Hydration structure and dynamics of K+ and Ca2+ in aqueous solution: Comparison of conventional QM/MM and ONIOM-XS MD simulations

Abstract Molecular dynamics (MD) simulations based on the conventional QM/MM scheme and ONIOM-XS method have been performed to investigate structural and dynamical properties of K+ and Ca2+ in water. Regarding the detailed analyses of the ONIOM-XS MD trajectories, the average hydration numbers for K+ and Ca2+ were found to be 6.3 and 7.6, respectively, compared with the corresponding values of 7.0 and 7.8 derived by the conventional QM/MM simulations. Together with the significant difference found in the comparison of the dynamics details, the ONIOM-XS method clearly shows its capability in predicting more reliable detailed knowledge of these hydrated ions.

[1]  K. Morokuma,et al.  ONIOM: A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels−Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition , 1996 .

[2]  Johannes Grotendorst,et al.  Modern methods and algorithms of quantum chemistry , 2000 .

[3]  Vassiliki-Alexandra Glezakou,et al.  Molecular simulation analysis and X-ray absorption measurement of Ca2+, K+ and Cl- ions in solution. , 2006, The journal of physical chemistry. B.

[4]  R. Howe,et al.  Ion hydration in aqueous CaCl2 solutions , 1980 .

[5]  W. R. Wadt,et al.  Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi , 1985 .

[6]  P. Brimblecombe,et al.  Chemistry of Atmospheres. , 1986 .

[7]  D. Xenides,et al.  Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study. , 2005, The Journal of chemical physics.

[8]  Bernd M. Rode,et al.  Dynamical properties of water molecules in the hydration shells of Na+ and K+: ab initio QM/MM molecular dynamics simulations , 2004 .

[9]  K. Morokuma,et al.  Combined quantum mechanics and molecular mechanics simulation of Ca2+/ammonia solution based on the ONIOM-XS method: Octahedral coordination and implication to biology , 2003 .

[10]  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.

[11]  Frank H. Stillinger,et al.  Revised central force potentials for water , 1978 .

[12]  Michele Parrinello,et al.  On the Quantum Nature of the Shared Proton in Hydrogen Bonds , 1997, Science.

[13]  G. Piccaluga,et al.  X‐ray diffraction study of the average solute species in CaCl2 aqueous solutions , 1976 .

[14]  Teerakiat Kerdcharoen,et al.  ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase , 2002 .

[15]  E. Stadtman,et al.  Oxidation of free amino acids and amino acid residues in proteins by radiolysis and by metal-catalyzed reactions. , 1993, Annual review of biochemistry.

[16]  M. Mezei,et al.  Monte Carlo studies of the structure of dilute aqueous sclutions of Li+, Na+, K+, F−, and Cl− , 1981 .

[17]  Klaus R. Liedl,et al.  BORN-OPPENHEIMER AB INITIO QM/MM DYNAMICS SIMULATIONS OF NA+ AND K+ IN WATER : FROM STRUCTURE MAKING TO STRUCTURE BREAKING EFFECTS , 1998 .

[18]  S. Heald,et al.  Understanding the effects of concentration on the solvation structure of Ca2+ in aqueous solution I: the perspective on local structure from EXAFS and XANES , 2003 .

[19]  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 .

[20]  U. Singh,et al.  A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .

[21]  Hung T. Tran,et al.  Characterization of dynamics and reactivities of solvated ions by ab initio simulations , 2004, J. Comput. Chem..

[22]  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.

[23]  I. Bakó,et al.  Ion pairing in aqueous calcium chloride solution: Molecular dynamics simulation and diffraction studies , 2006 .

[24]  H. Bradaczek,et al.  Molecular Dynamics Study of the Structure and Dynamics of the Hydration Shell of Alkaline and Alkaline-Earth Metal Cations , 1996 .

[25]  K. Heinzinger,et al.  An improved potential for non-rigid water molecules in the liquid phase , 1983 .

[26]  K. Tasaki,et al.  Observations concerning the treatment of long‐range interactions in molecular dynamics simulations , 1993, J. Comput. Chem..

[27]  Yizhak Marcus,et al.  Ionic radii in aqueous solutions , 1983 .

[28]  B. Rode,et al.  Ab initio QM/MM MD simulations of the hydrated Ca2+ ion , 2004 .

[29]  Klaus R. Liedl,et al.  Solvation of Ca2+ in Water Studied by Born−Oppenheimer ab Initio QM/MM Dynamics , 1997 .

[30]  Hannes H. Loeffler,et al.  Molecular dynamics simulations of Ca2+ in water: Comparison of a classical simulation including three-body corrections and Born–Oppenheimer ab initio and density functional theory quantum mechanical/molecular mechanics simulations , 2001 .

[31]  J. Phillips,et al.  Lithium and Medicine: Inorganic Pharmacology , 2010 .

[32]  B. Randolf,et al.  Hydration of sodium(I) and potassium(I) revisited: a comparative QM/MM and QMCF MD simulation study of weakly hydrated ions. , 2009, The journal of physical chemistry. A.

[33]  J. Enderby,et al.  Environment of Ca2+ ions in aqueous solvent , 1982, Nature.

[34]  Model extended X-ray absorption fine structure (EXAFS) spectra from molecular dynamics data for Ca2+ and Al3+ aqueous solutions , 2000 .

[35]  B. Rode,et al.  QM/MM dynamics of CH3COO(-)-water hydrogen bonds in aqueous solution. , 2010, The journal of physical chemistry. A.

[36]  Bernd M. Rode,et al.  Structure and dynamics of hydrated ions—new insights through quantum mechanical simulations , 2003 .

[37]  Brian J. Wright,et al.  Addition of Polarization and Diffuse Functions to the LANL2DZ Basis Set for P-Block Elements , 2001 .

[38]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[39]  Milton Blander,et al.  Chemical physics of ionic solutions: edited by B. E. Conway and R. G. Barradas. 622 pages, diagrams, illustr. 6 × 9 in. New York, Wiley and Sons, 1966. $25.00 , 1967 .

[40]  J. Rasaiah,et al.  Molecular Dynamics Simulation of Ion Mobility. 2. Alkali Metal and Halide Ions Using the SPC/E Model for Water at 25 °C† , 1996 .

[41]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[42]  Zaheer-ul-Haq,et al.  Classical and QM/MM MD simulations of sodium(I) and potassium(I) ions in aqueous solution , 2010 .

[43]  G. Brady Structure in Ionic Solutions. II , 1958 .

[44]  E. Clementi Determination of Liquid Water Structure: Coordination Numbers for Ions and Solvation for Biological Molecules , 1976 .

[45]  P. Hünenberger,et al.  Car-Parrinello Molecular Dynamics Simulations of CaCl2 Aqueous Solutions. , 2008, Journal of chemical theory and computation.

[46]  Bernd M. Rode,et al.  Ab initio QM/MM dynamics of anion–water hydrogen bonds in aqueous solution , 2005 .

[47]  Graham Hills,et al.  The computer simulation of polar liquids , 1979 .

[48]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.