1932

Abstract

Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biophys-070317-033349
2019-05-06
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/biophys/48/1/annurev-biophys-070317-033349.html?itemId=/content/journals/10.1146/annurev-biophys-070317-033349&mimeType=html&fmt=ahah

Literature Cited

  1. 1.
    Ahlstrand E, Zukerman Schpector J, Friedman R 2017. Computer simulations of alkali-acetate solutions: accuracy of the forcefields in difference concentrations. J. Chem. Phys. 147:194102
    [Google Scholar]
  2. 2.
    Albaugh A, Head-Gordon T 2017. A new method for treating Drude polarization in classical molecular simulation. J. Chem. Theory Comput. 13:5207–16
    [Google Scholar]
  3. 3.
    Albaugh A, Niklasson AMN, Head-Gordon T 2017. Accurate classical polarization solution with no self-consistent field iterations. J. Phys. Chem. Lett. 8:1714–23
    [Google Scholar]
  4. 4.
    Aviat F, Levitt A, Stamm B, Maday Y, Ren P et al. 2017. Truncated conjugate gradient: an optimal strategy for the analytical evaluation of the many-body polarization energy and forces in molecular simulations. J. Chem. Theory Comput. 13:180–90
    [Google Scholar]
  5. 5.
    Baker CM 2015. Polarizable force fields for molecular dynamics simulations of biomolecules. Wiley Interdiscip. Rev. Comput. Mol. Sci. 5:241–54
    [Google Scholar]
  6. 6.
    Bell DR, Qi R, Jing Z, Xiang JY, Mejias C et al. 2016. Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field. Phys. Chem. Chem. Phys. 18:30261–69
    [Google Scholar]
  7. 7.
    Boateng HA 2017. Mesh-free hierarchical clustering methods for fast evaluation of electrostatic interactions of point multipoles. J. Chem. Phys. 147:164104
    [Google Scholar]
  8. 8.
    Cerutti DS, Rice JE, Swope WC, Case DA 2013. Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization. J. Phys. Chem. B 117:2328–38
    [Google Scholar]
  9. 9.
    Chen J, Martínez TJ 2007. QTPIE: charge transfer with polarization current equalization. A fluctuating charge model with correct asymptotics. Chem. Phys. Lett. 438:315–20
    [Google Scholar]
  10. 10.
    Chodera JD, Swope WC, Noé F, Prinz J-H, Shirts MR, Pande VS 2011. Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. J. Chem. Phys. 134:244107
    [Google Scholar]
  11. 11.
    Cieplak P, Caldwell J, Kollman P 2001. Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N‐methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. J. Comput. Chem. 22:1048–57
    [Google Scholar]
  12. 12.
    Cisneros GA, Karttunen M, Ren P, Sagui C 2014. Classical electrostatics for biomolecular simulations. Chem. Rev. 114:779–814
    [Google Scholar]
  13. 13.
    Das AK, Demerdash ON, Head-Gordon T 2018. Improvements to the AMOEBA force field by introducing anisotropic atomic polarizability of the water molecule. J. Chem. Theory Comput. 14:6722–33
    [Google Scholar]
  14. 14.
    Davis JE, Patel S 2009. Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A. J. Phys. Chem. B 113:9183–96
    [Google Scholar]
  15. 15.
    Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT 2016. Further along the road less traveled: AMBER ff15ipq, an original protein force field built on a self-consistent physical model. J. Chem. Theory Comput. 12:3926–47
    [Google Scholar]
  16. 16.
    Demerdash O, Mao Y, Liu T, Head-Gordon M, Head-Gordon T 2017. Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations. J. Chem. Phys. 147:161721
    [Google Scholar]
  17. 17.
    Demerdash O, Wang L-P, Head-Gordon T 2018. Advanced models for water simulations. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8:e1355
    [Google Scholar]
  18. 18.
    Dhakshnamoorthy B, Rohaim A, Rui H, Blachowicz L, Roux B 2016. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Nat. . Commun 7:12753
    [Google Scholar]
  19. 19.
    Duke RE, Starovoytov ON, Piquemal J-P, Cisneros GA 2014. GEM*: a molecular electronic density-based force field for molecular dynamics simulations. J. Chem. Theory Comput. 10:1361–65
    [Google Scholar]
  20. 20.
    Dybeck EC, Schieber NP, Shirts MR 2016. Effects of a more accurate polarizable Hamiltonian on polymorph free energies computed efficiently by reweighting point-charge potentials. J. Chem. Theory Comput. 12:3491–505
    [Google Scholar]
  21. 21.
    Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y et al. 2017. OpenMM 7: rapid development of high performance algorithms for molecular dynamics. PLOS Comput. Biol. 13:7e1005659
    [Google Scholar]
  22. 22.
    Elber R 2016. Perspective: computer simulations of long time dynamics. J. Chem. Phys. 144:060901
    [Google Scholar]
  23. 23.
    El Hage K, Piquemal JP, Hobaika Z, Maroun RG, Gresh N 2013. Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds. ? J. Comput. Chem. 34:1125–35
    [Google Scholar]
  24. 24.
    Faradjian AK, Elber R 2004. Computing time scales from reaction coordinates by milestoning. J. Chem. Phys. 120:10880–89
    [Google Scholar]
  25. 25.
    Gao X-C, Hao Q, Wang C-S 2017. Improved polarizable dipole-dipole interaction model for hydrogen bonding, stacking, T-shaped, and X-H…π interactions. J. Chem. Theory Comput. 13:2730–41
    [Google Scholar]
  26. 26.
    Ghahremanpour MM, van Maaren PJ, Caleman C, Hutchison GR, van der Spoel D 2018. Polarizable Drude model with s-type Gaussian or Slater charge density for general molecular mechanics force fields. J. Chem. Theory Comput. 14:5553–66
    [Google Scholar]
  27. 27.
    Giese TJ, Panteva MT, Chen H, York DM 2015. Multipolar Ewald methods, 1: theory, accuracy, and performance. J. Chem. Theory Comput. 11:436–50
    [Google Scholar]
  28. 28.
    Gkionis K, Kruse H, Platts JA, Mladek A, Koca J, Sponer J 2014. Ion binding to quadruplex DNA stems. Comparison of MM and QM descriptions reveals sizable polarization effects not included in contemporary simulations. J. Chem. Theory Comput. 10:1326–40
    [Google Scholar]
  29. 29.
    Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R et al. 2016. Computational methodologies for real-space structural refinement of large macromolecular complexes. Annu. Rev. Biophys. 45:253–78
    [Google Scholar]
  30. 30.
    Gökcan H, Kratz E, Darden TA, Piquemal J-P, Cisneros GA 2018. QM/MM simulations with the Gaussian electrostatic model: a density-based polarizable potential. J. Phys. Chem. Lett. 9:3062–67
    [Google Scholar]
  31. 31.
    Gresh N, Cisneros GA, Darden TA, Piquemal J-P 2007. Anisotropic, polarizable molecular mechanics studies of inter- and intramolecular interactions and ligand–macromolecule complexes. A bottom-up strategy. J. Chem. Theory Comput. 3:1960–86
    [Google Scholar]
  32. 32.
    Gresh N, Perahia D, de Courcy B, Foret J, Roux C et al. 2016. Complexes of a Zn‐metalloenzyme binding site with hydroxamate‐containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown. J. Comput. Chem. 37:2770–82
    [Google Scholar]
  33. 33.
    Gresh N, Sponer JE, Devereux M, Gkionis K, de Courcy B et al. 2015. Stacked and H-bonded cytosine dimers. Analysis of the intermolecular interaction energies by parallel quantum chemistry and polarizable molecular mechanics. J. Phys. Chem. B 119:9477–95
    [Google Scholar]
  34. 34.
    Grossfield A, Ren P, Ponder JW 2003. Ion solvation thermodynamics from simulation with a polarizable force field. J. Am. Chem. Soc. 125:15671–82
    [Google Scholar]
  35. 35.
    Halgren TA, Damm W 2001. Polarizable force fields. Curr. Opin. Struct. Biol. 11:236–42
    [Google Scholar]
  36. 36.
    Harger M, Li D, Wang Z, Dalby K, Lagardère L et al. 2017. Tinker‐OpenMM: absolute and relative alchemical free energies using AMOEBA on GPUs. J. Comput. Chem. 38:2047–55
    [Google Scholar]
  37. 37.
    Heidar-Zadeh F, Ayers PW, Verstraelen T, Vinogradov I, Vöhringer-Martinez E, Bultinck P 2018. Information-theoretic approaches to atoms-in-molecules: Hirshfeld family of partitioning schemes. J. Phys. Chem. A 122:4219–45
    [Google Scholar]
  38. 38.
    Huang J, Lemkul JA, Eastman PK, MacKerell AD Jr 2018. Molecular dynamics simulations using the Drude polarizable force field on GPUs with OpenMM: implementation, validation, and benchmarks. J. Comput. Chem. 39:1682–89
    [Google Scholar]
  39. 39.
    Huang J, Simmonett AC, Pickard FC, MacKerell AD, Brooks BR 2017. Mapping the Drude polarizable force field onto a multipole and induced dipole model. J. Chem. Phys. 147:161702
    [Google Scholar]
  40. 40.
    Husic BE, Pande VS 2018. Markov state models: from an art to a science. J. Am. Chem. Soc. 140:2386–96
    [Google Scholar]
  41. 41.
    Jakobsen S, Jensen F 2014. Systematic improvement of potential-derived atomic multipoles and redundancy of the electrostatic parameter space. J. Chem. Theory Comput. 10:5493–504
    [Google Scholar]
  42. 42.
    Jakobsen S, Jensen F 2016. Searching the force field electrostatic multipole parameter space. J. Chem. Theory Comput. 12:1824–32
    [Google Scholar]
  43. 43.
    Jiao D, Golubkov PA, Darden TA, Ren P 2008. Calculation of protein–ligand binding free energy by using a polarizable potential. PNAS 105:6290–95
    [Google Scholar]
  44. 44.
    Jing Z, Liu C, Qi R, Ren P 2018. Many-body effect determines the selectivity for Ca2+ and Mg2+ in proteins. PNAS 115:E7495–501
    [Google Scholar]
  45. 45.
    Jorgensen WL, Schyman P 2012. Treatment of halogen bonding in the OPLS-AA force field: application to potent anti-HIV agents. J. Chem. Theory Comput. 8:3895–901
    [Google Scholar]
  46. 46.
    Kaminsky J, Jensen F 2016. Conformational interconversions of amino acid derivatives. J. Chem. Theory Comput. 12:694–705
    [Google Scholar]
  47. 47.
    Kolář MH, Hobza P 2016. Computer modeling of halogen bonds and other σ-hole interactions. Chem. Rev. 116:5155–87
    [Google Scholar]
  48. 48.
    Kramer C, Spinn A, Liedl KR 2014. Charge anisotropy: where atomic multipoles matter most. J. Chem. Theory Comput. 10:4488–96
    [Google Scholar]
  49. 49.
    Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal J-P, Cisneros GA 2016. LICHEM: a QM/MM program for simulations with multipolar and polarizable force fields. J. Comput. Chem. 37:1019–29
    [Google Scholar]
  50. 50.
    Kurnikov IV, Kurnikova M 2015. Modeling electronic polarizability changes in the course of a magnesium ion water ligand exchange process. J. Phys. Chem. B 119:10275–86
    [Google Scholar]
  51. 51.
    Kutzner C, Páll S, Fechner M, Esztermann A, de Groot BL, Grubmüller H 2015. Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. J. Comput. Chem. 36:1990–2008
    [Google Scholar]
  52. 52.
    Lagardère L, Jolly L-H, Lipparini F, Aviat F, Stamm B et al. 2018. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chem. Sci. 9:956–72
    [Google Scholar]
  53. 53.
    Laury ML, Wang L-P, Pande VS, Head-Gordon T, Ponder JW 2015. Revised parameters for the AMOEBA polarizable atomic multipole water model. J. Phys. Chem. B 119:9423–37
    [Google Scholar]
  54. 54.
    Lemkul JA, Huang J, MacKerell AD 2015. Induced dipole–dipole interactions influence the unfolding pathways of wild-type and mutant amyloid β-peptides. J. Phys. Chem. B 119:15574–82
    [Google Scholar]
  55. 55.
    Lemkul JA, Huang J, Roux B, MacKerell AD 2016. An empirical polarizable force field based on the classical Drude oscillator model: development history and recent applications. Chem. Rev. 116:4983–5013
    [Google Scholar]
  56. 56.
    Lemkul JA, MacKerell AD 2017. Polarizable force field for DNA based on the classical Drude oscillator: I. Refinement using quantum mechanical base stacking and conformational energetics. J. Chem. Theory Comput. 13:2053–71
    [Google Scholar]
  57. 57.
    Lemkul JA, Savelyev A, MacKerell AD 2014. Induced polarization influences the fundamental forces in DNA base flipping. J. Phys. Chem. Lett. 5:2077–83
    [Google Scholar]
  58. 58.
    Leontyev IV, Stuchebrukhov AA 2014. Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models. J. Chem. Phys. 141:014103
    [Google Scholar]
  59. 59.
    Li H, Chowdhary J, Huang L, He X, MacKerell AD, Roux B 2017. Drude polarizable force field for molecular dynamics simulations of saturated and unsaturated zwitterionic lipids. J. Chem. Theory Comput. 13:4535–52
    [Google Scholar]
  60. 60.
    Li Y, Li H, Pickard FC, Narayanan B, Sen FG et al. 2017. Machine learning force field parameters from ab initio data. J. Chem. Theory Comput. 13:4492–503
    [Google Scholar]
  61. 61.
    Liberatore E, Meli R, Rothlisberger U 2018. A versatile multiple time step scheme for efficient ab initio molecular dynamics simulations. J. Chem. Theory Comput. 14:2834–42
    [Google Scholar]
  62. 62.
    Lin B, Gao Y, Li Y, Zhang JZ, Mei Y 2014. Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin. J. Mol. Model. 20:2189
    [Google Scholar]
  63. 63.
    Lin D 2015. Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors. J. Chem. Phys. 143:114115
    [Google Scholar]
  64. 64.
    Lin F-Y, MacKerell AD 2018. Polarizable empirical force field for halogen-containing compounds based on the classical Drude oscillator. J. Chem. Theory Comput. 14:1083–98
    [Google Scholar]
  65. 65.
    Lin Z, van Gunsteren WF 2015. Effects of polarizable solvent models upon the relative stability of an α-helical and a β-hairpin structure of an alanine decapeptide. J. Chem. Theory Comput. 11:1983–86
    [Google Scholar]
  66. 66.
    Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E et al. 2015. Polarizable molecular dynamics in a polarizable continuum solvent. J. Chem. Theory Comput. 11:623–34
    [Google Scholar]
  67. 67.
    Liu C, Li Y, Han B-Y, Gong L-D, Lu L-N et al. 2017. Development of the ABEEMσπ polarization force field for base pairs with amino acid residue complexes. J. Chem. Theory Comput. 13:2098–111
    [Google Scholar]
  68. 68.
    Liu C, Qi R, Wang Q, Piquemal J-P, Ren P 2017. Capturing many-body interactions with classical dipole induction models. J. Chem. Theory Comput. 13:2751–61
    [Google Scholar]
  69. 69.
    Loco D, Buda F, Lugtenburg J, Mennucci B 2018. The dynamic origin of color tuning in proteins revealed by a carotenoid pigment. J. Phys. Chem. Lett. 9:2404–10
    [Google Scholar]
  70. 70.
    Loco D, Lagardère L, Caprasecca S, Lipparini F, Mennucci B, Piquemal J-P 2017. Hybrid QM/MM molecular dynamics with AMOEBA polarizable embedding. J. Chem. Theory Comput. 13:4025–33
    [Google Scholar]
  71. 71.
    Loco D, Polack É, Caprasecca S, Lagardère L, Lipparini F et al. 2016. A QM/MM approach using the AMOEBA polarizable embedding: from ground state energies to electronic excitations. J. Chem. Theory Comput. 12:3654–61
    [Google Scholar]
  72. 72.
    Lopes PEM, Huang J, Shim J, Luo Y, Li H et al. 2013. Polarizable force field for peptides and proteins based on the classical Drude oscillator. J. Chem. Theory Comput. 9:5430–49
    [Google Scholar]
  73. 73.
    Lu C, Li X, Wu D, Zheng L, Yang W 2016. Predictive sampling of rare conformational events in aqueous solution: designing a generalized orthogonal space tempering method. J. Chem. Theory Comput. 12:41–52
    [Google Scholar]
  74. 74.
    MacDermaid CM, Kaminski GA 2007. Electrostatic polarization is crucial for reproducing pKa shifts of carboxylic residues in turkey ovomucoid third domain. J. Phys. Chem. B 111:9036–44
    [Google Scholar]
  75. 75.
    Manin N, da Silva MC, Zdravkovic I, Eliseeva O, Dyshin A et al. 2016. LiCl solvation in N-methyl-acetamide (NMA) as a model for understanding Li+ binding to an amide plane. Phys. Chem. Chem. Phys. 18:4191–200
    [Google Scholar]
  76. 76.
    Mao Y, Demerdash O, Head-Gordon M, Head-Gordon T 2016. Assessing ion-water interactions in the AMOEBA force field using energy decomposition analysis of electronic structure calculations. J. Chem. Theory Comput. 12:5422–37
    [Google Scholar]
  77. 77.
    Margul DT, Tuckerman ME 2016. A stochastic, resonance-free multiple time-step algorithm for polarizable models that permits very large time steps. J. Chem. Theory Comput. 12:2170–80
    [Google Scholar]
  78. 78.
    Marshall GR 2013. Limiting assumptions in molecular modeling: electrostatics. J. Comput. Aided Mol. Des. 27:107–14
    [Google Scholar]
  79. 79.
    Mehandzhiyski AY, Riccardi E, van Erp TS, Koch H, Astrand PO et al. 2015. Density functional theory study on the interactions of metal ions with long chain deprotonated carboxylic acids. J. Phys. Chem. A 119:10195–203
    [Google Scholar]
  80. 80.
    Mei Y, Simmonett AC, Pickard FC, DiStasio RA, Brooks BR, Shao Y 2015. Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions. J. Phys. Chem. A 119:5865–82
    [Google Scholar]
  81. 81.
    Misquitta AJ, Stone AJ, Fazeli F 2014. Distributed multipoles from a robust basis-space implementation of the iterated stockholder atoms procedure. J. Chem. Theory Comput. 10:5405–18
    [Google Scholar]
  82. 82.
    Morrone JA, Markland TE, Ceriotti M, Berne BJ 2011. Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances. J. Chem. Phys. 134:014103
    [Google Scholar]
  83. 83.
    Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G 2015. The impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexes. Drug Discov. Today 20:686–702
    [Google Scholar]
  84. 84.
    Mu X, Wang Q, Wang L-P, Fried SD, Piquemal J-P et al. 2014. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J. Phys. Chem. B 118:6456–65
    [Google Scholar]
  85. 85.
    Nessler IJ, Litman JM, Schnieders MJ 2016. Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals. Phys. Chem. Chem. Phys. 18:30313–22
    [Google Scholar]
  86. 86.
    Ngo V, da Silva MC, Kubillus M, Li H, Roux B et al. 2015. Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins. J. Chem. Theory Comput. 11:4992–5001
    [Google Scholar]
  87. 87.
    Ouyang JF, Bettens RP 2016. When are many-body effects significant. ? J. Chem. Theory Comput. 12:5860–67
    [Google Scholar]
  88. 88.
    Patel S, Brooks CL III 2004. CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J. Comput. Chem. 25:1–16
    [Google Scholar]
  89. 89.
    Peng X, Zhang Y, Chu H, Li Y, Zhang D et al. 2016. Accurate evaluation of ion conductivity of the gramicidin A channel using a polarizable force field without any corrections. J. Chem. Theory Comput. 12:2973–82
    [Google Scholar]
  90. 90.
    Piotr C, François-Yves D, Yong D, Junmei W 2009. Polarization effects in molecular mechanical force fields. J. Phys. Condens. Matter 21:333102
    [Google Scholar]
  91. 91.
    Piquemal J-P, Cisneros GA, Reinhardt P, Gresh N, Darden TA 2006. Towards a force field based on density fitting. J. Chem. Phys. 124:104101
    [Google Scholar]
  92. 92.
    Piquemal J-P, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA 2006. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: from energetics to structure. J. Chem. Phys. 125:054511
    [Google Scholar]
  93. 93.
    Ponder JW, Wu C, Ren P, Pande VS, Chodera JD et al. 2010. Current status of the AMOEBA polarizable force field. J. Phys. Chem. B 114:2549–64
    [Google Scholar]
  94. 94.
    Qi R, Jing Z, Liu C, Piquemal J-P, Dalby KN, Ren P 2018. Elucidating the phosphate binding mode of PBP: the critical effect of buffer solution. J. Phys. Chem. B 122:6371–76
    [Google Scholar]
  95. 95.
    Qi R, Wang L-P, Wang Q, Pande VS, Ren P 2015. United polarizable multipole water model for molecular mechanics simulation. J. Chem. Phys. 143:014504
    [Google Scholar]
  96. 96.
    Qi R, Wang Q, Ren P 2016. General van der Waals potential for common organic molecules. Bioorg. Med. Chem. 24:4911–19
    [Google Scholar]
  97. 97.
    Qiao B, Skanthakumar S, Soderholm L 2018. Comparative CHARMM and AMOEBA simulations of lanthanide hydration energetics and experimental aqueous-solution structures. J. Chem. Theory Comput. 14:1781–90
    [Google Scholar]
  98. 98.
    Qiu F, Chamberlin A, Watkins BM, Ionescu A, Perez ME et al. 2016. Molecular mechanism of Zn2+ inhibition of a voltage-gated proton channel. PNAS 113:E5962–71
    [Google Scholar]
  99. 99.
    Rackers JA, Wang Q, Liu C, Piquemal J-P, Ren P, Ponder JW 2017. An optimized charge penetration model for use with the AMOEBA force field. Phys. Chem. Chem. Phys. 19:276–91
    [Google Scholar]
  100. 100.
    Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M et al. 2012. Biomolecular electrostatics and solvation: a computational perspective. Q. Rev. Biophys. 45:427–91
    [Google Scholar]
  101. 101.
    Ren P, Ponder JW 2003. Polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B 107:5933–47
    [Google Scholar]
  102. 102.
    Ren P, Wu C, Ponder JW 2011. Polarizable atomic multipole-based molecular mechanics for organic molecules. J. Chem. Theory Comput. 7:3143–61
    [Google Scholar]
  103. 103.
    Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC 2013. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald. J. Chem. Theory Comput. 9:3878–88
    [Google Scholar]
  104. 104.
    Satpati P, Clavaguéra C, Ohanessian G, Simonson T 2011. Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2. J. Phys. Chem. B 115:6749–63
    [Google Scholar]
  105. 105.
    Savelyev A, MacKerell AD 2014. All‐atom polarizable force field for DNA based on the classical Drude oscillator model. J. Comput. Chem. 35:1219–39
    [Google Scholar]
  106. 106.
    Savelyev A, MacKerell AD 2015. Differential impact of the monovalent ions Li+, Na+, K+, and Rb+ on DNA conformational properties. J. Phys. Chem. Lett. 6:212–16
    [Google Scholar]
  107. 107.
    Schnieders MJ, Baltrusaitis J, Shi Y, Chattree G, Zheng L et al. 2012. The structure, thermodynamics, and solubility of organic crystals from simulation with a polarizable force field. J. Chem. Theory Comput. 8:1721–36
    [Google Scholar]
  108. 108.
    Semrouni D, Isley WC, Clavaguéra C, Dognon J-P, Cramer CJ, Gagliardi L 2013. Ab initio extension of the AMOEBA polarizable force field to Fe2+. J. Chem. Theory Comput. 9:3062–71
    [Google Scholar]
  109. 109.
    Shi Y, Xia Z, Zhang J, Best R, Wu C et al. 2013. Polarizable atomic multipole-based AMOEBA force field for proteins. J. Chem. Theory Comput. 9:4046–63
    [Google Scholar]
  110. 110.
    Shi Y, Zhu CZ, Martin SF, Ren P 2012. Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations. J. Phys. Chem. B 116:1716–27
    [Google Scholar]
  111. 111.
    Simmonett AC, Pickard FC IV, Ponder JW, Brooks BR 2016. An empirical extrapolation scheme for efficient treatment of induced dipoles. J. Chem. Phys. 145:164101
    [Google Scholar]
  112. 112.
    Simmonett AC, Pickard FC IV, Schaefer HF III, Brooks BR 2014. An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald. J. Chem. Phys. 140:184101
    [Google Scholar]
  113. 113.
    Song J, Ji C, Zhang JZH 2013. The critical effect of polarization on the dynamical structure of guanine quadruplex DNA. Phys. Chem. Chem. Phys. 15:3846–54
    [Google Scholar]
  114. 114.
    Stern HA, Rittner F, Berne BJ, Friesner RA 2001. Combined fluctuating charge and polarizable dipole models: application to a five-site water potential function. J. Chem. Phys. 115:2237–51
    [Google Scholar]
  115. 115.
    Stone A 2016. The Theory of Intermolecular Forces Oxford, UK: Oxford Univ. Press
  116. 116.
    Sun R-N, Gong H 2017. Simulating the activation of voltage sensing domain for a voltage-gated sodium channel using polarizable force field. J. Phys. Chem. Lett. 8:901–8
    [Google Scholar]
  117. 117.
    Swope WC, Horn HW, Rice JE 2010. Accounting for polarization cost when using fixed charge force fields. I. Method for computing energy. J. Phys. Chem. B 114:8621–30
    [Google Scholar]
  118. 118.
    Tazi S, Molina JJ, Rotenberg B, Turq P, Vuilleumier R, Salanne M 2012. A transferable ab initio based force field for aqueous ions. J. Chem. Phys. 136:114507
    [Google Scholar]
  119. 119.
    Torabifard H, Cisneros GA 2017. Computational investigation of O2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O2 transport. Chem. Sci. 8:6230–38
    [Google Scholar]
  120. 120.
    Unke OT, Devereux M, Meuwly M 2017. Minimal distributed charges: multipolar quality at the cost of point charge electrostatics. J. Chem. Phys. 147:161712
    [Google Scholar]
  121. 121.
    Van Vleet MJ, Misquitta AJ, Schmidt JR 2018. New angles on standard force fields: toward a general approach for treating atomic-level anisotropy. J. Chem. Theory Comput. 14:739–58
    [Google Scholar]
  122. 122.
    Vergara-Jaque A, Fong P, Comer J 2017. Iodide binding in sodium-coupled cotransporters. J. Chem. Inform. Model. 57:3043–55
    [Google Scholar]
  123. 123.
    Verstraelen T, Vandenbrande S, Ayers PW 2014. Direct computation of parameters for accurate polarizable force fields. J. Chem. Phys. 141:194114
    [Google Scholar]
  124. 124.
    Vosmeer CR, Kiewisch K, Keijzer K, Visscher L, Geerke DP 2014. A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities. Phys. Chem. Chem. Phys. 16:17857–62
    [Google Scholar]
  125. 125.
    Vosmeer CR, Rustenburg AS, Rice JE, Horn HW, Swope WC, Geerke DP 2012. QM/MM-based fitting of atomic polarizabilities for use in condensed-phase biomolecular simulation. J. Chem. Theory Comput. 8:3839–53
    [Google Scholar]
  126. 126.
    Walsh TR, Knecht MR 2017. Biointerface structural effects on the properties and applications of bioinspired peptide-based nanomaterials. Chem. Rev. 117:12641–704
    [Google Scholar]
  127. 127.
    Wang H, Yang W 2016. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory. J. Chem. Phys. 144:224107
    [Google Scholar]
  128. 128.
    Wang J, Cieplak P, Li J, Cai Q, Hsieh M-J et al. 2012. Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization. J. Phys. Chem. B 116:7088–101
    [Google Scholar]
  129. 129.
    Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA 2004. Development and testing of a general amber force field. J. Comput. Chem. 25:1157–74
    [Google Scholar]
  130. 130.
    Wang L-P, Head-Gordon T, Ponder JW, Ren P, Chodera JD et al. 2013. Systematic improvement of a classical molecular model of water. J. Phys. Chem. B 117:9956–72
    [Google Scholar]
  131. 131.
    Wang L-P, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T et al. 2017. Building a more predictive protein force field: a systematic and reproducible route to AMBER-FB15. J. Phys. Chem. B 121:4023–39
    [Google Scholar]
  132. 132.
    Wang Q, Rackers JA, He C, Qi R, Narth C et al. 2015. General model for treating short-range electrostatic penetration in a molecular mechanics force field. J. Chem. Theory Comput. 11:2609–18
    [Google Scholar]
  133. 133.
    Warshel A, Kato M, Pisliakov AV 2007. Polarizable force fields: history, test cases, and prospects. J. Chem. Theory Comput. 3:2034–45
    [Google Scholar]
  134. 134.
    Wu H, Paul F, Wehmeyer C, Noé F 2016. Multiensemble Markov models of molecular thermodynamics and kinetics. PNAS 113:E3221–30
    [Google Scholar]
  135. 135.
    Wu JC, Chattree G, Ren P 2012. Automation of AMOEBA polarizable force field parameterization for small molecules. Theor. Chem. Acc. 131:1138
    [Google Scholar]
  136. 136.
    Wu X, Clavaguéra C, Lagardère L, Piquemal J-P, de la Lande A 2018. AMOEBA polarizable force field parameters of the heme cofactor in its ferrous and ferric forms. J. Chem. Theory Comput. 14:2705–20
    [Google Scholar]
  137. 137.
    Wu X, Pickard FC IV, Brooks BR 2016. Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor. J. Chem. Phys. 145:164110
    [Google Scholar]
  138. 138.
    Xia M, Chai Z, Wang D 2017. Polarizable and non-polarizable force field representations of ferric cation and validations. J. Phys. Chem. B 121:5718–29
    [Google Scholar]
  139. 139.
    Xiang JY, Ponder JW 2013. A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field. J. Comput. Chem. 34:739–49
    [Google Scholar]
  140. 140.
    Yang Z-Z, Wang JJ, Zhao D-X 2014. Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field. J. Comput. Chem. 35:1690–706
    [Google Scholar]
  141. 141.
    Yin J, Fenley AT, Henriksen NM, Gilson MK 2015. Toward improved force-field accuracy through sensitivity analysis of host-guest binding thermodynamics. J. Phys. Chem. B 119:10145–55
    [Google Scholar]
  142. 142.
    Zeng Q, Liang W 2015. Analytic energy gradient of excited electronic state within TDDFT/MMpol framework: benchmark tests and parallel implementation. J. Chem. Phys. 143:134104
    [Google Scholar]
  143. 143.
    Zhang C, Lu C, Jing Z, Wu C, Piquemal J-P et al. 2018. AMOEBA polarizable atomic multipole force field for nucleic acids. J. Chem. Theory Comput. 14:2084–108
    [Google Scholar]
  144. 144.
    Zhao D-X, Liu C, Wang F-F, Yu C-Y, Gong L-D et al. 2010. Development of a polarizable force field using multiple fluctuating charges per atom. J. Chem. Theory Comput. 6:795–804
    [Google Scholar]
  145. 145.
    Zhu Q, Lu Y, He X, Liu T, Chen H et al. 2017. Entropy and polarity control the partition and transportation of drug-like molecules in biological membrane. Sci. Rep. 7:17749
    [Google Scholar]
/content/journals/10.1146/annurev-biophys-070317-033349
Loading
/content/journals/10.1146/annurev-biophys-070317-033349
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error