Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.

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 Zn(2+) are derived from gas-phase ab initio calculation of Zn(2+)-water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn(2+) have been obtained by comparing the AMOEBA Zn(2+)-water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn(2+) solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time 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 Zn(2+)(H(2)O)(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 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 condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn(2+) in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn(2+)-water dimer. Indeed, in order to avoid overestimation of 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 in to the pairwise van der Waals contribution or treated explicitly.

[1]  L. Pedersen,et al.  Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks. , 2010, Journal of chemical theory and computation.

[2]  Margaret E. Johnson,et al.  Current status of the AMOEBA polarizable force field. , 2010, The journal of physical chemistry. B.

[3]  D. Rogers,et al.  Polarization and charge transfer in the hydration of chloride ions. , 2009, The Journal of chemical physics.

[4]  D. Rogers,et al.  Quasichemical and structural analysis of polarizable anion hydration. , 2009, The Journal of chemical physics.

[5]  Guohui Li,et al.  Trypsin‐ligand binding free energies from explicit and implicit solvent simulations with polarizable potential , 2009, J. Comput. Chem..

[6]  N. Gresh,et al.  Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Zn-metalloenzyme: Insights from electron localization function , 2009, Interdisciplinary Sciences: Computational Life Sciences.

[7]  Jean-Philip Piquemal,et al.  Fragment-Localized Kohn-Sham Orbitals via a Singles Configuration-Interaction Procedure and Application to Local Properties and Intermolecular Energy Decomposition Analysis. , 2008, Journal of chemical theory and computation.

[8]  N. Gresh,et al.  Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization? , 2008, Journal of chemical theory and computation.

[9]  Jean-Philip Piquemal,et al.  Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments , 2008, J. Comput. Chem..

[10]  Pengyu Y. Ren,et al.  Calculation of protein–ligand binding free energy by using a polarizable potential , 2008, Proceedings of the National Academy of Sciences.

[11]  Dimas Suárez,et al.  Monoligand Zn(II) Complexes:  Ab Initio Benchmark Calculations and Comparison with Density Functional Theory Methodologies. , 2008, Journal of chemical theory and computation.

[12]  Nohad Gresh,et al.  Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. , 2007, Journal of chemical theory and computation.

[13]  S. Durell,et al.  Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein. , 2007, Journal of the American Chemical Society.

[14]  Dimas Suárez,et al.  Quantum mechanical and molecular dynamics simulations of ureases and Zn β‐lactamases , 2006, Journal of computational chemistry.

[15]  Alan Grossfield,et al.  Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. , 2006, The journal of physical chemistry. B.

[16]  Pengyu Y. Ren,et al.  Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. , 2006, The Journal of chemical physics.

[17]  Armando Rossello,et al.  Amber force field implementation, molecular modelling study, synthesis and MMP-1/MMP-2 inhibition profile of (R)- and (S)-N-hydroxy-2-(N-isopropoxybiphenyl-4-ylsulfonamido)-3-methylbutanamides. , 2006, Bioorganic & medicinal chemistry.

[18]  B. Randolf,et al.  Temperature effects on the structural and dynamical properties of the Zn(II)-water complex in aqueous solution: a QM/MM molecular dynamics study. , 2006, The journal of physical chemistry. B.

[19]  M. Probst,et al.  On the performance of molecular polarization methods. II. Water and carbon tetrachloride close to a cation. , 2005, The Journal of chemical physics.

[20]  F. Gygi,et al.  A first-principles molecular dynamics study of calcium in water. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[21]  Nohad Gresh,et al.  Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short‐range contributions. Comparisons with parallel ab initio computations , 2005, J. Comput. Chem..

[22]  Nohad Gresh,et al.  Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo‐β‐lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry , 2005, J. Comput. Chem..

[23]  Thomas S Hofer,et al.  An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution. , 2005, The Journal of chemical physics.

[24]  Jean-Philip Piquemal,et al.  A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution , 2005, J. Comput. Chem..

[25]  Hannes H. Loeffler,et al.  Quantum mechanical/molecular mechanical molecular dynamic simulation of zinc(II) ion in water , 2005 .

[26]  A. Grossfield.  Dependence of ion hydration on the sign of the ion's charge. , 2005, The Journal of chemical physics.

[27]  Gabriel J. Cuello,et al.  Understanding the Effects of Concentration on the Solvation Structure of Ca2+ in Aqueous Solution. II: Insights into Longer Range Order from Neutron Diffraction Isotope Substitution , 2004 .

[28]  Pengyu Y. Ren,et al.  Temperature and Pressure Dependence of the AMOEBA Water Model , 2004 .

[29]  T. Ghosh,et al.  Size dependent ion hydration, its asymmetry, and convergence to macroscopic behavior. , 2004, The Journal of chemical physics.

[30]  L. Pratt,et al.  Hydration structure and free energy of biomolecularly specific aqueous dications, including Zn2+ and first transition row metals. , 2004, Journal of the American Chemical Society.

[31]  Pengyu Y. Ren,et al.  Ion solvation thermodynamics from simulation with a polarizable force field. , 2003, Journal of the American Chemical Society.

[32]  Michael R. Shirts,et al.  Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. , 2003, Physical review letters.

[33]  Pengyu Y. Ren,et al.  Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation , 2003 .

[34]  C. Dellago,et al.  Car-Parrinello molecular dynamics simulation of the calcium ion in liquid water , 2003 .

[35]  Ulf Ryde,et al.  Combined quantum and molecular mechanics calculations on metalloproteins. , 2003, Current opinion in chemical biology.

[36]  Pengyu Y. Ren,et al.  Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations , 2002, J. Comput. Chem..

[37]  V. Barone,et al.  Hydrogen and higher shell contributions in Zn2+, Ni2+, and Co2+ aqueous solutions: an X-ray absorption fine structure and molecular dynamics study. , 2002, Journal of the American Chemical Society.

[38]  Y. Pang.  Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method , 2001, Proteins.

[39]  K. Hermansson,et al.  Hydration of the calcium ion. An EXAFS, large-angle x-ray scattering, and molecular dynamics simulation study. , 2001, Journal of the American Chemical Society.

[40]  D. Covell,et al.  Reactivity of zinc finger cores: analysis of protein packing and electrostatic screening. , 2001, Journal of the American Chemical Society.

[41]  Nohad Gresh,et al.  Parallel ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligands , 2000, J. Comput. Chem..

[42]  Bernard Silvi,et al.  Computational Tools for the Electron Localization Function Topological Analysis , 1999, Comput. Chem..

[43]  L. Helm,et al.  Water exchange on metal ions: experiments and simulations , 1999 .

[44]  G. Hummer,et al.  Free energy of hydration of a molecular ionic solute: Tetramethylammonium ion , 1998 .

[45]  A. Kuzmin,et al.  X-ray absorption spectroscopy and molecular dynamics studies of hydration in aqueous solutions , 1997 .

[46]  Andreas Savin,et al.  ELF: The Electron Localization Function , 1997 .

[47]  H. Bradaczek,et al.  Molecular Dynamics Simulations of Zinc Ions in Water Using CHARMM , 1997 .

[48]  W. Lipscomb,et al.  Recent Advances in Zinc Enzymology , 1997 .

[49]  Nohad Gresh,et al.  Comparative binding energetics of Mg2+, Ca2+, Zn2+, and Cd2+ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation , 1996, J. Comput. Chem..

[50]  Bernd M. Rode,et al.  MONTE CARLO SIMULATIONS OF ZN(II) IN WATER INCLUDING THREE-BODY EFFECTS , 1996 .

[51]  Nohad Gresh,et al.  Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self‐consistent field supermolecular computations , 1995, J. Comput. Chem..

[52]  Robert Moszynski,et al.  Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes , 1994 .

[53]  A. Savin,et al.  Classification of chemical bonds based on topological analysis of electron localization functions , 1994, Nature.

[54]  Yizhak Marcus,et al.  A simple empirical model describing the thermodynamics of hydration of ions of widely varying charges, sizes, and shapes , 1994 .

[55]  H. Ohtaki,et al.  Structure and dynamics of hydrated ions , 1993 .

[56]  Thomas A. Halgren,et al.  The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters , 1992 .

[57]  Francesc Illas,et al.  Decomposition of the chemisorption bond by constrained variations: Order of the variations and construction of the variational spaces , 1992 .

[58]  B. Rode,et al.  Zinc ion in water : intermolecular potential with approximate three-body correction and Monte Carlo simulation , 1991 .

[59]  M. Bellissent-Funel,et al.  The dynamics of aqueous Zn2+ solutions: a study using incoherent quasi-elastic neutron scattering , 1990 .

[60]  Axel D. Becke,et al.  A Simple Measure of Electron Localization in Atomic and Molecular-Systems , 1990 .

[61]  T. H. Dunning.  Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[62]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[63]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[64]  William H. Fink,et al.  Frozen fragment reduced variational space analysis of hydrogen bonding interactions. Application to the water dimer , 1987 .

[65]  Harold Basch,et al.  Compact effective potentials and efficient shared‐exponent basis sets for the first‐ and second‐row atoms , 1984 .

[66]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[67]  W. Kutzelnigg.  The ‘‘primitive’’ wave function in the theory of intermolecular interactions , 1980 .

[68]  Barry Robson,et al.  Intermolecular Interactions: from diatomics to biopolymers , 1978 .

[69]  R. Caminiti,et al.  X-ray diffraction study of a “three-ion” aqueous solution , 1977 .

[70]  Charles H. Bennett,et al.  Efficient estimation of free energy differences from Monte Carlo data , 1976 .

[71]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[72]  R. Connick,et al.  Rate of water exchange from hydrated magnesium ion , 1970 .

[73]  D. Keilin,et al.  Carbonic anhydrase. Purification and nature of the enzyme. , 1940, The Biochemical journal.

[74]  M. Born.  Volumen und Hydratationswärme der Ionen , 1920 .

[75]  Nohad Gresh,et al.  Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics , 2009 .

[76]  Darrin M. York,et al.  Multi-scale Quantum Models for Biocatalysis , 2009 .

[77]  Elizabeth A. Amin,et al.  Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory. , 2008, Journal of chemical theory and computation.

[78]  J. Piquemal,et al.  What can be learnt on biologically relevant systems from the topological analysis of the electron localization function , 2008 .

[79]  Mark S. Gordon,et al.  Chapter 41 – Advances in electronic structure theory: GAMESS a decade later , 2005 .

[80]  R. Friesner,et al.  Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. , 2005, Annual review of physical chemistry.

[81]  Celeste Sagui,et al.  Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations. , 2004, The Journal of chemical physics.

[82]  V. Sapunov,et al.  A new table of the thermodynamic quantities of ionic hydration: values and some applications (enthalpy–entropy compensation and Born radii) , 2000 .

[83]  Bernard Pullman,et al.  Intermolecular interactions, from diatomics to biopolymers , 1978 .

[84]  Henry Margenau,et al.  Theory of intermolecular forces , 1969 .