Combining ab initio and density functional theories with semiempirical methods

被引:52
作者
Cui, Q [1 ]
Guo, H
Karplus, M
机构
[1] Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
[2] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA
[3] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA
[4] Univ Strasbourg, ISIS, Lab Chim Biophys, F-67000 Strasbourg, France
关键词
D O I
10.1063/1.1501134
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
For large reactive systems, the calculation of energies can be simplified by treating the active part with a high-level quantum mechanical (QM) (ab initio or density functional) approach and the environment with a less sophisticated semiempirical (SE) approach, as an improvement over the widely used hybrid quantum mechanical/molecular mechanical (QM/MM) methods. An example is the interaction between an active region of an enzyme and its immediate environment. One such method is the original "Our-own-N-layer Integrated molecular Orbital+Molecular Mechanics (ONIOM)" approach. In this paper, the interaction between the QM and SE region is described explicitly by two different schemes. In the iterative QM/SE schemes (QM/SE-I), the electrostatic interaction and polarization effects are introduced explicitly for both the QM and SE atoms by a self-consistent procedure based on either polarizable point charges or the electron density. In the noniterative QM/SE scheme, based on the ONIOM model (QM/SE-O), the exchange (Pauli repulsion) and charge transfer effects are taken into account at the SE level, in addition to the explicit electrostatic interaction and polarization between the two regions. Test calculations are made on a number of model systems (including small polar or charged molecules interacting with water and proton transfer reactions in the presence of polar molecules or an extended hydrogen-bond network). The quantitative accuracy of the results depend on several parameters, such as the charge-scaling/normalization factors for the SE charge and the QM/SE van der Waals parameters, which can be chosen to optimize the result. For the QM/SE-O approach, the results are more sensitive to the quality of the SE level (e.g., self-consistent-charge density-functional-tight-binding vs AM1) than the explicit interaction between QM and SE atoms. (C) 2002 American Institute of Physics.
引用
收藏
页码:5617 / 5631
页数:15
相关论文
共 86 条
[1]   Modeling of peptide hydrolysis by thermolysin.: A semiempirical and QM/MM study [J].
Antonczak, S ;
Monard, G ;
Ruiz-López, MF ;
Rivail, JL .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, 120 (34) :8825-8833
[2]   Hybrid models for combined quantum mechanical and molecular mechanical approaches [J].
Bakowies, D ;
Thiel, W .
JOURNAL OF PHYSICAL CHEMISTRY, 1996, 100 (25) :10580-10594
[3]   COMPUTER-SIMULATION AND ANALYSIS OF THE REACTION PATHWAY OF TRIOSEPHOSPHATE ISOMERASE [J].
BASH, PA ;
FIELD, MJ ;
DAVENPORT, RC ;
PETSKO, GA ;
RINGE, D ;
KARPLUS, M .
BIOCHEMISTRY, 1991, 30 (24) :5826-5832
[4]   FREE-ENERGY PERTURBATION METHOD FOR CHEMICAL-REACTIONS IN THE CONDENSED PHASE - A DYNAMICAL-APPROACH BASED ON A COMBINED QUANTUM AND MOLECULAR MECHANICS POTENTIAL [J].
BASH, PA ;
FIELD, MJ ;
KARPLUS, M .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1987, 109 (26) :8092-8094
[5]   Progress toward chemical accuracy in the computer simulation of condensed phase reactions [J].
Bash, PA ;
Ho, LL ;
MacKerell, AD ;
Levine, D ;
Hallstrom, P .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (08) :3698-3703
[6]   DENSITY-FUNCTIONAL EXCHANGE-ENERGY APPROXIMATION WITH CORRECT ASYMPTOTIC-BEHAVIOR [J].
BECKE, AD .
PHYSICAL REVIEW A, 1988, 38 (06) :3098-3100
[7]   Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations [J].
Cui, Q ;
Karplus, M .
JOURNAL OF CHEMICAL PHYSICS, 2000, 112 (03) :1133-1149
[8]   Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules [J].
Cui, Q ;
Karplus, M .
JOURNAL OF PHYSICAL CHEMISTRY B, 2000, 104 (15) :3721-3743
[9]   A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method [J].
Cui, Q ;
Elstner, M ;
Kaxiras, E ;
Frauenheim, T ;
Karplus, M .
JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (02) :569-585
[10]   Quantum mechanical/molecular mechanical studies of the triosephosphate isomerase-catalyzed reaction: Verification of methodology and analysis of reaction mechanisms [J].
Cui, Q ;
Karplus, M .
JOURNAL OF PHYSICAL CHEMISTRY B, 2002, 106 (07) :1768-1798