OPLS all-atom model for amines: Resolution of the amine hydration problem

被引:0
|
作者
机构
来源
J Am Chem Soc | / 20卷 / 4827-4836期
关键词
D O I
暂无
中图分类号
学科分类号
摘要
Classical force-field parameters have been developed for amines primarily by fitting to experimental data for pure liquids and to hydrogen-bond strengths from gas-phase ab initio calculations. The resultant parameters were used to calculate relative free energies of hydration for ammonia, methylamine, dimethylamine, and trimethylamine using free energy perturbation calculations in Monte Carlo simulations (MC/FEP). The results including the fact that the most favorable ΔGhyd occurs for methylamine are in excellent agreement with the experimental data, in contrast to numerous prior computational reports. The calculations reveal two opposing trends in water: increased contribution from hydrogen-bond acceptance and diminished contribution from hydrogen-bond donation with increasing methylation of the amines. The proper balance of hydrogen-bond strengths, which is achieved with the OPLS-AA force field, is essential for correct ordering of the free energies of hydration. MC simulations for the pure liquids of thirteen additional amines, not included in the original parametrization, then demonstrated the transferability of the force field. These simulations covered aliphatic as well as cyclic and aromatic amines. Furthermore, the appropriateness of the force field for less polar environments was confirmed through MC/FEP calculations of relative free energies of solvation and log P values in chloroform. It is apparent that the prior problems with classical force fields for amines were simply a result of nonoptimal parametrization rather than to a critical omission such as the lack of explicit polarization.
引用
收藏
相关论文
共 50 条
  • [31] A hybrid all-atom/coarse grain model for multiscale simulations of DNA
    Rodrigo Machado, Matias
    Daniel Dans, Pablo
    Pantano, Sergio
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2011, 13 (40) : 18134 - 18144
  • [32] Development of an anisotropic polarizable model for the all-atom AMOEBA force field
    Yang, Yanyan
    Jin, Qianqian
    Yin, Shiwei
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2024, 26 (35) : 22900 - 22911
  • [33] Free-energy function based on an all-atom model for proteins
    Yoshidome, Takashi
    Oda, Koji
    Harano, Yuichi
    Roth, Roland
    Sugita, Yuji
    Ikeguchi, Mitsunori
    Kinoshita, Masahiro
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009, 77 (04) : 950 - 961
  • [34] An all-atom model of the human cardiac sodium channel in a lipid bilayer
    Knotts, Garrett M.
    Lile, Spencer K.
    Campbell, Emily M.
    Agee, Taylor A.
    Liyanage, Senal D.
    Gwaltney, Steven R.
    Johnson, Christopher N.
    SCIENTIFIC REPORTS, 2024, 14 (01):
  • [35] All-Atom Model for Stabilization of α-Helical Structure in Peptides by Hydrocarbon Staples
    Kutchukian, Peter S.
    Yang, Jae Shick
    Verdine, Gregory L.
    Shakhnovich, Eugene I.
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2009, 131 (13) : 4622 - 4627
  • [36] A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations
    Strader, ML
    Feller, SE
    JOURNAL OF PHYSICAL CHEMISTRY A, 2002, 106 (06): : 1074 - 1080
  • [37] Folding and association of a homotetrameric protein complex in an all-atom Go model
    Berhanu, W. M.
    Jiang, P.
    Hansmann, U. H. E.
    PHYSICAL REVIEW E, 2013, 87 (01):
  • [38] The role of hydrophobic hydration in the LCST behaviour of POEGMA300 by all-atom molecular dynamics simulations
    Dalgakiran, Eray
    Tatlipinar, Hasan
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2018, 20 (22) : 15389 - 15399
  • [39] 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
  • [40] 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