Posts Tagged ‘Molecular geometry’
Monday, April 1st, 2019
Members of the chemical FAIR data community have just met in Orlando (with help from the NSF, the American National Science Foundation) to discuss how such data is progressing in chemistry. There are a lot of themes converging at the moment. Thus this article[1] extolls the virtues of having raw NMR data available in natural product research, to which we added that such raw data should also be made FAIR (Findable, Accessible, Interoperable and Reusable) by virtue of adding rich metadata and then properly registering it so that it can be searched. These themes are combined in another article which made a recent appearance.[2]
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References
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J.B. McAlpine, S. Chen, A. Kutateladze, J.B. MacMillan, G. Appendino, A. Barison, M.A. Beniddir, M.W. Biavatti, S. Bluml, A. Boufridi, M.S. Butler, R.J. Capon, Y.H. Choi, D. Coppage, P. Crews, M.T. Crimmins, M. Csete, P. Dewapriya, J.M. Egan, M.J. Garson, G. Genta-Jouve, W.H. Gerwick, H. Gross, M.K. Harper, P. Hermanto, J.M. Hook, L. Hunter, D. Jeannerat, N. Ji, T.A. Johnson, D.G.I. Kingston, H. Koshino, H. Lee, G. Lewin, J. Li, R.G. Linington, M. Liu, K.L. McPhail, T.F. Molinski, B.S. Moore, J. Nam, R.P. Neupane, M. Niemitz, J. Nuzillard, N.H. Oberlies, F.M.M. Ocampos, G. Pan, R.J. Quinn, D.S. Reddy, J. Renault, J. Rivera-Chávez, W. Robien, C.M. Saunders, T.J. Schmidt, C. Seger, B. Shen, C. Steinbeck, H. Stuppner, S. Sturm, O. Taglialatela-Scafati, D.J. Tantillo, R. Verpoorte, B. Wang, C.M. Williams, P.G. Williams, J. Wist, J. Yue, C. Zhang, Z. Xu, C. Simmler, D.C. Lankin, J. Bisson, and G.F. Pauli, "The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research", Natural Product Reports, vol. 36, pp. 35-107, 2019. http://dx.doi.org/10.1039/c7np00064b
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A. Barba, S. Dominguez, C. Cobas, D.P. Martinsen, C. Romain, H.S. Rzepa, and F. Seoane, "Workflows Allowing Creation of Journal Article Supporting Information and Findable, Accessible, Interoperable, and Reusable (FAIR)-Enabled Publication of Spectroscopic Data", ACS Omega, vol. 4, pp. 3280-3286, 2019. http://dx.doi.org/10.1021/acsomega.8b03005
Tags:American National Science Foundation, Bond length, ChemDraw, chemical, Chemical IT, Chemistry, City: Orlando, Company: NSF, Force field, Intermolecular forces, Molecular geometry, National Science Foundation, natural product, Natural sciences, Orlando, Physical organic chemistry, Physical sciences, Quantum chemistry, Science and technology in the United States, Stereochemistry, steric energy, steric energy test, Strain, suitable free tool, unstable natural product, X-ray
Posted in Uncategorised | No Comments »
Saturday, February 24th, 2018
Another post inspired by a comment on an earlier one; I had been discussing compounds of the type I.In (n=4,6) as possible candidates for hypervalency. The comment suggests the below as a similar analogue, deriving from observations made in 1989.[1]
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References
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Y. Mazaki, and K. Kobayashi, "Structure and intramolecular dynamics of bis(diisobutylselenocarbamoyl) triselenide as identified in solution by the 77Se-NMR spectroscopy", Tetrahedron Letters, vol. 30, pp. 2813-2816, 1989. http://dx.doi.org/10.1016/S0040-4039(00)99132-9
Tags:C, chemical bonding, Chemistry, free energy, Hypervalency, Hypervalent molecule, Matter, Molecular geometry, Nature, Nitrogen
Posted in Uncategorised | 3 Comments »
Tuesday, December 26th, 2017
Recollect the suggestion that diazomethane has hypervalent character[1]. When I looked into this, I came to the conclusion that it probably was mildly hypervalent, but on carbon and not nitrogen. Here I try some variations with substituents to see what light if any this casts.
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References
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M.C. Durrant, "A quantitative definition of hypervalency", Chemical Science, vol. 6, pp. 6614-6623, 2015. http://dx.doi.org/10.1039/C5SC02076J
Tags:chemical bonding, Chemistry, diazo, Diazo compounds, Diazomethane, diazomethane-like systems, Functional groups, Hypervalency, Hypervalent molecule, Molecular geometry, Organic chemistry, Recollects
Posted in Uncategorised | 8 Comments »
Saturday, December 23rd, 2017
In the previous post, I referred to a recently published review on hypervalency[1] which introduced a very simple way (the valence electron equivalent γ) of quantifying the effect. Diazomethane was cited as one example of a small molecule exhibiting hypervalency (on nitrogen) by this measure. Here I explore the effect of substituting diazomethane with cyano and nitro groups.‡
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References
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M.C. Durrant, "A quantitative definition of hypervalency", Chemical Science, vol. 6, pp. 6614-6623, 2015. http://dx.doi.org/10.1039/C5SC02076J
Tags:candidate for hypervalent carbon, chemical bonding, Hypervalency, Hypervalent molecule, Interesting chemistry, Molecular geometry
Posted in Uncategorised | No Comments »
Tuesday, November 7th, 2017
One thread that runs through this blog is that of hypervalency. It was therefore nice to come across a recent review of the concept[1] which revisits the topic, and where a helpful summary is given of the evolving meanings over time of the term hypervalent. The key phrase “it soon became clear that the two principles of the 2-centre-2-electron bond and the octet rule were sometimes in conflict” succinctly summarises the issue. Two molecules that are discussed in this review caught my eye, CLi6 and SeMe6. The former is stated as “anomalous in terms of the Lewis model“, but as I have shown in an earlier post, the carbon is in fact not anomalous in a Lewis sense because of a large degree of Li-Li bonding. When this is taken into account, the Lewis model of the carbon becomes more “normal”. Here I take a look at the other cited molecule, SeMe6.
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References
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M.C. Durrant, "A quantitative definition of hypervalency", Chemical Science, vol. 6, pp. 6614-6623, 2015. http://dx.doi.org/10.1039/c5sc02076j
Tags:chemical bonding, City: Aachen, Hypervalency, Hypervalent molecule, Molecular geometry
Posted in Uncategorised | 4 Comments »
Saturday, September 16th, 2017
Early in 2011, I wrote about how the diatomic molecule Be2 might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species. I yesterday updated this post with further suggestions and one of these inspired this follow-up.
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Tags:Be-Be double bond, Be-Be triple bond, Chemical bond, Chemistry, Cs-Cs double bond, Diatomic molecule, free energy, General chemistry, Interesting chemistry, K-K double bond, Li-Li double bond, Molecular geometry, Oxygen, Province/State: Be2, Quantum chemistry, Rb-Rb double bond, Stereochemistry
Posted in Uncategorised | 3 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 »
Monday, October 31st, 2016
Is asking a question such as “what is the smallest angle subtended at a chain of three connected 4-coordinate carbon atoms” just seeking another chemical record, or could it unearth interesting chemistry?
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Tags:animation, Bicyclic molecule, chemical record, Chemistry, City: Cambridge, Cycloalkane, Cyclopropanes, Java, Molecular geometry, Organic chemistry, potential energy surface, Safari, Web browser, X-ray
Posted in crystal_structure_mining, reaction mechanism | 7 Comments »
Monday, May 30th, 2016
This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry. This search arose because of a casual comment I made in the earlier post regarding possible cooperative effects between the two axial ligands (the ones with an angle of ~180 degrees subtended at silicon). Perhaps the geometries might expand upon this comment?
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Tags:Anomer, Anomeric effect, Carbohydrate chemistry, Carbohydrates, Chemical IT, Ligand, Molecular geometry, Physical organic chemistry, Stereochemistry, Stereoelectronic effect, Trigonal bipyramidal molecular geometry
Posted in crystal_structure_mining | 3 Comments »