Virtual Molecules

Here at this illustrious University, researchers have access to some pretty hefty supercomputing capabilities. It was actually the second most powerful academic supercomputer in Europe when it was initially set up. As a matter of fact, there are three disciplines which use more of the cluster’s computing power than anyone else — astronomers, chemists and computer scientists. Normally, I’d put in a joke here about clusters computing clusters (atom clusters, galaxy clusters…), but I’m not in a particularly nerdy mood, so I’ll let you make one up yourself.

Realising that I represent two of these three groups, it would be rude of me not to do some CPU-intensive uber-calculations, now wouldn’t it?

Well, in all seriousness, it’s mainly the fact that a big part of astrochemistry is spectroscopy, and a big part of theoretical spectroscopy is Density Functional Theory (DFT). DFT calculations let you map out the electron density of a molecule (as shown in this image of benzyne — redder means higher electron density). It’s a rather nicer method than having to use Schrodinger’s wave equation too. The Hartree-Fock (HF) method uses that, and it only really works for atomic hydrogen. Add any more electrons and it breaks (which is where the Born-Oppenheimer approximation comes in).

Anyway, DFT (and it’s younger sibling, time dependent DFT) approach the problem from the opposite perspective, building molecular orbitals from the top down, as opposed to the bottom up approach of HF calculations. Actually, DFT is pretty damn versatile. As well as calculating spectroscopic frequencies, you can use it to determine information on transition states, activation energies, potential energy surfaces…

But I should stop ranting now, because few people find theoretical chemistry that interesting (and most people find it rather scary). Incidentally, one of the most used computations astronomers like to play with are Monte Carlo simulations. Chances are, I’ll have to learn how to use them too at some point… But all in due time.

Suffice to say that my laptop now contains even more scientific software (namely Gabedit and GAMESS) for doing DFT work with. Gabedit, incidentally, is a GUI for most major computational chemistry software, and it’s pretty damn good. It’s nice to be able to run Linux apps through X11, though if I’m honest, most command line interfaces still intimidate me somewhat…

About Invader Xan

Molecular astrophysicist, usually found writing frenziedly, staring at the sky, or drinking mojitos.
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