Molecular Electrostatic Potential and Electron Density of Large Systems in Solution Computed with the Fragment Molecular Orbital Method

被引：17

作者：

Fedorov, Dmitri G. ^{[1
]}

Brekhov, Anton ^{[2
]}

Mironov, Vladimir ^{[2
]}

Alexeev, Yuri ^{[3
,4
]}

机构：

[1] Natl Inst Adv Ind Sci & Technol, Res Ctr Computat Design Adv Funct Mat CDFMat, Cent 2,Umezono 1-1-1, Tsukuba, Ibaraki 3058568, Japan

[2] Lomonosov Moscow State Univ, Dept Chem, Moscow 119991, Russia

[3] Argonne Natl Lab, Argonne Leadership Comp Facil, Argonne, IL 60439 USA

[4] Argonne Natl Lab, Computat Sci Div, Argonne, IL 60439 USA

来源：

JOURNAL OF PHYSICAL CHEMISTRY A | 2019年 / 123卷 / 29期

基金：

俄罗斯基础研究基金会;

关键词：

ENERGY DECOMPOSITION ANALYSIS; POISSON-BOLTZMANN EQUATION; SOLVENT INTERACTIONS; CHEMISTRY; BINDING; HF; ACCURATE;

D O I：

10.1021/acs.jpca.9b04936

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

A solvent screening model for the molecular electrostatic potential is developed for the fragment molecular orbital method combined with the polarizable continuum model at the Hartree-Fock and density functional theory levels. The accuracy of the generated potentials is established in comparison to calculations without fragmentation. Solvent effects upon the molecular electrostatic potential and electron density of solute are discussed. The method is applied to two proteins: chignolin (PDB: 1UAO) and ovine prostaglandin H(2) synthase-1 (1EQG).

引用

页码：6281 / 6290

页数：10

共 50 条

[31] Fragment-Molecular-Orbital-Method-Based ab Initio NMR Chemical-Shift Calculations for Large Molecular Systems
Gao, Qi
Yokojima, Satoshi
Fedorov, Dmitri G.
Kitaura, Kazuo
Sakurai, Minoru
Nakamura, Shinichiro
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (04) : 1428 - 1444
[32] Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method
Okiyama, Yoshio
Nakano, Tatsuya
Watanabe, Chiduru
Fukuzawa, Kaori
Komeiji, Yuto
Segawa, Katsunori
Mochizuki, Yuji
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, 2021, 94 (01) : 91 - 96
[33] Fragment molecular orbital method with density functional theory and DIIS convergence acceleration
Sugiki, SI
Kurita, N
Sengoku, Y
Sekino, H
CHEMICAL PHYSICS LETTERS, 2003, 382 (5-6) : 611 - 617
[34] Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method
Brorsen, Kurt R.
Zahariev, Federico
Nakata, Hiroya
Fedorov, Dmitri G.
Gordon, Mark S.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2014, 10 (12) : 5297 - 5307
[35] Simulations of infrared and Raman spectra in solution using the fragment molecular orbital method
Nakata, Hiroya
Fedorov, Dmitri G.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2019, 21 (25) : 13641 - 13652
[36] Polarization energies in the fragment molecular orbital method
Fedorov, Dmitri G.
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2022, 43 (16) : 1094 - 1103
[37] Exploring chemistry with the fragment molecular orbital method
Fedorov, Dmitri G.
Nagata, Takeshi
Kitaura, Kazuo
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2012, 14 (21) : 7562 - 7577
[38] Acceleration of fragment molecular orbital method with GPUs
Koga, Ryota
Furukawa, Yuki
Yasuda, Koji
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2011, 241
[39] Fragment molecular orbital method: application to polypeptides
Nakano, T
Kaminuma, T
Sato, T
Akiyama, Y
Uebayasi, M
Kitaura, K
CHEMICAL PHYSICS LETTERS, 2000, 318 (06) : 614 - 618
[40] Recent development of the fragment molecular orbital method
Kitaura, Kazuo
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2011, 241

← 1 2 3 4 5 →