July 1st, 2015
Recollect this earlier post on the topic of the Baeyer-Villiger reaction. In 1999 natural abundance kinetic isotope effects were reported[cite]10.1021/ja992016z[/cite] and I set out to calculate the values predicted for a particular model constructed using Quantum mechanics. This comparison of measurement and calculation is nowadays a standard verification of both experiment and theory. When the two disagree either the computational model is wrong or incomplete, or the remoter possibility that there is something not understood about the experiment.
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Tags: Dan Singleton, Donna Blackmond, energy method, Erik Plata, free energy method, Jordi Bures Amat, Keith Laidig, Kinetic isotope effect, Physical organic chemistry, Yale
Posted in reaction mechanism | 4 Comments »
June 26th, 2015
Open principles in the sciences in general and chemistry in particular are increasingly nowadays preached from funding councils down, but it can be more of a challenge to find innovative practitioners. Part of the problem perhaps is that many of the current reward systems for scientists do not always help promote openness. Jean-Claude Bradley was a young scientist who was passionately committed to practising open chemistry, even though when he started he could not have anticipated any honours for doing so. A year ago a one day meeting at Cambridge was held to celebrate his achievements, followed up with a special issue of the Journal of Cheminformatics. Peter Murray-Rust and I both contributed and following the meeting we decided to help promote Open Chemistry via an annual award to be called the Bradley-Mason prize. This would celebrate both “JC” himself and Nick Mason, who also made outstanding contributions to the cause whilst studying at Imperial College. The prize was initially to be given to an undergraduate student at Imperial, but was also extended to postgraduate students who have promoted and showcased open chemistry in their PhD researches.
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Tags: Cambridge, chemical data, Chemistry Central, Collective intelligence, Crowdsourcing, Doctor of Philosophy, Education, European Union, France, GITHUB INC., Imperial College, Jean Claude Bradley, lab on a chip, Lyon, Nick Mason, Nonprofit technology, Open content, Peter Murray-Rust, reward systems, Technology/Internet, Tom Arrow, Tom Phillips, Wikimedia Foundation, wikipedia, World Wide Web, young scientist
Posted in Bradley-Mason Prize for Open Chemistry, Chemical IT | 1 Comment »
June 20th, 2015
The university sector in the UK has quality inspections of its research outputs conducted every seven years, going by the name of REF or Research Excellence Framework. The next one is due around 2020, and already preparations are under way! Here I describe how I have interpreted one of its strictures; that all UK funded research outputs (i.e. research publications in international journals) must be made available in open unrestricted form within three months of the article being accepted for publication, or they will not be eligible for consideration in 2020.
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Tags: Academia, Academic publishing, Archival science, author, Data management, Digital library, EPrints, Institutional repository, Knowledge, Knowledge representation, Library science, metadata, Open access, PDF, personal web page, Preprint, Publishing, Repository, researcher, ROMEO GREEN, Science, Technology/Internet, United Kingdom, web server
Posted in Chemical IT | No Comments »
June 12th, 2015
In the preceding post, I discussed the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly pointed out on this blog that his was a mixed-phase reaction, and that mechanistic comparison with homogenous solutions may not be justified. An intriguing aspect of the (solution) mechanism would be whether the TI forms quickly and/or reversibly and what the position of any equilibrium between it and the starting ketone is. This reminded me of work we did some years ago,[cite]10.1021/jo00389a050[/cite] and here I discuss that.
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Tags: Anomer, Anomeric effect, Carbohydrate chemistry, Carbohydrates, Chemistry, Dan Singleton, homogenous solutions, Ketone, Meta-Chloroperoxybenzoic acid, Organic chemistry, Tetrahedral carbonyl addition compound
Posted in reaction mechanism | 2 Comments »
June 10th, 2015
I have blogged before about the mechanism of this classical oxidation reaction. Here I further explore computed models, and whether they match the observed kinetic isotope effects (KIE) obtained using the natural-abundance method described in the previous post.
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Tags: ATM, Baeyer–Villiger oxidation, Chemistry, Dipole, energy, energy gradient, Kinetic isotope effect, Physical organic chemistry
Posted in reaction mechanism | 4 Comments »
June 3rd, 2015
My PhD thesis involved determining kinetic isotope effects (KIE) for aromatic electrophilic substitution reactions in an effort to learn more about the nature of the transition states involved.[cite]10.1039/p29750001209[/cite] I learnt relatively little, mostly because a transition state geometry is defined by 3N-6 variables (N = number of atoms) and its force constants by even more and you get only one or two measured KIE per reaction; a rather under-defined problem in terms of data! So I decided to spend a PostDoc learning how to invert the problem by computing the anticipated isotope effects using quantum mechanics and then comparing the predictions with measured KIE.[cite]10.1021/ja00486a013[/cite] Although such computation allows access to ALL possible isotope effects, the problem is still under-defined because of the lack of measured KIE to compare the predictions with. In 1995 Dan Singleton and Allen Thomas reported an elegant strategy to this very problem by proposing a remarkably simple method for obtaining KIE using natural isotopic abundances.[cite]10.1021/ja00141a030[/cite] It allows isotope effects to be measured for all the positions in one of the reactant molecules by running the reaction close to completion and then recovering unreacted reactant and measuring the changes in its isotope abundances using NMR. The method has since been widely applied[cite]10.1021/ja109686[/cite],[cite]10.1021/ja205674x[/cite] and improved.[cite]10.1038/nchembio.352[/cite] Here I explore how measured and calculated KIE can be reconciled.
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Tags: Allen Thomas, calculated activation free energy, Chemistry, Dan Singleton, Deuterium, Diels–Alder reaction, Isotope, Isotopes, Kinetic isotope effect, Nuclear physics, Physical organic chemistry, shell solutions
Posted in reaction mechanism | 6 Comments »
May 30th, 2015
I am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool. One colleague asked for a demonstration and suggested exploring the classical Jahn-Teller effect (thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best example is illustrated by octahedral copper complexes which have a d9 electronic configuration. The eg level shown below is occupied by three electrons and which can therefore distort in one of two ways to eliminate the eg degeneracy by placing the odd electron into either a x2-y2 or a z2 orbital. Here I explore how this effect can be teased out of crystal structures.
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Tags: basic search, Chemical bond, chemical bonding, Chemistry, classical Jahn-Teller, clear Jahn-Teller, Coordination chemistry, Coordination complex, Copper(II) nitrate, dynamic Jahn-Teller, Edward Teller, Inorganic chemistry, Jahn-Teller, Jahn–Teller effect, Metal ions in aqueous solution, search criteria, Technology/Internet, Transition metals
Posted in Chemical IT, crystal_structure_mining | 1 Comment »
May 22nd, 2015
As I have noted elsewhere, Gilbert N. Lewis wrote a famous paper entitled “the atom and the molecule“, the centenary of which is coming up.[cite]10.1021/ja02261a002[/cite] In a short and rarely commented upon remark, he speculates about the shared electron pair structure of acetylene, R-X≡X-R (R=H, X=C). It could, he suggests, take up three forms. H-C:::C-H and two more which I show as he drew them. The first of these would now be called a bis-carbene and the second a biradical.
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Tags: Carbene, Carbenes, Chemistry, Cluster chemistry, food, Functional groups, Gilbert N. Lewis, Non-Kekulé molecule, Organic chemistry, Organic compounds
Posted in Chemical IT, Historical, Interesting chemistry | 1 Comment »
May 21st, 2015
A lunchtime conversation with a colleague had us both bemoaning the distorting influence on chemistry of bibliometrics, h-indices and journal impact factors, all very much a modern phenomenon of scientific publishing. Young academics on a promotion fast-track for example are apparently advised not to publish in a well-known journal devoted to organic chemistry because of its apparently “low” impact factor. Chris suggested that the real reason the impact factor was “low” is that this particular journal concentrates on full articles, which for a subject area such as organic chemistry can take years to assemble and hence years for others to assimilate and report their own results, and only then creating a citation for the first article. So this slow but steady evolution of citations in a long time frame apparently shows such a journal up as having less (short-term) impact than the fast-publishing notes-type variety where the impact is immediate but possibly less long-lived. That would be no reason of itself not to publish there of course!
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Tags: Academia, Academic publishing, Bibliometrics, Impact, Impact factor, Knowledge, Publishing, TWITTER INC.
Posted in Chemical IT | 1 Comment »
May 12th, 2015
The Bürgi–Dunitz angle is one of those memes that most students of organic chemistry remember. It hypothesizes the geometry of attack of a nucleophile on a trigonal unsaturated (sp2) carbon in a molecule such as ketone, aldehyde, ester, and amide carbonyl. Its value obviously depends on the exact system, but is generally taken to be in the range 105-107°. A very good test of this approach is to search the crystal structure database (this was how it was originally established[cite]10.1016/S0040-4020(01)90678-7[/cite]).
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Tags: alkene, Bürgi–Dunitz angle, Carbonyl, Chemistry, Functional groups, Group of Eight, Ketone, Organic chemistry, Organic compounds, Stall
Posted in Chemical IT, crystal_structure_mining | 3 Comments »