Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

被引:23
|
作者
Lee, Myung Won [1 ]
Meuwly, Markus [1 ]
机构
[1] Univ Basel, Dept Chem, CH-4056 Basel, Switzerland
基金
瑞士国家科学基金会;
关键词
MULTIPOLE ELECTROSTATICS; SOLVATION; POTENTIALS; MECHANICS; SOLVENT; WATER; CONTINUUM; DENSITY; MODEL; STABILITY;
D O I
10.1039/c3cp52713a
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
The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN- in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN-, the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.
引用
收藏
页码:20303 / 20312
页数:10
相关论文
共 50 条
  • [31] Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations
    Schwoerer, Magnus
    Breitenfeld, Benedikt
    Troester, Philipp
    Bauer, Sebastian
    Lorenzen, Konstantin
    Tavan, Paul
    Mathias, Gerald
    JOURNAL OF CHEMICAL PHYSICS, 2013, 138 (24):
  • [32] Experiment vs force fields: DNA conformation from molecular dynamics simulations
    Feig, M
    Pettitt, M
    JOURNAL OF PHYSICAL CHEMISTRY B, 1997, 101 (38): : 7361 - 7363
  • [33] Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations
    Klimovich, Pavel V.
    Mobley, David L.
    JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2010, 24 (04) : 307 - 316
  • [34] Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field
    Beckstein, Oliver
    Fourrier, Anais
    Iorga, Bogdan I.
    JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2014, 28 (03) : 265 - 276
  • [35] Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water
    Sun, Delin
    Lakkaraju, Sirish Kaushik
    Jo, Sunhwan
    MacKerell, Alexander D., Jr.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2018, 14 (10) : 5290 - 5302
  • [36] Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field
    Oliver Beckstein
    Anaïs Fourrier
    Bogdan I. Iorga
    Journal of Computer-Aided Molecular Design, 2014, 28 : 265 - 276
  • [37] Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations
    Pavel V. Klimovich
    David L. Mobley
    Journal of Computer-Aided Molecular Design, 2010, 24 : 307 - 316
  • [38] Efficient and accurate calculation of proline cis/trans isomerization free energies from Hamiltonian replica exchange molecular dynamics simulations
    Kienlein, Maximilian
    Zacharias, Martin
    Reif, Maria M.
    STRUCTURE, 2023, 31 (11) : 1473 - +
  • [39] Ab initio molecular dynamics calculations of ion hydration free energies
    Leung, Kevin
    Rempe, Susan B.
    von Lilienfeld, O. Anatole
    JOURNAL OF CHEMICAL PHYSICS, 2009, 130 (20):
  • [40] Comparison of solvation free energies and solvent structures of simple ions by integral theory and molecular dynamics simulations
    Joung, In Suk
    Luchko, Tyler
    Case, David A.
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2012, 243