Posts Tagged ‘Chemistry’
Saturday, April 15th, 2017
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
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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
Tags:calculated energy, chemical bonding, Chemistry, Crystal, crystallography, energy, energy calculation, Intermolecular forces, Nature, search query, search software, Supramolecular chemistry
Posted in crystal_structure_mining | 2 Comments »
Thursday, April 13th, 2017
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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Tags:Carbon, chemical bonding, Chemistry, Cyclopentadienyl anion, Graphite, Hydrogen bond, Intermolecular forces, Nature, Organic chemistry, search query, Stacking, Supramolecular chemistry, VDW
Posted in crystal_structure_mining | 1 Comment »
Sunday, April 9th, 2017
Both the cyclopropenium cation and the cyclopentadienide anion are well-known 4n+2-type aromatic ions, but could the two together form an ion-pair?
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Tags:Anions, Aromatization, Cation–pi interaction, Chemistry, Cyclopentadienyl anion, Interesting chemistry, Ion, Ion association, potential energy surface, Simple aromatic rings
Posted in crystal_structure_mining | 6 Comments »
Thursday, April 6th, 2017
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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Tags:Chemical bond, chemical bonding, Chemistry, Conformational isomerism, constrained search, Enol, free energy, Gauche effect, Hydrogen bond, Isomerism, Java, Physical organic chemistry, search query, Stereochemistry, Supramolecular chemistry
Posted in crystal_structure_mining, reaction mechanism | 2 Comments »
Saturday, April 1st, 2017
In a comment appended to an earlier post, I mused about the magnitude of the force constant relating to the interconversion between a classical and a non-classical structure for the norbornyl cation. Most calculations indicate the force constant for an “isolated” symmetrical cation is +ve, which means it is a true minimum and not a transition state for a [1,2] shift. The latter would have been required if the species equilibrated between two classical carbocations. I then pondered what might happen to both the magnitude and the sign of this force constant if various layers of solvation and eventually a counter-ion were to be applied to the molecule, so that a bridge of sorts between the different states of solid crystals, superacid and aqueous solutions might be built.
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Tags:Carbocations, chemical bonding, Chemistry, constant matrix/search direction, continuum model for water, gas phase, Interesting chemistry, Paul Schleyer, Physical organic chemistry, potential energy surface, Reactive intermediates, superacid and aqueous solutions
Posted in crystal_structure_mining, reaction mechanism | 7 Comments »
Friday, March 31st, 2017
Nowadays, data supporting most publications relating to the synthesis of organic compounds is more likely than not to be found in associated “supporting information” rather than the (often page limited) article itself. For example, this article[1] has an SI which is paginated at 907; almost a mini-database in its own right!† Here I ponder whether such dissemination of data is FAIR (Findable, accessible, interoperable and re-usable).[2]
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References
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J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. http://dx.doi.org/10.1021/jacs.6b13229
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M.D. Wilkinson, M. Dumontier, I.J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. Boiten, L.B. da Silva Santos, P.E. Bourne, J. Bouwman, A.J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C.T. Evelo, R. Finkers, A. Gonzalez-Beltran, A.J. Gray, P. Groth, C. Goble, J.S. Grethe, J. Heringa, P.A. ’t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S.J. Lusher, M.E. Martone, A. Mons, A.L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M.A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, and B. Mons, "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data, vol. 3, 2016. http://dx.doi.org/10.1038/sdata.2016.18
Tags:Carbon, chemical databases, chemical graveyard, Chemical IT, chemical spectra, Chemistry, digital signature, Nature, Organic, Organic chemistry, Organic compound, Organic food, search engines, Technology/Internet
Posted in Uncategorised | 3 Comments »
Friday, March 31st, 2017
Occasionally one comes across a web site that manages to combine being unusual, interesting and also useful. Thus www.molinsight.net is I think a unique chemistry resource for blind and visually impaired students.
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Tags:Chemistry, Electromagnetic radiation, Infrared, Infrared spectroscopy, Interesting chemistry, Multimodal interaction, Nuclear magnetic resonance, open source chemical structure editors, Sonification, spectroscopy, stereochemical utilities
Posted in Uncategorised | No Comments »
Saturday, March 25th, 2017
A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via a crystal structure, DOI:10.5517/CCDC.CSD.CC1M71QM[1]. Here is a similar proposal for penta-coordinate nitrogen.
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References
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M. Malischewski, and K. Seppelt, "Crystal Structure Determination of the Pentagonal‐Pyramidal Hexamethylbenzene Dication C6(CH3)62+", Angewandte Chemie International Edition, vol. 56, pp. 368-370, 2016. http://dx.doi.org/10.1002/anie.201608795
Tags:aromatic systems, Chemistry, Hexacoordinate, Hypervalency, Hypotheses, Interesting chemistry, Matter, Molecular geometry, Stereochemistry
Posted in Bond slam, crystal_structure_mining | 1 Comment »