Posts Tagged ‘Physical organic 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, 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
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Sunday, January 13th, 2019
Linear free energy relationships (LFER) are associated with the dawn of physical organic chemistry in the late 1930s and its objectives in understanding chemical reactivity as measured by reaction rates and equilibria.
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Tags:Benzoic acid, Chemical IT, Chemical kinetics, chemical reaction, chemical reactivity, chemist, Chemistry, Electrophilic aromatic substitution, energy point, Equations, Equilibrium chemistry, Equilibrium constant, free energy overall route, Hammett equation, Interesting chemistry, Linear free energy relationships, Natural sciences, Organic chemistry, Physical organic chemistry, Physical sciences, Reactivity
Posted in reaction mechanism | No Comments »
Thursday, January 3rd, 2019
There is emerging interest in cyclic conjugated molecules that happen to have triplet spin states and which might be expected to follow a 4n rule for aromaticity.[1] The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to be lower in energy. Here I explore some crystal structures containing this motif for possible insights.
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References
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A. Kostenko, B. Tumanskii, Y. Kobayashi, M. Nakamoto, A. Sekiguchi, and Y. Apeloig, "Spectroscopic Observation of the Triplet Diradical State of a Cyclobutadiene", Angewandte Chemie International Edition, vol. 56, pp. 10183-10187, 2017. http://dx.doi.org/10.1002/anie.201705228
Tags:antiaromaticity, aromaticity, Baird's rule, Conjugated system, crystal structure search, energy, Hückel's rule, Interesting chemistry, Nature, Physical organic chemistry, Physical sciences, search query, Triplet state
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Friday, December 21st, 2018
Five years back, I speculated about the mechanism of the epoxidation of ethene by a peracid, concluding that kinetic isotope effects provided interesting evidence that this mechanism is highly asynchronous and involves a so-called “hidden intermediate”. Here I revisit this reaction in which a small change is applied to the atoms involved.
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Tags:Chemical kinetics, chemical reaction, Chemistry, Deuterium, Interesting chemistry, Isotope effect, Kinetic isotope effect, Natural sciences, Organic chemistry, overall activation energy, pericyclic reaction, Physical organic chemistry, Physical sciences, potential energy surface, Rearrangement reactions
Posted in Uncategorised | 5 Comments »
Saturday, September 1st, 2018
I am exploring the fascinating diverse facets of a recently published laboratory experiment for undergraduate students.[1] Previously I looked at a possible mechanistic route for the reaction between an enal (a conjugated aldehyde-alkene) and benzyl chloride catalysed by base and a chiral amine, followed by the use of NMR coupling constants to assign relative stereochemistries. Here I take a look at some chiroptical techniques which can be used to assign absolute stereochemistries (configurations).
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References
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M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (E)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018. http://dx.doi.org/10.1021/acs.jchemed.7b00566
Tags:Absolute configuration, Biochemistry, bulk solutions, chemical transformations, Chemistry, Conformational isomerism, difficult energy difference, gas phase, higher energy forms, Interesting chemistry, Isomer, Isomerism, Nature, Physical organic chemistry, Polarization, spectroscopy, stereochemical product, Stereochemistry, Stereoisomerism, Vibrational circular dichroism
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Wednesday, August 22nd, 2018
Following the general recognition of carbon as being tetrahedrally tetravalent in 1869 (Paterno) and 1874 (Van’t Hoff and Le Bell), an early seminal exploitation of this to the conformation of cyclohexane was by Hermann Sachse in 1890.[1] This was verified when the Braggs in 1913[2], followed by an oft-cited article by Mohr in 1918,[3] established the crystal structure of diamond as comprising repeating rings in the chair conformation.† So by 1926, you might imagine that the shape (or conformation as we would now call it) of cyclohexane would be well-known. No quite so for everyone!
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References
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H. Sachse, "Ueber die geometrischen Isomerien der Hexamethylenderivate", Berichte der deutschen chemischen Gesellschaft, vol. 23, pp. 1363-1370, 1890. http://dx.doi.org/10.1002/cber.189002301216
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"The structure of the diamond", Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character, vol. 89, pp. 277-291, 1913. http://dx.doi.org/10.1098/rspa.1913.0084
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E. Mohr, "Die Baeyersche Spannungstheorie und die Struktur des Diamanten", Journal für Praktische Chemie, vol. 98, pp. 315-353, 1918. http://dx.doi.org/10.1002/prac.19180980123
Tags:Carbon, chair, Chemistry, Conformation, Cycloalkanes, cyclohexane, Cyclohexane conformation, Derek Barton, Hermann Sachse, Hoff, Imperial College Chemical Society, Interesting chemistry, Isomerism, Physical organic chemistry, R. F Hunter, Stereochemistry, Van 't Hof
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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 »
Thursday, March 23rd, 2017
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
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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
Tags:2-Norbornyl cation, Carbocations, chemical bonding, Chemistry, metal, Physical organic chemistry, Reactive intermediates, search query, tri-coordinate
Posted in crystal_structure_mining | 8 Comments »
Sunday, March 12th, 2017
This is another of those posts that has morphed from an earlier one noting the death of the great chemist George Olah. The discussion about the norbornyl cation concentrated on whether this species existed in a single minimum symmetric energy well (the non-classical Winstein/Olah proposal) or a double minimum well connected by a symmetric transition state (the classical Brown proposal). In a comment on the post, I added other examples in chemistry of single/double minima, mapped here to non-classical/classical structures. I now expand on the examples related to small aromatic or anti-aromatic rings.
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Tags:antiaromaticity, aromaticity, Évariste Galois, Carbocation, Chemistry, equilibrium minimum energy position, George Andrew Olah, George Olah, great chemist, Interesting chemistry, Jahn-Teller, minimum symmetric energy, Olah, Physical organic chemistry, Saul Winstein, symmetric energy potentials
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