Ab initio molecular dynamics: basic concepts, current trends and novel applications

The field of ab initio molecular dynamics (AIMD), in which finite temperature molecular dynamics (MD) trajectories are generated with forces obtained from accurate 'on the fly' electronic structure calculations, is a rapidly evolving and growing technology that allows chemical processes in condensed phases to be studied in an accurate and unbiased way. This article is intended to present the basics of the AIMD method as well as to provide a broad survey of the state of the art of the field and showcase some of its capabilities. Beginning with a derivation of the method from the Born–Oppenheimer approximation, issues including the density functional representation of electronic structure, basis sets, calculation of observables and the Car–Parrinello extended Lagrangian algorithm are discussed. A number of example applications, including liquid structure and dynamics and aqueous proton transport, are presented in order to highlight some of the current capabilities of the approach. Finally, advanced topics such as inclusion of nuclear quantum effects, excited states and scaling issues are addressed.

[1]  K. Venkatesan.  The crystal structure of ammonium perchlorate—NH4ClO4 , 1957 .

[2]  T. C. Waddington.  881. Infrared spectra, structure, and hydrogen-bonding in ammonium salts , 1958 .

[3]  S. Meiboom,et al.  NUCLEAR MAGNETIC RESONANCE STUDY OF THE PROTON TRANSFER IN WATER , 1961 .

[4]  P. A. Egelstaff.  Neutron scattering studies of liquid diffusion , 1962 .

[5]  R. Feynman,et al.  The Theory of a general quantum system interacting with a linear dissipative system , 1963 .

[6]  Manfred Eigen,et al.  Proton Transfer, Acid-Base Catalysis, and Enzymatic Hydrolysis. Part I: ELEMENTARY PROCESSES†‡ , 1964 .

[7]  P. Hohenberg,et al.  Inhomogeneous Electron Gas , 1964 .

[8]  P. Cossee,et al.  Ziegler-Natta catalysis III. Stereospecific polymerization of propene with the catalyst system TiCl3AlEt3 , 1964 .

[9]  N. Mermin.  Thermal Properties of the Inhomogeneous Electron Gas , 1965 .

[10]  W. Kohn,et al.  Self-Consistent Equations Including Exchange and Correlation Effects , 1965 .

[11]  R. Feynman,et al.  Quantum Mechanics and Path Integrals , 1965 .

[12]  C. Coulson,et al.  Interactions of H2O molecules in ice I. The dipole moment of an H2O molecule in ice , 1966, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[13]  H. Wise.  ELECTRICAL CONDUCTIVITY OF SOLID AMMONIUM PERCHLORATE. , 1967 .

[14]  J. Tully,et al.  Trajectory Surface Hopping Approach to Nonadiabatic Molecular Collisions: The Reaction of H+ with D2 , 1971 .

[15]  H. A. Levy,et al.  Liquid Water: Molecular Correlation Functions from X‐Ray Diffraction , 1971 .

[16]  E. M. Peterson,et al.  Self‐diffusion in liquid ammonia and deuteroammonia , 1973 .

[17]  L. Glasser.  Proton conduction and injection in solids , 1975 .

[18]  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.

[19]  P. Schuster,et al.  The Hydrogen bond : recent developments in theory and experiments , 1976 .

[20]  M. N. Afsar,et al.  Measurements of the optical constants of liquid H 2 O and D 2 O between 6 and 450 cm −1 , 1977 .

[21]  Arieh Warshel,et al.  An empirical valence bond approach for comparing reactions in solutions and in enzymes , 1980 .

[22]  A. Zunger,et al.  Self-interaction correction to density-functional approximations for many-electron systems , 1981 .

[23]  W. Rowe,et al.  Microwave spectroscopic study of malonaldehyde (3-hydroxy-2-propenal). 2. Structure, dipole moment, and tunneling , 1981 .

[24]  Steven G. Louie,et al.  Nonlinear ionic pseudopotentials in spin-density-functional calculations , 1982 .

[25]  Leonard Kleinman,et al.  Efficacious Form for Model Pseudopotentials , 1982 .

[26]  D. R. Hamann,et al.  Pseudopotentials that work: From H to Pu , 1982 .

[27]  R. Corn,et al.  Ammonium ion rotation in ammonium perchlorate as studied by infrared spectroscopy , 1983 .

[28]  G. Hall,et al.  State‐to‐state vibrational excitation of I2 in collisions with He , 1984 .

[29]  Quantum mechanical and molecular mechanical studies on a model for the dihydroxyacetone phosphate-glyceraldehyde phosphate isomerization catalyzed by triose phosphate isomerase (TIM) , 1984 .

[30]  E. Gross,et al.  Density-Functional Theory for Time-Dependent Systems , 1984 .

[31]  Richard W. Duerst,et al.  Microwave spectroscopic study of malonaldehyde. 3. Vibration-rotation interaction and one-dimensional model for proton tunneling , 1984 .

[32]  D. Ceperley,et al.  Simulation of quantum many-body systems by path-integral methods , 1984 .

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

[34]  J. Light,et al.  Generalized discrete variable approximation in quantum mechanics , 1985 .

[35]  R. Pecora.  Dynamic Light Scattering , 1985 .

[36]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[37]  Richard A. Friesner,et al.  Solution of self-consistent field electronic structure equations by a pseudospectral method , 1985 .

[38]  Alan K. Soper,et al.  A new determination of the structure of water at 25°C , 1986 .

[39]  J. Klinowski,et al.  Magic-angle-spinning NMR shows the aluminosilicate framework of ultramarine to be disordered , 1987, Nature.

[40]  Testa,et al.  Green's-function approach to linear response in solids. , 1987, Physical review letters.

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

[42]  G. Watson,et al.  Computer simulation , 1988 .

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

[44]  Jimmie D. Doll,et al.  Stationary phase Monte Carlo methods: An exact formulation , 1988 .

[45]  J. D. Doll,et al.  Quantum Monte Carlo dynamics: The stationary phase Monte Carlo path integral calculation of finite temperature time correlation functions , 1988 .

[46]  G. Ciccotti,et al.  Constrained reaction coordinate dynamics for the simulation of rare events , 1989 .

[47]  X. Gonze,et al.  Density-functional approach to nonlinear-response coefficients of solids. , 1989, Physical review. B, Condensed matter.

[48]  R. Parr.  Density-functional theory of atoms and molecules , 1989 .

[49]  A. Becke,et al.  Exchange holes in inhomogeneous systems: A coordinate-space model. , 1989, Physical review. A, General physics.

[50]  R. Dreizler,et al.  Density-Functional Theory , 1990 .

[51]  W. Kohn,et al.  Time-dependent density functional theory , 1990 .

[52]  J. Tully.  Molecular dynamics with electronic transitions , 1990 .

[53]  Scheffler,et al.  Ghost states for separable, norm-conserving, Iab initioP pseudopotentials. , 1990, Physical review. B, Condensed matter.

[54]  J. Muckerman.  Some useful discrete variable representations for problems in time-dependent and time-independent quantum mechanics , 1990 .

[55]  D. Vanderbilt,et al.  Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. , 1990, Physical review. B, Condensed matter.

[56]  D. Remler,et al.  Molecular dynamics without effective potentials via the Car-Parrinello approach , 1990 .

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

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

[59]  Martins,et al.  Efficient pseudopotentials for plane-wave calculations. , 1991, Physical review. B, Condensed matter.

[60]  J. Weigelt,et al.  Structure of calcium aluminosilicate glasses : wide-angle X-ray scattering and computer simulation , 1991 .

[61]  Lee,et al.  Implementation of ultrasoft pseudopotentials in ab initio molecular dynamics. , 1991, Physical review. B, Condensed matter.

[62]  Wang,et al.  Accurate and simple analytic representation of the electron-gas correlation energy. , 1992, Physical review. B, Condensed matter.

[63]  Galli,et al.  Large scale electronic structure calculations. , 1992, Physical review letters.

[64]  J. Gao,et al.  A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. , 1992, Science.

[65]  D. Colbert,et al.  A novel discrete variable representation for quantum mechanical reactive scattering via the S-matrix Kohn method , 1992 .

[66]  Parrinello,et al.  Adiabaticity in first-principles molecular dynamics. , 1992, Physical review. B, Condensed matter.

[67]  T. Arias,et al.  Iterative minimization techniques for ab initio total energy calculations: molecular dynamics and co , 1992 .

[68]  Theilhaber,et al.  Ab initio simulations of sodium using time-dependent density-functional theory. , 1992, Physical review. B, Condensed matter.

[69]  Axel D. Becke,et al.  Density-functional thermochemistry. I. The effect of the exchange-only gradient correction , 1992 .

[70]  M. Klein,et al.  Nosé-Hoover chains : the canonical ensemble via continuous dynamics , 1992 .

[71]  Lee,et al.  Ab initio studies on high pressure phases of ice. , 1992, Physical review letters.

[72]  Experimental and theoretical studies of malonaldehyde: vibrational analysis of a strongly intramolecularly hydrogen bonded compound , 1992 .

[73]  Lee,et al.  Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials. , 1993, Physical review. B, Condensed matter.

[74]  Kari Laasonen,et al.  Structures of small water clusters using gradient-corrected density functional theory , 1993 .

[75]  Fred Wudl,et al.  Inhibition of the HIV-1 protease by fullerene derivatives: model building studies and experimental verification , 1993 .

[76]  B. Berne,et al.  Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals , 1993 .

[77]  Barnett,et al.  Born-Oppenheimer molecular-dynamics simulations of finite systems: Structure and dynamics of (H2O)2. , 1993, Physical review. B, Condensed matter.

[78]  Cho,et al.  Wavelets in electronic structure calculations. , 1993, Physical review letters.

[79]  Arieh Warshel,et al.  Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches , 1993 .

[80]  D. Vanderbilt,et al.  Theory of polarization of crystalline solids. , 1993, Physical review. B, Condensed matter.

[81]  Kari Laasonen,et al.  ‘‘Ab initio’’ liquid water , 1993 .

[82]  P. Madden,et al.  Order N ab initio Molecular Dynamics with an Orbital-Free Density Functional , 1993 .

[83]  D. J. Tildesley,et al.  Computer simulation in chemical physics, NATO ASI Series C , 1993 .

[84]  B. Berne,et al.  A Born–Oppenheimer approximation for path integrals with an application to electron solvation in polarizable fluids , 1993 .

[85]  Lee,et al.  Ab initio studies on the structural and dynamical properties of ice. , 1993, Physical review. B, Condensed matter.

[86]  C. Wilkins,et al.  Synthesis of a fullerene derivative for the inhibition of HIV enzymes , 1993 .

[87]  Jianshu Cao,et al.  A new perspective on quantum time correlation functions , 1993 .

[88]  Martin,et al.  Unconstrained minimization approach for electronic computations that scales linearly with system size. , 1993, Physical review. B, Condensed matter.

[89]  Alavi,et al.  Ab initio molecular dynamics with excited electrons. , 1994, Physical review letters.

[90]  M. Klein,et al.  STRUCTURAL STUDY OF (H2O)20 AND (H2O)21H+ USING DENSITY FUNCTIONAL METHODS , 1994 .

[91]  T. Taylor,et al.  Allomyces in the Devonian , 1994, Nature.

[92]  Galli,et al.  Electronic-structure calculations and molecular-dynamics simulations with linear system-size scaling. , 1994, Physical review. B, Condensed matter.

[93]  M. Parrinello,et al.  Ab initio simulations of water and water ions , 1994 .

[94]  Raffaele Resta,et al.  MACROSCOPIC POLARIZATION IN CRYSTALLINE DIELECTRICS : THE GEOMETRIC PHASE APPROACH , 1994 .

[95]  Jianshu Cao,et al.  The formulation of quantum statistical mechanics based on the Feynman path centroid density. II. Dynamical properties , 1994 .

[96]  S. Scheiner,et al.  Excited-State Energetics and Proton-Transfer Barriers in Malonaldehyde , 1994 .

[97]  Michele Parrinello,et al.  Ab initio path-integral molecular dynamics , 1994 .

[98]  White,et al.  Implementation of gradient-corrected exchange-correlation potentials in Car-Parrinello total-energy calculations. , 1994, Physical review. B, Condensed matter.

[99]  Blöchl,et al.  Projector augmented-wave method. , 1994, Physical review. B, Condensed matter.

[100]  M. Klein,et al.  Ab initio molecular dynamics study of hydrochloric acid in water , 1994 .

[101]  M. Parrinello,et al.  Properties of supercritical water: an ab initio simulation , 1994 .

[102]  Kari Laasonen,et al.  Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water , 1995 .

[103]  Kari Laasonen,et al.  Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- ions in water , 1995 .

[104]  X. Gonze,et al.  Adiabatic density-functional perturbation theory. , 1995, Physical review. A, Atomic, molecular, and optical physics.

[105]  Superconducting domain walls from a supersymmetric action. , 1995, Physical review. D, Particles and fields.

[106]  E. Carter,et al.  Full Configuration Interaction Molecular Dynamics of Na2 and Na3 , 1995 .

[107]  M. Parrinello,et al.  Integrating the Car–Parrinello equations. III. Techniques for ultrasoft pseudopotentials , 1995 .

[108]  N. Agmon,et al.  The Grotthuss mechanism , 1995 .

[109]  Carla Andreani,et al.  Microscopic structure of low temperature liquid ammonia: A neutron diffraction experiment , 1995 .

[110]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[111]  Mark E. Tuckerman,et al.  Ab Initio Molecular Dynamics Simulations , 1996 .

[112]  Bernard R. Brooks,et al.  ENZYME MECHANISMS WITH HYBRID QUANTUM AND MOLECULAR MECHANICAL POTENTIALS.I. THEORETICAL CONSIDERATIONS , 1996 .

[113]  M. Parrinello,et al.  AB INITIO PATH INTEGRAL MOLECULAR DYNAMICS : BASIC IDEAS , 1996 .

[114]  Louie,et al.  Magnetic susceptibility of insulators from first principles. , 1996, Physical review letters.

[115]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[116]  Michele Parrinello,et al.  Efficient and general algorithms for path integral Car–Parrinello molecular dynamics , 1996 .

[117]  R. Schmidt,et al.  Non-adiabatic quantum molecular dynamics: basic formalism and case study , 1996 .

[118]  Michiel Sprik,et al.  Ab initio molecular dynamics simulation of liquid water: Comparison of three gradient‐corrected density functionals , 1996 .

[119]  Louie,et al.  Ab Initio Theory of NMR Chemical Shifts in Solids and Liquids. , 1996, Physical review letters.

[120]  Jean-Louis Rivail,et al.  HYBRID CLASSICAL QUANTUM FORCE FIELD FOR MODELING VERY LARGE MOLECULES , 1996 .

[121]  Ab initio molecular dynamics study of dilute hydrofluoric acid , 1996 .

[122]  Madden,et al.  Further orbital-free kinetic-energy functionals for ab initio molecular dynamics. , 1996, Physical review. B, Condensed matter.

[123]  M. Klein,et al.  Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A. , 1996, Biophysical journal.

[124]  Parrinello,et al.  New high-pressure phase of ice. , 1996, Physical review letters.

[125]  Anisotropic a-C:H from compression of polyacetylene. , 1996, Physical review letters.

[126]  Ab-initio simulation of phase transformations under pressure , 1996 .

[127]  Alan K. Soper,et al.  Empirical potential Monte Carlo simulation of fluid structure , 1996 .

[128]  N. Marzari,et al.  Maximally localized generalized Wannier functions for composite energy bands , 1997, cond-mat/9707145.

[129]  Bernd G. Pfrommer,et al.  {ital Ab initio} NMR Chemical Shift of Diamond, Chemical-Vapor-Deposited Diamond, and Amorphous Carbon , 1997 .

[130]  Michele Parrinello,et al.  From silicon to RNA: The coming of age of ab initio molecular dynamics , 1997 .

[131]  M. Gillan.  The virtual matter laboratory , 1997 .

[132]  M. Parrinello,et al.  Ab initio infrared spectrum of liquid water , 1997 .

[133]  Dennis R. Salahub,et al.  Hydrogen-bonding in glycine and malonaldehyde: Performance of the Lap1 correlation functional , 1997 .

[134]  Noam Agmon.  Estimation of the hydrogen-bond lengths to H3O+ and H5O2+ in liquid water , 1997 .

[135]  Nailong Wu.  The Maximum Entropy Method , 1997 .

[136]  J. Stebbins,et al.  NMR evidence for excess non-bridging oxygen in an aluminosilicate glass , 1997, Nature.

[137]  R. Car,et al.  Structure and hyperfine parameters of E'(1) centers in a-quartz and in vitreous SiO2 , 1997 .

[138]  R. Car,et al.  DYNAMICAL CHARGE TENSORS AND INFRARED SPECTRUM OF AMORPHOUS SIO2 , 1997 .

[139]  Michele Parrinello,et al.  A hybrid Gaussian and plane wave density functional scheme , 1997 .

[140]  F. Mota,et al.  Structure of the First Solvation Shell of the Hydroxide Anion. A Model Study Using OH-(H2O)n (n = 4, 5, 6, 7, 11, 17) Clusters , 1997 .

[141]  M. Klein,et al.  Ab initio study of aqueous hydrochloric acid , 1997 .

[142]  Alfredo Pasquarello,et al.  Origin of the High-Frequency Doublet in the Vibrational Spectrum of Vitreous SiO2 , 1997, Science.

[143]  Alan K. Soper,et al.  Site–site pair correlation functions of water from 25 to 400 °C: Revised analysis of new and old diffraction data , 1997 .

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

[145]  Structural chemistry: Oxygen bridges in molten glass , 1997, Nature.

[146]  C. Dellago,et al.  Transition path sampling and the calculation of rate constants , 1998 .

[147]  R. Resta,et al.  Quantum-Mechanical Position Operator in Extended Systems , 1998 .

[148]  Mark E. Tuckerman,et al.  Quantum Nuclear ab Initio Molecular Dynamics Study of Water Wires , 1998 .

[149]  Emily A. Carter,et al.  Orbital-free kinetic-energy functionals for the nearly free electron gas , 1998 .

[150]  M. Parrinello,et al.  The dissociation mechanism of H2O in water studied by first-principles molecular dynamics , 1998 .

[151]  H. Jónsson,et al.  Molecular multipole moments of water molecules in ice Ih , 1998 .

[152]  Kiyoyuki Terakura,et al.  First Principles Molecular Dynamics Study of Ziegler−Natta Heterogeneous Catalysis , 1998 .

[153]  Alfredo Pasquarello,et al.  Identification of Raman defect lines as signatures of ring structures in vitreous silica , 1998 .

[154]  Bernd G. Pfrommer,et al.  NMR Chemical Shifts in Hard Carbon Nitride Compounds , 1998 .

[155]  M. Parrinello,et al.  Molecular dynamics in low-spin excited states , 1998 .

[156]  Ab initio pseudopotentials for orbital-free density functionals , 1998 .

[157]  Ab initio molecular dynamics study of the reaction of water with formaldehyde in sulfuric acid solution. , 1998 .

[158]  Michiel Sprik,et al.  Free energy from constrained molecular dynamics , 1998 .

[159]  M. Parrinello,et al.  Tunnelling and zero-point motion in high-pressure ice , 1998, Nature.

[160]  V. Heine,et al.  Thermodynamics of Al/Al avoidance in the ordering of Al/Si tetrahedral framework structures , 1998 .

[161]  M. Parrinello,et al.  Ab Initio Infrared Absorption Study of the Hydrogen-Bond Symmetrization in Ice , 1998 .

[162]  Andreoni,et al.  The chemistry of water on alumina surfaces: reaction dynamics from first principles , 1998, Science.

[163]  K. Laasonen,et al.  Ab initio study of gas-phase sulphuric acid hydrates containing 1 to 3 water molecules , 1998 .

[164]  R. Car,et al.  Dynamic structure factor of vitreous silica from first principles: Comparison to neutron-inelastic-scattering experiments , 1998 .

[165]  Paul Tavan,et al.  A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields , 1999 .

[166]  C. H. Mak,et al.  A multilevel blocking approach to the sign problem in real-time quantum Monte Carlo simulations , 1999 .

[167]  M. Tsukada,et al.  Density-functional study of liquid methanol , 1999 .

[168]  P. Sipos,et al.  Dielectric Relaxation of Dilute Aqueous NaOH, NaAl(OH)4, and NaB(OH)4 , 1999 .

[169]  A. Soper,et al.  The structure of liquid methanol revisited: a neutron diffraction experiment at −80 °C and +25 °C , 1999 .

[170]  U. Rothlisberger,et al.  Ab initio molecular dynamics studies of a synthetic biomimetic model of galactose oxidase , 1999 .

[171]  M. Parrinello,et al.  The role of quantum effects and ionic defects in high-density ice , 1999 .

[172]  Mark E. Tuckerman,et al.  Quantum dynamics via adiabatic ab initio centroid molecular dynamics , 1999 .

[173]  Vittorio Rosato,et al.  An high performance Fortran implementation of a Tight-Binding Molecular Dynamics simulation , 1999 .

[174]  R. Car,et al.  Intermediate range order and bonding character in disordered network-forming systems , 1999 .

[175]  J. Tse,et al.  Catalysis of the reaction HCl+HOCl→H2O+Cl2 on an ice surface , 1999 .

[176]  Density-functional theory study of the catalytic oxidation of CO over transition metal surfaces , 1999, cond-mat/9905341.

[177]  M. Parrinello,et al.  The nature of the hydrated excess proton in water , 1999, Nature.

[178]  A. Alavi,et al.  The electrostatic properties of water molecules in condensed phases: an ab initio study , 1999 .

[179]  Evolution of Fragments Formed at the Rupture of a Knotted Alkane Molecule , 1999, cond-mat/9910219.

[180]  A. Marco Saitta,et al.  Influence of a knot on the strength of a polymer strand , 1999, Nature.

[181]  G. Voth,et al.  Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations , 1999 .

[182]  Tai-Sung Lee,et al.  A pseudobond approach to combining quantum mechanical and molecular mechanical methods , 1999 .

[183]  H. Jauslin,et al.  Grid methods and Hilbert space basis for simulations of quantum dynamics , 1999 .

[184]  Milan Hodošček,et al.  A Hybrid QM−MM Potential Employing Hartree−Fock or Density Functional Methods in the Quantum Region , 1999 .

[185]  Pier Luigi Silvestrelli,et al.  Maximally localized Wannier functions for simulations with supercells of general symmetry , 1999 .

[186]  Mark E. Tuckerman,et al.  A reciprocal space based method for treating long range interactions in ab initio and force-field-based calculations in clusters , 1999 .

[187]  SIGNATURE OF SURFACE STATES ON NMR CHEMICAL SHIFTS : A THEORETICAL PREDICTION , 1999 .

[188]  Christoph Dellago,et al.  On the calculation of reaction rate constants in the transition path ensemble , 1999 .

[189]  Michele Parrinello,et al.  Water Molecule Dipole in the Gas and in the Liquid Phase , 1999 .

[190]  J. Stebbins,et al.  The degree of aluminum avoidance in aluminosilicate glasses , 1999 .

[191]  Noam Agmon,et al.  Proton Solvation and Proton Mobility , 1999 .

[192]  M. Tuckerman,et al.  Simulation studies of liquid ammonia by classical ab initio, classical, and path-integral molecular dynamics , 1999 .

[193]  A. Marco Saitta,et al.  Polyethylene under tensil load: Strain energy storage and breaking of linear and knotted alkanes probed by first-principles molecular dynamics calculations , 1999 .

[194]  Thomas Gregor,et al.  A comparison of methods for the calculation of NMR chemical shifts , 1999 .

[195]  M. Parrinello,et al.  Solvated excess protons in water: quantum effects on the hydration structure , 2000 .

[196]  Matthias Krack,et al.  All-electron ab-initio molecular dynamics , 2000 .

[197]  Michele Parrinello,et al.  General and efficient algorithms for obtaining maximally localized Wannier functions , 2000 .

[198]  Christoph Dellago,et al.  Ab initio analysis of proton transfer dynamics in (H2O)3H , 2000 .

[199]  Michele Parrinello,et al.  First‐principles molecular dynamics simulations of models for the myoglobin active center , 2000 .

[200]  Bernd G. Pfrommer,et al.  NMR chemical shifts of ice and liquid water: The effects of condensation , 2000 .

[201]  M. Parrinello,et al.  First principles study of propene polymerization in Ziegler-Natta heterogeneous catalysis , 2000 .

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

[203]  A. Curioni,et al.  First-Principles Molecular Dynamics Simulations of H 2 O on α-Al 2 O 3 (0001) , 2000 .

[204]  M. Sprik.  Computation of the pK of liquid water using coordination constraints , 2000 .

[205]  S. Okazaki,et al.  Path integral molecular dynamics for Bose–Einstein and Fermi–Dirac statistics , 2000 .

[206]  M. Klein,et al.  Ab Initio Molecular Dynamics Study of the Superacid System SbF5/HF Solution , 2000 .

[207]  Dennis R. Salahub,et al.  New τ-dependent correlation functional combined with a modified Becke exchange , 2000 .

[208]  Daniel Sebastiani,et al.  Generalized variational density functional perturbation theory , 2000 .

[209]  Axel D. Becke,et al.  Simulation of delocalized exchange by local density functionals , 2000 .

[210]  Alan K. Soper,et al.  The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa , 2000 .

[211]  Bernd G. Pfrommer,et al.  Si-O-Si bond-angle distribution in vitreous silica from first-principles 29 Si NMR analysis , 2000 .

[212]  Mark E. Tuckerman,et al.  Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers , 2000 .

[213]  Paolo Carloni,et al.  Conformational flexibility of the catalytic Asp dyad in HIV‐1 protease: An ab initio study on the free enzyme , 2000, Proteins.

[214]  Noam Agmon.  Mechanism of hydroxide mobility , 2000 .

[215]  Weitao Yang,et al.  Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface , 2000 .

[216]  M. Parrinello,et al.  A Density Functional Theory Study of a Silica-Supported Zirconium Monohydride Catalyst for Depolymerization of Polyethylene , 2000 .

[217]  Greg L. Hura,et al.  What can x-ray scattering tell us about the radial distribution functions of water? , 2000 .

[218]  D. Salahub,et al.  Using a classical potential as an efficient importance function for sampling from an ab initio potential , 2000 .

[219]  C. Dellago,et al.  Autoionization in Liquid Water , 2001, Science.

[220]  M. Tuckerman,et al.  Heavy-atom skeleton quantization and proton tunneling in "intermediate-barrier" hydrogen bonds. , 2001, Physical review letters.

[221]  G. Scuseria,et al.  Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals , 2001 .

[222]  Radu Iftimie,et al.  Efficient ab initio sampling methods in rate constant calculations for proton-transfer reactions , 2001 .

[223]  M. Parrinello,et al.  A First Principles Exploration of a Variety of Active Surfaces and Catalytic Sites in Ziegler−Natta Heterogeneous Catalysis , 2001 .

[224]  Mark E. Tuckerman,et al.  Protonic Defects in Hydrogen Bonded Liquids: Structure and Dynamics in Ammonia and Comparison with Water† , 2001 .

[225]  Structural properties of molten silicates from ab initio molecular-dynamics simulations: Comparison between (formula presented) and (formula presented) , 2001, cond-mat/0109267.

[226]  J. A. Hernando.  Density functional theory in the canonical ensemble: I. General formalism , 2001 .

[227]  Daniel Sebastiani,et al.  A New ab-Initio Approach for NMR Chemical Shifts in Periodic Systems , 2001 .

[228]  Francesco Mauri,et al.  All-electron magnetic response with pseudopotentials: NMR chemical shifts , 2001 .

[229]  M. Parrinello,et al.  Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site. , 2001, Journal of the American Chemical Society.

[230]  N. Handy,et al.  Left-right correlation energy , 2001 .

[231]  R. Iftimie,et al.  Reaction mechanism and isotope effects derived from centroid transition state theory in intramolecular proton transfer reactions , 2001 .

[232]  Dawn A. Yarne,et al.  A dual length scale method for plane-wave-based, simulation studies of chemical systems modeled using mixed ab initio/empirical force field descriptions , 2001 .

[233]  First-Principles Molecular Dynamics Study of the Rupture Processes of a Bulklike Polyethylene Knot , 2001 .

[234]  F. Gygi,et al.  Dissociation of water under pressure. , 2001, Physical review letters.

[235]  Alessandro Curioni,et al.  DFT-based molecular dynamics as a new tool for computational biology: First applications and perspective , 2001, IBM J. Res. Dev..

[236]  B. Berne,et al.  Quantum time correlation functions from complex time Monte Carlo simulations: A maximum entropy approach , 2001 .

[237]  M Eichinger,et al.  Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study. , 2001, Biophysical journal.

[238]  Nicholas C. Handy,et al.  A dynamical correlation functional , 2002 .

[239]  M. Tuckerman,et al.  On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles , 2002 .

[240]  First-principles theory of the EPR g tensor in solids: defects in quartz. , 2001, Physical review letters.

[241]  M. V. Ganduglia-Pirovano,et al.  Catalysis and corrosion: the theoretical surface-science context , 2002 .

[242]  Sergey N. Maximoff,et al.  Functionals of quantities other than the electron density: Approximations to the exchange energy , 2002 .

[243]  Alessandro Laio,et al.  A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations , 2002 .

[244]  Tucker Carrington,et al.  A general framework for discrete variable representation basis sets , 2002 .

[245]  A. Gross,et al.  Quantum theory of dissociative chemisorption on metal surfaces. , 2002, Accounts of chemical research.

[246]  Why are insulators insulating and metals conducting , 2002 .

[247]  Mark E. Tuckerman,et al.  A new reciprocal space based treatment of long range interactions on surfaces , 2002 .

[248]  Roberto Car,et al.  Introduction to density-functional theory and ab-initio molecular dynamics , 2002 .

[249]  M. Tuckerman,et al.  Ab Initio Molecular Dynamics Investigation of the Concentration Dependence of Charged Defect Transport in Basic Solutions via Calculation of the Infrared Spectrum , 2002 .

[250]  M. Klein,et al.  First-principles study of aqueous hydroxide solutions. , 2002, Journal of the American Chemical Society.

[251]  N. Doltsinis,et al.  Nonadiabatic Car-Parrinello molecular dynamics. , 2002, Physical review letters.

[252]  M. Parrinello,et al.  The nature and transport mechanism of hydrated hydroxide ions in aqueous solution , 2002, Nature.

[253]  G. Voth,et al.  Car–Parrinello molecular dynamics simulation of liquid water: New results , 2002 .

[254]  Qin Wu,et al.  Empirical correction to density functional theory for van der Waals interactions , 2002 .

[255]  Michele Parrinello,et al.  Anharmonic Raman spectra in high-pressure ice from ab initio simulations. , 2002, Physical review letters.

[256]  Tamar Schlick,et al.  Computational Methods for Macromolecules: Challenges and Applications , 2002 .

[257]  David R. Bowler,et al.  Recent progress in linear scaling ab initio electronic structure techniques , 2002 .

[258]  Joseph A Morrone,et al.  Ab initio molecular dynamics study of proton mobility in liquid methanol , 2002 .

[259]  Stefan Grimme,et al.  Comparison of multireference Møller-Plesset theory and time-dependent methods for the calculation of vertical excitation energies of molecules , 2002 .