Screened Electrostatic Interactions in Molecular Mechanics

被引:39
|
作者
Wang, Bo
Truhlar, Donald G. [1 ]
机构
[1] Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA
关键词
ENERGY DECOMPOSITION ANALYSIS; FORCE-FIELD; BASIS-SETS; CHARGE PENETRATION; GAS-PHASE; POTENTIALS; DYNAMICS; DENSITY; MODEL; ENERGETICS;
D O I
10.1021/ct5005142
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
In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal/mol. We could have decreased the average errors further, but at the cost of sometimes significantly overestimating the screening; instead we chose a more conservative (safer) parametrization that systematically underestimates the screening (which by definition means it improves over point charges) and only occasionally overestimates it. Despite this conservative choice, we find that the screened MM method is even more accurate for the electrostatics than unscreened QM/MM calculations. This new method is easy to implement in any MM program, and it can be used to develop more physical force fields for molecular simulations.
引用
收藏
页码:4480 / 4487
页数:8
相关论文
共 50 条
  • [31] Electrostatic interactions between peptides and the molecular chaperone DnaK
    Liu, W
    Bratko, D
    Prausnitz, JM
    Blanch, HW
    JOURNAL OF PHYSICAL CHEMISTRY B, 2003, 107 (41): : 11563 - 11569
  • [32] Molecular Electrostatic Potential Topology Analysis of Noncovalent Interactions
    Suresh, Cherumuttathu H.
    Anila, Sebastian
    ACCOUNTS OF CHEMICAL RESEARCH, 2023, 56 (13) : 1884 - 1895
  • [33] Electrostatic interactions in molecular recognition of intrinsically disordered proteins
    Yang, Jing
    Zeng, Yifan
    Liu, Yunfei
    Gao, Meng
    Liu, Sen
    Su, Zhengding
    Huang, Yongqi
    JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2020, 38 (16): : 4883 - 4894
  • [34] Handling electrostatic interactions in molecular simulations: A systematic study
    Kolafa, Jiri
    Moucka, Filip
    Nezbeda, Ivo
    COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, 2008, 73 (04) : 481 - 506
  • [35] TREATMENT OF ELECTROSTATIC EFFECTS WITHIN THE MOLECULAR MECHANICS METHOD .2.
    DOSENMICOVIC, L
    JEREMIC, D
    ALLINGER, NL
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1983, 105 (07) : 1723 - 1733
  • [36] Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials
    Hassan, SA
    Mehler, EL
    Zhang, DQ
    Weinstein, H
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2003, 51 (01) : 109 - 125
  • [37] PATTERN-FORMATION IN SCREENED ELECTROSTATIC FIELDS
    LOUIS, E
    GUINEA, F
    PLA, O
    SANDER, LM
    PHYSICAL REVIEW LETTERS, 1992, 68 (02) : 209 - 212
  • [38] Parameterization of electrostatic interactions for molecular dynamics simulations of heterocyclic polymers
    Nazarychev, Victor M.
    Larin, Sergey V.
    Yakimansky, Alexander V.
    Lukasheva, Natalia V.
    Gurtovenko, Andrey A.
    Gofman, Iosif V.
    Yudin, Vladimir E.
    Svetlichnyi, Valentin M.
    Kenny, Jose M.
    Lyulin, Sergey V.
    JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 2015, 53 (13) : 912 - 923
  • [39] Novel molecular device based on electrostatic interactions in organic polymers
    Kwok, HL
    Xu, JB
    PROCEEDINGS OF THE SIXTH CHINESE OPTOELECTRONICS SYMPOSIUM, 2003, : 259 - 262
  • [40] Cooperativity from electrostatic interactions: understanding bistability in molecular crystals
    D'Avino, Gabriele
    Grisanti, Luca
    Painelli, Anna
    Guasch, Judith
    Ratera, Imma
    Veciana, Jaume
    CRYSTENGCOMM, 2009, 11 (10): : 2040 - 2047