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).
Posts Tagged ‘energy’
The stereochemistry of [8+2] pericyclic cycloadditions.
Sunday, July 10th, 2011Steve 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?
Déjà vu: Pirkle for a third time!
Wednesday, May 25th, 2011This molecule is not leaving me in peace. It and I first met in 1990 (DO: 10.1039/C39910000765), when we spotted the two unusual π-facial bonds formed when it forms a loose dimer. The next step was to use QTAIM to formalise this interaction, and this led to spotting a second one missed the first time round (labelled 2 in that post). Then a method known as NCI was tried, which revealed an H…H interaction, labelled ? in that post! Here I discuss the origins of the ?
The inner secrets of the DNA structure.
Wednesday, May 18th, 2011In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets.
Updating a worked problem in conformational analysis. Part 1: the question.
Friday, May 13th, 2011Conformational analysis comes from the classical renaissance of physical organic chemistry in the 1950s and 60s. The following problem is taken from E. D. Hughes and J. Wilby J. Chem. Soc., 1960, 4094-4101, DOI: 10.1039/JR9600004094, the essence of which is that Hofmann elimination of a neomenthyl derivative (C below) was observed as anomalously faster than its menthyl analogue. Of course, what is anomalous in one decade is a standard student problem (and one Nobel prize) five decades later.
Why are α-helices in proteins mostly right handed?
Saturday, April 9th, 2011Understanding why and how proteins fold continues to be a grand challenge in science. I have described how Wrinch in 1936 made a bold proposal for the mechanism, which however flew in the face of much of then known chemistry. Linus Pauling took most of the credit (and a Nobel prize) when in a famous paper[cite]10.1073/pnas.37.4.205[/cite] in 1951 he suggested a mechanism that involved (inter alia) the formation of what he termed α-helices. Jack Dunitz in 2001[cite]10.1002/1521-3773(20011119)40:22%3C4167::AID-ANIE4167%3E3.0.CO;2-Q[/cite] wrote a must-read article[cite]10.fgkwqb[/cite] on the topic of “Pauling’s Left-handed α-helix” (it is now known to be right handed). I thought I would revisit this famous example with a calculation of my own and here I have used the ωB97XD/6-311G(d,p) DFT procedure[cite]10.1021/ct100469b[/cite] to calculate some of the energy components of a small helix comprising (ala)6 in both left and right handed form.
The colour of Monastral blue (part 2).
Monday, April 4th, 2011Andy Mclean posted a comment to my story of copper phthalocyanine (Monastral blue). The issue was its colour, and more specifically why this pigment has two peaks λmax 610 and 710nm making it blue. The first was accurately reproduced by calculation on the monomer, but the second was absent with such a model. Andy suggested this latter was due to stacking. Here, the calculated spectrum of a stacked dimer is explored.
The thermodynamic energies of left and right handed DNA.
Saturday, March 5th, 2011In this earlier post, I noted some aspects of the calculated structures of both Z- and B-DNA duplexes. These calculations involved optimising the positions of around 250-254 atoms, for d(CGCG)2 and d(ATAT)2, an undertaking which has taken about two months of computer time! The geometries are finally optimised to the point where 2nd derivatives can be calculated, and which reveal up to 756 all-positive force constants and 6 translations and rotations which are close to zero! This now lets one compute the thermodynamic relative energies using ωB97XD/6-31G(d) (for 2nd derivatives) and 6-31G(d,p) (for dispersion terms). All geometries are optimized using a continuum solvent field (water), and are calculated, without a counterion, as hexa-anions. (more…)
Shorter is higher: the strange case of diberyllium.
Friday, January 21st, 2011Much of chemistry is about bonds, but sometimes it can also be about anti-bonds. It is also true that the simplest of molecules can have quite subtle properties. Thus most undergraduate courses in chemistry deal with how to describe the bonding in the diatomics of the first row of the periodic table. Often, only the series C2 to F2 is covered, so as to take into account the paramagnetism of dioxygen, and the triple bonded nature of dinitrogen (but never mentioning the strongest bond in the universe!). Rarely is diberyllium mentioned, and yet by its strangeness, it can also teach us a lot of chemistry.