September 3rd, 2011
The (hopefully tongue-in-cheek) title Mindless chemistry was given to an article reporting[1] an automated stochastic search procedure for locating all possible minima with a given composition using high-level quantum mechanical calculations. “Many new structures, often with nonintuitive geometries, were found”. Well, another approach is to follow unexpected hunches. One such was described in the previous post, and here I follow it to one logical conclusion.
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References
- P.P. Bera, K.W. Sattelmeyer, M. Saunders, H.F. Schaefer, and P.V.R. Schleyer, "Mindless Chemistry", The Journal of Physical Chemistry A, vol. 110, pp. 4287-4290, 2006. https://doi.org/10.1021/jp057107z
Tags: automated stochastic search procedure, free energy, metal, scientist, Tutorial material
Posted in Interesting chemistry | No Comments »
September 1st, 2011
I have mentioned Lewis a number of times in these posts; his suggestion of the shared electron covalent bond still underpins much chemical thinking. Take for example mechanistic speculations on the course of a reaction, a very common indulgence in almost all articles reporting such, and largely based on informed arrow pushing. This process is bound to follow the rules of reasonable Lewis structures for any putative intermediates. Here, I suggest that we are now firmly in an era where such speculations must of necessity be backed up by quantum mechanical estimates of the energies and structures. I would propose that journals routinely encourage referees to insist on such (additional) checks. Let me give one specific example of the need to do this (part of a follow up to an earlier article I blogged on previously).
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Tags: 3-dimethylcyclobutadiene, blog server, calixarene, chemical thinking, energy, free energy, Lewis, pericyclic, Petit, photolysis., square Me, suitable metal
Posted in Interesting chemistry | 2 Comments »
August 7th, 2011
I have often heard the question posed “how much of chemistry has been discovered?” Another might be “has most of chemistry, like low-hanging fruit, already been picked?“. Well, time and time again, one comes across examples which are only a simple diagram or so away from what might be found in any introductory chemistry text, and which would tend to indicate the answers to these questions is a resounding no. Take for example the three reactions shown below.
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Tags: basic boron, Tutorial material
Posted in Interesting chemistry | No Comments »
August 3rd, 2011
Unusual bonds are always intriguing, and the Xe-Xe bond is no exception. It was first reported (10.1002/anie.199702731) for the species Xe2+. Sb4F21– and its length (3.09Å) was claimed as “unsurpassed in length in main group chemistry by any other element -element bond”. Krapp and Frenking then creatively tweaked the bond (in a computer). The counterion was replaced by C60, and the two xenon atoms placed inside! Buckyballs have a fascinating ability to absorb electrons, up to six in fact, from whatever is placed inside the cavity, and so this assembly acts as a rather intriguing ion-pair. So the issue reduces to how many electrons does C60 manage to scavenge from two Xenon atoms, and what is the nature of any resulting bonding formed between these two atoms?
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Tags: endohedral complexes, Extreme chemical intimacy, ultimate chemical bond
Posted in Hypervalency, Interesting chemistry | 1 Comment »
August 2nd, 2011
In his famous lecture in 1959, C. P. Snow wrote about the breakdown in communications between the “two cultures” of modern society — the sciences and the humanities (arts). That was then. This is now, and the occasion of my visit to a spectacular “city of arts and sciences complex” in Europe. An un-missable exhibit representing science and life was the 15m high model of DNA. Now to be fair this is styled an artist’s impression, and one presumes that an artist is allowed license. But how much license? And at how much expense to the science? And is there a counterbalance to the art where the science is fastidiously (but artistically) preserved?
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Tags: artist, chemical diagram, chemist, DNA duplex, duplex DNA, Europe, Historical, scientist and the artist, sculptor and scientist
Posted in General | 1 Comment »
July 12th, 2011
In 1986 or so, molecular modelling came of age. Richard Counts, who ran an organisation called QCPE (here I had already submitted several of the program codes I had worked on) had a few years before contacted me to ask for my help with his Roadshow. He had started these in the USA as a means of promoting QCPE, which was the then main repository of chemistry codes, and as a means of showing people how to use the codes. My task was to organise a speakers list, the venue being in Oxford in a delightful house owned by the university computing services. Access to VAX computers was provided, via VT100 terminals. Amazingly, these terminals could do very primitive molecular graphics (using delightfully named escape codes, which I learnt to manipulate).
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Tags: 3D graphics, antimalarial, antimalarial pharmaceutical molecule, chemical, co-processor, Florida, Gainesville, George Purvis, Halofantrine, haptic device, Historical, HTML, Macintosh, Mike Webb, Ohio, Oxford, pharmaceutical, Richard Counts, security guard, tangled web, Tektronix, United Kingdom, United States, university computing services, University of Florida
Posted in Chemical IT, Interesting chemistry | 4 Comments »
July 10th, 2011
Steve Bachrach has blogged on the reaction shown below. If it were a pericyclic cycloaddition, both new bonds would form simultaneously, as shown with the indicated arrow pushing. Ten electrons would be involved, and in theory, the transition state would have 4n+2 aromaticity. In fact Fernandez, Sierra and Torres have reported that they can trap an intermediate zwitterion 2, and in this sense therefore, the reaction is not pericyclic but nucleophilic addition from the imine lone pair to the carbonyl of the ketene (it finds the half way stage convivial). But this got me thinking. Does this reaction have any pericyclic character at all? And if so, could it be enhanced by design?
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Tags: antarafacial, cycloaddition, energy, Fernandez, Möbius, pericyclic, Sierra, Steve Bachrach, Torres
Posted in Interesting chemistry | 2 Comments »
July 8th, 2011
Tags: Apple computer, Appletalk, Australia, chemical, copy-editor, ethernet, Eudora, Fibre optic, GBP, hand-drawn chemical diagrams, Historical, IBM, laser printer, Mac OS X, Macintosh, megabit network, mouse pointing device, multigate routers, operating system, Pirelli, Pittsburgh, proper network, Royal Society of Chemistry, stereographics device, telephone negotiation, Tim Berners-Lee, Webster multigate routers, XML
Posted in Chemical IT | 3 Comments »
July 7th, 2011
Computers and I go back a while (44 years to be precise), and it struck me (with some horror) that I have been around them for ~62% of the modern computing era (Babbage notwithstanding, ~1940 is normally taken as the start of the modern computing era). So indulge me whilst I record this perspective from the viewpoint of the computers I have used over this 62% of the computing era. Read the rest of this entry »
Tags: chemical shifts, chemistry department computer network, controller, director, fancy phototypesetter, Fortran, GBP, Guggenheim, Historical, IBM, ICT, Imperial College, Joana, London Computing Centre, Michael Dewar, obviously enlightened teacher, Paul Weiner, Peter Murray-Rust, programmer, steady state chemical kinetics, Tektronix, Texas, University of London, University of London Computing Centre, Wimbledon, word processor
Posted in Chemical IT | 5 Comments »
July 6th, 2011
A scalemic molecule is the term used by Eliel to describe any non-racemic chiral compound. Synthetic chemists imply it when they describe a synthetic product with an observable enantiomeric excess or ee (which can range from close to 0% to almost 100%). There are two cheminformatics questions of interest to me: Read the rest of this entry »
Tags: Cambridge, chemical substances, chiral, chiroptical, disorder, dissymetric, low energy, scalemic molecules, semantic web, synthetic product
Posted in Chemical IT | No Comments »