Wednesday, August 15, 2012

Avogadro: An advanced semantic chemical editor, visualization, and analysis platform


Readers of this blog will know that I am a fan of Avogadro.   A paper describing Avogadro has now been published in the open access Journal of Cheminformatics.  I am telling you this for two reasons:

1) The paper probably describes options in Avogadro you didn't know about, so check it out.

2) Please support the Avogadro developers by citing this paper when you are writing up projects where you have used Avogadro in some way.

This also seems a good time to say Thank You! to Geoff, Marcus, Donald, David, Tim, and Eva for all their hard work and, not least, for making it freely available to the rest of us.

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 

Tuesday, August 14, 2012

The Molecule Calculator

What is MolCalc?
MolCalc is a web interface that allows anyone to build (small*) molecules and estimate** molecular properties such as molecular structure, heats of formation, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies in a matter of seconds or minutes - depending on the size.  

MolCalc is designed for teaching as opposed to research - specifically for assignments in which students build their own molecules and estimate their own molecular properties.  (**MolCalc is therefore designed to run fast and the estimated molecular properties will not match experimental values exactly, and in some cases be quite different.)  The idea is to have students develop a “chemical intuition” about how molecular structure affects molecular properties, without performing the underlying calculations by hand (which would be near impossible for all but the simplest chemical systems).

How can I use MolCalc in teaching?
Just like a pocket calculator or a symbolic math program (such as Mathematica or MAPLE), MolCalc allows one to assign “higher level” chemical problems that are not practically possible to solve otherwise.  

For example, one might now ask students to compute the effect of a substituent on a particular vibration, and then rationalize the effect using molecular orbitals.  Or one might ask more open ended questions such as “build a molecule with an unusually long C-C single bond”.

How does MolCalc work?
In the Molecule Editor page the molecular structure is build using Jmol and energy minimized using the UFF force field as implemented in Jmol.

In the Molecule Calculator page the structure is re-optimized at the PM3 level of theory for a maximum of 50 steps.  This structure is then used to compute the heat of formation or vibrational frequencies at the PM3 level of theory, or the molecular orbitals using the RHF/STO-3G level of theory.  These calculations are performed with the GAMESS program. OpenBabel is used to manage input files and coordinate files.

*MolCalc 1.0 allows calculations on (closed shell) molecules with only doubly occupied molecular orbitals and with less than 11 non-hydrogen atoms.

Can I modify and/or install MolCalc on my own server?
Yes, MolCalc is distributed through github under the GPL license (

). You must obtain a copy of the GAMESS code separately from

The interface code uses PHP5, jQuery, HTML5, and CSS3 and is very modular.  It therefore quite easy to add new capabilities to MolCalc.

What if I find a bug in MolCalc?
Please report it here.
Who is involved with MolCalc?
MolCalc 1.0 is written by Jimmy Charnley Kromann based on an idea by Jan Jensen. Toke Fritzemeier wrote an early prototype.  The Molecule Editor was inspired, in part, by the Virtual Molecular Modeling Kit.


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Sunday, August 12, 2012

Perspective on Density Functional Theory by Kieron Burke

Kieron Burke has written a very readable perspective on density functional theory in Journal of Chemical Physics, who, very commendably, has made it freely accessible.

To whet your appetite here are some quotes from the paper:

If you wish to annoy and confuse a traditional quantum chemist, ask “How much correlation is there in the KS wavefunction?”

When teaching chemistry students, I explain that DFT is some algorithm meaning unreliable, while ab initio is Latin for too expensive.

Interestingly, I have recently co-authored an approximation with about 105 “empirical” parameters.111 Don Truhlar, eat your heart out!

Users should stick to the standard functionals (as most do, according to Fig. 1), or explain very carefully why not.
If you enjoyed the article you may also want to check out this presentation of Kieron's entitled "Density Functional Theory: A great physics success story"

Thanks to Sten Rettrup for alerting me this paper

Saturday, August 4, 2012