Posts Tagged ‘Quantum chemistry’
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, 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 Chemical IT | No Comments »
Monday, June 18th, 2018
It was about a year ago that I came across a profusion of colour in my local Park. Although colour in fact was the topic that sparked my interest in chemistry many years ago (the fantastic reds produced by diazocoupling reactions), I had never really tracked down the origin of colours in many flowers. It is of course a vast field. Here I take a look at just one class of molecule responsible for many flower colours, anthocyanidin, this being the sugar-free counterpart of the anthocyanins found in nature.
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Tags:Anthocyanidin, Anthocyanin, Chemistry, Delphinidin, HOMO/LUMO, Major, Molecular electronic transition, Molecule, Nature, PH indicators, Quantum chemistry, spectroscopy, Ultraviolet–visible spectroscopy
Posted in Interesting chemistry | 4 Comments »
Sunday, March 4th, 2018
A bond index (BI) approximately measures the totals of the bond orders at any given atom in a molecule. Here I ponder what the maximum values might be for elements with filled valence shells.
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Tags:Atom, Chemical bond, chemical bonding, chemical properties, Chemistry, metal bond indices, Molecule, Nature, Quantum chemistry, Residential REITs, Resonance, Tennessine, Valence, Valence electron
Posted in Interesting chemistry | No Comments »
Sunday, November 12th, 2017
A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons. Whereas the original VSEPR theory talks about five “electron pairs” totalling an octet-busting ten electrons surrounding chlorine, the electron density-based ELF approach located only ~6.8e surrounding the central chlorine and no “octet-busting”. The remaining electrons occupied fluorine lone pairs rather than the shared Cl-F regions. Here I take a look at ClMe3, as induced by the analysis of SeMe6.
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Tags:Chemical bond, chemical bonding, Chemistry, Chlorine, Covalent bond, Lone pair, Oxidizing agents, Quantum chemistry, Stereochemistry, Valence, VSEPR theory
Posted in Chemical IT, Hypervalency | 5 Comments »
Tuesday, October 24th, 2017
An N-B single bond is iso-electronic to a C-C single bond, as per below. So here is a simple question: what form does the distribution of the lengths of these two bonds take, as obtained from crystal structures?
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Tags:bond, Bond valence method, Chemical bond, chemical bonding, Chemistry, Covalent bond, crystal structure, Nature, Quantum chemistry, search query
Posted in crystal_structure_mining | 3 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, K-K double bond, Li-Li double bond, Molecular geometry, Oxygen, Province/State: Be2, Quantum chemistry, Rb-Rb double bond, Stereochemistry
Posted in Interesting chemistry | 3 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.
(more…)
Tags:Be-Be double bond, Be-Be triple bond, Chemical bond, Chemistry, Cs-Cs double bond, Diatomic molecule, free energy, General chemistry, K-K double bond, Li-Li double bond, Molecular geometry, Oxygen, Province/State: Be2, Quantum chemistry, Rb-Rb double bond, Stereochemistry
Posted in Interesting chemistry | 3 Comments »
Monday, March 20th, 2017
The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate (IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD).
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Tags:animation, chemical reaction, Chemistry, computational chemistry, computed potential energy surface, energy, Gaseous signaling molecules, Hydrogen, kinetic energy, kinetic energy contributions, Methane, Molecular dynamics, Physical chemistry, Quantum chemistry, Reaction coordinate, simulation, Theoretical chemistry
Posted in reaction mechanism | 2 Comments »
Wednesday, February 15th, 2017
This post arose from a comment attached to the post on Na2He and relating to peculiar and rare topological features of the electron density in molecules called non-nuclear attractors. This set me thinking about other molecules that might exhibit this and one of these is shown below.
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Tags:Attractor, brief search, Chemistry, Electron, Electron density, Hydrogen, Molecule, Nature, Physics, Quantum chemistry
Posted in Interesting chemistry | 11 Comments »