Posts Tagged ‘computational chemistry’
Thursday, May 2nd, 2019
Ken Houk’s group has recently published this study of cycloaddition reactions, using a combination of classical transition state location followed by molecular dynamics trajectory calculations,[1] and to which Steve Bachrach’s blog alerted me. The reaction struck me as being quite polar (with cyano groups) and so I took a look at the article to see what both the original[2] experimental conditions were and how the new simulations compared. The reaction itself is shown below.
(more…)
References
-
X. Xue, C.S. Jamieson, M. Garcia-Borràs, X. Dong, Z. Yang, and K.N. Houk, "Ambimodal Trispericyclic Transition State and Dynamic Control of Periselectivity", Journal of the American Chemical Society, vol. 141, pp. 1217-1221, 2019. http://dx.doi.org/10.1021/jacs.8b12674
-
C.Y. Liu, and S.T. Ding, "Cycloadditions of electron-deficient 8,8-disubstituted heptafulvenes to electron-rich 6,6-disubstituted fulvenes", The Journal of Organic Chemistry, vol. 57, pp. 4539-4544, 1992. http://dx.doi.org/10.1021/jo00042a039
Tags:Chemistry, computational chemistry, Implicit solvation, Ken Houk, Molecular dynamics, Molecular modelling, Natural sciences, Physical sciences, Solutions, Solvent, Solvent model, Solvents, Steve Bachrach, Theoretical chemistry
Posted in reaction mechanism | 2 Comments »
Thursday, April 4th, 2019
Previously, I explored the Graham reaction to form a diazirine. The second phase of the reaction involved an Sn2′ displacement of N-Cl forming C-Cl. Here I ask how facile the simpler displacement of C-Cl by another chlorine might be and whether the mechanism is Sn2 or the alternative Sn1.
The reason for posing this question is that as an Sn1 reaction, simply ionizing off the chlorine to form a diazacyclopropenium cation might be a very easy process. Why? Because the resulting cation is analogous to the cyclopropenium cation, famously proposed by Breslow as the first example of a 4n+2 aromatic ring for which the value of n is zero and not 1 as for benzene.[1] Another example of a famous “Sn1” reaction is the solvolysis of t-butyl chloride to form the very stable tertiary carbocation and chloride anion (except in fact that it is not an Sn1 reaction but an Sn2 one!)
(more…)
References
-
R. Breslow, "SYNTHESIS OF THE s-TRIPHENYLCYCLOPROPENYL CATION", Journal of the American Chemical Society, vol. 79, pp. 5318-5318, 1957. http://dx.doi.org/10.1021/ja01576a067
Tags:animation, Carbenium ion, Cations, Chemical elements, chemical reaction, Chemistry, Chlorine, computational chemistry, Cyclopropenium ion, Diazirine, energy, energy profile, free energy, Halogens, Natural sciences, Nucleophilic aromatic substitution, Oxidizing agents, Physical sciences, potential energy surface, SN1 reaction, Substitution reactions
Posted in reaction mechanism | No 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).
(more…)
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 »
Tuesday, October 4th, 2016
Tags:Analytical chemistry, chemical information, chemical insight, Cheminformatics, Chemistry, Chemometrics, Clyde Fare, Company: GitHub, computation chemical research projects, computational chemistry, computing, Cross-platform software, driver, GitHub, Jan Szopinski, machine learning, open sourcing software development, opensource healthchecker software, Peter Murray-Rust, public web sites, Python, quantum chemical calculation, quantum chemical codes, quantum chemical data, quantum chemical research, Quotation, Server & Database Software, simulation, Software, supervisor, sustainable software conference prize, Technology/Internet
Posted in Bradley-Mason Prize for Open Chemistry | No Comments »
Wednesday, August 19th, 2015
This post is prompted by the appearance of a retrospective special issue of C&E news, with what appears to be its very own Website: internet.cenmag.org. It contains articles and interviews with many interesting people, along with several variations on the historical (albeit rather USA-centric) perspectives and a time-line covers many of the key innovations (again, from a USA-perspective). Some subjects are covered in greater depth, including computational chemistry. The periodic table too gets coverage, but surprisingly that is not of Mark Winter’s WebElements, which carries the impressive 1993-2015 continuous timeline (hence 22 in the title!).
(more…)
Tags:computational chemistry, internet.cenmag.org, Mark Winter, Robert Cailliau, search.labs.datacite.org/help/examples, spin-off, the C&E news, Tim Berners-Lee, United States
Posted in Historical | No Comments »
Saturday, July 21st, 2012
I blogged about this two years ago and thought a brief update might be in order now. To support the discussions here, I often perform calculations, and most of these are then deposited into a DSpace digital repository, along with metadata. Anyone wishing to have the full details of any calculation can retrieve these from the repository. Now in 2012, such repositories are more important than ever.
(more…)
Tags:API, Chemspider, computational chemistry, Digital respository, Imperial College, InChI Key, Mark Hahnel, Matt Harvey, opendata, pubchem, QRCode, Skolnik, United Kingdom, wikipedia
Posted in Chemical IT | 1 Comment »
Friday, July 20th, 2012
Twenty years are acknowledged to be a long time in Internet/Web terms. In the early days (in 1994), it was a taken that the passage of 1 Web day in the Internet time-warp was ~≡ 7 for the rest of the world (the same factor as applied to the lives of canines). This temporal warping can also be said to apply to computational chemistry. I previously revisited some computational work done in 1992, and here I rediscover another investigation from that year[1] and that era. The aim in this post is to compare not only how the presentation of the results has changed, but how the computational models have as well.
(more…)
References
-
R.A. Batey, P. Grice, J.D. Harling, W.B. Motherwell, and H.S. Rzepa, "Origins of the regioselectivity of cyclopropylcarbinyl ring opening reactions in bicyclo [n.1.0] systems", Journal of the Chemical Society, Chemical Communications, pp. 942, 1992. http://dx.doi.org/10.1039/C39920000942
Tags:computational chemistry, hardware tools, Historical, Internet time-warp, Internet/Web terms, Reaction Mechanism, Skolnik, Web day
Posted in Uncategorized | No Comments »
Monday, April 30th, 2012
During the 1960s, a holy grail of synthetic chemists was to devise an efficient route to steroids. R. B. Woodward was one the chemists who undertook this challenge, starting from compounds known as dienones (e.g. 1) and their mysterious conversion to phenols (e.g. 2 or 3) under acidic conditions. This was also the golden era of mechanistic exploration, which coupled with an abundance of radioactive isotopes from the war effort had ignited the great dienone-phenol debates of that time (now largely forgotten). In a classic recording from the late 1970s, Woodward muses how chemistry had changed since he started in the early 1940s. In particular he notes how crystallography had revolutionised the reliability and speed of molecular structure determination. Here I speculate what he might have made of modern computational chemistry, and in particular whether it might cast new light on those mechanistic controversies of the past.
(more…)
Tags:computational chemist, computational chemistry, Historical, pericyclic, sigmatropic shifts, tracer labelling
Posted in Chemical IT, Interesting chemistry | 1 Comment »
Tuesday, March 13th, 2012
I wrote in an earlier post how Pauling’s Nobel prize-winning suggestion in February 1951 of an (left-handed) α-helical structure for proteins was based on the wrong absolute configuration of the amino acids (hence his helix should really have been the right-handed enantiomer). This was most famously established a few months later by Bijvoet’s definitive crystallographic determination of the absolute configuration of rubidium tartrate, published on August 18th, 1951 (there is no received date, but a preliminary communication of this result was made in April 1950). Well, a colleague (thanks Chris!) just wandered into my office and he drew my attention to an article by John Kirkwood (DOI: 10.1063/1.1700491) published in April 1952, but received July 20, 1951, carrying the assertion “The Fischer convention is confirmed as a structurally correct representation of absolute configuration“, and based on the two compounds 2,3-epoxybutane and 1,2-dichloropropane. Neither Bijvoet nor Kirkwood seem aware of the other’s work, which was based on crystallography for the first, and quantum computation for the second. Over the years, the first result has become the more famous, perhaps because Bijvoet’s result was mentioned early on by Watson and Crick in their own very famous 1953 publication of the helical structure of DNA. They do not mention Kirkwood’s result. Had they not been familiar with Bijvoet’s result, their helix too might have turned out a left-handed one!
(more…)
Tags:California, chiroptical spectroscopies, computational chemistry, Imperial College, Institute of Technology, John Kirkwood, Pasadena, spectroscopy
Posted in Chiroptics, Historical | 1 Comment »
Friday, October 28th, 2011
Moore’s law describes a long-term trend in the evolution of computing hardware, and it is often interpreted in terms of processing speed. Here I chart this rise in terms of the size of computable molecules. By computable I mean specifically how long it takes to predict the geometry of a given molecule using a quantum mechanical procedure.
(more…)
Tags:3g, chemical engineers, chemical reactor plants, computational chemistry, energy, energy function, hallucination, Historical, LSD, molecular systems, Paul Weiner, simulation, sojourn, Texas Tavern, X-ray
Posted in Interesting chemistry | No Comments »