Archive for January, 2016
Sunday, January 31st, 2016
Six years ago, I posted on the nature of a then recently reported[1] Cr-Cr quintuple bond. The topic resurfaced as part of the discussion on a more recent post on NSF3, and a sub-topic on the nature of the higher order bonding in C2. The comment made a connection between that discussion and the Cr-Cr bond alluded to above. I responded briefly to that comment, but because I want to include 3D rotatable surfaces, I expand the discussion here and not in the comment.‡
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References
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C. Hsu, J. Yu, C. Yen, G. Lee, Y. Wang, and Y. Tsai, "Quintuply‐Bonded Dichromium(I) Complexes Featuring Metal–Metal Bond Lengths of 1.74 Å", Angewandte Chemie International Edition, vol. 47, pp. 9933-9936, 2008. http://dx.doi.org/10.1002/anie.200803859
Tags:Chemical bond, chemical bonding, Electron, Electron configuration, energy, General, Interesting chemistry, Molecular orbital, Multi-configurational self-consistent field, Quantum chemistry, quintuple bond, search term, Transition metal, Valence bond theory
Posted in Uncategorised | 6 Comments »
Wednesday, January 20th, 2016
The original strategic objective of my PhD researches in 1972-74 was to explore how primary kinetic hydrogen isotope effects might be influenced by the underlying structures of the transition states involved. Earlier posts dealt with how one can construct quantum-chemical models of these transition states that fit the known properties of the reactions. Now, one can reverse the strategy by computing the expected variation with structure to see if anything interesting might emerge, and then if it does, open up the prospect of further exploration by experiment. Here I will use the base-catalysed enolisation of 1,3-dimethylindolin-2-ones and the decarboxylation of 3-indole carboxylates to explore this aspect.
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Tags:aqueous solution, Brian Challis, can construct quantum-chemical models, computed free energy barrier matches, Dan Singleton, free energy barrier, free energy barriers, Kinetic isotope effect, Organic chemistry, Physical organic chemistry, quantum-chemical models, supervisor
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Saturday, January 16th, 2016
The post on applying VSEPR ("valence shell electron pair repulsion") theory to the geometry of ClF3 has proved perennially popular. So here is a follow-up on another little molecue, F3SN. As the name implies, it is often represented with an S≡N bond. Here I take a look at the conventional analysis.
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Tags:Chemical bond, chemical bonding, Electron, Hypervalency, Lone pair, Molecular geometry, Octet rule, Quantum chemistry, Stereochemistry, Tetrahedral molecular geometry, Theoretical chemistry, Valence, VSEPR theory
Posted in Uncategorised | 110 Comments »
Sunday, January 10th, 2016
Earlier I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came models for both water and the general base catalysed ionization of indolinones. Here I explore general acid catalysis by evaluating the properties of two possible models for decarboxylation of 3-indole carboxylic acid, one involving proton transfer (PT) from neutral water in the presence of covalent un-ionized HCl (1) and one with PT from a protonated water resulting from ionised HCl (2).
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Tags:Acid, Acids, bicyclic network, carboxylic acid, free energy, Functional groups, Hydrogen bond, Indole, Interesting chemistry, transition state free energy
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Thursday, January 7th, 2016
This is the third and final study deriving from my Ph.D.[1]. The first two topics dealt with the mechanism of heteroaromatic electrophilic attack using either a diazonium cation or a proton as electrophile, followed by either proton abstraction or carbon dioxide loss from the resulting Wheland intermediate. This final study inverts this sequence by starting with the proton abstraction from an indolinone by a base to create/aromatize to a indole-2-enolate intermediate, which only then is followed by electrophilic attack (by iodine). Here I explore what light quantum chemical modelling might cast on the mechanism.
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References
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B.C. Challis, and H.S. Rzepa, "Heteroaromatic hydrogen exchange reactions. Part VIII. The ionisation of 1,3-dimethylindolin-2-one", Journal of the Chemical Society, Perkin Transactions 2, pp. 1822, 1975. http://dx.doi.org/10.1039/P29750001822
Tags:Arenium ion, Bases, diazo, Diazonium compound, Electrophile, Electrophilic aromatic substitution, Equilibrium chemistry, Fortran, Historical, Indole, light quantum chemical modelling, Metal ions in aqueous solution, Nuclear physics, Simple aromatic rings, Solutions
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Tuesday, January 5th, 2016
In May 2015, the EPSRC funding council in the UK required researchers to publish the outcomes of the funded work to include an OA (open access) version of the narrative and to cite the managed research data used to support the research with a DOI (digital object identifier). I was discussing these aspects with a senior manager (research outcomes) at the EPSRC and he asked me to provide some examples from my area of chemistry; here are some.
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Tags:Chemical IT
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Saturday, January 2nd, 2016
Another mechanistic study we started in 1972[1] is here 40+ years on subjected to quantum mechanical scrutiny.
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References
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B.C. Challis, and H.S. Rzepa, "Heteroaromatic hydrogen exchange reactions. Part 9. Acid catalysed decarboxylation of indole-3-carboxylic acids", Journal of the Chemical Society, Perkin Transactions 2, pp. 281, 1977. http://dx.doi.org/10.1039/P29770000281
Tags:aqueous ethanoic acid solutions, energy, ethanoic acid solutions, free energy barrier , Historical, quantum chemical modelling
Posted in reaction mechanism | No Comments »