{"found":53991,"hits":[{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

\"\"

\n

\n

Metadata are an essential way of enabling the discoverability and impact of scholarly resources such as (research) data and associated objects. It must adhere to a precisely described schema describing its properties,[1] and such a conformant metadata record is an mandatory component of a (research) data repository. Access to the record is by resolving the DOI (Digital object identifier) for any repository item, as for example:

\n

https://data.datacite.org/application/vnd.datacite.datacite+xml/10.14469/hpc/15994
\nhttps://data.datacite.org/application/vnd.datacite.datacite+xml/10.5281/zenodo.20657236

\n

where 10.14469/hpc/15994 and 10.5281/zenodo.20657236 are the (in this example two) DOIs registered for the same specific repository dataset. Two different repositories are shown here, because the metadata is still mostly captured using the user-interface of the relevant repository, and the richness or completeness of the metadata can differ greatly between repositories. Whilst the registered metadata record has some mandatory components, many more are optional and it is often the case that these optional components are either not supported via a visual interface by the repository, or the user choses to omit them (a complete or “rich” metadata entry could be quite tedious for a human). This aspect of human time and their attention span can often result in sparse metadata records.

\n

In some cases, the metadata is captured using a programmed workflow and then registered using the equivalent of a command line interface (API) which requires no user involvement or interactive user responses[2] and which tends to produce more systematically complete metadata records. Unfortunately, I think this mode of metadata provision must be relatively rare – although to be fair the metadata record itself does not carry details of the mechanism by which the metadata was populated. The two examples above were prepared using exactly the same API, and they largely differ in what elements of the total metadata schema each of the two repositories above actually support, rather than what a human had the patience for.

\n

So it is a welcome development that DataCite have recently made a Dashboard available that allows at a glance an inspection of either a specific metadata record or a collection of such records to be made. The start point is https://metadata.datacite.org/\u00a0and here you can filter the record by\u00a0a) the repository, further filtered by\u00a0b) registration year and c) resource type (Figure 1).\u00a0Thus:
\n\"\"

\n

Figure 1. The DataCite Metadata Dashboard,\u00a0showing a specified repository using the query
\nhttps://metadata.datacite.org/urks.helix?registrationYear=2026&resourceType=dataset

\n

This dashboard now allows you to easily compare the two metadata records noted above, with the help of an additional DOI query filter which can be used to further narrow it down to a single dataset (queries 1 and 2).

\n
    \n
  1. https://metadata.datacite.org/urks?registrationYear=2026&query=id:10.14469/HPC/15994
    2. \n
  2. https://metadata.datacite.org/cern.zenodo?registrationYear=2026&query=id:10.5281/zenodo.20657236
    3. \n
\n

A prominent difference between these queries is the Subjects metadata, with for example the subjectScheme\u00a0100% complete for example 1 (Figure 2) and 0% complete for example 2 (Figure 3).
\n\"\"

\n

Figure 2. The Subjects panel of the DataCite Metadata Dashboard,\u00a0for\u00a0DOI: 10.14469/HPC/15994

\n

\"\"

\n

Figure 3. The Subjects panel of the DataCite Metadata Dashboard,\u00a0for\u00a0DOI: 10.5281/zenodo.20657236

\n

Using the query filter to explore a range of other searches.

\n

Searches 3 and 4 specify an individual depositor by their ORCID identifier and 2026 as a publication year, for two different repositories.

\n
    \n
  1. https://metadata.datacite.org/bl.imperial?registrationYear=2026&query=contributors.nameIdentifiers.nameIdentifier:0000-0002-8635-8390+OR+creators.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390
    2. \n
  2. https://metadata.datacite.org/cern.zenodo?registrationYear=2026&query=contributors.nameIdentifiers.nameIdentifier:0000-0002-8635-8390+OR+creators.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390
    3. \n
\n

The Subjects panels\u00a0are shown in Figures 4 and 5. In these examples, both sets of depositions are made using the same automatic command line API[2] so human error or their lack of attention is not the cause of the differences.
\n\"\"

\n

Figure 4. The Subjects panel of the DataCite Metadata Dashboard for the bl.imperial repository for query 3.

\n

\"\"

\n

Figure 5. The Subjects panel of the DataCite Metadata Dashboard for the cern.zenodo repository for query 4.

\n

Search 5 shows more direct use of a Subject filter (Figure 6) and use of this filter ensures that again the subjects metadata panel is well populated.

\n
    \n
  1. https://metadata.datacite.org/urks?query=(media.media_type:application/zip+OR+media.media_type:chemical/x-mnova)+AND+
    \n(subjects.subjectScheme:*NMR_Nucleus)+AND+(subjects.subject:13C)+AND+
    \n(titles.title:*pyrazol*+OR+descriptions.description:*pyrazol*)
    2. \n
\n

\"\"

\n

Figure 6. The Subjects panel of the DataCite Metadata Dashboard for the urks repository for query 5.

\n

Query 6 (Figure 7) identifies datasets that have a directly associated journal article, showing the population of the “high impact” relatedIdentifier property.

\n
    \n
  1. https://metadata.datacite.org/urks?query=(types.resourceTypeGeneral:Dataset+OR+types.resourceTypeGeneral:Collection)+AND+
    \n(contributors.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390+OR+
    \ncreators.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390)+AND+(relatedIdentifiers.relatedIdentifierType:DOI+AND+
    \nrelatedIdentifiers.resourceTypeGeneral:JournalArticle+AND+relatedIdentifiers.relatedIdentifier:*)
    2. \n
\n

\"\"

\n

Figure 7. The RelatedIdentifiers\u00a0panel of the DataCite Metadata Dashboard for the urks repository for query 6.

\n

Query 7 showing again a very well populated Subjects panel (due of course to the filter applied below) with 100% occupancy of the subjectScheme.

\n
    \n
  1. https://metadata.datacite.org/urks?query=(media.media_type:chemical/x-gaussian-log+OR+
    \nmedia.media_type:chemical/x-gaussian-checkpoint)+AND+
    \n(titles.title:*Endo*+OR+
    \ndescriptions.description:*Endo*+OR+titles.title:*Exo*+OR+descriptions.description:*Exo*)+AND+
    \n(subjects.subjectScheme:*KIE*)+AND+
    \nsubjects.subject:1H/2H
    2. \n
\n

\"\"

\n

Figure 8. The Subjects\u00a0panel of the DataCite Metadata Dashboard for the urks repository for query 7.

\n

Query 8 shows how well populated the Subjects panel is for a whole range of users (excluding one subject-loving suspect!). It would be interesting to see if this population (albeit only 4.7%) was achieved by manual entry or by automatic API calls.

\n
    \n
  1. https://metadata.datacite.org/cern.zenodo?registrationYear=2026&query=+NOT+
    \n(contributors.nameIdentifiers.nameIdentifier:0000-0002-8635-8390+OR+
    \ncreators.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390)
    2. \n
\n

\"\"

\n

Figure 9. The Subjects panel of the DataCite Metadata Dashboard for the cern.zenodo repository for query 8.

\n

Example 9 uses the InvenioRDM repository system whilst 10 uses a bespoke repository created in 2016 with metadata richness in mind.[2] Both these examples were crafted “by hand” rather than using an API tool and are limited only by the user interfaces of either repository.

\n
    \n
  1. https://metadata.datacite.org/urks.helix?registrationYear=2026&query=id:10.82186/xjxch-zzb72
    2. \n
  2. https://metadata.datacite.org/bl.imperial?registrationYear=2024&query=id:10.14469/hpc/14835
    3. \n
\n

\"\"

\n

Figure 10. The Subjects panel of the DataCite Metadata Dashboard for query 9.
\n\"\"

\n

Figure 11. The Subjects panel of the DataCite Metadata Dashboard for query 10.

\n

Conclusions.

\n

It is to be hoped that analysis of research data metadata records using the DataCite tool will rapidly lead to a greater and richer population of these records. Wherever possible, these records should be populated using automated methods which do not rely on the patience of a human. My own candidate for increased population is the Subjects field, which can be readily automated and the presence of which allows finely tuned searches of the DataCite metadata store to be made.

\n
\n

DOI: 10.59350/ams3m-m3t92

\n

References

\n
  1. DataCite Metadata Working Group., \"DataCite Metadata Schema Documentation for the Publication and Citation of Research Data and Other Research Outputs v4.7\", DataCite, 2026. https://doi.org/10.14454/qdd3-ps68\n\n
    2. \n
  2. C. Cave-Ayland, M. Bearpark, C. Romain, and H. Rzepa, \"CHAMP is a HPC Access and Metadata Portal\", Journal of Open Source Software, vol. 7, pp. 3824, 2022. https://doi.org/10.21105/joss.03824\n\n
    3. \n
\n\n
","doi":"https://doi.org/10.59350/ams3m-m3t92","guid":"https://www.ch.ic.ac.uk/rzepa/blog/?p=31548","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1781654400,"reference":[{"id":"https://doi.org/10.14454/qdd3-ps68","unstructured":"DataCite Metadata Working Group, Liffers, M., Robertson, W., Ashton, J., Bernal, I., Devaraju, A., Elger, K., Habermann, T., Harrison, M., Kraus, R., Mathews, I., Medina-Smith, A., Moore, A. V., Padfield, J., Raugh, A., Shallcross, M., Strecker, D., Tarocco, N., Tvrdy, P., \u2026 El-Gebali, S. (2026). DataCite Metadata Schema Documentation for the Publication and Citation of Research Data and Other Research Outputs v4.7."},{"id":"https://doi.org/10.21105/joss.03824","unstructured":"Cave-Ayland, C., Bearpark, M., Romain, C., & Rzepa, H. (2022). CHAMP is a HPC Access and Metadata Portal. Journal of Open Source Software, 7(70), 3824."}],"rid":"se4bz-dxb91","summary":"Metadata are an essential way of enabling the discoverability and impact of scholarly resources such as (research) data and associated objects. It must adhere to a precisely described schema describing its properties,[1] and such a conformant metadata record is an mandatory component of a (research) data repository.","tags":["Chemical IT"],"title":"Evaluating metadata quality and completeness for research data using the new DataCite Tool.","updated_at":1787767377,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=31548","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemistry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

In 1988, Wilke[1] reported molecule 1

\n

\"A

A 24-annulene. Click for 3D.


\nIt was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned! The reason is that a 24- annulene belongs formally to a class of molecule with 4n (n=6) \u03c0-electrons, and which makes it antiaromatic according to the (extended) H\u00fcckel rule. This is a select class of molecule, of which the first two members are cyclobutadiene and cyclo-octatetraene. The first of these is exceptionally reactive and unstable and is the archetypal anti-aromatic molecule. The second is not actually unstable, but it is reactive and conventional wisdom has it that it avoids the undesirable antiaromaticity by adopting a highly non-planar tub shape and hence instead adopts reactive non-aromaticity. Both these examples have localized double bonds, a great contrast with the molecule which sandwiches them, cyclo-hexatriene (i.e. benzene). The reason for the resurgent interest is that a number of crystalline, apparently stable, antiaromatic molecules have recently been discovered, and ostensibly, molecule 1 belongs to this select class!

\n

\n

So is 1 actually anti-aromatic? Let us look at some of the ways in which this might be estimated.

\n
    \n
  1. One can inspect the bond lengths, measured from X-ray analysis. The longest is 1.463\u00c5, labelled a above, and it corresponds to a single bond (value from the crystal structure).
    2. \n
  2. If the molecule had a bond alternating structure, the adjacent bonds would be expected to be much shorter, in the region of 1.32\u00c5. In fact, they are rather longer, at 1.37\u00c5. Indeed, in the cycloheptatriene part of the molecule, the alternation is much less than one might expect of an anti-aromatic molecule, oscillating between 1.37 and 1.43\u00c5.
    3. \n
  3. One can also inspect aromaticity via a variety of magnetic indices. The simplest of these is the NICS probe. Placed at a ring centroid, a negative value of this index of around -10ppm indicates aromaticity (this is the value for benzene), whilst a strongly positive value (of up to +20 ppm) indicates anti-aromaticity. Molecule 1 has two potential centroids, one placed at the absolute centre of the system, and one placed at the centroid of the ~6-membered ring completed using bond b (in reality, the centroids were computed from the positions of ring critical points obtained from an AIM analysis). The NICS values at these two positions are both ~-4.4 ppm (See DOI: 10042/to-2156 for details of the calculation). These values does not indicate antiaromaticity! They could even be described as mildly aromatic. So what is going on?
    4. \n
  4. What about the chemical shifts of the other protons? All the hydrogens attached to sp2 carbons are predicted to resonate at around 6.7ppm (unfortunately Wilke does not report the experimental spectrum), which is typical of an aromatic system (anti-aromatic systems have high upfield shifts for such protons, at around 2ppm or even -2 ppm, see [2] for examples). The two protons of the methylene bridges are also quite different; 2.9 and 0.8 ppm. The latter is the proton endo to the cycloheptatrienyl ring, and is typical of a proton placed in the anisotropic magnetic shielding region of e.g. benzene. Thus the cycloheptatrienyl ring is itself behaving as if it were aromatic, whereas the overarching 24-annulene ring is certainly not behaving as if it were antiaromatic.
    5. \n
\n

One possible explanation involves a concept known as homoaromaticity. The bond marked as b could be regarded as completing the 6\u03c0-electron local aromaticity of that ring (it would be formally considered as a 1\u03c0-electron bond, with no underlying \u03c3-framework, see [3] for discussion). So has the case been made for 1 being the first clear cut example of a neutral homoaromatic molecule, containing no less than four rings exhibiting this type of aromaticity?

\n

There is one further concept that can be introduced. Clar (for a discussion, see DOI: [4] proposed that benzenoid 6\u03c0-electron local aromaticity is preferred to less local or more extended cyclic conjugations, if the two compete. Many examples in a type of compound known as polybenzenoid aromatics are known where the most favourable resonance structure is that which maximises the number of Clar rings. More recently, quite a few ostensibly antiaromatic molecules have been shown to attenuate this unfavourable effect by forming instead groups of aromatic Clar islands containing delocalized benzene like rings (discussion of this point can be found at [5]. In molecule 1, we could have a new phenomenon; a homoClar ring, formed to avoid antiaromaticity.

\n

For further discussion, see the comment posted to Steve Bachrach’s blog.

\n

References

\n
  1. G. Wilke, \"Contributions to Organo\u2010Nickel Chemistry\", Angewandte Chemie International Edition in English, vol. 27, pp. 185-206, 1988. https://doi.org/10.1002/anie.198801851\n\n
    2. \n
  2. H.S. Rzepa, \"Lemniscular Hexaphyrins as Examples of Aromatic and Antiaromatic Double-Twist M\u00f6bius Molecules\", Organic Letters, vol. 10, pp. 949-952, 2008. https://doi.org/10.1021/ol703129z\n\n
    3. \n
  3. https://doi.org/\n\n
    4. \n
  4. A.T. Balaban, P.V.R. Schleyer, and H.S. Rzepa, \"Crocker, Not Armit and Robinson, Begat the Six Aromatic Electrons\", Chemical Reviews, vol. 105, pp. 3436-3447, 2005. https://doi.org/10.1021/cr0300946\n\n
    5. \n
  5. C.S.M. Allan, and H.S. Rzepa, \"A computational investigation of the structure of polythiocyanogen\", Dalton Trans., pp. 6925-6932, 2008. https://doi.org/10.1039/b810147g\n\n
    6. \n
\n\n
","doi":"https://doi.org/10.59350/wnt2x-q6k53","guid":"http://www.ch.ic.ac.uk/rzepa/blog/?p=275","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2009/04/gaytab.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1239580800,"reference":[{"id":"https://doi.org/10.1002/anie.198801851","unstructured":"Wilke, G. (1988). Contributions to Organo\u2010Nickel Chemistry. Angewandte Chemie International Edition in English, 27(1), 185\u2013206."},{"id":"https://doi.org/10.1021/ol703129z","unstructured":"Rzepa, H. S. (2008). Lemniscular Hexaphyrins as Examples of Aromatic and Antiaromatic Double-Twist M\u00f6bius Molecules. Organic Letters, 10(5), 949\u2013952."},{"id":"https://doi.org/"},{"id":"https://doi.org/10.1021/cr0300946","unstructured":"Balaban, A. T., Schleyer, P. v R., & Rzepa, H. S. (2005). Crocker, Not Armit and Robinson, Begat the Six Aromatic Electrons. Chemical Reviews, 105(10), 3436\u20133447."},{"id":"https://doi.org/10.1039/b810147g","unstructured":"Allan, C. S. M., & Rzepa, H. S. (2008). A computational investigation of the structure of polythiocyanogen. Dalton Trans., (48), 6925\u20136932."}],"rid":"s8829-gfh38","summary":"In 1988, Wilke[1] reported molecule 1 A 24-annulene. Click for 3D. It was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned!","tags":["Interesting Chemistry","Anti-aromatic Systems","Chemical Shifts","Clar Islands","Steve Bachrach"],"title":"A molecule with an identity crisis: Aromatic or anti-aromatic?","updated_at":1787767330,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=275","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

In a previous post, I talked about a library of reaction pathway intrinsic reaction coordinates (IRCs) containing 115 examples of organic and organometallic reactions. Now (thanks Dean!) I have been alerted to a brand new databank of dynamics trajectories (DDT), with the focus on those reactions taught in undergraduate organic chemistry courses, some of which are shown below.

\n

\n

\"\"

\n

Each example takes the form of two movie animations, one showing the classical IRC path and the other the “major trajectory” (DT) resulting from a molecular dynamics calculation. The latter representation incorporates molecular vibrations into the picture, showing how they evolve from reactants into a reaction product over a time period. Dynamics are a more realistic picture of how a molecule actually reacts. Any given trajectory can follow its own path, but the most common path for it to take is indeed that defined by the IRC and here you can compare the two approaches. What is interesting of course are those examples where the IRC and DT differ, with perhaps the latter not necessarily following the minimum energy path charted by the former.\u2021 Even more fascinating are those non-classical reactions where a given IRC path, as defined by a single unique transition state at the top of the energy barrier, can nonetheless result in two or more different reaction outcomes. [1] See my analysis.

\n

This databank is still young, with eight reactions at the time this blog was written. Suggestions for new reactions are invited, and I do hope it grows rapidly. Also I look forward to a section describing the technicalities of how the DT are computed and what sorts of resources are required to do this routinely (an article describing the databank is being prepared). In particular, how do the computer time resources needed for IRC and DT compare? It is good indeed to see this dynamic picture entering into the undergraduate taught curriculum.

\n
\n

\u2021For an example of a differing outcome, see here.

\n

References

\n
  1. X.S. Bogle, and D.A. Singleton, \"Dynamic Origin of the Stereoselectivity of a Nucleophilic Substitution Reaction\", Organic Letters, vol. 14, pp. 2528-2531, 2012. https://doi.org/10.1021/ol300817a\n\n
    2. \n
\n\n
","doi":"https://doi.org/10.59350/aa792-4x456","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22259","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/04/MD-1024x340.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1587513600,"reference":[{"id":"https://doi.org/10.1021/ol300817a","unstructured":"Bogle, X. S., & Singleton, D. A. (2012). Dynamic Origin of the Stereoselectivity of a Nucleophilic Substitution Reaction. Organic Letters, 14(10), 2528\u20132531."}],"rid":"h4tp1-58f06","summary":"In a previous post, I talked about a library of reaction pathway intrinsic reaction coordinates (IRCs) containing 115 examples of organic and organometallic reactions.","tags":["Reaction Mechanism"],"title":"A databank of molecular dynamics reaction trajectories (DDT) focused on undergraduate teaching.","updated_at":1787767327,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22259","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

In 2013, I created an iTunesU library of 115\u00a0mechanistic types in organic and organometallic chemistry, illustrated using video animations of the intrinsic reaction coordinate (IRC) computed using a high level quantum mechanical procedure. Many of those examples first derived from posts here. That collection\u00a0 is still available and is viewable \u00a0in the iTunesU app on an iPhone or an iPad. The realisation struck me now\u2021 that one of the types not described in that library was Michael-type 1,4-nucleophilic addition to an activated alkene, as described at\u00a0Wikipedia. So here is that addition.

\n

\n

\"\"

\n

The base used will be NH3 and the activating groups R will all be formyl. The DFT computational method will be\u00a0\u03c9B97XD/Def2-TZVPP/SCRF=water and the FAIR data will collect at DOI: 10.14469/hpc/7027

\n

The full reaction mechanism can be represented as below \"\"

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Species\u0394\u0394G298, kcal/molFAIR Data DOI
Reactant0.07028
TS16.77029
Int1-7.77036
TS216.37031
Int2-8.77033
Int3-8.77035
TS39.67030
Product-13.27034
\n

The rate-limiting step of C-C bond formation is coupled with almost synchronous protonation on the remote oxygen. It is driven by reducing the dipole moment of the zwitterion Int1, as shown below.\"\"

\n

Attempts to find an analogous route with carbon protonation leading directly to the product did not succeed.

\n

\"\"

\n

By varying parameters such as the nature of the R groups or the base, one might be able to control the choreography of the C-C bond formation relative to the accompanying proton transfer to oxygen in TS2 (in the manner that was possible for e.g. peracid epoxidation[1]). These changes could then be subjected to e.g. the measurement of kinetic isotope effects and comparison with values calculated from the computational mechanism.

\n
\n

\u2021With Coronavirus now changing our lives and our work patterns, and having done my allowed quota of one exercise walk for the day at 06.30 (to avoid social contact, although in fact the park we went to had lots of other people exercising, even at that time) I settled down to think about what else could be done. The Michael reaction suddenly appeared! Locating transition states is one of those things that gives me considerable pleasure, and I have not reported any for a few posts now.

\n

References

\n
  1. J.E.M.N. Klein, G. Knizia, and H.S. Rzepa, \"Epoxidation of Alkenes by Peracids: From Textbook Mechanisms to a Quantum Mechanically Derived Curly\u2010Arrow Depiction\", ChemistryOpen, vol. 8, pp. 1244-1250, 2019. https://doi.org/10.1002/open.201900099\n\n
    2. \n
\n\n
","doi":"https://doi.org/10.59350/fsmz0-znr76","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=21982","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/03/michael1.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1585094400,"reference":[{"id":"https://doi.org/10.1002/open.201900099","unstructured":"Klein, J. E. M. N., Knizia, G., & Rzepa, H. S. (2019). Epoxidation of Alkenes by Peracids: From Textbook Mechanisms to a Quantum Mechanically Derived Curly\u2010Arrow Depiction. ChemistryOpen, 8(10), 1244\u20131250."}],"rid":"ce73r-n8g54","summary":"In 2013, I created an iTunesU library of 115 mechanistic types in organic and organometallic chemistry, illustrated using video animations of the intrinsic reaction coordinate (IRC) computed using a high level quantum mechanical procedure. Many of those examples first derived from posts here.","tags":["Reaction Mechanism"],"title":"The mechanism of Michael 1,4-Nucleophilic addition: a computationally derived reaction pathway.","updated_at":1787767326,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=21982","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Earlier, I explored the choreography or “timing”, of what might be described as the curly arrows for a typical taught reaction mechanism, the 1,4-addition of a nucleophile to an unsaturated carbonyl compound (scheme 1). I am now going to explore the consequences of changing one of the actors by adding the nucleophile to an unsaturated imine rather than carbonyl compound (scheme 2).\u00a0

\n

\n

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Scheme 1

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Scheme 2

\n

For the reaction shown in Scheme 1, the maximum energy point along the reaction path involves the formation of an S-C bond (arrow 2 in scheme 1) rather than transfer of a proton. Scheme 2 has a new actor in which NH replaces O and which is a better base (i.e. has a greater affinity for a proton). The mechanism again starts with arrows 1 and 2 launching proceedings. If you watch the animation below very carefully, you will notice that arrows 3 and 4 lag behind them. This means that you have to have the blue arrows\u00a01 and\u00a04 as distinctly separate arrows. An alternative depiction (and in truth very probably the depiction you would find in pretty much all text books and lecture notes) would be to combine arrows 1 and 4 into the single red arrow 8. If you do this however, you loose this subtle nuance to the mechanism.

\n

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Animated\u00a0Reaction coordinate for TS1 (scheme 2) Click to load 3D model

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0Energy along reaction coordinate for TS1 (Scheme 2)

\n

The product of this first step is a zwitterionic (internal ion-pair) compound. This then goes on to form the S-C bond (arrows 5–7) via TS2, with the energy of this second transition state being lower than than TS1.

\n
\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Animated reaction coordinate for TS2 (Scheme 2)

\n

\"\"

\n

The free energy barrier for this second step is low (\u0394G\u2020 0.6 kcal/mol) because it is an ion-pair reacting to form a neutral molecule, always a facile process. Because the slowest step in this reaction (TS1) involves a proton transfer, this should now show a primary deuterium kinetic isotope effect. Indeed this is calculated to have the value 4.0 at 298K.\u00a0There is a prediction for an experiment to undertake!

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Species
\n(FAIR Data: dt5d)		\n

Relative energy

\n

kcal/mol

\n
Reactant0.0
TS17.7
Zwitterion2.2
TS22.8
Product-12.5
\n

To sumarise

\n
    \n
  1. Changing a C=O group to a C=NH group changes the nature of the mechanism from concerted asynchrous to stepwise.
    2. \n
  2. As a result of this change, the highest energy step now involves asynchronous proton transfers rather than S-C bond formation.
    3. \n
  3. The curly arrows can be used to reflect these steps, with two (blue) arrows being preferred to a single (red) one.
    4. \n
\n

So by expanding the conventional number of curly arrows used to include extra ones capturing asynchronicity in the reaction, one can indeed add further information to the curly arrow formalism.

\n
\n

This post has DOI: dt6v

\n
\n\n
","doi":"https://doi.org/10.59350/vwqyw-gsh07","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22304","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/04/michael3.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1588896000,"rid":"rt5s7-dz079","summary":"Earlier, I explored the choreography or \"timing\", of what might be described as the curly arrows for a typical taught reaction mechanism, the 1,4-addition of a nucleophile to an unsaturated carbonyl compound (scheme 1). I am now going to explore the consequences of changing one of the actors by adding the nucleophile to an unsaturated [\u2026]","tags":["Curly Arrows","Reaction Mechanism"],"title":"Choreographing a chemical ballet: what happens if you change one of the actors?","updated_at":1787767322,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22304","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemistry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

The epoxidation of an alkene to give an oxirane is taught in introductory organic chemistry. Formulating an analogous mechanism for such reaction of an alkyne\u00a0sounds straightforward, but one gradually realises that it requires raiding knowledge from several other areas of (perhaps slightly more advanced) chemistry to achieve a joined up approach to the problem. I had indeed hinted in a\u00a0previous post that the mechanism for oxidation of acetylene to ketene might be an interesting arrow pushing challenge to set a bright tutorial group, and it was that self-hint that has led me to here.\u00a0I now explore how my “arrow pushing” intuition stands up to a computational examination.

\n

\n

\"\"

\n

The products of the reaction of an acetylene with mCPBA (m-chloroperbenzoic acid) are set out[1] and the primary step of the mechanism[1]\u00a0(this article declines to discuss the subsequent steps).\u00a0The primary product is the formation of oxirene 1, a 4\u03c0-annulene which then undergoes an electrocyclic pericyclic ring opening to give the formyl carbene 4 (or 2 or 3). This presumed intermediate is also presumed to be highly reactive, and likely to undergo a variety of reactions (for example it will insert into a C-H bond if given one). I concentrate initially on just one path, the Wolff rearrangement (a [1,2] sigmatropic pericyclic reaction) to give the ketene 7. The scheme above constitutes one of those mandatory mechanistic challenges that organic chemists, almost without exception, cannot resist trying to solve, in the same way that some people may be addicted to Sudoko puzzles! So now for the reality check.

\n
    \n
  1. The intrinsic reaction coordinate (IRC) for the reaction to form oxirene 1\u00a0is shown below (DOI: 10.14469/ch/10244). Its uneventful profile is deceptive.
    \"\"
    2. \n
  2. Look how delightfully non-linear the motions of the atoms are; one of the new C-O bonds clearly forms long before the second, in what is termed an asynchronous exothermic reaction. This is almost certainly due to the forming anti-aromaticity of the product, which tends to favour such asymmetry.
    \n
    \"\"

    IRC for per oxidation of acetylene. Click for 3D

    \n
    3. \n
  3. Easily overlooked however would be the nature of the resulting product, which is actually a hydrogen-bonded complex of the oxirene and the acetic acid. Oxirene is a planar ring with two \u03c0-electrons from the double bond, and two \u03c0Lp electrons from the oxygen. This makes it an anti-aromatic annulene, just like say cyclobutadiene. One aspect of this anti-aromaticity which is not often noted is that the anti-aromaticity makes these\u00a0\u03c0 electrons especially basic, and so it is with oxirene. The oxygen forms a remarkably short\u00a0(1.673\u00c5) hydrogen bond to the H-O part of the carboxylic acid (in the process slightly attenuating its otherwise unremitting anti-aromaticity).
    4. \n
  4. However, the IRC for the next stage is unexpected (DOI: 10.14469/ch/10245). According to the scheme above, the oxirene would ring open to give a carbene 3, at which point this species might be expected to steady\u00a0itself before deciding what pathway it\u00a0will undertake. Shown below is the route 1-3-6.\"\"\"\"\n
      \n
    • Starting at IRC=-8, the oxirene encounters a blip of a barrier at IRC=-3.5, but the potential never actually settles into the carbene 3. Instead, it sails past it without much of a rest, and its momentum carries it onwards to perform a [1,2] hydrogen migration (TS@IRC=0.0), before finally settling into the unexpected carbene intermediate 6.
      • \n
    • Species 6\u00a0is no longer anti-aromatic, the oxygen is less basic, and the consequence is that the hydrogen bond to the adjacent\u00a0H-O group lengthens to 1.998\u00c5. This is a splendid lesson in how anti-aromaticity affects basicity, and not a lesson we had been expecting.
      \n
      \"\"

      Ring opening of oxirene, with unexpected momentum!

      \n
      • \n
    \n
    5. \n
  5. What happens to 6? An electrocyclic ring opening occurs (DOI: 10.14469/ch/10246) with an odd abrupt start of the action at IRC=-4 and after the transition state, an exothermic descent to ketene 7.\"\"\"\"
    6. \n
  6. Note that the acetic acid fragment stays passive until late on, when it decides to re-form the hydrogen bond.
    \n
    \"\"

    Conversion of 6 to 7.

    \n
    7. \n
\n

Well, that was a complicated story, and we have learnt a lot about (anti)aromaticity and hydrogen bonds in the process. There is one fly in the ointment however. If you look that the barriers that have to be overcome for the sequence 1-3-6-7 to occur, they are all quite large. In fact, the original report (for di-t-butyl acetylene[1]) does say very little ketene is actually formed. The next step would be to find lower energy pathways for reaction (such as possibly involving 2 or 4). But I will save that for a future posta future post.

\n

References

\n
  1. J. Ciabattoni, R.A. Campbell, C.A. Renner, and P.W. Concannon, \"Peracid oxidation of acetylenes. 1,2-Methyl migration, cyclopropane formation, and stereoselective 1,5- and 1,6-transannular insertion\", Journal of the American Chemical Society, vol. 92, pp. 3826-3828, 1970. https://doi.org/10.1021/ja00715a068\n\n
    2. \n
\n\n
","doi":"https://doi.org/10.59350/82cmm-qmv79","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=5500","image":"http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2011/11/peracid.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1321401600,"reference":[{"id":"https://doi.org/10.1021/ja00715a068","unstructured":"Ciabattoni, J., Campbell, R. A., Renner, C. A., & Concannon, P. W. (1970). Peracid oxidation of acetylenes. 1,2-Methyl migration, cyclopropane formation, and stereoselective 1,5- and 1,6-transannular insertion. Journal of the American Chemical Society, 92(12), 3826\u20133828."}],"rid":"yvtse-n8f94","summary":"The epoxidation of an alkene to give an oxirane is taught in introductory organic chemistry. Formulating an analogous mechanism for such reaction of an alkyne sounds straightforward, but one gradually realises that it requires raiding knowledge from several other areas of (perhaps slightly more advanced) chemistry to achieve a joined up approach to the problem.","tags":["Curly Arrows","Anti-aromatic","Ketene","Lower Energy Pathways","Pericyclic"],"title":"The peroxidation of alkynes: things are not always what they seem.","updated_at":1787767319,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=5500","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemistry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts.

\n

\n
    \n
  1. I had noted that antiaromaticity in cyclopropenium anion is lessened by the system adopting gross geometric distortions, which take the anionic lone pair out of conjugation from the ring.
    2. \n
  2. Similarly, cyclobutadiene can form a complex with the guanidinium cation in which the anti-aromaticity is reduced by the formation of strong C…H-N hydrogen bonds.
    3. \n
  3. Unhappy with modelling a cation without a counter-ion, I added one. I noted that the cyclobutadiene+ ion pair was more stable in this more complete form.
    4. \n
  4. My next connection is to a post on how ethyne reacts with peracetic acid. The initial product of this reaction is oxirene, which like cyclobutadiene or cyclopropenium anion is anti-aromatic. This time, the liberated acetic acid forms a remarkably strong hydrogen bond to the oxygen of the antiaromatic ring as a way of reducing the antiaromaticity.\u00a0
    5. \n
  5. Particularly noteworthy was that the initial attack of oxygen on the alkyne was very asymmetric. This reminded of another post on the reaction of dichlorocarbene with ethene, which too is asymmetric, yet again to avoid an antiaromatic transition state. However, as the hydrogen bond\u00a0in 4 above get stronger, the antiaromatic oxirene becomes symmetrical again. It is as if the hydrogen bond had replaced the need for asymmetry (as with 2 above).
    6. \n
  6. Another asymmetric example is the 2+2 closed shell cycloaddition of two ethenes, which adopt a different form of distortion.
    7. \n
\n

The original alkyne+peracid study was conducted using a gas phase model. I decided to revisit it now, but to change the modelled medium from the gas phase to continuum water. I show the IRC (intrinsic reaction coordinates) for this reaction in continuum water followed by the gas phase below (click on the animations to see the transition state model).

\n

\"\"

\n

\"\"

\n

\"\"

\n

\"\"

\n

I want to compare the difference that introducing a model solvent (water) has made to the appearance of the reaction path.

\n
    \n
  1. In water, the symmetry of the forming antiaromatic oxirene ring is always maintained. There is no distortion; the combination of hydrogen bond, developing ionicity and its stabilization by the model solvent, appears to eliminate the need for such distortion. The free energy barrier, \u0394G\u2021 (\u03c9B97XD/6-311G(d,p) is 32.2 kcal/mol, outside of a room temperature reaction.
    2. \n
  2. In water, the proton transfer step comes much later, and is visible in the RMS gradient norm at +1.4.
    3. \n
  3. In the gas phase, the IRC is much more complex (as previously noted). Pronounced asymmetry develops, and this only resymmetrises late on, when the hydrogen bond forms.
    4. \n
  4. In the gas phase, the proton transfer occurs relatively early, and it cannot be found as a discrete feature in the RMS gradient norm plot.\u00a0
    5. \n
  5. If a more acidic peracid is introduced, say\u00a0CF3CO3H, and the reaction is again simulated in water, the proton transfer is further delayed (below), and the barrier drops to\u00a0\u0394G\u2021 25.9 kcal/mol, an entirely viable thermal reaction. I do not believe this particular variation has ever been tested experimentally;\u00a0anyone up for it?\u00a0\"\"
    6. \n
  6. The product of the CF3CO3H reaction is shown below. It has a remarkably short predicted hydrogen bond of\u00a01.55\u00c5\u00a0between the oxirene and the trifluoracetic acid.\"\"
    7. \n
\n

The take home message is that the very nature of a reaction, the geometry (symmetry) of the molecules taking part, and the timing of the changes can be very visibly changed by simulating the event with a solvent. In the past of course, all such computational studies were conducted purely as a gas phase model.

\n

Postscript: The above shows how even a change in continuum solvent can affect the features of the reaction path. A rather greater perturbation is to change e.g. the substituents on the alkyne. I have tried replacing one H with t-butyl, and the other with OH. The rationale for the former is that t-butyl acetylene is actually the substrate that this reaction has been performed on, and for OH that it pushes electrons into the oxirene, making it more anti-aromatic and hence more liable to avoid that antiaromaticity. Animation of the IRC for this combination is shown below. Notice how the reaction now proceeds in a concerted manner directly from the alkyne to the hydroxy-carbene, without any sign of an intervening oxirene.\u00a0\"\"

\n

The energy and gradient profiles for this variation are shown below. Notice in particular how the barrier has dropped; it is now a much easier reaction.\"\"

\n

\"\"

\n\n
","doi":"https://doi.org/10.59350/d7wf1-g4m48","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=7027","image":"http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2012/07/alkyne+pa_water.gif","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1341792000,"rid":"za66v-b9714","summary":"Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts.","tags":["Curly Arrows","Reaction Mechanism","Alkyne","Gas Phase","Gas Phase Model"],"title":"Joining up the pieces. Peroxidation of ethyne.","updated_at":1787767314,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=7027","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

I occasionally notice that posts that first appeared here many years ago suddenly attract attention. Thus this post, entitled The strongest bond in the universe, from ten years back, has suddently become the most popular, going from an average of 0-2 hits per day to 92 in a single day on May 22nd (most views appear to originate from India). I can only presume that a university there has set some course work on this topic and Google has helped some of the students identify my post. Well, re-reading something you wrote ten years ago can be unsettling. Are the conclusions still sound? Would I establish my claim the same way now? After all, one picks up a little more experience in ten years. So here is my revisitation.

\n

\n

The hypothesis was that mono and then diprotonating dinitrogen strengthened the N-N bond, in the sequence\u00a0N\u2261N \u2192 H-N\u2261N+ \u2192 H-N\u2261N-H2+ to the point that the latter was now a candidate for the strongest known bond between two (non-hydrogen) atoms. One of my original criteria was to calculate the N-N stretching wavenumber. To get this, I had to project out the coupling between the N-N stretching mode and the H-N modes in the latter two species. In the original discussion, Igor suggested another candidate O22+\u00a0in the comments. I speculated that the heavy atom diatomic force constant might be a better way of estimating how strong the bond was rather than the stretching wavenumber, but I never followed this up! So time to do so now.

\n

The calculations are now at the CCSD(T)/Def2-TZVPP level (FAIR DOI: 10.14469/hpc/7214).

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
SpeciesHeavy atom Force constant, mDyne/\u00c5Projected heavy atom stretch, cm-1Bond length, \u00c5
N\u2261N45.517723491.1029
HN\u2261N+50.266224691.0983
HN\u2261NH2+56.490326171.0859
O\u2261O2+44.954221841.0510
N\u2261O1+49.011923651.0678
HN\u2261O2+50.806124111.065
HN\u2261C38.440822341.175
\n

I did learn one new trick. To project out mode mixing between the hydrogen stretch and the heavy atom stretch, the hydrogen atom masses are now set at 10,000! This has the effect of suppressing any mode mixing, but it also results in exactly the same reduced mass for the NN stretch (14.0) for the three species N\u2261N, H-N\u2261N(+) and H-N\u2261N-H(2+), thus facilitating a like for like comparison. Ten years ago I had also tried the other direction, setting the mass of H to 0.001. Although this latter also eliminates the mode mixing, it does not result in the same reduced masses for the NN mode. So we will stick to the heavy hydrogen projection for comparisons.

\n

The force constant increases almost linearly on mono and then diprotonation of dinitrogen, reaching 56.5 mDyne/\u00c5. In comparison, both O22+ and NO1+ are a little lower. Does monoprotonating NO1+ strengthen its bond? Yes, but not quite surpassing HN\u2261NH2+. And the neutral HN\u2261C, which is isoelectronic with HN\u2261N+, also\u00a0shows a weaker bond.

\n

So my revisitation ten years on still shows that diprotonated nitrogen has the strongest bond (presumably in the universe), as now judged by the diatomic force constant. The hunt is still on for a species where the force constant between two non-hydrogen atoms is higher. Maybe I will return in another ten years to see the state of this challenge!

\n\n
","doi":"https://doi.org/10.59350/8n298-0ez38","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22378","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1590192000,"rid":"fwx4f-kv629","summary":"I occasionally notice that posts that first appeared here many years ago suddenly attract attention.","tags":["Interesting Chemistry"],"title":"The strongest bond in the universe: revisited ten years on.","updated_at":1787767310,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22378","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

My previous two posts on the topic of strongest bonds have involved mono and diprotonating N2 and using quantum mechanics to predict the effect this has on the N-N bond via its length and vibrational stetching mode. Such species are very unlikely to be easily observed for verification. But how about a metal M+ instead of H+? It turns out that structures containing the fragment Ru-N\u2261N-Ru are a small but well studied class of organometallic. Here is a search of the CSD crystal database for this motif.

\n

\n

\"\"

\n

The three examples showing the shortest N-N distances are shown below.[1],[2][3]

\n

\"\" \"\" \"\"

\n

The NN distances for these three examples are in the region of 1.1\u00c5. There are 39 structures in total, for a variety of other transition metals, with a length <1.15\u00c5. The angles subtended at N are close to linear;

\n

\"\"

\n

 

\n

For comparison, N2 itself entrained into a crystal structure has the value of ~1.096\u00c5 as measured at 80K (R-factor 0.84%)[4]) which is pretty similar to the value computed in the previous post (1.103\u00c5). \u00a0

\n

So the question to ask is whether any of these organometallic examples have an NN bond at least as strong as that in dinitrogen itself? Only a reliable value for the force constant will give us a clear picture, which however would be non-trivial for such species. But it does suggest that asking whether there could be a real candidate for the strongest bond in the universe other than N2 itself may not be entirely futile.

\n

 

\n

References

\n
  1. Y. Sun, H. Chan, and Z. Xie, \"Reaction Scope and Mechanism of Sterically Induced Ruthenium-Mediated Intramolecular Coupling of<i>o</i>-Carboranyl with Cyclopentadienyl. Synthesis and Structure of Ruthenium Complexes Incorporating Doubly Linked Cyclopentadienyl\u2212Carboranyl Ligands\", Organometallics, vol. 25, pp. 4188-4195, 2006. https://doi.org/10.1021/om0604122\n\n
    2. \n
  2. Y. Tanabe, S. Kuriyama, K. Arashiba, K. Nakajima, and Y. Nishibayashi, \"Synthesis and Reactivity of Ruthenium Complexes Bearing Arsenic-Containing Arsenic-Nitrogen-Arsenic-Type Pincer Ligand\", Organometallics, vol. 33, pp. 5295-5300, 2014. https://doi.org/10.1021/om5006116\n\n
    3. \n
  3. K. Abdur-Rashid, D.G. Gusev, A.J. Lough, and R.H. Morris, \"Synthesis and Characterization of RuH<sub>2</sub>(H<sub>2</sub>)<sub>2</sub>(P<sup>i</sup>Pr<sub>3</sub>)<sub>2</sub> and Related Chemistry. Evidence for a Bis(dihydrogen) Structure\", Organometallics, vol. 19, pp. 1652-1660, 2000. https://doi.org/10.1021/om990669i\n\n
    4. \n
  4. C. Dou, W. Kosaka, and H. Miyasaka, \"Gate-open-type Sorption in a Zigzag Paddlewheel Ru Dimer Chain Compound with a Phenylenediamine Linker Instructed by a Preliminary Structural Change of Desolvation\", Chemistry Letters, vol. 46, pp. 1288-1291, 2017. https://doi.org/10.1246/cl.170509\n\n
    5. \n
\n\n
","doi":"https://doi.org/10.59350/xrt9p-jjn04","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22391","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/05/Screenshot-33-1024x714.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1590364800,"reference":[{"id":"https://doi.org/10.1021/om0604122","unstructured":"Sun, Y., Chan, H.-S., & Xie, Z. (2006). Reaction Scope and Mechanism of Sterically Induced Ruthenium-Mediated Intramolecular Coupling ofo-Carboranyl with Cyclopentadienyl. Synthesis and Structure of Ruthenium Complexes Incorporating Doubly Linked Cyclopentadienyl\u2212Carboranyl Ligands. Organometallics, 25(17), 4188\u20134195."},{"id":"https://doi.org/10.1021/om5006116","unstructured":"Tanabe, Y., Kuriyama, S., Arashiba, K., Nakajima, K., & Nishibayashi, Y. (2014). Synthesis and Reactivity of Ruthenium Complexes Bearing Arsenic-Containing Arsenic-Nitrogen-Arsenic-Type Pincer Ligand. Organometallics, 33(19), 5295\u20135300."},{"id":"https://doi.org/10.1021/om990669i","unstructured":"Abdur-Rashid, K., Gusev, D. G., Lough, A. J., & Morris, R. H. (2000). Synthesis and Characterization of RuH2(H2)2(PiPr3)2 and Related Chemistry. Evidence for a Bis(dihydrogen) Structure. Organometallics, 19(9), 1652\u20131660."},{"id":"https://doi.org/10.1246/cl.170509","unstructured":"Dou, C., Kosaka, W., & Miyasaka, H. (2017). Gate-open-type Sorption in a Zigzag Paddlewheel Ru Dimer Chain Compound with a Phenylenediamine Linker Instructed by a Preliminary Structural Change of Desolvation. Chemistry Letters, 46(9), 1288\u20131291."}],"rid":"dwrdg-60564","summary":"My previous two posts on the topic of strongest bonds have involved mono and diprotonating N2 and using quantum mechanics to predict the effect this has on the N-N bond via its length and vibrational stetching mode. Such species are very unlikely to be easily observed for verification.","tags":["Crystal_structure_mining"],"title":"The strongest bond in the universe: A crystallographic reality check?","updated_at":1787767308,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22391","version":"v1"}},{"document":{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus “NU-1501-Al” can absorb 14 weight% of hydrogen. To power a low-polluting car with a 500 km range, about 4-5 kg of hydrogen gas would be need to be stored and released safely. The molecule is of interest since it opens a systematic strategy of synthetically driven optimisation towards a viable ultra-porous storage material,[1] much like a lead drug compound can be optimised.

\n

\n

I thought it would be informative to show a 3D interactive model of the crystal lattice here and so I went in search of coordinates. These are indeed available online. This is an example of scientific data Interoperability and Reuse, part of the FAIR\u00a0data acronym. Before showing the model, I thought it worth briefly describing the procedure for starting with deposited data and converting (interoperating) it to the model here.

\n
    \n
  1. The molecule is a so-called MOF, or Metal-Organic-Framework. The core organic framework in this case is composed of linked tryptycene derivatives. Shown below is the 3D structure of this linker, oriented here to show the three-fold symmetry (actually D3) of the molecule, rather than any attempt to reveal all the atoms without any hidden ones. To see the latter, you are encouraged to click on the diagram and view the molecule as a rotatable model instead. The coordinates below are optimised using molecular mechanics to reveal the role of the linker units.
    2. \n
\n
\"\"

Click for a rotatable 3D model.

\n
    \n
  1. The data comes in the form of a CIF (crystallographic information) file and needs to be loaded into software that can manipulate such a format. In this case a program called Mercury (from CCDC) is available. Doing so reveals two minor oddities, circled in red below. The phenomenon arises from disorder, or two or more structures each with what is called partial occupancy. In this case, the disorder is largely limited to a p-substituted phenyl spacer linkage, which can adopt one of two rotational positions in the structure. The projection below is now selected to reveal the disorder rather than the symmetry. \"\"
    2. \n
  2. I want to “inter-operate” these coordinates into something that can be modelled and for this, the structure has to be edited to reduce it to a single unambiguous model. My very simple expedient here was simply to remove extraneous disordered atoms entirely; since they are acting as a spacing unit, this is unlikely to change the overall picture.‡ Again, the projection below is selected to show the symmetry present and in particular the hexagonal-like channels that appear in the crystal lattice. To achieve this lattice, the unit cell has to be grown in all three directions using the calculate packing option in the Mercury program.\n
    3. \n
\n
\"\"

Click for 3D rotatable model

\n

Clearly, the hexagonal cavities formed can accommodate a large number of hydrogen molecules. As to why, it is no doubt complex, but I cannot help but notice that the surface of the cavity is lined with multiple C-H units from the aryl spacer units pointing inwards. Given that hydrogen is a very good inducer of dispersion attractions, it would be interesting indeed to see whether the very large number of H…H2 dispersion attractions possible inside the cavity of this species might at least in part be responsible for the ability of this framework to accommodate hydrogen (or methane) gas.[2] It would be good to have an estimate of the dispersion energy term for NU-1501-Al and related species and the contribution of this term to the overall thermodynamics of the system. By the same token, replacing the four aryl C-H units with C-F units (a weaker dispersion attractor, think non-stick teflon) should reduce the ability to absorb hydrogen if dispersion is indeed important.

\n
\n

‡On the other hand, if the orientation of the aryl C-H groups is important in terms of dispersion attractons, perhaps these groups are actually critical to the effect.

\n
\n

\n

References

\n
  1. Z. Chen, P. Li, R. Anderson, X. Wang, X. Zhang, L. Robison, L.R. Redfern, S. Moribe, T. Islamoglu, D.A. G\u00f3mez-Gualdr\u00f3n, T. Yildirim, J.F. Stoddart, and O.K. Farha, \"Balancing volumetric and gravimetric uptake in highly porous materials for clean energy\", Science, vol. 368, pp. 297-303, 2020. https://doi.org/10.1126/science.aaz8881\n\n
    2. \n
  2. S. R\u00f6sel, C. Balestrieri, and P.R. Schreiner, \"Sizing the role of London dispersion in the dissociation of all-meta tert-butyl hexaphenylethane\", Chemical Science, vol. 8, pp. 405-410, 2017. https://doi.org/10.1039/c6sc02727j\n\n
    3. \n
\n\n
","doi":"https://doi.org/10.59350/v0xea-7a521","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22231","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/04/typt2-1024x911.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1587254400,"reference":[{"id":"https://doi.org/10.1126/science.aaz8881","unstructured":"Chen, Z., Li, P., Anderson, R., Wang, X., Zhang, X., Robison, L., Redfern, L. R., Moribe, S., Islamoglu, T., G\u00f3mez-Gualdr\u00f3n, D. A., Yildirim, T., Stoddart, J. F., & Farha, O. K. (2020). Balancing volumetric and gravimetric uptake in highly porous materials for clean energy. Science, 368(6488), 297\u2013303."},{"id":"https://doi.org/10.1039/c6sc02727j","unstructured":"R\u00f6sel, S., Balestrieri, C., & Schreiner, P. R. (2017). Sizing the role of London dispersion in the dissociation of all-meta tert-butyl hexaphenylethane. Chemical Science, 8(1), 405\u2013410."}],"rid":"8ymfn-snz74","summary":"In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus \"NU-1501-Al\" can absorb 14 weight% of hydrogen.","tags":["Crystal_structure_mining","Interesting Chemistry"],"title":"A molecular sponge for hydrogen storage- the future for road transport?","updated_at":1787767306,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22231","version":"v1"}}],"items":[{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

\"\"

\n

\n

Metadata are an essential way of enabling the discoverability and impact of scholarly resources such as (research) data and associated objects. It must adhere to a precisely described schema describing its properties,[1] and such a conformant metadata record is an mandatory component of a (research) data repository. Access to the record is by resolving the DOI (Digital object identifier) for any repository item, as for example:

\n

https://data.datacite.org/application/vnd.datacite.datacite+xml/10.14469/hpc/15994
\nhttps://data.datacite.org/application/vnd.datacite.datacite+xml/10.5281/zenodo.20657236

\n

where 10.14469/hpc/15994 and 10.5281/zenodo.20657236 are the (in this example two) DOIs registered for the same specific repository dataset. Two different repositories are shown here, because the metadata is still mostly captured using the user-interface of the relevant repository, and the richness or completeness of the metadata can differ greatly between repositories. Whilst the registered metadata record has some mandatory components, many more are optional and it is often the case that these optional components are either not supported via a visual interface by the repository, or the user choses to omit them (a complete or “rich” metadata entry could be quite tedious for a human). This aspect of human time and their attention span can often result in sparse metadata records.

\n

In some cases, the metadata is captured using a programmed workflow and then registered using the equivalent of a command line interface (API) which requires no user involvement or interactive user responses[2] and which tends to produce more systematically complete metadata records. Unfortunately, I think this mode of metadata provision must be relatively rare – although to be fair the metadata record itself does not carry details of the mechanism by which the metadata was populated. The two examples above were prepared using exactly the same API, and they largely differ in what elements of the total metadata schema each of the two repositories above actually support, rather than what a human had the patience for.

\n

So it is a welcome development that DataCite have recently made a Dashboard available that allows at a glance an inspection of either a specific metadata record or a collection of such records to be made. The start point is https://metadata.datacite.org/\u00a0and here you can filter the record by\u00a0a) the repository, further filtered by\u00a0b) registration year and c) resource type (Figure 1).\u00a0Thus:
\n\"\"

\n

Figure 1. The DataCite Metadata Dashboard,\u00a0showing a specified repository using the query
\nhttps://metadata.datacite.org/urks.helix?registrationYear=2026&resourceType=dataset

\n

This dashboard now allows you to easily compare the two metadata records noted above, with the help of an additional DOI query filter which can be used to further narrow it down to a single dataset (queries 1 and 2).

\n
    \n
  1. https://metadata.datacite.org/urks?registrationYear=2026&query=id:10.14469/HPC/15994
    2. \n
  2. https://metadata.datacite.org/cern.zenodo?registrationYear=2026&query=id:10.5281/zenodo.20657236
    3. \n
\n

A prominent difference between these queries is the Subjects metadata, with for example the subjectScheme\u00a0100% complete for example 1 (Figure 2) and 0% complete for example 2 (Figure 3).
\n\"\"

\n

Figure 2. The Subjects panel of the DataCite Metadata Dashboard,\u00a0for\u00a0DOI: 10.14469/HPC/15994

\n

\"\"

\n

Figure 3. The Subjects panel of the DataCite Metadata Dashboard,\u00a0for\u00a0DOI: 10.5281/zenodo.20657236

\n

Using the query filter to explore a range of other searches.

\n

Searches 3 and 4 specify an individual depositor by their ORCID identifier and 2026 as a publication year, for two different repositories.

\n
    \n
  1. https://metadata.datacite.org/bl.imperial?registrationYear=2026&query=contributors.nameIdentifiers.nameIdentifier:0000-0002-8635-8390+OR+creators.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390
    2. \n
  2. https://metadata.datacite.org/cern.zenodo?registrationYear=2026&query=contributors.nameIdentifiers.nameIdentifier:0000-0002-8635-8390+OR+creators.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390
    3. \n
\n

The Subjects panels\u00a0are shown in Figures 4 and 5. In these examples, both sets of depositions are made using the same automatic command line API[2] so human error or their lack of attention is not the cause of the differences.
\n\"\"

\n

Figure 4. The Subjects panel of the DataCite Metadata Dashboard for the bl.imperial repository for query 3.

\n

\"\"

\n

Figure 5. The Subjects panel of the DataCite Metadata Dashboard for the cern.zenodo repository for query 4.

\n

Search 5 shows more direct use of a Subject filter (Figure 6) and use of this filter ensures that again the subjects metadata panel is well populated.

\n
    \n
  1. https://metadata.datacite.org/urks?query=(media.media_type:application/zip+OR+media.media_type:chemical/x-mnova)+AND+
    \n(subjects.subjectScheme:*NMR_Nucleus)+AND+(subjects.subject:13C)+AND+
    \n(titles.title:*pyrazol*+OR+descriptions.description:*pyrazol*)
    2. \n
\n

\"\"

\n

Figure 6. The Subjects panel of the DataCite Metadata Dashboard for the urks repository for query 5.

\n

Query 6 (Figure 7) identifies datasets that have a directly associated journal article, showing the population of the “high impact” relatedIdentifier property.

\n
    \n
  1. https://metadata.datacite.org/urks?query=(types.resourceTypeGeneral:Dataset+OR+types.resourceTypeGeneral:Collection)+AND+
    \n(contributors.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390+OR+
    \ncreators.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390)+AND+(relatedIdentifiers.relatedIdentifierType:DOI+AND+
    \nrelatedIdentifiers.resourceTypeGeneral:JournalArticle+AND+relatedIdentifiers.relatedIdentifier:*)
    2. \n
\n

\"\"

\n

Figure 7. The RelatedIdentifiers\u00a0panel of the DataCite Metadata Dashboard for the urks repository for query 6.

\n

Query 7 showing again a very well populated Subjects panel (due of course to the filter applied below) with 100% occupancy of the subjectScheme.

\n
    \n
  1. https://metadata.datacite.org/urks?query=(media.media_type:chemical/x-gaussian-log+OR+
    \nmedia.media_type:chemical/x-gaussian-checkpoint)+AND+
    \n(titles.title:*Endo*+OR+
    \ndescriptions.description:*Endo*+OR+titles.title:*Exo*+OR+descriptions.description:*Exo*)+AND+
    \n(subjects.subjectScheme:*KIE*)+AND+
    \nsubjects.subject:1H/2H
    2. \n
\n

\"\"

\n

Figure 8. The Subjects\u00a0panel of the DataCite Metadata Dashboard for the urks repository for query 7.

\n

Query 8 shows how well populated the Subjects panel is for a whole range of users (excluding one subject-loving suspect!). It would be interesting to see if this population (albeit only 4.7%) was achieved by manual entry or by automatic API calls.

\n
    \n
  1. https://metadata.datacite.org/cern.zenodo?registrationYear=2026&query=+NOT+
    \n(contributors.nameIdentifiers.nameIdentifier:0000-0002-8635-8390+OR+
    \ncreators.nameIdentifiers.nameIdentifier:*0000-0002-8635-8390)
    2. \n
\n

\"\"

\n

Figure 9. The Subjects panel of the DataCite Metadata Dashboard for the cern.zenodo repository for query 8.

\n

Example 9 uses the InvenioRDM repository system whilst 10 uses a bespoke repository created in 2016 with metadata richness in mind.[2] Both these examples were crafted “by hand” rather than using an API tool and are limited only by the user interfaces of either repository.

\n
    \n
  1. https://metadata.datacite.org/urks.helix?registrationYear=2026&query=id:10.82186/xjxch-zzb72
    2. \n
  2. https://metadata.datacite.org/bl.imperial?registrationYear=2024&query=id:10.14469/hpc/14835
    3. \n
\n

\"\"

\n

Figure 10. The Subjects panel of the DataCite Metadata Dashboard for query 9.
\n\"\"

\n

Figure 11. The Subjects panel of the DataCite Metadata Dashboard for query 10.

\n

Conclusions.

\n

It is to be hoped that analysis of research data metadata records using the DataCite tool will rapidly lead to a greater and richer population of these records. Wherever possible, these records should be populated using automated methods which do not rely on the patience of a human. My own candidate for increased population is the Subjects field, which can be readily automated and the presence of which allows finely tuned searches of the DataCite metadata store to be made.

\n
\n

DOI: 10.59350/ams3m-m3t92

\n

References

\n
  1. DataCite Metadata Working Group., \"DataCite Metadata Schema Documentation for the Publication and Citation of Research Data and Other Research Outputs v4.7\", DataCite, 2026. https://doi.org/10.14454/qdd3-ps68\n\n
    2. \n
  2. C. Cave-Ayland, M. Bearpark, C. Romain, and H. Rzepa, \"CHAMP is a HPC Access and Metadata Portal\", Journal of Open Source Software, vol. 7, pp. 3824, 2022. https://doi.org/10.21105/joss.03824\n\n
    3. \n
\n\n
","doi":"https://doi.org/10.59350/ams3m-m3t92","guid":"https://www.ch.ic.ac.uk/rzepa/blog/?p=31548","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1781654400,"reference":[{"id":"https://doi.org/10.14454/qdd3-ps68","unstructured":"DataCite Metadata Working Group, Liffers, M., Robertson, W., Ashton, J., Bernal, I., Devaraju, A., Elger, K., Habermann, T., Harrison, M., Kraus, R., Mathews, I., Medina-Smith, A., Moore, A. V., Padfield, J., Raugh, A., Shallcross, M., Strecker, D., Tarocco, N., Tvrdy, P., \u2026 El-Gebali, S. (2026). DataCite Metadata Schema Documentation for the Publication and Citation of Research Data and Other Research Outputs v4.7."},{"id":"https://doi.org/10.21105/joss.03824","unstructured":"Cave-Ayland, C., Bearpark, M., Romain, C., & Rzepa, H. (2022). CHAMP is a HPC Access and Metadata Portal. Journal of Open Source Software, 7(70), 3824."}],"rid":"se4bz-dxb91","summary":"Metadata are an essential way of enabling the discoverability and impact of scholarly resources such as (research) data and associated objects. It must adhere to a precisely described schema describing its properties,[1] and such a conformant metadata record is an mandatory component of a (research) data repository.","tags":["Chemical IT"],"title":"Evaluating metadata quality and completeness for research data using the new DataCite Tool.","updated_at":1787767377,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=31548","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemistry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

In 1988, Wilke[1] reported molecule 1

\n

\"A

A 24-annulene. Click for 3D.


\nIt was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned! The reason is that a 24- annulene belongs formally to a class of molecule with 4n (n=6) \u03c0-electrons, and which makes it antiaromatic according to the (extended) H\u00fcckel rule. This is a select class of molecule, of which the first two members are cyclobutadiene and cyclo-octatetraene. The first of these is exceptionally reactive and unstable and is the archetypal anti-aromatic molecule. The second is not actually unstable, but it is reactive and conventional wisdom has it that it avoids the undesirable antiaromaticity by adopting a highly non-planar tub shape and hence instead adopts reactive non-aromaticity. Both these examples have localized double bonds, a great contrast with the molecule which sandwiches them, cyclo-hexatriene (i.e. benzene). The reason for the resurgent interest is that a number of crystalline, apparently stable, antiaromatic molecules have recently been discovered, and ostensibly, molecule 1 belongs to this select class!

\n

\n

So is 1 actually anti-aromatic? Let us look at some of the ways in which this might be estimated.

\n
    \n
  1. One can inspect the bond lengths, measured from X-ray analysis. The longest is 1.463\u00c5, labelled a above, and it corresponds to a single bond (value from the crystal structure).
    2. \n
  2. If the molecule had a bond alternating structure, the adjacent bonds would be expected to be much shorter, in the region of 1.32\u00c5. In fact, they are rather longer, at 1.37\u00c5. Indeed, in the cycloheptatriene part of the molecule, the alternation is much less than one might expect of an anti-aromatic molecule, oscillating between 1.37 and 1.43\u00c5.
    3. \n
  3. One can also inspect aromaticity via a variety of magnetic indices. The simplest of these is the NICS probe. Placed at a ring centroid, a negative value of this index of around -10ppm indicates aromaticity (this is the value for benzene), whilst a strongly positive value (of up to +20 ppm) indicates anti-aromaticity. Molecule 1 has two potential centroids, one placed at the absolute centre of the system, and one placed at the centroid of the ~6-membered ring completed using bond b (in reality, the centroids were computed from the positions of ring critical points obtained from an AIM analysis). The NICS values at these two positions are both ~-4.4 ppm (See DOI: 10042/to-2156 for details of the calculation). These values does not indicate antiaromaticity! They could even be described as mildly aromatic. So what is going on?
    4. \n
  4. What about the chemical shifts of the other protons? All the hydrogens attached to sp2 carbons are predicted to resonate at around 6.7ppm (unfortunately Wilke does not report the experimental spectrum), which is typical of an aromatic system (anti-aromatic systems have high upfield shifts for such protons, at around 2ppm or even -2 ppm, see [2] for examples). The two protons of the methylene bridges are also quite different; 2.9 and 0.8 ppm. The latter is the proton endo to the cycloheptatrienyl ring, and is typical of a proton placed in the anisotropic magnetic shielding region of e.g. benzene. Thus the cycloheptatrienyl ring is itself behaving as if it were aromatic, whereas the overarching 24-annulene ring is certainly not behaving as if it were antiaromatic.
    5. \n
\n

One possible explanation involves a concept known as homoaromaticity. The bond marked as b could be regarded as completing the 6\u03c0-electron local aromaticity of that ring (it would be formally considered as a 1\u03c0-electron bond, with no underlying \u03c3-framework, see [3] for discussion). So has the case been made for 1 being the first clear cut example of a neutral homoaromatic molecule, containing no less than four rings exhibiting this type of aromaticity?

\n

There is one further concept that can be introduced. Clar (for a discussion, see DOI: [4] proposed that benzenoid 6\u03c0-electron local aromaticity is preferred to less local or more extended cyclic conjugations, if the two compete. Many examples in a type of compound known as polybenzenoid aromatics are known where the most favourable resonance structure is that which maximises the number of Clar rings. More recently, quite a few ostensibly antiaromatic molecules have been shown to attenuate this unfavourable effect by forming instead groups of aromatic Clar islands containing delocalized benzene like rings (discussion of this point can be found at [5]. In molecule 1, we could have a new phenomenon; a homoClar ring, formed to avoid antiaromaticity.

\n

For further discussion, see the comment posted to Steve Bachrach’s blog.

\n

References

\n
  1. G. Wilke, \"Contributions to Organo\u2010Nickel Chemistry\", Angewandte Chemie International Edition in English, vol. 27, pp. 185-206, 1988. https://doi.org/10.1002/anie.198801851\n\n
    2. \n
  2. H.S. Rzepa, \"Lemniscular Hexaphyrins as Examples of Aromatic and Antiaromatic Double-Twist M\u00f6bius Molecules\", Organic Letters, vol. 10, pp. 949-952, 2008. https://doi.org/10.1021/ol703129z\n\n
    3. \n
  3. https://doi.org/\n\n
    4. \n
  4. A.T. Balaban, P.V.R. Schleyer, and H.S. Rzepa, \"Crocker, Not Armit and Robinson, Begat the Six Aromatic Electrons\", Chemical Reviews, vol. 105, pp. 3436-3447, 2005. https://doi.org/10.1021/cr0300946\n\n
    5. \n
  5. C.S.M. Allan, and H.S. Rzepa, \"A computational investigation of the structure of polythiocyanogen\", Dalton Trans., pp. 6925-6932, 2008. https://doi.org/10.1039/b810147g\n\n
    6. \n
\n\n
","doi":"https://doi.org/10.59350/wnt2x-q6k53","guid":"http://www.ch.ic.ac.uk/rzepa/blog/?p=275","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2009/04/gaytab.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1239580800,"reference":[{"id":"https://doi.org/10.1002/anie.198801851","unstructured":"Wilke, G. (1988). Contributions to Organo\u2010Nickel Chemistry. Angewandte Chemie International Edition in English, 27(1), 185\u2013206."},{"id":"https://doi.org/10.1021/ol703129z","unstructured":"Rzepa, H. S. (2008). Lemniscular Hexaphyrins as Examples of Aromatic and Antiaromatic Double-Twist M\u00f6bius Molecules. Organic Letters, 10(5), 949\u2013952."},{"id":"https://doi.org/"},{"id":"https://doi.org/10.1021/cr0300946","unstructured":"Balaban, A. T., Schleyer, P. v R., & Rzepa, H. S. (2005). Crocker, Not Armit and Robinson, Begat the Six Aromatic Electrons. Chemical Reviews, 105(10), 3436\u20133447."},{"id":"https://doi.org/10.1039/b810147g","unstructured":"Allan, C. S. M., & Rzepa, H. S. (2008). A computational investigation of the structure of polythiocyanogen. Dalton Trans., (48), 6925\u20136932."}],"rid":"s8829-gfh38","summary":"In 1988, Wilke[1] reported molecule 1 A 24-annulene. Click for 3D. It was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned!","tags":["Interesting Chemistry","Anti-aromatic Systems","Chemical Shifts","Clar Islands","Steve Bachrach"],"title":"A molecule with an identity crisis: Aromatic or anti-aromatic?","updated_at":1787767330,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=275","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

In a previous post, I talked about a library of reaction pathway intrinsic reaction coordinates (IRCs) containing 115 examples of organic and organometallic reactions. Now (thanks Dean!) I have been alerted to a brand new databank of dynamics trajectories (DDT), with the focus on those reactions taught in undergraduate organic chemistry courses, some of which are shown below.

\n

\n

\"\"

\n

Each example takes the form of two movie animations, one showing the classical IRC path and the other the “major trajectory” (DT) resulting from a molecular dynamics calculation. The latter representation incorporates molecular vibrations into the picture, showing how they evolve from reactants into a reaction product over a time period. Dynamics are a more realistic picture of how a molecule actually reacts. Any given trajectory can follow its own path, but the most common path for it to take is indeed that defined by the IRC and here you can compare the two approaches. What is interesting of course are those examples where the IRC and DT differ, with perhaps the latter not necessarily following the minimum energy path charted by the former.\u2021 Even more fascinating are those non-classical reactions where a given IRC path, as defined by a single unique transition state at the top of the energy barrier, can nonetheless result in two or more different reaction outcomes. [1] See my analysis.

\n

This databank is still young, with eight reactions at the time this blog was written. Suggestions for new reactions are invited, and I do hope it grows rapidly. Also I look forward to a section describing the technicalities of how the DT are computed and what sorts of resources are required to do this routinely (an article describing the databank is being prepared). In particular, how do the computer time resources needed for IRC and DT compare? It is good indeed to see this dynamic picture entering into the undergraduate taught curriculum.

\n
\n

\u2021For an example of a differing outcome, see here.

\n

References

\n
  1. X.S. Bogle, and D.A. Singleton, \"Dynamic Origin of the Stereoselectivity of a Nucleophilic Substitution Reaction\", Organic Letters, vol. 14, pp. 2528-2531, 2012. https://doi.org/10.1021/ol300817a\n\n
    2. \n
\n\n
","doi":"https://doi.org/10.59350/aa792-4x456","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22259","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/04/MD-1024x340.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1587513600,"reference":[{"id":"https://doi.org/10.1021/ol300817a","unstructured":"Bogle, X. S., & Singleton, D. A. (2012). Dynamic Origin of the Stereoselectivity of a Nucleophilic Substitution Reaction. Organic Letters, 14(10), 2528\u20132531."}],"rid":"h4tp1-58f06","summary":"In a previous post, I talked about a library of reaction pathway intrinsic reaction coordinates (IRCs) containing 115 examples of organic and organometallic reactions.","tags":["Reaction Mechanism"],"title":"A databank of molecular dynamics reaction trajectories (DDT) focused on undergraduate teaching.","updated_at":1787767327,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22259","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

In 2013, I created an iTunesU library of 115\u00a0mechanistic types in organic and organometallic chemistry, illustrated using video animations of the intrinsic reaction coordinate (IRC) computed using a high level quantum mechanical procedure. Many of those examples first derived from posts here. That collection\u00a0 is still available and is viewable \u00a0in the iTunesU app on an iPhone or an iPad. The realisation struck me now\u2021 that one of the types not described in that library was Michael-type 1,4-nucleophilic addition to an activated alkene, as described at\u00a0Wikipedia. So here is that addition.

\n

\n

\"\"

\n

The base used will be NH3 and the activating groups R will all be formyl. The DFT computational method will be\u00a0\u03c9B97XD/Def2-TZVPP/SCRF=water and the FAIR data will collect at DOI: 10.14469/hpc/7027

\n

The full reaction mechanism can be represented as below \"\"

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Species\u0394\u0394G298, kcal/molFAIR Data DOI
Reactant0.07028
TS16.77029
Int1-7.77036
TS216.37031
Int2-8.77033
Int3-8.77035
TS39.67030
Product-13.27034
\n

The rate-limiting step of C-C bond formation is coupled with almost synchronous protonation on the remote oxygen. It is driven by reducing the dipole moment of the zwitterion Int1, as shown below.\"\"

\n

Attempts to find an analogous route with carbon protonation leading directly to the product did not succeed.

\n

\"\"

\n

By varying parameters such as the nature of the R groups or the base, one might be able to control the choreography of the C-C bond formation relative to the accompanying proton transfer to oxygen in TS2 (in the manner that was possible for e.g. peracid epoxidation[1]). These changes could then be subjected to e.g. the measurement of kinetic isotope effects and comparison with values calculated from the computational mechanism.

\n
\n

\u2021With Coronavirus now changing our lives and our work patterns, and having done my allowed quota of one exercise walk for the day at 06.30 (to avoid social contact, although in fact the park we went to had lots of other people exercising, even at that time) I settled down to think about what else could be done. The Michael reaction suddenly appeared! Locating transition states is one of those things that gives me considerable pleasure, and I have not reported any for a few posts now.

\n

References

\n
  1. J.E.M.N. Klein, G. Knizia, and H.S. Rzepa, \"Epoxidation of Alkenes by Peracids: From Textbook Mechanisms to a Quantum Mechanically Derived Curly\u2010Arrow Depiction\", ChemistryOpen, vol. 8, pp. 1244-1250, 2019. https://doi.org/10.1002/open.201900099\n\n
    2. \n
\n\n
","doi":"https://doi.org/10.59350/fsmz0-znr76","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=21982","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/03/michael1.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1585094400,"reference":[{"id":"https://doi.org/10.1002/open.201900099","unstructured":"Klein, J. E. M. N., Knizia, G., & Rzepa, H. S. (2019). Epoxidation of Alkenes by Peracids: From Textbook Mechanisms to a Quantum Mechanically Derived Curly\u2010Arrow Depiction. ChemistryOpen, 8(10), 1244\u20131250."}],"rid":"ce73r-n8g54","summary":"In 2013, I created an iTunesU library of 115 mechanistic types in organic and organometallic chemistry, illustrated using video animations of the intrinsic reaction coordinate (IRC) computed using a high level quantum mechanical procedure. Many of those examples first derived from posts here.","tags":["Reaction Mechanism"],"title":"The mechanism of Michael 1,4-Nucleophilic addition: a computationally derived reaction pathway.","updated_at":1787767326,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=21982","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Earlier, I explored the choreography or “timing”, of what might be described as the curly arrows for a typical taught reaction mechanism, the 1,4-addition of a nucleophile to an unsaturated carbonyl compound (scheme 1). I am now going to explore the consequences of changing one of the actors by adding the nucleophile to an unsaturated imine rather than carbonyl compound (scheme 2).\u00a0

\n

\n

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Scheme 1

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Scheme 2

\n

For the reaction shown in Scheme 1, the maximum energy point along the reaction path involves the formation of an S-C bond (arrow 2 in scheme 1) rather than transfer of a proton. Scheme 2 has a new actor in which NH replaces O and which is a better base (i.e. has a greater affinity for a proton). The mechanism again starts with arrows 1 and 2 launching proceedings. If you watch the animation below very carefully, you will notice that arrows 3 and 4 lag behind them. This means that you have to have the blue arrows\u00a01 and\u00a04 as distinctly separate arrows. An alternative depiction (and in truth very probably the depiction you would find in pretty much all text books and lecture notes) would be to combine arrows 1 and 4 into the single red arrow 8. If you do this however, you loose this subtle nuance to the mechanism.

\n

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Animated\u00a0Reaction coordinate for TS1 (scheme 2) Click to load 3D model

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0Energy along reaction coordinate for TS1 (Scheme 2)

\n

The product of this first step is a zwitterionic (internal ion-pair) compound. This then goes on to form the S-C bond (arrows 5–7) via TS2, with the energy of this second transition state being lower than than TS1.

\n
\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Animated reaction coordinate for TS2 (Scheme 2)

\n

\"\"

\n

The free energy barrier for this second step is low (\u0394G\u2020 0.6 kcal/mol) because it is an ion-pair reacting to form a neutral molecule, always a facile process. Because the slowest step in this reaction (TS1) involves a proton transfer, this should now show a primary deuterium kinetic isotope effect. Indeed this is calculated to have the value 4.0 at 298K.\u00a0There is a prediction for an experiment to undertake!

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Species
\n(FAIR Data: dt5d)		\n

Relative energy

\n

kcal/mol

\n
Reactant0.0
TS17.7
Zwitterion2.2
TS22.8
Product-12.5
\n

To sumarise

\n
    \n
  1. Changing a C=O group to a C=NH group changes the nature of the mechanism from concerted asynchrous to stepwise.
    2. \n
  2. As a result of this change, the highest energy step now involves asynchronous proton transfers rather than S-C bond formation.
    3. \n
  3. The curly arrows can be used to reflect these steps, with two (blue) arrows being preferred to a single (red) one.
    4. \n
\n

So by expanding the conventional number of curly arrows used to include extra ones capturing asynchronicity in the reaction, one can indeed add further information to the curly arrow formalism.

\n
\n

This post has DOI: dt6v

\n
\n\n
","doi":"https://doi.org/10.59350/vwqyw-gsh07","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22304","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/04/michael3.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1588896000,"rid":"rt5s7-dz079","summary":"Earlier, I explored the choreography or \"timing\", of what might be described as the curly arrows for a typical taught reaction mechanism, the 1,4-addition of a nucleophile to an unsaturated carbonyl compound (scheme 1). I am now going to explore the consequences of changing one of the actors by adding the nucleophile to an unsaturated [\u2026]","tags":["Curly Arrows","Reaction Mechanism"],"title":"Choreographing a chemical ballet: what happens if you change one of the actors?","updated_at":1787767322,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22304","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemistry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

The epoxidation of an alkene to give an oxirane is taught in introductory organic chemistry. Formulating an analogous mechanism for such reaction of an alkyne\u00a0sounds straightforward, but one gradually realises that it requires raiding knowledge from several other areas of (perhaps slightly more advanced) chemistry to achieve a joined up approach to the problem. I had indeed hinted in a\u00a0previous post that the mechanism for oxidation of acetylene to ketene might be an interesting arrow pushing challenge to set a bright tutorial group, and it was that self-hint that has led me to here.\u00a0I now explore how my “arrow pushing” intuition stands up to a computational examination.

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\n

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\n

The products of the reaction of an acetylene with mCPBA (m-chloroperbenzoic acid) are set out[1] and the primary step of the mechanism[1]\u00a0(this article declines to discuss the subsequent steps).\u00a0The primary product is the formation of oxirene 1, a 4\u03c0-annulene which then undergoes an electrocyclic pericyclic ring opening to give the formyl carbene 4 (or 2 or 3). This presumed intermediate is also presumed to be highly reactive, and likely to undergo a variety of reactions (for example it will insert into a C-H bond if given one). I concentrate initially on just one path, the Wolff rearrangement (a [1,2] sigmatropic pericyclic reaction) to give the ketene 7. The scheme above constitutes one of those mandatory mechanistic challenges that organic chemists, almost without exception, cannot resist trying to solve, in the same way that some people may be addicted to Sudoko puzzles! So now for the reality check.

\n
    \n
  1. The intrinsic reaction coordinate (IRC) for the reaction to form oxirene 1\u00a0is shown below (DOI: 10.14469/ch/10244). Its uneventful profile is deceptive.
    \"\"
    2. \n
  2. Look how delightfully non-linear the motions of the atoms are; one of the new C-O bonds clearly forms long before the second, in what is termed an asynchronous exothermic reaction. This is almost certainly due to the forming anti-aromaticity of the product, which tends to favour such asymmetry.
    \n
    \"\"

    IRC for per oxidation of acetylene. Click for 3D

    \n
    3. \n
  3. Easily overlooked however would be the nature of the resulting product, which is actually a hydrogen-bonded complex of the oxirene and the acetic acid. Oxirene is a planar ring with two \u03c0-electrons from the double bond, and two \u03c0Lp electrons from the oxygen. This makes it an anti-aromatic annulene, just like say cyclobutadiene. One aspect of this anti-aromaticity which is not often noted is that the anti-aromaticity makes these\u00a0\u03c0 electrons especially basic, and so it is with oxirene. The oxygen forms a remarkably short\u00a0(1.673\u00c5) hydrogen bond to the H-O part of the carboxylic acid (in the process slightly attenuating its otherwise unremitting anti-aromaticity).
    4. \n
  4. However, the IRC for the next stage is unexpected (DOI: 10.14469/ch/10245). According to the scheme above, the oxirene would ring open to give a carbene 3, at which point this species might be expected to steady\u00a0itself before deciding what pathway it\u00a0will undertake. Shown below is the route 1-3-6.\"\"\"\"\n
      \n
    • Starting at IRC=-8, the oxirene encounters a blip of a barrier at IRC=-3.5, but the potential never actually settles into the carbene 3. Instead, it sails past it without much of a rest, and its momentum carries it onwards to perform a [1,2] hydrogen migration (TS@IRC=0.0), before finally settling into the unexpected carbene intermediate 6.
      • \n
    • Species 6\u00a0is no longer anti-aromatic, the oxygen is less basic, and the consequence is that the hydrogen bond to the adjacent\u00a0H-O group lengthens to 1.998\u00c5. This is a splendid lesson in how anti-aromaticity affects basicity, and not a lesson we had been expecting.
      \n
      \"\"

      Ring opening of oxirene, with unexpected momentum!

      \n
      • \n
    \n
    5. \n
  5. What happens to 6? An electrocyclic ring opening occurs (DOI: 10.14469/ch/10246) with an odd abrupt start of the action at IRC=-4 and after the transition state, an exothermic descent to ketene 7.\"\"\"\"
    6. \n
  6. Note that the acetic acid fragment stays passive until late on, when it decides to re-form the hydrogen bond.
    \n
    \"\"

    Conversion of 6 to 7.

    \n
    7. \n
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Well, that was a complicated story, and we have learnt a lot about (anti)aromaticity and hydrogen bonds in the process. There is one fly in the ointment however. If you look that the barriers that have to be overcome for the sequence 1-3-6-7 to occur, they are all quite large. In fact, the original report (for di-t-butyl acetylene[1]) does say very little ketene is actually formed. The next step would be to find lower energy pathways for reaction (such as possibly involving 2 or 4). But I will save that for a future posta future post.

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References

\n
  1. J. Ciabattoni, R.A. Campbell, C.A. Renner, and P.W. Concannon, \"Peracid oxidation of acetylenes. 1,2-Methyl migration, cyclopropane formation, and stereoselective 1,5- and 1,6-transannular insertion\", Journal of the American Chemical Society, vol. 92, pp. 3826-3828, 1970. https://doi.org/10.1021/ja00715a068\n\n
    2. \n
\n\n
","doi":"https://doi.org/10.59350/82cmm-qmv79","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=5500","image":"http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2011/11/peracid.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1321401600,"reference":[{"id":"https://doi.org/10.1021/ja00715a068","unstructured":"Ciabattoni, J., Campbell, R. A., Renner, C. A., & Concannon, P. W. (1970). Peracid oxidation of acetylenes. 1,2-Methyl migration, cyclopropane formation, and stereoselective 1,5- and 1,6-transannular insertion. Journal of the American Chemical Society, 92(12), 3826\u20133828."}],"rid":"yvtse-n8f94","summary":"The epoxidation of an alkene to give an oxirane is taught in introductory organic chemistry. Formulating an analogous mechanism for such reaction of an alkyne sounds straightforward, but one gradually realises that it requires raiding knowledge from several other areas of (perhaps slightly more advanced) chemistry to achieve a joined up approach to the problem.","tags":["Curly Arrows","Anti-aromatic","Ketene","Lower Energy Pathways","Pericyclic"],"title":"The peroxidation of alkynes: things are not always what they seem.","updated_at":1787767319,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=5500","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemistry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
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Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts.

\n

\n
    \n
  1. I had noted that antiaromaticity in cyclopropenium anion is lessened by the system adopting gross geometric distortions, which take the anionic lone pair out of conjugation from the ring.
    2. \n
  2. Similarly, cyclobutadiene can form a complex with the guanidinium cation in which the anti-aromaticity is reduced by the formation of strong C…H-N hydrogen bonds.
    3. \n
  3. Unhappy with modelling a cation without a counter-ion, I added one. I noted that the cyclobutadiene+ ion pair was more stable in this more complete form.
    4. \n
  4. My next connection is to a post on how ethyne reacts with peracetic acid. The initial product of this reaction is oxirene, which like cyclobutadiene or cyclopropenium anion is anti-aromatic. This time, the liberated acetic acid forms a remarkably strong hydrogen bond to the oxygen of the antiaromatic ring as a way of reducing the antiaromaticity.\u00a0
    5. \n
  5. Particularly noteworthy was that the initial attack of oxygen on the alkyne was very asymmetric. This reminded of another post on the reaction of dichlorocarbene with ethene, which too is asymmetric, yet again to avoid an antiaromatic transition state. However, as the hydrogen bond\u00a0in 4 above get stronger, the antiaromatic oxirene becomes symmetrical again. It is as if the hydrogen bond had replaced the need for asymmetry (as with 2 above).
    6. \n
  6. Another asymmetric example is the 2+2 closed shell cycloaddition of two ethenes, which adopt a different form of distortion.
    7. \n
\n

The original alkyne+peracid study was conducted using a gas phase model. I decided to revisit it now, but to change the modelled medium from the gas phase to continuum water. I show the IRC (intrinsic reaction coordinates) for this reaction in continuum water followed by the gas phase below (click on the animations to see the transition state model).

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\"\"

\n

\"\"

\n

\"\"

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I want to compare the difference that introducing a model solvent (water) has made to the appearance of the reaction path.

\n
    \n
  1. In water, the symmetry of the forming antiaromatic oxirene ring is always maintained. There is no distortion; the combination of hydrogen bond, developing ionicity and its stabilization by the model solvent, appears to eliminate the need for such distortion. The free energy barrier, \u0394G\u2021 (\u03c9B97XD/6-311G(d,p) is 32.2 kcal/mol, outside of a room temperature reaction.
    2. \n
  2. In water, the proton transfer step comes much later, and is visible in the RMS gradient norm at +1.4.
    3. \n
  3. In the gas phase, the IRC is much more complex (as previously noted). Pronounced asymmetry develops, and this only resymmetrises late on, when the hydrogen bond forms.
    4. \n
  4. In the gas phase, the proton transfer occurs relatively early, and it cannot be found as a discrete feature in the RMS gradient norm plot.\u00a0
    5. \n
  5. If a more acidic peracid is introduced, say\u00a0CF3CO3H, and the reaction is again simulated in water, the proton transfer is further delayed (below), and the barrier drops to\u00a0\u0394G\u2021 25.9 kcal/mol, an entirely viable thermal reaction. I do not believe this particular variation has ever been tested experimentally;\u00a0anyone up for it?\u00a0\"\"
    6. \n
  6. The product of the CF3CO3H reaction is shown below. It has a remarkably short predicted hydrogen bond of\u00a01.55\u00c5\u00a0between the oxirene and the trifluoracetic acid.\"\"
    7. \n
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The take home message is that the very nature of a reaction, the geometry (symmetry) of the molecules taking part, and the timing of the changes can be very visibly changed by simulating the event with a solvent. In the past of course, all such computational studies were conducted purely as a gas phase model.

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Postscript: The above shows how even a change in continuum solvent can affect the features of the reaction path. A rather greater perturbation is to change e.g. the substituents on the alkyne. I have tried replacing one H with t-butyl, and the other with OH. The rationale for the former is that t-butyl acetylene is actually the substrate that this reaction has been performed on, and for OH that it pushes electrons into the oxirene, making it more anti-aromatic and hence more liable to avoid that antiaromaticity. Animation of the IRC for this combination is shown below. Notice how the reaction now proceeds in a concerted manner directly from the alkyne to the hydroxy-carbene, without any sign of an intervening oxirene.\u00a0\"\"

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The energy and gradient profiles for this variation are shown below. Notice in particular how the barrier has dropped; it is now a much easier reaction.\"\"

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\"\"

\n\n
","doi":"https://doi.org/10.59350/d7wf1-g4m48","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=7027","image":"http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2012/07/alkyne+pa_water.gif","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1341792000,"rid":"za66v-b9714","summary":"Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts.","tags":["Curly Arrows","Reaction Mechanism","Alkyne","Gas Phase","Gas Phase Model"],"title":"Joining up the pieces. Peroxidation of ethyne.","updated_at":1787767314,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=7027","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
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I occasionally notice that posts that first appeared here many years ago suddenly attract attention. Thus this post, entitled The strongest bond in the universe, from ten years back, has suddently become the most popular, going from an average of 0-2 hits per day to 92 in a single day on May 22nd (most views appear to originate from India). I can only presume that a university there has set some course work on this topic and Google has helped some of the students identify my post. Well, re-reading something you wrote ten years ago can be unsettling. Are the conclusions still sound? Would I establish my claim the same way now? After all, one picks up a little more experience in ten years. So here is my revisitation.

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The hypothesis was that mono and then diprotonating dinitrogen strengthened the N-N bond, in the sequence\u00a0N\u2261N \u2192 H-N\u2261N+ \u2192 H-N\u2261N-H2+ to the point that the latter was now a candidate for the strongest known bond between two (non-hydrogen) atoms. One of my original criteria was to calculate the N-N stretching wavenumber. To get this, I had to project out the coupling between the N-N stretching mode and the H-N modes in the latter two species. In the original discussion, Igor suggested another candidate O22+\u00a0in the comments. I speculated that the heavy atom diatomic force constant might be a better way of estimating how strong the bond was rather than the stretching wavenumber, but I never followed this up! So time to do so now.

\n

The calculations are now at the CCSD(T)/Def2-TZVPP level (FAIR DOI: 10.14469/hpc/7214).

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
SpeciesHeavy atom Force constant, mDyne/\u00c5Projected heavy atom stretch, cm-1Bond length, \u00c5
N\u2261N45.517723491.1029
HN\u2261N+50.266224691.0983
HN\u2261NH2+56.490326171.0859
O\u2261O2+44.954221841.0510
N\u2261O1+49.011923651.0678
HN\u2261O2+50.806124111.065
HN\u2261C38.440822341.175
\n

I did learn one new trick. To project out mode mixing between the hydrogen stretch and the heavy atom stretch, the hydrogen atom masses are now set at 10,000! This has the effect of suppressing any mode mixing, but it also results in exactly the same reduced mass for the NN stretch (14.0) for the three species N\u2261N, H-N\u2261N(+) and H-N\u2261N-H(2+), thus facilitating a like for like comparison. Ten years ago I had also tried the other direction, setting the mass of H to 0.001. Although this latter also eliminates the mode mixing, it does not result in the same reduced masses for the NN mode. So we will stick to the heavy hydrogen projection for comparisons.

\n

The force constant increases almost linearly on mono and then diprotonation of dinitrogen, reaching 56.5 mDyne/\u00c5. In comparison, both O22+ and NO1+ are a little lower. Does monoprotonating NO1+ strengthen its bond? Yes, but not quite surpassing HN\u2261NH2+. And the neutral HN\u2261C, which is isoelectronic with HN\u2261N+, also\u00a0shows a weaker bond.

\n

So my revisitation ten years on still shows that diprotonated nitrogen has the strongest bond (presumably in the universe), as now judged by the diatomic force constant. The hunt is still on for a species where the force constant between two non-hydrogen atoms is higher. Maybe I will return in another ten years to see the state of this challenge!

\n\n
","doi":"https://doi.org/10.59350/8n298-0ez38","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22378","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1590192000,"rid":"fwx4f-kv629","summary":"I occasionally notice that posts that first appeared here many years ago suddenly attract attention.","tags":["Interesting Chemistry"],"title":"The strongest bond in the universe: revisited ten years on.","updated_at":1787767310,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22378","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
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My previous two posts on the topic of strongest bonds have involved mono and diprotonating N2 and using quantum mechanics to predict the effect this has on the N-N bond via its length and vibrational stetching mode. Such species are very unlikely to be easily observed for verification. But how about a metal M+ instead of H+? It turns out that structures containing the fragment Ru-N\u2261N-Ru are a small but well studied class of organometallic. Here is a search of the CSD crystal database for this motif.

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\n

\"\"

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The three examples showing the shortest N-N distances are shown below.[1],[2][3]

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\"\" \"\" \"\"

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The NN distances for these three examples are in the region of 1.1\u00c5. There are 39 structures in total, for a variety of other transition metals, with a length <1.15\u00c5. The angles subtended at N are close to linear;

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\"\"

\n

 

\n

For comparison, N2 itself entrained into a crystal structure has the value of ~1.096\u00c5 as measured at 80K (R-factor 0.84%)[4]) which is pretty similar to the value computed in the previous post (1.103\u00c5). \u00a0

\n

So the question to ask is whether any of these organometallic examples have an NN bond at least as strong as that in dinitrogen itself? Only a reliable value for the force constant will give us a clear picture, which however would be non-trivial for such species. But it does suggest that asking whether there could be a real candidate for the strongest bond in the universe other than N2 itself may not be entirely futile.

\n

 

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References

\n
  1. Y. Sun, H. Chan, and Z. Xie, \"Reaction Scope and Mechanism of Sterically Induced Ruthenium-Mediated Intramolecular Coupling of<i>o</i>-Carboranyl with Cyclopentadienyl. Synthesis and Structure of Ruthenium Complexes Incorporating Doubly Linked Cyclopentadienyl\u2212Carboranyl Ligands\", Organometallics, vol. 25, pp. 4188-4195, 2006. https://doi.org/10.1021/om0604122\n\n
    2. \n
  2. Y. Tanabe, S. Kuriyama, K. Arashiba, K. Nakajima, and Y. Nishibayashi, \"Synthesis and Reactivity of Ruthenium Complexes Bearing Arsenic-Containing Arsenic-Nitrogen-Arsenic-Type Pincer Ligand\", Organometallics, vol. 33, pp. 5295-5300, 2014. https://doi.org/10.1021/om5006116\n\n
    3. \n
  3. K. Abdur-Rashid, D.G. Gusev, A.J. Lough, and R.H. Morris, \"Synthesis and Characterization of RuH<sub>2</sub>(H<sub>2</sub>)<sub>2</sub>(P<sup>i</sup>Pr<sub>3</sub>)<sub>2</sub> and Related Chemistry. Evidence for a Bis(dihydrogen) Structure\", Organometallics, vol. 19, pp. 1652-1660, 2000. https://doi.org/10.1021/om990669i\n\n
    4. \n
  4. C. Dou, W. Kosaka, and H. Miyasaka, \"Gate-open-type Sorption in a Zigzag Paddlewheel Ru Dimer Chain Compound with a Phenylenediamine Linker Instructed by a Preliminary Structural Change of Desolvation\", Chemistry Letters, vol. 46, pp. 1288-1291, 2017. https://doi.org/10.1246/cl.170509\n\n
    5. \n
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","doi":"https://doi.org/10.59350/xrt9p-jjn04","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22391","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/05/Screenshot-33-1024x714.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1590364800,"reference":[{"id":"https://doi.org/10.1021/om0604122","unstructured":"Sun, Y., Chan, H.-S., & Xie, Z. (2006). Reaction Scope and Mechanism of Sterically Induced Ruthenium-Mediated Intramolecular Coupling ofo-Carboranyl with Cyclopentadienyl. Synthesis and Structure of Ruthenium Complexes Incorporating Doubly Linked Cyclopentadienyl\u2212Carboranyl Ligands. Organometallics, 25(17), 4188\u20134195."},{"id":"https://doi.org/10.1021/om5006116","unstructured":"Tanabe, Y., Kuriyama, S., Arashiba, K., Nakajima, K., & Nishibayashi, Y. (2014). Synthesis and Reactivity of Ruthenium Complexes Bearing Arsenic-Containing Arsenic-Nitrogen-Arsenic-Type Pincer Ligand. Organometallics, 33(19), 5295\u20135300."},{"id":"https://doi.org/10.1021/om990669i","unstructured":"Abdur-Rashid, K., Gusev, D. G., Lough, A. J., & Morris, R. H. (2000). Synthesis and Characterization of RuH2(H2)2(PiPr3)2 and Related Chemistry. Evidence for a Bis(dihydrogen) Structure. Organometallics, 19(9), 1652\u20131660."},{"id":"https://doi.org/10.1246/cl.170509","unstructured":"Dou, C., Kosaka, W., & Miyasaka, H. (2017). Gate-open-type Sorption in a Zigzag Paddlewheel Ru Dimer Chain Compound with a Phenylenediamine Linker Instructed by a Preliminary Structural Change of Desolvation. Chemistry Letters, 46(9), 1288\u20131291."}],"rid":"dwrdg-60564","summary":"My previous two posts on the topic of strongest bonds have involved mono and diprotonating N2 and using quantum mechanics to predict the effect this has on the N-N bond via its length and vibrational stetching mode. Such species are very unlikely to be easily observed for verification.","tags":["Crystal_structure_mining"],"title":"The strongest bond in the universe: A crystallographic reality check?","updated_at":1787767308,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22391","version":"v1"},{"authors":[{"affiliation":[{"name":"Imperial College London, Chemstry"}],"contributor_roles":[],"family":"Rzepa","given":"Henry","url":"https://orcid.org/0000-0002-8635-8390"}],"blog":{"authors":[{"name":"Henry Rzepa","url":"https://orcid.org/0000-0002-8635-8390"}],"community_id":"8fb94c86-e95f-41cf-aac2-a2877ffc1b5f","created":1693094400,"current_feed_url":null,"description":"Chemistry with a twist","doi":"https://doi.org/10.59350/rzepa","favicon":"https://rogue-scholar.org/api/communities/8fb94c86-e95f-41cf-aac2-a2877ffc1b5f/logo","feed_format":"application/atom+xml","feed_url":"https://www.ch.ic.ac.uk/rzepa/blog/?feed=atom","filter":null,"generator":"WordPress","home_page_url":"https://www.ch.ic.ac.uk/rzepa/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"rzepa","status":"active","subfield":"1606","title":"Henry Rzepa's Blog","updated":1787733932,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
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In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus “NU-1501-Al” can absorb 14 weight% of hydrogen. To power a low-polluting car with a 500 km range, about 4-5 kg of hydrogen gas would be need to be stored and released safely. The molecule is of interest since it opens a systematic strategy of synthetically driven optimisation towards a viable ultra-porous storage material,[1] much like a lead drug compound can be optimised.

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I thought it would be informative to show a 3D interactive model of the crystal lattice here and so I went in search of coordinates. These are indeed available online. This is an example of scientific data Interoperability and Reuse, part of the FAIR\u00a0data acronym. Before showing the model, I thought it worth briefly describing the procedure for starting with deposited data and converting (interoperating) it to the model here.

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  1. The molecule is a so-called MOF, or Metal-Organic-Framework. The core organic framework in this case is composed of linked tryptycene derivatives. Shown below is the 3D structure of this linker, oriented here to show the three-fold symmetry (actually D3) of the molecule, rather than any attempt to reveal all the atoms without any hidden ones. To see the latter, you are encouraged to click on the diagram and view the molecule as a rotatable model instead. The coordinates below are optimised using molecular mechanics to reveal the role of the linker units.
    2. \n
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Click for a rotatable 3D model.

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  1. The data comes in the form of a CIF (crystallographic information) file and needs to be loaded into software that can manipulate such a format. In this case a program called Mercury (from CCDC) is available. Doing so reveals two minor oddities, circled in red below. The phenomenon arises from disorder, or two or more structures each with what is called partial occupancy. In this case, the disorder is largely limited to a p-substituted phenyl spacer linkage, which can adopt one of two rotational positions in the structure. The projection below is now selected to reveal the disorder rather than the symmetry. \"\"
    2. \n
  2. I want to “inter-operate” these coordinates into something that can be modelled and for this, the structure has to be edited to reduce it to a single unambiguous model. My very simple expedient here was simply to remove extraneous disordered atoms entirely; since they are acting as a spacing unit, this is unlikely to change the overall picture.‡ Again, the projection below is selected to show the symmetry present and in particular the hexagonal-like channels that appear in the crystal lattice. To achieve this lattice, the unit cell has to be grown in all three directions using the calculate packing option in the Mercury program.\n
    3. \n
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Click for 3D rotatable model

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Clearly, the hexagonal cavities formed can accommodate a large number of hydrogen molecules. As to why, it is no doubt complex, but I cannot help but notice that the surface of the cavity is lined with multiple C-H units from the aryl spacer units pointing inwards. Given that hydrogen is a very good inducer of dispersion attractions, it would be interesting indeed to see whether the very large number of H…H2 dispersion attractions possible inside the cavity of this species might at least in part be responsible for the ability of this framework to accommodate hydrogen (or methane) gas.[2] It would be good to have an estimate of the dispersion energy term for NU-1501-Al and related species and the contribution of this term to the overall thermodynamics of the system. By the same token, replacing the four aryl C-H units with C-F units (a weaker dispersion attractor, think non-stick teflon) should reduce the ability to absorb hydrogen if dispersion is indeed important.

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‡On the other hand, if the orientation of the aryl C-H groups is important in terms of dispersion attractons, perhaps these groups are actually critical to the effect.

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References

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  1. Z. Chen, P. Li, R. Anderson, X. Wang, X. Zhang, L. Robison, L.R. Redfern, S. Moribe, T. Islamoglu, D.A. G\u00f3mez-Gualdr\u00f3n, T. Yildirim, J.F. Stoddart, and O.K. Farha, \"Balancing volumetric and gravimetric uptake in highly porous materials for clean energy\", Science, vol. 368, pp. 297-303, 2020. https://doi.org/10.1126/science.aaz8881\n\n
    2. \n
  2. S. R\u00f6sel, C. Balestrieri, and P.R. Schreiner, \"Sizing the role of London dispersion in the dissociation of all-meta tert-butyl hexaphenylethane\", Chemical Science, vol. 8, pp. 405-410, 2017. https://doi.org/10.1039/c6sc02727j\n\n
    3. \n
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","doi":"https://doi.org/10.59350/v0xea-7a521","guid":"https://www.ch.imperial.ac.uk/rzepa/blog/?p=22231","image":"https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2020/04/typt2-1024x911.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1587254400,"reference":[{"id":"https://doi.org/10.1126/science.aaz8881","unstructured":"Chen, Z., Li, P., Anderson, R., Wang, X., Zhang, X., Robison, L., Redfern, L. R., Moribe, S., Islamoglu, T., G\u00f3mez-Gualdr\u00f3n, D. A., Yildirim, T., Stoddart, J. F., & Farha, O. K. (2020). Balancing volumetric and gravimetric uptake in highly porous materials for clean energy. Science, 368(6488), 297\u2013303."},{"id":"https://doi.org/10.1039/c6sc02727j","unstructured":"R\u00f6sel, S., Balestrieri, C., & Schreiner, P. R. (2017). Sizing the role of London dispersion in the dissociation of all-meta tert-butyl hexaphenylethane. Chemical Science, 8(1), 405\u2013410."}],"rid":"8ymfn-snz74","summary":"In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus \"NU-1501-Al\" can absorb 14 weight% of hydrogen.","tags":["Crystal_structure_mining","Interesting Chemistry"],"title":"A molecular sponge for hydrogen storage- the future for road transport?","updated_at":1787767306,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=22231","version":"v1"}],"out_of":53991,"page":1,"per_page":10,"total-results":53991}