Tag Archives: theoretical chemistry

Update: Installing Molden on 64bit Debian based GNU/Linux Systems

Quite some time ago, I have posted a script that attempts to install Molden. This has become a very popular post but when I read the script again recently, I felt a strong obligation to post a much cleaner way to do things. The following instructions should work for any Debian based GNU/Linux distribution. This includes Ubuntu, but – while in the past, I have been using Ubuntu myself – I cannot recommend it any longer because it does a poor job in respecting your freedom. If you like Ubuntu‘s look & feel but value your freedom, you might want to give Trisquel a try. Anyway, this is about getting Molden to work. Continue reading

Dimensional Abuse

(i) Homunculus next to a heap of smoking dimensions presenting a report: "I have written this report in atomic units. That means: reduced Planck constant = electric constant = mass of the electron = 1"

Click to enlarge – hover to read stupid comment.
(c) M.Klammler 2010, Creative Commons Share Alike.

Update on AB5 Molecule Conformation

Some time ago I posted a little program to calculate a rough approximation for the conformation of AB5 molecules with. As I started dealing with the stuff again I improved the program somewhat. First of all I corrected part of the “violent” code from the first version.

Secondly, I’ve added the possibility to assign relative charges to the ligands. You can Continue reading

Energy optimized arrangement in AB5-Molecules

In an AB5-molecule (i.e. an atom consisting of one (say positive charged) center atom and five negative charged ligands) the question of the molecule geometry seems to be very interesting. In the lectures we heard, that a bipyramidal arrangement will appear. I.e. all ligands on the surface of a sphere – the center atom of course in the center – such, that three of them form an equilateral triangle at the equator of the sphere and the other two take place at the poles. Interesting enough, one can calculate, that for this arrangement there is not an equal distribution of the energies between the ligands. That means, that the two ligands at the poles (we call it axial position) have a higher potential energy than the three in equatorial position. Since this isn’t trivial, a closer look might not be wrong. Continue reading