Posts Tagged ‘search query’

CH⋅⋅⋅π Interactions between methyl and carbonyl groups in proteins: a small molecule check.

Monday, May 29th, 2017
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Derek Lowe highlights a recent article[1] postulating CH⋅⋅⋅π interactions in proteins. Here I report a quick check using the small molecule crystal structure database (CSD).

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References

  1. F.A. Perras, D. Marion, J. Boisbouvier, D.L. Bryce, and M.J. Plevin, "Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins", Angewandte Chemie International Edition, vol. 56, pp. 7564-7567, 2017. http://dx.doi.org/10.1002/anie.201702626

How does carbon dioxide coordinate to a metal?

Saturday, May 6th, 2017
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Mention carbon dioxide (CO2) to most chemists and its properties as a metal ligand are not the first aspect that springs to mind. Here thought I might take a look at how it might act as such.

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π-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach?

Monday, April 17th, 2017
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Following on from my re-investigation of close hydrogen bonding contacts to the π-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469/hpc/2478) is similar to the previous one:

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π-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?

Saturday, April 15th, 2017
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Back in the early 1990s, we first discovered the delights of searching crystal structures for unusual bonding features.[1] One of the first cases was a search for hydrogen bonds formed to the π-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it’s now ten times larger) and the search software less powerful. So here is an update. 

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References

  1. H.S. Rzepa, M.H. Smith, and M.L. Webb, "A crystallographic AM1 and PM3 SCF-MO investigation of strong OH ⋯π-alkene and alkyne hydrogen bonding interactions", J. Chem. Soc., Perkin Trans. 2, pp. 703-707, 1994. http://dx.doi.org/10.1039/P29940000703

The π-π stacking of aromatic rings: what is their closest parallel approach?

Thursday, April 13th, 2017
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Layer stacking in structures such as graphite is well-studied. The separation between the π-π planes is ~3.35Å, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7Å). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW distance sum by up to ~0.8Å or even more? This question was prompted by the separation calculated for the ion-pair cyclopropenium cyclopentadienide (~2.6-2.8Å).

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The conformation of enols: revealed and explained.

Thursday, April 6th, 2017
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Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.

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Silyl cations?

Thursday, March 23rd, 2017
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It is not only the non-classical norbornyl cation that has proved controversial in the past. A colleague mentioned at lunch (thanks Paul!) that tri-coordinate group 14 cations such as R3Si+ have also had an interesting history.[1] Here I take a brief look at some of these systems.

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References

  1. J.B. Lambert, Y. Zhao, H. Wu, W.C. Tse, and B. Kuhlmann, "The Allyl Leaving Group Approach to Tricoordinate Silyl, Germyl, and Stannyl Cations", Journal of the American Chemical Society, vol. 121, pp. 5001-5008, 1999. http://dx.doi.org/10.1021/ja990389u

Stable “unstable” molecules: a crystallographic survey of cyclobutadienes and cyclo-octatetraenes.

Sunday, March 5th, 2017
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Cyclobutadiene is one of those small iconic molecules, the transience and instability of which was explained theoretically long before it was actually detected in 1965.[1] Given that instability, I was intrigued as to how many crystal structures might have been reported for this ring system, along with the rather more stable congener cyclo-octatetraene. Here is what I found.

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References

  1. L. Watts, J.D. Fitzpatrick, and R. Pettit, "Cyclobutadiene", Journal of the American Chemical Society, vol. 87, pp. 3253-3254, 1965. http://dx.doi.org/10.1021/ja01092a049

Molecules of the year? Pnictogen chains and 16 coordinate Cs.

Monday, December 19th, 2016
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I am completing my survey of the vote for molecule of the year candidates, which this year seems focused on chemical records of one type or another.

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Molecule of the year? “CrN123”, a molecule with three different types of Cr-N bond.

Friday, December 16th, 2016
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Here is a third candidate for the C&EN “molecule of the year” vote. This one was shortlisted because it is the first example of a metal-nitrogen complex exhibiting single, double and triple bonds from different nitrogens to the same metal[1] (XUZLUB has a 3D display available at DOI: 10.5517/CC1JYY6M). Since no calculation of its molecular properties was reported, I annotate some here.

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References

  1. E.P. Beaumier, B.S. Billow, A.K. Singh, S.M. Biros, and A.L. Odom, "A complex with nitrogen single, double, and triple bonds to the same chromium atom: synthesis, structure, and reactivity", Chem. Sci., vol. 7, pp. 2532-2536, 2016. http://dx.doi.org/10.1039/c5sc04608d