{"found":57962,"hits":[{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Pursuing the topic of halogen bonds, the system DABCO (a tertiary dibase) and iodine form an intriguing complex. Here I explore some unusual features of the structure HEKZOO[1] as published in 2012[2] and ask whether the bonding between the donor (N) and the acceptor (I-I) really is best described as a “non-covalent-interaction” (NCI) or not.

\n

\n

The crystal structure shows a repeating unit, with each DABCO surrounded by two I2 molecules aligned along the N-N axis. These linear chains are stacked in a dislocated manner induced by aligning to optimize the dispersion interactions between the iodines and the CH groups. The most surprising aspect is the N…I distance shown as 2.42Å. The van der Waals radii of N and I are respectively 1.55 + 1.98 = 3.53Å, a contraction of 1.1Å. The covalent radii are 0.75 + 1.33 = 2.08, an elongation of 0.34Å So is this a strong (non-covalent) interaction/contraction or a stretched weak covalent bond?

\n

I will start with a B3LYP+D3/Def2-TZVPP+PP calculation on the crystal geometry (below).

\n
\"Click

Click for 3D

\n

The short N…I distance has a computed Wiberg bond order of 0.26 (the I-I is 0.76) and an E(2) NBO donor-acceptor interaction energy of 40.1 kcal/mol. For comparison, the E(2) energies for conventional OH…O hydrogen bonds are around 10 kcal/mol. This makes the halogen bond a pretty strong interaction! But is it strong enough to call a bond? Indeed, do we have any means of deciding where the transition from a strong interaction to a weak bond occurs?

\n

A NCI analysis is shown below. This analysis filters out electron densities above 0.05au (which are considered as covalent values) and shows only the properties of the reduced density gradients below this value. The dispersion attractions between the DABCO hydrocarbon chains and the iodine molecules are very apparent, but the N…I is encircled with a strange feature, normally only seen for covalent bonds or transition state breaking/forming bonds. A strong hydrogen bond for example would show up as blue, and not this strange torus.

\n
\"Click

Click for 3D

\n

Reducing the threshold for covalent densities to be filtered out to 0.03au eliminates the N…I feature (it is now covalent by definition so to speak), but the I-I feature remains. One can see here that this NCI analysis does rather arbitrarily depend on what one considers the covalent density threshold to be, and as one moves up the periodic table, this density changes. What should the density for eg a N…I interaction/bond actually be? The value appropriate for N (0.05) or I (< 0.03)?
\n

\"Click

Click for 3D

\n

Next, I show the optimised geometry of the system above.[3] This is not a periodic boundary calculation and this lack of a surrounding environment is highlighted by the change in the structure. The N…I distance lengthens, and the iodines which have no DABCO to interact with lengthen more. One might conclude that the short N…I distance measured in the solid state structure is due to some degree of N…I compression induced by the linear chains of I-I…DABCO…I-I…DABCO…I-I aligning to maximise the interchain dispersion attractions. Thus the N…I “bond/interaction” is really a co-operative effect between the N…I atoms and the extended 3D structure of the molecule. The N…I contraction of 1.1Å noted above is in part due to the intrinsic halogen bond, but also in part due to dispersion attractions elsewhere!
\n\"DAB-opt\"

\n

So it does rather seem as if the DABCO-I2 complex sits very much in that awkward region in which the contracted N…I distance could either be described as a weak bond or a strong interaction.‡. Just like the infamous H…H bond in cis-butene, one cannot just regard a bond as a purely localised phenomenon, one must also take into account what is happening elsewhere in the total system. Halogen bonds could also be regarding as filling the gap spanned by recognised covalency and recognised hydrogen bonds. I note in passing that another “awkward” bond is the 4th in the diatomic C2[4] that has a bond energy of about 17 kcal/mol, again weak for a normal bond and strong for an interaction.

\n

In my next post on this theme, I will deal with another halogen bond that is found in a famous molecule known for a long time and which has another weird property.

\n
\n

‡Postscript. An ELF analysis reveals the following basin centroids. Basin 1 integrates to 2.00 electrons, basin 2 to 1.92. The asymmetry in the position of the basin centroid towards the nitrogen suggests it is not an equally shared covalent bond, as indeed the Wiberg bond order noted above also indicates. The I…I basin integrates to 1.86 electrons, indicating slightly reduced bonding (by donation into the sigma; orbital).
\n\"DABCO-I2-ELF\"

\n
\n

References

\n
  1. Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., \"CCDC 879935: Experimental Crystal Structure Determination\", 2013. https://doi.org/10.5517/ccyjn03\n\n
    2. \n
  2. A. Peuronen, A. Valkonen, M. Kortelainen, K. Rissanen, and M. Lahtinen, \"Halogen Bonding-Based \"Catch and Release\": Reversible Solid-State Entrapment of Elemental Iodine with Monoalkylated DABCO Salts\", Crystal Growth & Design, vol. 12, pp. 4157-4169, 2012. https://doi.org/10.1021/cg300669t\n\n
    3. \n
  3. H.S. Rzepa, \"Gaussian Job Archive for C12H24I8N4\", 2014. https://doi.org/10.6084/m9.figshare.1254779\n\n
    4. \n
  4. D. Danovich, P.C. Hiberty, W. Wu, H.S. Rzepa, and S. Shaik, \"The Nature of the Fourth Bond in the Ground State of C<sub>2</sub>: The Quadruple Bond Conundrum\", Chemistry \u2013 A European Journal, vol. 20, pp. 6220-6232, 2014. https://doi.org/10.1002/chem.201400356\n\n
    5. \n
\n\n
","doi":"https://doi.org/10.59350/mscek-qty92","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13105","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2014/11/HEKZOO.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1417305600,"reference":[{"id":"https://doi.org/10.5517/ccyjn03","unstructured":"Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., \"CCDC 879935: Experimental Crystal Structure Determination\", 2013."},{"id":"https://doi.org/10.1021/cg300669t","unstructured":"Peuronen, A., Valkonen, A., Kortelainen, M., Rissanen, K., & Lahtinen, M. (2012). Halogen Bonding-Based \"Catch and Release\": Reversible Solid-State Entrapment of Elemental Iodine with Monoalkylated DABCO Salts. Crystal Growth & Design, 12(8), 4157\u20134169."},{"id":"https://doi.org/10.6084/m9.figshare.1254779","unstructured":"Rzepa, H. S. (2014). Gaussian Job Archive for C12H24I8N4 [Dataset]. figshare."},{"id":"https://doi.org/10.1002/chem.201400356","unstructured":"Danovich, D., Hiberty, P. C., Wu, W., Rzepa, H. S., & Shaik, S. (2014). The Nature of the Fourth Bond in the Ground State of C2: The Quadruple Bond Conundrum. Chemistry \u2013 A European Journal, 20(21), 6220\u20136232."}],"rid":"16aqc-te677","summary":"Pursuing the topic of halogen bonds, the system DABCO (a tertiary dibase) and iodine form an intriguing complex. Here I explore some unusual features of the structure HEKZOO as published in 2012 and ask whether the bonding between the donor (N) and the acceptor (I-I) really is best described as a \"non-covalent-interaction\" (NCI) or not.","tags":["Interesting Chemistry","Bond Energy","Co-operative","Donor-acceptor Interaction Energy"],"title":"Halogen bonds 2: The DABCO-Iodine structure.","updated_at":1793349501,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13105","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

These posts contain the computed potential energy surfaces for a fair few “text-book” reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent,[1] as\u00a0prepared from di-iodomethane using zinc metal insertion into a C-I bond.
\n\"simmonds-smith\"

\n

\n

Two reactions it can be compared with are the epoxidation of ethene using a peracid and dichlorocyclopropanation. The latter is a four-electron pericyclic process, which is thermally forbidden. The outcome there is that the two new bonds form very asynchronously to avoid transition state antiaromaticity. The former is a more complex reaction, best described as a six-electron process\u00a0which allows both C…O bonds to form at the same rate. So which of these two does the\u00a0Simmons\u2013Smith mechanism correspond to?

\n

The calculation as undertaken at a \u03c9B97XD/Def2-TZVPD-PP (solvent=dichloromethane) level[2] shows the two C…C bonds forming at more or less the same rate. The reaction therefore resembles epoxidation rather than dichlorocyclopropanation.

\n

\"SS\"

\n

The\u00a0intrinsic reaction coordinate (IRC)[3] is shown below, revealing a concerted and almost synchronous reaction. The synchronicity is all the more surprising given the diversity of bonds forming/breaking.
\n\"SSa\"
\n\"SSE\"

\n

\"SSG\"

\n

There are slight and tantalizing hints that the alkene and the I-Zn-CH2-I components initially form a weak \u03c0-complex, which then rearranges into the TS, and then again a weak complex at the end. The NCI surfaces for both are shown below, and show clear signs of dispersion-like stabilisations for both of them!\u00a0The strange torus around the Zn-I bond is due to the need for a lower density threshold to filter out the covalent interactions.

\n
\"Click

Click for 3D

\n
\"Click

Click for 3D

\n

References

\n
  1. H.E. Simmons, and R.D. Smith, \"A NEW SYNTHESIS OF CYCLOPROPANES FROM OLEFINS\", Journal of the American Chemical Society, vol. 80, pp. 5323-5324, 1958. https://doi.org/10.1021/ja01552a080\n\n
    2. \n
  2. H.S. Rzepa, \"C 3 H 6 I 2 Zn 1\", 2014. https://doi.org/10.14469/ch/147617\n\n
    3. \n
  3. H.S. Rzepa, \"Gaussian Job Archive for C3H6I2Zn\", 2014. https://doi.org/10.6084/m9.figshare.1270441\n\n
    4. \n
\n\n
","doi":"https://doi.org/10.59350/51gb4-0qa77","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13174","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2014/12/simmonds-smith.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1418515200,"reference":[{"id":"https://doi.org/10.1021/ja01552a080","unstructured":"Simmons, H. E., & Smith, R. D. (1958). A NEW SYNTHESIS OF CYCLOPROPANES FROM OLEFINS. Journal of the American Chemical Society, 80(19), 5323\u20135324."},{"id":"https://doi.org/10.14469/ch/147617","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2014, December 13). C 3 H 6 I 2 Zn 1 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.6084/m9.figshare.1270441","unstructured":"Rzepa, H. S. (2014). Gaussian Job Archive for C3H6I2Zn [Dataset]. figshare."}],"rid":"ga6kw-98n08","summary":"These posts contain the computed potential energy surfaces for a fair few \"text-book\" reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent, as prepared from di-iodomethane using zinc metal insertion into a C-I bond.","tags":["Reaction Mechanism","Computed Potential Energy Surfaces","Di-iodomethane Using Zinc Metal Insertion","Simmons"],"title":"Cyclopropanation: the mechanism of the Simmons\u2013Smith reaction.","updated_at":1793349498,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13174","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

I have written earlier about the Amsterdam Manifesto. That arose out of a conference on the theme of “beyond the PDF“, with one simple question at its heart: what can be done to liberate data from containers it was not designed to be in? The latest meeting on this topic will happen in\u00a0January 2015 as FORCE2015.

\n

\n

The format is suitably modern, starting with a Hackathon, and then two days of talks, posters and demos. We will be presenting both a talk and a demo. In the spirit of emancipated data, we have placed the latter into a container that is most certainly not a PDF. That demo has been archived, and there assigned a DOI[1] and for good measure transcluded into this post in its entirety. We hope this demonstrates that such “containers” can be usefully moved around to where they might be needed. I should say that the core of this demo is not just the data, but the metadata associated with it. Metadata renders that data discoverable (mineable) and its usage measurable.†

\n

\n\n

\n

I hope to report here on anything interesting happening at the FORCE2015 event.

\n
\n

\u2021The format of this blog is a tiny bit too narrow for the demo to fit comfortably. Go see it here[1] and “enlarge” the view for a better experience.

\n

†Full details of this are in preparation.

\n

References

\n
  1. H.S. Rzepa, N. Mason, A. Mclean, and M. Harvey, \"Interoperability for Data Repositories. Machine Methods for Retrieving Data for Display or Mining Utilising Persistent (data-DOI) Identifiers\", 2014. https://doi.org/10.6084/m9.figshare.1266197\n\n
    2. \n
\n\n
","doi":"https://doi.org/10.59350/ek3ac-55t28","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13203","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1418774400,"reference":[{"id":"https://doi.org/10.6084/m9.figshare.1266197","unstructured":"Rzepa, H. S., Mason, N., Mclean, A., & Harvey, M. (2014). Interoperability for Data Repositories. Machine Methods for Retrieving Data for Display or Mining Utilising Persistent (data-DOI) Identifiers [Dataset]. figshare."}],"rid":"dx213-m8d70","summary":"I have written earlier about the Amsterdam Manifesto.","tags":["Chemical IT"],"title":"Data discoverability","updated_at":1793349494,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13203","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published[1]. That was then.

\n

\n

\"\"

\n

This is now. I have just finished a post on ring-opening reactions of oxirene, a 4n electron anti-aromatic ring. I was casting around for an example of a calculation done just before the modern Internet era, and happened upon the above. Although this was a mere 20 years ago, much of the detail had faded; I had not thought much about it in the intervening years, but I did recollect that although we had attributed the high stereoselectivity shown above to a stereoelectronic orbital alignment, I was not entirely happy with the interpretation. Put simply, we had relied on a molecular orbital diagram, and this diagram (in resplendent colour in the journal, one of the few being so published at that time, and for no colour charge to boot) was just too complicated. Arguably it was the fixated complexity (I remember at the time that it looked complicated no matter what the viewing angle was) that set me on the road to the use of the Web, and ultimately here to this blog. So I thought a re-analysis using modern algorithms and presentation might help simplify. The newly recalculated transition state (\u03c9B97XD/6-311G(d,p)[2] looks like:

\n
\"\"

Transition state for ring opening of a cyclopropene. Click for 3D.

\n
    \n
  1. The reaction is a 4n (n=1) electron electrocyclic ring opening and so according to the rules, should proceed with the formation/cleavage of an antarafacial bond. You might think that there are not quite enough substituents to reveal this stereochemistry, but there are if the carbene lone pair is included. So how to add the lone pair?
    2. \n
  2. Well, its coordinates can be computed using the ELF (electron localisation function). The relevant lone pair is ringed in red below. Using (old technology, i.e. a static figure) you may choose to believe me when I argue that this lone pair is above the plane of the forming ring from the perspective shown, whilst the terminus of the bond it forms is to the bottom. This defines an antarafacial component. Well, I might have carefully manipulated the viewing angle to show this. Now, in 2012 rather than 1992, you can load the 3D coordinates by clicking below, and check for yourself!
    \n
    \"\"

    Lone pair centroid for the transition state. Click for 3D

    \n
    3. \n
  3. What about the stereo-control? Take a look at the angle between the axis of the C-Cl bond (atoms ringed in blue) and the centroid of the carbene lone pair (red). It is about 162\u00b0, or almost anti-periplanar. A magic orientation in organic chemistry. Time to attack the orbitals again. Our published diagram looked as below. It shows the HOMO aligning with the LUMO+2 (if your eyes are not distracted by all the other detail).\"\"
    But we can now simplify such a complex molecular orbital by using instead a localized version, an NBO. A little explanation is needed. The NBO orbital shown with red/blue phases is antibonding for the C-Cl bond. That with orange/purple is the carbene lone pair. Where orange overlaps with red, we have a positive overlap that stabilises the system. The NBO E2 perturbation energy is around 4.6 kcal/mol. Although this may seem small, it is actually quite large for a through-space interaction of this type. It is this stabilisation (amounting to ~ 1.6 kcal/mol in free energy) that accounts for the high selectivity for the stereoisomer shown above.
    \n
    \"\"

    NBO for transition state. Click for 3D.

    \n
    4. \n
\n

Well, I think that the passage of 20 years has enabled us to tidy up the origins of the stereoelectronic effect responsible for controlling this reaction, and to produce clearer diagrams which the reader can interactively explore for themselves. It did take 20 years to join things up though!

\n

\"\"[3]

\n

References

\n
  1. M.S. Baird, J.R. Al Dulayymi, H.S. Rzepa, and V. Thoss, \"An unusual example of stereoelectronic control in the ring opening of 3,3-disubstituted 1,2-dichlorocyclopropenes\", Journal of the Chemical Society, Chemical Communications, pp. 1323, 1992. https://doi.org/10.1039/c39920001323\n\n
    2. \n
  2. H.S. Rzepa, \"C 5 H 5 Cl 3\", 2012. https://doi.org/10.14469/ch/14180\n\n
    3. \n
  3. H.S. Rzepa, \"Gaussian Job Archive for C5H5Cl3\", 2015. https://doi.org/10.6084/m9.figshare.1285422\n\n
    4. \n
\n\n
","doi":"https://doi.org/10.59350/1eja6-jjf31","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=7068","image":"http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2012/07/dichlorocarbene.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1342051200,"reference":[{"id":"https://doi.org/10.1039/c39920001323","unstructured":"Baird, M. S., Al Dulayymi, J. R., Rzepa, H. S., & Thoss, V. (1992). An unusual example of stereoelectronic control in the ring opening of 3,3-disubstituted 1,2-dichlorocyclopropenes. Journal of the Chemical Society, Chemical Communications, (18), 1323."},{"id":"https://doi.org/10.14469/ch/14180","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2012, July 10). C 5 H 5 Cl 3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.6084/m9.figshare.1285422","unstructured":"Rzepa, H. S. (2015). Gaussian Job Archive for C5H5Cl3 [Dataset]. figshare."}],"rid":"473qx-a2m96","summary":"Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published.","tags":["Interesting Chemistry","Reaction Mechanism","Cambridge","Chemist","Conformational Analysis"],"title":"More joining up of pieces. Stereocontrol in the ring opening of cyclopropenes.","updated_at":1793349492,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=7068","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

About two years ago, I posted on the distribution of readership of this blog. The passage of time has increased\u00a0this from 144 to 176 countries. There are apparently between 189-196 such, so not quite yet complete coverage! \"2015\"
\nOf course, it is the nature of the beast that whilst we can track countries, very little else is known about such readerships. Is the readership young or old, student or professor, chemist or not (although I fancy the latter is less likely). Another way of keeping tabs on some of the activity are aggregators such as Chemical Blogspace, which has been rather quiet recently. Perhaps we have become too obsessed by metrics, and with the Internet-of-things apparently the “next-big-thing”, the metrics are only likely to increase. This will only encourage “game playing“, and I urge you to see a prime example of this in the UK REF (research excellence framework), the measure which attempts to rank UK\u00a0universities in terms of their “excellence”.

\n

\n

Ah well, I had better leave this blog and go off and check on my h-index just in case it has notched up another integer.

\n\n
","doi":"https://doi.org/10.59350/rvgsd-85f42","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13243","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/01/2015.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1420675200,"rid":"2qr4p-1ck07","summary":"About two years ago, I posted on the distribution of readership of this blog. The passage of time has increased this from 144 to 176 countries. There are apparently between 189-196 such, so not quite yet complete coverage!","tags":["General","Chemist","Internet-of-things","Professor","United Kingdom"],"title":"The demographics of a blog readership \u2013 updated","updated_at":1793349489,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13243","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

The journal of chemical education has many little gems providing inspiration for laboratory experiments. Jonathan Piard reports one based on the reaction below[1]; here I investigate the mechanism of this transformation.

\n

\n

\"spiropyran\"
\nThere are two things going on here; an electrocyclic ring opening involving breaking the C-O bond, with\u00a0a cis/trans isomerism of the alkene (concurrent or consecutive). A crystal structure of the dinitro analogue establishes the trans stereochemistry[2]. This product zwitterion is highly coloured (blue-purple) unlike the colourless reactant. The rate at which this colour clears can be easily measured in a UV/visible spectrometer, and from this activation parameters are inferred\u00a0as a function of the solvent.

\n

Photochemically, this reaction is too complex to study quickly using computation, but the thermal back reaction is much easier. Applying the \u03c9B97XD/6-311G(d,p)/SCRF=solvent procedure and using the C-O bond as a reaction coordinate results in the following transition state[3] IRC profile[4] for DMSO as solvent,\u00a0here connecting to the\u00a0cis-alkene.\u00a0The thermal forward barrier for the C…O cleaving\u00a0is ~12 kcal/mol. More significantly, the back reaction is only <2 kcal mol, which is very much lower than that reported[1] (~22 kcal/mol) and makes the cis-alkene very much a transient species\u00a0and therefore not the\u00a0coloured species being measured.

\n

\"C-O-cleave\"

\n

A second transition state involving C=C bond rotation is located[5] and this yields the following IRC[6] to form the trans-alkene, with activation parameters listed below.\u00a0It is entirely probable however that the forward photochemical reaction follows a different course involving conical intersections; an interesting study in its own right, but beyond the scope of this post.

\n

\"cis-trans\"

\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
Measured and computed activation parameters for the thermal back\u00a0reaction
Solvent\u0394G298, kcal mol-1\u0394H, kcal mol-1\u0394S, cal K-1 mol-1
DMSO, measured22.026.4+14.6
toluene, measured19.014.3-15.6
DMSO, calc[5]21.220.4+2.6
toluene, calc[7]18.619.1+1.8
\n

The next issue surrounds the effect of solvent. Most spectacular are those of the\u00a0activation parameters for the thermal back-reaction. The measured activation entropy \u0394S changes with solvent by \u039430.2 cal, and the enthalpy \u0394H by \u039412.1 kcal, which are enormous solvent effects. Are they in fact real? It is reassuring at least that the calculated free energy agrees pretty closely with the measured values. So too does the decrease in\u00a0\u0394G in changing the solvent from DMSO to toluene (3.0 kcal/mol measured, 2.6 calculated).

\n

There is little sign of a large solvent effect in the calculated values. This could be for three reasons.

\n
    \n
  1. The first is that adding explicit, hydrogen-bonded solvent molecules to the system is essential. As the zwitterionic character is lost when the trans-alkene starts to rotate, the system will become less ionic, and hence shed solvent molecules and gain entropy. If the solvent is not capable of hydrogen bonding, as say toluene, these will not be shed and the entropy will not increase at the transition state. It is difficult however to reconcile this picture with the apparent large loss of entropy for toluene as solvent.
    2. \n
  2. The second reason is because of a complete change in mechanism, one not modelled here.
    3. \n
  3. For completeness, one should also mention that the measured values might simply be in error, either due to typographical mistakes or indeed in numerical analysis.
    4. \n
\n

I will conclude with the colour.\u00a0It is possible to compute the electronic excitations across the range 180-580nm, and I show below a difference spectrum (for DMSO as solvent) with the product +ve and the reactant \u00a0-ve. You can see the spectacular red-shift for the highly conjugated zwitterion! The absolute value of \u03bbmax is not red-shifted enough (by about 65 nm), but the effect remains real.
\n\"spiro\"

\n

The above experiment is for undergraduate chemistry laboratories. I suggest that a computational reality check could also easily be included into such a lab, and would certainly help give students a broader perspective.

\n

References

\n
  1. J. Piard, \"Influence of the Solvent on the Thermal Back Reaction of One Spiropyran\", Journal of Chemical Education, vol. 91, pp. 2105-2111, 2014. https://doi.org/10.1021/ed4005003\n\n
    2. \n
  2. J. Hobley, V. Malatesta, R. Millini, L. Montanari, and W. O Neil Parker, Jr, \"Proton exchange and isomerisation reactions of photochromic and reverse photochromic spiro-pyrans and their merocyanine forms\", Physical Chemistry Chemical Physics, vol. 1, pp. 3259-3267, 1999. https://doi.org/10.1039/a902379h\n\n
    3. \n
  3. H.S. Rzepa, \"C 19 H 18 N 2 O 3\", 2015. https://doi.org/10.14469/ch/189540\n\n
    4. \n
  4. H.S. Rzepa, \"C19H18N2O3\", 2015. https://doi.org/10.14469/ch/189573\n\n
    5. \n
  5. H.S. Rzepa, \"C 19 H 18 N 2 O 3\", 2015. https://doi.org/10.14469/ch/189546\n\n
    6. \n
  6. H.S. Rzepa, \"C19H18N2O3\", 2015. https://doi.org/10.14469/ch/189648\n\n
    7. \n
  7. H.S. Rzepa, \"C 19 H 18 N 2 O 3\", 2015. https://doi.org/10.14469/ch/189579\n\n
    8. \n
\n\n
","doi":"https://doi.org/10.59350/h3q65-w8y21","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13300","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/02/spiropyran4.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1423008000,"reference":[{"id":"https://doi.org/10.1021/ed4005003","unstructured":"Piard, J. (2014). Influence of the Solvent on the Thermal Back Reaction of One Spiropyran. Journal of Chemical Education, 91(12), 2105\u20132111."},{"id":"https://doi.org/10.1039/a902379h","unstructured":"Hobley, J., Malatesta, V., Millini, R., Montanari, L., & O Neil Parker, Jr, W. (1999). Proton exchange and isomerisation reactions of photochromic and reverse photochromic spiro-pyrans and their merocyanine forms. Physical Chemistry Chemical Physics, 1(14), 3259\u20133267."},{"id":"https://doi.org/10.14469/ch/189540","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 1). C 19 H 18 N 2 O 3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189573","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 4). C19H18N2O3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189546","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 1). C 19 H 18 N 2 O 3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189648","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C19H18N2O3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189579","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 4). C 19 H 18 N 2 O 3 [Archival collection]. Imperial College London."}],"rid":"jccrq-10321","summary":"The journal of chemical education has many little gems providing inspiration for laboratory experiments. Jonathan Piard reports one based on the reaction below; here I investigate the mechanism of this transformation.","tags":["Reaction Mechanism","Calculated Free Energy","Chemical Education","Jonathan Piard"],"title":"Mechanism of the solvatochromic reaction of a spiropyran.","updated_at":1793349486,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13300","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Steganone is an unusual natural product, known for about 40 years now. The assignment of its absolute configurations makes for an interesting, on occasion rather confusing, and perhaps not entirely atypical story. I will start with the modern accepted stereochemical structure of this molecule, which comes in the form of two separately isolable atropisomers.
\n\"steganone\"
\nThe first reported synthesis of this system in 1977 was racemic, and no stereochemistry is shown in the article (structure 2).[1] Three years later an “Asymmetric total synthesis of (-)steganone and revision of its absolute configuration” shows how the then accepted\u00a0configuration (structure 1 in this article) needs to be revised to the\u00a0enantiomer shown as\u00a0structure 12 in the article[2] and matching\u00a0the above representation. The system has continued to attract interest ever since[3],[4],[5],[6], not least because of the presence of axial chirality in the form of atropisomerism. Thus early on it was shown that the alternative atropisomer, the (aS,R,R) configuration initially emerges out of several syntheses, and has to be converted to the (aR,R,R) configuration by heating[3]. One could easily be fooled by such isomerism!

\n

\n

Absolute configurations can be established in several ways.

\n
    \n
  1. From precursors of known absolute configuration. This was the most common method until relatively recently, but it is very expensive since asymmetric syntheses are often much more complex and longer than racemic\u00a0ones. There is always a small residual doubt\u00a0that any\u00a0transformation in the synthesis might have altered the configuration in an unexpected manner.
    2. \n
  2. From an X-ray of the final configuration (Bijvoet). Very often the structure is determined on a derivative of the target compound (the original\u00a0may not form suitable crystals). There is also the doubt that the selected crystals may in fact be a minor form and do not represent the bulk of the system in solution. This is especially true where atropisomerism is concerned, since the solid state structure may not represent the same atropisomer present in solution.
    3. \n
  3. In the last decade or so, it has become more common to make use of the computation\u00a0of measured\u00a0chiroptical spectroscopies to see if they match.\u00a0It turns out that this method appears never to have been applied to Steganone, and here I attempt to rectify this.
    4. \n
\n

First, let us compute the optical rotation. The\u00a0(aR,R,R) stereoisomer is also known as (-)-Steganone, because the measured specific rotation is [\u03b1]589 -170\u00b0 \u00b1 30.[3] It is computed (MN12L/6-311++G(d,p)/SCRF=chloroform) as -240\u00b0, [\u03b1]365 -2251[7]. The other atropisomer (aS,R,R) is computed to be 4.5 kcal/mol higher in free energy\u00a0with\u00a0[\u03b1]589 +408\u00b0[8], and measured as +150.[3] There is some uncertainty in the computed values, since the rotations can be dependent on the conformation not only of the rings, but the substituents. You might imagine that the conformation of eg a -OMe group is unimportant, but this is not so. In this case, I have used a crystal structure of a related species to\u00a0serve as the start point for optimising the MeO\u00a0conformations. The greater mismatch between computation and experiment for the (aS,R,R) stereoisomer probably needs an exploration of more conformations of the -OMe groups. At least in both cases the signs match between computation and measurement.

\n

Next, the electronic circular dichroism (ECD), which has also been measured[3] for the (aR,R,R) isomer as \u0394\u03b5 201nm (-ve Cotton effect), 218 (+ve), 244 (-ve), 276 (+ve) 304 (-ve) and 337 (-ve). Bearing in mind that the baselines in ECD spectra are notoriously difficult to define (moving it up or down can easily invert a Cotton effect), the agreement with the calculated spectrum MN12L/6-311++G(d,p)/SCRF=chloroform, nstates=200)[9] might seem\u00a0reasonable, although the calculated version has more peaks in the region 225-265 than are reported (e.g. 235, +ve, 265, -ve).
\n\"(R,R)-steganone-9\"
\nThe (aS,R,R) isomer seems a less good fit. The +ve peak at 218 is missing, the +ve 276 peak matches better than the other isomer, but the 337nm peak is again the wrong sign.
\n\"(aS,R,R)-steganone\"

\n

Of course, in such a game it may be the DFT functional used for the simulation that itself might be misleading, MN12L in this case. Just to check, I also include the results using M062X[10] to see how variable these simulations might be. The measured peaks at 201, 218, 244 and 337nm match, but the ones at 276 and 304nm do not.

\n

\"s-m062x\"

\n

Although matching computed with measured ECD spectra is commonly used to assign absolute configurations of molecules, you can see from these results that the technique is not a cast iron one! Even scanning through myriad DFT procedures to find the one that fits best is probably not a complete solution either. Can anything be done to further increase confidence?

\n

How about\u00a0Vibrational Circular Dichroism (VCD) predictions?[11],[12]. Like ECD, VCD is also sensitive to conformation, which is why some modern instruments have low temperature probes operating at close to 0K which strive to capture only a single lowest energy conformation (although of course in any simulation, you have to identify that conformation reliably!). At some stage in the future, the VCD spectra of steganone might indeed be measured, and hence compared with the below. It might serve to increase confidence in the chiroptical methods as a means of assigning configuration.

\n

\"(aR,R,R)-steganone\" \"(aS,R,R)-steganone\"

\n

We might conclude from this short exploration of chiroptical spectroscopy that no one single measured or computed value can be absolutely definitive; rather it is the accumulation from various sources that builds up the case for a particular configuration. But at least the above simulations do serve to add some useful additional data for the record.

\n

References

\n
  1. D. Becker, L.R. Hughes, and R.A. Raphael, \"Total synthesis of the antileukaemic lignan (\u00b1)-steganacin\", J. Chem. Soc., Perkin Trans. 1, pp. 1674-1681, 1977. https://doi.org/10.1039/p19770001674\n\n
    2. \n
  2. J. Robin, O. Gringore, and E. Brown, \"Asymmetric total synthesis of the antileukaemic lignan precursor (-)steganone and revision of its absolute configuration\", Tetrahedron Letters, vol. 21, pp. 2709-2712, 1980. https://doi.org/10.1016/s0040-4039(00)78586-8\n\n
    3. \n
  3. E.R. Larson, and R.A. Raphael, \"Synthesis of (\u2013)-steganone\", J. Chem. Soc., Perkin Trans. 1, pp. 521-525, 1982. https://doi.org/10.1039/p19820000521\n\n
    4. \n
  4. A. Bradley, W.B. Motherwell, and F. Ujjainwalla, \"A concise approach towards the synthesis of steganone analogues\", Chemical Communications, pp. 917-918, 1999. https://doi.org/10.1039/a900743a\n\n
    5. \n
  5. M. Uemura, A. Daimon, and Y. Hayashi, \"An asymmetric synthesis of an axially chiral biaryl via an (arene)chromium complex: formal synthesis of (\u2013)-steganone\", J. Chem. Soc., Chem. Commun., vol. 0, pp. 1943-1944, 1995. https://doi.org/10.1039/c39950001943\n\n
    6. \n
  6. B. Yalcouye, S. Choppin, A. Panossian, F.R. Leroux, and F. Colobert, \"A Concise Atroposelective Formal Synthesis of (\u2013)\u2010Steganone\", European Journal of Organic Chemistry, vol. 2014, pp. 6285-6294, 2014. https://doi.org/10.1002/ejoc.201402761\n\n
    7. \n
  7. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189647\n\n
    8. \n
  8. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189646\n\n
    9. \n
  9. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189649\n\n
    10. \n
  10. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189657\n\n
    11. \n
  11. https://doi.org/\n\n
    12. \n
  12. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189651\n\n
    13. \n
\n\n
","doi":"https://doi.org/10.59350/5t09h-k5125","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13353","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/02/steganone3.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1423526400,"reference":[{"id":"https://doi.org/10.1039/p19770001674","unstructured":"Becker, D., Hughes, L. R., & Raphael, R. A. (1977). Total synthesis of the antileukaemic lignan (\u00b1)-steganacin. J. Chem. Soc., Perkin Trans. 1, (14), 1674\u20131681."},{"id":"https://doi.org/10.1016/s0040-4039(00)78586-8","unstructured":"Robin, J. P., Gringore, O., & Brown, E. (1980). Asymmetric total synthesis of the antileukaemic lignan precursor (-)steganone and revision of its absolute configuration. Tetrahedron Letters, 21(28), 2709\u20132712."},{"id":"https://doi.org/10.1039/p19820000521","unstructured":"Larson, E. R., & Raphael, R. A. (1982). Synthesis of (\u2013)-steganone. J. Chem. Soc., Perkin Trans. 1, (0), 521\u2013525."},{"id":"https://doi.org/10.1039/a900743a","unstructured":"Bradley, A., Motherwell, W. B., & Ujjainwalla, F. (1999). A concise approach towards the synthesis of steganone analogues. Chemical Communications, (10), 917\u2013918."},{"id":"https://doi.org/10.1039/c39950001943","unstructured":"Uemura, M., Daimon, A., & Hayashi, Y. (1995). An asymmetric synthesis of an axially chiral biaryl via an (arene)chromium complex: formal synthesis of (\u2013)-steganone. J. Chem. Soc., Chem. Commun., 0(19), 1943\u20131944."},{"id":"https://doi.org/10.1002/ejoc.201402761","unstructured":"Yalcouye, B., Choppin, S., Panossian, A., Leroux, F. R., & Colobert, F. (2014). A Concise Atroposelective Formal Synthesis of (\u2013)\u2010Steganone. European Journal of Organic Chemistry, 2014(28), 6285\u20136294."},{"id":"https://doi.org/10.14469/ch/189647","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C 22 H 20 O 8 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189646","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C 22 H 20 O 8 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189649","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C 22 H 20 O 8 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189657","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 10). C 22 H 20 O 8 [Archival collection]. Imperial College London."},{"id":"https://doi.org/"},{"id":"https://doi.org/10.14469/ch/189651","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C 22 H 20 O 8 [Archival collection]. Imperial College London."}],"rid":"btpcq-vd795","summary":" Steganone is an unusual natural product, known for about 40 years now. The assignment of its absolute configurations makes for an interesting, on occasion rather confusing, and perhaps not entirely atypical story. I will start with the modern accepted stereochemical structure of this molecule, which comes in the form of two separately isolable atropisomers.","tags":["Interesting Chemistry","Free Energy","Lowest Energy Conformation","Natural Product","Simulation"],"title":"Chiroptical spectroscopy of the natural product Steganone.","updated_at":1793349483,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13353","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

The title of this post refers to the site\u00a0http://howopenisit.org/\u00a0 which is in effect a license scraper for journal articles. In the past 2-3 years in the UK, we have been able to make use of grants to our university to pay publishers to convert our publications into Open Access (also called GOLD). I thought I might check out a few of my recent publications to see what\u00a0http://howopenisit.org/\u00a0makes of them.

\n

\n

This was catalysed by an\u00a0article\u00a0which revealed that UK universities spent \u00a39M in 2014 on the purchase of such openness. One of the “challenges” identified\u00a0is the difficulty in converting such payment into an article that actually is open. Apparently, publishers make not a few mistakes in their quality controls in ensuring it is so, relying on irate authors informing them of such mistakes. This can be quite tedious to do, and so a tool that largely automates this checking is most useful. So here we go.

\n
    \n
  1. doi: 10.1039/C3SC53416B[1] This is a good start. The output looks like thus. Green is GOLD so to speak. Well done the Royal Society of Chemistry.
    \n\"10.1039:C3SC53416B\"
    2. \n
  2. doi: 10.1021/ci500302p[2] from the ACS this time. Pink, but at least free to read. Quite what that means is less certain. There is an adage, “the right to read means the right to mine” presumably means this article is OK to mine, but then why does it not say so?\"10.1021:ci500302p\"
    3. \n
  3. doi: 10.1002/anie.201405238[3]. Pink again, but the colour now simply means no information about the license could be obtained from the publisher (Wiley). \"10.1002:anie.201405238\"
    4. \n
\n

I ran a few more and sadly the third of the above, “no information” was the most common response. And the legal response is invariably that if no information can be obtained, the answer is NO, it is not free to read. In other words, not providing a license is just as bad as saying it’s not free to read.

\n

Article aggregators such as Symplectic do not yet perform the service above (which to be fair is still in beta), and so I cannot yet check how many GOLD articles there are to my name. I think it should be about 8, and I might add that the time I have to spend in arranging for this to happen is not negligible. Hell, I could probably have found a few more reactions mechanism in the time I have spent on achieving GOLD. This is one of those topics which would be interesting to revisit say in five years time to see how the world has changed. So I leave this little time capsule and will update it then!

\n

References

\n
  1. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-Garc\u00eda, M.J. Harvey, N.J. Mason, and H.S. Rzepa, \"The Houk\u2013List transition states for organocatalytic mechanisms revisited\", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b\n\n
    2. \n
  2. M.J. Harvey, N.J. Mason, and H.S. Rzepa, \"Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks\", Journal of Chemical Information and Modeling, vol. 54, pp. 2627-2635, 2014. https://doi.org/10.1021/ci500302p\n\n
    3. \n
  3. A. Jana, I. Omlor, V. Huch, H.S. Rzepa, and D. Scheschkewitz, \"N\u2010Heterocyclic Carbene Coordinated Neutral and Cationic Heavier Cyclopropylidenes\", Angewandte Chemie International Edition, vol. 53, pp. 9953-9956, 2014. https://doi.org/10.1002/anie.201405238\n\n
    4. \n
\n\n
","doi":"https://doi.org/10.59350/yejb8-b6m51","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13387","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/02/10.1039C3SC53416B.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1423699200,"reference":[{"id":"https://doi.org/10.1039/c3sc53416b","unstructured":"Armstrong, A., Boto, R. A., Dingwall, P., Contreras-Garc\u00eda, J., Harvey, M. J., Mason, N. J., & Rzepa, H. S. (2014). The Houk\u2013List transition states for organocatalytic mechanisms revisited. Chem. Sci., 5(5), 2057\u20132071."},{"id":"https://doi.org/10.1021/ci500302p","unstructured":"Harvey, M. J., Mason, N. J., & Rzepa, H. S. (2014). Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks. Journal of Chemical Information and Modeling, 54(10), 2627\u20132635."},{"id":"https://doi.org/10.1002/anie.201405238","unstructured":"Jana, A., Omlor, I., Huch, V., Rzepa, H. S., & Scheschkewitz, D. (2014). N\u2010Heterocyclic Carbene Coordinated Neutral and Cationic Heavier Cyclopropylidenes. Angewandte Chemie International Edition, 53(37), 9953\u20139956."}],"rid":"4cym7-4c738","summary":"The title of this post refers to the site http://howopenisit.org/ which is in effect a license scraper for journal articles.","tags":["Chemical IT","General","ACS","GBP","Royal Society Of Chemistry"],"title":"How-open-is-it?","updated_at":1793349479,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13387","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Why is this post orphaned from the previous? In order to have the opportunity of noting that treating iodine computationally can be a little different from the procedures used for F, Cl and Br.

\n

\n

As the nuclear charge increases proceeding down the periodic table, the inner electron shells start becoming relativistic. Iodine is the first halogen where this might really start to matter.* There are two ways in which one can compute molecules with I; the first adopts the same procedure as for the earlier halogens, whereby all the electrons are described by basis functions (called an all-electron basis). This effect does not really include the effects of relativistic contractions on the inner (1s) shell unless special relativistic Hamiltonians are also used. The second replaces these inner cores with a pseudopotential, and this does incorporate some of the relativistic effects. To find out how much this might matter, I have included both types:

\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
I
nI-HH-O
11.637\u2020/1.623\u20212.032/2.060[1]
21.657/1.6411.863/1.889[2]
31.696/1.6751.641/1.670[3]
4\u00a02.316/2.3041.014/1.015[4]
\n

\u2020Non-relativistic calculation with an all-electron 6-311G(d,p) basis on I, 6-311++G(2d,2p) on O and H. \u2021Def2-TZVPPD basis, with pseudopotential just on I.

\n

As with bromine, iodine shows a precipitous ionisation when the 4th water molecule is added. In the previous post, I compared this with pKa values, and a comment\u00a0posted there reminded us that a pKa is measured for macroscopic bulk water and that all sorts of new effects due to free energy/entropy, continuum solvation and much else will take hold. But qualitatively at least, the ionisation of HI in a gas-phase cluster of water molecules seems to match the bulk properties. Relativistic effects do not appear to play a major role here.

\n
\n

*Whilst such effects can be prominent for I, arguably they actually start at Cl via an effect called spin-orbit (SO) coupling. This manifests in the calculation of chemical magnetic shieldings. If one uses standard GIAO NMR theories, one can calculate shieldings for e.g. C pretty accurately. But with Cl, the shieldings may be SO-perturbed by about 3ppm, with Br it’s about 12 ppm and with I it reaches 50 ppm![5]

\n

References

\n
  1. H.S. Rzepa, \"H 3 I 1 O 1\", 2015. https://doi.org/10.14469/ch/190924\n\n
    2. \n
  2. H.S. Rzepa, \"H 5 I 1 O 2\", 2015. https://doi.org/10.14469/ch/190921\n\n
    3. \n
  3. H.S. Rzepa, \"H 7 I 1 O 3\", 2015. https://doi.org/10.14469/ch/190925\n\n
    4. \n
  4. H.S. Rzepa, \"H 9 I 1 O 4\", 2015. https://doi.org/10.14469/ch/190927\n\n
    5. \n
  5. D.C. Braddock, and H.S. Rzepa, \"Structural Reassignment of Obtusallenes V, VI, and VII by GIAO-Based Density Functional Prediction\", Journal of Natural Products, vol. 71, pp. 728-730, 2008. https://doi.org/10.1021/np0705918\n\n
    6. \n
\n\n
","doi":"https://doi.org/10.59350/8vk4h-a6g91","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13488","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1425081600,"reference":[{"id":"https://doi.org/10.14469/ch/190924","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 28). H 3 I 1 O 1 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/190921","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 28). H 5 I 1 O 2 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/190925","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 28). H 7 I 1 O 3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/190927","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 28). H 9 I 1 O 4 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.1021/np0705918","unstructured":"Braddock, D. C., & Rzepa, H. S. (2008). Structural Reassignment of Obtusallenes V, VI, and VII by GIAO-Based Density Functional Prediction. Journal of Natural Products, 71(4), 728\u2013730."}],"rid":"81cy7-rrb59","summary":"Why is this post orphaned from the previous? In order to have the opportunity of noting that treating iodine computationally can be a little different from the procedures used for F, Cl and Br.","tags":["General","Interesting Chemistry","Chemical Magnetic Shieldings","Free Energy/entropy","Gas-phase Cluster"],"title":"How many water molecules does it take to ionise HI?","updated_at":1793349476,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13488","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

My previous posts have covered the ionization by a small number of discrete water molecules of the series of halogen acids, ranging from HI (the strongest, pKa -10) via HF (weaker, pKa 3.1) to the pseudo-halogen HCN (the weakest, pKa 9.2). Here I try out some even stronger acids to see what the least number of water molecule needed to ionize these might be.

\n

\n

Firstly what must surely be the ultimate acid H(CHB11Cl11), discovered by Christopher Reed[1] in 2006. This is so strong that it appears that it can even largely ionize itself; the form on the right (below) is the cationic acid, the form on the left is its anionic base. The proton itself is bridged[2] between the two in a manner similar to the structure of one form of HCl.4H2O reported in the earlier post on the topic.

\n
\"Click

Click for 3D

\n

So it comes as no surprise‡ to find[3] that just one water molecule can also ionize H(CHB11Cl11) to the anionic form (CHB11Cl11)–.

\n
\"Click

Click for 3D

\n

How about triflic acid, CF3SO2OH, pKa -16), which is also a fair bit more acidic than HI? Here, only three waters are needed (\u03c9B97XD/6-311++G(2d,2p) prediction) to ionise to triflate anion.[4]

\n
\"Click

Click for 3D

\n

So, if there a system which is ionised by precisely two water molecules I will record it here.

\n
\n

‡Perhaps also no surprise is that one H2S molecule can also perform this ionisation.[5] This leads us into another exploration, using molecules other than water to perform these ionisations.

\n

References

\n
  1. E.S. Stoyanov, S.P. Hoffmann, M. Juhasz, and C.A. Reed, \"The Structure of the Strongest Br\u00f8nsted Acid:\u2009 The Carborane Acid H(CHB<sub>11</sub>Cl<sub>11</sub>)\", Journal of the American Chemical Society, vol. 128, pp. 3160-3161, 2006. https://doi.org/10.1021/ja058581l\n\n
    2. \n
  2. Stoyanov, E.S.., Hoffmann, S.P.., Juhasz, M.., and Reed, C.A.., \"CCDC 606170: Experimental Crystal Structure Determination\", 2006. https://doi.org/10.5517/ccnbrwl\n\n
    3. \n
  3. H.S. Rzepa, \"C 1 H 4 B 11 Cl 11 O 1\", 2015. https://doi.org/10.14469/ch/191134\n\n
    4. \n
  4. H.S. Rzepa, \"C 1 H 7 F 3 O 6 S 1\", 2015. https://doi.org/10.14469/ch/191129\n\n
    5. \n
  5. H.S. Rzepa, \"C 1 H 4 B 11 Cl 11 S 1\", 2015. https://doi.org/10.14469/ch/191135\n\n
    6. \n
\n\n
","doi":"https://doi.org/10.59350/y2b56-3b715","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13618","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/03/LEHZOO.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1426377600,"reference":[{"id":"https://doi.org/10.1021/ja058581l","unstructured":"Stoyanov, E. S., Hoffmann, S. P., Juhasz, M., & Reed, C. A. (2006). The Structure of the Strongest Br\u00f8nsted Acid: The Carborane Acid H(CHB11Cl11). Journal of the American Chemical Society, 128(10), 3160\u20133161."},{"id":"https://doi.org/10.5517/ccnbrwl","unstructured":"Stoyanov, E.S.., Hoffmann, S.P.., Juhasz, M.., and Reed, C.A.., \"CCDC 606170: Experimental Crystal Structure Determination\", 2006."},{"id":"https://doi.org/10.14469/ch/191134","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, March 16). C 1 H 4 B 11 Cl 11 O 1 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/191129","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, March 15). C 1 H 7 F 3 O 6 S 1 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/191135","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, March 16). C 1 H 4 B 11 Cl 11 S 1 [Archival collection]. Imperial College London."}],"rid":"p2p2m-4j396","summary":"My previous posts have covered the ionization by a small number of discrete water molecules of the series of halogen acids, ranging from HI (the strongest, pKa -10) via HF (weaker, pKa 3.1) to the pseudo-halogen HCN (the weakest, pKa 9.2). Here I try out some even stronger acids to see what the least number of water [\u2026]","tags":["Interesting Chemistry","Christopher Reed","Ohio","Pence"],"title":"Ionizing ultra-strong acids with water molecules.","updated_at":1793349474,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13618","version":"v1"}}],"items":[{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Pursuing the topic of halogen bonds, the system DABCO (a tertiary dibase) and iodine form an intriguing complex. Here I explore some unusual features of the structure HEKZOO[1] as published in 2012[2] and ask whether the bonding between the donor (N) and the acceptor (I-I) really is best described as a “non-covalent-interaction” (NCI) or not.

\n

\n

The crystal structure shows a repeating unit, with each DABCO surrounded by two I2 molecules aligned along the N-N axis. These linear chains are stacked in a dislocated manner induced by aligning to optimize the dispersion interactions between the iodines and the CH groups. The most surprising aspect is the N…I distance shown as 2.42Å. The van der Waals radii of N and I are respectively 1.55 + 1.98 = 3.53Å, a contraction of 1.1Å. The covalent radii are 0.75 + 1.33 = 2.08, an elongation of 0.34Å So is this a strong (non-covalent) interaction/contraction or a stretched weak covalent bond?

\n

I will start with a B3LYP+D3/Def2-TZVPP+PP calculation on the crystal geometry (below).

\n
\"Click

Click for 3D

\n

The short N…I distance has a computed Wiberg bond order of 0.26 (the I-I is 0.76) and an E(2) NBO donor-acceptor interaction energy of 40.1 kcal/mol. For comparison, the E(2) energies for conventional OH…O hydrogen bonds are around 10 kcal/mol. This makes the halogen bond a pretty strong interaction! But is it strong enough to call a bond? Indeed, do we have any means of deciding where the transition from a strong interaction to a weak bond occurs?

\n

A NCI analysis is shown below. This analysis filters out electron densities above 0.05au (which are considered as covalent values) and shows only the properties of the reduced density gradients below this value. The dispersion attractions between the DABCO hydrocarbon chains and the iodine molecules are very apparent, but the N…I is encircled with a strange feature, normally only seen for covalent bonds or transition state breaking/forming bonds. A strong hydrogen bond for example would show up as blue, and not this strange torus.

\n
\"Click

Click for 3D

\n

Reducing the threshold for covalent densities to be filtered out to 0.03au eliminates the N…I feature (it is now covalent by definition so to speak), but the I-I feature remains. One can see here that this NCI analysis does rather arbitrarily depend on what one considers the covalent density threshold to be, and as one moves up the periodic table, this density changes. What should the density for eg a N…I interaction/bond actually be? The value appropriate for N (0.05) or I (< 0.03)?
\n

\"Click

Click for 3D

\n

Next, I show the optimised geometry of the system above.[3] This is not a periodic boundary calculation and this lack of a surrounding environment is highlighted by the change in the structure. The N…I distance lengthens, and the iodines which have no DABCO to interact with lengthen more. One might conclude that the short N…I distance measured in the solid state structure is due to some degree of N…I compression induced by the linear chains of I-I…DABCO…I-I…DABCO…I-I aligning to maximise the interchain dispersion attractions. Thus the N…I “bond/interaction” is really a co-operative effect between the N…I atoms and the extended 3D structure of the molecule. The N…I contraction of 1.1Å noted above is in part due to the intrinsic halogen bond, but also in part due to dispersion attractions elsewhere!
\n\"DAB-opt\"

\n

So it does rather seem as if the DABCO-I2 complex sits very much in that awkward region in which the contracted N…I distance could either be described as a weak bond or a strong interaction.‡. Just like the infamous H…H bond in cis-butene, one cannot just regard a bond as a purely localised phenomenon, one must also take into account what is happening elsewhere in the total system. Halogen bonds could also be regarding as filling the gap spanned by recognised covalency and recognised hydrogen bonds. I note in passing that another “awkward” bond is the 4th in the diatomic C2[4] that has a bond energy of about 17 kcal/mol, again weak for a normal bond and strong for an interaction.

\n

In my next post on this theme, I will deal with another halogen bond that is found in a famous molecule known for a long time and which has another weird property.

\n
\n

‡Postscript. An ELF analysis reveals the following basin centroids. Basin 1 integrates to 2.00 electrons, basin 2 to 1.92. The asymmetry in the position of the basin centroid towards the nitrogen suggests it is not an equally shared covalent bond, as indeed the Wiberg bond order noted above also indicates. The I…I basin integrates to 1.86 electrons, indicating slightly reduced bonding (by donation into the sigma; orbital).
\n\"DABCO-I2-ELF\"

\n
\n

References

\n
  1. Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., \"CCDC 879935: Experimental Crystal Structure Determination\", 2013. https://doi.org/10.5517/ccyjn03\n\n
    2. \n
  2. A. Peuronen, A. Valkonen, M. Kortelainen, K. Rissanen, and M. Lahtinen, \"Halogen Bonding-Based \"Catch and Release\": Reversible Solid-State Entrapment of Elemental Iodine with Monoalkylated DABCO Salts\", Crystal Growth & Design, vol. 12, pp. 4157-4169, 2012. https://doi.org/10.1021/cg300669t\n\n
    3. \n
  3. H.S. Rzepa, \"Gaussian Job Archive for C12H24I8N4\", 2014. https://doi.org/10.6084/m9.figshare.1254779\n\n
    4. \n
  4. D. Danovich, P.C. Hiberty, W. Wu, H.S. Rzepa, and S. Shaik, \"The Nature of the Fourth Bond in the Ground State of C<sub>2</sub>: The Quadruple Bond Conundrum\", Chemistry \u2013 A European Journal, vol. 20, pp. 6220-6232, 2014. https://doi.org/10.1002/chem.201400356\n\n
    5. \n
\n\n
","doi":"https://doi.org/10.59350/mscek-qty92","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13105","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2014/11/HEKZOO.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1417305600,"reference":[{"id":"https://doi.org/10.5517/ccyjn03","unstructured":"Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., \"CCDC 879935: Experimental Crystal Structure Determination\", 2013."},{"id":"https://doi.org/10.1021/cg300669t","unstructured":"Peuronen, A., Valkonen, A., Kortelainen, M., Rissanen, K., & Lahtinen, M. (2012). Halogen Bonding-Based \"Catch and Release\": Reversible Solid-State Entrapment of Elemental Iodine with Monoalkylated DABCO Salts. Crystal Growth & Design, 12(8), 4157\u20134169."},{"id":"https://doi.org/10.6084/m9.figshare.1254779","unstructured":"Rzepa, H. S. (2014). Gaussian Job Archive for C12H24I8N4 [Dataset]. figshare."},{"id":"https://doi.org/10.1002/chem.201400356","unstructured":"Danovich, D., Hiberty, P. C., Wu, W., Rzepa, H. S., & Shaik, S. (2014). The Nature of the Fourth Bond in the Ground State of C2: The Quadruple Bond Conundrum. Chemistry \u2013 A European Journal, 20(21), 6220\u20136232."}],"rid":"16aqc-te677","summary":"Pursuing the topic of halogen bonds, the system DABCO (a tertiary dibase) and iodine form an intriguing complex. Here I explore some unusual features of the structure HEKZOO as published in 2012 and ask whether the bonding between the donor (N) and the acceptor (I-I) really is best described as a \"non-covalent-interaction\" (NCI) or not.","tags":["Interesting Chemistry","Bond Energy","Co-operative","Donor-acceptor Interaction Energy"],"title":"Halogen bonds 2: The DABCO-Iodine structure.","updated_at":1793349501,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13105","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

These posts contain the computed potential energy surfaces for a fair few “text-book” reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent,[1] as\u00a0prepared from di-iodomethane using zinc metal insertion into a C-I bond.
\n\"simmonds-smith\"

\n

\n

Two reactions it can be compared with are the epoxidation of ethene using a peracid and dichlorocyclopropanation. The latter is a four-electron pericyclic process, which is thermally forbidden. The outcome there is that the two new bonds form very asynchronously to avoid transition state antiaromaticity. The former is a more complex reaction, best described as a six-electron process\u00a0which allows both C…O bonds to form at the same rate. So which of these two does the\u00a0Simmons\u2013Smith mechanism correspond to?

\n

The calculation as undertaken at a \u03c9B97XD/Def2-TZVPD-PP (solvent=dichloromethane) level[2] shows the two C…C bonds forming at more or less the same rate. The reaction therefore resembles epoxidation rather than dichlorocyclopropanation.

\n

\"SS\"

\n

The\u00a0intrinsic reaction coordinate (IRC)[3] is shown below, revealing a concerted and almost synchronous reaction. The synchronicity is all the more surprising given the diversity of bonds forming/breaking.
\n\"SSa\"
\n\"SSE\"

\n

\"SSG\"

\n

There are slight and tantalizing hints that the alkene and the I-Zn-CH2-I components initially form a weak \u03c0-complex, which then rearranges into the TS, and then again a weak complex at the end. The NCI surfaces for both are shown below, and show clear signs of dispersion-like stabilisations for both of them!\u00a0The strange torus around the Zn-I bond is due to the need for a lower density threshold to filter out the covalent interactions.

\n
\"Click

Click for 3D

\n
\"Click

Click for 3D

\n

References

\n
  1. H.E. Simmons, and R.D. Smith, \"A NEW SYNTHESIS OF CYCLOPROPANES FROM OLEFINS\", Journal of the American Chemical Society, vol. 80, pp. 5323-5324, 1958. https://doi.org/10.1021/ja01552a080\n\n
    2. \n
  2. H.S. Rzepa, \"C 3 H 6 I 2 Zn 1\", 2014. https://doi.org/10.14469/ch/147617\n\n
    3. \n
  3. H.S. Rzepa, \"Gaussian Job Archive for C3H6I2Zn\", 2014. https://doi.org/10.6084/m9.figshare.1270441\n\n
    4. \n
\n\n
","doi":"https://doi.org/10.59350/51gb4-0qa77","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13174","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2014/12/simmonds-smith.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1418515200,"reference":[{"id":"https://doi.org/10.1021/ja01552a080","unstructured":"Simmons, H. E., & Smith, R. D. (1958). A NEW SYNTHESIS OF CYCLOPROPANES FROM OLEFINS. Journal of the American Chemical Society, 80(19), 5323\u20135324."},{"id":"https://doi.org/10.14469/ch/147617","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2014, December 13). C 3 H 6 I 2 Zn 1 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.6084/m9.figshare.1270441","unstructured":"Rzepa, H. S. (2014). Gaussian Job Archive for C3H6I2Zn [Dataset]. figshare."}],"rid":"ga6kw-98n08","summary":"These posts contain the computed potential energy surfaces for a fair few \"text-book\" reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent, as prepared from di-iodomethane using zinc metal insertion into a C-I bond.","tags":["Reaction Mechanism","Computed Potential Energy Surfaces","Di-iodomethane Using Zinc Metal Insertion","Simmons"],"title":"Cyclopropanation: the mechanism of the Simmons\u2013Smith reaction.","updated_at":1793349498,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13174","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

I have written earlier about the Amsterdam Manifesto. That arose out of a conference on the theme of “beyond the PDF“, with one simple question at its heart: what can be done to liberate data from containers it was not designed to be in? The latest meeting on this topic will happen in\u00a0January 2015 as FORCE2015.

\n

\n

The format is suitably modern, starting with a Hackathon, and then two days of talks, posters and demos. We will be presenting both a talk and a demo. In the spirit of emancipated data, we have placed the latter into a container that is most certainly not a PDF. That demo has been archived, and there assigned a DOI[1] and for good measure transcluded into this post in its entirety. We hope this demonstrates that such “containers” can be usefully moved around to where they might be needed. I should say that the core of this demo is not just the data, but the metadata associated with it. Metadata renders that data discoverable (mineable) and its usage measurable.†

\n

\n\n

\n

I hope to report here on anything interesting happening at the FORCE2015 event.

\n
\n

\u2021The format of this blog is a tiny bit too narrow for the demo to fit comfortably. Go see it here[1] and “enlarge” the view for a better experience.

\n

†Full details of this are in preparation.

\n

References

\n
  1. H.S. Rzepa, N. Mason, A. Mclean, and M. Harvey, \"Interoperability for Data Repositories. Machine Methods for Retrieving Data for Display or Mining Utilising Persistent (data-DOI) Identifiers\", 2014. https://doi.org/10.6084/m9.figshare.1266197\n\n
    2. \n
\n\n
","doi":"https://doi.org/10.59350/ek3ac-55t28","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13203","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1418774400,"reference":[{"id":"https://doi.org/10.6084/m9.figshare.1266197","unstructured":"Rzepa, H. S., Mason, N., Mclean, A., & Harvey, M. (2014). Interoperability for Data Repositories. Machine Methods for Retrieving Data for Display or Mining Utilising Persistent (data-DOI) Identifiers [Dataset]. figshare."}],"rid":"dx213-m8d70","summary":"I have written earlier about the Amsterdam Manifesto.","tags":["Chemical IT"],"title":"Data discoverability","updated_at":1793349494,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13203","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published[1]. That was then.

\n

\n

\"\"

\n

This is now. I have just finished a post on ring-opening reactions of oxirene, a 4n electron anti-aromatic ring. I was casting around for an example of a calculation done just before the modern Internet era, and happened upon the above. Although this was a mere 20 years ago, much of the detail had faded; I had not thought much about it in the intervening years, but I did recollect that although we had attributed the high stereoselectivity shown above to a stereoelectronic orbital alignment, I was not entirely happy with the interpretation. Put simply, we had relied on a molecular orbital diagram, and this diagram (in resplendent colour in the journal, one of the few being so published at that time, and for no colour charge to boot) was just too complicated. Arguably it was the fixated complexity (I remember at the time that it looked complicated no matter what the viewing angle was) that set me on the road to the use of the Web, and ultimately here to this blog. So I thought a re-analysis using modern algorithms and presentation might help simplify. The newly recalculated transition state (\u03c9B97XD/6-311G(d,p)[2] looks like:

\n
\"\"

Transition state for ring opening of a cyclopropene. Click for 3D.

\n
    \n
  1. The reaction is a 4n (n=1) electron electrocyclic ring opening and so according to the rules, should proceed with the formation/cleavage of an antarafacial bond. You might think that there are not quite enough substituents to reveal this stereochemistry, but there are if the carbene lone pair is included. So how to add the lone pair?
    2. \n
  2. Well, its coordinates can be computed using the ELF (electron localisation function). The relevant lone pair is ringed in red below. Using (old technology, i.e. a static figure) you may choose to believe me when I argue that this lone pair is above the plane of the forming ring from the perspective shown, whilst the terminus of the bond it forms is to the bottom. This defines an antarafacial component. Well, I might have carefully manipulated the viewing angle to show this. Now, in 2012 rather than 1992, you can load the 3D coordinates by clicking below, and check for yourself!
    \n
    \"\"

    Lone pair centroid for the transition state. Click for 3D

    \n
    3. \n
  3. What about the stereo-control? Take a look at the angle between the axis of the C-Cl bond (atoms ringed in blue) and the centroid of the carbene lone pair (red). It is about 162\u00b0, or almost anti-periplanar. A magic orientation in organic chemistry. Time to attack the orbitals again. Our published diagram looked as below. It shows the HOMO aligning with the LUMO+2 (if your eyes are not distracted by all the other detail).\"\"
    But we can now simplify such a complex molecular orbital by using instead a localized version, an NBO. A little explanation is needed. The NBO orbital shown with red/blue phases is antibonding for the C-Cl bond. That with orange/purple is the carbene lone pair. Where orange overlaps with red, we have a positive overlap that stabilises the system. The NBO E2 perturbation energy is around 4.6 kcal/mol. Although this may seem small, it is actually quite large for a through-space interaction of this type. It is this stabilisation (amounting to ~ 1.6 kcal/mol in free energy) that accounts for the high selectivity for the stereoisomer shown above.
    \n
    \"\"

    NBO for transition state. Click for 3D.

    \n
    4. \n
\n

Well, I think that the passage of 20 years has enabled us to tidy up the origins of the stereoelectronic effect responsible for controlling this reaction, and to produce clearer diagrams which the reader can interactively explore for themselves. It did take 20 years to join things up though!

\n

\"\"[3]

\n

References

\n
  1. M.S. Baird, J.R. Al Dulayymi, H.S. Rzepa, and V. Thoss, \"An unusual example of stereoelectronic control in the ring opening of 3,3-disubstituted 1,2-dichlorocyclopropenes\", Journal of the Chemical Society, Chemical Communications, pp. 1323, 1992. https://doi.org/10.1039/c39920001323\n\n
    2. \n
  2. H.S. Rzepa, \"C 5 H 5 Cl 3\", 2012. https://doi.org/10.14469/ch/14180\n\n
    3. \n
  3. H.S. Rzepa, \"Gaussian Job Archive for C5H5Cl3\", 2015. https://doi.org/10.6084/m9.figshare.1285422\n\n
    4. \n
\n\n
","doi":"https://doi.org/10.59350/1eja6-jjf31","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=7068","image":"http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2012/07/dichlorocarbene.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1342051200,"reference":[{"id":"https://doi.org/10.1039/c39920001323","unstructured":"Baird, M. S., Al Dulayymi, J. R., Rzepa, H. S., & Thoss, V. (1992). An unusual example of stereoelectronic control in the ring opening of 3,3-disubstituted 1,2-dichlorocyclopropenes. Journal of the Chemical Society, Chemical Communications, (18), 1323."},{"id":"https://doi.org/10.14469/ch/14180","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2012, July 10). C 5 H 5 Cl 3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.6084/m9.figshare.1285422","unstructured":"Rzepa, H. S. (2015). Gaussian Job Archive for C5H5Cl3 [Dataset]. figshare."}],"rid":"473qx-a2m96","summary":"Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published.","tags":["Interesting Chemistry","Reaction Mechanism","Cambridge","Chemist","Conformational Analysis"],"title":"More joining up of pieces. Stereocontrol in the ring opening of cyclopropenes.","updated_at":1793349492,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=7068","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

About two years ago, I posted on the distribution of readership of this blog. The passage of time has increased\u00a0this from 144 to 176 countries. There are apparently between 189-196 such, so not quite yet complete coverage! \"2015\"
\nOf course, it is the nature of the beast that whilst we can track countries, very little else is known about such readerships. Is the readership young or old, student or professor, chemist or not (although I fancy the latter is less likely). Another way of keeping tabs on some of the activity are aggregators such as Chemical Blogspace, which has been rather quiet recently. Perhaps we have become too obsessed by metrics, and with the Internet-of-things apparently the “next-big-thing”, the metrics are only likely to increase. This will only encourage “game playing“, and I urge you to see a prime example of this in the UK REF (research excellence framework), the measure which attempts to rank UK\u00a0universities in terms of their “excellence”.

\n

\n

Ah well, I had better leave this blog and go off and check on my h-index just in case it has notched up another integer.

\n\n
","doi":"https://doi.org/10.59350/rvgsd-85f42","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13243","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/01/2015.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1420675200,"rid":"2qr4p-1ck07","summary":"About two years ago, I posted on the distribution of readership of this blog. The passage of time has increased this from 144 to 176 countries. There are apparently between 189-196 such, so not quite yet complete coverage!","tags":["General","Chemist","Internet-of-things","Professor","United Kingdom"],"title":"The demographics of a blog readership \u2013 updated","updated_at":1793349489,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13243","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

The journal of chemical education has many little gems providing inspiration for laboratory experiments. Jonathan Piard reports one based on the reaction below[1]; here I investigate the mechanism of this transformation.

\n

\n

\"spiropyran\"
\nThere are two things going on here; an electrocyclic ring opening involving breaking the C-O bond, with\u00a0a cis/trans isomerism of the alkene (concurrent or consecutive). A crystal structure of the dinitro analogue establishes the trans stereochemistry[2]. This product zwitterion is highly coloured (blue-purple) unlike the colourless reactant. The rate at which this colour clears can be easily measured in a UV/visible spectrometer, and from this activation parameters are inferred\u00a0as a function of the solvent.

\n

Photochemically, this reaction is too complex to study quickly using computation, but the thermal back reaction is much easier. Applying the \u03c9B97XD/6-311G(d,p)/SCRF=solvent procedure and using the C-O bond as a reaction coordinate results in the following transition state[3] IRC profile[4] for DMSO as solvent,\u00a0here connecting to the\u00a0cis-alkene.\u00a0The thermal forward barrier for the C…O cleaving\u00a0is ~12 kcal/mol. More significantly, the back reaction is only <2 kcal mol, which is very much lower than that reported[1] (~22 kcal/mol) and makes the cis-alkene very much a transient species\u00a0and therefore not the\u00a0coloured species being measured.

\n

\"C-O-cleave\"

\n

A second transition state involving C=C bond rotation is located[5] and this yields the following IRC[6] to form the trans-alkene, with activation parameters listed below.\u00a0It is entirely probable however that the forward photochemical reaction follows a different course involving conical intersections; an interesting study in its own right, but beyond the scope of this post.

\n

\"cis-trans\"

\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
Measured and computed activation parameters for the thermal back\u00a0reaction
Solvent\u0394G298, kcal mol-1\u0394H, kcal mol-1\u0394S, cal K-1 mol-1
DMSO, measured22.026.4+14.6
toluene, measured19.014.3-15.6
DMSO, calc[5]21.220.4+2.6
toluene, calc[7]18.619.1+1.8
\n

The next issue surrounds the effect of solvent. Most spectacular are those of the\u00a0activation parameters for the thermal back-reaction. The measured activation entropy \u0394S changes with solvent by \u039430.2 cal, and the enthalpy \u0394H by \u039412.1 kcal, which are enormous solvent effects. Are they in fact real? It is reassuring at least that the calculated free energy agrees pretty closely with the measured values. So too does the decrease in\u00a0\u0394G in changing the solvent from DMSO to toluene (3.0 kcal/mol measured, 2.6 calculated).

\n

There is little sign of a large solvent effect in the calculated values. This could be for three reasons.

\n
    \n
  1. The first is that adding explicit, hydrogen-bonded solvent molecules to the system is essential. As the zwitterionic character is lost when the trans-alkene starts to rotate, the system will become less ionic, and hence shed solvent molecules and gain entropy. If the solvent is not capable of hydrogen bonding, as say toluene, these will not be shed and the entropy will not increase at the transition state. It is difficult however to reconcile this picture with the apparent large loss of entropy for toluene as solvent.
    2. \n
  2. The second reason is because of a complete change in mechanism, one not modelled here.
    3. \n
  3. For completeness, one should also mention that the measured values might simply be in error, either due to typographical mistakes or indeed in numerical analysis.
    4. \n
\n

I will conclude with the colour.\u00a0It is possible to compute the electronic excitations across the range 180-580nm, and I show below a difference spectrum (for DMSO as solvent) with the product +ve and the reactant \u00a0-ve. You can see the spectacular red-shift for the highly conjugated zwitterion! The absolute value of \u03bbmax is not red-shifted enough (by about 65 nm), but the effect remains real.
\n\"spiro\"

\n

The above experiment is for undergraduate chemistry laboratories. I suggest that a computational reality check could also easily be included into such a lab, and would certainly help give students a broader perspective.

\n

References

\n
  1. J. Piard, \"Influence of the Solvent on the Thermal Back Reaction of One Spiropyran\", Journal of Chemical Education, vol. 91, pp. 2105-2111, 2014. https://doi.org/10.1021/ed4005003\n\n
    2. \n
  2. J. Hobley, V. Malatesta, R. Millini, L. Montanari, and W. O Neil Parker, Jr, \"Proton exchange and isomerisation reactions of photochromic and reverse photochromic spiro-pyrans and their merocyanine forms\", Physical Chemistry Chemical Physics, vol. 1, pp. 3259-3267, 1999. https://doi.org/10.1039/a902379h\n\n
    3. \n
  3. H.S. Rzepa, \"C 19 H 18 N 2 O 3\", 2015. https://doi.org/10.14469/ch/189540\n\n
    4. \n
  4. H.S. Rzepa, \"C19H18N2O3\", 2015. https://doi.org/10.14469/ch/189573\n\n
    5. \n
  5. H.S. Rzepa, \"C 19 H 18 N 2 O 3\", 2015. https://doi.org/10.14469/ch/189546\n\n
    6. \n
  6. H.S. Rzepa, \"C19H18N2O3\", 2015. https://doi.org/10.14469/ch/189648\n\n
    7. \n
  7. H.S. Rzepa, \"C 19 H 18 N 2 O 3\", 2015. https://doi.org/10.14469/ch/189579\n\n
    8. \n
\n\n
","doi":"https://doi.org/10.59350/h3q65-w8y21","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13300","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/02/spiropyran4.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1423008000,"reference":[{"id":"https://doi.org/10.1021/ed4005003","unstructured":"Piard, J. (2014). Influence of the Solvent on the Thermal Back Reaction of One Spiropyran. Journal of Chemical Education, 91(12), 2105\u20132111."},{"id":"https://doi.org/10.1039/a902379h","unstructured":"Hobley, J., Malatesta, V., Millini, R., Montanari, L., & O Neil Parker, Jr, W. (1999). Proton exchange and isomerisation reactions of photochromic and reverse photochromic spiro-pyrans and their merocyanine forms. Physical Chemistry Chemical Physics, 1(14), 3259\u20133267."},{"id":"https://doi.org/10.14469/ch/189540","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 1). C 19 H 18 N 2 O 3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189573","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 4). C19H18N2O3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189546","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 1). C 19 H 18 N 2 O 3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189648","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C19H18N2O3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189579","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 4). C 19 H 18 N 2 O 3 [Archival collection]. Imperial College London."}],"rid":"jccrq-10321","summary":"The journal of chemical education has many little gems providing inspiration for laboratory experiments. Jonathan Piard reports one based on the reaction below; here I investigate the mechanism of this transformation.","tags":["Reaction Mechanism","Calculated Free Energy","Chemical Education","Jonathan Piard"],"title":"Mechanism of the solvatochromic reaction of a spiropyran.","updated_at":1793349486,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13300","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Steganone is an unusual natural product, known for about 40 years now. The assignment of its absolute configurations makes for an interesting, on occasion rather confusing, and perhaps not entirely atypical story. I will start with the modern accepted stereochemical structure of this molecule, which comes in the form of two separately isolable atropisomers.
\n\"steganone\"
\nThe first reported synthesis of this system in 1977 was racemic, and no stereochemistry is shown in the article (structure 2).[1] Three years later an “Asymmetric total synthesis of (-)steganone and revision of its absolute configuration” shows how the then accepted\u00a0configuration (structure 1 in this article) needs to be revised to the\u00a0enantiomer shown as\u00a0structure 12 in the article[2] and matching\u00a0the above representation. The system has continued to attract interest ever since[3],[4],[5],[6], not least because of the presence of axial chirality in the form of atropisomerism. Thus early on it was shown that the alternative atropisomer, the (aS,R,R) configuration initially emerges out of several syntheses, and has to be converted to the (aR,R,R) configuration by heating[3]. One could easily be fooled by such isomerism!

\n

\n

Absolute configurations can be established in several ways.

\n
    \n
  1. From precursors of known absolute configuration. This was the most common method until relatively recently, but it is very expensive since asymmetric syntheses are often much more complex and longer than racemic\u00a0ones. There is always a small residual doubt\u00a0that any\u00a0transformation in the synthesis might have altered the configuration in an unexpected manner.
    2. \n
  2. From an X-ray of the final configuration (Bijvoet). Very often the structure is determined on a derivative of the target compound (the original\u00a0may not form suitable crystals). There is also the doubt that the selected crystals may in fact be a minor form and do not represent the bulk of the system in solution. This is especially true where atropisomerism is concerned, since the solid state structure may not represent the same atropisomer present in solution.
    3. \n
  3. In the last decade or so, it has become more common to make use of the computation\u00a0of measured\u00a0chiroptical spectroscopies to see if they match.\u00a0It turns out that this method appears never to have been applied to Steganone, and here I attempt to rectify this.
    4. \n
\n

First, let us compute the optical rotation. The\u00a0(aR,R,R) stereoisomer is also known as (-)-Steganone, because the measured specific rotation is [\u03b1]589 -170\u00b0 \u00b1 30.[3] It is computed (MN12L/6-311++G(d,p)/SCRF=chloroform) as -240\u00b0, [\u03b1]365 -2251[7]. The other atropisomer (aS,R,R) is computed to be 4.5 kcal/mol higher in free energy\u00a0with\u00a0[\u03b1]589 +408\u00b0[8], and measured as +150.[3] There is some uncertainty in the computed values, since the rotations can be dependent on the conformation not only of the rings, but the substituents. You might imagine that the conformation of eg a -OMe group is unimportant, but this is not so. In this case, I have used a crystal structure of a related species to\u00a0serve as the start point for optimising the MeO\u00a0conformations. The greater mismatch between computation and experiment for the (aS,R,R) stereoisomer probably needs an exploration of more conformations of the -OMe groups. At least in both cases the signs match between computation and measurement.

\n

Next, the electronic circular dichroism (ECD), which has also been measured[3] for the (aR,R,R) isomer as \u0394\u03b5 201nm (-ve Cotton effect), 218 (+ve), 244 (-ve), 276 (+ve) 304 (-ve) and 337 (-ve). Bearing in mind that the baselines in ECD spectra are notoriously difficult to define (moving it up or down can easily invert a Cotton effect), the agreement with the calculated spectrum MN12L/6-311++G(d,p)/SCRF=chloroform, nstates=200)[9] might seem\u00a0reasonable, although the calculated version has more peaks in the region 225-265 than are reported (e.g. 235, +ve, 265, -ve).
\n\"(R,R)-steganone-9\"
\nThe (aS,R,R) isomer seems a less good fit. The +ve peak at 218 is missing, the +ve 276 peak matches better than the other isomer, but the 337nm peak is again the wrong sign.
\n\"(aS,R,R)-steganone\"

\n

Of course, in such a game it may be the DFT functional used for the simulation that itself might be misleading, MN12L in this case. Just to check, I also include the results using M062X[10] to see how variable these simulations might be. The measured peaks at 201, 218, 244 and 337nm match, but the ones at 276 and 304nm do not.

\n

\"s-m062x\"

\n

Although matching computed with measured ECD spectra is commonly used to assign absolute configurations of molecules, you can see from these results that the technique is not a cast iron one! Even scanning through myriad DFT procedures to find the one that fits best is probably not a complete solution either. Can anything be done to further increase confidence?

\n

How about\u00a0Vibrational Circular Dichroism (VCD) predictions?[11],[12]. Like ECD, VCD is also sensitive to conformation, which is why some modern instruments have low temperature probes operating at close to 0K which strive to capture only a single lowest energy conformation (although of course in any simulation, you have to identify that conformation reliably!). At some stage in the future, the VCD spectra of steganone might indeed be measured, and hence compared with the below. It might serve to increase confidence in the chiroptical methods as a means of assigning configuration.

\n

\"(aR,R,R)-steganone\" \"(aS,R,R)-steganone\"

\n

We might conclude from this short exploration of chiroptical spectroscopy that no one single measured or computed value can be absolutely definitive; rather it is the accumulation from various sources that builds up the case for a particular configuration. But at least the above simulations do serve to add some useful additional data for the record.

\n

References

\n
  1. D. Becker, L.R. Hughes, and R.A. Raphael, \"Total synthesis of the antileukaemic lignan (\u00b1)-steganacin\", J. Chem. Soc., Perkin Trans. 1, pp. 1674-1681, 1977. https://doi.org/10.1039/p19770001674\n\n
    2. \n
  2. J. Robin, O. Gringore, and E. Brown, \"Asymmetric total synthesis of the antileukaemic lignan precursor (-)steganone and revision of its absolute configuration\", Tetrahedron Letters, vol. 21, pp. 2709-2712, 1980. https://doi.org/10.1016/s0040-4039(00)78586-8\n\n
    3. \n
  3. E.R. Larson, and R.A. Raphael, \"Synthesis of (\u2013)-steganone\", J. Chem. Soc., Perkin Trans. 1, pp. 521-525, 1982. https://doi.org/10.1039/p19820000521\n\n
    4. \n
  4. A. Bradley, W.B. Motherwell, and F. Ujjainwalla, \"A concise approach towards the synthesis of steganone analogues\", Chemical Communications, pp. 917-918, 1999. https://doi.org/10.1039/a900743a\n\n
    5. \n
  5. M. Uemura, A. Daimon, and Y. Hayashi, \"An asymmetric synthesis of an axially chiral biaryl via an (arene)chromium complex: formal synthesis of (\u2013)-steganone\", J. Chem. Soc., Chem. Commun., vol. 0, pp. 1943-1944, 1995. https://doi.org/10.1039/c39950001943\n\n
    6. \n
  6. B. Yalcouye, S. Choppin, A. Panossian, F.R. Leroux, and F. Colobert, \"A Concise Atroposelective Formal Synthesis of (\u2013)\u2010Steganone\", European Journal of Organic Chemistry, vol. 2014, pp. 6285-6294, 2014. https://doi.org/10.1002/ejoc.201402761\n\n
    7. \n
  7. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189647\n\n
    8. \n
  8. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189646\n\n
    9. \n
  9. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189649\n\n
    10. \n
  10. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189657\n\n
    11. \n
  11. https://doi.org/\n\n
    12. \n
  12. H.S. Rzepa, \"C 22 H 20 O 8\", 2015. https://doi.org/10.14469/ch/189651\n\n
    13. \n
\n\n
","doi":"https://doi.org/10.59350/5t09h-k5125","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13353","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/02/steganone3.svg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1423526400,"reference":[{"id":"https://doi.org/10.1039/p19770001674","unstructured":"Becker, D., Hughes, L. R., & Raphael, R. A. (1977). Total synthesis of the antileukaemic lignan (\u00b1)-steganacin. J. Chem. Soc., Perkin Trans. 1, (14), 1674\u20131681."},{"id":"https://doi.org/10.1016/s0040-4039(00)78586-8","unstructured":"Robin, J. P., Gringore, O., & Brown, E. (1980). Asymmetric total synthesis of the antileukaemic lignan precursor (-)steganone and revision of its absolute configuration. Tetrahedron Letters, 21(28), 2709\u20132712."},{"id":"https://doi.org/10.1039/p19820000521","unstructured":"Larson, E. R., & Raphael, R. A. (1982). Synthesis of (\u2013)-steganone. J. Chem. Soc., Perkin Trans. 1, (0), 521\u2013525."},{"id":"https://doi.org/10.1039/a900743a","unstructured":"Bradley, A., Motherwell, W. B., & Ujjainwalla, F. (1999). A concise approach towards the synthesis of steganone analogues. Chemical Communications, (10), 917\u2013918."},{"id":"https://doi.org/10.1039/c39950001943","unstructured":"Uemura, M., Daimon, A., & Hayashi, Y. (1995). An asymmetric synthesis of an axially chiral biaryl via an (arene)chromium complex: formal synthesis of (\u2013)-steganone. J. Chem. Soc., Chem. Commun., 0(19), 1943\u20131944."},{"id":"https://doi.org/10.1002/ejoc.201402761","unstructured":"Yalcouye, B., Choppin, S., Panossian, A., Leroux, F. R., & Colobert, F. (2014). A Concise Atroposelective Formal Synthesis of (\u2013)\u2010Steganone. European Journal of Organic Chemistry, 2014(28), 6285\u20136294."},{"id":"https://doi.org/10.14469/ch/189647","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C 22 H 20 O 8 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189646","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C 22 H 20 O 8 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189649","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C 22 H 20 O 8 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/189657","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 10). C 22 H 20 O 8 [Archival collection]. Imperial College London."},{"id":"https://doi.org/"},{"id":"https://doi.org/10.14469/ch/189651","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 9). C 22 H 20 O 8 [Archival collection]. Imperial College London."}],"rid":"btpcq-vd795","summary":" Steganone is an unusual natural product, known for about 40 years now. The assignment of its absolute configurations makes for an interesting, on occasion rather confusing, and perhaps not entirely atypical story. I will start with the modern accepted stereochemical structure of this molecule, which comes in the form of two separately isolable atropisomers.","tags":["Interesting Chemistry","Free Energy","Lowest Energy Conformation","Natural Product","Simulation"],"title":"Chiroptical spectroscopy of the natural product Steganone.","updated_at":1793349483,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13353","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

The title of this post refers to the site\u00a0http://howopenisit.org/\u00a0 which is in effect a license scraper for journal articles. In the past 2-3 years in the UK, we have been able to make use of grants to our university to pay publishers to convert our publications into Open Access (also called GOLD). I thought I might check out a few of my recent publications to see what\u00a0http://howopenisit.org/\u00a0makes of them.

\n

\n

This was catalysed by an\u00a0article\u00a0which revealed that UK universities spent \u00a39M in 2014 on the purchase of such openness. One of the “challenges” identified\u00a0is the difficulty in converting such payment into an article that actually is open. Apparently, publishers make not a few mistakes in their quality controls in ensuring it is so, relying on irate authors informing them of such mistakes. This can be quite tedious to do, and so a tool that largely automates this checking is most useful. So here we go.

\n
    \n
  1. doi: 10.1039/C3SC53416B[1] This is a good start. The output looks like thus. Green is GOLD so to speak. Well done the Royal Society of Chemistry.
    \n\"10.1039:C3SC53416B\"
    2. \n
  2. doi: 10.1021/ci500302p[2] from the ACS this time. Pink, but at least free to read. Quite what that means is less certain. There is an adage, “the right to read means the right to mine” presumably means this article is OK to mine, but then why does it not say so?\"10.1021:ci500302p\"
    3. \n
  3. doi: 10.1002/anie.201405238[3]. Pink again, but the colour now simply means no information about the license could be obtained from the publisher (Wiley). \"10.1002:anie.201405238\"
    4. \n
\n

I ran a few more and sadly the third of the above, “no information” was the most common response. And the legal response is invariably that if no information can be obtained, the answer is NO, it is not free to read. In other words, not providing a license is just as bad as saying it’s not free to read.

\n

Article aggregators such as Symplectic do not yet perform the service above (which to be fair is still in beta), and so I cannot yet check how many GOLD articles there are to my name. I think it should be about 8, and I might add that the time I have to spend in arranging for this to happen is not negligible. Hell, I could probably have found a few more reactions mechanism in the time I have spent on achieving GOLD. This is one of those topics which would be interesting to revisit say in five years time to see how the world has changed. So I leave this little time capsule and will update it then!

\n

References

\n
  1. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-Garc\u00eda, M.J. Harvey, N.J. Mason, and H.S. Rzepa, \"The Houk\u2013List transition states for organocatalytic mechanisms revisited\", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b\n\n
    2. \n
  2. M.J. Harvey, N.J. Mason, and H.S. Rzepa, \"Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks\", Journal of Chemical Information and Modeling, vol. 54, pp. 2627-2635, 2014. https://doi.org/10.1021/ci500302p\n\n
    3. \n
  3. A. Jana, I. Omlor, V. Huch, H.S. Rzepa, and D. Scheschkewitz, \"N\u2010Heterocyclic Carbene Coordinated Neutral and Cationic Heavier Cyclopropylidenes\", Angewandte Chemie International Edition, vol. 53, pp. 9953-9956, 2014. https://doi.org/10.1002/anie.201405238\n\n
    4. \n
\n\n
","doi":"https://doi.org/10.59350/yejb8-b6m51","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13387","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/02/10.1039C3SC53416B.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1423699200,"reference":[{"id":"https://doi.org/10.1039/c3sc53416b","unstructured":"Armstrong, A., Boto, R. A., Dingwall, P., Contreras-Garc\u00eda, J., Harvey, M. J., Mason, N. J., & Rzepa, H. S. (2014). The Houk\u2013List transition states for organocatalytic mechanisms revisited. Chem. Sci., 5(5), 2057\u20132071."},{"id":"https://doi.org/10.1021/ci500302p","unstructured":"Harvey, M. J., Mason, N. J., & Rzepa, H. S. (2014). Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks. Journal of Chemical Information and Modeling, 54(10), 2627\u20132635."},{"id":"https://doi.org/10.1002/anie.201405238","unstructured":"Jana, A., Omlor, I., Huch, V., Rzepa, H. S., & Scheschkewitz, D. (2014). N\u2010Heterocyclic Carbene Coordinated Neutral and Cationic Heavier Cyclopropylidenes. Angewandte Chemie International Edition, 53(37), 9953\u20139956."}],"rid":"4cym7-4c738","summary":"The title of this post refers to the site http://howopenisit.org/ which is in effect a license scraper for journal articles.","tags":["Chemical IT","General","ACS","GBP","Royal Society Of Chemistry"],"title":"How-open-is-it?","updated_at":1793349479,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13387","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
\n

Why is this post orphaned from the previous? In order to have the opportunity of noting that treating iodine computationally can be a little different from the procedures used for F, Cl and Br.

\n

\n

As the nuclear charge increases proceeding down the periodic table, the inner electron shells start becoming relativistic. Iodine is the first halogen where this might really start to matter.* There are two ways in which one can compute molecules with I; the first adopts the same procedure as for the earlier halogens, whereby all the electrons are described by basis functions (called an all-electron basis). This effect does not really include the effects of relativistic contractions on the inner (1s) shell unless special relativistic Hamiltonians are also used. The second replaces these inner cores with a pseudopotential, and this does incorporate some of the relativistic effects. To find out how much this might matter, I have included both types:

\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
I
nI-HH-O
11.637\u2020/1.623\u20212.032/2.060[1]
21.657/1.6411.863/1.889[2]
31.696/1.6751.641/1.670[3]
4\u00a02.316/2.3041.014/1.015[4]
\n

\u2020Non-relativistic calculation with an all-electron 6-311G(d,p) basis on I, 6-311++G(2d,2p) on O and H. \u2021Def2-TZVPPD basis, with pseudopotential just on I.

\n

As with bromine, iodine shows a precipitous ionisation when the 4th water molecule is added. In the previous post, I compared this with pKa values, and a comment\u00a0posted there reminded us that a pKa is measured for macroscopic bulk water and that all sorts of new effects due to free energy/entropy, continuum solvation and much else will take hold. But qualitatively at least, the ionisation of HI in a gas-phase cluster of water molecules seems to match the bulk properties. Relativistic effects do not appear to play a major role here.

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*Whilst such effects can be prominent for I, arguably they actually start at Cl via an effect called spin-orbit (SO) coupling. This manifests in the calculation of chemical magnetic shieldings. If one uses standard GIAO NMR theories, one can calculate shieldings for e.g. C pretty accurately. But with Cl, the shieldings may be SO-perturbed by about 3ppm, with Br it’s about 12 ppm and with I it reaches 50 ppm![5]

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References

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  1. H.S. Rzepa, \"H 3 I 1 O 1\", 2015. https://doi.org/10.14469/ch/190924\n\n
    2. \n
  2. H.S. Rzepa, \"H 5 I 1 O 2\", 2015. https://doi.org/10.14469/ch/190921\n\n
    3. \n
  3. H.S. Rzepa, \"H 7 I 1 O 3\", 2015. https://doi.org/10.14469/ch/190925\n\n
    4. \n
  4. H.S. Rzepa, \"H 9 I 1 O 4\", 2015. https://doi.org/10.14469/ch/190927\n\n
    5. \n
  5. D.C. Braddock, and H.S. Rzepa, \"Structural Reassignment of Obtusallenes V, VI, and VII by GIAO-Based Density Functional Prediction\", Journal of Natural Products, vol. 71, pp. 728-730, 2008. https://doi.org/10.1021/np0705918\n\n
    6. \n
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","doi":"https://doi.org/10.59350/8vk4h-a6g91","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13488","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1425081600,"reference":[{"id":"https://doi.org/10.14469/ch/190924","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 28). H 3 I 1 O 1 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/190921","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 28). H 5 I 1 O 2 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/190925","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 28). H 7 I 1 O 3 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/190927","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, February 28). H 9 I 1 O 4 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.1021/np0705918","unstructured":"Braddock, D. C., & Rzepa, H. S. (2008). Structural Reassignment of Obtusallenes V, VI, and VII by GIAO-Based Density Functional Prediction. Journal of Natural Products, 71(4), 728\u2013730."}],"rid":"81cy7-rrb59","summary":"Why is this post orphaned from the previous? In order to have the opportunity of noting that treating iodine computationally can be a little different from the procedures used for F, Cl and Br.","tags":["General","Interesting Chemistry","Chemical Magnetic Shieldings","Free Energy/entropy","Gas-phase Cluster"],"title":"How many water molecules does it take to ionise HI?","updated_at":1793349476,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13488","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/041kmwe10","name":"Imperial College London"}],"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":1793273213,"use_api":true},"blog_name":"Henry Rzepa's Blog","blog_slug":"rzepa","content_html":"
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My previous posts have covered the ionization by a small number of discrete water molecules of the series of halogen acids, ranging from HI (the strongest, pKa -10) via HF (weaker, pKa 3.1) to the pseudo-halogen HCN (the weakest, pKa 9.2). Here I try out some even stronger acids to see what the least number of water molecule needed to ionize these might be.

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Firstly what must surely be the ultimate acid H(CHB11Cl11), discovered by Christopher Reed[1] in 2006. This is so strong that it appears that it can even largely ionize itself; the form on the right (below) is the cationic acid, the form on the left is its anionic base. The proton itself is bridged[2] between the two in a manner similar to the structure of one form of HCl.4H2O reported in the earlier post on the topic.

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\"Click

Click for 3D

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So it comes as no surprise‡ to find[3] that just one water molecule can also ionize H(CHB11Cl11) to the anionic form (CHB11Cl11)–.

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\"Click

Click for 3D

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How about triflic acid, CF3SO2OH, pKa -16), which is also a fair bit more acidic than HI? Here, only three waters are needed (\u03c9B97XD/6-311++G(2d,2p) prediction) to ionise to triflate anion.[4]

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\"Click

Click for 3D

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So, if there a system which is ionised by precisely two water molecules I will record it here.

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‡Perhaps also no surprise is that one H2S molecule can also perform this ionisation.[5] This leads us into another exploration, using molecules other than water to perform these ionisations.

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References

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  1. E.S. Stoyanov, S.P. Hoffmann, M. Juhasz, and C.A. Reed, \"The Structure of the Strongest Br\u00f8nsted Acid:\u2009 The Carborane Acid H(CHB<sub>11</sub>Cl<sub>11</sub>)\", Journal of the American Chemical Society, vol. 128, pp. 3160-3161, 2006. https://doi.org/10.1021/ja058581l\n\n
    2. \n
  2. Stoyanov, E.S.., Hoffmann, S.P.., Juhasz, M.., and Reed, C.A.., \"CCDC 606170: Experimental Crystal Structure Determination\", 2006. https://doi.org/10.5517/ccnbrwl\n\n
    3. \n
  3. H.S. Rzepa, \"C 1 H 4 B 11 Cl 11 O 1\", 2015. https://doi.org/10.14469/ch/191134\n\n
    4. \n
  4. H.S. Rzepa, \"C 1 H 7 F 3 O 6 S 1\", 2015. https://doi.org/10.14469/ch/191129\n\n
    5. \n
  5. H.S. Rzepa, \"C 1 H 4 B 11 Cl 11 S 1\", 2015. https://doi.org/10.14469/ch/191135\n\n
    6. \n
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","doi":"https://doi.org/10.59350/y2b56-3b715","guid":"http://www.ch.imperial.ac.uk/rzepa/blog/?p=13618","image":"http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/03/LEHZOO.jpg","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1426377600,"reference":[{"id":"https://doi.org/10.1021/ja058581l","unstructured":"Stoyanov, E. S., Hoffmann, S. P., Juhasz, M., & Reed, C. A. (2006). The Structure of the Strongest Br\u00f8nsted Acid: The Carborane Acid H(CHB11Cl11). Journal of the American Chemical Society, 128(10), 3160\u20133161."},{"id":"https://doi.org/10.5517/ccnbrwl","unstructured":"Stoyanov, E.S.., Hoffmann, S.P.., Juhasz, M.., and Reed, C.A.., \"CCDC 606170: Experimental Crystal Structure Determination\", 2006."},{"id":"https://doi.org/10.14469/ch/191134","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, March 16). C 1 H 4 B 11 Cl 11 O 1 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/191129","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, March 15). C 1 H 7 F 3 O 6 S 1 [Archival collection]. Imperial College London."},{"id":"https://doi.org/10.14469/ch/191135","unstructured":"Rzepa, H. S., Imperial College London, Imperial College London, & Rzepa, H. S. (2015, March 16). C 1 H 4 B 11 Cl 11 S 1 [Archival collection]. Imperial College London."}],"rid":"p2p2m-4j396","summary":"My previous posts have covered the ionization by a small number of discrete water molecules of the series of halogen acids, ranging from HI (the strongest, pKa -10) via HF (weaker, pKa 3.1) to the pseudo-halogen HCN (the weakest, pKa 9.2). Here I try out some even stronger acids to see what the least number of water [\u2026]","tags":["Interesting Chemistry","Christopher Reed","Ohio","Pence"],"title":"Ionizing ultra-strong acids with water molecules.","updated_at":1793349474,"url":"https://www.ch.ic.ac.uk/rzepa/blog/?p=13618","version":"v1"}],"out_of":57962,"page":1,"per_page":10,"total-results":57962}