Friday, April 4, 2014

New manuscript: A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+


After a long fight, I can finally say that I've submitted the method I've been working on. PM6-D3H+. Well, the method is actually 'stolen' pieces from other great work, implemented in GAMESS.

The MS is submitted to +PeerJ and is therefore also available on preprint:
https://peerj.com/preprints/353v1

Abstract:
We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and $\ge$ 3 imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g. when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.

The method is implemented in GAMESS, and will be available to public as soon as possible.

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