{"found":55754,"hits":[{"document":{"authors":[{"contributor_roles":[],"family":"Crueger","given":"Jens"}],"blog":{"authors":[{"name":"Redaktion iRights.info"}],"community_id":"7d3b25fd-a4a8-4155-8e76-99d6be06706a","created":1694736000,"current_feed_url":null,"description":"Urheberrecht und kreatives Schaffen in der digitalen Welt","doi":"https://doi.org/10.59350/irights","favicon":"https://rogue-scholar.org/api/communities/7d3b25fd-a4a8-4155-8e76-99d6be06706a/logo","feed_format":"application/atom+xml","feed_url":"https://irights.info/feed/atom","filter":null,"generator":"Other","home_page_url":"https://irights.info/","issn":null,"language":"deu","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"irights","status":"active","subfield":"3308","title":"iRights.info","updated":1789026321,"use_api":false},"blog_name":"iRights.info","blog_slug":"irights","content_html":"<p>In the media and on social media, there has been a growing number of concerned reports about AI companies that are buying up used books in large quantities and in a rather ominous manner. It is speculated that the large quantities of books acquired in this way are scanned, used for AI training, and irretrievably destroyed in the process. It is often suggested that copyright law is the reason why the books are being destroyed. Can this assumption be substantiated?<br/>\n<span id=\"more-32898\"></span></p>\n<h2>The Destructive Scanning of Books</h2>\n<p>The retro-digitization (usually referred to simply as \"digitization\") of books is typically carried out using scanning technology. Modern book scanners are capable of scanning books non-destructively. However, non-destructive scanning of books is a complex process, as irregularities caused by the book's binding must be compensated for during the scanning process.</p>\n<p>In contrast, in so-called destructive scanning, the book's binding is mechanically removed. This turns a book into a loose collection of pages that can be conveniently digitized using a sheet-fed scanner. Once the scanning process is complete, the book pages are then disposed of as waste paper.</p>\n<h2>Why Antiquarian Bookstores Are Important for AI Training</h2>\n<p>Digital data sources, such as web archives, have long been incorporated into the training of current AI models. The digitization of printed books is now the next stage in data acquisition. According to observers, tech companies are particularly focused on non-fiction books published between the 1970s and the 1990s.</p>\n<p>These books are likely to be of interest for three reasons: First, nonfiction books are valuable for AI training because of their content; they contain factual information that is still largely accurate and is integrated into linguistically sophisticated patterns of argumentation. Second, book titles published before the mid-1990s were generally released exclusively as print editions and have not been digitized since. Third, books from the period in question are still predominantly subject to copyright, which expires only 70 years after the author's death in both Germany and the U.S.</p>\n<p>Obtaining scans of these books from dubious third-party sources would be illegal. Therefore, from a copyright perspective, the purchased print editions of these books are particularly valuable to the companies.</p>\n<h2>Technical Reasons for Destructive Scanning</h2>\n<p>But why do AI companies accept the destruction of the books during the scanning process?</p>\n<p>First, technical aspects play a significant role in large-scale retro-digitization of books: As explained at the outset, destructive scanning is simpler, faster, and therefore more cost-effective. Although the AI industry appears economically strong, observers interpret the decision to use the most cost-effective digitization method as an indication of cost pressure in this \"<a href=\"https://arstechnica.com/ai/2025/06/anthropic-destroyed-millions-of-print-books-to-build-its-ai-models/\" rel=\"noopener\" target=\"_blank\">highly competitive industry</a>.\"</p>\n<p>Competitive considerations may also play a role, because while the books in question are not particularly old or unique, many of them are nevertheless rarely available on the antiquarian book market due to low print runs and scarcity. Whoever buys them first effectively removes them from the competition's reach, thereby gaining a small advantage for their AI model.</p>\n<h2>Destructive Scanning Out of Concern for Copyright?</h2>\n<p>A lawsuit between three plaintiff authors and the AI company Anthropic before the United States District Court for the Northern District of California (<a href=\"https://copyrightalliance.org/wp-content/uploads/2025/06/Bartz-v.-Anthropic-Order.pdf\" rel=\"noopener\" target=\"_blank\">Bartz v. Anthropic</a>) established a legal precedent regarding destructive book scanning in 2025.</p>\n<p>The central question here was whether destructive scanning, on the one hand, and the training of AI models using the content of acquired digitized books, on the other, fall under the so-called \"fair use principle.\"</p>\n<div class=\"merksatz\"><strong>What is the fair use principle?</strong><br/>\nThe fair use principle is a legal doctrine found in some common law countries. It permits the use of copyrighted material for purposes of public education or intellectual production without requiring authorization for such use. Classic areas of application for fair use include commentary, criticism, parody, news reporting, research, and scholarship. Under German copyright law, instead of a general clause like fair use, there are narrow exceptions that permit certain uses (such as quotations, caricatures, parodies, educational and scholarly purposes, reporting on current events, etc.) regardless of the copyright holder's consent.</div>\n<p>The two central questions to be decided by the court must be considered separately:</p>\n<p>First, whether training AI models with the content of purchased digitized books is protected by the fair use doctrine.</p>\n<p>Second, whether destructive scanning constitutes a copyright-relevant copy of a work.</p>\n<p><a href=\"https://copyrightalliance.org/wp-content/uploads/2025/06/Bartz-v.-Anthropic-Order.pdf\" rel=\"noopener\" target=\"_blank\">According to Judge William Alsup</a>, training AI models using the content of purchased digitized books was \"transformative in the truest sense of the word\" and therefore protected by the fair use doctrine. Destructive scanning should be classified as \"replacement scanning,\" in which a printed work is replaced by a digital work. This conversion of a purchased printed book into a digital book was classified by the court as a \"<a href=\"https://copyrightalliance.org/wp-content/uploads/2025/06/Bartz-v.-Anthropic-Order.pdf\" rel=\"noopener\" target=\"_blank\">format change</a>\" rather than a copy and is therefore also covered by fair use.</p>\n<h2>A Landmark Ruling with Significant Implications</h2>\n<p>The rule on format conversion\u2014also known as the \"<a href=\"https://www.technollama.co.uk/fahrenheit-451-or-rainbows-end-ai-books-and-copyright-law\" rel=\"noopener\" target=\"_blank\">format-shifting rationale</a>\"\u2014thus promises, according to this landmark ruling, a certain degree of legal certainty for AI companies that destroy the books they have acquired for AI training through destructive scanning. The method that is more efficient from a technical standpoint is therefore also the more legally advisable one.</p>\n<p>However, it is a fallacy to assume that the court's ruling <em>requires</em> AI companies to destroy the digitized books. The lawsuit merely examined the specific digitization process as applied by Anthropic as part of \"Project Panama\"\u2014and classified it as fair use.</p>\n<h2>E-books Instead of Print Books?</h2>\n<p>If e-books were used for training instead of their printed counterparts, the time-consuming step of scanning\u2014and the associated issues of transportation, storage, and reuse\u2014would be eliminated.</p>\n<p>However, e-books can only become training data for AI models in two ways: the legal way\u2014that is, with the involvement of the rights holders of those e-books\u2014or by training with pirated copies. For AI companies, the legal route entails a significantly higher \"<a href=\"https://www.nytimes.com/2025/09/05/technology/anthropic-settlement-copyright-ai.html\" rel=\"noopener\" target=\"_blank\">legal/practice/business slog</a>\" (quote from Anthropic co-founder and CEO Dario Amodei).</p>\n<p>Training AI with pirated copies of e-books <a href=\"https://truthonthemarket.com/2025/06/24/bartz-v-anthropic-mapping-fair-use-boundaries-in-the-age-of-generative-ai/\" rel=\"noopener\" target=\"_blank\">is not covered by fair use</a> and thus constitutes a clear copyright infringement, Judge Alsup ruled.</p>\n<h2>Fears of 'Fahrenheit 451' Scenarios</h2>\n<p>Reports of AI companies purchasing large quantities of books from used bookstores have sparked, in some cases, fierce reactions in the media. The media discussion often references Ray Bradbury's novel *<a href=\"https://en.wikipedia.org/wiki/Fahrenheit_451\" rel=\"noopener\" target=\"_blank\">Fahrenheit 451</a>*, a dystopia in which books are banned.</p>\n<p>A closer look at the relevant court ruling in this specific case reveals that there is no legal obligation to destroy retro-digitized books. Economic reasons for choosing the most cost-effective digitization method therefore appear to be the decisive factor when the AI industry employs destructive book scanning. Against the backdrop of the actions taken by major AI companies, calls for open-source AI models are currently growing louder, and with regard to the retro-digitization of books, there are also increasing calls for \"<a href=\"https://www.rbb24.de/kultur/beitrag/2026/08/buecher-antiquariate-bestellungen-ki-training-vermutet.html\" rel=\"noopener\" target=\"_blank\">an open-source initiative or a similar nonprofit project.</a>\"</p>\n<div class=\"merksatz\">\n<h2>Would you like to support iRights.info?</h2>\n<p><strong><a href=\"https://irights.info/\">iRights.info</a> provides information and explanations on the subject of \"Copyright and creativity in the digital world\". All texts are published free of charge and openly licensed.</strong></p>\n<p><strong>If you like, you can support us via the <a href=\"https://www.betterplace.org/de/projects/120241-irights-info-informationsplattform-zum-urheberrecht-in-der-digitalen-welt\">donation platform Betterplace</a> and receive a donation receip. Betterplace accepts PayPal, direct debit, credit card, paydirekt or bank transfer.</strong></p>\n<p><strong>We would be particularly pleased to receive a regular contribution, for example as a monthly standing order. The <a href=\"https://irights.info/was-ist-irightsinfo-projekttrger\">non-profit organization iRights e.V.</a> would like to thank you for your support!<br/>\n</strong></p>\n<hr/>\n<p><strong>DOI for this text: \u00b7 Automatic DOI assignment for blogs via <a href=\"https://rogue-scholar.org/de/blogs/irights\">The Rogue Scholar</a></strong></p>\n</div>\n<p><script async=\"async\" src=\"https://www.betterplace.org/de/widgets/overlays/EjCxZ8kpYxhZeyTSTKxRZ33M.js\" type=\"text/javascript\"></script></p>\n<p>The post <a href=\"https://irights.info/artikel/out-of-concern-for-copyright-ai-companies-and-their-destructive-scanning-of-books/32898\">Out of Concern for Copyright? AI Companies and Their Destructive Scanning of Books</a> appeared first on <a href=\"https://irights.info\">iRights.info</a>.</p>","doi":"https://doi.org/10.59350/ksfmn-23248","guid":"https://irights.info/?post_type=custom_artikel&p=32898","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788998400,"rid":"bznwv-d6252","summary":"In the media and on social media, there has been a growing number of concerned reports about AI companies that are buying up used books in large quantities and in a rather ominous manner. It is speculated that the large quantities of books acquired in this way are scanned, used for AI training, and irretrievably [\u2026] The post Out of Concern for Copyright? AI Companies and Their Destructive Scanning of Books appeared first on iRights.info.","tags":["B\u00fccher","English","Generative KI","Urheberrecht","Urteile"],"title":"Out of Concern for Copyright? AI Companies and Their Destructive Scanning of Books","updated_at":1789029454,"url":"https://irights.info/artikel/out-of-concern-for-copyright-ai-companies-and-their-destructive-scanning-of-books/32898","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"University of Wroc\u0142aw, Chemistry"}],"contributor_roles":[],"family":"Janeta","given":"Mateusz","url":"https://orcid.org/0000-0003-2197-7913"}],"blog":{"authors":null,"community_id":"c21eed24-c860-43d0-997c-0bc782922544","created":1788652800,"current_feed_url":null,"description":null,"doi":"https://doi.org/10.59350/silsesquioxane","favicon":"https://rogue-scholar.org/api/communities/c21eed24-c860-43d0-997c-0bc782922544/logo","feed_format":"application/atom+xml","feed_url":"https://silsesquioxane.blogspot.com/feeds/posts/default","filter":null,"generator":"Blogger","home_page_url":"https://silsesquioxane.blogspot.com/","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"silsesquioxane","status":"active","subfield":"1604","title":"Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry","updated":1789025287,"use_api":true},"blog_name":"Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry","blog_slug":"silsesquioxane","content_html":"<p>\u4e2d\u6587\u7248\u672c / Chinese version: <a href=\"https://silsesquioxane.blogspot.com/p/poss.html\">POSS \u4e8c\u6c1f\u787c\u5149\u50ac\u5316\u5242:\u786b\u919a\u9009\u62e9\u6027\u6c27\u5316\u5236\u4e9a\u781c</a></p>\n<div \"times=\"\" 0px=\"\" 1.75;=\"\" 17px;=\"\" 780px;\"=\"\" auto;=\"\" font-size:=\"\" iowan=\"\" line-height:=\"\" margin:=\"\" max-width:=\"\" new=\"\" old=\"\" roman\",=\"\" serif;=\"\" style=\"color: #24292f; font-family: Georgia, \" style\",=\"\"><p style=\"background: rgb(245, 248, 251); border-left: 4px solid rgb(15, 76, 129); border-radius: 0px 6px 6px 0px; color: #1f2937; font-size: 18px; margin: 0px 0px 1.4em; padding: 1.1em 1.3em; text-align: justify;\"><a href=\"https://pubs.rsc.org/en/content/articlelanding/2025/qi/d5qi00323g\" style=\"display: inline-block; float: left; margin-bottom: 1em; margin-right: 1em;\"><img alt=\"silsesquioxane difluoroboron complexes\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieZxQDVRgNeI8fmnmqP8Q-yYBJlE79nqTichFmo5SytMhZfFD9URo5d6StOfaKM95COqeqIfh2B72C6LWys5dyJBBhR_9TiY3UJG08-bqRwv6I6yfBgCvyAfYfQ3BvBcaZ5gedOnqAAkaqMwyhpv_luxChyTOmfKo_RZwCcEmXc_iEntpFdRVVGSMD-6g/w99-h91/Research%20Highlights%20-%20Copy.png\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\" title=\"silsesquioxane difluoroboron complexes\"/></a>The publication titled <em>\"Polyhedral oligomeric silsesquioxane difluoroboron complexes as cooperative octo-site catalysts for the photooxidation of sulfides to sulfoxides\"</em> by Mateusz Janeta and S\u0142awomir Szafert, published in <em>Inorganic Chemistry Frontiers</em> on April 17, 2025, presents a study on the development of novel metal-free photocatalysts. These catalysts are based on <a href=\"https://silsesquioxane.blogspot.com/2020/08/structures-of-silsesquioxanes.html\">polyhedral oligomeric silsesquioxanes (POSS)</a> functionalized with difluoroboron complexes.</p><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicis9mjsH6kdFSZV6z_G5Je8C8Hh2k2lBZY37-2lORlb-SKPFVcoqRaCb5VKVneVxEaKFKPRQedPuA-b2vgw-M-M1ApfyZ0ClrEmPOsRQ94ixndI5gc3cm4Tki_wTipJ6IJseAOn-KG9GnEQ1q1RDdMdtLwT4X6P25el1n-6U8u8dGuZ0R7QLzz6WJX5Y/s2042/d5qi00323g-s1_hi-res.gif\" style=\"display: block;\"><img alt=\"Synthetic scheme for POSS-sal-BF2, POSS-tert-BF2, and POSS-npht-BF2 difluoroboron photocatalysts with isolated yields\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicis9mjsH6kdFSZV6z_G5Je8C8Hh2k2lBZY37-2lORlb-SKPFVcoqRaCb5VKVneVxEaKFKPRQedPuA-b2vgw-M-M1ApfyZ0ClrEmPOsRQ94ixndI5gc3cm4Tki_wTipJ6IJseAOn-KG9GnEQ1q1RDdMdtLwT4X6P25el1n-6U8u8dGuZ0R7QLzz6WJX5Y/s1600/d5qi00323g-s1_hi-res.gif\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\"/></a></div><div style=\"margin: 2em 0px; text-align: center;\"><div 0.85em=\"\" 0px;=\"\" 1.55;=\"\" 14px;=\"\" 92%;=\"\" arial,=\"\" auto=\"\" center;\"=\"\" font-size:=\"\" helvetica,=\"\" line-height:=\"\" margin:=\"\" max-width:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"color: #5f6b7a; font-family: -apple-system, BlinkMacSystemFont, \" text-align:=\"\" ui\",=\"\"><strong>Scheme 1.</strong> Synthesis of POSS-sal-BF<sub>2</sub>, POSS-<i>tert</i>-BF<sub>2</sub>, and POSS-npht-BF<sub>2</sub>. Isolated yields in parentheses.</div></div><h2 0.01em;=\"\" 0.35em;\"=\"\" 0.9em;=\"\" 0px=\"\" 2.4em=\"\" 22px;=\"\" 700;=\"\" arial,=\"\" font-size:=\"\" font-weight:=\"\" helvetica,=\"\" letter-spacing:=\"\" margin:=\"\" padding-bottom:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: -apple-system, BlinkMacSystemFont, \" ui\",=\"\">Key Highlights</h2><ul style=\"list-style: none; margin: 0px 0px 1.3em; padding-left: 0px;\"><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Catalyst design.</strong> The researchers synthesized three new difluoroboron-functionalized POSS complexes, namely POSS-<i>tert</i>-BF<sub>2</sub>, POSS-sal-BF<sub>2</sub>, and POSS-npht-BF<sub>2</sub>, derived from <a href=\"https://silsesquioxane.blogspot.com/2026/08/rationally-designed-octa-imine.html\">imine-functionalized POSS</a>s.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Photocatalytic performance.</strong> These complexes demonstrated exceptional efficiency in the aerobic photooxidation of sulfides to sulfoxides, significantly outperforming their silsesquioxane-free counterparts. Notably, POSS-<i>tert</i>-BF<sub>2</sub> exhibited a high singlet oxygen quantum yield of 48%.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Intramolecular cooperative activity.</strong> The study demonstrates the feasibility of intramolecular cooperative activity in catalytic reactions and identifies the key factors influencing its effectiveness. The octahedral structure of POSS provides multiple active sites, which enhances catalytic performance.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Environmental advantages.</strong> The catalysts operate under mild conditions, using molecular oxygen as the oxidant and avoiding toxic heavy metals and hazardous reagents, in keeping with the principles of green chemistry.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Reusability.</strong> POSS-<i>tert</i>-BF<sub>2</sub> retained its catalytic activity over multiple cycles with minimal loss of efficiency, which indicates good stability and recyclability.</li></ul><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">This research underscores the potential of POSS-based difluoroboron complexes as efficient, sustainable, and reusable photocatalysts for the selective oxidation of sulfides to sulfoxides, with implications for pharmaceutical synthesis and environmental applications.</p><h2 0.01em;=\"\" 0.35em;\"=\"\" 0.9em;=\"\" 0px=\"\" 2.4em=\"\" 22px;=\"\" 700;=\"\" arial,=\"\" font-size:=\"\" font-weight:=\"\" helvetica,=\"\" letter-spacing:=\"\" margin:=\"\" padding-bottom:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: -apple-system, BlinkMacSystemFont, \" ui\",=\"\">Singlet Oxygen Quantum Yields</h2><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The singlet oxygen quantum yield (SOQY, \u03a6(<sup>1</sup>O<sub>2</sub>)) was determined by monitoring the photooxidation of DPA in methanol in the presence of the POSS derivatives. Changes in the DPA absorbance at 391 nm were measured over time using low concentrations of photosensitizer and DPA in order to minimize potential quenching of <sup>1</sup>O<sub>2</sub> by the photocatalyst. The SOQY values were calculated by plotting the change in DPA absorbance against irradiation time.</p><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The calculated \u03a6(<sup>1</sup>O<sub>2</sub>) values for POSS-<i>tert</i>-BF<sub>2</sub>, POSS-sal-BF<sub>2</sub>, POSS-npht-BF<sub>2</sub>, prop-<i>tert</i>-BF<sub>2</sub>, prop-sal-BF<sub>2</sub>, and prop-npht-BF<sub>2</sub> were 48%, 35%, 46%, 27%, 26%, and 18%, respectively, which highlights the high efficiency of POSS-<i>tert</i>-BF<sub>2</sub> in generating singlet oxygen. A higher singlet oxygen quantum yield, and therefore a higher degree of DPA oxidation, was obtained for the octametallic POSS-<i>tert</i>-BF<sub>2</sub>, POSS-sal-BF<sub>2</sub>, and POSS-npht-BF<sub>2</sub> than for the monometallic analogues prop-<i>tert</i>-BF<sub>2</sub>, prop-sal-BF<sub>2</sub>, and prop-npht-BF<sub>2</sub> under the same reaction conditions. This can be attributed to the intramolecular cooperative effect in compounds bearing the POSS moiety, which was investigated further.</p><h2 0.01em;=\"\" 0.35em;\"=\"\" 0.9em;=\"\" 0px=\"\" 2.4em=\"\" 22px;=\"\" 700;=\"\" arial,=\"\" font-size:=\"\" font-weight:=\"\" helvetica,=\"\" letter-spacing:=\"\" margin:=\"\" padding-bottom:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: -apple-system, BlinkMacSystemFont, \" ui\",=\"\">Photocatalytic Oxidation of Sulfides to Sulfoxides</h2><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">Recent studies have demonstrated the powerful photocatalytic capabilities of POSS-<i>tert</i>-BF<sub>2</sub>, a boron difluoride-functionalized polyhedral oligomeric silsesquioxane. This system shows a significant singlet oxygen quantum yield and generates multiple reactive oxygen species, which makes it highly effective in oxidative transformations.</p><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGPDjOyYlHzrOYGxeMI0OB6IRK3YMTkGn-n2waYjgZk6kbRfiDXEj2hnvOcNsPufgKayUlp7u2Dc6AP88RRs3Ubpzndy6buIHplCht01xR16XIVH2w0ecdlv26wlBrjFUyMfo4oBSs31HoQxhslYF_qSsdDATij1dOta0wqD6i3jyyhkIkUwYc8ZTsoek/s1337/untitled.png\" style=\"display: block;\"><img alt=\"Photooxidation of thioanisole to sulfoxide catalyzed by the POSS-tert-BF2 photocatalyst\" border=\"0\" height=\"125\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGPDjOyYlHzrOYGxeMI0OB6IRK3YMTkGn-n2waYjgZk6kbRfiDXEj2hnvOcNsPufgKayUlp7u2Dc6AP88RRs3Ubpzndy6buIHplCht01xR16XIVH2w0ecdlv26wlBrjFUyMfo4oBSs31HoQxhslYF_qSsdDATij1dOta0wqD6i3jyyhkIkUwYc8ZTsoek/w400-h125/untitled.png\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\" width=\"400\"/></a></div><p style=\"margin: 0px 0px 1.15em; text-align: justify;\"><strong>Key findings from the study</strong></p><ul style=\"list-style: none; margin: 0px 0px 1.3em; padding-left: 0px;\"><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">Oxidation of thioanisole (0.425 mmol in MeOH) reached full conversion in 40 minutes using only 0.5 mol% of POSS-<i>tert</i>-BF<sub>2</sub> under a 150 W medium-pressure mercury lamp.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">The process achieved a turnover number of 1582 and a turnover frequency of 2373 h<sup>\u22121</sup>.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">Scale-up experiments gave a 98% yield.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">The external quantum efficiency of the system was 59%, determined by ferrioxalate actinometry.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">Control experiments conducted without light, without photosensitizer, or under anaerobic conditions showed negligible conversion, which confirms the photocatalytic nature of the mechanism.</li></ul><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The conversion of thioanisole was only 30% in pure DCM, whereas under the same reaction conditions in MeOH the conversion increased to 99%. Protic solvents such as MeOH and H<sub>2</sub>O are known to stabilize the intermediate involved in the formation of <sup>1</sup>O<sub>2</sub> and thereby to accelerate photooxidation. These differences in conversion also suggest that <sup>1</sup>O<sub>2</sub> can be identified as one of the reactive oxygen species involved in the photooxidation of thioanisole.</p><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">Comparing the activity of POSS compounds bearing various substituents on the phenyl ring, we observed that introducing steric hindrance, as in the <i>tert</i>-butyl groups at the 3- and 5-positions of the phenyl ring in POSS-<i>tert</i>-BF<sub>2</sub>, significantly increased the reaction efficiency, giving 99% conversion in 40 minutes compared with 70% for POSS-sal-BF<sub>2</sub>, which lacks bulky substituents. Introducing steric hindrance at the 5,6-positions of the phenyl ring in POSS-npht-BF<sub>2</sub>, by replacing the phenyl ring with a naphthalene ring, also improved the efficiency relative to POSS-sal-BF<sub>2</sub>, although it remained lower than that of POSS-<i>tert</i>-BF<sub>2</sub>. This underscores the critical role of steric hindrance at the 3-position of the phenyl ring in promoting the conversion of thioanisole. POSS-<i>tert</i>-BF<sub>2</sub> therefore exhibits high efficiency in the photocatalytic oxidation of thioanisole and was studied in greater detail.</p><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The reaction progress was monitored in real time by NMR spectroscopy, which revealed that the conversion of thioanisole to methyl phenyl sulfoxide with POSS-<i>tert</i>-BF<sub>2</sub> as the photosensitizer increased steadily over time, reaching complete conversion within 40 minutes in accordance with zero-order kinetics. By comparison, the use of prop-<i>tert</i>-BF<sub>2</sub> resulted in only 65% substrate conversion after 40 minutes, with full conversion achieved after 60 minutes. These findings clearly demonstrate the superior reaction efficiency and faster catalytic performance of POSS-<i>tert</i>-BF<sub>2</sub> relative to prop-<i>tert</i>-BF<sub>2</sub>.</p><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The higher conversion of thioanisole obtained with the octametallic POSS-<i>tert</i>-BF<sub>2</sub> (99%) than with the monometallic analogue prop-<i>tert</i>-BF<sub>2</sub> (65%) under the same reaction conditions supports the occurrence of intramolecular cooperative catalysis in POSS-<i>tert</i>-BF<sub>2</sub>. This observation is consistent with the enhancement recorded in the singlet oxygen quantum yields. A similar intramolecular cooperative effect was previously reported for Zn<sub>4</sub>@POSS-1, which contains the POSS-1 ligand, in the formation of cyclic carbonates from epoxides.<sup>37</sup> A comparable enhancement in efficiency was observed for POSS-sal-BF<sub>2</sub> and POSS-npht-BF<sub>2</sub>. Comparing the activity of POSS-npht-BF<sub>2</sub> with that of prop-npht-BF<sub>2</sub>, a higher yield of 90% versus 60% was obtained for POSS-npht-BF<sub>2</sub>. The activity of POSS-sal-BF<sub>2</sub> is likewise higher than that of prop-sal-BF<sub>2</sub>, at 70% versus 59%.</p><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUwpLnjAXZSC6ygXAgF63Zrl3x_7KgzLvUNA4rb-s5E-g4kZK680L0zDhG36E-UF4oMdI8VGmPdTHz3Ab-zbHXHV1PtwGoLD3sVBigGJq4tPls-65zHlheLwPkRqaNm8OgMb0_YrueLw1YCH2TY-kykyjySIibkOu-GT3DwP_jGhjDBPlIpYmKDH5a4Fw/s979/d5qi00323g-s4_hi-res.gif\" style=\"display: block;\"><img alt=\"Proposed photocatalytic mechanism of POSS-tert-BF2 for sulfide oxidation via singlet oxygen\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUwpLnjAXZSC6ygXAgF63Zrl3x_7KgzLvUNA4rb-s5E-g4kZK680L0zDhG36E-UF4oMdI8VGmPdTHz3Ab-zbHXHV1PtwGoLD3sVBigGJq4tPls-65zHlheLwPkRqaNm8OgMb0_YrueLw1YCH2TY-kykyjySIibkOu-GT3DwP_jGhjDBPlIpYmKDH5a4Fw/s1600/d5qi00323g-s4_hi-res.gif\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\"/></a><div 0.85em=\"\" 0px;=\"\" 1.55;=\"\" 14px;=\"\" 92%;=\"\" arial,=\"\" auto=\"\" font-size:=\"\" helvetica,=\"\" left;\"=\"\" line-height:=\"\" margin:=\"\" max-width:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"color: #5f6b7a; font-family: -apple-system, BlinkMacSystemFont, \" text-align:=\"\" ui\",=\"\"><strong>Scheme 2.</strong> Proposed reaction mechanisms of sulfide-selective oxidation by POSS-<i>tert</i>-BF<sub>2</sub> in the presence of O<sub>2</sub>.</div></div><h2 0.01em;=\"\" 0.35em;\"=\"\" 0.9em;=\"\" 0px=\"\" 2.4em=\"\" 22px;=\"\" 700;=\"\" arial,=\"\" font-size:=\"\" font-weight:=\"\" helvetica,=\"\" letter-spacing:=\"\" margin:=\"\" padding-bottom:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: -apple-system, BlinkMacSystemFont, \" ui\",=\"\">Substrate Scope</h2><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">To assess the versatility of POSS-<i>tert</i>-BF<sub>2</sub> as a photocatalyst in the photooxidation of thioanisole derivatives in methanol, a series of substrates bearing various substituents was evaluated. Thioanisole derivatives containing the electron-donating group \u2013CH<sub>3</sub> and the electron-withdrawing groups \u2013CN, \u2013CHO, and \u2013C(O)CH<sub>3</sub> achieved high yields of 99%, 82%, 78%, and 96%, respectively. Bromine-substituted derivatives at the <i>ortho</i> and <i>meta</i> positions also gave high yields of 99%.</p><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj9AZsfRpRiHgq_DmcJyRfS2Gxiap-Fqr57sV4g7FXk4ke0hyNpW29pJDqxmkGoJPRmeYPbRr9HVE2xNfOHwF7Hq2_GJBENjc2b3hqNVcL17mqJRiFJoqaV17G5pFGomj7U8FBXJyreBKkpJehrEsuHWeWQDWBSQgx7Cl2hYJCv6iyHhZ0ruxCiBYdjdWk/s979/d5qi00323g-s3_hi-res.gif\" style=\"display: block;\"><img alt=\"Substrate scope showing sulfoxide product yields from POSS catalyzed sulfide photooxidation\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj9AZsfRpRiHgq_DmcJyRfS2Gxiap-Fqr57sV4g7FXk4ke0hyNpW29pJDqxmkGoJPRmeYPbRr9HVE2xNfOHwF7Hq2_GJBENjc2b3hqNVcL17mqJRiFJoqaV17G5pFGomj7U8FBXJyreBKkpJehrEsuHWeWQDWBSQgx7Cl2hYJCv6iyHhZ0ruxCiBYdjdWk/s1600/d5qi00323g-s3_hi-res.gif\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\"/></a></div><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">These results highlight the potential of POSS-based systems in green and efficient photocatalytic oxidation chemistry.</p><div style=\"background: rgb(245, 247, 251); border-left: 4px solid rgb(15, 76, 129); color: #333333; font-size: 0.86em; line-height: 1.75; margin: 2em 0px 1em; padding: 14px 20px;\"><strong style=\"color: #0f4c81; display: block; font-size: 0.75em; letter-spacing: 0.08em; margin-bottom: 6px; text-transform: uppercase;\">Full Citation</strong>Mateusz Janeta and S\u0142awomir Szafert. \"Polyhedral oligomeric silsesquioxane difluoroboron complexes as cooperative octo-site catalysts for the photooxidation of sulfides to sulfoxides.\" <em>Inorganic Chemistry Frontiers</em>, 2025, <strong>12</strong>, 4666-4676.<br/>DOI: <a href=\"https://doi.org/10.1039/D5QI00323G\" rel=\"noopener\" target=\"_blank\">10.1039/D5QI00323G</a><br/>Full text: <a href=\"https://pubs.rsc.org/en/content/articlelanding/2025/qi/d5qi00323g\" rel=\"noopener\" target=\"_blank\">Inorganic Chemistry Frontiers \u2192 RSC Publishing</a></div><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://pubs.rsc.org/en/content/articlelanding/2025/qi/d5qi00323g\" style=\"display: block;\" target=\"_blank\"><img alt=\"Research highlights infographic summarizing POSS BF2 photocatalyst performance and singlet oxygen quantum yields\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2rAfRA7RUKjArioYslyjzxJDAO5r4XnObrT9xqirLaaETjeAmvL25VLCegDVm8IGP8b2CjM9NfGU87inA2pr2mfB95hr0VbjT2dj-zjQ7PFvWoJDx_5NUUY8t-GVjFwaJV4Hsu2PDt65coyoZwTaSsb1NS-m930wkHYXloGLxGx-pzQYVfL96cVKiG28/s1600/Research%20Highlights.png\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\"/></a></div></div>","doi":"https://doi.org/10.59350/pznaw-y5e39","guid":"tag:blogger.com,1999:blog-2875892712213933214.post-4039579808081725822","image":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieZxQDVRgNeI8fmnmqP8Q-yYBJlE79nqTichFmo5SytMhZfFD9URo5d6StOfaKM95COqeqIfh2B72C6LWys5dyJBBhR_9TiY3UJG08-bqRwv6I6yfBgCvyAfYfQ3BvBcaZ5gedOnqAAkaqMwyhpv_luxChyTOmfKo_RZwCcEmXc_iEntpFdRVVGSMD-6g/s72-w99-h91-c/Research%20Highlights%20-%20Copy.png","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788998400,"rid":"8jtxv-rdg17","summary":"\u4e2d\u6587\u7248\u672c / Chinese version: POSS \u4e8c\u6c1f\u787c\u5149\u50ac\u5316\u5242:\u786b\u919a\u9009\u62e9\u6027\u6c27\u5316\u5236\u4e9a\u781c The publication titled <em> \"Polyhedral oligomeric silsesquioxane difluoroboron complexes as cooperative octo-site catalysts for the photooxidation of sulfides to sulfoxides\" </em> by Mateusz Janeta and S\u0142awomir Szafert, published in <em> Inorganic Chemistry Frontiers </em> on April 17, 2025, presents a study on the development of novel metal-free photocatalysts.","tags":["Catalysis","Imine-POSS","Photochemistry","POSS","POSS Functionalization"],"title":"POSS Difluoroboron Photocatalysts for Sulfide Oxidation","updated_at":1789025423,"url":"https://silsesquioxane.blogspot.com/2026/09/poss-difluoroboron-photocatalysts-for.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Bielefeld University, Medical Faculty"}],"contributor_roles":[],"family":"Friederichs","given":"Hendrik","url":"https://orcid.org/0000-0001-9671-5235"}],"blog":{"authors":null,"community_id":"304adf51-cbb7-4ff1-a505-1dc06082fbad","created":1776988800,"current_feed_url":null,"description":"Aktuelle Einblicke aus der medizinischen Bildungsforschung \u2014 evidenzbasiert, verst\u00e4ndlich, mit gelegentlichem Augenzwinkern.","doi":"https://doi.org/10.59350/medical_education","favicon":"https://rogue-scholar.org/api/communities/304adf51-cbb7-4ff1-a505-1dc06082fbad/logo","feed_format":"application/rss+xml","feed_url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/blog.xml","filter":null,"generator":"Quarto","home_page_url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/blog.html","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"medical_education","status":"active","subfield":"2739","title":"Entscheiden(d) lernen","updated":1788991200,"use_api":null},"blog_name":"Entscheiden(d) lernen","blog_slug":"medical_education","content_html":"<p><img class=\"preview-image img-fluid\" src=\"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/FriederichsH_impostor.png\"/></p>\n<p><em>Im Oktober beginnen viele junge Menschen ihr Medizinstudium. Viele von ihnen werden in den ersten Wochen denselben Gedanken haben, n\u00e4mlich dass alle anderen im H\u00f6rsaal besser vorbereitet, kl\u00fcger und sicherer wirken als sie selbst. Dieser Gedanke hat einen Namen, er ist gut untersucht, und er ist erstaunlich verbreitet.</em></p>\n<section class=\"level2\" id=\"der-gedanke-in-der-ersten-woche\">\n<h2 class=\"anchored\" data-anchor-id=\"der-gedanke-in-der-ersten-woche\">Der Gedanke in der ersten Woche</h2>\n<p>Die allererste Vorlesung. Um Euch herum sitzen Leute, die sich offenbar m\u00fchelos Fachbegriffe merken, die im Seminar als Erste die Hand heben und die schon wissen, wo die Bibliothek ist. Ihr selbst habt das Gef\u00fchl, durch einen Zufall hier gelandet zu sein. Die Zulassung war Gl\u00fcck, der gute Abiturschnitt eine Verkettung g\u00fcnstiger Umst\u00e4nde, und irgendwann wird jemand merken, dass Ihr eigentlich gar nicht hierhergeh\u00f6rt.</p>\n<p>Wenn Euch das bekannt vorkommt, seid Ihr in gro\u00dfer Gesellschaft. Zwei Metaanalysen aus diesem Jahr kommen unabh\u00e4ngig voneinander zu dem Ergebnis, dass etwa die H\u00e4lfte aller Medizinstudierenden weltweit ausgepr\u00e4gte Impostor-Gef\u00fchle berichtet <span class=\"citation\" data-cites=\"10.1007/s10459-026-10513-3 10.1371/journal.pone.0351713\">[1, 2]</span>. Zum Studienstart liegt der Anteil noch deutlich h\u00f6her. In einer L\u00e4ngsschnittstudie mit 257 Erstsemestern hatten fast neun von zehn schon in den ersten Wochen hohe Werte, und bis zum Jahresende stiegen sie weiter <span class=\"citation\" data-cites=\"10.22454/FamMed.2021.799997\">[3]</span>.</p>\n</section>\n<section class=\"level2\" id=\"was-das-impostor-ph\u00e4nomen-ist\">\n<h2 class=\"anchored\" data-anchor-id=\"was-das-impostor-ph\u00e4nomen-ist\">Was das Impostor-Ph\u00e4nomen ist</h2>\n<p>Beschrieben haben es die Psychologinnen Pauline Clance und Suzanne Imes 1978 bei mehr als 150 beruflich sehr erfolgreichen Frauen. Ihre Klientinnen waren \u00fcberzeugt, ihre Erfolge nicht verdient zu haben, und lebten in der Erwartung, irgendwann als Betr\u00fcgerinnen entlarvt zu werden <span class=\"citation\" data-cites=\"10.1037/h0086006\">[4]</span>. Das T\u00fcckische daran ist ein Kreislauf. Wer vor einer Pr\u00fcfung \u00fcberm\u00e4\u00dfig viel lernt und besteht, schreibt das dem Flei\u00df zu, nicht der eigenen F\u00e4higkeit. Wer aufgeschoben hat und trotzdem durchkommt, schreibt es dem Gl\u00fcck zu. In beiden F\u00e4llen bleibt die eigene Kompetenz unsichtbar, und die n\u00e4chste Pr\u00fcfung beginnt mit denselben Zweifeln.</p>\n<p>Zwei Dinge sind dabei wichtig. Das Impostor-Ph\u00e4nomen ist <strong>keine</strong> Krankheit und <strong>keine</strong> Diagnose, es steht in keinem Klassifikationssystem. Und der verbreitete Begriff \"Impostor-Syndrom\" f\u00fchrt in die Irre, weil er nahelegt, das Problem s\u00e4\u00dfe in der Person. Eine Forschungsgruppe hat 2020 daf\u00fcr pl\u00e4diert, das Ph\u00e4nomen konsequent im Kontext zu betrachten, also in den Umgebungen, die solche Gef\u00fchle hervorrufen <span class=\"citation\" data-cites=\"10.3389/fpsyg.2020.575024\">[5]</span>. Genau darum geht es im n\u00e4chsten Abschnitt.</p>\n</section>\n<section class=\"level2\" id=\"warum-ausgerechnet-das-medizinstudium\">\n<h2 class=\"anchored\" data-anchor-id=\"warum-ausgerechnet-das-medizinstudium\">Warum ausgerechnet das Medizinstudium</h2>\n<p>Die Antwort beginnt mit der Auswahl. Wer einen Medizinstudienplatz bekommt, geh\u00f6rte an der Schule zu den Besten. Im H\u00f6rsaal sitzen dann 300 Menschen, auf die das gleiche zutrifft, und die vertraute Referenzgruppe ist \u00fcber Nacht verschwunden. Wer sich bisher am oberen Rand verortet hat, findet sich pl\u00f6tzlich in der Mitte wieder, ohne dass sich an den eigenen F\u00e4higkeiten etwas ge\u00e4ndert h\u00e4tte.</p>\n<p>Dazu kommt eine Kultur, die Perfektion als Normalzustand behandelt. Ein \u00dcberblick \u00fcber die Literatur beschreibt, wie das Medizinstudium hohe Anspr\u00fcche und Selbstkritik nicht nur anzieht, sondern aktiv trainiert <span class=\"citation\" data-cites=\"10.5116/ijme.5f54.c8f8\">[6]</span>. Eine britische Studie fand, dass die Impostor-Werte umso h\u00f6her lagen, je weiter unten jemand im Pr\u00fcfungsranking stand <span class=\"citation\" data-cites=\"10.1007/s40670-022-01675-x\">[7]</span>. Das klingt zun\u00e4chst naheliegend, hat aber eine Pointe. In einer Gruppe, in der alle zu den Besten ihres Jahrgangs geh\u00f6rten, muss ein Ranking trotzdem die H\u00e4lfte in die untere H\u00e4lfte sortieren. Es verteilt also Zweifel an Menschen, deren Leistung sich gar nicht verschlechtert hat.</p>\n<p>Ein dritter Faktor ist die Frage, ob man sich zugeh\u00f6rig f\u00fchlt. Kanadische Studierende, die im Studium erlebten, dass sie etwas k\u00f6nnen und dass sie aus eigenem Antrieb lernen, berichteten deutlich weniger Impostor-Gef\u00fchle. Wer sich dagegen vor allem von au\u00dfen getrieben f\u00fchlte, von Noten, Erwartungen und Vergleich, berichtete mehr davon <span class=\"citation\" data-cites=\"10.1080/10401334.2022.2056741\">[8]</span>. Und wer an seiner Fakult\u00e4t zu einer Minderheit geh\u00f6rt, ist besonders betroffen. In den USA berichteten Studierende aus unterrepr\u00e4sentierten Gruppen an \u00fcberwiegend wei\u00dfen Fakult\u00e4ten fast dreimal so h\u00e4ufig starke Impostor-Gef\u00fchle wie an Hochschulen mit \u00fcberwiegend schwarzer Studierendenschaft <span class=\"citation\" data-cites=\"10.1016/j.jnma.2023.01.012\">[9]</span>.</p>\n<p>Das Impostor-Gef\u00fchl ist also weniger eine Eigenschaft, die man mitbringt, als eine Reaktion auf eine Situation. Das erkl\u00e4rt, warum es in \u00dcbergangsphasen am st\u00e4rksten ist, nach dem Studienstart, beim Eintritt in die Klinik, zu Beginn der Weiterbildung. So z. B. hatten britische Chirurg*innen in Weiterbildung deutlich h\u00f6here Werte als ihre fertig ausgebildeten Kolleg*innen <span class=\"citation\" data-cites=\"10.1136/bmjopen-2025-100557\">[10]</span>. Es wird besser, aber nicht von allein und nicht schnell.</p>\n</section>\n<section class=\"level2\" id=\"warum-es-nicht-egal-ist\">\n<h2 class=\"anchored\" data-anchor-id=\"warum-es-nicht-egal-ist\">Warum es nicht egal ist</h2>\n<p>Man k\u00f6nnte einwenden, ein bisschen Selbstzweifel schadet nicht. Ein bisschen stimmt das auch. Problematisch wird es, wenn die Zweifel anhalten. Bei \u00c4rzt*innen in Weiterbildung war ein ausgepr\u00e4gtes Impostor-Erleben ein eigenst\u00e4ndiger Risikofaktor f\u00fcr Angstsymptome und Burnout <span class=\"citation\" data-cites=\"10.1080/0142159X.2022.2028751\">[11]</span>, und bei einer Studie an mehr als 3.000 US-\u00c4rzt*innen verdoppelte es die Wahrscheinlichkeit f\u00fcr Burnout <span class=\"citation\" data-cites=\"10.1016/j.mayocp.2022.06.021\">[12]</span>. Bei Erstsemestern hing anhaltendes Impostor-Erleben mit geringerem Selbstmitgef\u00fchl und mehr psychischer Belastung zusammen <span class=\"citation\" data-cites=\"10.22454/FamMed.2021.799997\">[3]</span>. Wer merkt, dass die Zweifel nicht mehr nur vor Pr\u00fcfungen kommen, sondern den Alltag bestimmen, sollte das ernst nehmen und die Beratungsangebote der Universit\u00e4t nutzen. Die sind genau daf\u00fcr da.</p>\n</section>\n<section class=\"level2\" id=\"was-hilft\">\n<h2 class=\"anchored\" data-anchor-id=\"was-hilft\">Was hilft</h2>\n<p>Noch 2020 stellte das gr\u00f6\u00dfte systematische Review zum Thema fest, dass es keine einzige evaluierte Ma\u00dfnahme gegen das Impostor-Ph\u00e4nomen gab <span class=\"citation\" data-cites=\"10.1007/s11606-019-05364-1\">[13]</span>. Seitdem hat sich einiges getan.</p>\n<p>Am besten belegt ist Gruppencoaching. In zwei randomisierten Studien mit zusammen mehr als 1.100 \u00c4rztinnen in Weiterbildung senkte ein sechsmonatiges Online-Programm Impostor-Werte und emotionale Ersch\u00f6pfung und st\u00e4rkte das Selbstmitgef\u00fchl <span class=\"citation\" data-cites=\"10.1001/jamanetworkopen.2022.10752 10.1001/jamanetworkopen.2023.35541\">[14, 15]</span>. Ein Umbrella-Review von 2026, das 16 \u00dcbersichtsarbeiten zusammenfasst, sieht Potenzial in Coaching, Online-Modulen und achtsamkeitsbasierten Ans\u00e4tzen, mahnt aber, dass hochwertige Interventionsstudien noch selten sind <span class=\"citation\" data-cites=\"10.1111/medu.70076\">[16]</span>.</p>\n<p>F\u00fcr den Studienstart ist ein anderer Befund vielleicht wichtiger. Schon ein einzelner Workshop, in dem Erstsemester das Ph\u00e4nomen kennenlernen und merken, dass es fast allen so geht, ver\u00e4ndert etwas. Nach einem solchen Workshop konnten neun von zehn Erstsemestern das Muster bei sich selbst erkennen <span class=\"citation\" data-cites=\"10.1016/j.heliyon.2024.e29478\">[17]</span>, und in einer Orientierungswoche sank der Anteil mit starken Impostor-Gef\u00fchlen um zehn Prozentpunkte <span class=\"citation\" data-cites=\"10.1093/milmed/usaf068\">[18]</span>. Der Wirkmechanismus hei\u00dft Normalisierung. Das Gef\u00fchl, allein damit zu sein, ist ein gro\u00dfer Teil des Problems, und es l\u00f6st sich in dem Moment auf, in dem die Nachbarin im H\u00f6rsaal dasselbe erz\u00e4hlt. Strukturierte Peer-Treffen f\u00fcr Studienanf\u00e4nger*innen zielen genau darauf <span class=\"citation\" data-cites=\"10.1186/s12909-026-09041-w\">[19]</span>.</p>\n<p>Was Ihr selbst tun k\u00f6nnt, l\u00e4sst sich aus dieser Evidenz ableiten. Redet dar\u00fcber, mit Kommiliton*innen und mit Lehrenden, denn die Wahrscheinlichkeit, dass Euer Gegen\u00fcber es kennt, liegt bei etwa f\u00fcnfzig Prozent. Schreibt Euch auf, was Ihr gut k\u00f6nnt, nicht nur, was Ihr noch nicht k\u00f6nnt, denn der Impostor-Kreislauf lebt davon, Erfolge zu vergessen. Und wechselt den Vergleichsma\u00dfstab. Die Frage ist nicht, ob Ihr besser seid als die Person neben Euch, sondern ob Ihr mehr k\u00f6nnt als vor vier Wochen.</p>\n<div class=\"callout callout-style-default callout-tip callout-titled\">\n<div aria-controls=\"callout-1\" aria-expanded=\"false\" aria-label=\"Toggle callout\" class=\"callout-header d-flex align-content-center collapsed\" data-bs-target=\".callout-1-contents\" data-bs-toggle=\"collapse\">\n<div class=\"callout-icon-container\">\n<i class=\"callout-icon\"></i>\n</div>\n<div class=\"callout-title-container flex-fill\">\n<span class=\"screen-reader-only\">Tipp</span>F\u00fcr Statistik-Interessierte \u2014 die Zahlen hinter dem Impostor-Ph\u00e4nomen\n</div>\n<div class=\"callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end\"><i class=\"callout-toggle\"></i></div>\n</div>\n<div class=\"callout-1-contents callout-collapse collapse\" id=\"callout-1\">\n<div class=\"callout-body-container callout-body\">\n<p>Die meisten Studien nutzen die Clance Impostor Phenomenon Scale (CIPS, 20 Items, Wertebereich 20 bis 100). Ab 62 Punkten gelten Impostor-Gef\u00fchle als \"h\u00e4ufig\", ab 81 als \"intensiv\". Diese Grenzen sind Konvention, nicht Diagnosekriterium, und sie erkl\u00e4ren einen Teil der Streuung zwischen den Studien.</p>\n<p><strong>Zwei Metaanalysen, ein Bild.</strong> Omar et al.\u00a0poolten 34 Studien mit 9.550 Medizinstudierenden und fanden eine Pr\u00e4valenz von 49 % (95 %-KI 43 bis 54 %, I\u00b2 = 95,6 %). Frauen lagen bei 51 %, M\u00e4nner bei 40 % (p = 0,021). Mit der CIPS ergaben sich 53 %, mit der Young Impostor Scale 38 % <span class=\"citation\" data-cites=\"10.1007/s10459-026-10513-3\">[1]</span>. Vera-Ponce et al.\u00a0poolten 26 CIPS-Studien mit 9.110 Studierenden und kamen auf 54,2 % (95 %-KI 47,0 bis 61,3 %, I\u00b2 = 98 %), ohne Unterschied zwischen vorklinischem (48,9 %) und klinischem Abschnitt (46,8 %, !) und ohne zeitlichen Trend zwischen 2018 und 2024 <span class=\"citation\" data-cites=\"10.1371/journal.pone.0351713\">[2]</span>. Bei I\u00b2-Werten \u00fcber 95 % beschreibt der gepoolte Wert eine Gr\u00f6\u00dfenordnung, keine gemeinsame Realit\u00e4t.</p>\n<p><strong>Der Studienstart in Zahlen.</strong> Rosenthal et al.\u00a0befragten 257 Erstsemester zu Beginn und am Ende des ersten Jahres. 87 % hatten anfangs hohe oder sehr hohe Werte, die bis zum Jahresende signifikant anstiegen (p &lt; 0,001). Hohe Werte gingen mit deutlich geringerem Selbstmitgef\u00fchl einher (d = 1,62) <span class=\"citation\" data-cites=\"10.22454/FamMed.2021.799997\">[3]</span>. Houseknecht et al.\u00a0beobachteten 110 Studierende \u00fcber drei Jahre und fanden steigende Impostor-Werte (p = 0,011) bei sinkender professioneller Identifikation <span class=\"citation\" data-cites=\"10.1007/s40670-019-00718-0\">[20]</span>. Kim et al.\u00a0verfolgten eine Kohorte von der Orientierungswoche bis zum Ende des 16-monatigen vorklinischen Abschnitts. Der mittlere CIPS-Wert blieb praktisch unver\u00e4ndert (68,3 gegen\u00fcber 68,1), die Ausl\u00f6ser verschoben sich aber vom Zulassungsgl\u00fcck zum Vergleich mit anderen <span class=\"citation\" data-cites=\"10.1093/milmed/usaf373\">[21]</span>.</p>\n<p><strong>Europ\u00e4ische Stichproben.</strong> Unter 457 schwedischen Medizinstudierenden lagen 58,4 % \u00fcber dem CIPS-Grenzwert, Frauen mit 67,4 gegen\u00fcber 59,3 Punkten (d = 0,47). Resilienz korrelierte moderat negativ mit Impostor-Werten (r = \u22120,41) <span class=\"citation\" data-cites=\"10.1186/s12909-024-05788-2\">[22]</span>. In Ume\u00e5 lagen 64 % von 968 Studierenden verschiedener F\u00e4cher \u00fcber dem Grenzwert, und weder Semester noch Alter machten einen Unterschied <span class=\"citation\" data-cites=\"10.3389/fmed.2025.1623792\">[23]</span>. F\u00fcr Deutschland gibt es bislang keine vergleichbare Erhebung.</p>\n<p><strong>Umgebung und Ranking.</strong> Franchi und Russell-Sewell fanden bei 191 britischen Studierenden einen mittleren CIPS-Wert von 65,8, bei 65,4 % \u00fcber dem Grenzwert; pro Dezil weiter unten im Pr\u00fcfungsranking stieg der Wert um 1,12 Punkte (p &lt; 0,05) <span class=\"citation\" data-cites=\"10.1007/s40670-022-01675-x\">[7]</span>. Bei Neufeld et al.\u00a0erkl\u00e4rte die Befriedigung der psychologischen Grundbed\u00fcrfnisse 21,8 % der Varianz, das Kompetenzerleben allein hatte ein \u03b2 von \u22120,49 <span class=\"citation\" data-cites=\"10.1080/10401334.2022.2056741\">[8]</span>. Rice et al.\u00a0berichten f\u00fcr Studierende aus unterrepr\u00e4sentierten Gruppen an \u00fcberwiegend wei\u00dfen Fakult\u00e4ten eine Odds Ratio von 2,75 (95 %-KI 1,65 bis 4,58) gegen\u00fcber historisch schwarzen Hochschulen <span class=\"citation\" data-cites=\"10.1016/j.jnma.2023.01.012\">[9]</span>. In der britischen Unfallchirurgie lagen Trainees bei 70,6 Punkten, Consultants bei 59,8 <span class=\"citation\" data-cites=\"10.1136/bmjopen-2025-100557\">[10]</span>.</p>\n<p><strong>Folgen.</strong> Bei 269 \u00c4rzt*innen in Weiterbildung war das Impostor-Erleben ein unabh\u00e4ngiger Risikofaktor f\u00fcr Angst (RR = 3,64; 95 %-KI 1,96 bis 6,76) und Burnout (RR = 1,82; 95 %-KI 1,07 bis 3,08) <span class=\"citation\" data-cites=\"10.1080/0142159X.2022.2028751\">[11]</span>. Bei 3.116 US-\u00c4rzt*innen war intensives Impostor-Erleben mit h\u00f6heren Odds f\u00fcr Burnout (OR = 2,13; 95 %-KI 1,43 bis 3,19) und f\u00fcr Suizidgedanken (OR = 2,62; 95 %-KI 1,46 bis 4,65) verbunden <span class=\"citation\" data-cites=\"10.1016/j.mayocp.2022.06.021\">[12]</span>. Bei 226 Medizinstudierenden vermittelte das Impostor-Ph\u00e4nomen den Zusammenhang zwischen maladaptivem Perfektionismus und Suizidgedanken (indirekter Effekt B = 0,07; 95 %-KI 0,03 bis 0,13); das ist eine Mediation in Querschnittsdaten, keine Kausalkette <span class=\"citation\" data-cites=\"10.1007/s40596-021-01503-1\">[24]</span>.</p>\n<p><strong>Interventionen.</strong> Fainstad et al.\u00a0randomisierten 101 Assistenz\u00e4rztinnen; das Impostor-Ma\u00df sank in der Coaching-Gruppe um 1,16 Punkte und stieg in der Kontrollgruppe um 0,11 (p = 0,003) <span class=\"citation\" data-cites=\"10.1001/jamanetworkopen.2022.10752\">[14]</span>. Die multizentrische Replikation mit 1.017 Teilnehmerinnen fand eine Differenz von \u22121,28 Punkten (95 %-KI \u22121,63 bis \u22120,93) <span class=\"citation\" data-cites=\"10.1001/jamanetworkopen.2023.35541\">[15]</span>. Nach zw\u00f6lf Monaten war der Impostor-Effekt nicht mehr signifikant (p = 0,081), das Selbstmitgef\u00fchl blieb verbessert <span class=\"citation\" data-cites=\"10.1097/JHM-D-23-00232\">[25]</span>. Ein systematisches Review von sechs Online-Interventionen fand nur zwei RCTs <span class=\"citation\" data-cites=\"10.1186/s12909-024-06340-y\">[26]</span>. Die Orientierungswochen-Workshops sind unkontrollierte Vorher-Nachher-Vergleiche, mit 53 % gegen\u00fcber 43 % mit h\u00e4ufigem oder intensivem Impostor-Erleben bei 222 Studierenden <span class=\"citation\" data-cites=\"10.1093/milmed/usaf068\">[18]</span>, 91,6 % Wiedererkennung bei 49 Erstsemestern <span class=\"citation\" data-cites=\"10.1016/j.heliyon.2024.e29478\">[17]</span>, 96 % bei 21 Assistenz\u00e4rzt*innen <span class=\"citation\" data-cites=\"10.15766/mep_2374-8265.11004\">[27]</span>.</p>\n</div>\n</div>\n</div>\n</section>\n<section class=\"level2\" id=\"was-wir-noch-nicht-wissen\">\n<h2 class=\"anchored\" data-anchor-id=\"was-wir-noch-nicht-wissen\">Was wir (noch) nicht wissen</h2>\n<ul>\n<li><strong>Ob wir alle dasselbe messen.</strong> Je nach Instrument liegt die Pr\u00e4valenz zwischen 38 und 54 %, und die Grenzwerte der CIPS sind Konvention. Ein systematisches Review der Skalen fand keinen Goldstandard <span class=\"citation\" data-cites=\"10.3389/fpsyg.2019.00671\">[28]</span>.</li>\n<li><strong>Was in Deutschland gilt.</strong> Die Daten stammen aus Nordamerika, Skandinavien, Gro\u00dfbritannien und Asien. F\u00fcr deutsche Medizinfakult\u00e4ten mit ihrem Auswahlverfahren und ihrem Curriculum gibt es keine Erhebung.</li>\n<li><strong>Ob Workshops mehr sind als ein Strohfeuer.</strong> Die Evidenz f\u00fcr Normalisierungsworkshops beruht auf Vorher-Nachher-Vergleichen ohne Kontrollgruppe. Ob der Effekt \u00fcber die Orientierungswoche hinaus h\u00e4lt, ist offen.</li>\n<li><strong>Wie viel davon Gef\u00fchl und wie viel davon Umgebung ist.</strong> Wenn Zugeh\u00f6rigkeit und Ranking die Werte so stark verschieben, ist unklar, welcher Anteil \u00fcberhaupt durch individuelle Ma\u00dfnahmen erreichbar ist.</li>\n</ul>\n</section>\n<section class=\"level2\" id=\"fazit\">\n<h2 class=\"anchored\" data-anchor-id=\"fazit\">Fazit</h2>\n<ul>\n<li>Etwa die H\u00e4lfte aller Medizinstudierenden kennt das Gef\u00fchl, nicht wirklich hierherzugeh\u00f6ren, zu Studienbeginn noch mehr. Wer es hat, ist damit nicht die Ausnahme, sondern die Regel.</li>\n<li>Das Gef\u00fchl ist keine Schw\u00e4che und keine Diagnose, sondern eine Reaktion auf eine Umgebung aus Auswahl, Vergleich und Perfektionsanspruch.</li>\n<li>Es h\u00e4ngt mit Angst, Ersch\u00f6pfung und psychischer Belastung zusammen, wenn es anh\u00e4lt. Dann ist es ein Grund, sich Unterst\u00fctzung zu holen.</li>\n<li>Gruppencoaching wirkt nachweislich, die Wirkung auf das Impostor-Erleben verblasst aber nach einem Jahr. Was (hoffentlich) bleibt, ist ein freundlicherer Umgang mit sich selbst.</li>\n<li>Der einfachste wirksame Schritt ist, dar\u00fcber zu sprechen. Die Person neben Euch kennt es sehr wahrscheinlich auch.</li>\n</ul>\n<div class=\"callout callout-style-default callout-note callout-titled\">\n<div aria-controls=\"callout-2\" aria-expanded=\"false\" aria-label=\"Toggle callout\" class=\"callout-header d-flex align-content-center collapsed\" data-bs-target=\".callout-2-contents\" data-bs-toggle=\"collapse\">\n<div class=\"callout-icon-container\">\n<i class=\"callout-icon\"></i>\n</div>\n<div class=\"callout-title-container flex-fill\">\n<span class=\"screen-reader-only\">Hinweis</span>Transparenzkasten\n</div>\n<div class=\"callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end\"><i class=\"callout-toggle\"></i></div>\n</div>\n<div class=\"callout-2-contents callout-collapse collapse\" id=\"callout-2\">\n<div class=\"callout-body-container callout-body\">\n<p><strong>Transparenzhinweis:</strong></p>\n<ul>\n<li><strong>Interessenkonflikte:</strong> Keine angegeben.</li>\n<li><strong>Finanzierung:</strong> Keine Angabe.</li>\n<li><strong>KI-Nutzung:</strong> Claude (Anthropic) wurde zur strukturellen Konzeption und zur sprachlichen Bearbeitung auf Basis eines vom Autor verfassten und immer wieder \u00fcberarbeiteten Gedankengangs eingesetzt.</li>\n<li><strong>Eigene Beteiligung:</strong> Der Autor ist in der medizinischen Ausbildungsforschung t\u00e4tig und hat auch mal Medizin studiert. Obwohl er heute Arzt und Professor ist, ist er im Studium durch Pr\u00fcfungen durchgefallen und kennt das Impostor-Gef\u00fchl sehr gut (auch wenn er das damals nicht so sch\u00f6n benennen konnte).</li>\n</ul>\n</div>\n</div>\n</div>\n</section>\n<section class=\"level2\" id=\"referenzen\">\n</section>\n<div class=\"default\" id=\"quarto-appendix\"><section class=\"quarto-appendix-contents\" id=\"quarto-bibliography\"><h2 class=\"anchored quarto-appendix-heading\">Referenzen</h2><div class=\"references csl-bib-body\" id=\"refs\">\n<div class=\"csl-entry\" id=\"ref-10.1007/s10459-026-10513-3\">\n1. Omar YM, Khattab YA, Abdelmageed A, Messak M, Mandour Y, Shabeeb AE, u.\u00a0a. The impostor phenomenon construct in medical education: a meta-analysis of its prevalence and a critical appraisal of its measurement. Advances in Health Sciences Education. 2026. <a href=\"https://doi.org/10.1007/s10459-026-10513-3\">https://doi.org/10.1007/s10459-026-10513-3</a>.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1371/journal.pone.0351713\">\n2. Vera-Ponce VJ, Huaman-Vega CH, Zuzunaga-Montoya FE, Guerrero Uceda CI, Le\u00f3n-Figueroa DA, Rivera-Lozada O, u.\u00a0a. <a href=\"https://doi.org/10.1371/journal.pone.0351713\">Global prevalence of impostor phenomenon in medical students: A systematic review and meta-analysis</a>. PLOS One. 2026;21:e0351713.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.22454/FamMed.2021.799997\">\n3. Rosenthal S, Schlussel Y, Yaden MB, DeSantis J, Trayes K, Pohl C, u.\u00a0a. <a href=\"https://doi.org/10.22454/fammed.2021.799997\">Persistent Impostor Phenomenon Is Associated With Distress in Medical Students</a>. Family Medicine. 2021;53:118\u201322.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1037/h0086006\">\n4. Clance PR, Imes SA. <a href=\"https://doi.org/10.1037/h0086006\">The imposter phenomenon in high achieving women: Dynamics and therapeutic intervention.</a> Psychotherapy: Theory, Research &amp;amp; Practice. 1978;15:241\u20137.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.3389/fpsyg.2020.575024\">\n5. Feenstra S, Begeny CT, Ryan MK, Rink FA, Stoker JI, Jordan J. <a href=\"https://doi.org/10.3389/fpsyg.2020.575024\">Contextualizing the Impostor <span>\"Syndrome\"</span></a>. Frontiers in Psychology. 2020;11.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.5116/ijme.5f54.c8f8\">\n6. Thomas M, Bigatti S. <a href=\"https://doi.org/10.5116/ijme.5f54.c8f8\">Perfectionism, impostor phenomenon, and mental health in medicine: a literature review</a>. International Journal of Medical Education. 2020;11:201\u201313.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1007/s40670-022-01675-x\">\n7. Franchi T, Russell-Sewell N. <a href=\"https://doi.org/10.1007/s40670-022-01675-x\">Medical Students and the Impostor Phenomenon: A Coexistence Precipitated and Perpetuated by the Educational Environment?</a> Medical Science Educator. 2022;33:27\u201338.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1080/10401334.2022.2056741\">\n8. Neufeld A, Babenko O, Lai H, Svrcek C, Malin G. <a href=\"https://doi.org/10.1080/10401334.2022.2056741\">Why Do We Feel Like Intellectual Frauds? A Self-Determination Theory Perspective on the Impostor Phenomenon in Medical Students</a>. Teaching and Learning in Medicine. 2022;35:180\u201392.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1016/j.jnma.2023.01.012\">\n9. Rice J, Rosario-Williams B, Williams F, West-Livingston L, Savage D, Wilensky JA, u.\u00a0a. <a href=\"https://doi.org/10.1016/j.jnma.2023.01.012\">Impostor syndrome among minority medical students who are underrepresented in medicine</a>. Journal of the National Medical Association. 2023;115:191\u20138.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1136/bmjopen-2025-100557\">\n10. Kamran Siddiqui Z, Tomlinson J, Scantlebury A, Jayasuriya R, Church H, Grove A. <a href=\"https://doi.org/10.1136/bmjopen-2025-100557\">Hidden barriers to leadership: a cross-sectional survey of prevalence and predictors of Imposter Phenomenon in Trauma and Orthopaedic surgery in the UK</a>. BMJ Open. 2025;15:e100557.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1080/0142159X.2022.2028751\">\n11. Liu RQ, Davidson J, Van Hooren TA, Van Koughnett JAM, Jones S, Ott MC. <a href=\"https://doi.org/10.1080/0142159x.2022.2028751\">Impostorism and anxiety contribute to burnout among resident physicians</a>. Medical Teacher. 2022;44:758\u201364.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1016/j.mayocp.2022.06.021\">\n12. Shanafelt TD, Dyrbye LN, Sinsky C, Trockel M, Makowski MS, Tutty M, u.\u00a0a. <a href=\"https://doi.org/10.1016/j.mayocp.2022.06.021\">Imposter Phenomenon in US Physicians Relative to the US Working Population</a>. Mayo Clinic Proceedings. 2022;97:1981\u201393.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1007/s11606-019-05364-1\">\n13. Bravata DM, Watts SA, Keefer AL, Madhusudhan DK, Taylor KT, Clark DM, u.\u00a0a. <a href=\"https://doi.org/10.1007/s11606-019-05364-1\">Prevalence, Predictors, and Treatment of Impostor Syndrome: a Systematic Review</a>. Journal of General Internal Medicine. 2019;35:1252\u201375.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1001/jamanetworkopen.2022.10752\">\n14. Fainstad T, Mann A, Suresh K, Shah P, Dieujuste N, Thurmon K, u.\u00a0a. <a href=\"https://doi.org/10.1001/jamanetworkopen.2022.10752\">Effect of a Novel Online Group-Coaching Program to Reduce Burnout in Female Resident Physicians: A Randomized Clinical Trial</a>. JAMA Network Open. 2022;5:e2210752.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1001/jamanetworkopen.2023.35541\">\n15. Mann A, Shah AN, Thibodeau PS, Dyrbye L, Syed A, Woodward MA, u.\u00a0a. <a href=\"https://doi.org/10.1001/jamanetworkopen.2023.35541\">Online Well-Being Group Coaching Program for Women Physician Trainees: A Randomized Clinical Trial</a>. JAMA Network Open. 2023;6:e2335541.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1111/medu.70076\">\n16. Gisselbaek M, Seyour M, Saxena S, Berger\u2010Estilita J, LaDonna KA, Elia N, u.\u00a0a. <a href=\"https://doi.org/10.1111/medu.70076\">Rethinking the impostor phenomenon: An umbrella review of concept, context and interventions</a>. Medical Education. 2025;60:607\u201324.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1016/j.heliyon.2024.e29478\">\n17. Wrench A, Padilla M, O'Malley C, Levy A. <a href=\"https://doi.org/10.1016/j.heliyon.2024.e29478\">Impostor phenomenon: Prevalence among 1st year medical students and strategies for mitigation</a>. Heliyon. 2024;10:e29478.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1093/milmed/usaf068\">\n18. Kim E, Dupont J, Durning SJ, Landoll R, Soh M. <a href=\"https://doi.org/10.1093/milmed/usaf068\">Mitigating Impostor Phenomenon of Onboarding Military Medical Students: A Workshop Utilizing Situated Learning Theory</a>. Military Medicine. 2025;190:e2153\u20139.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1186/s12909-026-09041-w\">\n19. Polemidiotis M, Sayani N, O'Kelly S, Sreenan S, Brennan M. <a href=\"https://doi.org/10.1186/s12909-026-09041-w\">Structured peer engagement for early-stage medical students provides a safe space and creates a sense of community, combatting imposter syndrome and improving wellbeing</a>. BMC Medical Education. 2026;26.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1007/s40670-019-00718-0\">\n20. Houseknecht VE, Roman B, Stolfi A, Borges NJ. <a href=\"https://doi.org/10.1007/s40670-019-00718-0\">A Longitudinal Assessment of Professional Identity, Wellness, Imposter Phenomenon, and Calling to Medicine Among Medical Students</a>. Medical Science Educator. 2019;29:493\u20137.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1093/milmed/usaf373\">\n21. Kim E, Dupont J, Durning SJ, Bulaklak J, Crosier A, Soh M. <a href=\"https://doi.org/10.1093/milmed/usaf373\">Exploring Impostor Phenomenon During Pre-Clerkship Period in Military Medical School</a>. Military Medicine. 2025;191:e413\u201320.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1186/s12909-024-05788-2\">\n22. Kristoffersson E, Boman J, Bitar A. <a href=\"https://doi.org/10.1186/s12909-024-05788-2\">Impostor phenomenon and its association with resilience in medical education \u2013 a questionnaire study among Swedish medical students</a>. BMC Medical Education. 2024;24.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.3389/fmed.2025.1623792\">\n23. Jansson A, Boman J, Sch\u00e9le I, Holmstr\u00f6m S, Rozental A, Semb O, u.\u00a0a. <a href=\"https://doi.org/10.3389/fmed.2025.1623792\">Impostor phenomenon and its association with perceived stress and anxiety among students in medical and social sciences at a Swedish university</a>. Frontiers in Medicine. 2025;12.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1007/s40596-021-01503-1\">\n24. Brennan-Wydra E, Chung HW, Angoff N, ChenFeng J, Phillips A, Schreiber J, u.\u00a0a. <a href=\"https://doi.org/10.1007/s40596-021-01503-1\">Maladaptive Perfectionism, Impostor Phenomenon, and Suicidal Ideation Among Medical Students</a>. Academic Psychiatry. 2021;45:708\u201315.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1097/JHM-D-23-00232\">\n25. Fainstad T, Syed A, Thibodeau PS, Vinaithirthan V, Jones CD, Mann A. <a href=\"https://doi.org/10.1097/jhm-d-23-00232\">Long-Term Impact of an Online Physician Group-Coaching Program to Improve Burnout and Self-Compassion in Trainees</a>. Journal of Healthcare Management. 2024;69:414\u201323.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1186/s12909-024-06340-y\">\n26. Hsu C-L, Liu C-H, Huang C-C, Chen H-L, Chiu Y-L, Yang C-W. <a href=\"https://doi.org/10.1186/s12909-024-06340-y\">The effectiveness of online educational interventions on impostor syndrome and burnout among medical trainees: a systematic review</a>. BMC Medical Education. 2024;24.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.15766/mep_2374-8265.11004\">\n27. Baumann N, Faulk C, Vanderlan J, Chen J, Bhayani RK. Small-Group Discussion Sessions on Imposter Syndrome. MedEdPORTAL. 2020. <a href=\"https://doi.org/10.15766/mep_2374-8265.11004\">https://doi.org/10.15766/mep_2374-8265.11004</a>.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.3389/fpsyg.2019.00671\">\n28. Mak KKL, Kleitman S, Abbott MJ. <a href=\"https://doi.org/10.3389/fpsyg.2019.00671\">Impostor Phenomenon Measurement Scales: A Systematic Review</a>. Frontiers in Psychology. 2019;10.\n</div>\n</div></section><section class=\"quarto-appendix-contents\" id=\"quarto-reuse\"><h2 class=\"anchored quarto-appendix-heading\">Wiederverwendung</h2><div class=\"quarto-appendix-contents\"><div><a href=\"https://creativecommons.org/licenses/by/4.0/deed.de\" rel=\"license\">CC BY 4.0</a></div></div></section><section class=\"quarto-appendix-contents\" id=\"quarto-citation\"><h2 class=\"anchored quarto-appendix-heading\">Zitat</h2><div><div class=\"quarto-appendix-secondary-label\">Mit BibTeX zitieren:</div><pre class=\"sourceCode code-with-copy quarto-appendix-bibtex\"><code class=\"sourceCode bibtex\">@misc{friederichs2026,\n  author = {Friederichs, Hendrik},\n  title = {Das Impostor-Ph\u00e4nomen \u2013 was mache ich hier?},\n  date = {2026-09-10},\n  url = {https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/},\n  doi = { 10.59350/0vw9m-k3092},\n  langid = {de}\n}\n</code></pre><div class=\"quarto-appendix-secondary-label\">Bitte zitieren Sie diese Arbeit als:</div><div class=\"csl-entry quarto-appendix-citeas\" id=\"ref-friederichs2026\">\n1. Friederichs H. <a href=\"https://doi.org/ 10.59350/0vw9m-k3092\">Das\nImpostor-Ph\u00e4nomen \u2013 was mache ich hier?</a> 2026.\n</div></div></section></div>","doi":"https://doi.org/10.59350/9dyyf-tve84","guid":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/","image":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/FriederichsH_impostor.png","language":"de","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788912000,"reference":[{"id":"https://doi.org/10.1007/s10459-026-10513-3","unstructured":"Omar, Y. M., Khattab, Y. A., Abdelmageed, A., Messak, M., Mandour, Y., Shabeeb, A. E., Zakaria, A. M., &amp; Abouelmagd, M. E. (2026). The impostor phenomenon construct in medical education: a meta-analysis of its prevalence and a critical appraisal of its measurement. <i>Advances in Health Sciences Education</i>."},{"id":"https://doi.org/10.1371/journal.pone.0351713","unstructured":"Vera-Ponce, V. J., Huaman-Vega, C. H., Zuzunaga-Montoya, F. E., Guerrero Uceda, C. I., Le\u00f3n-Figueroa, D. A., Rivera-Lozada, O., Aguirre-Milachay, E., Gutierrez De Carrillo, C. I., Valladares-Garrido, M. J., &amp; Forero, D. A. (2026). Global prevalence of impostor phenomenon in medical students: A systematic review and meta-analysis. <i>PLOS One</i>, <i>21</i>(8), e0351713."},{"id":"https://doi.org/10.22454/fammed.2021.799997","unstructured":"Rosenthal, S., Schlussel, Y., Yaden, M. B., DeSantis, J., Trayes, K., Pohl, C., &amp; Hojat, M. (2021). 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Perfectionism, impostor phenomenon, and mental health in medicine: a literature review. <i>International Journal of Medical Education</i>, <i>11</i>, 201\u2013213."},{"id":"https://doi.org/10.1007/s40670-022-01675-x","unstructured":"Franchi, T., &amp; Russell-Sewell, N. (2022). Medical Students and the Impostor Phenomenon: A Coexistence Precipitated and Perpetuated by the Educational Environment?. <i>Medical Science Educator</i>, <i>33</i>(1), 27\u201338."},{"id":"https://doi.org/10.1080/10401334.2022.2056741","unstructured":"Neufeld, A., Babenko, O., Lai, H., Svrcek, C., &amp; Malin, G. (2022). Why Do We Feel Like Intellectual Frauds? A Self-Determination Theory Perspective on the Impostor Phenomenon in Medical Students. <i>Teaching and Learning in Medicine</i>, <i>35</i>(2), 180\u2013192."},{"id":"https://doi.org/10.1016/j.jnma.2023.01.012","unstructured":"Rice, J., Rosario-Williams, B., Williams, F., West-Livingston, L., Savage, D., Wilensky, J. A., &amp; Landry, A. (2023). 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Impostor phenomenon: Prevalence among 1st year medical students and strategies for mitigation. <i>Heliyon</i>, <i>10</i>(8), e29478."},{"id":"https://doi.org/10.1093/milmed/usaf068","unstructured":"Kim, E., Dupont, J., Durning, S. J., Landoll, R., &amp; Soh, M. (2025). Mitigating Impostor Phenomenon of Onboarding Military Medical Students: A Workshop Utilizing Situated Learning Theory. <i>Military Medicine</i>, <i>190</i>(9-10), e2153\u2013e2159."},{"id":"https://doi.org/10.1186/s12909-026-09041-w","unstructured":"Polemidiotis, M., Sayani, N., O'Kelly, S., Sreenan, S., &amp; Brennan, M. (2026). Structured peer engagement for early-stage medical students provides a safe space and creates a sense of community, combatting imposter syndrome and improving wellbeing. <i>BMC Medical Education</i>, <i>26</i>(1)."},{"id":"https://doi.org/10.1007/s40670-019-00718-0","unstructured":"Houseknecht, V. E., Roman, B., Stolfi, A., &amp; Borges, N. J. (2019). A Longitudinal Assessment of Professional Identity, Wellness, Imposter Phenomenon, and Calling to Medicine Among Medical Students. <i>Medical Science Educator</i>, <i>29</i>(2), 493\u2013497."},{"id":"https://doi.org/10.1093/milmed/usaf373","unstructured":"Kim, E., Dupont, J., Durning, S. J., Bulaklak, J., Crosier, A., &amp; Soh, M. (2025). Exploring Impostor Phenomenon During Pre-Clerkship Period in Military Medical School. <i>Military Medicine</i>, <i>191</i>(1-2), e413\u2013e420."},{"id":"https://doi.org/10.1186/s12909-024-05788-2","unstructured":"Kristoffersson, E., Boman, J., &amp; Bitar, A. (2024). Impostor phenomenon and its association with resilience in medical education \u2013 a questionnaire study among Swedish medical students. <i>BMC Medical Education</i>, <i>24</i>(1)."},{"id":"https://doi.org/10.3389/fmed.2025.1623792","unstructured":"Jansson, A., Boman, J., Sch\u00e9le, I., Holmstr\u00f6m, S., Rozental, A., Semb, O., Fahlstr\u00f6m, M., Stenman, L., Bitar, A., &amp; Lindquist, D. (2025). Impostor phenomenon and its association with perceived stress and anxiety among students in medical and social sciences at a Swedish university. <i>Frontiers in Medicine</i>, <i>12</i>."},{"id":"https://doi.org/10.1007/s40596-021-01503-1","unstructured":"Brennan-Wydra, E., Chung, H. W., Angoff, N., ChenFeng, J., Phillips, A., Schreiber, J., Young, C., &amp; Wilkins, K. (2021). Maladaptive Perfectionism, Impostor Phenomenon, and Suicidal Ideation Among Medical Students. <i>Academic Psychiatry</i>, <i>45</i>(6), 708\u2013715."},{"id":"https://doi.org/10.1097/jhm-d-23-00232","unstructured":"Fainstad, T., Syed, A., Thibodeau, P. S., Vinaithirthan, V., Jones, C. D., &amp; Mann, A. (2024). Long-Term Impact of an Online Physician Group-Coaching Program to Improve Burnout and Self-Compassion in Trainees. <i>Journal of Healthcare Management</i>, <i>69</i>(6), 414\u2013423."},{"id":"https://doi.org/10.1186/s12909-024-06340-y","unstructured":"Hsu, C.-L., Liu, C.-H., Huang, C.-C., Chen, H.-L., Chiu, Y.-L., &amp; Yang, C.-W. (2024). The effectiveness of online educational interventions on impostor syndrome and burnout among medical trainees: a systematic review. <i>BMC Medical Education</i>, <i>24</i>(1)."},{"id":"https://doi.org/10.15766/mep_2374-8265.11004","unstructured":"Baumann, N., Faulk, C., Vanderlan, J., Chen, J., &amp; Bhayani, R. K. (2020). Small-Group Discussion Sessions on Imposter Syndrome. <i>MedEdPORTAL</i>."},{"id":"https://doi.org/10.3389/fpsyg.2019.00671","unstructured":"Mak, K. K. L., Kleitman, S., &amp; Abbott, M. J. (2019). Impostor Phenomenon Measurement Scales: A Systematic Review. <i>Frontiers in Psychology</i>, <i>10</i>."}],"rid":"sy0q1-4yg31","summary":"<em> Im Oktober beginnen viele junge Menschen ihr Medizinstudium. Viele von ihnen werden in den ersten Wochen denselben Gedanken haben, n\u00e4mlich dass alle anderen im H\u00f6rsaal besser vorbereitet, kl\u00fcger und sicherer wirken als sie selbst. Dieser Gedanke hat einen Namen, er ist gut untersucht, und er ist erstaunlich verbreitet. </em> Der Gedanke in der ersten Woche Die allererste Vorlesung.","tags":["Studierende","Studienstart","Wohlbefinden","Lernen"],"title":"Das Impostor-Ph\u00e4nomen \u2013 was mache ich hier?","updated_at":1789025415,"url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/","version":"v1"}},{"document":{"authors":[{"contributor_roles":[],"family":"Bekkers","given":"Rene"}],"blog":{"authors":null,"community_id":"c04223e6-4d3d-42ad-a718-878a8fc35d32","created":1739059200,"current_feed_url":null,"description":"Rene Bekkers","doi":"https://doi.org/10.59350/renebekkers","favicon":"https://rogue-scholar.org/api/communities/c04223e6-4d3d-42ad-a718-878a8fc35d32/logo","feed_format":"application/atom+xml","feed_url":"https://renebekkers.wordpress.com/feed/atom","filter":null,"generator":"WordPress.com","home_page_url":"https://renebekkers.wordpress.com","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"renebekkers","status":"active","subfield":"1404","title":"Rene Bekkers","updated":1788987428,"use_api":true},"blog_name":"Rene Bekkers","blog_slug":"renebekkers","content_html":"<p class=\"wp-block-paragraph\">Why is the share of income and wealth that people give to charities lower when their income and wealth are higher? Are more generous persons less likely to accumulate wealth? Or does wealth make people care less about those in need? Can fundraising organizations increase generosity by soliciting gifts in different ways?</p>\n\n\n\n<p class=\"wp-block-paragraph\">Fifteen years of data from the Giving in the Netherlands Panel Survey (Bekkers, De Wit &amp; Wiepking, 2017, p. 65: Figure 24, reproduced below) indicate that households with lower incomes in the Netherlands are more generous than households with higher incomes. In the period 2001-2017, the 10% lowest income households spent about 1.2% of their income on gifts to charitable causes, almost three times as much as the 10% highest incomes (0.4%).  </p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img src=\"https://renebekkers.wordpress.com/wp-content/uploads/2019/11/generosity_decile_nl.png\" alt=\"\" /></figure>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https://www.cbs.nl/nl-nl/maatwerk/2022/10/particuliere-huishoudens-naar-vermogensklassen-2020-\">Register data from Statistics Netherlands</a> on charitable deductions in the income tax indicate a similar pattern for wealth. Households with up to \u20ac5k in wealth deduct gifts worth 1% of their wealth. The wealthiest households, a group of 8,100 households with average wealth of 23.8 million, deduct gifts worth 0.06% of their wealth. </p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img src=\"https://renebekkers.wordpress.com/wp-content/uploads/2024/07/deductions_bywealth.png\" alt=\"\" /></figure>\n\n\n\n<p class=\"wp-block-paragraph\">The project will draw upon unique administrative and survey data from the Netherlands and will conduct new field experiments to test interventions that could increase generosity. This will be the first study tracking changes in wealth and generosity in the Netherlands over the life course, as well as after death through bequests. The research will benefit from collaboration with fundraising organizations in the Netherlands, and an international board of advisors, consisting of Mark Ottoni-Wilhelm at Indiana University in the US, Sarah Smith at the University of Bristol in the UK, and Hans Schmeets at Statistics Netherlands. </p>\n\n\n\n<p class=\"wp-block-paragraph\">The research proposal is also unique in its openness. I work from the principle that transparency supports the reliability of science. Throughout the application process, I have posted all materials for the proposal on a publicly available repository at the Open Science Framework, <a href=\"https://osf.io/e3mux/\">https://osf.io/e3mux/</a>. The repository includes <a href=\"https://osf.io/t6cav\">the initial idea</a>, an extensive document with <a href=\"https://osf.io/45dky\">answers to frequently asked questions</a>, the <a href=\"https://osf.io/59jvk\">full proposal</a>, as well as the <a href=\"https://osf.io/d8gez\">external peer review reports on the full proposal and my responses</a>. </p>\n\n\n\n<p class=\"wp-block-paragraph\">With a grant from the Netherlands Organization for Scientific Research (NWO), I have formed a team to answer these questions at VU Amsterdam with two postdoctoral researchers, Marlou Ramaekers and Wahideh Achbari, and a research assistant, Max Littel. Starting 1 January 2026 the two postdocs have commenced with analyses of survey data and the design of experiments. Read more about the results here: </p>\n\n\n\n<figure class=\"wp-block-embed is-type-wp-embed is-provider-rene-bekkers wp-block-embed-rene-bekkers\"><div class=\"wp-block-embed__wrapper\">\n<blockquote class=\"wp-embedded-content\" data-secret=\"YhT1gkX1YB\"><a href=\"https://renebekkers.wordpress.com/new-research/\">Current research</a></blockquote><iframe loading=\"lazy\" class=\"wp-embedded-content\" sandbox=\"allow-scripts\" security=\"restricted\" style=\"position: absolute; visibility: hidden;\" title=\"&#8220;Current research&#8221; &#8212; Rene Bekkers\" src=\"https://renebekkers.wordpress.com/new-research/embed/#?secret=JHcNNv9Xmb#?secret=YhT1gkX1YB\" data-secret=\"YhT1gkX1YB\" width=\"500\" height=\"282\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\"></iframe>\n</div></figure>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>References</strong></p>\n\n\n\n<p class=\"wp-block-paragraph\">Bekkers, R. (2024). Generating Generosity. Proposal for the NWO SSH Open Competition L 2023. <a href=\"https://osf.io/59jvk\">https://osf.io/59jvk</a></p>\n\n\n\n<p class=\"wp-block-paragraph\">Bekkers, R., De Wit, A. &amp; Wiepking, P. (2017).&nbsp;<a href=\"https://renebekkers.wordpress.com/wp-content/uploads/2018/06/bekkers_dewit_wiepking_17.pdf\">Jubileumspecial: Twintig jaar&nbsp;</a><em><a href=\"https://renebekkers.wordpress.com/wp-content/uploads/2018/06/bekkers_dewit_wiepking_17.pdf\">Geven in Nederland</a>.&nbsp;</em>Pp. 61-94 in: Bekkers, R. Schuyt, T.N.M., &amp; Gouwenberg, B.M. (Eds.).&nbsp;<em>Geven in Nederland 2017: Giften, Sponsoring, Legaten en Vrijwilligerswerk.&nbsp;</em>Amsterdam: Lenthe.</p>\n\n\n\n<p class=\"wp-block-paragraph\"></p>","doi":"https://doi.org/10.59350/28h2k-27w63","guid":"https://renebekkers.wordpress.com/?p=3843","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1721692800,"reference":[{"id":"https://osf.io/59jvk","unstructured":"Unknown title"},{"id":"https://renebekkers.wordpress.com/wp-content/uploads/2018/06/bekkers_dewit_wiepking_17.pdf","unstructured":"Unknown title"}],"rid":"4m7ah-xzm26","summary":"Why is the share of income and wealth that people give to charities lower when their income and wealth are higher? Are more generous persons less likely to accumulate wealth? Or does wealth make people care less about those in need? Can fundraising organizations increase generosity by soliciting gifts in different ways?","tags":["Altruism","Bequests","Center For Philanthropic Studies","Charitable Organizations","Data"],"title":"Generating Generosity","updated_at":1789025413,"url":"https://renebekkers.wordpress.com/2024/07/23/generating-generosity/","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"University of Wroc\u0142aw, Chemistry"}],"contributor_roles":[],"family":"Janeta","given":"Mateusz","url":"https://orcid.org/0000-0003-2197-7913"}],"blog":{"authors":null,"community_id":"c21eed24-c860-43d0-997c-0bc782922544","created":1788652800,"current_feed_url":null,"description":null,"doi":"https://doi.org/10.59350/silsesquioxane","favicon":"https://rogue-scholar.org/api/communities/c21eed24-c860-43d0-997c-0bc782922544/logo","feed_format":"application/atom+xml","feed_url":"https://silsesquioxane.blogspot.com/feeds/posts/default","filter":null,"generator":"Blogger","home_page_url":"https://silsesquioxane.blogspot.com/","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"silsesquioxane","status":"active","subfield":"1604","title":"Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry","updated":1789025287,"use_api":true},"blog_name":"Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry","blog_slug":"silsesquioxane","content_html":"<!--META DESCRIPTION (set separately in Blogger: Settings \u2192 Search preferences \u2192 Meta tags):\nPOSS poly(1-haloacetylene) networks synthesized by catalyst-free, oxygen-initiated solid-state polymerization achieve band gaps of 2.38\u20132.79 eV.-->\n<div style=\"color: #24292f; font-family: Georgia, serif; font-size: 17px; line-height: 1.75; margin: 0px auto; max-width: 780px;\">\n<p>\u4e2d\u6587\u7248\u672c / Chinese version: <a href=\"https://silsesquioxane.blogspot.com/p/poss-1.html\">POSS \u805a(1-\u5364\u4ee3\u4e59\u7094):\u65e0\u50ac\u5316\u5242\u56fa\u76f8\u805a\u5408\u8def\u7ebf</a></p>\n<!--REVISED OPENING PARAGRAPH (section 3d)-->\n<p style=\"background: rgb(245, 248, 251); border-left: 4px solid rgb(15, 76, 129); border-radius: 0px 6px 6px 0px; font-size: 18px; margin: 0px 0px 1.15em; padding: 1.1em 1.3em; text-align: justify;\">Polyhedral oligomeric silsesquioxane (POSS) poly(1-haloacetylene) conjugated networks have been synthesized by Marta Cieplucha, Mateusz Janeta, and S\u0142awomir Szafert at the Faculty of Chemistry, University of Wroc\u0142aw, as reported in <em>Materials Chemistry Frontiers</em> in 2025. Three octa-functionalized monomers, POSS-C2Cl, POSS-C2Br, and POSS-C2I, were prepared by amide coupling of <a href=\"https://silsesquioxane.blogspot.com/2020/08/octa-aminopropyl-silsesquioxane.html\">octa(3-aminopropyl)silsesquioxane</a> with the corresponding 4-(haloethynyl)benzoyl chloride and were shown to undergo thermal polymerization in the solid state without any transition metal catalyst, yielding highly cross-linked poly(1-haloacetylene) networks. This work constitutes the first reported polymerization of a 1-iodoethyne derivative and the first example of 1-haloalkyne polymerization achieved entirely in the absence of metal-based initiators.</p>\n<!--H2 SUBHEADING 1-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Synthesis of Octa-Functionalized POSS Haloalkyne Monomers</h2>\n<figure style=\"margin: 1.5em 0px 2em; text-align: center;\">\n<img alt=\"Synthesis of POSS haloalkyne monomers POSS-C2Cl, POSS-C2Br, and POSS-C2I by amide coupling\" src=\"https://blogger.googleusercontent.com/img/a/AVvXsEjNZtnjmDuWrpEQtGeKyAee5oekwAxIf7crv-ugMF7tJbPW9pQ7cqzmxI03Vpn4-OdAz4DCT6asX1sixDnnMcDkYNXwxQufcUZXSicjajZ1NMDdOyV2Oc0nQiZ9XQypF-4-pnyOr2ZqFKl2LkwTkuiSLYKor_qSsKOgZso40Zsh7LxXW1XUEDqBl5F-UYE\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; max-width: 100%;\"/>\n<figcaption style=\"color: #5f6b7a; font-family: Arial, Helvetica, sans-serif; font-size: 14px; margin-top: 8px; text-align: center;\">\n<strong>Scheme 1.</strong> Synthesis of 1-haloethynyl-functionalized POSS-based monomers. Reaction of octa(3-aminopropyl)silsesquioxane hydrochloride (OAS-POSS) with 4-(haloethynyl)benzoyl chloride (8.2 equiv.) and Et<sub>3</sub>N (16.2 equiv.) in DMF at 0 \u00b0C affords POSS-C2Cl (70%), POSS-C2Br (60%), and POSS-C2I (71%) as the fully octa-substituted amide-linked products.\n    </figcaption>\n</figure>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The three monomers were synthesized by reacting octa(3-aminopropyl)silsesquioxane with the corresponding 4-(haloethynyl)benzoyl chloride in the presence of triethylamine in DMF at 0 degrees Celsius, affording the amide-linked, octa-functional POSS derivatives in isolated yields of 60 to 71 percent. Comprehensive solution and solid-state characterization, including proton and carbon-13 NMR spectroscopy, silicon-29 NMR, nitrogen-15 CP-MAS NMR, DRIFT spectroscopy, and mass spectrometry, confirmed complete octa-substitution, the integrity of the T<sub>8</sub> silsesquioxane cage throughout the synthesis, and the presence of intact haloalkyne functionality in each monomer. The characteristic acetylene stretching vibration near 2197 per centimeter in the DRIFT spectra provided the most direct spectroscopic signature of the C triple bond C unit, and a single symmetric resonance near negative 66 ppm in the silicon-29 NMR spectra confirmed that all eight silicon atoms of the cubic cage remained crystallographically equivalent and that no <a href=\"https://silsesquioxane.blogspot.com/2025/04/unraveling-structure-of.html\">cage rearrangement</a> occurred.</p>\n<!--H2 SUBHEADING 2-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Catalyst-Free, Oxygen-Initiated Solid-State Thermal Polymerization</h2>\n<figure style=\"margin: 1.5em 0px 2em; text-align: center;\">\n<img alt=\"Catalyst-free solid-state polymerization of POSS haloalkyne monomers to poly(1-haloacetylene) T8 cage networks\" src=\"https://blogger.googleusercontent.com/img/a/AVvXsEgE29uI3HKoQpLJ3Y5pqHiEhvtqpxZ4qpbGpo5iOZ0t2KmYXih0B3JmWFiYpzzcv_jP1HRIjTCFc1o8v4VYOrsHENi9n3YA-RzHax_1il4hAsAeJsZRf4cjzjuusB9Ho4Vz2oTLGrEEhVLWkTwtF5JDpc-J6jYrnAS0B-VLBgBJJPCn8jMVWCTmK5XW4Ow\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; max-width: 100%;\"/>\n<figcaption style=\"color: #5f6b7a; font-family: Arial, Helvetica, sans-serif; font-size: 14px; margin-top: 8px; text-align: center;\">\n<strong>Scheme 2.</strong> Catalyst-free solid-state thermal polymerization of POSS-C2X (X = Cl, Br, I) to yield the highly cross-linked polyPOSS-C2X networks. Each of the eight peripheral 1-haloalkyne groups undergoes conversion of the carbon\u2013carbon triple bond to a double bond, generating a three-dimensional poly(1-haloacetylene) network anchored to and propagating from the rigid cubic POSS core. The red fragments on the right represent the newly formed polymer backbone segments connecting adjacent POSS units.\n    </figcaption>\n</figure>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The discovery of solid-state thermal polymerization arose from differential thermal analysis, which revealed distinct exothermic events for each monomer in the temperature range of approximately 130 to 273 degrees Celsius with no accompanying mass loss in the thermogravimetric traces \u2014 the defining signature of a solid-state reaction rather than a decomposition process. The irreversibility of the transformation was confirmed by differential scanning calorimetry: an exothermic peak observed in the first heating cycle was replaced in subsequent cycles by a glass transition temperature characteristic of polymeric materials. Control experiments conducted under strictly oxygen-free conditions in an argon-filled glovebox produced no evidence of polymerization by DRIFT spectroscopy, establishing that molecular oxygen plays a critical initiating role, most plausibly through peroxyl radical formation at elevated temperatures.</p>\n<!--H2 SUBHEADING 3-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Spectroscopic Confirmation of Poly(1-haloacetylene) Network Formation</h2>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The structural transformation from monomer to polymer was confirmed orthogonally by solid-state carbon-13 CP-MAS NMR, DRIFT, and Raman spectroscopy, as well as by XPS analysis. In the carbon-13 CP-MAS spectrum of polyPOSS-C2Br, the signals at 78.3 and 51.7 ppm assigned to the sp-hybridized alkyne carbons disappeared completely, replaced by two new resonances at 139.0 and 135.2 ppm attributable to the sp2-hybridized vinyl carbons of the polyhaloacetylene backbone. The alkyne stretching band at 2197 per centimeter vanished entirely in the DRIFT spectrum of the polymer, while a new absorption at 1768 per centimeter confirmed the formation of the conjugated C=CBr stretching mode. Raman spectroscopy identified new bands at 1580 and 1555 per centimeter characteristic of the trans-polyhaloacetylene backbone, and XPS data confirmed the change in the bromine bonding environment from sp-carbon in the monomer to sp2-carbon in the polymer, ruling out significant side reactions. The silicon-29 CP-MAS spectrum retained a single symmetric resonance at negative 66.2 ppm, confirming complete preservation of the T<sub>8</sub> cage throughout polymerization.</p>\n<!--H2 SUBHEADING 4-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Polymerization Kinetics and Activation Energies by the Kissinger Method</h2>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">\n    Polymerization kinetics, monitored by time-resolved Raman spectroscopy under isothermal conditions, followed a pseudo-second-order model for all three monomers. For POSS-C2Br at 165 degrees Celsius, more than 47 percent conversion was achieved within the first 10 minutes and full conversion within 6 hours. For POSS-C2Cl at 145 degrees Celsius and POSS-C2I at 175 degrees Celsius, complete conversion required 24 and 25 hours, respectively. Apparent activation energies determined by the Kissinger method from non-isothermal DTA experiments were 179 kJ/mol for POSS-C2Br, 209 kJ/mol for POSS-C2Cl, and 217 kJ/mol for POSS-C2I, values substantially higher than those for classical radical polymerizations of vinyl monomers, reflecting the greater energetic barrier of triple bond activation under solid-state constraints.\n  </p>\n<!--H2 SUBHEADING 5-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Thermal Stability, Insolubility, and Optical Band Gaps of the Cross-Linked Networks</h2>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">\n    All three polymers are completely insoluble in common organic solvents and thermally stable up to decomposition onset temperatures of 267, 287, and 309 degrees Celsius for polyPOSS-C2Br, polyPOSS-C2Cl, and polyPOSS-C2I, respectively. The three-dimensional cross-linking topology enforced by the cubic POSS scaffold, where eight alkyne groups per cage simultaneously engage in polymerization, is responsible for the exceptional insolubility and mechanical robustness of the resulting networks. Glass transition temperatures of 51, 140, and 211 degrees Celsius for the chloro, bromo, and iodo polymers, respectively, confirm that all three materials behave as glassy solids at ambient temperature.\n  </p>\n<figure style=\"margin: 1.5em 0px 2em; text-align: center;\">\n<img alt=\"Bar chart of direct and indirect optical band gaps of polyPOSS-C2Cl, polyPOSS-C2Br, and polyPOSS-C2I determined by Tauc plot analysis of solid-state UV-Vis absorption spectra showing systematic decrease from 2.79 eV to 2.38 eV with increasing halogen polarizability\" src=\"https://blogger.googleusercontent.com/img/a/AVvXsEjiUpAMs8KBXZJLeTW7wxcQW4hreTQjZDsxfXj7i1WD2sU7RPc3YFpc3owbUMHKxU0ChmSrOhGQt_eKUuV957YpkgxtkvNZR5V_AT1f6H1NRJh6ceD6VNzMHzcD0B5WnlRsmHDSyhRbJYcI77ij3Z7yqnIH85UMKlXQzIgoueTIXG7IzzuLJxmedy74_XA=s1600\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; max-width: 100%;\"/>\n<figcaption style=\"color: #5f6b7a; font-family: Arial, Helvetica, sans-serif; font-size: 14px; margin-top: 8px; text-align: center;\">\n<strong>Fig. 8.</strong> Direct (blue bars) and indirect (dark red bars) optical band gaps of polyPOSS-C2Cl, polyPOSS-C2Br, and polyPOSS-C2I determined by Tauc plot analysis of solid-state UV-Vis absorption spectra, with structural fragments of the corresponding repeating units shown below each column. The direct band gap decreases systematically from 2.79 eV (Cl) to 2.74 eV (Br) to 2.38 eV (I), reflecting the increasing polarizability of the halogen substituent incorporated directly into the polymer backbone.\n    </figcaption>\n</figure>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">\n    The optical properties of the polymers, investigated by solid-state UV-Vis spectroscopy and Tauc plot analysis, reveal direct optical band gaps of 2.79 eV for polyPOSS-C2Cl, 2.74 eV for polyPOSS-C2Br, and 2.38 eV for polyPOSS-C2I. All three values fall within the visible light range of 1 to 3 eV considered optimal for photovoltaic and optoelectronic applications. The absorption profiles of all polymers are substantially broader and red-shifted relative to their monomers, consistent with the formation of an extended pi-conjugated system along the polyhaloacetylene backbone. The systematic narrowing of the band gap from the chloro to the iodo polymer reflects the increase in halogen polarizability and its influence on the electronic structure of the conjugated chain. Indirect band gaps were additionally identified at 2.19 eV for polyPOSS-C2Cl, 1.57 eV for polyPOSS-C2Br, and 1.47 eV for polyPOSS-C2I, extending the optical response of the iodo polymer well into the near-infrared region.\n  </p>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">Taken together, this work establishes a new synthetic paradigm for the preparation of hybrid conjugated polymer networks by harnessing the geometric rigidity and thermal robustness of the cubic POSS scaffold to direct three-dimensional cross-linking of poly(1-haloacetylene) chains through a catalyst-free, oxygen-initiated solid-state process. The resulting materials combine the semiconducting properties of halogenated polyacetylenes with the exceptional thermal stability and structural precision of silsesquioxane-based hybrid architectures, positioning them as promising candidates for exploration in organic photovoltaics, field-effect transistors, <a href=\"https://silsesquioxane.blogspot.com/2021/04/advanced-fluorescent-silsesquioxane.html\">chemical sensors</a>, and electrochromic devices. This study continues and expands the broader research program of the Janeta and Szafert groups at the University of Wroc\u0142aw on functional POSS-based hybrid materials, which has previously encompassed <a href=\"https://silsesquioxane.blogspot.com/2018/07/porous-silsesquioxane-imine-frameworks.html\">imine-functionalized POSS for supramolecular assembly and iodine capture</a>, <a href=\"https://silsesquioxane.blogspot.com/2026/02/zinc-imine-poss-quattro-site-catalyst.html\">zinc-POSS complexes for catalytic CO<sub>2</sub> cycloaddition</a>, and <a href=\"https://silsesquioxane.blogspot.com/2025/04/poss-as-photocatalyst.html\">difluoroboron-POSS photocatalysts for the selective oxidation of sulfides to sulfoxides</a>.</p>\n<!--UPDATED CITATION BLOCK (section 3h)-->\n<div style=\"background-color: #f7f7fb; border-left: 4px solid rgb(15, 76, 129); border-radius: 0px 6px 6px 0px; font-family: Arial, Helvetica, sans-serif; font-size: 0.92em; line-height: 1.6; margin-top: 32px; padding: 12px 16px;\">\n<strong>Original Publication</strong><br/>\n    Cieplucha, M.; Janeta, M.; Szafert, S.\n    Hybrid inorganic\u2013organic polyhedral oligomeric silsesquioxane-based poly(1-haloacetylene)s: thermal, solid-state polymerization.\n    <em>Materials Chemistry Frontiers</em> <strong>2025</strong>, <strong>9</strong>, 3034.<br/>\n    DOI: <a href=\"https://doi.org/10.1039/d5qm00583c\" rel=\"noopener noreferrer\" target=\"_blank\">10.1039/d5qm00583c</a>\n    \u00a0|\u00a0\n    <a href=\"https://pubs.rsc.org/en/content/articlelanding/2025/qm/d5qm00583c\" rel=\"noopener noreferrer\" target=\"_blank\">View at RSC Publishing</a>\n</div>\n<hr style=\"border: 0px; border-top: 1px solid rgb(227, 232, 238); margin: 2.2em 0px 1.4em;\"/>\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Cite this post</h2>\n<p style=\"color: #5f6b7a; font-family: Arial, Helvetica, sans-serif; font-size: 14px; margin: 0px 0px 0.8em;\">This post has its own persistent identifier. Please use the DOI below when citing it.</p>\n<p style=\"color: #24292f; font-family: Georgia, serif; font-size: 16px; line-height: 1.7; margin: 0px 0px 1.15em; text-align: left;\">Janeta, M. (2026). POSS Poly(1-Haloacetylene): Catalyst-Free Solid-State Route. <em>Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry</em>. <a href=\"https://doi.org/10.59350/3pnqc-4p954\">https://doi.org/10.59350/3pnqc-4p954</a></p>\n<script type=\"application/ld+json\">\n{\n  \"@context\": \"https://schema.org\",\n  \"@type\": \"BlogPosting\",\n  \"headline\": \"POSS Poly(1-Haloacetylene): Catalyst-Free Solid-State Route\",\n  \"url\": \"https://silsesquioxane.blogspot.com/2026/08/hybrid-inorganicorganic-poss-based.html\",\n  \"mainEntityOfPage\": \"https://silsesquioxane.blogspot.com/2026/08/hybrid-inorganicorganic-poss-based.html\",\n  \"identifier\": \"https://doi.org/10.59350/3pnqc-4p954\",\n  \"sameAs\": [\n    \"https://doi.org/10.59350/3pnqc-4p954\",\n    \"https://rogue-scholar.org/records/9951n-bhj92\"\n  ],\n  \"datePublished\": \"2026-09-01\",\n  \"inLanguage\": \"en\",\n  \"license\": \"https://creativecommons.org/licenses/by/4.0/\",\n  \"author\": {\n    \"@type\": \"Person\",\n    \"name\": \"Mateusz Janeta\",\n    \"url\": \"https://sites.google.com/view/mateusz-janeta/\"\n  },\n  \"citation\": {\n    \"@type\": \"ScholarlyArticle\",\n    \"name\": \"Hybrid inorganic-organic polyhedral oligomeric silsesquioxane-based poly(1-haloacetylene)s: thermal, solid-state polymerization\",\n    \"identifier\": \"https://doi.org/10.1039/d5qm00583c\"\n  }\n}\n</script>\n</div>","doi":"https://doi.org/10.59350/92dfm-jvk79","guid":"tag:blogger.com,1999:blog-2875892712213933214.post-6710372823875080355","image":"https://blogger.googleusercontent.com/img/a/AVvXsEjNZtnjmDuWrpEQtGeKyAee5oekwAxIf7crv-ugMF7tJbPW9pQ7cqzmxI03Vpn4-OdAz4DCT6asX1sixDnnMcDkYNXwxQufcUZXSicjajZ1NMDdOyV2Oc0nQiZ9XQypF-4-pnyOr2ZqFKl2LkwTkuiSLYKor_qSsKOgZso40Zsh7LxXW1XUEDqBl5F-UYE=s72-c","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788998400,"rid":"111ng-se271","summary":"\u4e2d\u6587\u7248\u672c / Chinese version: POSS \u805a(1-\u5364\u4ee3\u4e59\u7094):\u65e0\u50ac\u5316\u5242\u56fa\u76f8\u805a\u5408\u8def\u7ebf Polyhedral oligomeric silsesquioxane (POSS) poly(1-haloacetylene) conjugated networks have been synthesized by Marta Cieplucha, Mateusz Janeta, and S\u0142awomir Szafert at the Faculty of Chemistry, University of Wroc\u0142aw, as reported in <em> Materials Chemistry Frontiers </em> in 2025.","tags":["Hybrid Materials","Polymer Nanocomposites","POSS","POSS Functionalization","POSS Synthesis"],"title":"POSS Poly(1-Haloacetylene): Catalyst-Free Solid-State Route","updated_at":1789025413,"url":"https://silsesquioxane.blogspot.com/2026/09/poss-poly1-haloacetylene-catalyst-free.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"National Autonomous University of Mexico, Instituto de Qu\u00edmica"}],"contributor_roles":[],"family":"Barroso-Flores","given":"Joaqu\u00edn","url":"https://orcid.org/0000-0003-0554-7569"}],"blog":{"authors":null,"community_id":"9ddd7090-8504-47e7-9389-267cfac8c5f6","created":1753833600,"current_feed_url":null,"description":"Scientific log of a computational chemist - \"Make like a molecule and React!\"","doi":"https://doi.org/10.59350/joaquinbarroso","favicon":"https://rogue-scholar.org/api/communities/9ddd7090-8504-47e7-9389-267cfac8c5f6/logo","feed_format":"application/atom+xml","feed_url":"https://joaquinbarroso.com/feed/atom/","filter":null,"generator":"WordPress.com","home_page_url":"https://joaquinbarroso.com","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"joaquinbarroso","status":"active","subfield":"1606","title":"Dr. Joaquin Barroso's Blog","updated":1788965940,"use_api":null},"blog_name":"Dr. Joaquin Barroso's Blog","blog_slug":"joaquinbarroso","content_html":"<p class=\"wp-block-paragraph\">This a guest post by Yamil Hern\u00e1ndez, first year PhD student on loan from Puebla, who is working with us in photosynthesis related projects for his thesis. </p>\n<p class=\"wp-block-paragraph\">VMD (Visual Molecular Dynamics) is a free widely known visualizer developed by the Theoretical and Computational Biophysics Group from the University of Illinois. It is primarily used to analyze and visualize molecular dynamics (MD) results, as well as to prepare biological systems for further simulations. However, VMD is highly versatile; its functionalities extend far beyond MD, making it an excellent tool for analyzing molecular results from quantum mechanical calculations. In this blog post, we delve into some of these non-standard applications of VMD</p>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7065\" data-attachment-id=\"7065\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture0\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg\" data-orig-size=\"1194,794\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture0/\" height=\"680\" sizes=\"(max-width: 1024px) 100vw, 1024px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=1024\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=1024 1024w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=768 768w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg 1194w\" width=\"1024\"/></a></figure>\n<h2 class=\"wp-block-heading\">1. Plotting Frontier Molecular Orbitals (FMO) and Electrostatic Potential (ESP)</h2>\n<p class=\"wp-block-paragraph\">VMD is able to plot .cube files, which can be generated by quantum chemistry software or analysis tools like GaussView, Chemcraft, or Multiwfn. </p>\n<p class=\"wp-block-paragraph\">In the following example, we use a glucose molecule optimized at the B3LYP-D3/6-311+G** level of theory using the SMD implicit solvent model to simulate an acqueous environment in ORCA 6.1. FMO and ESP .cube files were generated using Multiwfn. </p>\n<h2 class=\"wp-block-heading\">1.1 Frontier Molecular Orbitals (FMO)</h2>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">Load each orbital .cube file as a <strong>New Molecule</strong> (separated molecule ID's). This will display the molecule framework. You can customize the molecular representation as described below. Change the <strong>Coloring Method</strong> to <strong>Element</strong> so the atoms are distinct. (In this example we changed the carbon color to silver in <strong>Color Controls</strong> window.)</p>\n<p class=\"wp-block-paragraph\">Open the <strong>Graphical Representation</strong> window. Let's walk through plotting the HOMO (the process for the LUMO or any other orbital is identical).</p>\n<p class=\"wp-block-paragraph\">With the orbital molecule selected in <strong>Graphical Representation</strong>, click <strong>Create Rep</strong> twice to generate two identical duplicate layers.</p>\n<p class=\"wp-block-paragraph\">Select the first new representation layer: </p>\n<ul class=\"wp-block-list\">\n<li>Change the <strong>Coloring Method</strong> to <strong>Volume</strong> and the <strong>Drawing Method</strong> to <strong>Isosurface</strong>.</li>\n<li>Change the <strong>Draw</strong> dropdown from Points to Solid Surface.</li>\n<li>Set the <strong>isovalue</strong> to 0.02 (the standard threshold for molecular orbitals). Part of the orbital surface will appear in white.</li>\n<li>Switch to <strong>Trajectory</strong> tab in the same window and adjust the <strong>Color Scale Data Range </strong>from -0.1 to 0.1 to apply the phase color.</li>\n</ul>\n<p class=\"wp-block-paragraph\">Select the second duplicate representation layer to map the complementary lobe:  </p>\n<ul class=\"wp-block-list\">\n<li>Repeat the exact same steps, but set the <strong>isovalue</strong> to -0.02.</li>\n</ul>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped wp-block-gallery-1 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7073\" data-attachment-id=\"7073\" data-comments-opened=\"1\" data-id=\"7073\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture0a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg\" data-orig-size=\"778,572\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture0a/\" height=\"572\" sizes=\"(max-width: 778px) 100vw, 778px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=778\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg 778w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=768 768w\" width=\"778\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7068\" data-attachment-id=\"7068\" data-comments-opened=\"1\" data-id=\"7068\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture1a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg\" data-orig-size=\"780,599\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture1a/\" height=\"599\" sizes=\"(max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=768 768w\" width=\"780\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7067\" data-attachment-id=\"7067\" data-comments-opened=\"1\" data-id=\"7067\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture1b\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg\" data-orig-size=\"781,594\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture1b/\" height=\"594\" loading=\"lazy\" sizes=\"auto, (max-width: 781px) 100vw, 781px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=781\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg 781w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=768 768w\" width=\"781\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1c.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7066\" data-attachment-id=\"7066\" data-comments-opened=\"1\" data-id=\"7066\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture1c\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1c-e1788930730384.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1c-e1788930730384.jpg\" data-orig-size=\"690,549\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture1c/\" height=\"621\" loading=\"lazy\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1c.jpg?w=781\" width=\"781\"/></a></figure>\n</figure>\n</div>\n</div>\n<h2 class=\"wp-block-heading\">1.2 Electrostatic Potential (ESP) and other mapped surfaces</h2>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">This procedure applies to most property-mapped volumetric surfaces saved as .cube files. Mapping <strong>ESP</strong> requires two files: the electron density .cuve and the <strong>ESP</strong> .cube files.</p>\n<p class=\"wp-block-paragraph\"><strong>Go to File -&gt; New Molecule</strong> and load the electronic density .cube file first.</p>\n<p class=\"wp-block-paragraph\">Next, select that same molecule ID in the <strong>Load files for</strong>: dropdown menu and load the ESP .cube file into it. The molecule ID should now contain two volumetric datasets (Vol 0 and Vol 1).</p>\n<p class=\"wp-block-paragraph\">Open <strong>Graphical Representations</strong> and customize your underlying molecular structure.</p>\n<p class=\"wp-block-paragraph\">Click <strong>Create Rep</strong> to make a new layer for the surface:</p>\n<ul class=\"wp-block-list\">\n<li>Set<strong> Coloring Method</strong> to <strong>Volume</strong> and <strong>Drawing</strong> <strong>Method</strong> to <strong>Isosurface</strong>.</li>\n<li>Set <strong>Draw</strong> option to<em> Solid Surface</em>.</li>\n<li>Ensure the <strong>Vol</strong> dropdown is set to vol0 corresponding to the electron density .cube file.</li>\n<li>Set the <strong>isovalue</strong> to 0.0004 (atomic units), which is standard for defining the molecular surface.</li>\n</ul>\n<p class=\"wp-block-paragraph\">To map the ESP gradient to this density surface: </p>\n<ul class=\"wp-block-list\">\n<li>Look at the small dropdown menu located between <strong>Coloring Method</strong> and <strong>Material</strong> (It defaults to vol0). Change this to vol1 (the ESP dataset).</li>\n<li>Go to <strong>Trajectory</strong> tab and set the <strong>Color Scale Data Range</strong> from negative to positive values.</li>\n</ul>\n<p class=\"wp-block-paragraph\">By default, VMD applies a Red-White-Blue (RWB) color scale. If you prefer the RGB gradient, open the <strong>Color Controls </strong>window, navigate to the <strong>Color Scale</strong> tab, and change the <strong>Method</strong> to <strong>RGB</strong>.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped wp-block-gallery-2 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7053\" data-attachment-id=\"7053\" data-comments-opened=\"1\" data-id=\"7053\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg\" data-orig-size=\"781,631\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3a-2/\" height=\"631\" loading=\"lazy\" sizes=\"auto, (max-width: 781px) 100vw, 781px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=781\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg 781w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=768 768w\" width=\"781\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7052\" data-attachment-id=\"7052\" data-comments-opened=\"1\" data-id=\"7052\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3b\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg\" data-orig-size=\"779,568\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3b/\" height=\"568\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=768 768w\" width=\"779\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7051\" data-attachment-id=\"7051\" data-comments-opened=\"1\" data-id=\"7051\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3c\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg\" data-orig-size=\"780,639\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3c/\" height=\"639\" loading=\"lazy\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=768 768w\" width=\"780\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7050\" data-attachment-id=\"7050\" data-comments-opened=\"1\" data-id=\"7050\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3d\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg\" data-orig-size=\"780,626\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3d/\" height=\"626\" loading=\"lazy\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=768 768w\" width=\"780\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7049\" data-attachment-id=\"7049\" data-comments-opened=\"1\" data-id=\"7049\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3e\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg\" data-orig-size=\"780,568\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3e/\" height=\"568\" loading=\"lazy\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=768 768w\" width=\"780\"/></a></figure>\n</figure>\n</div>\n</div>\n<h2 class=\"wp-block-heading\">2 Comparison of Molecular Geometries</h2>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">VMD allows you to compare two or more geometries of the same molecule using two different approaches. Crucially, all geometries must share the same atom numbering. To illustrate this process we'll use different geometries of Chlorophyll-a.</p>\n<p class=\"wp-block-paragraph\">One common way to compare molecules is by overlapping them.</p>\n<p class=\"wp-block-paragraph\">First, load the different molecular files into separate molecule IDs:</p>\n<ul class=\"wp-block-list\">\n<li>Go to file menu and click on New Molecule. </li>\n</ul>\n<ul class=\"wp-block-list\">\n<li>In Molecular File Browser, select the file for your first structure and load it. </li>\n</ul>\n<ul class=\"wp-block-list\">\n<li>For the second structure, ensure that Load files for: is set to New Molecule to avoid overwriting the first one, then select and load the file. </li>\n</ul>\n<p class=\"wp-block-paragraph\">Once all structures are loaded, they will appear piled up on top of each other in the OpenGL window.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped wp-block-gallery-3 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7073\" data-attachment-id=\"7073\" data-comments-opened=\"1\" data-id=\"7073\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture0a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg\" data-orig-size=\"778,572\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture0a/\" height=\"572\" sizes=\"(max-width: 778px) 100vw, 778px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=778\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg 778w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=768 768w\" width=\"778\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7085\" data-attachment-id=\"7085\" data-comments-opened=\"1\" data-id=\"7085\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg\" data-orig-size=\"780,473\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4-2/\" height=\"473\" loading=\"lazy\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=768 768w\" width=\"780\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7084\" data-attachment-id=\"7084\" data-comments-opened=\"1\" data-id=\"7084\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg\" data-orig-size=\"779,466\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4a/\" height=\"466\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=768 768w\" width=\"779\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7083\" data-attachment-id=\"7083\" data-comments-opened=\"1\" data-id=\"7083\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4b\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg\" data-orig-size=\"866,528\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4b/\" height=\"528\" loading=\"lazy\" sizes=\"auto, (max-width: 866px) 100vw, 866px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=866\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg 866w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=768 768w\" width=\"866\"/></a></figure>\n</figure>\n</div>\n</div>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">Before overlaping the structures, let's customize the visualization. For better clarity, a white background with distinct color for each molecule is recommended</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">Close <strong>Molecular File Browser</strong>\u00a0and open the <strong>Color Controls</strong>\u00a0window by clicking on <strong>Graphics \u2192</strong>\u00a0<strong>Colors\u2026</strong>.</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">To change the background, select <strong>Display</strong>\u00a0from the <em>Categories</em>\u00a0list, choose <strong>Background</strong>\u00a0from the <em>Names</em>\u00a0list, and select your preferred color.</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">By default, the loaded molecules will still share the same color. To fix this, close <strong>Color Controls</strong>\u00a0and open <strong>Representations</strong> under the <strong>Graphics</strong>\u00a0menu.</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">At the top of <strong>Graphical Representation</strong>\u00a0window, select your molecule one by one. For each molecule, change the <strong>Coloring Method</strong>\u00a0to <strong>Molecule</strong>, the <strong>Drawing Method</strong>\u00a0to <strong>CPK</strong>, and the <strong>Material</strong>\u00a0to <strong>Glossy</strong>.***</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">Optionally, you can turn off the Axes and the <strong>Depth Cueing</strong>\u00a0in <strong>Display</strong>\u00a0main menu for a cleaner look.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped is-style-rectangular wp-block-gallery-4 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7082\" data-attachment-id=\"7082\" data-comments-opened=\"1\" data-id=\"7082\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4c\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg\" data-orig-size=\"779,547\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4c/\" height=\"547\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=768 768w\" width=\"779\"/></figure>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7081\" data-attachment-id=\"7081\" data-comments-opened=\"1\" data-id=\"7081\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4d\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg\" data-orig-size=\"866,516\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4d/\" height=\"516\" loading=\"lazy\" sizes=\"auto, (max-width: 866px) 100vw, 866px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=866\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg 866w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=768 768w\" width=\"866\"/></figure>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7080\" data-attachment-id=\"7080\" data-comments-opened=\"1\" data-id=\"7080\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4e\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg\" data-orig-size=\"866,523\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4e/\" height=\"523\" loading=\"lazy\" sizes=\"auto, (max-width: 866px) 100vw, 866px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=866\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg 866w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=768 768w\" width=\"866\"/></figure>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7079\" data-attachment-id=\"7079\" data-comments-opened=\"1\" data-id=\"7079\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4f\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg\" data-orig-size=\"866,518\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4f/\" height=\"518\" loading=\"lazy\" sizes=\"auto, (max-width: 866px) 100vw, 866px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=866\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg 866w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=768 768w\" width=\"866\"/></figure>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7078\" data-attachment-id=\"7078\" data-comments-opened=\"1\" data-id=\"7078\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4g\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg\" data-orig-size=\"865,518\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4g/\" height=\"518\" loading=\"lazy\" sizes=\"auto, (max-width: 865px) 100vw, 865px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=865\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg 865w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=768 768w\" width=\"865\"/></figure>\n</figure>\n</div>\n</div>\n<p class=\"wp-block-paragraph\">Now that each structure has a distinct \"ball-and-stick\" representation, we can proceed with the structural alignment: </p>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">Close <strong>Graphical Representation</strong>\u00a0window and navigate to <strong>Extensions \u2192 Analysis \u2192 RMSD Calculator</strong>.</p>\n<p class=\"wp-block-paragraph\">In the <strong>RMSD Tool</strong>\u00a0window, locate the next box that defaults to <em>protein (or residue 5 to 85)</em>\u00a0and replace it with the specific index numbers of the atoms you want to use for the alignment. This should be conserved atoms that do not change position significantly between structures.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7077\" data-attachment-id=\"7077\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4i\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg\" data-orig-size=\"779,514\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4i/\" height=\"514\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=768 768w\" width=\"779\"/></a></figure>\n</div>\n</div>\n<p class=\"wp-block-paragraph\">NOTE: <em>VMD uses zero-based indexing</em>. To select specific atoms, type <em>index 0 1 2 3</em>\u00a0or <em>index 0 to 3</em>.</p>\n<p class=\"wp-block-paragraph\">Uncheck the <strong>Backbone only </strong>option. By default, the alignment uses the <strong>Top</strong>\u00a0molecule as reference. You can change this by clicking the <strong>Selected</strong>\u00a0radio button and choosing your reference molecule.</p>\n<p class=\"wp-block-paragraph\">Click the <strong>Align</strong>\u00a0button at the top right of the window.</p>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">Once the structures are aligned, calculating the Root-Mean-Square-Deviation (RMSD) is straightforward.</p>\n<p class=\"wp-block-paragraph\">Click the <strong>RMSD</strong>\u00a0button at the top of tool. The calculated value will appear in the list.</p>\n<p class=\"wp-block-paragraph\">It is important to remember that VMD calculates the RMSD strictly based on the special distance deviation between the atoms of the reference structure (A<sub>a</sub><sup>ref</sup>) and the comparison structure (A<sub>a</sub><sup>comp</sup>). VMD does <strong>not</strong>\u00a0compare internal coordinates like bond lengths, angles or dihedrals.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped wp-block-gallery-5 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7077\" data-attachment-id=\"7077\" data-comments-opened=\"1\" data-id=\"7077\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4i\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg\" data-orig-size=\"779,514\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4i/\" height=\"514\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=768 768w\" width=\"779\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7076\" data-attachment-id=\"7076\" data-comments-opened=\"1\" data-id=\"7076\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4j\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg\" data-orig-size=\"865,521\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4j/\" height=\"521\" loading=\"lazy\" sizes=\"auto, (max-width: 865px) 100vw, 865px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=865\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg 865w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=768 768w\" width=\"865\"/></a></figure>\n</figure>\n</div>\n</div>","doi":"https://doi.org/10.59350/nw7bh-1ne53","guid":"http://joaquinbarroso.com/?p=7029","image":"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=1024","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788912000,"rid":"bjznx-ybs76","summary":"This a guest post by Yamil Hern\u00e1ndez, first year PhD student on loan from Puebla, who is working with us in photosynthesis related projects for his thesis. VMD (Visual Molecular Dynamics) is a free widely known visualizer developed by the Theoretical and Computational Biophysics Group from the University of Illinois.","tags":["Computational Chemistry","GaussView","Quantum Mechanics","Theoretical Chemistry","Visualization"],"title":"VMD not for Bio, but for CompChem","updated_at":1789025412,"url":"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/05a28rw58","name":"ETH Zurich"}],"contributor_roles":[],"family":"Rutz","given":"Adriano","url":"https://orcid.org/0000-0003-0443-9902"}],"blog":{"authors":[{"name":"Adriano Rutz","url":"https://orcid.org/0000-0003-0443-9902"}],"community_id":"9d85a476-b411-4d80-89d5-500bb0f3750d","created":1780876800,"current_feed_url":null,"description":"Personal website of Adriano Rutz","doi":"https://doi.org/10.59350/adafede","favicon":"https://rogue-scholar.org/api/communities/9d85a476-b411-4d80-89d5-500bb0f3750d/logo","feed_format":"application/feed+json","feed_url":"https://adafede.github.io/posts.json","filter":null,"generator":"Other","home_page_url":"https://adafede.github.io","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":null,"slug":"adafede","status":"active","subfield":"1312","title":"Adriano Rutz","updated":1788983002,"use_api":null},"blog_name":"Adriano Rutz","blog_slug":"adafede","content_html":"<script async=\"\" crossorigin=\"anonymous\" defer=\"\" src=\"https://scripts.simpleanalyticscdn.com/latest.js\">\n</script><p>I have finally opened a <code>Posts</code> section on my website! Every post should now automatically get a DOI.</p>\n<p>This is something I have wanted to do for a long time, largely inspired by the tireless and consistent example set by <a href=\"https://scholia.toolforge.org/author/Q20895241\">Egon Willighagen</a> <span class=\"citation\" data-cites=\"willighagen2024a willighagen2024b willighagen2025\">(Willighagen 2024b, 2024a, 2025)</span>.</p>\n<p>It was today's post of <span class=\"citation\" data-cites=\"fenner2025\">(Fenner 2025)</span> that finally motivated me to look into it again. That led me down a productive rabbit hole to set up Rogue Scholar: first landing on <span class=\"citation\" data-cites=\"voncsefalvay2023\">(Csefalvay 2023)</span>'s excellent guide, and then <span class=\"citation\" data-cites=\"fruehwald2025\">(Fruehwald 2025)</span>'s clear write-up, both of which made the process of integrating Rogue Scholar into a Quarto-based site surprisingly smooth.</p>\n<p>All the changes are documented in the following commit:</p>\n<p><a class=\"uri\" href=\"https://github.com/Adafede/adafede.github.io/commit/bc2dfe6f\">https://github.com/Adafede/adafede.github.io/commit/bc2dfe6f</a></p>\n<p>If you care about attribution, long-term archiving, DOIs and metadata, I highly recommend looking into <a href=\"https://rogue-scholar.org/\">Rogue Scholar</a>.</p>\n<p><strong>Edit (1):</strong> I realized that integrating <a href=\"https://sparontologies.github.io/cito/current/cito.html\">CiTO</a> could be a significant enhancement. With some effort (and thanks again to Egon), I managed to implement a working solution for the HTML and PDF outputs, see <span class=\"citation\" data-cites=\"willighagen2023\">(Willighagen 2023)</span>. However, the solution for the XML feed still feels suboptimal.</p>\n<p><strong>Edit (2):</strong> After some help from Egon and <a href=\"https://scholia.toolforge.org/author/Q30532925\">Martin</a>, I could improve my feed with correct CiTO annotations and their cool custom json feed, see: <a class=\"uri\" href=\"https://adafede.github.io/posts.json\">https://adafede.github.io/posts.json</a>!</p>\n<section class=\"level2\" id=\"references\">\n<h2 class=\"anchored\" data-anchor-id=\"references\">References</h2>\n<div class=\"references csl-bib-body hanging-indent\" id=\"refs\">\n<div class=\"csl-entry\" id=\"ref-voncsefalvay2023\">\nCsefalvay, Chris von. 2023. <em>Auto-DOI for Quarto Posts via Rogue Scholar</em>. <a href=\"http://dx.doi.org/10.59350/5hxdg-fz574\">http://dx.doi.org/10.59350/5hxdg-fz574</a>.\n<span class=\"cito\"> [cito:obtainsBackgroundFrom]</span></div>\n<div class=\"csl-entry\" id=\"ref-fenner2025\">\nFenner, Martin. 2025. <em>Rogue Scholar Citation Tracking Launches to Production</em>. <a href=\"http://dx.doi.org/10.53731/zyg15-qv911\">http://dx.doi.org/10.53731/zyg15-qv911</a>.\n<span class=\"cito\"> [cito:obtainsBackgroundFrom]</span></div>\n<div class=\"csl-entry\" id=\"ref-fruehwald2025\">\nFruehwald, Josef. 2025. <em>Setting up Rogue Scholar</em>. <a href=\"http://dx.doi.org/10.59350/3fp6d-e6z90\">http://dx.doi.org/10.59350/3fp6d-e6z90</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-willighagen2023\">\nWillighagen, Egon. 2023. <span>\"Two Years of Explicit CiTO Annotations.\"</span> <em>Journal of Cheminformatics</em> 15 (1). <a href=\"https://doi.org/10.1186/s13321-023-00683-2\">https://doi.org/10.1186/s13321-023-00683-2</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-willighagen2024b\">\nWillighagen, Egon. 2024a. <em>FAIR Blog-to-Blog Citations</em>. <a href=\"http://dx.doi.org/10.59350/er1mn-m5q69\">http://dx.doi.org/10.59350/er1mn-m5q69</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n<div class=\"csl-entry\" id=\"ref-willighagen2024a\">\nWillighagen, Egon. 2024b. <em>GoatCounter, Rogue Scholar and More New Things</em>. <a href=\"http://dx.doi.org/10.59350/8x2f1-h6d21\">http://dx.doi.org/10.59350/8x2f1-h6d21</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n<div class=\"csl-entry\" id=\"ref-willighagen2025\">\nWillighagen, Egon. 2025. <em>Blog Updates</em>. <a href=\"http://dx.doi.org/10.59350/cf885-kee54\">http://dx.doi.org/10.59350/cf885-kee54</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n</div>\n</section>\n<div class=\"default\" id=\"quarto-appendix\"><section class=\"quarto-appendix-contents\" id=\"quarto-reuse\"><h2 class=\"anchored quarto-appendix-heading\">Reuse</h2><div class=\"quarto-appendix-contents\"><div><a href=\"https://creativecommons.org/licenses/by/4.0/\" rel=\"license\">CC BY 4.0</a></div></div></section><section class=\"quarto-appendix-contents\" id=\"quarto-citation\"><h2 class=\"anchored quarto-appendix-heading\">Citation</h2><div><div class=\"quarto-appendix-secondary-label\">BibTeX citation:</div><pre class=\"sourceCode code-with-copy quarto-appendix-bibtex\"><code class=\"sourceCode bibtex\">@online{rutz2025,\n  author = {{Adriano Rutz}},\n  title = {Open {Science} {Upgrade:} {Adding} {Blog} {Posts} to My\n    {Website} and {Linking} to {Rogue} {Scholar}},\n  date = {2025-08-04},\n  url = {https://adafede.github.io/posts/2025-08-04_rogue_scholar.html},\n  doi = {10.59350/yckwd-9vm79},\n  langid = {en}\n}\n</code></pre><div class=\"quarto-appendix-secondary-label\">For attribution, please cite this work as:</div><div class=\"csl-entry quarto-appendix-citeas\" id=\"ref-rutz2025\">\nAdriano Rutz. 2025. <span>\"Open Science Upgrade: Adding Blog Posts to My\nWebsite and Linking to Rogue Scholar.\"</span> August 4. <a href=\"https://doi.org/10.59350/yckwd-9vm79\">https://doi.org/10.59350/yckwd-9vm79</a>.\n</div></div></section></div>","doi":"https://doi.org/10.59350/yckwd-9vm79","guid":"https://doi.org/10.59350/yckwd-9vm79","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1754265600,"reference":[{"id":"https://doi.org/10.59350/5hxdg-fz574","unstructured":"von Csefalvay, C. (2023, November 13). Auto-DOI for Quarto posts via Rogue Scholar. <i>Chris Von Csefalvay</i>.  <b>[cito:obtainsBackgroundFrom]</b>"},{"id":"https://doi.org/10.53731/zyg15-qv911","unstructured":"Fenner, M. (2025, August 4). Rogue Scholar citation tracking launches to production. <i>Front Matter</i>.  <b>[cito:obtainsBackgroundFrom]</b>"},{"id":"https://doi.org/10.59350/3fp6d-e6z90","unstructured":"Fruehwald, J. (2025, July 31). Setting Up Rogue Scholar. <i>V\u00e6l Space</i>.  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.1186/s13321-023-00683-2","unstructured":"Willighagen, E. (2023). Two years of explicit CiTO annotations. <i>Journal of Cheminformatics</i>, <i>15</i>(1).  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.59350/er1mn-m5q69","unstructured":"Willighagen, E. (2024, December 30). FAIR blog-to-blog citations. <i>Chem-bla-ics</i>.  <b>[cito:cites]</b>"},{"id":"https://doi.org/10.59350/8x2f1-h6d21","unstructured":"Willighagen, E. (2024, July 21). GoatCounter, Rogue Scholar and more new things. <i>Chem-bla-ics</i>.  <b>[cito:cites]</b>"},{"id":"https://doi.org/10.59350/cf885-kee54","unstructured":"Willighagen, E. (2025, January 19). Blog updates. <i>Chem-bla-ics</i>.  <b>[cito:cites]</b>"}],"rid":"9hzx0-g6543","summary":"I have finally opened a Posts section on my website! Every post should now automatically get a DOI.","tags":["Open Science"],"title":"Open Science Upgrade: Adding Blog Posts to my Website and Linking to Rogue Scholar","updated_at":1789025409,"url":"https://adafede.github.io/posts/2025-08-04_rogue_scholar.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/05a28rw58","name":"ETH Zurich"}],"contributor_roles":[],"family":"Rutz","given":"Adriano","url":"https://orcid.org/0000-0003-0443-9902"}],"blog":{"authors":[{"name":"Adriano Rutz","url":"https://orcid.org/0000-0003-0443-9902"}],"community_id":"9d85a476-b411-4d80-89d5-500bb0f3750d","created":1780876800,"current_feed_url":null,"description":"Personal website of Adriano Rutz","doi":"https://doi.org/10.59350/adafede","favicon":"https://rogue-scholar.org/api/communities/9d85a476-b411-4d80-89d5-500bb0f3750d/logo","feed_format":"application/feed+json","feed_url":"https://adafede.github.io/posts.json","filter":null,"generator":"Other","home_page_url":"https://adafede.github.io","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":null,"slug":"adafede","status":"active","subfield":"1312","title":"Adriano Rutz","updated":1788983002,"use_api":null},"blog_name":"Adriano Rutz","blog_slug":"adafede","content_html":"<script async=\"\" crossorigin=\"anonymous\" defer=\"\" src=\"https://scripts.simpleanalyticscdn.com/latest.js\">\n</script><p>Five years ago, <a about=\"wd:Q104225190\" href=\"https://www.wikidata.org/wiki/Q104225190\">LOTUS</a> <span class=\"citation\" data-cites=\"Rutz2022\">(Rutz et al. 2022)</span> started as a small attempt to cultivate the flow of chemical knowledge, in the same way we study how metabolites flow through living systems, rather than to build <em>yet another database</em>.</p>\n<p>The idea was simple. Natural products data should be open, structured, reusable, and belong to everyone.</p>\n<p>Like many community-driven efforts, LOTUS had bursts of activity, long pauses, and years of invisible maintenance. From the outside, silence can look like disappearance. From the inside, it usually means people are still doing the work; slowly, carefully, and often without announcements.</p>\n<section class=\"level2\" id=\"from-isolated-datasets-to-global-outreach\">\n<h2 class=\"anchored\" data-anchor-id=\"from-isolated-datasets-to-global-outreach\">From isolated datasets to global outreach</h2>\n<p>The early focus of LOTUS was necessarily inward: assembling data, cleaning records, releasing versions. We built a website, curated entries, and archived releases.</p>\n<p>But we slowly realized something uncomfortable: data stored in a repository, even a good one, does not automatically live.</p>\n<p>Archiving on <a about=\"wd:Q22661177\" href=\"https://www.wikidata.org/wiki/Q22661177\">Zenodo</a> (<a class=\"uri\" href=\"https://zenodo.org/communities/the-lotus-initiative\">https://zenodo.org/communities/the-lotus-initiative</a>) was the right thing to do, but archived data is mostly silent data. It waits to be discovered, and versioning remains labor-intensive.</p>\n<p>What we really needed were entry points where people already were.</p>\n<p><a about=\"wd:Q52\" href=\"https://www.wikidata.org/wiki/Q52\">Wikipedia</a> , <a about=\"wd:Q2013\" href=\"https://www.wikidata.org/wiki/Q2013\">Wikidata</a> , and <a about=\"wd:Q45340488\" href=\"https://www.wikidata.org/wiki/Q45340488\">Scholia</a> building on top of it are not dissemination platforms in the classical sense. They are circulatory systems. They persist because communities maintain them.</p>\n<p>The <a about=\"wd:Q134520857\" href=\"https://www.wikidata.org/wiki/Q134520857\">Scholia Chemistry preprint</a> <span class=\"citation\" data-cites=\"Willighagen2025b\">(Willighagen et al. 2025)</span> co-authored with <a about=\"wd:Q20895241\" href=\"https://www.wikidata.org/wiki/Q20895241\">Egon</a> , <a about=\"wd:Q43744369\" href=\"https://www.wikidata.org/wiki/Q43744369\">Denise</a> , <a about=\"wd:Q20895785\" href=\"https://www.wikidata.org/wiki/Q20895785\">Daniel</a> , and <a about=\"wd:Q20980928\" href=\"https://www.wikidata.org/wiki/Q20980928\">Finn</a> belongs to this continuity. It does not introduce a new platform. It offers a lens for communities to see what they already collectively know.</p>\n<section class=\"level3\" id=\"making-knowledge-visible-the-wikipedia-p703-module\">\n<h3 class=\"anchored\" data-anchor-id=\"making-knowledge-visible-the-wikipedia-p703-module\">Making knowledge visible: the Wikipedia P703 module</h3>\n<blockquote class=\"blockquote\">\n<p>Knowledge needs channels, not just reservoirs.</p>\n</blockquote>\n<p>One important step was enabling Wikipedia articles and <a about=\"wd:Q15515987\" href=\"https://www.wikidata.org/wiki/Q15515987\">infoboxes</a> to directly access <em>found in taxon</em> (<a about=\"wd:Property:P703\" href=\"https://www.wikidata.org/wiki/Property:P703\">P703</a>) relationships from Wikidata in an efficient way.</p>\n<p>This sounds like a small technical detail. It is not.</p>\n<p>The idea had circulated quietly for years, in hallway conversations, chats, and conferences. I also mentioned it during the <a about=\"wd:Q133846580\" href=\"https://www.wikidata.org/wiki/Q133846580\">WikiCite 2025</a> conference last August, but it took time before conditions were right. Infrastructure work rarely happens on schedule. It almost never happens on stage. It happens in version histories, talk pages, and tiny edits that fix one Lua bug, enabling thousands of articles to improve forever.</p>\n<p>Once data is in Wikidata, it can flow into thousands of chemical articles, in dozens of languages, without duplication or translation overhead. It becomes visible to non-experts, students, and readers who will never see a database interface. This is how open data becomes public knowledge.</p>\n<p>These <a about=\"wd:Q15184295\" href=\"https://www.wikidata.org/wiki/Q15184295\">modules</a> are now available on multiple Wikipedias:</p>\n<ul>\n<li><a about=\"wd:Q328\" href=\"https://www.wikidata.org/wiki/Q328\">English</a> : <a href=\"https://en.wikipedia.org/wiki/Module:P703\">Module:P703</a></li>\n<li><a about=\"wd:Q8447\" href=\"https://www.wikidata.org/wiki/Q8447\">French</a> : <a href=\"https://fr.wikipedia.org/wiki/Module:P703\">Module:P703</a></li>\n<li><a about=\"wd:Q48183\" href=\"https://www.wikidata.org/wiki/Q48183\">German</a> : <a href=\"https://de.wikipedia.org/wiki/Modul:P703\">Modul:P703</a></li>\n<li><a about=\"wd:Q11920\" href=\"https://www.wikidata.org/wiki/Q11920\">Italian</a> : <a href=\"https://it.wikipedia.org/wiki/Modulo:P703\">Modulo:P703</a></li>\n</ul>\n<p>If you speak another language, feel free to copy them and increase their use.</p>\n<p>Initially, I tried to reuse existing modules, and quickly learned why module reuse across Wikipedias is famously difficult. Each wiki evolves its own ecosystem of dependencies, conventions, and technical debt. So the modules were written fully contained, independent of language-specific infrastructure. Only lines that need to be changed are the language-specific translations at the top of the module, trying to follow <a about=\"wd:Q3141064\" href=\"https://www.wikidata.org/wiki/Q3141064\">18n</a>.</p>\n<p>These modules are not a new website or a new interface. They are simply better plumbing.</p>\n<div class=\"quarto-figure quarto-figure-center\">\n<figure class=\"figure\">\n<p><img class=\"img-fluid figure-img\" src=\"https://adafede.github.io/images/screenshots/screenshot_p703_module.png\"/></p>\n<figcaption>Screenshot of the P703 module on English Wikipedia</figcaption>\n</figure>\n</div>\n<p>By default, only <code>5</code> <a about=\"wd:Q16521\" href=\"https://www.wikidata.org/wiki/Q16521\">organisms</a> are shown, keeping the text clean and readable. But the magic is in how the module handles the rest: each taxon links to its Wikipedia article, and if no article exists in the current language, the module gracefully redirects to an equivalent page in another wiki. A beautiful example of this is <code>war</code> for <a href=\"https://war.wikipedia.org/wiki/Quassia_africana\">Quassia africana</a>.</p>\n</section>\n<section class=\"level3\" id=\"reaching-non-experts\">\n<h3 class=\"anchored\" data-anchor-id=\"reaching-non-experts\">Reaching non-experts</h3>\n<blockquote class=\"blockquote\">\n<p>Not everyone wants to learn SPARQL.</p>\n</blockquote>\n<p>I have heard this sentiment countless times. Regardless of personal preferences, if we want the data to truly live, it must reach as many people as possible.</p>\n<p>Small tools like the <a href=\"https://adafede.github.io/marimo/apps/lotus_wikidata_explorer.html\">LOTUS Wikidata Explorer</a> help lower that barrier. It is imperfect. It is still growing. But it already allows chemists, curators, and students to access and export data in formats they can actually use.</p>\n<p>The principle is simple: knowledge only flows when it reaches people. The data must be seen, explored, and reused. Only then does it fulfill its purpose.</p>\n<div class=\"quarto-figure quarto-figure-center\">\n<figure class=\"figure\">\n<p><img class=\"img-fluid figure-img\" src=\"https://adafede.github.io/images/screenshots/screenshot_lotus_wikidata_explorer.png\"/></p>\n<figcaption>Screenshot of the LOTUS Wikidata Explorer interface</figcaption>\n</figure>\n</div>\n<p>On a more technical note, the LOTUS Wikidata Explorer leverages the powerful <a about=\"wd:Q101200819\" href=\"https://www.wikidata.org/wiki/Q101200819\">IDSM</a> endpoint <span class=\"citation\" data-cites=\"Galgonek2021\">(Galgonek and Vondr\u00e1\u0161ek 2021)</span>, which allows for chemical similarity searches thanks to <a about=\"wd:Q55016200\" href=\"https://www.wikidata.org/wiki/Q55016200\">Sachem</a> <span class=\"citation\" data-cites=\"Kratochvl2018\">(Kratochv\u00edl et al. 2018)</span>. Its speed for large-scale queries could never have been reached without <a about=\"wd:Q111016295\" href=\"https://www.wikidata.org/wiki/Q111016295\">QLever</a> <span class=\"citation\" data-cites=\"Bast2017\">(Bast and Buchhold 2017)</span>, and chemical depictions come from <a about=\"wd:Q137800121\" href=\"https://www.wikidata.org/wiki/Q137800121\">CDK Depict</a>.</p>\n<p>It returns structured metadata for traceability and reproducibility, together with hashes that uniquely identify the query and its results. It can be queried programmatically via simple API calls, for example <code>?taxon=Gentianaceae</code> or <code>?smiles=c1ccccc1&amp;formula_filter=true&amp;f_state=required</code>. It works directly in the browser without requiring heavy dependencies, almost everything works out of the box.</p>\n<p>Alternatively, users can take advantage of a local version, for example to extract a small, personal <a about=\"wd:Q33002955\" href=\"https://www.wikidata.org/wiki/Q33002955\">knowledge graph</a> in <a about=\"wd:Q114409\" href=\"https://www.wikidata.org/wiki/Q114409\">TTL</a> format, or to export all or selected LOTUS data in more chemistry-friendly formats such as <a about=\"wd:Q2063\" href=\"https://www.wikidata.org/wiki/Q2063\">JSON</a> or <a about=\"wd:Q935809\" href=\"https://www.wikidata.org/wiki/Q935809\">CSV</a>, ready for analysis, visualization, or integration into other workflows.</p>\n<p>For example, to export a complete or filtered snapshot locally:</p>\n<div class=\"cell\">\n<div class=\"code-copy-outer-scaffold\"><div class=\"sourceCode cell-code\" id=\"cb1\" style=\"background: #f1f3f5;\"><pre class=\"sourceCode r code-with-copy\"><code class=\"sourceCode r\"><span id=\"cb1-1\">uvx \\</span>\n<span id=\"cb1-2\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>from \\</span>\n<span id=\"cb1-3\">  git<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">+</span>https<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span><span class=\"er\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">//</span>github.com<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">/</span>adafede<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">/</span>marimo \\</span>\n<span id=\"cb1-4\">  lotus_wikidata_explorer \\</span>\n<span id=\"cb1-5\">  export \\</span>\n<span id=\"cb1-6\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>taxon <span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">\"*\"</span> \\   <span class=\"co\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\"># to get all taxa, else \"Gentianaceae\", for example</span></span>\n<span id=\"cb1-7\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>format csv \\  <span class=\"co\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\"># also supports json, ttl</span></span>\n<span id=\"cb1-8\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>output <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">20260119</span>_lotus.csv.gz \\</span>\n<span id=\"cb1-9\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>compress \\</span>\n<span id=\"cb1-10\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>verbose</span></code></pre></div></div>\n</div>\n<p>And if you are curious where halogenated compounds appear most often, you can simply ask:</p>\n<div class=\"cell\">\n<div class=\"code-copy-outer-scaffold\"><div class=\"sourceCode cell-code\" id=\"cb2\" style=\"background: #f1f3f5;\"><pre class=\"sourceCode r code-with-copy\"><code class=\"sourceCode r\"><span id=\"cb2-1\">xan dedup <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">20260119</span>_lotus.csv.gz \\</span>\n<span id=\"cb2-2\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>select compound_inchikey,molecular_formula,taxon_name <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-3\">  xan select compound_inchikey,molecular_formula,taxon_name <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-4\">  xan filter <span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">\"contains(molecular_formula, 'Br') or</span></span>\n<span id=\"cb2-5\"><span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">              contains(molecular_formula, 'Cl') or</span></span>\n<span id=\"cb2-6\"><span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">              contains(molecular_formula, 'F') or</span></span>\n<span id=\"cb2-7\"><span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">              contains(molecular_formula, 'I')\"</span> <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-8\">  xan filter <span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">'!contains(molecular_formula, \"Fe\")'</span> <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-9\">  xan freq <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">-</span>s taxon_name <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-10\">  xan hist <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">-</span>l value <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">-</span>R</span></code></pre></div></div>\n</div>\n<div class=\"cell\">\n<div class=\"code-copy-outer-scaffold\"><div class=\"sourceCode cell-code\" id=\"cb3\" style=\"background: #f1f3f5;\"><pre class=\"sourceCode r code-with-copy\"><code class=\"sourceCode r\"><span id=\"cb3-1\">Histogram <span class=\"cf\" style=\"color: #003B4F;\nbackground-color: null;\nfont-weight: bold;\nfont-style: inherit;\">for</span> <span class=\"fu\" style=\"color: #4758AB;\nbackground-color: null;\nfont-style: inherit;\">taxon_name</span> (bars<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span> <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">11</span>, sum<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span> <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">11</span>,<span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">604</span>, max<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span> <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">10</span>,<span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">060</span>)<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span></span>\n<span id=\"cb3-2\"></span>\n<span id=\"cb3-3\">Streptomyces            <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>   <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">374</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">3.22</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0\u25a0\u25a0                                                                                                   <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-4\">Laurencia dendroidea    <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>   <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">314</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">2.71</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0\u25a0\u25a0                                                                                                   <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-5\">Laurencia obtusa        <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>   <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">184</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">1.59</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0                                                                                                     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-6\">Pseudoceratina purpurea <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>   <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">112</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.97</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0                                                                                                     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-7\">Aplysia dactylomela     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">99</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.85</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0                                                                                                     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-8\">Nostoc                  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">99</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.85</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0                                                                                                     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-9\">Laurencia nipponica     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">95</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.82</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0                                                                                                      <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-10\">Portieria hornemannii   <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">94</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.81</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0                                                                                                      <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-11\">Lyngbya majuscula       <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">88</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.76</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0                                                                                                      <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-12\">Chaetomium globosum     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">85</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.73</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0                                                                                                      <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-13\"><span class=\"er\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">&lt;</span>rest<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">&gt;</span>                  <span class=\"er\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">|</span><span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">10</span>,<span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">060</span>  <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">86.69</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span></code></pre></div></div>\n</div>\n</section>\n</section>\n<section class=\"level2\" id=\"making-flow-reliable-curation-and-standards\">\n<h2 class=\"anchored\" data-anchor-id=\"making-flow-reliable-curation-and-standards\">Making flow reliable: curation and standards</h2>\n<blockquote class=\"blockquote\">\n<p>At some point, flow only runs if it is maintained.</p>\n</blockquote>\n<p>As I do not post as often as I probably should, here are some other pointers to related work and discussions from the past months, for those who want to follow the flow a bit further:</p>\n<section class=\"level3\" id=\"blue-obelisk\">\n<h3 class=\"anchored\" data-anchor-id=\"blue-obelisk\">Blue Obelisk</h3>\n<ul>\n<li>Following some ideas he had to improve Scholia Chemistry, Egon initiated the Blue Obelisk Wikidata Chemistry Curation project: <a class=\"uri\" href=\"https://blueobelisk.github.io/wikidata-chemistry-curation/\">https://blueobelisk.github.io/wikidata-chemistry-curation/</a>. I then joined and contributed to some parts, maybe you will find out which ones!</li>\n<li>Contributions were also made to the Blue Obelisk IUPAC Names project (also led by Egon): <a class=\"uri\" href=\"https://github.com/BlueObelisk/iupac-names\">https://github.com/BlueObelisk/iupac-names</a>, integrating Wikidata-derived name-compound pairs. See <a class=\"uri\" href=\"https://github.com/Adafede/wd-labels-to-iupac\">https://github.com/Adafede/wd-labels-to-iupac</a> and <a class=\"uri\" href=\"https://chem-bla-ics.linkedchemistry.info/2025/08/09/one-million-iupac-names-4.html\">https://chem-bla-ics.linkedchemistry.info/2025/08/09/one-million-iupac-names-4.html</a> <span class=\"citation\" data-cites=\"Willighagen2025c\">(Willighagen 2025)</span> These bridges allow names and identifiers to circulate consistently across systems.</li>\n</ul>\n</section>\n<section class=\"level3\" id=\"reactions-flow\">\n<h3 class=\"anchored\" data-anchor-id=\"reactions-flow\">Reactions flow</h3>\n<p>Recently, I also contributed to improving how <a about=\"wd:Q36534\" href=\"https://www.wikidata.org/wiki/Q36534\">chemical reactions</a> are modeled in Wikidata.</p>\n<p>Previously, many reactions were modeled as <a about=\"wd:Property:P31\" href=\"https://www.wikidata.org/wiki/Property:P31\">instances of</a> \"chemical reaction\", which violated disjointness, see <span class=\"citation\" data-cites=\"Doan2025\">(Do\u01e7an and Patel-Schneider 2025)</span>.</p>\n<p>The introduction of <a about=\"wd:Q137796968\" href=\"https://www.wikidata.org/wiki/Q137796968\">type of chemical reaction</a> now allows reactions to be classified more precisely, while preserving their hierarchy using <a about=\"wd:Property:P279\" href=\"https://www.wikidata.org/wiki/Property:P279\">subclass of</a>.</p>\n</section>\n<section class=\"level3\" id=\"wikifunctions\">\n<h3 class=\"anchored\" data-anchor-id=\"wikifunctions\">Wikifunctions</h3>\n<p>Out of curiosity, I also made a small contribution to chemistry-related functions in <a about=\"wd:Q104587954\" href=\"https://www.wikidata.org/wiki/Q104587954\">Wikifunctions</a>: <a href=\"https://www.wikifunctions.org/view/en/Z30950\">Z30950</a>. It validates <a about=\"wd:Q102507\" href=\"https://www.wikidata.org/wiki/Q102507\">CAS Registry Numbers</a>. It does one thing, and it does it reliably.</p>\n<p>It is tiny. But it is a seed.</p>\n</section>\n</section>\n<section class=\"level2\" id=\"looking-forward-flowing-knowledge-flowing-metabolites\">\n<h2 class=\"anchored\" data-anchor-id=\"looking-forward-flowing-knowledge-flowing-metabolites\">Looking forward: flowing knowledge, flowing metabolites</h2>\n<p>Projects like Wikifunctions and <a about=\"wd:Q96807071\" href=\"https://www.wikidata.org/wiki/Q96807071\">Abstract Wikipedia</a> point to the next phase of open knowledge: knowledge that is not only stored, but executed, reused, and recombined.</p>\n<p>A global, open <a about=\"wd:Q12149006\" href=\"https://www.wikidata.org/wiki/Q12149006\">metabolomics</a> knowledge graph is slowly taking shape, one where chemical structures, organisms, reactions, and evidence can finally be traced together.</p>\n<p>LOTUS is no longer an initiative. It is one contributor among many in that graph.</p>\n<p>If you edit Wikipedia, curate Wikidata, maintain a SPARQL endpoint, write a template, review a module, or fix a tiny detail no one will notice, <em>thank you</em>. <strong>This work only matters because you are here</strong>.</p>\n<section class=\"level3\" id=\"references\">\n<h3 class=\"anchored\" data-anchor-id=\"references\">References</h3>\n<div class=\"references csl-bib-body hanging-indent\" id=\"refs\">\n<div class=\"csl-entry\" id=\"ref-Bast2017\">\nBast, Hannah, and Bj\u00f6rn Buchhold. 2017. <span>\"QLever: A Query Engine for Efficient SPARQL+text Search.\"</span> <em>Proceedings of the 2017 ACM on Conference on Information and Knowledge Management</em>, CIKM '17, November, 647\u201356. <a href=\"https://doi.org/10.1145/3132847.3132921\">https://doi.org/10.1145/3132847.3132921</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-Doan2025\">\nDo\u01e7an, Ege Atacan, and Peter F. Patel-Schneider. 2025. <span>\"Disjointness Violations in Wikidata.\"</span> In <em>Knowledge Graphs and Semantic Web</em>. Springer Nature Switzerland. <a href=\"https://doi.org/10.1007/978-3-031-81221-7_18\">https://doi.org/10.1007/978-3-031-81221-7_18</a>.\n<span class=\"cito\"> [cito:citesAsRecommendedReading]</span></div>\n<div class=\"csl-entry\" id=\"ref-Galgonek2021\">\nGalgonek, Jakub, and Ji\u0159\u00ed Vondr\u00e1\u0161ek. 2021. <span>\"IDSM ChemWebRDF: SPARQLing Small-Molecule Datasets.\"</span> <em>Journal of Cheminformatics</em> 13 (1). <a href=\"https://doi.org/10.1186/s13321-021-00515-1\">https://doi.org/10.1186/s13321-021-00515-1</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-Kratochvl2018\">\nKratochv\u00edl, Miroslav, Ji\u0159\u00ed Vondr\u00e1\u0161ek, and Jakub Galgonek. 2018. <span>\"Sachem: A Chemical Cartridge for High-Performance Substructure Search.\"</span> <em>Journal of Cheminformatics</em> 10 (1). <a href=\"https://doi.org/10.1186/s13321-018-0282-y\">https://doi.org/10.1186/s13321-018-0282-y</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-Rutz2022\">\nRutz, Adriano, Maria Sorokina, Jakub Galgonek, et al. 2022. <span>\"The LOTUS Initiative for Open Knowledge Management in Natural Products Research.\"</span> <em>eLife</em> 11 (May). <a href=\"https://doi.org/10.7554/elife.70780\">https://doi.org/10.7554/elife.70780</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n<div class=\"csl-entry\" id=\"ref-Willighagen2025c\">\nWillighagen, Egon. 2025. August. <a href=\"https://doi.org/10.59350/krw9n-dv417\">https://doi.org/10.59350/krw9n-dv417</a>.\n<span class=\"cito\"> [cito:citesAsRecommendedReading]</span></div>\n<div class=\"csl-entry\" id=\"ref-Willighagen2025b\">\nWillighagen, Egon, Denise Slenter, Adriano Rutz, Daniel Mietchen, and Finn Nielsen. 2025. <em>Scholia Chemistry: Access to Chemistry in Wikidata</em>. May. <a href=\"https://doi.org/10.26434/chemrxiv-2025-53n0w\">https://doi.org/10.26434/chemrxiv-2025-53n0w</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n</div>\n</section>\n</section>\n<div class=\"default\" id=\"quarto-appendix\"><section class=\"quarto-appendix-contents\" id=\"quarto-reuse\"><h2 class=\"anchored quarto-appendix-heading\">Reuse</h2><div class=\"quarto-appendix-contents\"><div><a href=\"https://creativecommons.org/licenses/by/4.0/\" rel=\"license\">CC BY 4.0</a></div></div></section><section class=\"quarto-appendix-contents\" id=\"quarto-citation\"><h2 class=\"anchored quarto-appendix-heading\">Citation</h2><div><div class=\"quarto-appendix-secondary-label\">BibTeX citation:</div><pre class=\"sourceCode code-with-copy quarto-appendix-bibtex\"><code class=\"sourceCode bibtex\">@online{rutz2026,\n  author = {{Adriano Rutz}},\n  title = {Cultivating {Knowledge} {Flow} in {Open} {Chemistry}},\n  date = {2026-01-20},\n  url = {https://adafede.github.io/posts/2026-01-20_chem_flow.html},\n  doi = {10.59350/sk00y-3gh44},\n  langid = {en}\n}\n</code></pre><div class=\"quarto-appendix-secondary-label\">For attribution, please cite this work as:</div><div class=\"csl-entry quarto-appendix-citeas\" id=\"ref-rutz2026\">\nAdriano Rutz. 2026. <span>\"Cultivating Knowledge Flow in Open\nChemistry.\"</span> January 20. <a href=\"https://doi.org/10.59350/sk00y-3gh44\">https://doi.org/10.59350/sk00y-3gh44</a>.\n</div></div></section></div>","doi":"https://doi.org/10.59350/sk00y-3gh44","guid":"https://doi.org/10.59350/sk00y-3gh44","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1768867200,"reference":[{"id":"https://doi.org/10.1145/3132847.3132921","unstructured":"Bast, H., &amp; Buchhold, B. (2017). QLever. In <i>Proceedings of the 2017 ACM on Conference on Information and Knowledge Management</i> (pp. 647\u2013656). ACM.  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.1007/978-3-031-81221-7_18","unstructured":"Do\u01e7an, E. A., &amp; Patel-Schneider, P. F. (2025). Disjointness Violations in\u00a0Wikidata. In <i>Lecture Notes in Computer Science</i> (pp. 259\u2013274). Springer Nature Switzerland.  <b>[cito:citesAsRecommendedReading]</b>"},{"id":"https://doi.org/10.1186/s13321-021-00515-1","unstructured":"Galgonek, J., &amp; Vondr\u00e1\u0161ek, J. (2021). IDSM ChemWebRDF: SPARQLing small-molecule datasets. <i>Journal of Cheminformatics</i>, <i>13</i>(1).  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.1186/s13321-018-0282-y","unstructured":"Kratochv\u00edl, M., Vondr\u00e1\u0161ek, J., &amp; Galgonek, J. (2018). Sachem: a chemical cartridge for high-performance substructure search. <i>Journal of Cheminformatics</i>, <i>10</i>(1).  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.7554/elife.70780","unstructured":"Rutz, A., Sorokina, M., Galgonek, J., Mietchen, D., Willighagen, E., Gaudry, A., Graham, J. G., Stephan, R., Page, R., Vondr\u00e1\u0161ek, J., Steinbeck, C., Pauli, G. F., Wolfender, J.-L., Bisson, J., &amp; Allard, P.-M. (2022). The LOTUS initiative for open knowledge management in natural products research. <i>eLife</i>, <i>11</i>.  <b>[cito:cites]</b>"},{"id":"https://doi.org/10.59350/krw9n-dv417","unstructured":"Willighagen, E. (2025, August 9). One Million IUPAC names #4: a lot is happening. <i>Chem-bla-ics</i>.  <b>[cito:citesAsRecommendedReading]</b>"},{"id":"https://doi.org/10.26434/chemrxiv-2025-53n0w","unstructured":"Willighagen, E., Slenter, D., Rutz, A., Mietchen, D., &amp; Nielsen, F. (2025). <i>Scholia Chemistry: access to chemistry in Wikidata</i>. American Chemical Society (ACS).  <b>[cito:cites]</b>"}],"rid":"80nkb-cq953","summary":"Five years ago, LOTUS (Rutz et al. 2022) started as a small attempt to cultivate the flow of chemical knowledge, in the same way we study how metabolites flow through living systems, rather than to build yet another database.","tags":["Chemistry","LOTUS","Open Science","Wikidata"],"title":"Cultivating Knowledge Flow in Open Chemistry","updated_at":1789025407,"url":"https://adafede.github.io/posts/2026-01-20_chem_flow.html","version":"v1"}},{"document":{"authors":[{"contributor_roles":[],"name":"Adapt Research"}],"blog":{"authors":null,"community_id":"bfd37b46-cbce-4a47-9a9d-fdc1d9c8b8d2","created":1753833600,"current_feed_url":null,"description":"As we build our world we build our minds","doi":"https://doi.org/10.59350/adaptresearchwriting","favicon":"https://rogue-scholar.org/api/communities/bfd37b46-cbce-4a47-9a9d-fdc1d9c8b8d2/logo","feed_format":"application/atom+xml","feed_url":"https://adaptresearchwriting.com/feed/atom/","filter":null,"generator":"WordPress.com","home_page_url":"https://adaptresearchwriting.com","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"adaptresearchwriting","status":"active","subfield":"2306","title":"Adapt Research Ltd","updated":1789011219,"use_api":null},"blog_name":"Adapt Research Ltd","blog_slug":"adaptresearchwriting","content_html":"<p class=\"wp-block-paragraph\"><em>Introducing our new preprint on evolutionary governance for systemic and global catastrophic risk</em></p>\n<p class=\"wp-block-paragraph\">By Matt Boyd</p>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7917\" data-attachment-id=\"7917\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"image\" data-large-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=840\" data-orig-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png\" data-orig-size=\"936,528\" data-permalink=\"https://adaptresearchwriting.com/2026/09/10/the-metacrisis-is-a-degradation-of-evolvability-why-global-risk-needs-evolutionary-explanation-and-governance/image-80/\" height=\"528\" sizes=\"(max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 1362px) 62vw, 840px\" src=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=936\" srcset=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png 936w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=150 150w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=300 300w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=768 768w\" width=\"936\"/><figcaption class=\"wp-element-caption\">Photo by <a href=\"https://unsplash.com/@jplenio?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Johannes Plenio</a> on <a href=\"https://unsplash.com/photos/silhouette-photo-of-group-people-standing-on-grass-aWDgqexSxA0?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Unsplash</a></figcaption></figure>\n<p class=\"wp-block-paragraph\"><strong>TLDR/Summary</strong></p>\n<ul class=\"wp-block-list\">\n<li>Nothing about human society and its generation of global risk makes sense except in the light of evolution. I've been building that claim through my recent <a href=\"https://adaptresearchwriting.com/2026/06/03/what-the-latest-european-risk-analysis-conference-means-for-global-risk-and-new-zealand/\">posts</a> and <a href=\"https://adaptresearchwriting.com/2026/02/04/is-there-a-meta-crisis-yes/\">conference talks</a>.</li>\n<li>A new <a href=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/260831-evolvability-metacrisis-v8.pdf\">preprint</a> I've developed with Nick Wilson, and now under peer-review, brings all this together in a technical paper: <a href=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/260831-evolvability-metacrisis-v8.pdf\">The Metacrisis as a Degradation of Evolvability</a>.</li>\n<li>Five research communities working on global risk are converging, often unawares, on the extended evolutionary framework. We name it, systematise it from first principles, and draw out what it implies for governance of global risk.</li>\n<li>Risk-generating architectures recur wherever certain evolutionary dynamics obtain; the <em>metacrisis</em> is the simultaneous degradation of five conditions of evolvability (variation, modularity, selective-environment stability, transmission fidelity, and outlaw/defector suppression)</li>\n<li>Global risk governance must therefore act on those conditions, above all on suppressing defectors.</li>\n<li>The evolutionary lens is not the answer to everything, but our paper deliberately pushes it as far as we can, because evolution keeps seeping through the gaps in other explanations and joining them together.</li>\n<li>The upshot is a change in what governance is <em>for</em>: less for specifying solutions, and more about engineering, nudging and continually readjusting the conditions under which good solutions can arise, spread and hold.</li>\n</ul>\n<p class=\"wp-block-paragraph\"><strong>Two intellectual strands twisted together</strong></p>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7919\" data-attachment-id=\"7919\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"image\" data-large-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=840\" data-orig-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png\" data-orig-size=\"936,526\" data-permalink=\"https://adaptresearchwriting.com/2026/09/10/the-metacrisis-is-a-degradation-of-evolvability-why-global-risk-needs-evolutionary-explanation-and-governance/image-81/\" height=\"526\" sizes=\"(max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 1362px) 62vw, 840px\" src=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=936\" srcset=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png 936w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=150 150w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=300 300w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=768 768w\" width=\"936\"/><figcaption class=\"wp-element-caption\">Photo by <a href=\"https://unsplash.com/@warrenumoh?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Warren Umoh</a> on <a href=\"https://unsplash.com/photos/dna-double-helix-structure--qycBqByWIY?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Unsplash</a></figcaption></figure>\n<p class=\"wp-block-paragraph\">This post has been a long time coming. In 2007 I wrote a Masters thesis in philosophy, on cultural evolution and the information environment we have created. That was back when \"meme\" still had a technical definition, Dawkins's unit of cultural inheritance, and did not yet mean a picture of a cat that goes viral. My thesis argued meme theory was useful in understanding how culture evolves.</p>\n<p class=\"wp-block-paragraph\">My 2011 PhD took the next step: technologies play a privileged causal role in psychological development, and as we invent new ones, we change the developmental environment for present and subsequent generations, thereby driving evolution of the mind, cumulative niche construction applied to human cognition.</p>\n<p class=\"wp-block-paragraph\">Both theses were under Kim Sterelny, whose work on cumulative culture runs through our new preprint too.</p>\n<p class=\"wp-block-paragraph\">For over a decade since, I have worked on global catastrophic risk, studying pandemics, nuclear winter, island refuges, and national risk assessment. It was seemingly inevitable that the two strands; evolution and global risk would meet.</p>\n<p class=\"wp-block-paragraph\">Dobzhansky said nothing in biology makes sense except in the light of evolution.</p>\n<p class=\"wp-block-paragraph\">I'll appropriate that: nothing about human society, and about why it keeps generating risks we know how to avoid, makes sense except in the light of evolution.</p>\n<p class=\"wp-block-paragraph\">Regular readers of this blog will have seen the argument assembling. In February I asked <a href=\"https://adaptresearchwriting.com/2026/02/04/is-there-a-meta-crisis-yes/\">whether there is really a \"meta\"-crisis</a>. In May I <a href=\"https://adaptresearchwriting.com/2026/06/03/what-the-latest-european-risk-analysis-conference-means-for-global-risk-and-new-zealand/\">presented</a> an early version of this argument at the European risk-analysis conference. In July I wrote a <a href=\"https://adaptresearchwriting.com/2026/07/06/polycrisis-metacrisis-systemic-risk-a-definitional-field-guide-to-the-reality-of-everything/\">definitional field guide</a> following a chain of four questions:</p>\n<ul class=\"wp-block-list\">\n<li>What could go badly wrong? That's <strong>global catastrophic risk</strong>.</li>\n<li>How do failures spread? That's <strong>systemic risk</strong>, where a tightly-coupled world is a <em>generator</em> of hazards, not a bystander.</li>\n<li>How do crises compound? That's <strong>polycrisis</strong>, the causal entanglement of crises such that the whole is worse than the sum of its parts.</li>\n<li>And why do we keep generating a fragile world?</li>\n</ul>\n<p class=\"wp-block-paragraph\">I now turn to this fourth question.</p>\n<p class=\"wp-block-paragraph\"><strong>Rising global risk despite known fixes</strong></p>\n<p class=\"wp-block-paragraph\">The major global hazards were identified decades ago, and so were fixes: disarmament, emissions reduction, health-security investment, limits to extraction. The Club of Rome laid much of it out in 1972. Yet emissions have risen since the Paris Agreement, arms-control treaties have lapsed, and by most measures the world is more exposed. Humanity is not ignorant of what threatens it. What's missing is second-order understanding: <em>why</em> we consistently fail, and <em>at what level</em> to intervene.</p>\n<p class=\"wp-block-paragraph\"><strong>Five fields, one grey elephant</strong></p>\n<p class=\"wp-block-paragraph\">Our new preprint begins by outlining the communities working on these problems of global risk. National risk assessment and disaster risk reduction handle hazards, mostly natural, mostly after the fact. Global catastrophic risk studies confront rare but devastating events. Systemic-risk analysis maps feedback-rich networks and names risk-creating actors. Polycrisis scholarship traces entanglement and attractor states, including the Cascade Institute's <a href=\"https://adaptresearchwriting.com/2025/11/11/mapping-pathways-through-the-polycrisis-the-cascade-institutes-new-model-for-navigating-global-systemic-risk/\">\"Illiberal Decline\" and \"Mad Max\"</a> basins. Behavioural and evolutionary science speaks of traps, ratchets and a \"human behavioural crisis\".</p>\n<p class=\"wp-block-paragraph\">Each field is like a blind monk with a hand on an elephant, describing in rich detail what they feel, but unable to articulate the whole. Each field reaches for the same vocabulary of adaptation, selection, co-evolution, traps, ratchets. Some is generic systems talk. A surprising amount is specifically evolutionary, used by fields with no evolutionary self-conception. That is latent Darwinism and it signals intellectual convergence.</p>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7921\" data-attachment-id=\"7921\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"image\" data-large-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png?w=468\" data-orig-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png\" data-orig-size=\"468,354\" data-permalink=\"https://adaptresearchwriting.com/2026/09/10/the-metacrisis-is-a-degradation-of-evolvability-why-global-risk-needs-evolutionary-explanation-and-governance/image-82/\" height=\"354\" sizes=\"(max-width: 468px) 85vw, 468px\" src=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png?w=468\" srcset=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png 468w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png?w=150 150w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png?w=300 300w\" width=\"468\"/><figcaption class=\"wp-element-caption\"><em>Image credit: romana klee on Flickr</em></figcaption></figure>\n<p class=\"wp-block-paragraph\"><strong>Evolution is not a metaphor here</strong></p>\n<p class=\"wp-block-paragraph\">In risk science, grey elephants are a metaphor for big obvious risks, charging right towards us, that everyone can see plainly, yet no one acts.</p>\n<p class=\"wp-block-paragraph\">In our pre-print evolution is not a metaphor. We deploy a precise version of evolution, not a simplified high school one, and certainly not the discredited \"Social Darwinism\" that confused selective success with moral merit.</p>\n<p class=\"wp-block-paragraph\">Natural selection is an abstract process that arises wherever there is heritable variation, differences in success that depend on it, and differential persistence as a result. Dennett called this <em>substrate neutrality</em>: the logic doesn't care what the variants are made of. Genes are one substrate. Firms, institutions, legal codes, professional norms, technologies and ideas are others, to varying degrees. Bicycle design lineages show the adaptive-radiation signature of biological clades, and no designer intended it.</p>\n<p class=\"wp-block-paragraph\">This instantiation comes in degrees, and where any human system sits on Godfrey-Smith's continuum of \"<a href=\"https://academic.oup.com/book/4808\">Darwinian populations</a>\" is an empirical question. But human systems are also designed, meaning that intention and the invisible hand of evolution operate simultaneously. Because no actor can intend outcomes everywhere and all the time, much of what results in human systems evolved rather than being designed.</p>\n<p class=\"wp-block-paragraph\">This is where the social sciences fit, and our framing does not replace economics, political science or the study of human decision-making. Those describe real mechanisms, and human choice is a genuine causal element in the system. What evolution adds is the <em>ultimate</em> level of explanation, in Mayr's sense, not how each mechanism or complex system feature works but <em>why</em> it exists and persists, shaping power and possibility.</p>\n<p class=\"wp-block-paragraph\">Deliberate decisions exist in a selective environment that determines which decisions get retained and copied. The framework is \"extended\" because inheritance runs through several channels at different speeds (genes, memes, laws, education syllabi, technologies), because we actively construct the niches that then impose selection back on human activities, and because not all cultural change is adaptive. For example, prestige, conformity and familiarity spread variants regardless of merit.</p>\n<p class=\"wp-block-paragraph\"><strong>Why we keep building a fragile world</strong></p>\n<p class=\"wp-block-paragraph\">Our new paper groups global risk by examples of its driving dynamics rather than by hazard.</p>\n<ul class=\"wp-block-list\">\n<li><em>Multilevel selection.</em> What's adaptive for one actor (individual, firm, nation) is often destructive for the commons that sustains it. Muir bred hens individually for egg yield and got flocks that feather-pecked and cannibalised themselves. Selecting whole cages for productivity produced cooperative, higher-yield flocks. Scale that up and you have excessive carbon emissions, overfishing, aquifer depletion, and antimicrobial resistance. Firms are rewarded for maximising extraction even when run by people who grasped the consequences decades ago.</li>\n<li><em>Arms races.</em> Red Queen dynamics where everyone must invest more merely to hold position. In frontier AI, safety spending is individually costly and competitively detrimental if an organisation's rivals don't match it, so the field races to deploy. Non-reckless actors are simply outcompeted. Global risks from nuclear weapon stockpiling and gain-of-function research share this structure.</li>\n<li><em>Lock-in and fitness traps.</em> Configurations stable under current pressures but globally suboptimal, can be hard to leave because improving requires first getting worse. Fossil fuel infrastructure is the obvious case, where build out has constrained changes that are now possible.</li>\n<li><em>Transmission bias.</em> Cultural evolution selects for what is readily learned and passed on, not for what is true, and engagement-optimised platforms erode the shared map of reality on which collective action depends and the information scaffolding which centuries of cultural evolution had built.</li>\n</ul>\n<p class=\"wp-block-paragraph\">These are not accidents or failures of will. They are predictable outputs of evolutionary selection at several scales at once. Where the selective environment has been deliberately re-engineered, on the other hand, the Montreal Protocol, verified arms control from the late 1980s, Ostrom's management of the commons, the dynamics have sometimes been beaten. In each case a suppression or coordination mechanism was built and protected, converting locally advantageous defection into a losing move.</p>\n<p class=\"wp-block-paragraph\"><strong>Evolvability, and Metacrisis defined</strong></p>\n<p class=\"wp-block-paragraph\">Evolvability is a system's capacity to generate, transmit and retain complex adaptations. Biological theory and computer science treat it as something that must be built into a system, not assumed. It rests on five conditions:</p>\n<ul class=\"wp-block-list\">\n<li><strong>Variation</strong>: a supply of diverse candidate solutions</li>\n<li><strong>Modularity</strong>: semi-independent parts that can change without dragging the whole down</li>\n<li><strong>Stability of the selective environment</strong>: pressure consistent enough for adaptation to accumulate</li>\n<li><strong>Fidelity of transmission</strong>: reliable inheritance of what works, with error-correction</li>\n<li><strong>Outlaw/defector suppression</strong>: containment of entities that gain locally by breaking cooperative rules or exploiting commons</li>\n</ul>\n<p class=\"wp-block-paragraph\">A definition of the metacrisis follows: <strong>the metacrisis is the simultaneous degradation of these conditions in the systems meant to govern or mitigate global risk.</strong></p>\n<p class=\"wp-block-paragraph\">This is not any particular crisis, or even a polycrisis, but a crisis of the capacity to adapt to crisis at all. That is why governance fails <em>consistently</em> across unrelated domains.</p>\n<p class=\"wp-block-paragraph\">Each evolvability condition is observable. Food-system homogenisation onto a few crops and chokepoints is a variation failure. The T\u014dhoku earthquake, Suez canal blockage and Hormuz fuel crisis rippling through stripped-out supply chains are modularity failures. Policy reversal each electoral cycle is a stability failure that selects against long-horizon investment. The pandemic plans and stockpiles accumulated after SARS in 2003 and the 2009 pandemic, then largely lost before 2020, are an inheritance fidelity failure.</p>\n<p class=\"wp-block-paragraph\">Importantly, evolvability is value-neutral, given that a cancer can be highly evolvable inside the body. So, capacity for evolvability must be paired with a fitness function worth sustaining, and what fast cultural evolution actually selects for is rarely wellbeing or planetary sustainability, but profit, votes, engagement or military advantage. Also, evolvability sits at an interior optimum. If there is too much variation then inheritance is destroyed, if too much stability then maladaptation can become entrenched. As an example, German scientific forestry optimised what it could count and discovered, rotations later, the ecological relationships it had discarded.</p>\n<p class=\"wp-block-paragraph\"><strong>Outlaws, and the lesson from cancer</strong></p>\n<p class=\"wp-block-paragraph\">Defector/outlaw suppression matters most, not only is suppressing outlaws constitutive of evolvability (multiplication of rogue genes that degrade organism fitness, across generations, is a biological example of 'outlaws'), but outlaw activity can undermine the other necessary criteria. At every major evolutionary transition, from cells to organisms to societies, the higher-level unit exists only because it continually constrains, regulates, or suppresses, lower-level strategies that benefit themselves at the expense of the whole.</p>\n<p class=\"wp-block-paragraph\">That is a decisive argument against purely non-interventionist, market-only solutions to large scale risk.</p>\n<p class=\"wp-block-paragraph\">An outlaw need not be conscious or act illegally, since firms externalising costs, states leaving treaties, platforms amplifying misinformation, or farmers applying excess nitrogen fertilizer, may be responding to legitimate incentives.</p>\n<p class=\"wp-block-paragraph\">Increasingly, though, outlaws attack the suppressors. At the height of the US opioid epidemic, wholesalers did not evade the DEA, instead they disabled it through lobbying, a revolving-door attorney and a 2016 statute. All this is the governance analogue of a tumour co-opting the immune cells sent to kill it.</p>\n<p class=\"wp-block-paragraph\">Cancer's evolutionary biology supplies four transferable principles against this kind of defection, namely:</p>\n<ul class=\"wp-block-list\">\n<li>Redundant, multi-layer suppression (single point solutions are insufficient)</li>\n<li>Calibrating rather than maximising enforcement, since maximal enforcement selects for resistant evasion, just as chemotherapy can select for resistant tumours</li>\n<li>Protecting the suppressors from capture</li>\n<li>Suppressing early, before risk generating actors become too big or organised to constrain</li>\n</ul>\n<p class=\"wp-block-paragraph\"><strong>Global overshoot, and walking some of it back</strong></p>\n<p class=\"wp-block-paragraph\">Unconstrained market dynamics constitute a selection environment with a fitness function of short-run return measured in profits. Under it humanity has transgressed several planetary boundaries, oversupplied what pays (extraction, coupling, engagement, throughput) and undersupplied what doesn't (slack, buffers, prevention, institutional memory). No institution was mandated to preserve resilience, so resilience was competed away, then we struck Covid-19, the Russian Invasion of Ukraine, the US assaults on Iran, and potentially worse global shocks to come.</p>\n<p class=\"wp-block-paragraph\">Reducing catastrophic risk means walking some of this back. We need to incentivise retreat from planetary boundaries, rebuild buffers, accepting that some efficiency was borrowed against the future. The evolutionary framing doesn't make that easy. It explains why it hasn't happened on its own and won't at the global level.</p>\n<p class=\"wp-block-paragraph\">Our <a href=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/260831-evolvability-metacrisis-v8.pdf\">pre-print</a> lays all this out, describing the current dynamics, explaining why they persist, and offering a pathway forward.</p>\n<p class=\"wp-block-paragraph\"><strong>New Zealand in the present</strong></p>\n<p class=\"wp-block-paragraph\">My book club is currently reading the Helen Clark Foundation's 2026 release \"<a href=\"https://www.helenclark.foundation/facing-up-to-our-future\">Facing Up to Our Future</a>\", which consists of twenty short policy chapters on the long-run problems no single government seems able to solve. What strikes me is how much of our pre-print's machinery is in there, independently arrived at across multiple fields of policy and economy, but never framed in evolutionary terms such that the big picture dynamics are clear.</p>\n<p class=\"wp-block-paragraph\">The book's framing is often a diagnosis of the metacrisis, speaking of political regimes structurally incapable of addressing decades-long problems, which is a claim about degraded adaptive capacity rather than about any one policy. The opening economic chapters then supply the conditions one by one.</p>\n<ul class=\"wp-block-list\">\n<li><em>Variation.</em> Competition policy and industrial policy are, in these terms, about the supply of candidate solutions. New Zealand's supermarket duopoly is a monoculture, with two dominant variants there is little for selection to work on, evolvability is throttled at the source, lock-in takes hold to the detriment of the higher-level system, namely New Zealand society.</li>\n<li><em>Modularity.</em> Niche construction (in our paper's sense) has created entrenchment in the energy market, incumbents whose infrastructure and integration and coalitions favour their own continuation and cannot be teased apart one by one to change, limiting what the system can become.</li>\n<li><em>Stability of the selective environment.</em> The book's recurring complaint about inconsistent, reversible policy is a stability failure. Investment flows to long-horizon adaptative solutions only where this action is predictably rewarded over time.</li>\n<li><em>Defector suppression.</em> New Zealand's regulatory environment is full of tools that lack bite, such as a passive Commerce Commission, captured regulation and high barriers to market entry. This is suppression architecture that has stopped suppressing what disrupts the cooperative whole, permits externalities, allows fragilities to expand, and fails to preserve modularity, or variation.</li>\n</ul>\n<p class=\"wp-block-paragraph\">Industrial policy to mitigate the contribution to global risk made across various industries, as well as investment in appropriate infrastructure, skills and training can shape evolvability. But only if paired with a meaningful fitness function, ie incentives and punishments tied to risk reduction and wellbeing, otherwise we simply accelerate adaptation in whatever direction the market was already heading.</p>\n<p class=\"wp-block-paragraph\">Unfortunately, market solutions alone will never overcome the outlaw/defector problem, because the market is where defection is rewarded. Good industrial policy grounded in evolutionary theory and tied to global risk reduction is the alternative, and is necessary otherwise, in the end, we all lose.</p>\n<p class=\"wp-block-paragraph\">The point is not that policy accounts need our pre-print. It is that the relevant dynamics are already and everywhere operating. There is some understanding of them across standard systems and economic thinking. But the evolutionary dynamics need to be understood better, deeper and more broadly, because they are foundational rather than incidental to reducing global systemic and catastrophic risk.</p>\n<p class=\"wp-block-paragraph\"><strong>Credit to others, and our contribution</strong></p>\n<p class=\"wp-block-paragraph\">None of this work comes out of thin air. <a href=\"https://www.cambridge.org/core/journals/global-sustainability/article/systemic-contributions-to-global-catastrophic-risk/C9DCBFE8C24F8CA1505F61DC61E9822B\">Arnscheidt and colleagues</a> have named risk-creating actors as a primary driver of global catastrophic risk. <a href=\"https://link.springer.com/article/10.1007/s13753-025-00636-3\">Liu and Renn</a> call for biomimetic designs \"tested by natural selection\". <a href=\"https://www.cambridge.org/core/journals/global-sustainability/article/both-adaptive-and-transformative-capacities-are-necessary-to-navigate-global-polycrisis/0FB17EA1F8BD5EF4AE6F15EBB0390267\">S\u00f8gaard J\u00f8rgensen</a>'s group catalogues Anthropocene traps and now speaks of a \"co-evolutionary struggle\" between resilience capacity and the polycrisis. <a href=\"https://www.tandfonline.com/doi/full/10.1080/02604027.2025.2572007\">H\u00e4m\u00e4l\u00e4inen's</a> cybernetic \"complexity gap\" is a functional analogue of evolvability. <a href=\"https://pubmed.ncbi.nlm.nih.gov/37952628/\">Waring and colleagues</a> treat the Anthropocene as an evolutionary ratchet. There are many other examples.</p>\n<p class=\"wp-block-paragraph\">These are real advances, mostly arrived at inductively and in fragments. What no one has done is articulate the complete framing from first principles, ie evolution as the substrate-neutral generative process, evolvability as an organising concept, and tied these to a formal definition of the metacrisis in these terms, with suppression as constitutive rather than optional. Several of these frameworks omit outlaw suppression entirely. Synthesising all this is what our pre-print attempts.</p>\n<p class=\"wp-block-paragraph\"><strong>Our deliberate overreach</strong></p>\n<p class=\"wp-block-paragraph\">Our paper is intentionally provocative and probably pushes the explanation a little further than is warranted. Not all cultural change follows Darwinian dynamics tightly, and institutions, unlike tumours, can foresee consequences and redesign themselves. Every concept we import from biology is because of the shared selective structure, not the disanalogous features.</p>\n<p class=\"wp-block-paragraph\">But this extended framework supplies machinery for the loose cases too, namely niche construction, transmission biases, developmental plasticity, multiple inheritance channels, and so on. Our aim was to cast the net wide, to show there is a broader way of thinking about global systemic and catastrophic risk that supplies coherence and ultimate explanation, providing the <em>why</em> to supplement the <em>what</em>.</p>\n<p class=\"wp-block-paragraph\"><strong>Towards action</strong></p>\n<p class=\"wp-block-paragraph\">Our approach would shift the object of global risk governance. We don't specify precise solutions, but instead recommend engineering, nudging and continually readjusting the evolutionary factors so that adaptive solutions to specified fitness problems, evolve naturally:</p>\n<ul class=\"wp-block-list\">\n<li><strong>Shape the fitness function</strong>: make biosphere persistence and human wellbeing what actually wins and stop feeding risk-creating actors with subsidies and support.</li>\n<li><strong>Stabilise the selective environment:</strong> with wise durable policy contracts insulated from electoral cycles.</li>\n<li><strong>Curate variation and modularity:</strong> mandated buffers, supply-chain and planetary-boundary examiners embedded in firms on the bank-examiner model, modular refuges, rural revitalization, or transition towns that preserve capability through catastrophe.</li>\n<li><strong>Protect transmission of adaptations:</strong> ring-fenced prevention budgets (eg pandemic PPE), institutional memory, error-correction of the information commons.</li>\n<li>Above all, <strong>build and protect multi-layer suppression</strong>: early, calibrated, capture-resistant control of defectors that win locally at the expense of humanity.</li>\n<li><strong>Act regionally and at bloc level</strong>, where cooperation is more evolvable than at global scale.</li>\n</ul>\n<p class=\"wp-block-paragraph\">Because each evolvability condition is observable, the five can form a dashboard tracking the direction of travel of global risk-governance capacity, and the framework makes falsifiable predictions, for example interventions that robustly alter the selection environment should outperform those that just alter actors' knowledge or goals.</p>\n<p class=\"wp-block-paragraph\"><strong>How this fits alongside existing work</strong></p>\n<p class=\"wp-block-paragraph\">Our work is integrative and complementary, not competitive. The <a href=\"https://cascadeinstitute.org/\">Cascade Institute's</a> <a href=\"https://adaptresearchwriting.com/2025/11/11/mapping-pathways-through-the-polycrisis-the-cascade-institutes-new-model-for-navigating-global-systemic-risk/\">Polycrisis CORE model</a> maps the global system attractor basins. The evolutionary account explains the forces pulling toward them and which levers change the gradient. The <a href=\"https://www.asranetwork.org/insights/facing-global-risks-with-honest-hope-report\">Accelerator for Systemic Risk Assessment</a> has built assessment capacity, and evolvability supplies what to assess and why. Oliver and colleagues' systemic-risk \"<a href=\"https://www.cambridge.org/core/journals/global-sustainability/article/appraising-cascading-systemic-risks-watchpoints-and-interventions-methodological-reflections/672D6A4430F1BBADF800464C9DA45C20\">watchpoints</a>\" are a step toward a dashboard. Richardson et al.'s <a href=\"https://www.cambridge.org/core/journals/global-sustainability/article/principles-for-just-and-effective-systemic-risk-governance/15DAE61A09BE55307C0484F362C38F08\">normative principles</a> in the context of global risk are where the fitness function gets its ethics. Complexity science explains how systems become fragile, and the evolutionary account explains why fragile architectures keep being selected despite full awareness.</p>\n<p class=\"wp-block-paragraph\">The risk community has spent enormous effort cataloguing what is going wrong. An evolutionary reading names, monitors and builds the conditions that determine what can be redesigned to go right. The invisible hand has been running on our institutions all along. The task is to make it visible, and to direct it.</p>\n<p class=\"wp-block-paragraph\">Read our new preprint<a href=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/260831-evolvability-metacrisis-v8.pdf\"> here</a> (currently under peer-review)</p>","doi":"https://doi.org/10.59350/kjv4n-j7x81","guid":"http://adaptresearchwriting.com/?p=7916","image":"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=936","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788998400,"rid":"eyq54-0w016","summary":"Introducing our new preprint on evolutionary governance for systemic and global catastrophic risk By Matt Boyd TLDR/Summary Two intellectual strands twisted together This post has been a long time coming. In 2007 I wrote a Masters thesis in philosophy, on cultural evolution and the information environment we have created.","title":"The Metacrisis is a Degradation of Evolvability: Why Global Risk Needs Evolutionary Explanation and Governance","updated_at":1789025406,"url":"https://adaptresearchwriting.com/2026/09/10/the-metacrisis-is-a-degradation-of-evolvability-why-global-risk-needs-evolutionary-explanation-and-governance/","version":"v1"}},{"document":{"authors":[{"contributor_roles":[],"name":"@edent"}],"blog":{"authors":null,"community_id":"61ce553a-bafd-4aba-a952-d3bab5e85bcc","created":1788652800,"current_feed_url":null,"description":"Regular nonsense about tech and its effects \ud83d\ude43","doi":"https://doi.org/10.59350/shkspr","favicon":"https://rogue-scholar.org/api/communities/61ce553a-bafd-4aba-a952-d3bab5e85bcc/logo","feed_format":"application/atom+xml","feed_url":"https://shkspr.mobi/blog/feed/atom/?cat=-1982&HTTP_REFERER=DOI","filter":null,"generator":"WordPress","home_page_url":"https://shkspr.mobi/blog","issn":"2753-1570","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"shkspr","status":"active","subfield":"1712","title":"Terence Eden's Blog","updated":1788867291,"use_api":false},"blog_name":"Terence Eden's Blog","blog_slug":"shkspr","content_html":"<html><head></head><body><img src=\"https://shkspr.mobi/blog/wp-content/uploads/2020/08/Invisible-Agents.jpg\" alt=\"\" width=\"358\" height=\"550\" class=\"alignleft size-full wp-image-36319\">\n\n<blockquote><p>It would be easy for the modern reader to conclude that women had no place in the world of early modern espionage, with a few seventeenth-century women spies identified and then relegated to the footnotes of history. If even the espionage carried out by Susan Hyde, sister of Edward Hyde, Earl of Clarendon, during the turbulent decades of civil strife in Britain can escape the historiographer's gaze, then how many more like her lurk in the archives?</p>\n\n<p>Nadine Akkerman's search for an answer to this question has led to the writing of Invisible Agents, the very first study to analyse the role of early modern women spies, demonstrating that the allegedly-male world of the spy was more than merely infiltrated by women. This compelling and ground-breaking contribution to the history of espionage details a series of case studies in which women \u2014 from playwright to postmistress, from lady-in-waiting to laundry woman \u2014 acted as spies, sourcing and passing on confidential information on account of political and religious convictions or to obtain money or power.</p></blockquote>\n\n<p>It's rare that I abandon a book - but I gave up half way through this and skimmed to the end. In theory, this should be an exciting book - Spies! Sex! State Secrets!  But it quickly becomes little more than a list of names, dates, and locations.</p>\n\n<p>There's a tantalising glimpse into the tradecraft of spies. An all-too-brief chapter on codes, ciphers, physical deceptions, and invisible inks.  But it doesn't go into any depth.  I'd have liked to have learned about how these evolved, and a bit more about the cat-and-mouse game between spy and spycatcher.</p>\n\n<p>The book is expertly researched - and draws upon multiple sources. But much of the quoted material is <em>physically</em> hard to read. Some abbreviations have been expanded with <em>italics</em> part way through words - but original archaic spelling is preserved. Deletions and insertions are also marked. Which leads to quotes like this:</p>\n\n<blockquote><p>he [Charles Lyttelton] [\u2026] had several ^tymes^ mett w<i>i</i>th the sa<i>i</i>d Maior [Henry] Norwood [\u2026] and p<i>ar</i>ticularly 4 or 5 tymes at the <del>Earl</del> ^Lady^ Newports ^in Lincolns Inn ffeilds^, where there haue been in her Company as he remembers (besides those of her family) one Mr Beuerly &amp; one Mr Browne a kinsman of <i>th</i>e Lo<i>rd</i> Harberts ^&amp; some others whom he remembers not^.</p></blockquote>\n\n<p>The mix of italics and regular text is just unpleasant to read.</p>\n\n<p>It is great to see that women were capable of committing treason, and it is interesting to see how they fared and the punishment they received. But the vast cast of characters is unweildly, and the timeline is muddled unless you're already an expert in the era.</p>\n\n<p>I'm sure it's a fine academic work - but it was too much of a slog for this casual reader.</p>\n</body></html>","doi":"https://doi.org/10.59350/sm876-7gs33","guid":"https://shkspr.mobi/blog/?p=36316","image":"https://shkspr.mobi/blog/wp-content/uploads/2020/08/Invisible-Agents.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1598054400,"rid":"dge5e-3cr20","summary":"It's rare that I abandon a book - but I gave up half way through this and skimmed to the end. In theory, this should be an exciting book - Spies! Sex! State Secrets! But it quickly becomes little more than a list of names, dates, and locations. There's a tantalising glimpse into the tradecraft of spies. An all-too-brief chapter on codes, ciphers, physical deceptions, and invisible inks. But it doesn't go into any depth.","tags":["/etc/","Book Review"],"title":"Book Review: Invisible Agents: Women and Espionage in Seventeenth-Century Britain","updated_at":1789023249,"url":"https://shkspr.mobi/blog/2020/08/book-review-invisible-agents-women-and-espionage-in-seventeenth-century-britain/","version":"v1"}}],"items":[{"authors":[{"contributor_roles":[],"family":"Crueger","given":"Jens"}],"blog":{"authors":[{"name":"Redaktion iRights.info"}],"community_id":"7d3b25fd-a4a8-4155-8e76-99d6be06706a","created":1694736000,"current_feed_url":null,"description":"Urheberrecht und kreatives Schaffen in der digitalen Welt","doi":"https://doi.org/10.59350/irights","favicon":"https://rogue-scholar.org/api/communities/7d3b25fd-a4a8-4155-8e76-99d6be06706a/logo","feed_format":"application/atom+xml","feed_url":"https://irights.info/feed/atom","filter":null,"generator":"Other","home_page_url":"https://irights.info/","issn":null,"language":"deu","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"irights","status":"active","subfield":"3308","title":"iRights.info","updated":1789026321,"use_api":false},"blog_name":"iRights.info","blog_slug":"irights","content_html":"<p>In the media and on social media, there has been a growing number of concerned reports about AI companies that are buying up used books in large quantities and in a rather ominous manner. It is speculated that the large quantities of books acquired in this way are scanned, used for AI training, and irretrievably destroyed in the process. It is often suggested that copyright law is the reason why the books are being destroyed. Can this assumption be substantiated?<br/>\n<span id=\"more-32898\"></span></p>\n<h2>The Destructive Scanning of Books</h2>\n<p>The retro-digitization (usually referred to simply as \"digitization\") of books is typically carried out using scanning technology. Modern book scanners are capable of scanning books non-destructively. However, non-destructive scanning of books is a complex process, as irregularities caused by the book's binding must be compensated for during the scanning process.</p>\n<p>In contrast, in so-called destructive scanning, the book's binding is mechanically removed. This turns a book into a loose collection of pages that can be conveniently digitized using a sheet-fed scanner. Once the scanning process is complete, the book pages are then disposed of as waste paper.</p>\n<h2>Why Antiquarian Bookstores Are Important for AI Training</h2>\n<p>Digital data sources, such as web archives, have long been incorporated into the training of current AI models. The digitization of printed books is now the next stage in data acquisition. According to observers, tech companies are particularly focused on non-fiction books published between the 1970s and the 1990s.</p>\n<p>These books are likely to be of interest for three reasons: First, nonfiction books are valuable for AI training because of their content; they contain factual information that is still largely accurate and is integrated into linguistically sophisticated patterns of argumentation. Second, book titles published before the mid-1990s were generally released exclusively as print editions and have not been digitized since. Third, books from the period in question are still predominantly subject to copyright, which expires only 70 years after the author's death in both Germany and the U.S.</p>\n<p>Obtaining scans of these books from dubious third-party sources would be illegal. Therefore, from a copyright perspective, the purchased print editions of these books are particularly valuable to the companies.</p>\n<h2>Technical Reasons for Destructive Scanning</h2>\n<p>But why do AI companies accept the destruction of the books during the scanning process?</p>\n<p>First, technical aspects play a significant role in large-scale retro-digitization of books: As explained at the outset, destructive scanning is simpler, faster, and therefore more cost-effective. Although the AI industry appears economically strong, observers interpret the decision to use the most cost-effective digitization method as an indication of cost pressure in this \"<a href=\"https://arstechnica.com/ai/2025/06/anthropic-destroyed-millions-of-print-books-to-build-its-ai-models/\" rel=\"noopener\" target=\"_blank\">highly competitive industry</a>.\"</p>\n<p>Competitive considerations may also play a role, because while the books in question are not particularly old or unique, many of them are nevertheless rarely available on the antiquarian book market due to low print runs and scarcity. Whoever buys them first effectively removes them from the competition's reach, thereby gaining a small advantage for their AI model.</p>\n<h2>Destructive Scanning Out of Concern for Copyright?</h2>\n<p>A lawsuit between three plaintiff authors and the AI company Anthropic before the United States District Court for the Northern District of California (<a href=\"https://copyrightalliance.org/wp-content/uploads/2025/06/Bartz-v.-Anthropic-Order.pdf\" rel=\"noopener\" target=\"_blank\">Bartz v. Anthropic</a>) established a legal precedent regarding destructive book scanning in 2025.</p>\n<p>The central question here was whether destructive scanning, on the one hand, and the training of AI models using the content of acquired digitized books, on the other, fall under the so-called \"fair use principle.\"</p>\n<div class=\"merksatz\"><strong>What is the fair use principle?</strong><br/>\nThe fair use principle is a legal doctrine found in some common law countries. It permits the use of copyrighted material for purposes of public education or intellectual production without requiring authorization for such use. Classic areas of application for fair use include commentary, criticism, parody, news reporting, research, and scholarship. Under German copyright law, instead of a general clause like fair use, there are narrow exceptions that permit certain uses (such as quotations, caricatures, parodies, educational and scholarly purposes, reporting on current events, etc.) regardless of the copyright holder's consent.</div>\n<p>The two central questions to be decided by the court must be considered separately:</p>\n<p>First, whether training AI models with the content of purchased digitized books is protected by the fair use doctrine.</p>\n<p>Second, whether destructive scanning constitutes a copyright-relevant copy of a work.</p>\n<p><a href=\"https://copyrightalliance.org/wp-content/uploads/2025/06/Bartz-v.-Anthropic-Order.pdf\" rel=\"noopener\" target=\"_blank\">According to Judge William Alsup</a>, training AI models using the content of purchased digitized books was \"transformative in the truest sense of the word\" and therefore protected by the fair use doctrine. Destructive scanning should be classified as \"replacement scanning,\" in which a printed work is replaced by a digital work. This conversion of a purchased printed book into a digital book was classified by the court as a \"<a href=\"https://copyrightalliance.org/wp-content/uploads/2025/06/Bartz-v.-Anthropic-Order.pdf\" rel=\"noopener\" target=\"_blank\">format change</a>\" rather than a copy and is therefore also covered by fair use.</p>\n<h2>A Landmark Ruling with Significant Implications</h2>\n<p>The rule on format conversion\u2014also known as the \"<a href=\"https://www.technollama.co.uk/fahrenheit-451-or-rainbows-end-ai-books-and-copyright-law\" rel=\"noopener\" target=\"_blank\">format-shifting rationale</a>\"\u2014thus promises, according to this landmark ruling, a certain degree of legal certainty for AI companies that destroy the books they have acquired for AI training through destructive scanning. The method that is more efficient from a technical standpoint is therefore also the more legally advisable one.</p>\n<p>However, it is a fallacy to assume that the court's ruling <em>requires</em> AI companies to destroy the digitized books. The lawsuit merely examined the specific digitization process as applied by Anthropic as part of \"Project Panama\"\u2014and classified it as fair use.</p>\n<h2>E-books Instead of Print Books?</h2>\n<p>If e-books were used for training instead of their printed counterparts, the time-consuming step of scanning\u2014and the associated issues of transportation, storage, and reuse\u2014would be eliminated.</p>\n<p>However, e-books can only become training data for AI models in two ways: the legal way\u2014that is, with the involvement of the rights holders of those e-books\u2014or by training with pirated copies. For AI companies, the legal route entails a significantly higher \"<a href=\"https://www.nytimes.com/2025/09/05/technology/anthropic-settlement-copyright-ai.html\" rel=\"noopener\" target=\"_blank\">legal/practice/business slog</a>\" (quote from Anthropic co-founder and CEO Dario Amodei).</p>\n<p>Training AI with pirated copies of e-books <a href=\"https://truthonthemarket.com/2025/06/24/bartz-v-anthropic-mapping-fair-use-boundaries-in-the-age-of-generative-ai/\" rel=\"noopener\" target=\"_blank\">is not covered by fair use</a> and thus constitutes a clear copyright infringement, Judge Alsup ruled.</p>\n<h2>Fears of 'Fahrenheit 451' Scenarios</h2>\n<p>Reports of AI companies purchasing large quantities of books from used bookstores have sparked, in some cases, fierce reactions in the media. The media discussion often references Ray Bradbury's novel *<a href=\"https://en.wikipedia.org/wiki/Fahrenheit_451\" rel=\"noopener\" target=\"_blank\">Fahrenheit 451</a>*, a dystopia in which books are banned.</p>\n<p>A closer look at the relevant court ruling in this specific case reveals that there is no legal obligation to destroy retro-digitized books. Economic reasons for choosing the most cost-effective digitization method therefore appear to be the decisive factor when the AI industry employs destructive book scanning. Against the backdrop of the actions taken by major AI companies, calls for open-source AI models are currently growing louder, and with regard to the retro-digitization of books, there are also increasing calls for \"<a href=\"https://www.rbb24.de/kultur/beitrag/2026/08/buecher-antiquariate-bestellungen-ki-training-vermutet.html\" rel=\"noopener\" target=\"_blank\">an open-source initiative or a similar nonprofit project.</a>\"</p>\n<div class=\"merksatz\">\n<h2>Would you like to support iRights.info?</h2>\n<p><strong><a href=\"https://irights.info/\">iRights.info</a> provides information and explanations on the subject of \"Copyright and creativity in the digital world\". All texts are published free of charge and openly licensed.</strong></p>\n<p><strong>If you like, you can support us via the <a href=\"https://www.betterplace.org/de/projects/120241-irights-info-informationsplattform-zum-urheberrecht-in-der-digitalen-welt\">donation platform Betterplace</a> and receive a donation receip. Betterplace accepts PayPal, direct debit, credit card, paydirekt or bank transfer.</strong></p>\n<p><strong>We would be particularly pleased to receive a regular contribution, for example as a monthly standing order. The <a href=\"https://irights.info/was-ist-irightsinfo-projekttrger\">non-profit organization iRights e.V.</a> would like to thank you for your support!<br/>\n</strong></p>\n<hr/>\n<p><strong>DOI for this text: \u00b7 Automatic DOI assignment for blogs via <a href=\"https://rogue-scholar.org/de/blogs/irights\">The Rogue Scholar</a></strong></p>\n</div>\n<p><script async=\"async\" src=\"https://www.betterplace.org/de/widgets/overlays/EjCxZ8kpYxhZeyTSTKxRZ33M.js\" type=\"text/javascript\"></script></p>\n<p>The post <a href=\"https://irights.info/artikel/out-of-concern-for-copyright-ai-companies-and-their-destructive-scanning-of-books/32898\">Out of Concern for Copyright? AI Companies and Their Destructive Scanning of Books</a> appeared first on <a href=\"https://irights.info\">iRights.info</a>.</p>","doi":"https://doi.org/10.59350/ksfmn-23248","guid":"https://irights.info/?post_type=custom_artikel&p=32898","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788998400,"rid":"bznwv-d6252","summary":"In the media and on social media, there has been a growing number of concerned reports about AI companies that are buying up used books in large quantities and in a rather ominous manner. It is speculated that the large quantities of books acquired in this way are scanned, used for AI training, and irretrievably [\u2026] The post Out of Concern for Copyright? AI Companies and Their Destructive Scanning of Books appeared first on iRights.info.","tags":["B\u00fccher","English","Generative KI","Urheberrecht","Urteile"],"title":"Out of Concern for Copyright? AI Companies and Their Destructive Scanning of Books","updated_at":1789029454,"url":"https://irights.info/artikel/out-of-concern-for-copyright-ai-companies-and-their-destructive-scanning-of-books/32898","version":"v1"},{"authors":[{"affiliation":[{"name":"University of Wroc\u0142aw, Chemistry"}],"contributor_roles":[],"family":"Janeta","given":"Mateusz","url":"https://orcid.org/0000-0003-2197-7913"}],"blog":{"authors":null,"community_id":"c21eed24-c860-43d0-997c-0bc782922544","created":1788652800,"current_feed_url":null,"description":null,"doi":"https://doi.org/10.59350/silsesquioxane","favicon":"https://rogue-scholar.org/api/communities/c21eed24-c860-43d0-997c-0bc782922544/logo","feed_format":"application/atom+xml","feed_url":"https://silsesquioxane.blogspot.com/feeds/posts/default","filter":null,"generator":"Blogger","home_page_url":"https://silsesquioxane.blogspot.com/","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"silsesquioxane","status":"active","subfield":"1604","title":"Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry","updated":1789025287,"use_api":true},"blog_name":"Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry","blog_slug":"silsesquioxane","content_html":"<p>\u4e2d\u6587\u7248\u672c / Chinese version: <a href=\"https://silsesquioxane.blogspot.com/p/poss.html\">POSS \u4e8c\u6c1f\u787c\u5149\u50ac\u5316\u5242:\u786b\u919a\u9009\u62e9\u6027\u6c27\u5316\u5236\u4e9a\u781c</a></p>\n<div \"times=\"\" 0px=\"\" 1.75;=\"\" 17px;=\"\" 780px;\"=\"\" auto;=\"\" font-size:=\"\" iowan=\"\" line-height:=\"\" margin:=\"\" max-width:=\"\" new=\"\" old=\"\" roman\",=\"\" serif;=\"\" style=\"color: #24292f; font-family: Georgia, \" style\",=\"\"><p style=\"background: rgb(245, 248, 251); border-left: 4px solid rgb(15, 76, 129); border-radius: 0px 6px 6px 0px; color: #1f2937; font-size: 18px; margin: 0px 0px 1.4em; padding: 1.1em 1.3em; text-align: justify;\"><a href=\"https://pubs.rsc.org/en/content/articlelanding/2025/qi/d5qi00323g\" style=\"display: inline-block; float: left; margin-bottom: 1em; margin-right: 1em;\"><img alt=\"silsesquioxane difluoroboron complexes\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieZxQDVRgNeI8fmnmqP8Q-yYBJlE79nqTichFmo5SytMhZfFD9URo5d6StOfaKM95COqeqIfh2B72C6LWys5dyJBBhR_9TiY3UJG08-bqRwv6I6yfBgCvyAfYfQ3BvBcaZ5gedOnqAAkaqMwyhpv_luxChyTOmfKo_RZwCcEmXc_iEntpFdRVVGSMD-6g/w99-h91/Research%20Highlights%20-%20Copy.png\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\" title=\"silsesquioxane difluoroboron complexes\"/></a>The publication titled <em>\"Polyhedral oligomeric silsesquioxane difluoroboron complexes as cooperative octo-site catalysts for the photooxidation of sulfides to sulfoxides\"</em> by Mateusz Janeta and S\u0142awomir Szafert, published in <em>Inorganic Chemistry Frontiers</em> on April 17, 2025, presents a study on the development of novel metal-free photocatalysts. These catalysts are based on <a href=\"https://silsesquioxane.blogspot.com/2020/08/structures-of-silsesquioxanes.html\">polyhedral oligomeric silsesquioxanes (POSS)</a> functionalized with difluoroboron complexes.</p><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicis9mjsH6kdFSZV6z_G5Je8C8Hh2k2lBZY37-2lORlb-SKPFVcoqRaCb5VKVneVxEaKFKPRQedPuA-b2vgw-M-M1ApfyZ0ClrEmPOsRQ94ixndI5gc3cm4Tki_wTipJ6IJseAOn-KG9GnEQ1q1RDdMdtLwT4X6P25el1n-6U8u8dGuZ0R7QLzz6WJX5Y/s2042/d5qi00323g-s1_hi-res.gif\" style=\"display: block;\"><img alt=\"Synthetic scheme for POSS-sal-BF2, POSS-tert-BF2, and POSS-npht-BF2 difluoroboron photocatalysts with isolated yields\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicis9mjsH6kdFSZV6z_G5Je8C8Hh2k2lBZY37-2lORlb-SKPFVcoqRaCb5VKVneVxEaKFKPRQedPuA-b2vgw-M-M1ApfyZ0ClrEmPOsRQ94ixndI5gc3cm4Tki_wTipJ6IJseAOn-KG9GnEQ1q1RDdMdtLwT4X6P25el1n-6U8u8dGuZ0R7QLzz6WJX5Y/s1600/d5qi00323g-s1_hi-res.gif\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\"/></a></div><div style=\"margin: 2em 0px; text-align: center;\"><div 0.85em=\"\" 0px;=\"\" 1.55;=\"\" 14px;=\"\" 92%;=\"\" arial,=\"\" auto=\"\" center;\"=\"\" font-size:=\"\" helvetica,=\"\" line-height:=\"\" margin:=\"\" max-width:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"color: #5f6b7a; font-family: -apple-system, BlinkMacSystemFont, \" text-align:=\"\" ui\",=\"\"><strong>Scheme 1.</strong> Synthesis of POSS-sal-BF<sub>2</sub>, POSS-<i>tert</i>-BF<sub>2</sub>, and POSS-npht-BF<sub>2</sub>. Isolated yields in parentheses.</div></div><h2 0.01em;=\"\" 0.35em;\"=\"\" 0.9em;=\"\" 0px=\"\" 2.4em=\"\" 22px;=\"\" 700;=\"\" arial,=\"\" font-size:=\"\" font-weight:=\"\" helvetica,=\"\" letter-spacing:=\"\" margin:=\"\" padding-bottom:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: -apple-system, BlinkMacSystemFont, \" ui\",=\"\">Key Highlights</h2><ul style=\"list-style: none; margin: 0px 0px 1.3em; padding-left: 0px;\"><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Catalyst design.</strong> The researchers synthesized three new difluoroboron-functionalized POSS complexes, namely POSS-<i>tert</i>-BF<sub>2</sub>, POSS-sal-BF<sub>2</sub>, and POSS-npht-BF<sub>2</sub>, derived from <a href=\"https://silsesquioxane.blogspot.com/2026/08/rationally-designed-octa-imine.html\">imine-functionalized POSS</a>s.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Photocatalytic performance.</strong> These complexes demonstrated exceptional efficiency in the aerobic photooxidation of sulfides to sulfoxides, significantly outperforming their silsesquioxane-free counterparts. Notably, POSS-<i>tert</i>-BF<sub>2</sub> exhibited a high singlet oxygen quantum yield of 48%.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Intramolecular cooperative activity.</strong> The study demonstrates the feasibility of intramolecular cooperative activity in catalytic reactions and identifies the key factors influencing its effectiveness. The octahedral structure of POSS provides multiple active sites, which enhances catalytic performance.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Environmental advantages.</strong> The catalysts operate under mild conditions, using molecular oxygen as the oxidant and avoiding toxic heavy metals and hazardous reagents, in keeping with the principles of green chemistry.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\"><strong>Reusability.</strong> POSS-<i>tert</i>-BF<sub>2</sub> retained its catalytic activity over multiple cycles with minimal loss of efficiency, which indicates good stability and recyclability.</li></ul><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">This research underscores the potential of POSS-based difluoroboron complexes as efficient, sustainable, and reusable photocatalysts for the selective oxidation of sulfides to sulfoxides, with implications for pharmaceutical synthesis and environmental applications.</p><h2 0.01em;=\"\" 0.35em;\"=\"\" 0.9em;=\"\" 0px=\"\" 2.4em=\"\" 22px;=\"\" 700;=\"\" arial,=\"\" font-size:=\"\" font-weight:=\"\" helvetica,=\"\" letter-spacing:=\"\" margin:=\"\" padding-bottom:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: -apple-system, BlinkMacSystemFont, \" ui\",=\"\">Singlet Oxygen Quantum Yields</h2><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The singlet oxygen quantum yield (SOQY, \u03a6(<sup>1</sup>O<sub>2</sub>)) was determined by monitoring the photooxidation of DPA in methanol in the presence of the POSS derivatives. Changes in the DPA absorbance at 391 nm were measured over time using low concentrations of photosensitizer and DPA in order to minimize potential quenching of <sup>1</sup>O<sub>2</sub> by the photocatalyst. The SOQY values were calculated by plotting the change in DPA absorbance against irradiation time.</p><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The calculated \u03a6(<sup>1</sup>O<sub>2</sub>) values for POSS-<i>tert</i>-BF<sub>2</sub>, POSS-sal-BF<sub>2</sub>, POSS-npht-BF<sub>2</sub>, prop-<i>tert</i>-BF<sub>2</sub>, prop-sal-BF<sub>2</sub>, and prop-npht-BF<sub>2</sub> were 48%, 35%, 46%, 27%, 26%, and 18%, respectively, which highlights the high efficiency of POSS-<i>tert</i>-BF<sub>2</sub> in generating singlet oxygen. A higher singlet oxygen quantum yield, and therefore a higher degree of DPA oxidation, was obtained for the octametallic POSS-<i>tert</i>-BF<sub>2</sub>, POSS-sal-BF<sub>2</sub>, and POSS-npht-BF<sub>2</sub> than for the monometallic analogues prop-<i>tert</i>-BF<sub>2</sub>, prop-sal-BF<sub>2</sub>, and prop-npht-BF<sub>2</sub> under the same reaction conditions. This can be attributed to the intramolecular cooperative effect in compounds bearing the POSS moiety, which was investigated further.</p><h2 0.01em;=\"\" 0.35em;\"=\"\" 0.9em;=\"\" 0px=\"\" 2.4em=\"\" 22px;=\"\" 700;=\"\" arial,=\"\" font-size:=\"\" font-weight:=\"\" helvetica,=\"\" letter-spacing:=\"\" margin:=\"\" padding-bottom:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: -apple-system, BlinkMacSystemFont, \" ui\",=\"\">Photocatalytic Oxidation of Sulfides to Sulfoxides</h2><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">Recent studies have demonstrated the powerful photocatalytic capabilities of POSS-<i>tert</i>-BF<sub>2</sub>, a boron difluoride-functionalized polyhedral oligomeric silsesquioxane. This system shows a significant singlet oxygen quantum yield and generates multiple reactive oxygen species, which makes it highly effective in oxidative transformations.</p><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGPDjOyYlHzrOYGxeMI0OB6IRK3YMTkGn-n2waYjgZk6kbRfiDXEj2hnvOcNsPufgKayUlp7u2Dc6AP88RRs3Ubpzndy6buIHplCht01xR16XIVH2w0ecdlv26wlBrjFUyMfo4oBSs31HoQxhslYF_qSsdDATij1dOta0wqD6i3jyyhkIkUwYc8ZTsoek/s1337/untitled.png\" style=\"display: block;\"><img alt=\"Photooxidation of thioanisole to sulfoxide catalyzed by the POSS-tert-BF2 photocatalyst\" border=\"0\" height=\"125\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGPDjOyYlHzrOYGxeMI0OB6IRK3YMTkGn-n2waYjgZk6kbRfiDXEj2hnvOcNsPufgKayUlp7u2Dc6AP88RRs3Ubpzndy6buIHplCht01xR16XIVH2w0ecdlv26wlBrjFUyMfo4oBSs31HoQxhslYF_qSsdDATij1dOta0wqD6i3jyyhkIkUwYc8ZTsoek/w400-h125/untitled.png\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\" width=\"400\"/></a></div><p style=\"margin: 0px 0px 1.15em; text-align: justify;\"><strong>Key findings from the study</strong></p><ul style=\"list-style: none; margin: 0px 0px 1.3em; padding-left: 0px;\"><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">Oxidation of thioanisole (0.425 mmol in MeOH) reached full conversion in 40 minutes using only 0.5 mol% of POSS-<i>tert</i>-BF<sub>2</sub> under a 150 W medium-pressure mercury lamp.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">The process achieved a turnover number of 1582 and a turnover frequency of 2373 h<sup>\u22121</sup>.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">Scale-up experiments gave a 98% yield.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">The external quantum efficiency of the system was 59%, determined by ferrioxalate actinometry.</li><li style=\"border-left: 3px solid rgb(219, 228, 238); margin: 0px 0px 0.85em; padding-left: 1.1em; text-align: justify;\">Control experiments conducted without light, without photosensitizer, or under anaerobic conditions showed negligible conversion, which confirms the photocatalytic nature of the mechanism.</li></ul><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The conversion of thioanisole was only 30% in pure DCM, whereas under the same reaction conditions in MeOH the conversion increased to 99%. Protic solvents such as MeOH and H<sub>2</sub>O are known to stabilize the intermediate involved in the formation of <sup>1</sup>O<sub>2</sub> and thereby to accelerate photooxidation. These differences in conversion also suggest that <sup>1</sup>O<sub>2</sub> can be identified as one of the reactive oxygen species involved in the photooxidation of thioanisole.</p><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">Comparing the activity of POSS compounds bearing various substituents on the phenyl ring, we observed that introducing steric hindrance, as in the <i>tert</i>-butyl groups at the 3- and 5-positions of the phenyl ring in POSS-<i>tert</i>-BF<sub>2</sub>, significantly increased the reaction efficiency, giving 99% conversion in 40 minutes compared with 70% for POSS-sal-BF<sub>2</sub>, which lacks bulky substituents. Introducing steric hindrance at the 5,6-positions of the phenyl ring in POSS-npht-BF<sub>2</sub>, by replacing the phenyl ring with a naphthalene ring, also improved the efficiency relative to POSS-sal-BF<sub>2</sub>, although it remained lower than that of POSS-<i>tert</i>-BF<sub>2</sub>. This underscores the critical role of steric hindrance at the 3-position of the phenyl ring in promoting the conversion of thioanisole. POSS-<i>tert</i>-BF<sub>2</sub> therefore exhibits high efficiency in the photocatalytic oxidation of thioanisole and was studied in greater detail.</p><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The reaction progress was monitored in real time by NMR spectroscopy, which revealed that the conversion of thioanisole to methyl phenyl sulfoxide with POSS-<i>tert</i>-BF<sub>2</sub> as the photosensitizer increased steadily over time, reaching complete conversion within 40 minutes in accordance with zero-order kinetics. By comparison, the use of prop-<i>tert</i>-BF<sub>2</sub> resulted in only 65% substrate conversion after 40 minutes, with full conversion achieved after 60 minutes. These findings clearly demonstrate the superior reaction efficiency and faster catalytic performance of POSS-<i>tert</i>-BF<sub>2</sub> relative to prop-<i>tert</i>-BF<sub>2</sub>.</p><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The higher conversion of thioanisole obtained with the octametallic POSS-<i>tert</i>-BF<sub>2</sub> (99%) than with the monometallic analogue prop-<i>tert</i>-BF<sub>2</sub> (65%) under the same reaction conditions supports the occurrence of intramolecular cooperative catalysis in POSS-<i>tert</i>-BF<sub>2</sub>. This observation is consistent with the enhancement recorded in the singlet oxygen quantum yields. A similar intramolecular cooperative effect was previously reported for Zn<sub>4</sub>@POSS-1, which contains the POSS-1 ligand, in the formation of cyclic carbonates from epoxides.<sup>37</sup> A comparable enhancement in efficiency was observed for POSS-sal-BF<sub>2</sub> and POSS-npht-BF<sub>2</sub>. Comparing the activity of POSS-npht-BF<sub>2</sub> with that of prop-npht-BF<sub>2</sub>, a higher yield of 90% versus 60% was obtained for POSS-npht-BF<sub>2</sub>. The activity of POSS-sal-BF<sub>2</sub> is likewise higher than that of prop-sal-BF<sub>2</sub>, at 70% versus 59%.</p><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUwpLnjAXZSC6ygXAgF63Zrl3x_7KgzLvUNA4rb-s5E-g4kZK680L0zDhG36E-UF4oMdI8VGmPdTHz3Ab-zbHXHV1PtwGoLD3sVBigGJq4tPls-65zHlheLwPkRqaNm8OgMb0_YrueLw1YCH2TY-kykyjySIibkOu-GT3DwP_jGhjDBPlIpYmKDH5a4Fw/s979/d5qi00323g-s4_hi-res.gif\" style=\"display: block;\"><img alt=\"Proposed photocatalytic mechanism of POSS-tert-BF2 for sulfide oxidation via singlet oxygen\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUwpLnjAXZSC6ygXAgF63Zrl3x_7KgzLvUNA4rb-s5E-g4kZK680L0zDhG36E-UF4oMdI8VGmPdTHz3Ab-zbHXHV1PtwGoLD3sVBigGJq4tPls-65zHlheLwPkRqaNm8OgMb0_YrueLw1YCH2TY-kykyjySIibkOu-GT3DwP_jGhjDBPlIpYmKDH5a4Fw/s1600/d5qi00323g-s4_hi-res.gif\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\"/></a><div 0.85em=\"\" 0px;=\"\" 1.55;=\"\" 14px;=\"\" 92%;=\"\" arial,=\"\" auto=\"\" font-size:=\"\" helvetica,=\"\" left;\"=\"\" line-height:=\"\" margin:=\"\" max-width:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"color: #5f6b7a; font-family: -apple-system, BlinkMacSystemFont, \" text-align:=\"\" ui\",=\"\"><strong>Scheme 2.</strong> Proposed reaction mechanisms of sulfide-selective oxidation by POSS-<i>tert</i>-BF<sub>2</sub> in the presence of O<sub>2</sub>.</div></div><h2 0.01em;=\"\" 0.35em;\"=\"\" 0.9em;=\"\" 0px=\"\" 2.4em=\"\" 22px;=\"\" 700;=\"\" arial,=\"\" font-size:=\"\" font-weight:=\"\" helvetica,=\"\" letter-spacing:=\"\" margin:=\"\" padding-bottom:=\"\" roboto,=\"\" sans-serif;=\"\" segoe=\"\" style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: -apple-system, BlinkMacSystemFont, \" ui\",=\"\">Substrate Scope</h2><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">To assess the versatility of POSS-<i>tert</i>-BF<sub>2</sub> as a photocatalyst in the photooxidation of thioanisole derivatives in methanol, a series of substrates bearing various substituents was evaluated. Thioanisole derivatives containing the electron-donating group \u2013CH<sub>3</sub> and the electron-withdrawing groups \u2013CN, \u2013CHO, and \u2013C(O)CH<sub>3</sub> achieved high yields of 99%, 82%, 78%, and 96%, respectively. Bromine-substituted derivatives at the <i>ortho</i> and <i>meta</i> positions also gave high yields of 99%.</p><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj9AZsfRpRiHgq_DmcJyRfS2Gxiap-Fqr57sV4g7FXk4ke0hyNpW29pJDqxmkGoJPRmeYPbRr9HVE2xNfOHwF7Hq2_GJBENjc2b3hqNVcL17mqJRiFJoqaV17G5pFGomj7U8FBXJyreBKkpJehrEsuHWeWQDWBSQgx7Cl2hYJCv6iyHhZ0ruxCiBYdjdWk/s979/d5qi00323g-s3_hi-res.gif\" style=\"display: block;\"><img alt=\"Substrate scope showing sulfoxide product yields from POSS catalyzed sulfide photooxidation\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj9AZsfRpRiHgq_DmcJyRfS2Gxiap-Fqr57sV4g7FXk4ke0hyNpW29pJDqxmkGoJPRmeYPbRr9HVE2xNfOHwF7Hq2_GJBENjc2b3hqNVcL17mqJRiFJoqaV17G5pFGomj7U8FBXJyreBKkpJehrEsuHWeWQDWBSQgx7Cl2hYJCv6iyHhZ0ruxCiBYdjdWk/s1600/d5qi00323g-s3_hi-res.gif\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\"/></a></div><p style=\"margin: 0px 0px 1.15em; text-align: justify;\">These results highlight the potential of POSS-based systems in green and efficient photocatalytic oxidation chemistry.</p><div style=\"background: rgb(245, 247, 251); border-left: 4px solid rgb(15, 76, 129); color: #333333; font-size: 0.86em; line-height: 1.75; margin: 2em 0px 1em; padding: 14px 20px;\"><strong style=\"color: #0f4c81; display: block; font-size: 0.75em; letter-spacing: 0.08em; margin-bottom: 6px; text-transform: uppercase;\">Full Citation</strong>Mateusz Janeta and S\u0142awomir Szafert. \"Polyhedral oligomeric silsesquioxane difluoroboron complexes as cooperative octo-site catalysts for the photooxidation of sulfides to sulfoxides.\" <em>Inorganic Chemistry Frontiers</em>, 2025, <strong>12</strong>, 4666-4676.<br/>DOI: <a href=\"https://doi.org/10.1039/D5QI00323G\" rel=\"noopener\" target=\"_blank\">10.1039/D5QI00323G</a><br/>Full text: <a href=\"https://pubs.rsc.org/en/content/articlelanding/2025/qi/d5qi00323g\" rel=\"noopener\" target=\"_blank\">Inorganic Chemistry Frontiers \u2192 RSC Publishing</a></div><div style=\"margin: 2em 0px; text-align: center;\"><a href=\"https://pubs.rsc.org/en/content/articlelanding/2025/qi/d5qi00323g\" style=\"display: block;\" target=\"_blank\"><img alt=\"Research highlights infographic summarizing POSS BF2 photocatalyst performance and singlet oxygen quantum yields\" border=\"0\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2rAfRA7RUKjArioYslyjzxJDAO5r4XnObrT9xqirLaaETjeAmvL25VLCegDVm8IGP8b2CjM9NfGU87inA2pr2mfB95hr0VbjT2dj-zjQ7PFvWoJDx_5NUUY8t-GVjFwaJV4Hsu2PDt65coyoZwTaSsb1NS-m930wkHYXloGLxGx-pzQYVfL96cVKiG28/s1600/Research%20Highlights.png\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; display: block; height: auto; margin: 0px auto; max-width: 100%;\"/></a></div></div>","doi":"https://doi.org/10.59350/pznaw-y5e39","guid":"tag:blogger.com,1999:blog-2875892712213933214.post-4039579808081725822","image":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieZxQDVRgNeI8fmnmqP8Q-yYBJlE79nqTichFmo5SytMhZfFD9URo5d6StOfaKM95COqeqIfh2B72C6LWys5dyJBBhR_9TiY3UJG08-bqRwv6I6yfBgCvyAfYfQ3BvBcaZ5gedOnqAAkaqMwyhpv_luxChyTOmfKo_RZwCcEmXc_iEntpFdRVVGSMD-6g/s72-w99-h91-c/Research%20Highlights%20-%20Copy.png","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788998400,"rid":"8jtxv-rdg17","summary":"\u4e2d\u6587\u7248\u672c / Chinese version: POSS \u4e8c\u6c1f\u787c\u5149\u50ac\u5316\u5242:\u786b\u919a\u9009\u62e9\u6027\u6c27\u5316\u5236\u4e9a\u781c The publication titled <em> \"Polyhedral oligomeric silsesquioxane difluoroboron complexes as cooperative octo-site catalysts for the photooxidation of sulfides to sulfoxides\" </em> by Mateusz Janeta and S\u0142awomir Szafert, published in <em> Inorganic Chemistry Frontiers </em> on April 17, 2025, presents a study on the development of novel metal-free photocatalysts.","tags":["Catalysis","Imine-POSS","Photochemistry","POSS","POSS Functionalization"],"title":"POSS Difluoroboron Photocatalysts for Sulfide Oxidation","updated_at":1789025423,"url":"https://silsesquioxane.blogspot.com/2026/09/poss-difluoroboron-photocatalysts-for.html","version":"v1"},{"authors":[{"affiliation":[{"name":"Bielefeld University, Medical Faculty"}],"contributor_roles":[],"family":"Friederichs","given":"Hendrik","url":"https://orcid.org/0000-0001-9671-5235"}],"blog":{"authors":null,"community_id":"304adf51-cbb7-4ff1-a505-1dc06082fbad","created":1776988800,"current_feed_url":null,"description":"Aktuelle Einblicke aus der medizinischen Bildungsforschung \u2014 evidenzbasiert, verst\u00e4ndlich, mit gelegentlichem Augenzwinkern.","doi":"https://doi.org/10.59350/medical_education","favicon":"https://rogue-scholar.org/api/communities/304adf51-cbb7-4ff1-a505-1dc06082fbad/logo","feed_format":"application/rss+xml","feed_url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/blog.xml","filter":null,"generator":"Quarto","home_page_url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/blog.html","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"medical_education","status":"active","subfield":"2739","title":"Entscheiden(d) lernen","updated":1788991200,"use_api":null},"blog_name":"Entscheiden(d) lernen","blog_slug":"medical_education","content_html":"<p><img class=\"preview-image img-fluid\" src=\"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/FriederichsH_impostor.png\"/></p>\n<p><em>Im Oktober beginnen viele junge Menschen ihr Medizinstudium. Viele von ihnen werden in den ersten Wochen denselben Gedanken haben, n\u00e4mlich dass alle anderen im H\u00f6rsaal besser vorbereitet, kl\u00fcger und sicherer wirken als sie selbst. Dieser Gedanke hat einen Namen, er ist gut untersucht, und er ist erstaunlich verbreitet.</em></p>\n<section class=\"level2\" id=\"der-gedanke-in-der-ersten-woche\">\n<h2 class=\"anchored\" data-anchor-id=\"der-gedanke-in-der-ersten-woche\">Der Gedanke in der ersten Woche</h2>\n<p>Die allererste Vorlesung. Um Euch herum sitzen Leute, die sich offenbar m\u00fchelos Fachbegriffe merken, die im Seminar als Erste die Hand heben und die schon wissen, wo die Bibliothek ist. Ihr selbst habt das Gef\u00fchl, durch einen Zufall hier gelandet zu sein. Die Zulassung war Gl\u00fcck, der gute Abiturschnitt eine Verkettung g\u00fcnstiger Umst\u00e4nde, und irgendwann wird jemand merken, dass Ihr eigentlich gar nicht hierhergeh\u00f6rt.</p>\n<p>Wenn Euch das bekannt vorkommt, seid Ihr in gro\u00dfer Gesellschaft. Zwei Metaanalysen aus diesem Jahr kommen unabh\u00e4ngig voneinander zu dem Ergebnis, dass etwa die H\u00e4lfte aller Medizinstudierenden weltweit ausgepr\u00e4gte Impostor-Gef\u00fchle berichtet <span class=\"citation\" data-cites=\"10.1007/s10459-026-10513-3 10.1371/journal.pone.0351713\">[1, 2]</span>. Zum Studienstart liegt der Anteil noch deutlich h\u00f6her. In einer L\u00e4ngsschnittstudie mit 257 Erstsemestern hatten fast neun von zehn schon in den ersten Wochen hohe Werte, und bis zum Jahresende stiegen sie weiter <span class=\"citation\" data-cites=\"10.22454/FamMed.2021.799997\">[3]</span>.</p>\n</section>\n<section class=\"level2\" id=\"was-das-impostor-ph\u00e4nomen-ist\">\n<h2 class=\"anchored\" data-anchor-id=\"was-das-impostor-ph\u00e4nomen-ist\">Was das Impostor-Ph\u00e4nomen ist</h2>\n<p>Beschrieben haben es die Psychologinnen Pauline Clance und Suzanne Imes 1978 bei mehr als 150 beruflich sehr erfolgreichen Frauen. Ihre Klientinnen waren \u00fcberzeugt, ihre Erfolge nicht verdient zu haben, und lebten in der Erwartung, irgendwann als Betr\u00fcgerinnen entlarvt zu werden <span class=\"citation\" data-cites=\"10.1037/h0086006\">[4]</span>. Das T\u00fcckische daran ist ein Kreislauf. Wer vor einer Pr\u00fcfung \u00fcberm\u00e4\u00dfig viel lernt und besteht, schreibt das dem Flei\u00df zu, nicht der eigenen F\u00e4higkeit. Wer aufgeschoben hat und trotzdem durchkommt, schreibt es dem Gl\u00fcck zu. In beiden F\u00e4llen bleibt die eigene Kompetenz unsichtbar, und die n\u00e4chste Pr\u00fcfung beginnt mit denselben Zweifeln.</p>\n<p>Zwei Dinge sind dabei wichtig. Das Impostor-Ph\u00e4nomen ist <strong>keine</strong> Krankheit und <strong>keine</strong> Diagnose, es steht in keinem Klassifikationssystem. Und der verbreitete Begriff \"Impostor-Syndrom\" f\u00fchrt in die Irre, weil er nahelegt, das Problem s\u00e4\u00dfe in der Person. Eine Forschungsgruppe hat 2020 daf\u00fcr pl\u00e4diert, das Ph\u00e4nomen konsequent im Kontext zu betrachten, also in den Umgebungen, die solche Gef\u00fchle hervorrufen <span class=\"citation\" data-cites=\"10.3389/fpsyg.2020.575024\">[5]</span>. Genau darum geht es im n\u00e4chsten Abschnitt.</p>\n</section>\n<section class=\"level2\" id=\"warum-ausgerechnet-das-medizinstudium\">\n<h2 class=\"anchored\" data-anchor-id=\"warum-ausgerechnet-das-medizinstudium\">Warum ausgerechnet das Medizinstudium</h2>\n<p>Die Antwort beginnt mit der Auswahl. Wer einen Medizinstudienplatz bekommt, geh\u00f6rte an der Schule zu den Besten. Im H\u00f6rsaal sitzen dann 300 Menschen, auf die das gleiche zutrifft, und die vertraute Referenzgruppe ist \u00fcber Nacht verschwunden. Wer sich bisher am oberen Rand verortet hat, findet sich pl\u00f6tzlich in der Mitte wieder, ohne dass sich an den eigenen F\u00e4higkeiten etwas ge\u00e4ndert h\u00e4tte.</p>\n<p>Dazu kommt eine Kultur, die Perfektion als Normalzustand behandelt. Ein \u00dcberblick \u00fcber die Literatur beschreibt, wie das Medizinstudium hohe Anspr\u00fcche und Selbstkritik nicht nur anzieht, sondern aktiv trainiert <span class=\"citation\" data-cites=\"10.5116/ijme.5f54.c8f8\">[6]</span>. Eine britische Studie fand, dass die Impostor-Werte umso h\u00f6her lagen, je weiter unten jemand im Pr\u00fcfungsranking stand <span class=\"citation\" data-cites=\"10.1007/s40670-022-01675-x\">[7]</span>. Das klingt zun\u00e4chst naheliegend, hat aber eine Pointe. In einer Gruppe, in der alle zu den Besten ihres Jahrgangs geh\u00f6rten, muss ein Ranking trotzdem die H\u00e4lfte in die untere H\u00e4lfte sortieren. Es verteilt also Zweifel an Menschen, deren Leistung sich gar nicht verschlechtert hat.</p>\n<p>Ein dritter Faktor ist die Frage, ob man sich zugeh\u00f6rig f\u00fchlt. Kanadische Studierende, die im Studium erlebten, dass sie etwas k\u00f6nnen und dass sie aus eigenem Antrieb lernen, berichteten deutlich weniger Impostor-Gef\u00fchle. Wer sich dagegen vor allem von au\u00dfen getrieben f\u00fchlte, von Noten, Erwartungen und Vergleich, berichtete mehr davon <span class=\"citation\" data-cites=\"10.1080/10401334.2022.2056741\">[8]</span>. Und wer an seiner Fakult\u00e4t zu einer Minderheit geh\u00f6rt, ist besonders betroffen. In den USA berichteten Studierende aus unterrepr\u00e4sentierten Gruppen an \u00fcberwiegend wei\u00dfen Fakult\u00e4ten fast dreimal so h\u00e4ufig starke Impostor-Gef\u00fchle wie an Hochschulen mit \u00fcberwiegend schwarzer Studierendenschaft <span class=\"citation\" data-cites=\"10.1016/j.jnma.2023.01.012\">[9]</span>.</p>\n<p>Das Impostor-Gef\u00fchl ist also weniger eine Eigenschaft, die man mitbringt, als eine Reaktion auf eine Situation. Das erkl\u00e4rt, warum es in \u00dcbergangsphasen am st\u00e4rksten ist, nach dem Studienstart, beim Eintritt in die Klinik, zu Beginn der Weiterbildung. So z. B. hatten britische Chirurg*innen in Weiterbildung deutlich h\u00f6here Werte als ihre fertig ausgebildeten Kolleg*innen <span class=\"citation\" data-cites=\"10.1136/bmjopen-2025-100557\">[10]</span>. Es wird besser, aber nicht von allein und nicht schnell.</p>\n</section>\n<section class=\"level2\" id=\"warum-es-nicht-egal-ist\">\n<h2 class=\"anchored\" data-anchor-id=\"warum-es-nicht-egal-ist\">Warum es nicht egal ist</h2>\n<p>Man k\u00f6nnte einwenden, ein bisschen Selbstzweifel schadet nicht. Ein bisschen stimmt das auch. Problematisch wird es, wenn die Zweifel anhalten. Bei \u00c4rzt*innen in Weiterbildung war ein ausgepr\u00e4gtes Impostor-Erleben ein eigenst\u00e4ndiger Risikofaktor f\u00fcr Angstsymptome und Burnout <span class=\"citation\" data-cites=\"10.1080/0142159X.2022.2028751\">[11]</span>, und bei einer Studie an mehr als 3.000 US-\u00c4rzt*innen verdoppelte es die Wahrscheinlichkeit f\u00fcr Burnout <span class=\"citation\" data-cites=\"10.1016/j.mayocp.2022.06.021\">[12]</span>. Bei Erstsemestern hing anhaltendes Impostor-Erleben mit geringerem Selbstmitgef\u00fchl und mehr psychischer Belastung zusammen <span class=\"citation\" data-cites=\"10.22454/FamMed.2021.799997\">[3]</span>. Wer merkt, dass die Zweifel nicht mehr nur vor Pr\u00fcfungen kommen, sondern den Alltag bestimmen, sollte das ernst nehmen und die Beratungsangebote der Universit\u00e4t nutzen. Die sind genau daf\u00fcr da.</p>\n</section>\n<section class=\"level2\" id=\"was-hilft\">\n<h2 class=\"anchored\" data-anchor-id=\"was-hilft\">Was hilft</h2>\n<p>Noch 2020 stellte das gr\u00f6\u00dfte systematische Review zum Thema fest, dass es keine einzige evaluierte Ma\u00dfnahme gegen das Impostor-Ph\u00e4nomen gab <span class=\"citation\" data-cites=\"10.1007/s11606-019-05364-1\">[13]</span>. Seitdem hat sich einiges getan.</p>\n<p>Am besten belegt ist Gruppencoaching. In zwei randomisierten Studien mit zusammen mehr als 1.100 \u00c4rztinnen in Weiterbildung senkte ein sechsmonatiges Online-Programm Impostor-Werte und emotionale Ersch\u00f6pfung und st\u00e4rkte das Selbstmitgef\u00fchl <span class=\"citation\" data-cites=\"10.1001/jamanetworkopen.2022.10752 10.1001/jamanetworkopen.2023.35541\">[14, 15]</span>. Ein Umbrella-Review von 2026, das 16 \u00dcbersichtsarbeiten zusammenfasst, sieht Potenzial in Coaching, Online-Modulen und achtsamkeitsbasierten Ans\u00e4tzen, mahnt aber, dass hochwertige Interventionsstudien noch selten sind <span class=\"citation\" data-cites=\"10.1111/medu.70076\">[16]</span>.</p>\n<p>F\u00fcr den Studienstart ist ein anderer Befund vielleicht wichtiger. Schon ein einzelner Workshop, in dem Erstsemester das Ph\u00e4nomen kennenlernen und merken, dass es fast allen so geht, ver\u00e4ndert etwas. Nach einem solchen Workshop konnten neun von zehn Erstsemestern das Muster bei sich selbst erkennen <span class=\"citation\" data-cites=\"10.1016/j.heliyon.2024.e29478\">[17]</span>, und in einer Orientierungswoche sank der Anteil mit starken Impostor-Gef\u00fchlen um zehn Prozentpunkte <span class=\"citation\" data-cites=\"10.1093/milmed/usaf068\">[18]</span>. Der Wirkmechanismus hei\u00dft Normalisierung. Das Gef\u00fchl, allein damit zu sein, ist ein gro\u00dfer Teil des Problems, und es l\u00f6st sich in dem Moment auf, in dem die Nachbarin im H\u00f6rsaal dasselbe erz\u00e4hlt. Strukturierte Peer-Treffen f\u00fcr Studienanf\u00e4nger*innen zielen genau darauf <span class=\"citation\" data-cites=\"10.1186/s12909-026-09041-w\">[19]</span>.</p>\n<p>Was Ihr selbst tun k\u00f6nnt, l\u00e4sst sich aus dieser Evidenz ableiten. Redet dar\u00fcber, mit Kommiliton*innen und mit Lehrenden, denn die Wahrscheinlichkeit, dass Euer Gegen\u00fcber es kennt, liegt bei etwa f\u00fcnfzig Prozent. Schreibt Euch auf, was Ihr gut k\u00f6nnt, nicht nur, was Ihr noch nicht k\u00f6nnt, denn der Impostor-Kreislauf lebt davon, Erfolge zu vergessen. Und wechselt den Vergleichsma\u00dfstab. Die Frage ist nicht, ob Ihr besser seid als die Person neben Euch, sondern ob Ihr mehr k\u00f6nnt als vor vier Wochen.</p>\n<div class=\"callout callout-style-default callout-tip callout-titled\">\n<div aria-controls=\"callout-1\" aria-expanded=\"false\" aria-label=\"Toggle callout\" class=\"callout-header d-flex align-content-center collapsed\" data-bs-target=\".callout-1-contents\" data-bs-toggle=\"collapse\">\n<div class=\"callout-icon-container\">\n<i class=\"callout-icon\"></i>\n</div>\n<div class=\"callout-title-container flex-fill\">\n<span class=\"screen-reader-only\">Tipp</span>F\u00fcr Statistik-Interessierte \u2014 die Zahlen hinter dem Impostor-Ph\u00e4nomen\n</div>\n<div class=\"callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end\"><i class=\"callout-toggle\"></i></div>\n</div>\n<div class=\"callout-1-contents callout-collapse collapse\" id=\"callout-1\">\n<div class=\"callout-body-container callout-body\">\n<p>Die meisten Studien nutzen die Clance Impostor Phenomenon Scale (CIPS, 20 Items, Wertebereich 20 bis 100). Ab 62 Punkten gelten Impostor-Gef\u00fchle als \"h\u00e4ufig\", ab 81 als \"intensiv\". Diese Grenzen sind Konvention, nicht Diagnosekriterium, und sie erkl\u00e4ren einen Teil der Streuung zwischen den Studien.</p>\n<p><strong>Zwei Metaanalysen, ein Bild.</strong> Omar et al.\u00a0poolten 34 Studien mit 9.550 Medizinstudierenden und fanden eine Pr\u00e4valenz von 49 % (95 %-KI 43 bis 54 %, I\u00b2 = 95,6 %). Frauen lagen bei 51 %, M\u00e4nner bei 40 % (p = 0,021). Mit der CIPS ergaben sich 53 %, mit der Young Impostor Scale 38 % <span class=\"citation\" data-cites=\"10.1007/s10459-026-10513-3\">[1]</span>. Vera-Ponce et al.\u00a0poolten 26 CIPS-Studien mit 9.110 Studierenden und kamen auf 54,2 % (95 %-KI 47,0 bis 61,3 %, I\u00b2 = 98 %), ohne Unterschied zwischen vorklinischem (48,9 %) und klinischem Abschnitt (46,8 %, !) und ohne zeitlichen Trend zwischen 2018 und 2024 <span class=\"citation\" data-cites=\"10.1371/journal.pone.0351713\">[2]</span>. Bei I\u00b2-Werten \u00fcber 95 % beschreibt der gepoolte Wert eine Gr\u00f6\u00dfenordnung, keine gemeinsame Realit\u00e4t.</p>\n<p><strong>Der Studienstart in Zahlen.</strong> Rosenthal et al.\u00a0befragten 257 Erstsemester zu Beginn und am Ende des ersten Jahres. 87 % hatten anfangs hohe oder sehr hohe Werte, die bis zum Jahresende signifikant anstiegen (p &lt; 0,001). Hohe Werte gingen mit deutlich geringerem Selbstmitgef\u00fchl einher (d = 1,62) <span class=\"citation\" data-cites=\"10.22454/FamMed.2021.799997\">[3]</span>. Houseknecht et al.\u00a0beobachteten 110 Studierende \u00fcber drei Jahre und fanden steigende Impostor-Werte (p = 0,011) bei sinkender professioneller Identifikation <span class=\"citation\" data-cites=\"10.1007/s40670-019-00718-0\">[20]</span>. Kim et al.\u00a0verfolgten eine Kohorte von der Orientierungswoche bis zum Ende des 16-monatigen vorklinischen Abschnitts. Der mittlere CIPS-Wert blieb praktisch unver\u00e4ndert (68,3 gegen\u00fcber 68,1), die Ausl\u00f6ser verschoben sich aber vom Zulassungsgl\u00fcck zum Vergleich mit anderen <span class=\"citation\" data-cites=\"10.1093/milmed/usaf373\">[21]</span>.</p>\n<p><strong>Europ\u00e4ische Stichproben.</strong> Unter 457 schwedischen Medizinstudierenden lagen 58,4 % \u00fcber dem CIPS-Grenzwert, Frauen mit 67,4 gegen\u00fcber 59,3 Punkten (d = 0,47). Resilienz korrelierte moderat negativ mit Impostor-Werten (r = \u22120,41) <span class=\"citation\" data-cites=\"10.1186/s12909-024-05788-2\">[22]</span>. In Ume\u00e5 lagen 64 % von 968 Studierenden verschiedener F\u00e4cher \u00fcber dem Grenzwert, und weder Semester noch Alter machten einen Unterschied <span class=\"citation\" data-cites=\"10.3389/fmed.2025.1623792\">[23]</span>. F\u00fcr Deutschland gibt es bislang keine vergleichbare Erhebung.</p>\n<p><strong>Umgebung und Ranking.</strong> Franchi und Russell-Sewell fanden bei 191 britischen Studierenden einen mittleren CIPS-Wert von 65,8, bei 65,4 % \u00fcber dem Grenzwert; pro Dezil weiter unten im Pr\u00fcfungsranking stieg der Wert um 1,12 Punkte (p &lt; 0,05) <span class=\"citation\" data-cites=\"10.1007/s40670-022-01675-x\">[7]</span>. Bei Neufeld et al.\u00a0erkl\u00e4rte die Befriedigung der psychologischen Grundbed\u00fcrfnisse 21,8 % der Varianz, das Kompetenzerleben allein hatte ein \u03b2 von \u22120,49 <span class=\"citation\" data-cites=\"10.1080/10401334.2022.2056741\">[8]</span>. Rice et al.\u00a0berichten f\u00fcr Studierende aus unterrepr\u00e4sentierten Gruppen an \u00fcberwiegend wei\u00dfen Fakult\u00e4ten eine Odds Ratio von 2,75 (95 %-KI 1,65 bis 4,58) gegen\u00fcber historisch schwarzen Hochschulen <span class=\"citation\" data-cites=\"10.1016/j.jnma.2023.01.012\">[9]</span>. In der britischen Unfallchirurgie lagen Trainees bei 70,6 Punkten, Consultants bei 59,8 <span class=\"citation\" data-cites=\"10.1136/bmjopen-2025-100557\">[10]</span>.</p>\n<p><strong>Folgen.</strong> Bei 269 \u00c4rzt*innen in Weiterbildung war das Impostor-Erleben ein unabh\u00e4ngiger Risikofaktor f\u00fcr Angst (RR = 3,64; 95 %-KI 1,96 bis 6,76) und Burnout (RR = 1,82; 95 %-KI 1,07 bis 3,08) <span class=\"citation\" data-cites=\"10.1080/0142159X.2022.2028751\">[11]</span>. Bei 3.116 US-\u00c4rzt*innen war intensives Impostor-Erleben mit h\u00f6heren Odds f\u00fcr Burnout (OR = 2,13; 95 %-KI 1,43 bis 3,19) und f\u00fcr Suizidgedanken (OR = 2,62; 95 %-KI 1,46 bis 4,65) verbunden <span class=\"citation\" data-cites=\"10.1016/j.mayocp.2022.06.021\">[12]</span>. Bei 226 Medizinstudierenden vermittelte das Impostor-Ph\u00e4nomen den Zusammenhang zwischen maladaptivem Perfektionismus und Suizidgedanken (indirekter Effekt B = 0,07; 95 %-KI 0,03 bis 0,13); das ist eine Mediation in Querschnittsdaten, keine Kausalkette <span class=\"citation\" data-cites=\"10.1007/s40596-021-01503-1\">[24]</span>.</p>\n<p><strong>Interventionen.</strong> Fainstad et al.\u00a0randomisierten 101 Assistenz\u00e4rztinnen; das Impostor-Ma\u00df sank in der Coaching-Gruppe um 1,16 Punkte und stieg in der Kontrollgruppe um 0,11 (p = 0,003) <span class=\"citation\" data-cites=\"10.1001/jamanetworkopen.2022.10752\">[14]</span>. Die multizentrische Replikation mit 1.017 Teilnehmerinnen fand eine Differenz von \u22121,28 Punkten (95 %-KI \u22121,63 bis \u22120,93) <span class=\"citation\" data-cites=\"10.1001/jamanetworkopen.2023.35541\">[15]</span>. Nach zw\u00f6lf Monaten war der Impostor-Effekt nicht mehr signifikant (p = 0,081), das Selbstmitgef\u00fchl blieb verbessert <span class=\"citation\" data-cites=\"10.1097/JHM-D-23-00232\">[25]</span>. Ein systematisches Review von sechs Online-Interventionen fand nur zwei RCTs <span class=\"citation\" data-cites=\"10.1186/s12909-024-06340-y\">[26]</span>. Die Orientierungswochen-Workshops sind unkontrollierte Vorher-Nachher-Vergleiche, mit 53 % gegen\u00fcber 43 % mit h\u00e4ufigem oder intensivem Impostor-Erleben bei 222 Studierenden <span class=\"citation\" data-cites=\"10.1093/milmed/usaf068\">[18]</span>, 91,6 % Wiedererkennung bei 49 Erstsemestern <span class=\"citation\" data-cites=\"10.1016/j.heliyon.2024.e29478\">[17]</span>, 96 % bei 21 Assistenz\u00e4rzt*innen <span class=\"citation\" data-cites=\"10.15766/mep_2374-8265.11004\">[27]</span>.</p>\n</div>\n</div>\n</div>\n</section>\n<section class=\"level2\" id=\"was-wir-noch-nicht-wissen\">\n<h2 class=\"anchored\" data-anchor-id=\"was-wir-noch-nicht-wissen\">Was wir (noch) nicht wissen</h2>\n<ul>\n<li><strong>Ob wir alle dasselbe messen.</strong> Je nach Instrument liegt die Pr\u00e4valenz zwischen 38 und 54 %, und die Grenzwerte der CIPS sind Konvention. Ein systematisches Review der Skalen fand keinen Goldstandard <span class=\"citation\" data-cites=\"10.3389/fpsyg.2019.00671\">[28]</span>.</li>\n<li><strong>Was in Deutschland gilt.</strong> Die Daten stammen aus Nordamerika, Skandinavien, Gro\u00dfbritannien und Asien. F\u00fcr deutsche Medizinfakult\u00e4ten mit ihrem Auswahlverfahren und ihrem Curriculum gibt es keine Erhebung.</li>\n<li><strong>Ob Workshops mehr sind als ein Strohfeuer.</strong> Die Evidenz f\u00fcr Normalisierungsworkshops beruht auf Vorher-Nachher-Vergleichen ohne Kontrollgruppe. Ob der Effekt \u00fcber die Orientierungswoche hinaus h\u00e4lt, ist offen.</li>\n<li><strong>Wie viel davon Gef\u00fchl und wie viel davon Umgebung ist.</strong> Wenn Zugeh\u00f6rigkeit und Ranking die Werte so stark verschieben, ist unklar, welcher Anteil \u00fcberhaupt durch individuelle Ma\u00dfnahmen erreichbar ist.</li>\n</ul>\n</section>\n<section class=\"level2\" id=\"fazit\">\n<h2 class=\"anchored\" data-anchor-id=\"fazit\">Fazit</h2>\n<ul>\n<li>Etwa die H\u00e4lfte aller Medizinstudierenden kennt das Gef\u00fchl, nicht wirklich hierherzugeh\u00f6ren, zu Studienbeginn noch mehr. Wer es hat, ist damit nicht die Ausnahme, sondern die Regel.</li>\n<li>Das Gef\u00fchl ist keine Schw\u00e4che und keine Diagnose, sondern eine Reaktion auf eine Umgebung aus Auswahl, Vergleich und Perfektionsanspruch.</li>\n<li>Es h\u00e4ngt mit Angst, Ersch\u00f6pfung und psychischer Belastung zusammen, wenn es anh\u00e4lt. Dann ist es ein Grund, sich Unterst\u00fctzung zu holen.</li>\n<li>Gruppencoaching wirkt nachweislich, die Wirkung auf das Impostor-Erleben verblasst aber nach einem Jahr. Was (hoffentlich) bleibt, ist ein freundlicherer Umgang mit sich selbst.</li>\n<li>Der einfachste wirksame Schritt ist, dar\u00fcber zu sprechen. Die Person neben Euch kennt es sehr wahrscheinlich auch.</li>\n</ul>\n<div class=\"callout callout-style-default callout-note callout-titled\">\n<div aria-controls=\"callout-2\" aria-expanded=\"false\" aria-label=\"Toggle callout\" class=\"callout-header d-flex align-content-center collapsed\" data-bs-target=\".callout-2-contents\" data-bs-toggle=\"collapse\">\n<div class=\"callout-icon-container\">\n<i class=\"callout-icon\"></i>\n</div>\n<div class=\"callout-title-container flex-fill\">\n<span class=\"screen-reader-only\">Hinweis</span>Transparenzkasten\n</div>\n<div class=\"callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end\"><i class=\"callout-toggle\"></i></div>\n</div>\n<div class=\"callout-2-contents callout-collapse collapse\" id=\"callout-2\">\n<div class=\"callout-body-container callout-body\">\n<p><strong>Transparenzhinweis:</strong></p>\n<ul>\n<li><strong>Interessenkonflikte:</strong> Keine angegeben.</li>\n<li><strong>Finanzierung:</strong> Keine Angabe.</li>\n<li><strong>KI-Nutzung:</strong> Claude (Anthropic) wurde zur strukturellen Konzeption und zur sprachlichen Bearbeitung auf Basis eines vom Autor verfassten und immer wieder \u00fcberarbeiteten Gedankengangs eingesetzt.</li>\n<li><strong>Eigene Beteiligung:</strong> Der Autor ist in der medizinischen Ausbildungsforschung t\u00e4tig und hat auch mal Medizin studiert. Obwohl er heute Arzt und Professor ist, ist er im Studium durch Pr\u00fcfungen durchgefallen und kennt das Impostor-Gef\u00fchl sehr gut (auch wenn er das damals nicht so sch\u00f6n benennen konnte).</li>\n</ul>\n</div>\n</div>\n</div>\n</section>\n<section class=\"level2\" id=\"referenzen\">\n</section>\n<div class=\"default\" id=\"quarto-appendix\"><section class=\"quarto-appendix-contents\" id=\"quarto-bibliography\"><h2 class=\"anchored quarto-appendix-heading\">Referenzen</h2><div class=\"references csl-bib-body\" id=\"refs\">\n<div class=\"csl-entry\" id=\"ref-10.1007/s10459-026-10513-3\">\n1. Omar YM, Khattab YA, Abdelmageed A, Messak M, Mandour Y, Shabeeb AE, u.\u00a0a. The impostor phenomenon construct in medical education: a meta-analysis of its prevalence and a critical appraisal of its measurement. Advances in Health Sciences Education. 2026. <a href=\"https://doi.org/10.1007/s10459-026-10513-3\">https://doi.org/10.1007/s10459-026-10513-3</a>.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1371/journal.pone.0351713\">\n2. Vera-Ponce VJ, Huaman-Vega CH, Zuzunaga-Montoya FE, Guerrero Uceda CI, Le\u00f3n-Figueroa DA, Rivera-Lozada O, u.\u00a0a. <a href=\"https://doi.org/10.1371/journal.pone.0351713\">Global prevalence of impostor phenomenon in medical students: A systematic review and meta-analysis</a>. PLOS One. 2026;21:e0351713.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.22454/FamMed.2021.799997\">\n3. Rosenthal S, Schlussel Y, Yaden MB, DeSantis J, Trayes K, Pohl C, u.\u00a0a. <a href=\"https://doi.org/10.22454/fammed.2021.799997\">Persistent Impostor Phenomenon Is Associated With Distress in Medical Students</a>. Family Medicine. 2021;53:118\u201322.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1037/h0086006\">\n4. Clance PR, Imes SA. <a href=\"https://doi.org/10.1037/h0086006\">The imposter phenomenon in high achieving women: Dynamics and therapeutic intervention.</a> Psychotherapy: Theory, Research &amp;amp; Practice. 1978;15:241\u20137.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.3389/fpsyg.2020.575024\">\n5. Feenstra S, Begeny CT, Ryan MK, Rink FA, Stoker JI, Jordan J. <a href=\"https://doi.org/10.3389/fpsyg.2020.575024\">Contextualizing the Impostor <span>\"Syndrome\"</span></a>. Frontiers in Psychology. 2020;11.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.5116/ijme.5f54.c8f8\">\n6. Thomas M, Bigatti S. <a href=\"https://doi.org/10.5116/ijme.5f54.c8f8\">Perfectionism, impostor phenomenon, and mental health in medicine: a literature review</a>. International Journal of Medical Education. 2020;11:201\u201313.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1007/s40670-022-01675-x\">\n7. Franchi T, Russell-Sewell N. <a href=\"https://doi.org/10.1007/s40670-022-01675-x\">Medical Students and the Impostor Phenomenon: A Coexistence Precipitated and Perpetuated by the Educational Environment?</a> Medical Science Educator. 2022;33:27\u201338.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1080/10401334.2022.2056741\">\n8. Neufeld A, Babenko O, Lai H, Svrcek C, Malin G. <a href=\"https://doi.org/10.1080/10401334.2022.2056741\">Why Do We Feel Like Intellectual Frauds? A Self-Determination Theory Perspective on the Impostor Phenomenon in Medical Students</a>. Teaching and Learning in Medicine. 2022;35:180\u201392.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1016/j.jnma.2023.01.012\">\n9. Rice J, Rosario-Williams B, Williams F, West-Livingston L, Savage D, Wilensky JA, u.\u00a0a. <a href=\"https://doi.org/10.1016/j.jnma.2023.01.012\">Impostor syndrome among minority medical students who are underrepresented in medicine</a>. Journal of the National Medical Association. 2023;115:191\u20138.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1136/bmjopen-2025-100557\">\n10. Kamran Siddiqui Z, Tomlinson J, Scantlebury A, Jayasuriya R, Church H, Grove A. <a href=\"https://doi.org/10.1136/bmjopen-2025-100557\">Hidden barriers to leadership: a cross-sectional survey of prevalence and predictors of Imposter Phenomenon in Trauma and Orthopaedic surgery in the UK</a>. BMJ Open. 2025;15:e100557.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1080/0142159X.2022.2028751\">\n11. Liu RQ, Davidson J, Van Hooren TA, Van Koughnett JAM, Jones S, Ott MC. <a href=\"https://doi.org/10.1080/0142159x.2022.2028751\">Impostorism and anxiety contribute to burnout among resident physicians</a>. Medical Teacher. 2022;44:758\u201364.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1016/j.mayocp.2022.06.021\">\n12. Shanafelt TD, Dyrbye LN, Sinsky C, Trockel M, Makowski MS, Tutty M, u.\u00a0a. <a href=\"https://doi.org/10.1016/j.mayocp.2022.06.021\">Imposter Phenomenon in US Physicians Relative to the US Working Population</a>. Mayo Clinic Proceedings. 2022;97:1981\u201393.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1007/s11606-019-05364-1\">\n13. Bravata DM, Watts SA, Keefer AL, Madhusudhan DK, Taylor KT, Clark DM, u.\u00a0a. <a href=\"https://doi.org/10.1007/s11606-019-05364-1\">Prevalence, Predictors, and Treatment of Impostor Syndrome: a Systematic Review</a>. Journal of General Internal Medicine. 2019;35:1252\u201375.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1001/jamanetworkopen.2022.10752\">\n14. Fainstad T, Mann A, Suresh K, Shah P, Dieujuste N, Thurmon K, u.\u00a0a. <a href=\"https://doi.org/10.1001/jamanetworkopen.2022.10752\">Effect of a Novel Online Group-Coaching Program to Reduce Burnout in Female Resident Physicians: A Randomized Clinical Trial</a>. JAMA Network Open. 2022;5:e2210752.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1001/jamanetworkopen.2023.35541\">\n15. Mann A, Shah AN, Thibodeau PS, Dyrbye L, Syed A, Woodward MA, u.\u00a0a. <a href=\"https://doi.org/10.1001/jamanetworkopen.2023.35541\">Online Well-Being Group Coaching Program for Women Physician Trainees: A Randomized Clinical Trial</a>. JAMA Network Open. 2023;6:e2335541.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1111/medu.70076\">\n16. Gisselbaek M, Seyour M, Saxena S, Berger\u2010Estilita J, LaDonna KA, Elia N, u.\u00a0a. <a href=\"https://doi.org/10.1111/medu.70076\">Rethinking the impostor phenomenon: An umbrella review of concept, context and interventions</a>. Medical Education. 2025;60:607\u201324.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1016/j.heliyon.2024.e29478\">\n17. Wrench A, Padilla M, O'Malley C, Levy A. <a href=\"https://doi.org/10.1016/j.heliyon.2024.e29478\">Impostor phenomenon: Prevalence among 1st year medical students and strategies for mitigation</a>. Heliyon. 2024;10:e29478.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1093/milmed/usaf068\">\n18. Kim E, Dupont J, Durning SJ, Landoll R, Soh M. <a href=\"https://doi.org/10.1093/milmed/usaf068\">Mitigating Impostor Phenomenon of Onboarding Military Medical Students: A Workshop Utilizing Situated Learning Theory</a>. Military Medicine. 2025;190:e2153\u20139.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1186/s12909-026-09041-w\">\n19. Polemidiotis M, Sayani N, O'Kelly S, Sreenan S, Brennan M. <a href=\"https://doi.org/10.1186/s12909-026-09041-w\">Structured peer engagement for early-stage medical students provides a safe space and creates a sense of community, combatting imposter syndrome and improving wellbeing</a>. BMC Medical Education. 2026;26.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1007/s40670-019-00718-0\">\n20. Houseknecht VE, Roman B, Stolfi A, Borges NJ. <a href=\"https://doi.org/10.1007/s40670-019-00718-0\">A Longitudinal Assessment of Professional Identity, Wellness, Imposter Phenomenon, and Calling to Medicine Among Medical Students</a>. Medical Science Educator. 2019;29:493\u20137.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1093/milmed/usaf373\">\n21. Kim E, Dupont J, Durning SJ, Bulaklak J, Crosier A, Soh M. <a href=\"https://doi.org/10.1093/milmed/usaf373\">Exploring Impostor Phenomenon During Pre-Clerkship Period in Military Medical School</a>. Military Medicine. 2025;191:e413\u201320.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1186/s12909-024-05788-2\">\n22. Kristoffersson E, Boman J, Bitar A. <a href=\"https://doi.org/10.1186/s12909-024-05788-2\">Impostor phenomenon and its association with resilience in medical education \u2013 a questionnaire study among Swedish medical students</a>. BMC Medical Education. 2024;24.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.3389/fmed.2025.1623792\">\n23. Jansson A, Boman J, Sch\u00e9le I, Holmstr\u00f6m S, Rozental A, Semb O, u.\u00a0a. <a href=\"https://doi.org/10.3389/fmed.2025.1623792\">Impostor phenomenon and its association with perceived stress and anxiety among students in medical and social sciences at a Swedish university</a>. Frontiers in Medicine. 2025;12.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1007/s40596-021-01503-1\">\n24. Brennan-Wydra E, Chung HW, Angoff N, ChenFeng J, Phillips A, Schreiber J, u.\u00a0a. <a href=\"https://doi.org/10.1007/s40596-021-01503-1\">Maladaptive Perfectionism, Impostor Phenomenon, and Suicidal Ideation Among Medical Students</a>. Academic Psychiatry. 2021;45:708\u201315.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1097/JHM-D-23-00232\">\n25. Fainstad T, Syed A, Thibodeau PS, Vinaithirthan V, Jones CD, Mann A. <a href=\"https://doi.org/10.1097/jhm-d-23-00232\">Long-Term Impact of an Online Physician Group-Coaching Program to Improve Burnout and Self-Compassion in Trainees</a>. Journal of Healthcare Management. 2024;69:414\u201323.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.1186/s12909-024-06340-y\">\n26. Hsu C-L, Liu C-H, Huang C-C, Chen H-L, Chiu Y-L, Yang C-W. <a href=\"https://doi.org/10.1186/s12909-024-06340-y\">The effectiveness of online educational interventions on impostor syndrome and burnout among medical trainees: a systematic review</a>. BMC Medical Education. 2024;24.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.15766/mep_2374-8265.11004\">\n27. Baumann N, Faulk C, Vanderlan J, Chen J, Bhayani RK. Small-Group Discussion Sessions on Imposter Syndrome. MedEdPORTAL. 2020. <a href=\"https://doi.org/10.15766/mep_2374-8265.11004\">https://doi.org/10.15766/mep_2374-8265.11004</a>.\n</div>\n<div class=\"csl-entry\" id=\"ref-10.3389/fpsyg.2019.00671\">\n28. Mak KKL, Kleitman S, Abbott MJ. <a href=\"https://doi.org/10.3389/fpsyg.2019.00671\">Impostor Phenomenon Measurement Scales: A Systematic Review</a>. Frontiers in Psychology. 2019;10.\n</div>\n</div></section><section class=\"quarto-appendix-contents\" id=\"quarto-reuse\"><h2 class=\"anchored quarto-appendix-heading\">Wiederverwendung</h2><div class=\"quarto-appendix-contents\"><div><a href=\"https://creativecommons.org/licenses/by/4.0/deed.de\" rel=\"license\">CC BY 4.0</a></div></div></section><section class=\"quarto-appendix-contents\" id=\"quarto-citation\"><h2 class=\"anchored quarto-appendix-heading\">Zitat</h2><div><div class=\"quarto-appendix-secondary-label\">Mit BibTeX zitieren:</div><pre class=\"sourceCode code-with-copy quarto-appendix-bibtex\"><code class=\"sourceCode bibtex\">@misc{friederichs2026,\n  author = {Friederichs, Hendrik},\n  title = {Das Impostor-Ph\u00e4nomen \u2013 was mache ich hier?},\n  date = {2026-09-10},\n  url = {https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/},\n  doi = { 10.59350/0vw9m-k3092},\n  langid = {de}\n}\n</code></pre><div class=\"quarto-appendix-secondary-label\">Bitte zitieren Sie diese Arbeit als:</div><div class=\"csl-entry quarto-appendix-citeas\" id=\"ref-friederichs2026\">\n1. Friederichs H. <a href=\"https://doi.org/ 10.59350/0vw9m-k3092\">Das\nImpostor-Ph\u00e4nomen \u2013 was mache ich hier?</a> 2026.\n</div></div></section></div>","doi":"https://doi.org/10.59350/9dyyf-tve84","guid":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/","image":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/FriederichsH_impostor.png","language":"de","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788912000,"reference":[{"id":"https://doi.org/10.1007/s10459-026-10513-3","unstructured":"Omar, Y. M., Khattab, Y. A., Abdelmageed, A., Messak, M., Mandour, Y., Shabeeb, A. E., Zakaria, A. M., &amp; Abouelmagd, M. E. (2026). The impostor phenomenon construct in medical education: a meta-analysis of its prevalence and a critical appraisal of its measurement. <i>Advances in Health Sciences Education</i>."},{"id":"https://doi.org/10.1371/journal.pone.0351713","unstructured":"Vera-Ponce, V. J., Huaman-Vega, C. H., Zuzunaga-Montoya, F. E., Guerrero Uceda, C. I., Le\u00f3n-Figueroa, D. A., Rivera-Lozada, O., Aguirre-Milachay, E., Gutierrez De Carrillo, C. I., Valladares-Garrido, M. J., &amp; Forero, D. A. (2026). Global prevalence of impostor phenomenon in medical students: A systematic review and meta-analysis. <i>PLOS One</i>, <i>21</i>(8), e0351713."},{"id":"https://doi.org/10.22454/fammed.2021.799997","unstructured":"Rosenthal, S., Schlussel, Y., Yaden, M. B., DeSantis, J., Trayes, K., Pohl, C., &amp; Hojat, M. (2021). 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Impostor phenomenon: Prevalence among 1st year medical students and strategies for mitigation. <i>Heliyon</i>, <i>10</i>(8), e29478."},{"id":"https://doi.org/10.1093/milmed/usaf068","unstructured":"Kim, E., Dupont, J., Durning, S. J., Landoll, R., &amp; Soh, M. (2025). Mitigating Impostor Phenomenon of Onboarding Military Medical Students: A Workshop Utilizing Situated Learning Theory. <i>Military Medicine</i>, <i>190</i>(9-10), e2153\u2013e2159."},{"id":"https://doi.org/10.1186/s12909-026-09041-w","unstructured":"Polemidiotis, M., Sayani, N., O'Kelly, S., Sreenan, S., &amp; Brennan, M. (2026). Structured peer engagement for early-stage medical students provides a safe space and creates a sense of community, combatting imposter syndrome and improving wellbeing. <i>BMC Medical Education</i>, <i>26</i>(1)."},{"id":"https://doi.org/10.1007/s40670-019-00718-0","unstructured":"Houseknecht, V. E., Roman, B., Stolfi, A., &amp; Borges, N. J. (2019). A Longitudinal Assessment of Professional Identity, Wellness, Imposter Phenomenon, and Calling to Medicine Among Medical Students. <i>Medical Science Educator</i>, <i>29</i>(2), 493\u2013497."},{"id":"https://doi.org/10.1093/milmed/usaf373","unstructured":"Kim, E., Dupont, J., Durning, S. J., Bulaklak, J., Crosier, A., &amp; Soh, M. (2025). Exploring Impostor Phenomenon During Pre-Clerkship Period in Military Medical School. <i>Military Medicine</i>, <i>191</i>(1-2), e413\u2013e420."},{"id":"https://doi.org/10.1186/s12909-024-05788-2","unstructured":"Kristoffersson, E., Boman, J., &amp; Bitar, A. (2024). Impostor phenomenon and its association with resilience in medical education \u2013 a questionnaire study among Swedish medical students. <i>BMC Medical Education</i>, <i>24</i>(1)."},{"id":"https://doi.org/10.3389/fmed.2025.1623792","unstructured":"Jansson, A., Boman, J., Sch\u00e9le, I., Holmstr\u00f6m, S., Rozental, A., Semb, O., Fahlstr\u00f6m, M., Stenman, L., Bitar, A., &amp; Lindquist, D. (2025). Impostor phenomenon and its association with perceived stress and anxiety among students in medical and social sciences at a Swedish university. <i>Frontiers in Medicine</i>, <i>12</i>."},{"id":"https://doi.org/10.1007/s40596-021-01503-1","unstructured":"Brennan-Wydra, E., Chung, H. W., Angoff, N., ChenFeng, J., Phillips, A., Schreiber, J., Young, C., &amp; Wilkins, K. (2021). Maladaptive Perfectionism, Impostor Phenomenon, and Suicidal Ideation Among Medical Students. <i>Academic Psychiatry</i>, <i>45</i>(6), 708\u2013715."},{"id":"https://doi.org/10.1097/jhm-d-23-00232","unstructured":"Fainstad, T., Syed, A., Thibodeau, P. S., Vinaithirthan, V., Jones, C. D., &amp; Mann, A. (2024). Long-Term Impact of an Online Physician Group-Coaching Program to Improve Burnout and Self-Compassion in Trainees. <i>Journal of Healthcare Management</i>, <i>69</i>(6), 414\u2013423."},{"id":"https://doi.org/10.1186/s12909-024-06340-y","unstructured":"Hsu, C.-L., Liu, C.-H., Huang, C.-C., Chen, H.-L., Chiu, Y.-L., &amp; Yang, C.-W. (2024). The effectiveness of online educational interventions on impostor syndrome and burnout among medical trainees: a systematic review. <i>BMC Medical Education</i>, <i>24</i>(1)."},{"id":"https://doi.org/10.15766/mep_2374-8265.11004","unstructured":"Baumann, N., Faulk, C., Vanderlan, J., Chen, J., &amp; Bhayani, R. K. (2020). Small-Group Discussion Sessions on Imposter Syndrome. <i>MedEdPORTAL</i>."},{"id":"https://doi.org/10.3389/fpsyg.2019.00671","unstructured":"Mak, K. K. L., Kleitman, S., &amp; Abbott, M. J. (2019). Impostor Phenomenon Measurement Scales: A Systematic Review. <i>Frontiers in Psychology</i>, <i>10</i>."}],"rid":"sy0q1-4yg31","summary":"<em> Im Oktober beginnen viele junge Menschen ihr Medizinstudium. Viele von ihnen werden in den ersten Wochen denselben Gedanken haben, n\u00e4mlich dass alle anderen im H\u00f6rsaal besser vorbereitet, kl\u00fcger und sicherer wirken als sie selbst. Dieser Gedanke hat einen Namen, er ist gut untersucht, und er ist erstaunlich verbreitet. </em> Der Gedanke in der ersten Woche Die allererste Vorlesung.","tags":["Studierende","Studienstart","Wohlbefinden","Lernen"],"title":"Das Impostor-Ph\u00e4nomen \u2013 was mache ich hier?","updated_at":1789025415,"url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-09-10-impostor/","version":"v1"},{"authors":[{"contributor_roles":[],"family":"Bekkers","given":"Rene"}],"blog":{"authors":null,"community_id":"c04223e6-4d3d-42ad-a718-878a8fc35d32","created":1739059200,"current_feed_url":null,"description":"Rene Bekkers","doi":"https://doi.org/10.59350/renebekkers","favicon":"https://rogue-scholar.org/api/communities/c04223e6-4d3d-42ad-a718-878a8fc35d32/logo","feed_format":"application/atom+xml","feed_url":"https://renebekkers.wordpress.com/feed/atom","filter":null,"generator":"WordPress.com","home_page_url":"https://renebekkers.wordpress.com","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"renebekkers","status":"active","subfield":"1404","title":"Rene Bekkers","updated":1788987428,"use_api":true},"blog_name":"Rene Bekkers","blog_slug":"renebekkers","content_html":"<p class=\"wp-block-paragraph\">Why is the share of income and wealth that people give to charities lower when their income and wealth are higher? Are more generous persons less likely to accumulate wealth? Or does wealth make people care less about those in need? Can fundraising organizations increase generosity by soliciting gifts in different ways?</p>\n\n\n\n<p class=\"wp-block-paragraph\">Fifteen years of data from the Giving in the Netherlands Panel Survey (Bekkers, De Wit &amp; Wiepking, 2017, p. 65: Figure 24, reproduced below) indicate that households with lower incomes in the Netherlands are more generous than households with higher incomes. In the period 2001-2017, the 10% lowest income households spent about 1.2% of their income on gifts to charitable causes, almost three times as much as the 10% highest incomes (0.4%).  </p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img src=\"https://renebekkers.wordpress.com/wp-content/uploads/2019/11/generosity_decile_nl.png\" alt=\"\" /></figure>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https://www.cbs.nl/nl-nl/maatwerk/2022/10/particuliere-huishoudens-naar-vermogensklassen-2020-\">Register data from Statistics Netherlands</a> on charitable deductions in the income tax indicate a similar pattern for wealth. Households with up to \u20ac5k in wealth deduct gifts worth 1% of their wealth. The wealthiest households, a group of 8,100 households with average wealth of 23.8 million, deduct gifts worth 0.06% of their wealth. </p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img src=\"https://renebekkers.wordpress.com/wp-content/uploads/2024/07/deductions_bywealth.png\" alt=\"\" /></figure>\n\n\n\n<p class=\"wp-block-paragraph\">The project will draw upon unique administrative and survey data from the Netherlands and will conduct new field experiments to test interventions that could increase generosity. This will be the first study tracking changes in wealth and generosity in the Netherlands over the life course, as well as after death through bequests. The research will benefit from collaboration with fundraising organizations in the Netherlands, and an international board of advisors, consisting of Mark Ottoni-Wilhelm at Indiana University in the US, Sarah Smith at the University of Bristol in the UK, and Hans Schmeets at Statistics Netherlands. </p>\n\n\n\n<p class=\"wp-block-paragraph\">The research proposal is also unique in its openness. I work from the principle that transparency supports the reliability of science. Throughout the application process, I have posted all materials for the proposal on a publicly available repository at the Open Science Framework, <a href=\"https://osf.io/e3mux/\">https://osf.io/e3mux/</a>. The repository includes <a href=\"https://osf.io/t6cav\">the initial idea</a>, an extensive document with <a href=\"https://osf.io/45dky\">answers to frequently asked questions</a>, the <a href=\"https://osf.io/59jvk\">full proposal</a>, as well as the <a href=\"https://osf.io/d8gez\">external peer review reports on the full proposal and my responses</a>. </p>\n\n\n\n<p class=\"wp-block-paragraph\">With a grant from the Netherlands Organization for Scientific Research (NWO), I have formed a team to answer these questions at VU Amsterdam with two postdoctoral researchers, Marlou Ramaekers and Wahideh Achbari, and a research assistant, Max Littel. Starting 1 January 2026 the two postdocs have commenced with analyses of survey data and the design of experiments. Read more about the results here: </p>\n\n\n\n<figure class=\"wp-block-embed is-type-wp-embed is-provider-rene-bekkers wp-block-embed-rene-bekkers\"><div class=\"wp-block-embed__wrapper\">\n<blockquote class=\"wp-embedded-content\" data-secret=\"YhT1gkX1YB\"><a href=\"https://renebekkers.wordpress.com/new-research/\">Current research</a></blockquote><iframe loading=\"lazy\" class=\"wp-embedded-content\" sandbox=\"allow-scripts\" security=\"restricted\" style=\"position: absolute; visibility: hidden;\" title=\"&#8220;Current research&#8221; &#8212; Rene Bekkers\" src=\"https://renebekkers.wordpress.com/new-research/embed/#?secret=JHcNNv9Xmb#?secret=YhT1gkX1YB\" data-secret=\"YhT1gkX1YB\" width=\"500\" height=\"282\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\"></iframe>\n</div></figure>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>References</strong></p>\n\n\n\n<p class=\"wp-block-paragraph\">Bekkers, R. (2024). Generating Generosity. Proposal for the NWO SSH Open Competition L 2023. <a href=\"https://osf.io/59jvk\">https://osf.io/59jvk</a></p>\n\n\n\n<p class=\"wp-block-paragraph\">Bekkers, R., De Wit, A. &amp; Wiepking, P. (2017).&nbsp;<a href=\"https://renebekkers.wordpress.com/wp-content/uploads/2018/06/bekkers_dewit_wiepking_17.pdf\">Jubileumspecial: Twintig jaar&nbsp;</a><em><a href=\"https://renebekkers.wordpress.com/wp-content/uploads/2018/06/bekkers_dewit_wiepking_17.pdf\">Geven in Nederland</a>.&nbsp;</em>Pp. 61-94 in: Bekkers, R. Schuyt, T.N.M., &amp; Gouwenberg, B.M. (Eds.).&nbsp;<em>Geven in Nederland 2017: Giften, Sponsoring, Legaten en Vrijwilligerswerk.&nbsp;</em>Amsterdam: Lenthe.</p>\n\n\n\n<p class=\"wp-block-paragraph\"></p>","doi":"https://doi.org/10.59350/28h2k-27w63","guid":"https://renebekkers.wordpress.com/?p=3843","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1721692800,"reference":[{"id":"https://osf.io/59jvk","unstructured":"Unknown title"},{"id":"https://renebekkers.wordpress.com/wp-content/uploads/2018/06/bekkers_dewit_wiepking_17.pdf","unstructured":"Unknown title"}],"rid":"4m7ah-xzm26","summary":"Why is the share of income and wealth that people give to charities lower when their income and wealth are higher? Are more generous persons less likely to accumulate wealth? Or does wealth make people care less about those in need? Can fundraising organizations increase generosity by soliciting gifts in different ways?","tags":["Altruism","Bequests","Center For Philanthropic Studies","Charitable Organizations","Data"],"title":"Generating Generosity","updated_at":1789025413,"url":"https://renebekkers.wordpress.com/2024/07/23/generating-generosity/","version":"v1"},{"authors":[{"affiliation":[{"name":"University of Wroc\u0142aw, Chemistry"}],"contributor_roles":[],"family":"Janeta","given":"Mateusz","url":"https://orcid.org/0000-0003-2197-7913"}],"blog":{"authors":null,"community_id":"c21eed24-c860-43d0-997c-0bc782922544","created":1788652800,"current_feed_url":null,"description":null,"doi":"https://doi.org/10.59350/silsesquioxane","favicon":"https://rogue-scholar.org/api/communities/c21eed24-c860-43d0-997c-0bc782922544/logo","feed_format":"application/atom+xml","feed_url":"https://silsesquioxane.blogspot.com/feeds/posts/default","filter":null,"generator":"Blogger","home_page_url":"https://silsesquioxane.blogspot.com/","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"silsesquioxane","status":"active","subfield":"1604","title":"Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry","updated":1789025287,"use_api":true},"blog_name":"Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry","blog_slug":"silsesquioxane","content_html":"<!--META DESCRIPTION (set separately in Blogger: Settings \u2192 Search preferences \u2192 Meta tags):\nPOSS poly(1-haloacetylene) networks synthesized by catalyst-free, oxygen-initiated solid-state polymerization achieve band gaps of 2.38\u20132.79 eV.-->\n<div style=\"color: #24292f; font-family: Georgia, serif; font-size: 17px; line-height: 1.75; margin: 0px auto; max-width: 780px;\">\n<p>\u4e2d\u6587\u7248\u672c / Chinese version: <a href=\"https://silsesquioxane.blogspot.com/p/poss-1.html\">POSS \u805a(1-\u5364\u4ee3\u4e59\u7094):\u65e0\u50ac\u5316\u5242\u56fa\u76f8\u805a\u5408\u8def\u7ebf</a></p>\n<!--REVISED OPENING PARAGRAPH (section 3d)-->\n<p style=\"background: rgb(245, 248, 251); border-left: 4px solid rgb(15, 76, 129); border-radius: 0px 6px 6px 0px; font-size: 18px; margin: 0px 0px 1.15em; padding: 1.1em 1.3em; text-align: justify;\">Polyhedral oligomeric silsesquioxane (POSS) poly(1-haloacetylene) conjugated networks have been synthesized by Marta Cieplucha, Mateusz Janeta, and S\u0142awomir Szafert at the Faculty of Chemistry, University of Wroc\u0142aw, as reported in <em>Materials Chemistry Frontiers</em> in 2025. Three octa-functionalized monomers, POSS-C2Cl, POSS-C2Br, and POSS-C2I, were prepared by amide coupling of <a href=\"https://silsesquioxane.blogspot.com/2020/08/octa-aminopropyl-silsesquioxane.html\">octa(3-aminopropyl)silsesquioxane</a> with the corresponding 4-(haloethynyl)benzoyl chloride and were shown to undergo thermal polymerization in the solid state without any transition metal catalyst, yielding highly cross-linked poly(1-haloacetylene) networks. This work constitutes the first reported polymerization of a 1-iodoethyne derivative and the first example of 1-haloalkyne polymerization achieved entirely in the absence of metal-based initiators.</p>\n<!--H2 SUBHEADING 1-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Synthesis of Octa-Functionalized POSS Haloalkyne Monomers</h2>\n<figure style=\"margin: 1.5em 0px 2em; text-align: center;\">\n<img alt=\"Synthesis of POSS haloalkyne monomers POSS-C2Cl, POSS-C2Br, and POSS-C2I by amide coupling\" src=\"https://blogger.googleusercontent.com/img/a/AVvXsEjNZtnjmDuWrpEQtGeKyAee5oekwAxIf7crv-ugMF7tJbPW9pQ7cqzmxI03Vpn4-OdAz4DCT6asX1sixDnnMcDkYNXwxQufcUZXSicjajZ1NMDdOyV2Oc0nQiZ9XQypF-4-pnyOr2ZqFKl2LkwTkuiSLYKor_qSsKOgZso40Zsh7LxXW1XUEDqBl5F-UYE\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; max-width: 100%;\"/>\n<figcaption style=\"color: #5f6b7a; font-family: Arial, Helvetica, sans-serif; font-size: 14px; margin-top: 8px; text-align: center;\">\n<strong>Scheme 1.</strong> Synthesis of 1-haloethynyl-functionalized POSS-based monomers. Reaction of octa(3-aminopropyl)silsesquioxane hydrochloride (OAS-POSS) with 4-(haloethynyl)benzoyl chloride (8.2 equiv.) and Et<sub>3</sub>N (16.2 equiv.) in DMF at 0 \u00b0C affords POSS-C2Cl (70%), POSS-C2Br (60%), and POSS-C2I (71%) as the fully octa-substituted amide-linked products.\n    </figcaption>\n</figure>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The three monomers were synthesized by reacting octa(3-aminopropyl)silsesquioxane with the corresponding 4-(haloethynyl)benzoyl chloride in the presence of triethylamine in DMF at 0 degrees Celsius, affording the amide-linked, octa-functional POSS derivatives in isolated yields of 60 to 71 percent. Comprehensive solution and solid-state characterization, including proton and carbon-13 NMR spectroscopy, silicon-29 NMR, nitrogen-15 CP-MAS NMR, DRIFT spectroscopy, and mass spectrometry, confirmed complete octa-substitution, the integrity of the T<sub>8</sub> silsesquioxane cage throughout the synthesis, and the presence of intact haloalkyne functionality in each monomer. The characteristic acetylene stretching vibration near 2197 per centimeter in the DRIFT spectra provided the most direct spectroscopic signature of the C triple bond C unit, and a single symmetric resonance near negative 66 ppm in the silicon-29 NMR spectra confirmed that all eight silicon atoms of the cubic cage remained crystallographically equivalent and that no <a href=\"https://silsesquioxane.blogspot.com/2025/04/unraveling-structure-of.html\">cage rearrangement</a> occurred.</p>\n<!--H2 SUBHEADING 2-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Catalyst-Free, Oxygen-Initiated Solid-State Thermal Polymerization</h2>\n<figure style=\"margin: 1.5em 0px 2em; text-align: center;\">\n<img alt=\"Catalyst-free solid-state polymerization of POSS haloalkyne monomers to poly(1-haloacetylene) T8 cage networks\" src=\"https://blogger.googleusercontent.com/img/a/AVvXsEgE29uI3HKoQpLJ3Y5pqHiEhvtqpxZ4qpbGpo5iOZ0t2KmYXih0B3JmWFiYpzzcv_jP1HRIjTCFc1o8v4VYOrsHENi9n3YA-RzHax_1il4hAsAeJsZRf4cjzjuusB9Ho4Vz2oTLGrEEhVLWkTwtF5JDpc-J6jYrnAS0B-VLBgBJJPCn8jMVWCTmK5XW4Ow\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; max-width: 100%;\"/>\n<figcaption style=\"color: #5f6b7a; font-family: Arial, Helvetica, sans-serif; font-size: 14px; margin-top: 8px; text-align: center;\">\n<strong>Scheme 2.</strong> Catalyst-free solid-state thermal polymerization of POSS-C2X (X = Cl, Br, I) to yield the highly cross-linked polyPOSS-C2X networks. Each of the eight peripheral 1-haloalkyne groups undergoes conversion of the carbon\u2013carbon triple bond to a double bond, generating a three-dimensional poly(1-haloacetylene) network anchored to and propagating from the rigid cubic POSS core. The red fragments on the right represent the newly formed polymer backbone segments connecting adjacent POSS units.\n    </figcaption>\n</figure>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The discovery of solid-state thermal polymerization arose from differential thermal analysis, which revealed distinct exothermic events for each monomer in the temperature range of approximately 130 to 273 degrees Celsius with no accompanying mass loss in the thermogravimetric traces \u2014 the defining signature of a solid-state reaction rather than a decomposition process. The irreversibility of the transformation was confirmed by differential scanning calorimetry: an exothermic peak observed in the first heating cycle was replaced in subsequent cycles by a glass transition temperature characteristic of polymeric materials. Control experiments conducted under strictly oxygen-free conditions in an argon-filled glovebox produced no evidence of polymerization by DRIFT spectroscopy, establishing that molecular oxygen plays a critical initiating role, most plausibly through peroxyl radical formation at elevated temperatures.</p>\n<!--H2 SUBHEADING 3-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Spectroscopic Confirmation of Poly(1-haloacetylene) Network Formation</h2>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">The structural transformation from monomer to polymer was confirmed orthogonally by solid-state carbon-13 CP-MAS NMR, DRIFT, and Raman spectroscopy, as well as by XPS analysis. In the carbon-13 CP-MAS spectrum of polyPOSS-C2Br, the signals at 78.3 and 51.7 ppm assigned to the sp-hybridized alkyne carbons disappeared completely, replaced by two new resonances at 139.0 and 135.2 ppm attributable to the sp2-hybridized vinyl carbons of the polyhaloacetylene backbone. The alkyne stretching band at 2197 per centimeter vanished entirely in the DRIFT spectrum of the polymer, while a new absorption at 1768 per centimeter confirmed the formation of the conjugated C=CBr stretching mode. Raman spectroscopy identified new bands at 1580 and 1555 per centimeter characteristic of the trans-polyhaloacetylene backbone, and XPS data confirmed the change in the bromine bonding environment from sp-carbon in the monomer to sp2-carbon in the polymer, ruling out significant side reactions. The silicon-29 CP-MAS spectrum retained a single symmetric resonance at negative 66.2 ppm, confirming complete preservation of the T<sub>8</sub> cage throughout polymerization.</p>\n<!--H2 SUBHEADING 4-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Polymerization Kinetics and Activation Energies by the Kissinger Method</h2>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">\n    Polymerization kinetics, monitored by time-resolved Raman spectroscopy under isothermal conditions, followed a pseudo-second-order model for all three monomers. For POSS-C2Br at 165 degrees Celsius, more than 47 percent conversion was achieved within the first 10 minutes and full conversion within 6 hours. For POSS-C2Cl at 145 degrees Celsius and POSS-C2I at 175 degrees Celsius, complete conversion required 24 and 25 hours, respectively. Apparent activation energies determined by the Kissinger method from non-isothermal DTA experiments were 179 kJ/mol for POSS-C2Br, 209 kJ/mol for POSS-C2Cl, and 217 kJ/mol for POSS-C2I, values substantially higher than those for classical radical polymerizations of vinyl monomers, reflecting the greater energetic barrier of triple bond activation under solid-state constraints.\n  </p>\n<!--H2 SUBHEADING 5-->\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Thermal Stability, Insolubility, and Optical Band Gaps of the Cross-Linked Networks</h2>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">\n    All three polymers are completely insoluble in common organic solvents and thermally stable up to decomposition onset temperatures of 267, 287, and 309 degrees Celsius for polyPOSS-C2Br, polyPOSS-C2Cl, and polyPOSS-C2I, respectively. The three-dimensional cross-linking topology enforced by the cubic POSS scaffold, where eight alkyne groups per cage simultaneously engage in polymerization, is responsible for the exceptional insolubility and mechanical robustness of the resulting networks. Glass transition temperatures of 51, 140, and 211 degrees Celsius for the chloro, bromo, and iodo polymers, respectively, confirm that all three materials behave as glassy solids at ambient temperature.\n  </p>\n<figure style=\"margin: 1.5em 0px 2em; text-align: center;\">\n<img alt=\"Bar chart of direct and indirect optical band gaps of polyPOSS-C2Cl, polyPOSS-C2Br, and polyPOSS-C2I determined by Tauc plot analysis of solid-state UV-Vis absorption spectra showing systematic decrease from 2.79 eV to 2.38 eV with increasing halogen polarizability\" src=\"https://blogger.googleusercontent.com/img/a/AVvXsEjiUpAMs8KBXZJLeTW7wxcQW4hreTQjZDsxfXj7i1WD2sU7RPc3YFpc3owbUMHKxU0ChmSrOhGQt_eKUuV957YpkgxtkvNZR5V_AT1f6H1NRJh6ceD6VNzMHzcD0B5WnlRsmHDSyhRbJYcI77ij3Z7yqnIH85UMKlXQzIgoueTIXG7IzzuLJxmedy74_XA=s1600\" style=\"border-radius: 8px; box-shadow: rgba(15, 23, 42, 0.12) 0px 2px 12px; max-width: 100%;\"/>\n<figcaption style=\"color: #5f6b7a; font-family: Arial, Helvetica, sans-serif; font-size: 14px; margin-top: 8px; text-align: center;\">\n<strong>Fig. 8.</strong> Direct (blue bars) and indirect (dark red bars) optical band gaps of polyPOSS-C2Cl, polyPOSS-C2Br, and polyPOSS-C2I determined by Tauc plot analysis of solid-state UV-Vis absorption spectra, with structural fragments of the corresponding repeating units shown below each column. The direct band gap decreases systematically from 2.79 eV (Cl) to 2.74 eV (Br) to 2.38 eV (I), reflecting the increasing polarizability of the halogen substituent incorporated directly into the polymer backbone.\n    </figcaption>\n</figure>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">\n    The optical properties of the polymers, investigated by solid-state UV-Vis spectroscopy and Tauc plot analysis, reveal direct optical band gaps of 2.79 eV for polyPOSS-C2Cl, 2.74 eV for polyPOSS-C2Br, and 2.38 eV for polyPOSS-C2I. All three values fall within the visible light range of 1 to 3 eV considered optimal for photovoltaic and optoelectronic applications. The absorption profiles of all polymers are substantially broader and red-shifted relative to their monomers, consistent with the formation of an extended pi-conjugated system along the polyhaloacetylene backbone. The systematic narrowing of the band gap from the chloro to the iodo polymer reflects the increase in halogen polarizability and its influence on the electronic structure of the conjugated chain. Indirect band gaps were additionally identified at 2.19 eV for polyPOSS-C2Cl, 1.57 eV for polyPOSS-C2Br, and 1.47 eV for polyPOSS-C2I, extending the optical response of the iodo polymer well into the near-infrared region.\n  </p>\n<p style=\"margin: 0px 0px 1.15em; text-align: justify;\">Taken together, this work establishes a new synthetic paradigm for the preparation of hybrid conjugated polymer networks by harnessing the geometric rigidity and thermal robustness of the cubic POSS scaffold to direct three-dimensional cross-linking of poly(1-haloacetylene) chains through a catalyst-free, oxygen-initiated solid-state process. The resulting materials combine the semiconducting properties of halogenated polyacetylenes with the exceptional thermal stability and structural precision of silsesquioxane-based hybrid architectures, positioning them as promising candidates for exploration in organic photovoltaics, field-effect transistors, <a href=\"https://silsesquioxane.blogspot.com/2021/04/advanced-fluorescent-silsesquioxane.html\">chemical sensors</a>, and electrochromic devices. This study continues and expands the broader research program of the Janeta and Szafert groups at the University of Wroc\u0142aw on functional POSS-based hybrid materials, which has previously encompassed <a href=\"https://silsesquioxane.blogspot.com/2018/07/porous-silsesquioxane-imine-frameworks.html\">imine-functionalized POSS for supramolecular assembly and iodine capture</a>, <a href=\"https://silsesquioxane.blogspot.com/2026/02/zinc-imine-poss-quattro-site-catalyst.html\">zinc-POSS complexes for catalytic CO<sub>2</sub> cycloaddition</a>, and <a href=\"https://silsesquioxane.blogspot.com/2025/04/poss-as-photocatalyst.html\">difluoroboron-POSS photocatalysts for the selective oxidation of sulfides to sulfoxides</a>.</p>\n<!--UPDATED CITATION BLOCK (section 3h)-->\n<div style=\"background-color: #f7f7fb; border-left: 4px solid rgb(15, 76, 129); border-radius: 0px 6px 6px 0px; font-family: Arial, Helvetica, sans-serif; font-size: 0.92em; line-height: 1.6; margin-top: 32px; padding: 12px 16px;\">\n<strong>Original Publication</strong><br/>\n    Cieplucha, M.; Janeta, M.; Szafert, S.\n    Hybrid inorganic\u2013organic polyhedral oligomeric silsesquioxane-based poly(1-haloacetylene)s: thermal, solid-state polymerization.\n    <em>Materials Chemistry Frontiers</em> <strong>2025</strong>, <strong>9</strong>, 3034.<br/>\n    DOI: <a href=\"https://doi.org/10.1039/d5qm00583c\" rel=\"noopener noreferrer\" target=\"_blank\">10.1039/d5qm00583c</a>\n    \u00a0|\u00a0\n    <a href=\"https://pubs.rsc.org/en/content/articlelanding/2025/qm/d5qm00583c\" rel=\"noopener noreferrer\" target=\"_blank\">View at RSC Publishing</a>\n</div>\n<hr style=\"border: 0px; border-top: 1px solid rgb(227, 232, 238); margin: 2.2em 0px 1.4em;\"/>\n<h2 style=\"border-bottom: 2px solid rgb(227, 232, 238); color: #0f4c81; font-family: Georgia, serif; font-size: 1.25em; font-weight: bold; margin: 1.6em 0px 0.5em; padding-bottom: 0.35em;\">Cite this post</h2>\n<p style=\"color: #5f6b7a; font-family: Arial, Helvetica, sans-serif; font-size: 14px; margin: 0px 0px 0.8em;\">This post has its own persistent identifier. Please use the DOI below when citing it.</p>\n<p style=\"color: #24292f; font-family: Georgia, serif; font-size: 16px; line-height: 1.7; margin: 0px 0px 1.15em; text-align: left;\">Janeta, M. (2026). POSS Poly(1-Haloacetylene): Catalyst-Free Solid-State Route. <em>Polyhedral Oligomeric Silsesquioxane (POSS) Chemistry</em>. <a href=\"https://doi.org/10.59350/3pnqc-4p954\">https://doi.org/10.59350/3pnqc-4p954</a></p>\n<script type=\"application/ld+json\">\n{\n  \"@context\": \"https://schema.org\",\n  \"@type\": \"BlogPosting\",\n  \"headline\": \"POSS Poly(1-Haloacetylene): Catalyst-Free Solid-State Route\",\n  \"url\": \"https://silsesquioxane.blogspot.com/2026/08/hybrid-inorganicorganic-poss-based.html\",\n  \"mainEntityOfPage\": \"https://silsesquioxane.blogspot.com/2026/08/hybrid-inorganicorganic-poss-based.html\",\n  \"identifier\": \"https://doi.org/10.59350/3pnqc-4p954\",\n  \"sameAs\": [\n    \"https://doi.org/10.59350/3pnqc-4p954\",\n    \"https://rogue-scholar.org/records/9951n-bhj92\"\n  ],\n  \"datePublished\": \"2026-09-01\",\n  \"inLanguage\": \"en\",\n  \"license\": \"https://creativecommons.org/licenses/by/4.0/\",\n  \"author\": {\n    \"@type\": \"Person\",\n    \"name\": \"Mateusz Janeta\",\n    \"url\": \"https://sites.google.com/view/mateusz-janeta/\"\n  },\n  \"citation\": {\n    \"@type\": \"ScholarlyArticle\",\n    \"name\": \"Hybrid inorganic-organic polyhedral oligomeric silsesquioxane-based poly(1-haloacetylene)s: thermal, solid-state polymerization\",\n    \"identifier\": \"https://doi.org/10.1039/d5qm00583c\"\n  }\n}\n</script>\n</div>","doi":"https://doi.org/10.59350/92dfm-jvk79","guid":"tag:blogger.com,1999:blog-2875892712213933214.post-6710372823875080355","image":"https://blogger.googleusercontent.com/img/a/AVvXsEjNZtnjmDuWrpEQtGeKyAee5oekwAxIf7crv-ugMF7tJbPW9pQ7cqzmxI03Vpn4-OdAz4DCT6asX1sixDnnMcDkYNXwxQufcUZXSicjajZ1NMDdOyV2Oc0nQiZ9XQypF-4-pnyOr2ZqFKl2LkwTkuiSLYKor_qSsKOgZso40Zsh7LxXW1XUEDqBl5F-UYE=s72-c","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788998400,"rid":"111ng-se271","summary":"\u4e2d\u6587\u7248\u672c / Chinese version: POSS \u805a(1-\u5364\u4ee3\u4e59\u7094):\u65e0\u50ac\u5316\u5242\u56fa\u76f8\u805a\u5408\u8def\u7ebf Polyhedral oligomeric silsesquioxane (POSS) poly(1-haloacetylene) conjugated networks have been synthesized by Marta Cieplucha, Mateusz Janeta, and S\u0142awomir Szafert at the Faculty of Chemistry, University of Wroc\u0142aw, as reported in <em> Materials Chemistry Frontiers </em> in 2025.","tags":["Hybrid Materials","Polymer Nanocomposites","POSS","POSS Functionalization","POSS Synthesis"],"title":"POSS Poly(1-Haloacetylene): Catalyst-Free Solid-State Route","updated_at":1789025413,"url":"https://silsesquioxane.blogspot.com/2026/09/poss-poly1-haloacetylene-catalyst-free.html","version":"v1"},{"authors":[{"affiliation":[{"name":"National Autonomous University of Mexico, Instituto de Qu\u00edmica"}],"contributor_roles":[],"family":"Barroso-Flores","given":"Joaqu\u00edn","url":"https://orcid.org/0000-0003-0554-7569"}],"blog":{"authors":null,"community_id":"9ddd7090-8504-47e7-9389-267cfac8c5f6","created":1753833600,"current_feed_url":null,"description":"Scientific log of a computational chemist - \"Make like a molecule and React!\"","doi":"https://doi.org/10.59350/joaquinbarroso","favicon":"https://rogue-scholar.org/api/communities/9ddd7090-8504-47e7-9389-267cfac8c5f6/logo","feed_format":"application/atom+xml","feed_url":"https://joaquinbarroso.com/feed/atom/","filter":null,"generator":"WordPress.com","home_page_url":"https://joaquinbarroso.com","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"joaquinbarroso","status":"active","subfield":"1606","title":"Dr. Joaquin Barroso's Blog","updated":1788965940,"use_api":null},"blog_name":"Dr. Joaquin Barroso's Blog","blog_slug":"joaquinbarroso","content_html":"<p class=\"wp-block-paragraph\">This a guest post by Yamil Hern\u00e1ndez, first year PhD student on loan from Puebla, who is working with us in photosynthesis related projects for his thesis. </p>\n<p class=\"wp-block-paragraph\">VMD (Visual Molecular Dynamics) is a free widely known visualizer developed by the Theoretical and Computational Biophysics Group from the University of Illinois. It is primarily used to analyze and visualize molecular dynamics (MD) results, as well as to prepare biological systems for further simulations. However, VMD is highly versatile; its functionalities extend far beyond MD, making it an excellent tool for analyzing molecular results from quantum mechanical calculations. In this blog post, we delve into some of these non-standard applications of VMD</p>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7065\" data-attachment-id=\"7065\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture0\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg\" data-orig-size=\"1194,794\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture0/\" height=\"680\" sizes=\"(max-width: 1024px) 100vw, 1024px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=1024\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=1024 1024w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=768 768w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg 1194w\" width=\"1024\"/></a></figure>\n<h2 class=\"wp-block-heading\">1. Plotting Frontier Molecular Orbitals (FMO) and Electrostatic Potential (ESP)</h2>\n<p class=\"wp-block-paragraph\">VMD is able to plot .cube files, which can be generated by quantum chemistry software or analysis tools like GaussView, Chemcraft, or Multiwfn. </p>\n<p class=\"wp-block-paragraph\">In the following example, we use a glucose molecule optimized at the B3LYP-D3/6-311+G** level of theory using the SMD implicit solvent model to simulate an acqueous environment in ORCA 6.1. FMO and ESP .cube files were generated using Multiwfn. </p>\n<h2 class=\"wp-block-heading\">1.1 Frontier Molecular Orbitals (FMO)</h2>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">Load each orbital .cube file as a <strong>New Molecule</strong> (separated molecule ID's). This will display the molecule framework. You can customize the molecular representation as described below. Change the <strong>Coloring Method</strong> to <strong>Element</strong> so the atoms are distinct. (In this example we changed the carbon color to silver in <strong>Color Controls</strong> window.)</p>\n<p class=\"wp-block-paragraph\">Open the <strong>Graphical Representation</strong> window. Let's walk through plotting the HOMO (the process for the LUMO or any other orbital is identical).</p>\n<p class=\"wp-block-paragraph\">With the orbital molecule selected in <strong>Graphical Representation</strong>, click <strong>Create Rep</strong> twice to generate two identical duplicate layers.</p>\n<p class=\"wp-block-paragraph\">Select the first new representation layer: </p>\n<ul class=\"wp-block-list\">\n<li>Change the <strong>Coloring Method</strong> to <strong>Volume</strong> and the <strong>Drawing Method</strong> to <strong>Isosurface</strong>.</li>\n<li>Change the <strong>Draw</strong> dropdown from Points to Solid Surface.</li>\n<li>Set the <strong>isovalue</strong> to 0.02 (the standard threshold for molecular orbitals). Part of the orbital surface will appear in white.</li>\n<li>Switch to <strong>Trajectory</strong> tab in the same window and adjust the <strong>Color Scale Data Range </strong>from -0.1 to 0.1 to apply the phase color.</li>\n</ul>\n<p class=\"wp-block-paragraph\">Select the second duplicate representation layer to map the complementary lobe:  </p>\n<ul class=\"wp-block-list\">\n<li>Repeat the exact same steps, but set the <strong>isovalue</strong> to -0.02.</li>\n</ul>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped wp-block-gallery-1 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7073\" data-attachment-id=\"7073\" data-comments-opened=\"1\" data-id=\"7073\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture0a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg\" data-orig-size=\"778,572\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture0a/\" height=\"572\" sizes=\"(max-width: 778px) 100vw, 778px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=778\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg 778w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=768 768w\" width=\"778\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7068\" data-attachment-id=\"7068\" data-comments-opened=\"1\" data-id=\"7068\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture1a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg\" data-orig-size=\"780,599\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture1a/\" height=\"599\" sizes=\"(max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1a.jpg?w=768 768w\" width=\"780\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7067\" data-attachment-id=\"7067\" data-comments-opened=\"1\" data-id=\"7067\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture1b\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg\" data-orig-size=\"781,594\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture1b/\" height=\"594\" loading=\"lazy\" sizes=\"auto, (max-width: 781px) 100vw, 781px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=781\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg 781w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1b.jpg?w=768 768w\" width=\"781\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1c.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7066\" data-attachment-id=\"7066\" data-comments-opened=\"1\" data-id=\"7066\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture1c\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1c-e1788930730384.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1c-e1788930730384.jpg\" data-orig-size=\"690,549\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture1c/\" height=\"621\" loading=\"lazy\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture1c.jpg?w=781\" width=\"781\"/></a></figure>\n</figure>\n</div>\n</div>\n<h2 class=\"wp-block-heading\">1.2 Electrostatic Potential (ESP) and other mapped surfaces</h2>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">This procedure applies to most property-mapped volumetric surfaces saved as .cube files. Mapping <strong>ESP</strong> requires two files: the electron density .cuve and the <strong>ESP</strong> .cube files.</p>\n<p class=\"wp-block-paragraph\"><strong>Go to File -&gt; New Molecule</strong> and load the electronic density .cube file first.</p>\n<p class=\"wp-block-paragraph\">Next, select that same molecule ID in the <strong>Load files for</strong>: dropdown menu and load the ESP .cube file into it. The molecule ID should now contain two volumetric datasets (Vol 0 and Vol 1).</p>\n<p class=\"wp-block-paragraph\">Open <strong>Graphical Representations</strong> and customize your underlying molecular structure.</p>\n<p class=\"wp-block-paragraph\">Click <strong>Create Rep</strong> to make a new layer for the surface:</p>\n<ul class=\"wp-block-list\">\n<li>Set<strong> Coloring Method</strong> to <strong>Volume</strong> and <strong>Drawing</strong> <strong>Method</strong> to <strong>Isosurface</strong>.</li>\n<li>Set <strong>Draw</strong> option to<em> Solid Surface</em>.</li>\n<li>Ensure the <strong>Vol</strong> dropdown is set to vol0 corresponding to the electron density .cube file.</li>\n<li>Set the <strong>isovalue</strong> to 0.0004 (atomic units), which is standard for defining the molecular surface.</li>\n</ul>\n<p class=\"wp-block-paragraph\">To map the ESP gradient to this density surface: </p>\n<ul class=\"wp-block-list\">\n<li>Look at the small dropdown menu located between <strong>Coloring Method</strong> and <strong>Material</strong> (It defaults to vol0). Change this to vol1 (the ESP dataset).</li>\n<li>Go to <strong>Trajectory</strong> tab and set the <strong>Color Scale Data Range</strong> from negative to positive values.</li>\n</ul>\n<p class=\"wp-block-paragraph\">By default, VMD applies a Red-White-Blue (RWB) color scale. If you prefer the RGB gradient, open the <strong>Color Controls </strong>window, navigate to the <strong>Color Scale</strong> tab, and change the <strong>Method</strong> to <strong>RGB</strong>.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped wp-block-gallery-2 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7053\" data-attachment-id=\"7053\" data-comments-opened=\"1\" data-id=\"7053\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg\" data-orig-size=\"781,631\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3a-2/\" height=\"631\" loading=\"lazy\" sizes=\"auto, (max-width: 781px) 100vw, 781px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=781\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg 781w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3a-1.jpg?w=768 768w\" width=\"781\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7052\" data-attachment-id=\"7052\" data-comments-opened=\"1\" data-id=\"7052\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3b\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg\" data-orig-size=\"779,568\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3b/\" height=\"568\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3b.jpg?w=768 768w\" width=\"779\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7051\" data-attachment-id=\"7051\" data-comments-opened=\"1\" data-id=\"7051\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3c\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg\" data-orig-size=\"780,639\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3c/\" height=\"639\" loading=\"lazy\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3c.jpg?w=768 768w\" width=\"780\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7050\" data-attachment-id=\"7050\" data-comments-opened=\"1\" data-id=\"7050\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3d\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg\" data-orig-size=\"780,626\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3d/\" height=\"626\" loading=\"lazy\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3d.jpg?w=768 768w\" width=\"780\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7049\" data-attachment-id=\"7049\" data-comments-opened=\"1\" data-id=\"7049\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture3e\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg\" data-orig-size=\"780,568\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture3e/\" height=\"568\" loading=\"lazy\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture3e.jpg?w=768 768w\" width=\"780\"/></a></figure>\n</figure>\n</div>\n</div>\n<h2 class=\"wp-block-heading\">2 Comparison of Molecular Geometries</h2>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">VMD allows you to compare two or more geometries of the same molecule using two different approaches. Crucially, all geometries must share the same atom numbering. To illustrate this process we'll use different geometries of Chlorophyll-a.</p>\n<p class=\"wp-block-paragraph\">One common way to compare molecules is by overlapping them.</p>\n<p class=\"wp-block-paragraph\">First, load the different molecular files into separate molecule IDs:</p>\n<ul class=\"wp-block-list\">\n<li>Go to file menu and click on New Molecule. </li>\n</ul>\n<ul class=\"wp-block-list\">\n<li>In Molecular File Browser, select the file for your first structure and load it. </li>\n</ul>\n<ul class=\"wp-block-list\">\n<li>For the second structure, ensure that Load files for: is set to New Molecule to avoid overwriting the first one, then select and load the file. </li>\n</ul>\n<p class=\"wp-block-paragraph\">Once all structures are loaded, they will appear piled up on top of each other in the OpenGL window.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped wp-block-gallery-3 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7073\" data-attachment-id=\"7073\" data-comments-opened=\"1\" data-id=\"7073\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture0a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg\" data-orig-size=\"778,572\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture0a/\" height=\"572\" sizes=\"(max-width: 778px) 100vw, 778px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=778\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg 778w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0a.jpg?w=768 768w\" width=\"778\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7085\" data-attachment-id=\"7085\" data-comments-opened=\"1\" data-id=\"7085\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg\" data-orig-size=\"780,473\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4-2/\" height=\"473\" loading=\"lazy\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=780\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg 780w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4.jpg?w=768 768w\" width=\"780\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7084\" data-attachment-id=\"7084\" data-comments-opened=\"1\" data-id=\"7084\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4a\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg\" data-orig-size=\"779,466\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4a/\" height=\"466\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4a.jpg?w=768 768w\" width=\"779\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7083\" data-attachment-id=\"7083\" data-comments-opened=\"1\" data-id=\"7083\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4b\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg\" data-orig-size=\"866,528\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4b/\" height=\"528\" loading=\"lazy\" sizes=\"auto, (max-width: 866px) 100vw, 866px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=866\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg 866w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4b.jpg?w=768 768w\" width=\"866\"/></a></figure>\n</figure>\n</div>\n</div>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">Before overlaping the structures, let's customize the visualization. For better clarity, a white background with distinct color for each molecule is recommended</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">Close <strong>Molecular File Browser</strong>\u00a0and open the <strong>Color Controls</strong>\u00a0window by clicking on <strong>Graphics \u2192</strong>\u00a0<strong>Colors\u2026</strong>.</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">To change the background, select <strong>Display</strong>\u00a0from the <em>Categories</em>\u00a0list, choose <strong>Background</strong>\u00a0from the <em>Names</em>\u00a0list, and select your preferred color.</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">By default, the loaded molecules will still share the same color. To fix this, close <strong>Color Controls</strong>\u00a0and open <strong>Representations</strong> under the <strong>Graphics</strong>\u00a0menu.</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">At the top of <strong>Graphical Representation</strong>\u00a0window, select your molecule one by one. For each molecule, change the <strong>Coloring Method</strong>\u00a0to <strong>Molecule</strong>, the <strong>Drawing Method</strong>\u00a0to <strong>CPK</strong>, and the <strong>Material</strong>\u00a0to <strong>Glossy</strong>.***</p>\n<p class=\"wp-block-paragraph\"></p>\n<p class=\"wp-block-paragraph\">Optionally, you can turn off the Axes and the <strong>Depth Cueing</strong>\u00a0in <strong>Display</strong>\u00a0main menu for a cleaner look.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped is-style-rectangular wp-block-gallery-4 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7082\" data-attachment-id=\"7082\" data-comments-opened=\"1\" data-id=\"7082\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4c\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg\" data-orig-size=\"779,547\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4c/\" height=\"547\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4c.jpg?w=768 768w\" width=\"779\"/></figure>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7081\" data-attachment-id=\"7081\" data-comments-opened=\"1\" data-id=\"7081\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4d\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg\" data-orig-size=\"866,516\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4d/\" height=\"516\" loading=\"lazy\" sizes=\"auto, (max-width: 866px) 100vw, 866px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=866\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg 866w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4d.jpg?w=768 768w\" width=\"866\"/></figure>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7080\" data-attachment-id=\"7080\" data-comments-opened=\"1\" data-id=\"7080\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4e\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg\" data-orig-size=\"866,523\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4e/\" height=\"523\" loading=\"lazy\" sizes=\"auto, (max-width: 866px) 100vw, 866px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=866\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg 866w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4e.jpg?w=768 768w\" width=\"866\"/></figure>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7079\" data-attachment-id=\"7079\" data-comments-opened=\"1\" data-id=\"7079\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4f\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg\" data-orig-size=\"866,518\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4f/\" height=\"518\" loading=\"lazy\" sizes=\"auto, (max-width: 866px) 100vw, 866px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=866\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg 866w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4f.jpg?w=768 768w\" width=\"866\"/></figure>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7078\" data-attachment-id=\"7078\" data-comments-opened=\"1\" data-id=\"7078\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4g\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg\" data-orig-size=\"865,518\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4g/\" height=\"518\" loading=\"lazy\" sizes=\"auto, (max-width: 865px) 100vw, 865px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=865\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg 865w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4g.jpg?w=768 768w\" width=\"865\"/></figure>\n</figure>\n</div>\n</div>\n<p class=\"wp-block-paragraph\">Now that each structure has a distinct \"ball-and-stick\" representation, we can proceed with the structural alignment: </p>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">Close <strong>Graphical Representation</strong>\u00a0window and navigate to <strong>Extensions \u2192 Analysis \u2192 RMSD Calculator</strong>.</p>\n<p class=\"wp-block-paragraph\">In the <strong>RMSD Tool</strong>\u00a0window, locate the next box that defaults to <em>protein (or residue 5 to 85)</em>\u00a0and replace it with the specific index numbers of the atoms you want to use for the alignment. This should be conserved atoms that do not change position significantly between structures.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7077\" data-attachment-id=\"7077\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4i\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg\" data-orig-size=\"779,514\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4i/\" height=\"514\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=768 768w\" width=\"779\"/></a></figure>\n</div>\n</div>\n<p class=\"wp-block-paragraph\">NOTE: <em>VMD uses zero-based indexing</em>. To select specific atoms, type <em>index 0 1 2 3</em>\u00a0or <em>index 0 to 3</em>.</p>\n<p class=\"wp-block-paragraph\">Uncheck the <strong>Backbone only </strong>option. By default, the alignment uses the <strong>Top</strong>\u00a0molecule as reference. You can change this by clicking the <strong>Selected</strong>\u00a0radio button and choosing your reference molecule.</p>\n<p class=\"wp-block-paragraph\">Click the <strong>Align</strong>\u00a0button at the top right of the window.</p>\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p class=\"wp-block-paragraph\">Once the structures are aligned, calculating the Root-Mean-Square-Deviation (RMSD) is straightforward.</p>\n<p class=\"wp-block-paragraph\">Click the <strong>RMSD</strong>\u00a0button at the top of tool. The calculated value will appear in the list.</p>\n<p class=\"wp-block-paragraph\">It is important to remember that VMD calculates the RMSD strictly based on the special distance deviation between the atoms of the reference structure (A<sub>a</sub><sup>ref</sup>) and the comparison structure (A<sub>a</sub><sup>comp</sup>). VMD does <strong>not</strong>\u00a0compare internal coordinates like bond lengths, angles or dihedrals.</p>\n</div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-gallery has-nested-images columns-1 is-cropped wp-block-gallery-5 is-layout-flex wp-block-gallery-is-layout-flex\" data-carousel-extra='{\"blog_id\":6713037,\"permalink\":\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/\"}'>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7077\" data-attachment-id=\"7077\" data-comments-opened=\"1\" data-id=\"7077\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4i\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg\" data-orig-size=\"779,514\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4i/\" height=\"514\" loading=\"lazy\" sizes=\"auto, (max-width: 779px) 100vw, 779px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=779\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg 779w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4i.jpg?w=768 768w\" width=\"779\"/></a></figure>\n<figure class=\"wp-block-image size-large\"><a href=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7076\" data-attachment-id=\"7076\" data-comments-opened=\"1\" data-id=\"7076\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"Picture4j\" data-large-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=616\" data-orig-file=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg\" data-orig-size=\"865,521\" data-permalink=\"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/picture4j/\" height=\"521\" loading=\"lazy\" sizes=\"auto, (max-width: 865px) 100vw, 865px\" src=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=865\" srcset=\"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg 865w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=150 150w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=300 300w, https://joaquinbarroso.com/wp-content/uploads/2026/09/picture4j.jpg?w=768 768w\" width=\"865\"/></a></figure>\n</figure>\n</div>\n</div>","doi":"https://doi.org/10.59350/nw7bh-1ne53","guid":"http://joaquinbarroso.com/?p=7029","image":"https://joaquinbarroso.com/wp-content/uploads/2026/09/picture0.jpg?w=1024","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788912000,"rid":"bjznx-ybs76","summary":"This a guest post by Yamil Hern\u00e1ndez, first year PhD student on loan from Puebla, who is working with us in photosynthesis related projects for his thesis. VMD (Visual Molecular Dynamics) is a free widely known visualizer developed by the Theoretical and Computational Biophysics Group from the University of Illinois.","tags":["Computational Chemistry","GaussView","Quantum Mechanics","Theoretical Chemistry","Visualization"],"title":"VMD not for Bio, but for CompChem","updated_at":1789025412,"url":"https://joaquinbarroso.com/2026/09/09/vmd-not-for-bio-but-for-compchem/","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/05a28rw58","name":"ETH Zurich"}],"contributor_roles":[],"family":"Rutz","given":"Adriano","url":"https://orcid.org/0000-0003-0443-9902"}],"blog":{"authors":[{"name":"Adriano Rutz","url":"https://orcid.org/0000-0003-0443-9902"}],"community_id":"9d85a476-b411-4d80-89d5-500bb0f3750d","created":1780876800,"current_feed_url":null,"description":"Personal website of Adriano Rutz","doi":"https://doi.org/10.59350/adafede","favicon":"https://rogue-scholar.org/api/communities/9d85a476-b411-4d80-89d5-500bb0f3750d/logo","feed_format":"application/feed+json","feed_url":"https://adafede.github.io/posts.json","filter":null,"generator":"Other","home_page_url":"https://adafede.github.io","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":null,"slug":"adafede","status":"active","subfield":"1312","title":"Adriano Rutz","updated":1788983002,"use_api":null},"blog_name":"Adriano Rutz","blog_slug":"adafede","content_html":"<script async=\"\" crossorigin=\"anonymous\" defer=\"\" src=\"https://scripts.simpleanalyticscdn.com/latest.js\">\n</script><p>I have finally opened a <code>Posts</code> section on my website! Every post should now automatically get a DOI.</p>\n<p>This is something I have wanted to do for a long time, largely inspired by the tireless and consistent example set by <a href=\"https://scholia.toolforge.org/author/Q20895241\">Egon Willighagen</a> <span class=\"citation\" data-cites=\"willighagen2024a willighagen2024b willighagen2025\">(Willighagen 2024b, 2024a, 2025)</span>.</p>\n<p>It was today's post of <span class=\"citation\" data-cites=\"fenner2025\">(Fenner 2025)</span> that finally motivated me to look into it again. That led me down a productive rabbit hole to set up Rogue Scholar: first landing on <span class=\"citation\" data-cites=\"voncsefalvay2023\">(Csefalvay 2023)</span>'s excellent guide, and then <span class=\"citation\" data-cites=\"fruehwald2025\">(Fruehwald 2025)</span>'s clear write-up, both of which made the process of integrating Rogue Scholar into a Quarto-based site surprisingly smooth.</p>\n<p>All the changes are documented in the following commit:</p>\n<p><a class=\"uri\" href=\"https://github.com/Adafede/adafede.github.io/commit/bc2dfe6f\">https://github.com/Adafede/adafede.github.io/commit/bc2dfe6f</a></p>\n<p>If you care about attribution, long-term archiving, DOIs and metadata, I highly recommend looking into <a href=\"https://rogue-scholar.org/\">Rogue Scholar</a>.</p>\n<p><strong>Edit (1):</strong> I realized that integrating <a href=\"https://sparontologies.github.io/cito/current/cito.html\">CiTO</a> could be a significant enhancement. With some effort (and thanks again to Egon), I managed to implement a working solution for the HTML and PDF outputs, see <span class=\"citation\" data-cites=\"willighagen2023\">(Willighagen 2023)</span>. However, the solution for the XML feed still feels suboptimal.</p>\n<p><strong>Edit (2):</strong> After some help from Egon and <a href=\"https://scholia.toolforge.org/author/Q30532925\">Martin</a>, I could improve my feed with correct CiTO annotations and their cool custom json feed, see: <a class=\"uri\" href=\"https://adafede.github.io/posts.json\">https://adafede.github.io/posts.json</a>!</p>\n<section class=\"level2\" id=\"references\">\n<h2 class=\"anchored\" data-anchor-id=\"references\">References</h2>\n<div class=\"references csl-bib-body hanging-indent\" id=\"refs\">\n<div class=\"csl-entry\" id=\"ref-voncsefalvay2023\">\nCsefalvay, Chris von. 2023. <em>Auto-DOI for Quarto Posts via Rogue Scholar</em>. <a href=\"http://dx.doi.org/10.59350/5hxdg-fz574\">http://dx.doi.org/10.59350/5hxdg-fz574</a>.\n<span class=\"cito\"> [cito:obtainsBackgroundFrom]</span></div>\n<div class=\"csl-entry\" id=\"ref-fenner2025\">\nFenner, Martin. 2025. <em>Rogue Scholar Citation Tracking Launches to Production</em>. <a href=\"http://dx.doi.org/10.53731/zyg15-qv911\">http://dx.doi.org/10.53731/zyg15-qv911</a>.\n<span class=\"cito\"> [cito:obtainsBackgroundFrom]</span></div>\n<div class=\"csl-entry\" id=\"ref-fruehwald2025\">\nFruehwald, Josef. 2025. <em>Setting up Rogue Scholar</em>. <a href=\"http://dx.doi.org/10.59350/3fp6d-e6z90\">http://dx.doi.org/10.59350/3fp6d-e6z90</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-willighagen2023\">\nWillighagen, Egon. 2023. <span>\"Two Years of Explicit CiTO Annotations.\"</span> <em>Journal of Cheminformatics</em> 15 (1). <a href=\"https://doi.org/10.1186/s13321-023-00683-2\">https://doi.org/10.1186/s13321-023-00683-2</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-willighagen2024b\">\nWillighagen, Egon. 2024a. <em>FAIR Blog-to-Blog Citations</em>. <a href=\"http://dx.doi.org/10.59350/er1mn-m5q69\">http://dx.doi.org/10.59350/er1mn-m5q69</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n<div class=\"csl-entry\" id=\"ref-willighagen2024a\">\nWillighagen, Egon. 2024b. <em>GoatCounter, Rogue Scholar and More New Things</em>. <a href=\"http://dx.doi.org/10.59350/8x2f1-h6d21\">http://dx.doi.org/10.59350/8x2f1-h6d21</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n<div class=\"csl-entry\" id=\"ref-willighagen2025\">\nWillighagen, Egon. 2025. <em>Blog Updates</em>. <a href=\"http://dx.doi.org/10.59350/cf885-kee54\">http://dx.doi.org/10.59350/cf885-kee54</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n</div>\n</section>\n<div class=\"default\" id=\"quarto-appendix\"><section class=\"quarto-appendix-contents\" id=\"quarto-reuse\"><h2 class=\"anchored quarto-appendix-heading\">Reuse</h2><div class=\"quarto-appendix-contents\"><div><a href=\"https://creativecommons.org/licenses/by/4.0/\" rel=\"license\">CC BY 4.0</a></div></div></section><section class=\"quarto-appendix-contents\" id=\"quarto-citation\"><h2 class=\"anchored quarto-appendix-heading\">Citation</h2><div><div class=\"quarto-appendix-secondary-label\">BibTeX citation:</div><pre class=\"sourceCode code-with-copy quarto-appendix-bibtex\"><code class=\"sourceCode bibtex\">@online{rutz2025,\n  author = {{Adriano Rutz}},\n  title = {Open {Science} {Upgrade:} {Adding} {Blog} {Posts} to My\n    {Website} and {Linking} to {Rogue} {Scholar}},\n  date = {2025-08-04},\n  url = {https://adafede.github.io/posts/2025-08-04_rogue_scholar.html},\n  doi = {10.59350/yckwd-9vm79},\n  langid = {en}\n}\n</code></pre><div class=\"quarto-appendix-secondary-label\">For attribution, please cite this work as:</div><div class=\"csl-entry quarto-appendix-citeas\" id=\"ref-rutz2025\">\nAdriano Rutz. 2025. <span>\"Open Science Upgrade: Adding Blog Posts to My\nWebsite and Linking to Rogue Scholar.\"</span> August 4. <a href=\"https://doi.org/10.59350/yckwd-9vm79\">https://doi.org/10.59350/yckwd-9vm79</a>.\n</div></div></section></div>","doi":"https://doi.org/10.59350/yckwd-9vm79","guid":"https://doi.org/10.59350/yckwd-9vm79","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1754265600,"reference":[{"id":"https://doi.org/10.59350/5hxdg-fz574","unstructured":"von Csefalvay, C. (2023, November 13). Auto-DOI for Quarto posts via Rogue Scholar. <i>Chris Von Csefalvay</i>.  <b>[cito:obtainsBackgroundFrom]</b>"},{"id":"https://doi.org/10.53731/zyg15-qv911","unstructured":"Fenner, M. (2025, August 4). Rogue Scholar citation tracking launches to production. <i>Front Matter</i>.  <b>[cito:obtainsBackgroundFrom]</b>"},{"id":"https://doi.org/10.59350/3fp6d-e6z90","unstructured":"Fruehwald, J. (2025, July 31). Setting Up Rogue Scholar. <i>V\u00e6l Space</i>.  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.1186/s13321-023-00683-2","unstructured":"Willighagen, E. (2023). Two years of explicit CiTO annotations. <i>Journal of Cheminformatics</i>, <i>15</i>(1).  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.59350/er1mn-m5q69","unstructured":"Willighagen, E. (2024, December 30). FAIR blog-to-blog citations. <i>Chem-bla-ics</i>.  <b>[cito:cites]</b>"},{"id":"https://doi.org/10.59350/8x2f1-h6d21","unstructured":"Willighagen, E. (2024, July 21). GoatCounter, Rogue Scholar and more new things. <i>Chem-bla-ics</i>.  <b>[cito:cites]</b>"},{"id":"https://doi.org/10.59350/cf885-kee54","unstructured":"Willighagen, E. (2025, January 19). Blog updates. <i>Chem-bla-ics</i>.  <b>[cito:cites]</b>"}],"rid":"9hzx0-g6543","summary":"I have finally opened a Posts section on my website! Every post should now automatically get a DOI.","tags":["Open Science"],"title":"Open Science Upgrade: Adding Blog Posts to my Website and Linking to Rogue Scholar","updated_at":1789025409,"url":"https://adafede.github.io/posts/2025-08-04_rogue_scholar.html","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/05a28rw58","name":"ETH Zurich"}],"contributor_roles":[],"family":"Rutz","given":"Adriano","url":"https://orcid.org/0000-0003-0443-9902"}],"blog":{"authors":[{"name":"Adriano Rutz","url":"https://orcid.org/0000-0003-0443-9902"}],"community_id":"9d85a476-b411-4d80-89d5-500bb0f3750d","created":1780876800,"current_feed_url":null,"description":"Personal website of Adriano Rutz","doi":"https://doi.org/10.59350/adafede","favicon":"https://rogue-scholar.org/api/communities/9d85a476-b411-4d80-89d5-500bb0f3750d/logo","feed_format":"application/feed+json","feed_url":"https://adafede.github.io/posts.json","filter":null,"generator":"Other","home_page_url":"https://adafede.github.io","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":null,"slug":"adafede","status":"active","subfield":"1312","title":"Adriano Rutz","updated":1788983002,"use_api":null},"blog_name":"Adriano Rutz","blog_slug":"adafede","content_html":"<script async=\"\" crossorigin=\"anonymous\" defer=\"\" src=\"https://scripts.simpleanalyticscdn.com/latest.js\">\n</script><p>Five years ago, <a about=\"wd:Q104225190\" href=\"https://www.wikidata.org/wiki/Q104225190\">LOTUS</a> <span class=\"citation\" data-cites=\"Rutz2022\">(Rutz et al. 2022)</span> started as a small attempt to cultivate the flow of chemical knowledge, in the same way we study how metabolites flow through living systems, rather than to build <em>yet another database</em>.</p>\n<p>The idea was simple. Natural products data should be open, structured, reusable, and belong to everyone.</p>\n<p>Like many community-driven efforts, LOTUS had bursts of activity, long pauses, and years of invisible maintenance. From the outside, silence can look like disappearance. From the inside, it usually means people are still doing the work; slowly, carefully, and often without announcements.</p>\n<section class=\"level2\" id=\"from-isolated-datasets-to-global-outreach\">\n<h2 class=\"anchored\" data-anchor-id=\"from-isolated-datasets-to-global-outreach\">From isolated datasets to global outreach</h2>\n<p>The early focus of LOTUS was necessarily inward: assembling data, cleaning records, releasing versions. We built a website, curated entries, and archived releases.</p>\n<p>But we slowly realized something uncomfortable: data stored in a repository, even a good one, does not automatically live.</p>\n<p>Archiving on <a about=\"wd:Q22661177\" href=\"https://www.wikidata.org/wiki/Q22661177\">Zenodo</a> (<a class=\"uri\" href=\"https://zenodo.org/communities/the-lotus-initiative\">https://zenodo.org/communities/the-lotus-initiative</a>) was the right thing to do, but archived data is mostly silent data. It waits to be discovered, and versioning remains labor-intensive.</p>\n<p>What we really needed were entry points where people already were.</p>\n<p><a about=\"wd:Q52\" href=\"https://www.wikidata.org/wiki/Q52\">Wikipedia</a> , <a about=\"wd:Q2013\" href=\"https://www.wikidata.org/wiki/Q2013\">Wikidata</a> , and <a about=\"wd:Q45340488\" href=\"https://www.wikidata.org/wiki/Q45340488\">Scholia</a> building on top of it are not dissemination platforms in the classical sense. They are circulatory systems. They persist because communities maintain them.</p>\n<p>The <a about=\"wd:Q134520857\" href=\"https://www.wikidata.org/wiki/Q134520857\">Scholia Chemistry preprint</a> <span class=\"citation\" data-cites=\"Willighagen2025b\">(Willighagen et al. 2025)</span> co-authored with <a about=\"wd:Q20895241\" href=\"https://www.wikidata.org/wiki/Q20895241\">Egon</a> , <a about=\"wd:Q43744369\" href=\"https://www.wikidata.org/wiki/Q43744369\">Denise</a> , <a about=\"wd:Q20895785\" href=\"https://www.wikidata.org/wiki/Q20895785\">Daniel</a> , and <a about=\"wd:Q20980928\" href=\"https://www.wikidata.org/wiki/Q20980928\">Finn</a> belongs to this continuity. It does not introduce a new platform. It offers a lens for communities to see what they already collectively know.</p>\n<section class=\"level3\" id=\"making-knowledge-visible-the-wikipedia-p703-module\">\n<h3 class=\"anchored\" data-anchor-id=\"making-knowledge-visible-the-wikipedia-p703-module\">Making knowledge visible: the Wikipedia P703 module</h3>\n<blockquote class=\"blockquote\">\n<p>Knowledge needs channels, not just reservoirs.</p>\n</blockquote>\n<p>One important step was enabling Wikipedia articles and <a about=\"wd:Q15515987\" href=\"https://www.wikidata.org/wiki/Q15515987\">infoboxes</a> to directly access <em>found in taxon</em> (<a about=\"wd:Property:P703\" href=\"https://www.wikidata.org/wiki/Property:P703\">P703</a>) relationships from Wikidata in an efficient way.</p>\n<p>This sounds like a small technical detail. It is not.</p>\n<p>The idea had circulated quietly for years, in hallway conversations, chats, and conferences. I also mentioned it during the <a about=\"wd:Q133846580\" href=\"https://www.wikidata.org/wiki/Q133846580\">WikiCite 2025</a> conference last August, but it took time before conditions were right. Infrastructure work rarely happens on schedule. It almost never happens on stage. It happens in version histories, talk pages, and tiny edits that fix one Lua bug, enabling thousands of articles to improve forever.</p>\n<p>Once data is in Wikidata, it can flow into thousands of chemical articles, in dozens of languages, without duplication or translation overhead. It becomes visible to non-experts, students, and readers who will never see a database interface. This is how open data becomes public knowledge.</p>\n<p>These <a about=\"wd:Q15184295\" href=\"https://www.wikidata.org/wiki/Q15184295\">modules</a> are now available on multiple Wikipedias:</p>\n<ul>\n<li><a about=\"wd:Q328\" href=\"https://www.wikidata.org/wiki/Q328\">English</a> : <a href=\"https://en.wikipedia.org/wiki/Module:P703\">Module:P703</a></li>\n<li><a about=\"wd:Q8447\" href=\"https://www.wikidata.org/wiki/Q8447\">French</a> : <a href=\"https://fr.wikipedia.org/wiki/Module:P703\">Module:P703</a></li>\n<li><a about=\"wd:Q48183\" href=\"https://www.wikidata.org/wiki/Q48183\">German</a> : <a href=\"https://de.wikipedia.org/wiki/Modul:P703\">Modul:P703</a></li>\n<li><a about=\"wd:Q11920\" href=\"https://www.wikidata.org/wiki/Q11920\">Italian</a> : <a href=\"https://it.wikipedia.org/wiki/Modulo:P703\">Modulo:P703</a></li>\n</ul>\n<p>If you speak another language, feel free to copy them and increase their use.</p>\n<p>Initially, I tried to reuse existing modules, and quickly learned why module reuse across Wikipedias is famously difficult. Each wiki evolves its own ecosystem of dependencies, conventions, and technical debt. So the modules were written fully contained, independent of language-specific infrastructure. Only lines that need to be changed are the language-specific translations at the top of the module, trying to follow <a about=\"wd:Q3141064\" href=\"https://www.wikidata.org/wiki/Q3141064\">18n</a>.</p>\n<p>These modules are not a new website or a new interface. They are simply better plumbing.</p>\n<div class=\"quarto-figure quarto-figure-center\">\n<figure class=\"figure\">\n<p><img class=\"img-fluid figure-img\" src=\"https://adafede.github.io/images/screenshots/screenshot_p703_module.png\"/></p>\n<figcaption>Screenshot of the P703 module on English Wikipedia</figcaption>\n</figure>\n</div>\n<p>By default, only <code>5</code> <a about=\"wd:Q16521\" href=\"https://www.wikidata.org/wiki/Q16521\">organisms</a> are shown, keeping the text clean and readable. But the magic is in how the module handles the rest: each taxon links to its Wikipedia article, and if no article exists in the current language, the module gracefully redirects to an equivalent page in another wiki. A beautiful example of this is <code>war</code> for <a href=\"https://war.wikipedia.org/wiki/Quassia_africana\">Quassia africana</a>.</p>\n</section>\n<section class=\"level3\" id=\"reaching-non-experts\">\n<h3 class=\"anchored\" data-anchor-id=\"reaching-non-experts\">Reaching non-experts</h3>\n<blockquote class=\"blockquote\">\n<p>Not everyone wants to learn SPARQL.</p>\n</blockquote>\n<p>I have heard this sentiment countless times. Regardless of personal preferences, if we want the data to truly live, it must reach as many people as possible.</p>\n<p>Small tools like the <a href=\"https://adafede.github.io/marimo/apps/lotus_wikidata_explorer.html\">LOTUS Wikidata Explorer</a> help lower that barrier. It is imperfect. It is still growing. But it already allows chemists, curators, and students to access and export data in formats they can actually use.</p>\n<p>The principle is simple: knowledge only flows when it reaches people. The data must be seen, explored, and reused. Only then does it fulfill its purpose.</p>\n<div class=\"quarto-figure quarto-figure-center\">\n<figure class=\"figure\">\n<p><img class=\"img-fluid figure-img\" src=\"https://adafede.github.io/images/screenshots/screenshot_lotus_wikidata_explorer.png\"/></p>\n<figcaption>Screenshot of the LOTUS Wikidata Explorer interface</figcaption>\n</figure>\n</div>\n<p>On a more technical note, the LOTUS Wikidata Explorer leverages the powerful <a about=\"wd:Q101200819\" href=\"https://www.wikidata.org/wiki/Q101200819\">IDSM</a> endpoint <span class=\"citation\" data-cites=\"Galgonek2021\">(Galgonek and Vondr\u00e1\u0161ek 2021)</span>, which allows for chemical similarity searches thanks to <a about=\"wd:Q55016200\" href=\"https://www.wikidata.org/wiki/Q55016200\">Sachem</a> <span class=\"citation\" data-cites=\"Kratochvl2018\">(Kratochv\u00edl et al. 2018)</span>. Its speed for large-scale queries could never have been reached without <a about=\"wd:Q111016295\" href=\"https://www.wikidata.org/wiki/Q111016295\">QLever</a> <span class=\"citation\" data-cites=\"Bast2017\">(Bast and Buchhold 2017)</span>, and chemical depictions come from <a about=\"wd:Q137800121\" href=\"https://www.wikidata.org/wiki/Q137800121\">CDK Depict</a>.</p>\n<p>It returns structured metadata for traceability and reproducibility, together with hashes that uniquely identify the query and its results. It can be queried programmatically via simple API calls, for example <code>?taxon=Gentianaceae</code> or <code>?smiles=c1ccccc1&amp;formula_filter=true&amp;f_state=required</code>. It works directly in the browser without requiring heavy dependencies, almost everything works out of the box.</p>\n<p>Alternatively, users can take advantage of a local version, for example to extract a small, personal <a about=\"wd:Q33002955\" href=\"https://www.wikidata.org/wiki/Q33002955\">knowledge graph</a> in <a about=\"wd:Q114409\" href=\"https://www.wikidata.org/wiki/Q114409\">TTL</a> format, or to export all or selected LOTUS data in more chemistry-friendly formats such as <a about=\"wd:Q2063\" href=\"https://www.wikidata.org/wiki/Q2063\">JSON</a> or <a about=\"wd:Q935809\" href=\"https://www.wikidata.org/wiki/Q935809\">CSV</a>, ready for analysis, visualization, or integration into other workflows.</p>\n<p>For example, to export a complete or filtered snapshot locally:</p>\n<div class=\"cell\">\n<div class=\"code-copy-outer-scaffold\"><div class=\"sourceCode cell-code\" id=\"cb1\" style=\"background: #f1f3f5;\"><pre class=\"sourceCode r code-with-copy\"><code class=\"sourceCode r\"><span id=\"cb1-1\">uvx \\</span>\n<span id=\"cb1-2\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>from \\</span>\n<span id=\"cb1-3\">  git<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">+</span>https<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span><span class=\"er\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">//</span>github.com<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">/</span>adafede<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">/</span>marimo \\</span>\n<span id=\"cb1-4\">  lotus_wikidata_explorer \\</span>\n<span id=\"cb1-5\">  export \\</span>\n<span id=\"cb1-6\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>taxon <span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">\"*\"</span> \\   <span class=\"co\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\"># to get all taxa, else \"Gentianaceae\", for example</span></span>\n<span id=\"cb1-7\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>format csv \\  <span class=\"co\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\"># also supports json, ttl</span></span>\n<span id=\"cb1-8\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>output <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">20260119</span>_lotus.csv.gz \\</span>\n<span id=\"cb1-9\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>compress \\</span>\n<span id=\"cb1-10\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>verbose</span></code></pre></div></div>\n</div>\n<p>And if you are curious where halogenated compounds appear most often, you can simply ask:</p>\n<div class=\"cell\">\n<div class=\"code-copy-outer-scaffold\"><div class=\"sourceCode cell-code\" id=\"cb2\" style=\"background: #f1f3f5;\"><pre class=\"sourceCode r code-with-copy\"><code class=\"sourceCode r\"><span id=\"cb2-1\">xan dedup <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">20260119</span>_lotus.csv.gz \\</span>\n<span id=\"cb2-2\">  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">--</span>select compound_inchikey,molecular_formula,taxon_name <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-3\">  xan select compound_inchikey,molecular_formula,taxon_name <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-4\">  xan filter <span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">\"contains(molecular_formula, 'Br') or</span></span>\n<span id=\"cb2-5\"><span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">              contains(molecular_formula, 'Cl') or</span></span>\n<span id=\"cb2-6\"><span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">              contains(molecular_formula, 'F') or</span></span>\n<span id=\"cb2-7\"><span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">              contains(molecular_formula, 'I')\"</span> <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-8\">  xan filter <span class=\"st\" style=\"color: #20794D;\nbackground-color: null;\nfont-style: inherit;\">'!contains(molecular_formula, \"Fe\")'</span> <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-9\">  xan freq <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">-</span>s taxon_name <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span> \\</span>\n<span id=\"cb2-10\">  xan hist <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">-</span>l value <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">-</span>R</span></code></pre></div></div>\n</div>\n<div class=\"cell\">\n<div class=\"code-copy-outer-scaffold\"><div class=\"sourceCode cell-code\" id=\"cb3\" style=\"background: #f1f3f5;\"><pre class=\"sourceCode r code-with-copy\"><code class=\"sourceCode r\"><span id=\"cb3-1\">Histogram <span class=\"cf\" style=\"color: #003B4F;\nbackground-color: null;\nfont-weight: bold;\nfont-style: inherit;\">for</span> <span class=\"fu\" style=\"color: #4758AB;\nbackground-color: null;\nfont-style: inherit;\">taxon_name</span> (bars<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span> <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">11</span>, sum<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span> <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">11</span>,<span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">604</span>, max<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span> <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">10</span>,<span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">060</span>)<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">:</span></span>\n<span id=\"cb3-2\"></span>\n<span id=\"cb3-3\">Streptomyces            <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>   <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">374</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">3.22</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0\u25a0\u25a0                                                                                                   <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-4\">Laurencia dendroidea    <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>   <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">314</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">2.71</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0\u25a0\u25a0                                                                                                   <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-5\">Laurencia obtusa        <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>   <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">184</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">1.59</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0                                                                                                     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-6\">Pseudoceratina purpurea <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>   <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">112</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.97</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0                                                                                                     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-7\">Aplysia dactylomela     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">99</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.85</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0                                                                                                     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-8\">Nostoc                  <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">99</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.85</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0                                                                                                     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-9\">Laurencia nipponica     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">95</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.82</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0                                                                                                      <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-10\">Portieria hornemannii   <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">94</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.81</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0                                                                                                      <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-11\">Lyngbya majuscula       <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">88</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.76</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0                                                                                                      <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-12\">Chaetomium globosum     <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>    <span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">85</span>   <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">0.73</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0                                                                                                      <span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span>\n<span id=\"cb3-13\"><span class=\"er\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">&lt;</span>rest<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">&gt;</span>                  <span class=\"er\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">|</span><span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">10</span>,<span class=\"dv\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">060</span>  <span class=\"fl\" style=\"color: #AD0000;\nbackground-color: null;\nfont-style: inherit;\">86.69</span>%<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span>\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0\u25a0<span class=\"sc\" style=\"color: #5E5E5E;\nbackground-color: null;\nfont-style: inherit;\">|</span></span></code></pre></div></div>\n</div>\n</section>\n</section>\n<section class=\"level2\" id=\"making-flow-reliable-curation-and-standards\">\n<h2 class=\"anchored\" data-anchor-id=\"making-flow-reliable-curation-and-standards\">Making flow reliable: curation and standards</h2>\n<blockquote class=\"blockquote\">\n<p>At some point, flow only runs if it is maintained.</p>\n</blockquote>\n<p>As I do not post as often as I probably should, here are some other pointers to related work and discussions from the past months, for those who want to follow the flow a bit further:</p>\n<section class=\"level3\" id=\"blue-obelisk\">\n<h3 class=\"anchored\" data-anchor-id=\"blue-obelisk\">Blue Obelisk</h3>\n<ul>\n<li>Following some ideas he had to improve Scholia Chemistry, Egon initiated the Blue Obelisk Wikidata Chemistry Curation project: <a class=\"uri\" href=\"https://blueobelisk.github.io/wikidata-chemistry-curation/\">https://blueobelisk.github.io/wikidata-chemistry-curation/</a>. I then joined and contributed to some parts, maybe you will find out which ones!</li>\n<li>Contributions were also made to the Blue Obelisk IUPAC Names project (also led by Egon): <a class=\"uri\" href=\"https://github.com/BlueObelisk/iupac-names\">https://github.com/BlueObelisk/iupac-names</a>, integrating Wikidata-derived name-compound pairs. See <a class=\"uri\" href=\"https://github.com/Adafede/wd-labels-to-iupac\">https://github.com/Adafede/wd-labels-to-iupac</a> and <a class=\"uri\" href=\"https://chem-bla-ics.linkedchemistry.info/2025/08/09/one-million-iupac-names-4.html\">https://chem-bla-ics.linkedchemistry.info/2025/08/09/one-million-iupac-names-4.html</a> <span class=\"citation\" data-cites=\"Willighagen2025c\">(Willighagen 2025)</span> These bridges allow names and identifiers to circulate consistently across systems.</li>\n</ul>\n</section>\n<section class=\"level3\" id=\"reactions-flow\">\n<h3 class=\"anchored\" data-anchor-id=\"reactions-flow\">Reactions flow</h3>\n<p>Recently, I also contributed to improving how <a about=\"wd:Q36534\" href=\"https://www.wikidata.org/wiki/Q36534\">chemical reactions</a> are modeled in Wikidata.</p>\n<p>Previously, many reactions were modeled as <a about=\"wd:Property:P31\" href=\"https://www.wikidata.org/wiki/Property:P31\">instances of</a> \"chemical reaction\", which violated disjointness, see <span class=\"citation\" data-cites=\"Doan2025\">(Do\u01e7an and Patel-Schneider 2025)</span>.</p>\n<p>The introduction of <a about=\"wd:Q137796968\" href=\"https://www.wikidata.org/wiki/Q137796968\">type of chemical reaction</a> now allows reactions to be classified more precisely, while preserving their hierarchy using <a about=\"wd:Property:P279\" href=\"https://www.wikidata.org/wiki/Property:P279\">subclass of</a>.</p>\n</section>\n<section class=\"level3\" id=\"wikifunctions\">\n<h3 class=\"anchored\" data-anchor-id=\"wikifunctions\">Wikifunctions</h3>\n<p>Out of curiosity, I also made a small contribution to chemistry-related functions in <a about=\"wd:Q104587954\" href=\"https://www.wikidata.org/wiki/Q104587954\">Wikifunctions</a>: <a href=\"https://www.wikifunctions.org/view/en/Z30950\">Z30950</a>. It validates <a about=\"wd:Q102507\" href=\"https://www.wikidata.org/wiki/Q102507\">CAS Registry Numbers</a>. It does one thing, and it does it reliably.</p>\n<p>It is tiny. But it is a seed.</p>\n</section>\n</section>\n<section class=\"level2\" id=\"looking-forward-flowing-knowledge-flowing-metabolites\">\n<h2 class=\"anchored\" data-anchor-id=\"looking-forward-flowing-knowledge-flowing-metabolites\">Looking forward: flowing knowledge, flowing metabolites</h2>\n<p>Projects like Wikifunctions and <a about=\"wd:Q96807071\" href=\"https://www.wikidata.org/wiki/Q96807071\">Abstract Wikipedia</a> point to the next phase of open knowledge: knowledge that is not only stored, but executed, reused, and recombined.</p>\n<p>A global, open <a about=\"wd:Q12149006\" href=\"https://www.wikidata.org/wiki/Q12149006\">metabolomics</a> knowledge graph is slowly taking shape, one where chemical structures, organisms, reactions, and evidence can finally be traced together.</p>\n<p>LOTUS is no longer an initiative. It is one contributor among many in that graph.</p>\n<p>If you edit Wikipedia, curate Wikidata, maintain a SPARQL endpoint, write a template, review a module, or fix a tiny detail no one will notice, <em>thank you</em>. <strong>This work only matters because you are here</strong>.</p>\n<section class=\"level3\" id=\"references\">\n<h3 class=\"anchored\" data-anchor-id=\"references\">References</h3>\n<div class=\"references csl-bib-body hanging-indent\" id=\"refs\">\n<div class=\"csl-entry\" id=\"ref-Bast2017\">\nBast, Hannah, and Bj\u00f6rn Buchhold. 2017. <span>\"QLever: A Query Engine for Efficient SPARQL+text Search.\"</span> <em>Proceedings of the 2017 ACM on Conference on Information and Knowledge Management</em>, CIKM '17, November, 647\u201356. <a href=\"https://doi.org/10.1145/3132847.3132921\">https://doi.org/10.1145/3132847.3132921</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-Doan2025\">\nDo\u01e7an, Ege Atacan, and Peter F. Patel-Schneider. 2025. <span>\"Disjointness Violations in Wikidata.\"</span> In <em>Knowledge Graphs and Semantic Web</em>. Springer Nature Switzerland. <a href=\"https://doi.org/10.1007/978-3-031-81221-7_18\">https://doi.org/10.1007/978-3-031-81221-7_18</a>.\n<span class=\"cito\"> [cito:citesAsRecommendedReading]</span></div>\n<div class=\"csl-entry\" id=\"ref-Galgonek2021\">\nGalgonek, Jakub, and Ji\u0159\u00ed Vondr\u00e1\u0161ek. 2021. <span>\"IDSM ChemWebRDF: SPARQLing Small-Molecule Datasets.\"</span> <em>Journal of Cheminformatics</em> 13 (1). <a href=\"https://doi.org/10.1186/s13321-021-00515-1\">https://doi.org/10.1186/s13321-021-00515-1</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-Kratochvl2018\">\nKratochv\u00edl, Miroslav, Ji\u0159\u00ed Vondr\u00e1\u0161ek, and Jakub Galgonek. 2018. <span>\"Sachem: A Chemical Cartridge for High-Performance Substructure Search.\"</span> <em>Journal of Cheminformatics</em> 10 (1). <a href=\"https://doi.org/10.1186/s13321-018-0282-y\">https://doi.org/10.1186/s13321-018-0282-y</a>.\n<span class=\"cito\"> [cito:usesMethodIn]</span></div>\n<div class=\"csl-entry\" id=\"ref-Rutz2022\">\nRutz, Adriano, Maria Sorokina, Jakub Galgonek, et al. 2022. <span>\"The LOTUS Initiative for Open Knowledge Management in Natural Products Research.\"</span> <em>eLife</em> 11 (May). <a href=\"https://doi.org/10.7554/elife.70780\">https://doi.org/10.7554/elife.70780</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n<div class=\"csl-entry\" id=\"ref-Willighagen2025c\">\nWillighagen, Egon. 2025. August. <a href=\"https://doi.org/10.59350/krw9n-dv417\">https://doi.org/10.59350/krw9n-dv417</a>.\n<span class=\"cito\"> [cito:citesAsRecommendedReading]</span></div>\n<div class=\"csl-entry\" id=\"ref-Willighagen2025b\">\nWillighagen, Egon, Denise Slenter, Adriano Rutz, Daniel Mietchen, and Finn Nielsen. 2025. <em>Scholia Chemistry: Access to Chemistry in Wikidata</em>. May. <a href=\"https://doi.org/10.26434/chemrxiv-2025-53n0w\">https://doi.org/10.26434/chemrxiv-2025-53n0w</a>.\n<span class=\"cito\"> [cito:cites]</span></div>\n</div>\n</section>\n</section>\n<div class=\"default\" id=\"quarto-appendix\"><section class=\"quarto-appendix-contents\" id=\"quarto-reuse\"><h2 class=\"anchored quarto-appendix-heading\">Reuse</h2><div class=\"quarto-appendix-contents\"><div><a href=\"https://creativecommons.org/licenses/by/4.0/\" rel=\"license\">CC BY 4.0</a></div></div></section><section class=\"quarto-appendix-contents\" id=\"quarto-citation\"><h2 class=\"anchored quarto-appendix-heading\">Citation</h2><div><div class=\"quarto-appendix-secondary-label\">BibTeX citation:</div><pre class=\"sourceCode code-with-copy quarto-appendix-bibtex\"><code class=\"sourceCode bibtex\">@online{rutz2026,\n  author = {{Adriano Rutz}},\n  title = {Cultivating {Knowledge} {Flow} in {Open} {Chemistry}},\n  date = {2026-01-20},\n  url = {https://adafede.github.io/posts/2026-01-20_chem_flow.html},\n  doi = {10.59350/sk00y-3gh44},\n  langid = {en}\n}\n</code></pre><div class=\"quarto-appendix-secondary-label\">For attribution, please cite this work as:</div><div class=\"csl-entry quarto-appendix-citeas\" id=\"ref-rutz2026\">\nAdriano Rutz. 2026. <span>\"Cultivating Knowledge Flow in Open\nChemistry.\"</span> January 20. <a href=\"https://doi.org/10.59350/sk00y-3gh44\">https://doi.org/10.59350/sk00y-3gh44</a>.\n</div></div></section></div>","doi":"https://doi.org/10.59350/sk00y-3gh44","guid":"https://doi.org/10.59350/sk00y-3gh44","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1768867200,"reference":[{"id":"https://doi.org/10.1145/3132847.3132921","unstructured":"Bast, H., &amp; Buchhold, B. (2017). QLever. In <i>Proceedings of the 2017 ACM on Conference on Information and Knowledge Management</i> (pp. 647\u2013656). ACM.  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.1007/978-3-031-81221-7_18","unstructured":"Do\u01e7an, E. A., &amp; Patel-Schneider, P. F. (2025). Disjointness Violations in\u00a0Wikidata. In <i>Lecture Notes in Computer Science</i> (pp. 259\u2013274). Springer Nature Switzerland.  <b>[cito:citesAsRecommendedReading]</b>"},{"id":"https://doi.org/10.1186/s13321-021-00515-1","unstructured":"Galgonek, J., &amp; Vondr\u00e1\u0161ek, J. (2021). IDSM ChemWebRDF: SPARQLing small-molecule datasets. <i>Journal of Cheminformatics</i>, <i>13</i>(1).  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.1186/s13321-018-0282-y","unstructured":"Kratochv\u00edl, M., Vondr\u00e1\u0161ek, J., &amp; Galgonek, J. (2018). Sachem: a chemical cartridge for high-performance substructure search. <i>Journal of Cheminformatics</i>, <i>10</i>(1).  <b>[cito:usesMethodIn]</b>"},{"id":"https://doi.org/10.7554/elife.70780","unstructured":"Rutz, A., Sorokina, M., Galgonek, J., Mietchen, D., Willighagen, E., Gaudry, A., Graham, J. G., Stephan, R., Page, R., Vondr\u00e1\u0161ek, J., Steinbeck, C., Pauli, G. F., Wolfender, J.-L., Bisson, J., &amp; Allard, P.-M. (2022). The LOTUS initiative for open knowledge management in natural products research. <i>eLife</i>, <i>11</i>.  <b>[cito:cites]</b>"},{"id":"https://doi.org/10.59350/krw9n-dv417","unstructured":"Willighagen, E. (2025, August 9). One Million IUPAC names #4: a lot is happening. <i>Chem-bla-ics</i>.  <b>[cito:citesAsRecommendedReading]</b>"},{"id":"https://doi.org/10.26434/chemrxiv-2025-53n0w","unstructured":"Willighagen, E., Slenter, D., Rutz, A., Mietchen, D., &amp; Nielsen, F. (2025). <i>Scholia Chemistry: access to chemistry in Wikidata</i>. American Chemical Society (ACS).  <b>[cito:cites]</b>"}],"rid":"80nkb-cq953","summary":"Five years ago, LOTUS (Rutz et al. 2022) started as a small attempt to cultivate the flow of chemical knowledge, in the same way we study how metabolites flow through living systems, rather than to build yet another database.","tags":["Chemistry","LOTUS","Open Science","Wikidata"],"title":"Cultivating Knowledge Flow in Open Chemistry","updated_at":1789025407,"url":"https://adafede.github.io/posts/2026-01-20_chem_flow.html","version":"v1"},{"authors":[{"contributor_roles":[],"name":"Adapt Research"}],"blog":{"authors":null,"community_id":"bfd37b46-cbce-4a47-9a9d-fdc1d9c8b8d2","created":1753833600,"current_feed_url":null,"description":"As we build our world we build our minds","doi":"https://doi.org/10.59350/adaptresearchwriting","favicon":"https://rogue-scholar.org/api/communities/bfd37b46-cbce-4a47-9a9d-fdc1d9c8b8d2/logo","feed_format":"application/atom+xml","feed_url":"https://adaptresearchwriting.com/feed/atom/","filter":null,"generator":"WordPress.com","home_page_url":"https://adaptresearchwriting.com","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"adaptresearchwriting","status":"active","subfield":"2306","title":"Adapt Research Ltd","updated":1789011219,"use_api":null},"blog_name":"Adapt Research Ltd","blog_slug":"adaptresearchwriting","content_html":"<p class=\"wp-block-paragraph\"><em>Introducing our new preprint on evolutionary governance for systemic and global catastrophic risk</em></p>\n<p class=\"wp-block-paragraph\">By Matt Boyd</p>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7917\" data-attachment-id=\"7917\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"image\" data-large-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=840\" data-orig-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png\" data-orig-size=\"936,528\" data-permalink=\"https://adaptresearchwriting.com/2026/09/10/the-metacrisis-is-a-degradation-of-evolvability-why-global-risk-needs-evolutionary-explanation-and-governance/image-80/\" height=\"528\" sizes=\"(max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 1362px) 62vw, 840px\" src=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=936\" srcset=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png 936w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=150 150w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=300 300w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=768 768w\" width=\"936\"/><figcaption class=\"wp-element-caption\">Photo by <a href=\"https://unsplash.com/@jplenio?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Johannes Plenio</a> on <a href=\"https://unsplash.com/photos/silhouette-photo-of-group-people-standing-on-grass-aWDgqexSxA0?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Unsplash</a></figcaption></figure>\n<p class=\"wp-block-paragraph\"><strong>TLDR/Summary</strong></p>\n<ul class=\"wp-block-list\">\n<li>Nothing about human society and its generation of global risk makes sense except in the light of evolution. I've been building that claim through my recent <a href=\"https://adaptresearchwriting.com/2026/06/03/what-the-latest-european-risk-analysis-conference-means-for-global-risk-and-new-zealand/\">posts</a> and <a href=\"https://adaptresearchwriting.com/2026/02/04/is-there-a-meta-crisis-yes/\">conference talks</a>.</li>\n<li>A new <a href=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/260831-evolvability-metacrisis-v8.pdf\">preprint</a> I've developed with Nick Wilson, and now under peer-review, brings all this together in a technical paper: <a href=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/260831-evolvability-metacrisis-v8.pdf\">The Metacrisis as a Degradation of Evolvability</a>.</li>\n<li>Five research communities working on global risk are converging, often unawares, on the extended evolutionary framework. We name it, systematise it from first principles, and draw out what it implies for governance of global risk.</li>\n<li>Risk-generating architectures recur wherever certain evolutionary dynamics obtain; the <em>metacrisis</em> is the simultaneous degradation of five conditions of evolvability (variation, modularity, selective-environment stability, transmission fidelity, and outlaw/defector suppression)</li>\n<li>Global risk governance must therefore act on those conditions, above all on suppressing defectors.</li>\n<li>The evolutionary lens is not the answer to everything, but our paper deliberately pushes it as far as we can, because evolution keeps seeping through the gaps in other explanations and joining them together.</li>\n<li>The upshot is a change in what governance is <em>for</em>: less for specifying solutions, and more about engineering, nudging and continually readjusting the conditions under which good solutions can arise, spread and hold.</li>\n</ul>\n<p class=\"wp-block-paragraph\"><strong>Two intellectual strands twisted together</strong></p>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7919\" data-attachment-id=\"7919\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"image\" data-large-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=840\" data-orig-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png\" data-orig-size=\"936,526\" data-permalink=\"https://adaptresearchwriting.com/2026/09/10/the-metacrisis-is-a-degradation-of-evolvability-why-global-risk-needs-evolutionary-explanation-and-governance/image-81/\" height=\"526\" sizes=\"(max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 1362px) 62vw, 840px\" src=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=936\" srcset=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png 936w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=150 150w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=300 300w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-1.png?w=768 768w\" width=\"936\"/><figcaption class=\"wp-element-caption\">Photo by <a href=\"https://unsplash.com/@warrenumoh?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Warren Umoh</a> on <a href=\"https://unsplash.com/photos/dna-double-helix-structure--qycBqByWIY?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Unsplash</a></figcaption></figure>\n<p class=\"wp-block-paragraph\">This post has been a long time coming. In 2007 I wrote a Masters thesis in philosophy, on cultural evolution and the information environment we have created. That was back when \"meme\" still had a technical definition, Dawkins's unit of cultural inheritance, and did not yet mean a picture of a cat that goes viral. My thesis argued meme theory was useful in understanding how culture evolves.</p>\n<p class=\"wp-block-paragraph\">My 2011 PhD took the next step: technologies play a privileged causal role in psychological development, and as we invent new ones, we change the developmental environment for present and subsequent generations, thereby driving evolution of the mind, cumulative niche construction applied to human cognition.</p>\n<p class=\"wp-block-paragraph\">Both theses were under Kim Sterelny, whose work on cumulative culture runs through our new preprint too.</p>\n<p class=\"wp-block-paragraph\">For over a decade since, I have worked on global catastrophic risk, studying pandemics, nuclear winter, island refuges, and national risk assessment. It was seemingly inevitable that the two strands; evolution and global risk would meet.</p>\n<p class=\"wp-block-paragraph\">Dobzhansky said nothing in biology makes sense except in the light of evolution.</p>\n<p class=\"wp-block-paragraph\">I'll appropriate that: nothing about human society, and about why it keeps generating risks we know how to avoid, makes sense except in the light of evolution.</p>\n<p class=\"wp-block-paragraph\">Regular readers of this blog will have seen the argument assembling. In February I asked <a href=\"https://adaptresearchwriting.com/2026/02/04/is-there-a-meta-crisis-yes/\">whether there is really a \"meta\"-crisis</a>. In May I <a href=\"https://adaptresearchwriting.com/2026/06/03/what-the-latest-european-risk-analysis-conference-means-for-global-risk-and-new-zealand/\">presented</a> an early version of this argument at the European risk-analysis conference. In July I wrote a <a href=\"https://adaptresearchwriting.com/2026/07/06/polycrisis-metacrisis-systemic-risk-a-definitional-field-guide-to-the-reality-of-everything/\">definitional field guide</a> following a chain of four questions:</p>\n<ul class=\"wp-block-list\">\n<li>What could go badly wrong? That's <strong>global catastrophic risk</strong>.</li>\n<li>How do failures spread? That's <strong>systemic risk</strong>, where a tightly-coupled world is a <em>generator</em> of hazards, not a bystander.</li>\n<li>How do crises compound? That's <strong>polycrisis</strong>, the causal entanglement of crises such that the whole is worse than the sum of its parts.</li>\n<li>And why do we keep generating a fragile world?</li>\n</ul>\n<p class=\"wp-block-paragraph\">I now turn to this fourth question.</p>\n<p class=\"wp-block-paragraph\"><strong>Rising global risk despite known fixes</strong></p>\n<p class=\"wp-block-paragraph\">The major global hazards were identified decades ago, and so were fixes: disarmament, emissions reduction, health-security investment, limits to extraction. The Club of Rome laid much of it out in 1972. Yet emissions have risen since the Paris Agreement, arms-control treaties have lapsed, and by most measures the world is more exposed. Humanity is not ignorant of what threatens it. What's missing is second-order understanding: <em>why</em> we consistently fail, and <em>at what level</em> to intervene.</p>\n<p class=\"wp-block-paragraph\"><strong>Five fields, one grey elephant</strong></p>\n<p class=\"wp-block-paragraph\">Our new preprint begins by outlining the communities working on these problems of global risk. National risk assessment and disaster risk reduction handle hazards, mostly natural, mostly after the fact. Global catastrophic risk studies confront rare but devastating events. Systemic-risk analysis maps feedback-rich networks and names risk-creating actors. Polycrisis scholarship traces entanglement and attractor states, including the Cascade Institute's <a href=\"https://adaptresearchwriting.com/2025/11/11/mapping-pathways-through-the-polycrisis-the-cascade-institutes-new-model-for-navigating-global-systemic-risk/\">\"Illiberal Decline\" and \"Mad Max\"</a> basins. Behavioural and evolutionary science speaks of traps, ratchets and a \"human behavioural crisis\".</p>\n<p class=\"wp-block-paragraph\">Each field is like a blind monk with a hand on an elephant, describing in rich detail what they feel, but unable to articulate the whole. Each field reaches for the same vocabulary of adaptation, selection, co-evolution, traps, ratchets. Some is generic systems talk. A surprising amount is specifically evolutionary, used by fields with no evolutionary self-conception. That is latent Darwinism and it signals intellectual convergence.</p>\n<figure class=\"wp-block-image size-large\"><img alt=\"\" aperture\":\"0\",\"credit\":\"\",\"camera\":\"\",\"caption\":\"\",\"created_timestamp\":\"0\",\"copyright\":\"\",\"focal_length\":\"0\",\"iso\":\"0\",\"shutter_speed\":\"0\",\"title\":\"\",\"orientation\":\"0\",\"alt\":\"\"}\"=\"\" class=\"wp-image-7921\" data-attachment-id=\"7921\" data-comments-opened=\"1\" data-image-caption=\"\" data-image-description=\"\" data-image-meta=\"{\" data-image-title=\"image\" data-large-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png?w=468\" data-orig-file=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png\" data-orig-size=\"468,354\" data-permalink=\"https://adaptresearchwriting.com/2026/09/10/the-metacrisis-is-a-degradation-of-evolvability-why-global-risk-needs-evolutionary-explanation-and-governance/image-82/\" height=\"354\" sizes=\"(max-width: 468px) 85vw, 468px\" src=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png?w=468\" srcset=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png 468w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png?w=150 150w, https://adaptresearchwriting.com/wp-content/uploads/2026/09/image-2.png?w=300 300w\" width=\"468\"/><figcaption class=\"wp-element-caption\"><em>Image credit: romana klee on Flickr</em></figcaption></figure>\n<p class=\"wp-block-paragraph\"><strong>Evolution is not a metaphor here</strong></p>\n<p class=\"wp-block-paragraph\">In risk science, grey elephants are a metaphor for big obvious risks, charging right towards us, that everyone can see plainly, yet no one acts.</p>\n<p class=\"wp-block-paragraph\">In our pre-print evolution is not a metaphor. We deploy a precise version of evolution, not a simplified high school one, and certainly not the discredited \"Social Darwinism\" that confused selective success with moral merit.</p>\n<p class=\"wp-block-paragraph\">Natural selection is an abstract process that arises wherever there is heritable variation, differences in success that depend on it, and differential persistence as a result. Dennett called this <em>substrate neutrality</em>: the logic doesn't care what the variants are made of. Genes are one substrate. Firms, institutions, legal codes, professional norms, technologies and ideas are others, to varying degrees. Bicycle design lineages show the adaptive-radiation signature of biological clades, and no designer intended it.</p>\n<p class=\"wp-block-paragraph\">This instantiation comes in degrees, and where any human system sits on Godfrey-Smith's continuum of \"<a href=\"https://academic.oup.com/book/4808\">Darwinian populations</a>\" is an empirical question. But human systems are also designed, meaning that intention and the invisible hand of evolution operate simultaneously. Because no actor can intend outcomes everywhere and all the time, much of what results in human systems evolved rather than being designed.</p>\n<p class=\"wp-block-paragraph\">This is where the social sciences fit, and our framing does not replace economics, political science or the study of human decision-making. Those describe real mechanisms, and human choice is a genuine causal element in the system. What evolution adds is the <em>ultimate</em> level of explanation, in Mayr's sense, not how each mechanism or complex system feature works but <em>why</em> it exists and persists, shaping power and possibility.</p>\n<p class=\"wp-block-paragraph\">Deliberate decisions exist in a selective environment that determines which decisions get retained and copied. The framework is \"extended\" because inheritance runs through several channels at different speeds (genes, memes, laws, education syllabi, technologies), because we actively construct the niches that then impose selection back on human activities, and because not all cultural change is adaptive. For example, prestige, conformity and familiarity spread variants regardless of merit.</p>\n<p class=\"wp-block-paragraph\"><strong>Why we keep building a fragile world</strong></p>\n<p class=\"wp-block-paragraph\">Our new paper groups global risk by examples of its driving dynamics rather than by hazard.</p>\n<ul class=\"wp-block-list\">\n<li><em>Multilevel selection.</em> What's adaptive for one actor (individual, firm, nation) is often destructive for the commons that sustains it. Muir bred hens individually for egg yield and got flocks that feather-pecked and cannibalised themselves. Selecting whole cages for productivity produced cooperative, higher-yield flocks. Scale that up and you have excessive carbon emissions, overfishing, aquifer depletion, and antimicrobial resistance. Firms are rewarded for maximising extraction even when run by people who grasped the consequences decades ago.</li>\n<li><em>Arms races.</em> Red Queen dynamics where everyone must invest more merely to hold position. In frontier AI, safety spending is individually costly and competitively detrimental if an organisation's rivals don't match it, so the field races to deploy. Non-reckless actors are simply outcompeted. Global risks from nuclear weapon stockpiling and gain-of-function research share this structure.</li>\n<li><em>Lock-in and fitness traps.</em> Configurations stable under current pressures but globally suboptimal, can be hard to leave because improving requires first getting worse. Fossil fuel infrastructure is the obvious case, where build out has constrained changes that are now possible.</li>\n<li><em>Transmission bias.</em> Cultural evolution selects for what is readily learned and passed on, not for what is true, and engagement-optimised platforms erode the shared map of reality on which collective action depends and the information scaffolding which centuries of cultural evolution had built.</li>\n</ul>\n<p class=\"wp-block-paragraph\">These are not accidents or failures of will. They are predictable outputs of evolutionary selection at several scales at once. Where the selective environment has been deliberately re-engineered, on the other hand, the Montreal Protocol, verified arms control from the late 1980s, Ostrom's management of the commons, the dynamics have sometimes been beaten. In each case a suppression or coordination mechanism was built and protected, converting locally advantageous defection into a losing move.</p>\n<p class=\"wp-block-paragraph\"><strong>Evolvability, and Metacrisis defined</strong></p>\n<p class=\"wp-block-paragraph\">Evolvability is a system's capacity to generate, transmit and retain complex adaptations. Biological theory and computer science treat it as something that must be built into a system, not assumed. It rests on five conditions:</p>\n<ul class=\"wp-block-list\">\n<li><strong>Variation</strong>: a supply of diverse candidate solutions</li>\n<li><strong>Modularity</strong>: semi-independent parts that can change without dragging the whole down</li>\n<li><strong>Stability of the selective environment</strong>: pressure consistent enough for adaptation to accumulate</li>\n<li><strong>Fidelity of transmission</strong>: reliable inheritance of what works, with error-correction</li>\n<li><strong>Outlaw/defector suppression</strong>: containment of entities that gain locally by breaking cooperative rules or exploiting commons</li>\n</ul>\n<p class=\"wp-block-paragraph\">A definition of the metacrisis follows: <strong>the metacrisis is the simultaneous degradation of these conditions in the systems meant to govern or mitigate global risk.</strong></p>\n<p class=\"wp-block-paragraph\">This is not any particular crisis, or even a polycrisis, but a crisis of the capacity to adapt to crisis at all. That is why governance fails <em>consistently</em> across unrelated domains.</p>\n<p class=\"wp-block-paragraph\">Each evolvability condition is observable. Food-system homogenisation onto a few crops and chokepoints is a variation failure. The T\u014dhoku earthquake, Suez canal blockage and Hormuz fuel crisis rippling through stripped-out supply chains are modularity failures. Policy reversal each electoral cycle is a stability failure that selects against long-horizon investment. The pandemic plans and stockpiles accumulated after SARS in 2003 and the 2009 pandemic, then largely lost before 2020, are an inheritance fidelity failure.</p>\n<p class=\"wp-block-paragraph\">Importantly, evolvability is value-neutral, given that a cancer can be highly evolvable inside the body. So, capacity for evolvability must be paired with a fitness function worth sustaining, and what fast cultural evolution actually selects for is rarely wellbeing or planetary sustainability, but profit, votes, engagement or military advantage. Also, evolvability sits at an interior optimum. If there is too much variation then inheritance is destroyed, if too much stability then maladaptation can become entrenched. As an example, German scientific forestry optimised what it could count and discovered, rotations later, the ecological relationships it had discarded.</p>\n<p class=\"wp-block-paragraph\"><strong>Outlaws, and the lesson from cancer</strong></p>\n<p class=\"wp-block-paragraph\">Defector/outlaw suppression matters most, not only is suppressing outlaws constitutive of evolvability (multiplication of rogue genes that degrade organism fitness, across generations, is a biological example of 'outlaws'), but outlaw activity can undermine the other necessary criteria. At every major evolutionary transition, from cells to organisms to societies, the higher-level unit exists only because it continually constrains, regulates, or suppresses, lower-level strategies that benefit themselves at the expense of the whole.</p>\n<p class=\"wp-block-paragraph\">That is a decisive argument against purely non-interventionist, market-only solutions to large scale risk.</p>\n<p class=\"wp-block-paragraph\">An outlaw need not be conscious or act illegally, since firms externalising costs, states leaving treaties, platforms amplifying misinformation, or farmers applying excess nitrogen fertilizer, may be responding to legitimate incentives.</p>\n<p class=\"wp-block-paragraph\">Increasingly, though, outlaws attack the suppressors. At the height of the US opioid epidemic, wholesalers did not evade the DEA, instead they disabled it through lobbying, a revolving-door attorney and a 2016 statute. All this is the governance analogue of a tumour co-opting the immune cells sent to kill it.</p>\n<p class=\"wp-block-paragraph\">Cancer's evolutionary biology supplies four transferable principles against this kind of defection, namely:</p>\n<ul class=\"wp-block-list\">\n<li>Redundant, multi-layer suppression (single point solutions are insufficient)</li>\n<li>Calibrating rather than maximising enforcement, since maximal enforcement selects for resistant evasion, just as chemotherapy can select for resistant tumours</li>\n<li>Protecting the suppressors from capture</li>\n<li>Suppressing early, before risk generating actors become too big or organised to constrain</li>\n</ul>\n<p class=\"wp-block-paragraph\"><strong>Global overshoot, and walking some of it back</strong></p>\n<p class=\"wp-block-paragraph\">Unconstrained market dynamics constitute a selection environment with a fitness function of short-run return measured in profits. Under it humanity has transgressed several planetary boundaries, oversupplied what pays (extraction, coupling, engagement, throughput) and undersupplied what doesn't (slack, buffers, prevention, institutional memory). No institution was mandated to preserve resilience, so resilience was competed away, then we struck Covid-19, the Russian Invasion of Ukraine, the US assaults on Iran, and potentially worse global shocks to come.</p>\n<p class=\"wp-block-paragraph\">Reducing catastrophic risk means walking some of this back. We need to incentivise retreat from planetary boundaries, rebuild buffers, accepting that some efficiency was borrowed against the future. The evolutionary framing doesn't make that easy. It explains why it hasn't happened on its own and won't at the global level.</p>\n<p class=\"wp-block-paragraph\">Our <a href=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/260831-evolvability-metacrisis-v8.pdf\">pre-print</a> lays all this out, describing the current dynamics, explaining why they persist, and offering a pathway forward.</p>\n<p class=\"wp-block-paragraph\"><strong>New Zealand in the present</strong></p>\n<p class=\"wp-block-paragraph\">My book club is currently reading the Helen Clark Foundation's 2026 release \"<a href=\"https://www.helenclark.foundation/facing-up-to-our-future\">Facing Up to Our Future</a>\", which consists of twenty short policy chapters on the long-run problems no single government seems able to solve. What strikes me is how much of our pre-print's machinery is in there, independently arrived at across multiple fields of policy and economy, but never framed in evolutionary terms such that the big picture dynamics are clear.</p>\n<p class=\"wp-block-paragraph\">The book's framing is often a diagnosis of the metacrisis, speaking of political regimes structurally incapable of addressing decades-long problems, which is a claim about degraded adaptive capacity rather than about any one policy. The opening economic chapters then supply the conditions one by one.</p>\n<ul class=\"wp-block-list\">\n<li><em>Variation.</em> Competition policy and industrial policy are, in these terms, about the supply of candidate solutions. New Zealand's supermarket duopoly is a monoculture, with two dominant variants there is little for selection to work on, evolvability is throttled at the source, lock-in takes hold to the detriment of the higher-level system, namely New Zealand society.</li>\n<li><em>Modularity.</em> Niche construction (in our paper's sense) has created entrenchment in the energy market, incumbents whose infrastructure and integration and coalitions favour their own continuation and cannot be teased apart one by one to change, limiting what the system can become.</li>\n<li><em>Stability of the selective environment.</em> The book's recurring complaint about inconsistent, reversible policy is a stability failure. Investment flows to long-horizon adaptative solutions only where this action is predictably rewarded over time.</li>\n<li><em>Defector suppression.</em> New Zealand's regulatory environment is full of tools that lack bite, such as a passive Commerce Commission, captured regulation and high barriers to market entry. This is suppression architecture that has stopped suppressing what disrupts the cooperative whole, permits externalities, allows fragilities to expand, and fails to preserve modularity, or variation.</li>\n</ul>\n<p class=\"wp-block-paragraph\">Industrial policy to mitigate the contribution to global risk made across various industries, as well as investment in appropriate infrastructure, skills and training can shape evolvability. But only if paired with a meaningful fitness function, ie incentives and punishments tied to risk reduction and wellbeing, otherwise we simply accelerate adaptation in whatever direction the market was already heading.</p>\n<p class=\"wp-block-paragraph\">Unfortunately, market solutions alone will never overcome the outlaw/defector problem, because the market is where defection is rewarded. Good industrial policy grounded in evolutionary theory and tied to global risk reduction is the alternative, and is necessary otherwise, in the end, we all lose.</p>\n<p class=\"wp-block-paragraph\">The point is not that policy accounts need our pre-print. It is that the relevant dynamics are already and everywhere operating. There is some understanding of them across standard systems and economic thinking. But the evolutionary dynamics need to be understood better, deeper and more broadly, because they are foundational rather than incidental to reducing global systemic and catastrophic risk.</p>\n<p class=\"wp-block-paragraph\"><strong>Credit to others, and our contribution</strong></p>\n<p class=\"wp-block-paragraph\">None of this work comes out of thin air. <a href=\"https://www.cambridge.org/core/journals/global-sustainability/article/systemic-contributions-to-global-catastrophic-risk/C9DCBFE8C24F8CA1505F61DC61E9822B\">Arnscheidt and colleagues</a> have named risk-creating actors as a primary driver of global catastrophic risk. <a href=\"https://link.springer.com/article/10.1007/s13753-025-00636-3\">Liu and Renn</a> call for biomimetic designs \"tested by natural selection\". <a href=\"https://www.cambridge.org/core/journals/global-sustainability/article/both-adaptive-and-transformative-capacities-are-necessary-to-navigate-global-polycrisis/0FB17EA1F8BD5EF4AE6F15EBB0390267\">S\u00f8gaard J\u00f8rgensen</a>'s group catalogues Anthropocene traps and now speaks of a \"co-evolutionary struggle\" between resilience capacity and the polycrisis. <a href=\"https://www.tandfonline.com/doi/full/10.1080/02604027.2025.2572007\">H\u00e4m\u00e4l\u00e4inen's</a> cybernetic \"complexity gap\" is a functional analogue of evolvability. <a href=\"https://pubmed.ncbi.nlm.nih.gov/37952628/\">Waring and colleagues</a> treat the Anthropocene as an evolutionary ratchet. There are many other examples.</p>\n<p class=\"wp-block-paragraph\">These are real advances, mostly arrived at inductively and in fragments. What no one has done is articulate the complete framing from first principles, ie evolution as the substrate-neutral generative process, evolvability as an organising concept, and tied these to a formal definition of the metacrisis in these terms, with suppression as constitutive rather than optional. Several of these frameworks omit outlaw suppression entirely. Synthesising all this is what our pre-print attempts.</p>\n<p class=\"wp-block-paragraph\"><strong>Our deliberate overreach</strong></p>\n<p class=\"wp-block-paragraph\">Our paper is intentionally provocative and probably pushes the explanation a little further than is warranted. Not all cultural change follows Darwinian dynamics tightly, and institutions, unlike tumours, can foresee consequences and redesign themselves. Every concept we import from biology is because of the shared selective structure, not the disanalogous features.</p>\n<p class=\"wp-block-paragraph\">But this extended framework supplies machinery for the loose cases too, namely niche construction, transmission biases, developmental plasticity, multiple inheritance channels, and so on. Our aim was to cast the net wide, to show there is a broader way of thinking about global systemic and catastrophic risk that supplies coherence and ultimate explanation, providing the <em>why</em> to supplement the <em>what</em>.</p>\n<p class=\"wp-block-paragraph\"><strong>Towards action</strong></p>\n<p class=\"wp-block-paragraph\">Our approach would shift the object of global risk governance. We don't specify precise solutions, but instead recommend engineering, nudging and continually readjusting the evolutionary factors so that adaptive solutions to specified fitness problems, evolve naturally:</p>\n<ul class=\"wp-block-list\">\n<li><strong>Shape the fitness function</strong>: make biosphere persistence and human wellbeing what actually wins and stop feeding risk-creating actors with subsidies and support.</li>\n<li><strong>Stabilise the selective environment:</strong> with wise durable policy contracts insulated from electoral cycles.</li>\n<li><strong>Curate variation and modularity:</strong> mandated buffers, supply-chain and planetary-boundary examiners embedded in firms on the bank-examiner model, modular refuges, rural revitalization, or transition towns that preserve capability through catastrophe.</li>\n<li><strong>Protect transmission of adaptations:</strong> ring-fenced prevention budgets (eg pandemic PPE), institutional memory, error-correction of the information commons.</li>\n<li>Above all, <strong>build and protect multi-layer suppression</strong>: early, calibrated, capture-resistant control of defectors that win locally at the expense of humanity.</li>\n<li><strong>Act regionally and at bloc level</strong>, where cooperation is more evolvable than at global scale.</li>\n</ul>\n<p class=\"wp-block-paragraph\">Because each evolvability condition is observable, the five can form a dashboard tracking the direction of travel of global risk-governance capacity, and the framework makes falsifiable predictions, for example interventions that robustly alter the selection environment should outperform those that just alter actors' knowledge or goals.</p>\n<p class=\"wp-block-paragraph\"><strong>How this fits alongside existing work</strong></p>\n<p class=\"wp-block-paragraph\">Our work is integrative and complementary, not competitive. The <a href=\"https://cascadeinstitute.org/\">Cascade Institute's</a> <a href=\"https://adaptresearchwriting.com/2025/11/11/mapping-pathways-through-the-polycrisis-the-cascade-institutes-new-model-for-navigating-global-systemic-risk/\">Polycrisis CORE model</a> maps the global system attractor basins. The evolutionary account explains the forces pulling toward them and which levers change the gradient. The <a href=\"https://www.asranetwork.org/insights/facing-global-risks-with-honest-hope-report\">Accelerator for Systemic Risk Assessment</a> has built assessment capacity, and evolvability supplies what to assess and why. Oliver and colleagues' systemic-risk \"<a href=\"https://www.cambridge.org/core/journals/global-sustainability/article/appraising-cascading-systemic-risks-watchpoints-and-interventions-methodological-reflections/672D6A4430F1BBADF800464C9DA45C20\">watchpoints</a>\" are a step toward a dashboard. Richardson et al.'s <a href=\"https://www.cambridge.org/core/journals/global-sustainability/article/principles-for-just-and-effective-systemic-risk-governance/15DAE61A09BE55307C0484F362C38F08\">normative principles</a> in the context of global risk are where the fitness function gets its ethics. Complexity science explains how systems become fragile, and the evolutionary account explains why fragile architectures keep being selected despite full awareness.</p>\n<p class=\"wp-block-paragraph\">The risk community has spent enormous effort cataloguing what is going wrong. An evolutionary reading names, monitors and builds the conditions that determine what can be redesigned to go right. The invisible hand has been running on our institutions all along. The task is to make it visible, and to direct it.</p>\n<p class=\"wp-block-paragraph\">Read our new preprint<a href=\"https://adaptresearchwriting.com/wp-content/uploads/2026/09/260831-evolvability-metacrisis-v8.pdf\"> here</a> (currently under peer-review)</p>","doi":"https://doi.org/10.59350/kjv4n-j7x81","guid":"http://adaptresearchwriting.com/?p=7916","image":"https://adaptresearchwriting.com/wp-content/uploads/2026/09/image.png?w=936","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1788998400,"rid":"eyq54-0w016","summary":"Introducing our new preprint on evolutionary governance for systemic and global catastrophic risk By Matt Boyd TLDR/Summary Two intellectual strands twisted together This post has been a long time coming. In 2007 I wrote a Masters thesis in philosophy, on cultural evolution and the information environment we have created.","title":"The Metacrisis is a Degradation of Evolvability: Why Global Risk Needs Evolutionary Explanation and Governance","updated_at":1789025406,"url":"https://adaptresearchwriting.com/2026/09/10/the-metacrisis-is-a-degradation-of-evolvability-why-global-risk-needs-evolutionary-explanation-and-governance/","version":"v1"},{"authors":[{"contributor_roles":[],"name":"@edent"}],"blog":{"authors":null,"community_id":"61ce553a-bafd-4aba-a952-d3bab5e85bcc","created":1788652800,"current_feed_url":null,"description":"Regular nonsense about tech and its effects \ud83d\ude43","doi":"https://doi.org/10.59350/shkspr","favicon":"https://rogue-scholar.org/api/communities/61ce553a-bafd-4aba-a952-d3bab5e85bcc/logo","feed_format":"application/atom+xml","feed_url":"https://shkspr.mobi/blog/feed/atom/?cat=-1982&HTTP_REFERER=DOI","filter":null,"generator":"WordPress","home_page_url":"https://shkspr.mobi/blog","issn":"2753-1570","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"shkspr","status":"active","subfield":"1712","title":"Terence Eden's Blog","updated":1788867291,"use_api":false},"blog_name":"Terence Eden's Blog","blog_slug":"shkspr","content_html":"<html><head></head><body><img src=\"https://shkspr.mobi/blog/wp-content/uploads/2020/08/Invisible-Agents.jpg\" alt=\"\" width=\"358\" height=\"550\" class=\"alignleft size-full wp-image-36319\">\n\n<blockquote><p>It would be easy for the modern reader to conclude that women had no place in the world of early modern espionage, with a few seventeenth-century women spies identified and then relegated to the footnotes of history. If even the espionage carried out by Susan Hyde, sister of Edward Hyde, Earl of Clarendon, during the turbulent decades of civil strife in Britain can escape the historiographer's gaze, then how many more like her lurk in the archives?</p>\n\n<p>Nadine Akkerman's search for an answer to this question has led to the writing of Invisible Agents, the very first study to analyse the role of early modern women spies, demonstrating that the allegedly-male world of the spy was more than merely infiltrated by women. This compelling and ground-breaking contribution to the history of espionage details a series of case studies in which women \u2014 from playwright to postmistress, from lady-in-waiting to laundry woman \u2014 acted as spies, sourcing and passing on confidential information on account of political and religious convictions or to obtain money or power.</p></blockquote>\n\n<p>It's rare that I abandon a book - but I gave up half way through this and skimmed to the end. In theory, this should be an exciting book - Spies! Sex! State Secrets!  But it quickly becomes little more than a list of names, dates, and locations.</p>\n\n<p>There's a tantalising glimpse into the tradecraft of spies. An all-too-brief chapter on codes, ciphers, physical deceptions, and invisible inks.  But it doesn't go into any depth.  I'd have liked to have learned about how these evolved, and a bit more about the cat-and-mouse game between spy and spycatcher.</p>\n\n<p>The book is expertly researched - and draws upon multiple sources. But much of the quoted material is <em>physically</em> hard to read. Some abbreviations have been expanded with <em>italics</em> part way through words - but original archaic spelling is preserved. Deletions and insertions are also marked. Which leads to quotes like this:</p>\n\n<blockquote><p>he [Charles Lyttelton] [\u2026] had several ^tymes^ mett w<i>i</i>th the sa<i>i</i>d Maior [Henry] Norwood [\u2026] and p<i>ar</i>ticularly 4 or 5 tymes at the <del>Earl</del> ^Lady^ Newports ^in Lincolns Inn ffeilds^, where there haue been in her Company as he remembers (besides those of her family) one Mr Beuerly &amp; one Mr Browne a kinsman of <i>th</i>e Lo<i>rd</i> Harberts ^&amp; some others whom he remembers not^.</p></blockquote>\n\n<p>The mix of italics and regular text is just unpleasant to read.</p>\n\n<p>It is great to see that women were capable of committing treason, and it is interesting to see how they fared and the punishment they received. But the vast cast of characters is unweildly, and the timeline is muddled unless you're already an expert in the era.</p>\n\n<p>I'm sure it's a fine academic work - but it was too much of a slog for this casual reader.</p>\n</body></html>","doi":"https://doi.org/10.59350/sm876-7gs33","guid":"https://shkspr.mobi/blog/?p=36316","image":"https://shkspr.mobi/blog/wp-content/uploads/2020/08/Invisible-Agents.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1598054400,"rid":"dge5e-3cr20","summary":"It's rare that I abandon a book - but I gave up half way through this and skimmed to the end. In theory, this should be an exciting book - Spies! Sex! State Secrets! But it quickly becomes little more than a list of names, dates, and locations. There's a tantalising glimpse into the tradecraft of spies. An all-too-brief chapter on codes, ciphers, physical deceptions, and invisible inks. But it doesn't go into any depth.","tags":["/etc/","Book Review"],"title":"Book Review: Invisible Agents: Women and Espionage in Seventeenth-Century Britain","updated_at":1789023249,"url":"https://shkspr.mobi/blog/2020/08/book-review-invisible-agents-women-and-espionage-in-seventeenth-century-britain/","version":"v1"}],"out_of":55754,"page":1,"per_page":10,"total-results":55754}
