This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Kromann JC, Christensen A, Steinmann C, Korth M, Jensen JH.2014. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+. PeerJ PrePrints2:e353v1https://doi.org/10.7287/peerj.preprints.353v1
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.
"Following" is like subscribing to any updates related to a preprint.
These updates will appear in your home dashboard each time you visit PeerJ.
You can also choose to receive updates via daily or weekly email digests.
If you are following multiple preprints then we will send you
no more than one email per day or week based on your preferences.
Note: You are now also subscribed to the subject areas of this preprint
and will receive updates in the daily or weekly email digests if turned on.
You can add specific subject areas through your profile settings.