Archive for the ‘Interesting chemistry’ Category
Thursday, November 10th, 2011
Fascination with nano-objects, molecules which resemble every day devices, is increasing. Thus the world’s smallest car has just been built[1]. The mechanics of such a device can often be understood in terms of chemical concepts taught to most students. So I thought I would have a go at this one!
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References
- T. Kudernac, N. Ruangsupapichat, M. Parschau, B. Maciá, N. Katsonis, S.R. Harutyunyan, K. Ernst, and B.L. Feringa, "Electrically driven directional motion of a four-wheeled molecule on a metal surface", Nature, vol. 479, pp. 208-211, 2011. https://doi.org/10.1038/nature10587
Tags:car drives, car rattling, chemical concepts, chemical name atropisomerism, chemical perspective, conformational analysis, day devices, energy, energy difference, Hubert Maehr, molecular car, nanocar, PDF, smallest car, Taxol
Posted in General, Interesting chemistry | 3 Comments »
Friday, November 4th, 2011
An attosecond is 10-18s. The chemistry that takes place on this timescale is called electron dynamics. For example, it is the time taken for an electron to traverse the 1s orbit in a hydrogen atom. And chemists are starting to manipulate electrons (and hence chemistry) on this timescale; for example a recent article (DOI: 10.1021/ja206193t) describes how to control the electrons in benzene using attosecond laser pulses.
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Tags:attosecond, chemical processes, exasecond, free energy barrier, G/RT, Inga Ulusoy, laser, Mathias Nest, Tutorial material
Posted in General, Interesting chemistry | 1 Comment »
Tuesday, November 1st, 2011
My previous post introduced the interesting guts of taxol. Two different isomers can exist, and these are called atropisomers; one has the carbonyl group pointing up, the other down. The barrier to their interconversion in this case is generated by a rotation about the two single bonds connecting the carbonyl group to the rest of the molecule. Introductory chemistry tells us that the barrier for rotation about such single bonds is low (i.e. fast at room temperature). But is that true here?
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Tags:animation, conformational analysis, Taxol, Tutorial material
Posted in Interesting chemistry | 4 Comments »
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.
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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 »
Friday, October 21st, 2011
Organic chemists have been making (more or less pure) molecules for the best part of 180 years. Occasionally, these ancient samples are unearthed in cupboards, and then the hunt for their origin starts. I have previously described tracking down the structure of a 120 year-old sample of a naphthalene derivative. But I visited a colleague's office today, and recollected having seen a well-made wooden display cabinet there on a previous visit. Today I took a photo of one of the samples:
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Tags:August von Hofmann, chemicals, detective, first professor, Haifa, Historical, Institute of Technology, professor of organic chemistry in the UK, Technion, United Kingdom, worth preserving chemical samples
Posted in Interesting chemistry | 1 Comment »
Sunday, October 16th, 2011
I asked a while back whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust more recently). A case for doing so might be my post of about a year ago, addressing why borane reduces a carboxylic acid, but not its ester, where I suggested a possible mechanism. Well, colleagues have raised some interesting questions, both on the blog itself and more silently by email to me. As a result, I have tried to address some of these questions, and accordingly my original scheme needs some revision! This sort of iterative process of getting to the truth with the help of the community (a kind of crowd-sourced chemistry) is where I feel blogs do have a genuine role to play.
The reduction of a carboxylic acid by borane
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Tags:activation energy, animation, carboxylic acid, carboxylic ester, diborane, free energy, pericyclic, Peter Murray-Rust, Reaction Mechanism, reduction, Tutorial material
Posted in Interesting chemistry | 8 Comments »
Monday, October 10th, 2011
I wrote earlier about the strangely close contact between two hydrogen atoms in cis-butene. The topology of the electron density showed characteristics of a bond, but is it a consensual union? The two hydrogens approach closer than their van der Waals radii would suggest is normal, so something is happening, but that something need not be what chemists might choose to call a “bond“. An NCI (non-covalent analysis) hinted that any stability due to the electron topologic characteristics of a bond (the BCP) might be more than offset by the repulsive nature of the adjacent ring critical point (RCP). Here I offer an alternative explanation for why the two hydrogens approach so closely.
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Tags:conformational analysis, energy, energy decreases, smallest energy gap, Tutorial material
Posted in General, Interesting chemistry | 9 Comments »
Friday, October 7th, 2011
The properties of electrons are studied by both chemists and physicists. At the boundaries of these two disciplines, sometimes interesting differences in interpretation emerge. One of the most controversial is that due to Bader (for a recent review, see DOI: 10.1021/jp102748b) a physicist who brought the mathematical rigor of electronic topology to bear upon molecules. The title of his review is revealing: “Definition of Molecular Structure: By Choice or by Appeal to Observation?”. He argues that electron density is observable, and that what chemists call a bond should be defined by that observable (with the implication that chemists instead often resort to arbitrary choice). Here I explore one molecule which could be said to be the focus of the differences between physics and chemistry; cis-but-2-ene.
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Tags:CCP, chemical picture, chemist, conformational analysis, energy, Julia Contreras-Garcia, physicist
Posted in General, Interesting chemistry | 6 Comments »
Monday, September 26th, 2011
To (mis)quote Oscar Wilde again, ““To lose one methyl group may be regarded as a misfortune; to lose both looks like carelessness.” Here, I refer to the (past) tendency of molecular modellers to simplify molecular structures. Thus in 1977, quantum molecular modelling, even at the semi-empirical level, was beset by lost groups. One of my early efforts (DOI: 10.1021/ja00465a005) was selected for study because it had nothing left to lose; the mass spectrometric fragmentation of the radical cations of methane and ethane. Methyl, phenyl and other “large” groups were routinely replaced by hydrogen in order to enable the study. Cations indeed were always of interest to modellers; the relative lack of electrons almost always meant unusual or interesting structures and reactions (including this controversial species, DOI: 10.1021/ja00444a012). Inured to such functional loss, we modellers forgot that (unless in a mass spectrometer), cations have to have a counter anion. Here I explore one example of the model being complete(d).
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Tags:bonded systems, energy difference drops, free energy, model, Oscar, potential energy surface, Steve Bachrach, using perchlorate
Posted in Interesting chemistry | 7 Comments »
