Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field
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作者:
Wu, Johnny C.
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机构:
Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USAUniv Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
Wu, Johnny C.
[2
]
Piquemal, Jean-Philip
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h-index: 0
机构:
Univ Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
CNRS, Chim Theor Lab, UMR 7616, F-75005 Paris, FranceUniv Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
Piquemal, Jean-Philip
[1
,3
]
Chaudret, Robin
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机构:
Univ Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
CNRS, Chim Theor Lab, UMR 7616, F-75005 Paris, FranceUniv Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
Chaudret, Robin
[1
,3
]
Reinhardt, Peter
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机构:
Univ Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
CNRS, Chim Theor Lab, UMR 7616, F-75005 Paris, FranceUniv Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
Reinhardt, Peter
[1
,3
]
Ren, Pengyu
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机构:
Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USAUniv Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
Ren, Pengyu
[2
]
机构:
[1] Univ Paris 06, UPMC, Chim Theor Lab, UMR 7616, F-75005 Paris, France
The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn2+ are derived from gas-phase ab initio calculation of the Zn2+-water dimer. The Thole-based dipole polarization is adjusted on the basis of the constrained space orbital variations (CSOV) calculation, while the symmetry adapted perturbation theory (SAPT) approach is also discussed. The vdW parameters of Zn2+ have been obtained by comparing the AMOEBA Zn2+ water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn2+ solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence lime, and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive reduced variational space (RVS) and electron localization function (ELF) computations in order to unravel the nature of the bonding in Zn2+(H2O)(n) (n = 1, 6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of the Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal ligand bonds. Induction could be dominated by polarization when the system approaches the condensed phase and the covalent effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn2+ in bulk water, one should therefore avoid overfilling to the ab initio charge transfer energy of the Zn2+-water dimer. Indeed, in order to avoid overestimation of the condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated into the pairwise van der Waals contribution or treated explicitly.
机构:
Univ So Calif, Dept Chem, Los Angeles, CA 90089 USAUniv So Calif, Dept Chem, Los Angeles, CA 90089 USA
Henke, Paul S.
Mak, Chi H.
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Univ So Calif, Dept Chem, Los Angeles, CA 90089 USA
Univ So Calif, Ctr Appl Math Sci, Los Angeles, CA 90089 USAUniv So Calif, Dept Chem, Los Angeles, CA 90089 USA
机构:
CNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Gresh, Nohad
El Hage, Krystel
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机构:
CNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Univ St Joseph, Unite Biochim, Beirut, LebanonCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
El Hage, Krystel
Perahia, David
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机构:
Ecole Normale Super, UMR 8113, LBPA, Paris, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Perahia, David
Piquemal, Jean-Philip
论文数: 0引用数: 0
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机构:
UPMC, Univ Paris 04, Lab Chim Theor, CNRS,UMR7616, Paris, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Piquemal, Jean-Philip
Berthomieu, Catherine
论文数: 0引用数: 0
h-index: 0
机构:
CEA, DSV, IBEB, Lab Interact Prot Met, St Paul Les Durance, France
CNRS, UMR Biol Vegetale & Microbiol Environm, St Paul Les Durance, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Berthomieu, Catherine
Berthomieu, Dorothee
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CNRS UM2 UM1 ENSCM, UMR 5253, Inst Charles Gerhardt, F-34296 Montpellier 5, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
机构:
Hong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R ChinaHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Pan, Cong
Liu, Chengwen
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h-index: 0
机构:
Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USAHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Liu, Chengwen
Peng, Junhui
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h-index: 0
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Hong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R ChinaHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Peng, Junhui
Ren, Pengyu
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h-index: 0
机构:
Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USAHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Ren, Pengyu
Huang, Xuhui
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机构:
Hong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Hong Kong Univ Sci & Technol, Ctr Syst Biol & Human Hlth, State Key Lab Mol Neurosci, Kowloon, Hong Kong, Peoples R ChinaHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
机构:
Nanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R ChinaNanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R China
Gu, Shuyin
Chen, Kai
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Nanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R ChinaNanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R China
Chen, Kai
Jin, Yezhi
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Nanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R ChinaNanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R China
Jin, Yezhi
Yang, Xiaoning
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Nanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R ChinaNanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R China
机构:
Univ So Calif, Dept Chem, Los Angeles, CA 90089 USAUniv So Calif, Dept Chem, Los Angeles, CA 90089 USA
Henke, Paul S.
Mak, Chi H.
论文数: 0引用数: 0
h-index: 0
机构:
Univ So Calif, Dept Chem, Los Angeles, CA 90089 USA
Univ So Calif, Ctr Appl Math Sci, Los Angeles, CA 90089 USAUniv So Calif, Dept Chem, Los Angeles, CA 90089 USA
机构:
CNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Gresh, Nohad
El Hage, Krystel
论文数: 0引用数: 0
h-index: 0
机构:
CNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Univ St Joseph, Unite Biochim, Beirut, LebanonCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
El Hage, Krystel
Perahia, David
论文数: 0引用数: 0
h-index: 0
机构:
Ecole Normale Super, UMR 8113, LBPA, Paris, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Perahia, David
Piquemal, Jean-Philip
论文数: 0引用数: 0
h-index: 0
机构:
UPMC, Univ Paris 04, Lab Chim Theor, CNRS,UMR7616, Paris, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Piquemal, Jean-Philip
Berthomieu, Catherine
论文数: 0引用数: 0
h-index: 0
机构:
CEA, DSV, IBEB, Lab Interact Prot Met, St Paul Les Durance, France
CNRS, UMR Biol Vegetale & Microbiol Environm, St Paul Les Durance, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
Berthomieu, Catherine
Berthomieu, Dorothee
论文数: 0引用数: 0
h-index: 0
机构:
CNRS UM2 UM1 ENSCM, UMR 5253, Inst Charles Gerhardt, F-34296 Montpellier 5, FranceCNRS, UMR 8601, UFR Biomed, Chem & Biol Nucleostides & Immunol Therapy CBNIT, Paris, France
机构:
Hong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R ChinaHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Pan, Cong
Liu, Chengwen
论文数: 0引用数: 0
h-index: 0
机构:
Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USAHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Liu, Chengwen
Peng, Junhui
论文数: 0引用数: 0
h-index: 0
机构:
Hong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R ChinaHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Peng, Junhui
Ren, Pengyu
论文数: 0引用数: 0
h-index: 0
机构:
Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USAHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Ren, Pengyu
Huang, Xuhui
论文数: 0引用数: 0
h-index: 0
机构:
Hong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
Hong Kong Univ Sci & Technol, Ctr Syst Biol & Human Hlth, State Key Lab Mol Neurosci, Kowloon, Hong Kong, Peoples R ChinaHong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Peoples R China
机构:
Nanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R ChinaNanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R China
Gu, Shuyin
Chen, Kai
论文数: 0引用数: 0
h-index: 0
机构:
Nanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R ChinaNanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R China
Chen, Kai
Jin, Yezhi
论文数: 0引用数: 0
h-index: 0
机构:
Nanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R ChinaNanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R China
Jin, Yezhi
Yang, Xiaoning
论文数: 0引用数: 0
h-index: 0
机构:
Nanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R ChinaNanjing Tech Univ, Coll Chem Engn, State Key Lab Mat Oriented Chem Engn, Nanjing, Peoples R China