DALTON mol File Input Generator for Open Babel

Because of my new engagement with DALTON, I felt there was a serious lack of availability in the open source tool chain that I am used to: There is no input file generator in Open Babel for DALTON, until now.

Through a series of commits in my own fork of the official Open Babel repository, I've added a basic mol file input generator (and reader too!). The commits have been marked with a pull request to be merged into the official repository, but it looks like it is only updated every now and then. If you want to get all crazy right away, clone my repository and get cracking.

Experienced users with DALTON knows that there are two input files. the molecule file and the DALTON input file (dal file). The mol file contains the coordinates of the atoms, their charge and the basis set for the computation. The dal file tells DALTON what to actually do with the content of the mol file. Thus, the dal file is about the quantum chemistry which is traditionally left out in Open Babel and I've only focused on getting the mol-file ready - most users of DALTON use a single dal file anyways and use different mol files. I guess my own scripts to make easy conversions to and from DALTON are now void (at least partially).

Hooray for Open Source!

Addendum: I should mention that coordinates can also be extracted from DALTON log files. As I myself do not (usually) have a need beyond coordinate extractions I will leave it as is for now.

NMR shielding constants through polarizable embedding

After I finished my Ph.D. in the Jan Jensen group, I've begun working at the University of Southern Denmark with Jacob Kongsted.

Apart from using DALTON instead of GAMESS I've also switched gears and I am now focused on an advanced form of QM/MM which is called polarizable embedding (see this paywalled link for details). Basically your gas-phase Fock operator is extended with interactions from the surroundings. In the language of polarizable embedding (PE) we constructs the effective Fock operator here for Hartree-Fock

$\hat{f}_{eff} = \hat{f}_{HF} + \hat{\nu}_{PE}$

The PE is a sum of interactions from the surroundings onto a molecule of interest. I will deal with the specifics of the PE approach later on.

This is all fine and dandy, but until now the PE model has focused solely on electronic molecular properties. I've extended it so you can calculate nuclear magnetic shielding constants in the PE model using London atomic orbitals (you might know them as Gauge-Including Atomic Orbitals) with contributions from charges, dipoles (induced and static) and quadrupoles. The hope is that we need a small QM region due to a very high-quality potential compared to previous QM/MM studie (see here for an example of needed more than 1000 atoms for converged NMR shieldings).

We'll see how it goes.