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

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Standard

A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method : PM6-D3H+. / Kromann, Jimmy Charnley; Christensen, Anders Steen; Svendsen, Casper Steinmann; Korth, Martin; Jensen, Jan Halborg.

I: PeerJ, Bind 2, 2014, s. e449.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Kromann, JC, Christensen, AS, Svendsen, CS, Korth, M & Jensen, JH 2014, 'A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+', PeerJ, bind 2, s. e449. https://doi.org/10.7717/peerj.449

APA

Kromann, J. C., Christensen, A. S., Svendsen, C. S., Korth, M., & Jensen, J. H. (2014). A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+. PeerJ, 2, e449. https://doi.org/10.7717/peerj.449

Vancouver

Kromann JC, Christensen AS, Svendsen CS, Korth M, Jensen JH. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+. PeerJ. 2014;2:e449. https://doi.org/10.7717/peerj.449

Author

Kromann, Jimmy Charnley ; Christensen, Anders Steen ; Svendsen, Casper Steinmann ; Korth, Martin ; Jensen, Jan Halborg. / A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method : PM6-D3H+. I: PeerJ. 2014 ; Bind 2. s. e449.

Bibtex

@article{7ec88e0447f24096adcfd51b9eeaeb75,
title = "A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+",
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 3 or more 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.",
author = "Kromann, {Jimmy Charnley} and Christensen, {Anders Steen} and Svendsen, {Casper Steinmann} and Martin Korth and Jensen, {Jan Halborg}",
note = "OA",
year = "2014",
doi = "10.7717/peerj.449",
language = "English",
volume = "2",
pages = "e449",
journal = "PeerJ",
issn = "2167-8359",
publisher = "PeerJ",

}

RIS

TY - JOUR

T1 - A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method

T2 - PM6-D3H+

AU - Kromann, Jimmy Charnley

AU - Christensen, Anders Steen

AU - Svendsen, Casper Steinmann

AU - Korth, Martin

AU - Jensen, Jan Halborg

N1 - OA

PY - 2014

Y1 - 2014

N2 - 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 3 or more 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.

AB - 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 3 or more 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.

U2 - 10.7717/peerj.449

DO - 10.7717/peerj.449

M3 - Journal article

C2 - 25024918

VL - 2

SP - e449

JO - PeerJ

JF - PeerJ

SN - 2167-8359

ER -

ID: 131121638