QuanPol: A full spectrum and seamless QM/MM program

The quantum chemistry polarizable force field program (QuanPol) is implemented to perform combined quantum mechanical and molecular mechanical (QM/MM) calculations with induced dipole polarizable force fields and induced surface charge continuum solvation models. The QM methods include Hartree–Fock method, density functional theory method (DFT), generalized valence bond theory method, multiconfiguration self‐consistent field method, Møller–Plesset perturbation theory method, and time‐dependent DFT method. The induced dipoles of the MM atoms and the induced surface charges of the continuum solvation model are self‐consistently and variationally determined together with the QM wavefunction. The MM force field methods can be user specified, or a standard force field such as MMFF94, Chemistry at Harvard Molecular Mechanics (CHARMM), Assisted Model Building with Energy Refinement (AMBER), and Optimized Potentials for Liquid Simulations‐All Atom (OPLS‐AA). Analytic gradients for all of these methods are implemented so geometry optimization and molecular dynamics (MD) simulation can be performed. MD free energy perturbation and umbrella sampling methods are also implemented. © 2013 Wiley Periodicals, Inc.

[1]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[2]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[3]  Michael W. Schmidt,et al.  Scalable implementation of analytic gradients for second-order Z-averaged perturbation theory using the distributed data interface. , 2006, The Journal of chemical physics.

[4]  Piet Th. van Duijnen,et al.  A discrete solvent reaction field model for calculating molecular linear response properties in solution , 2003 .

[5]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[6]  F.J.Olivares del Valle,et al.  ASEP/MD: A program for the calculation of solvent effects combining QM/MM methods and the mean field approximation ☆ , 2003 .

[7]  Donald G Truhlar,et al.  Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. , 2005, The journal of physical chemistry. A.

[8]  Thomas A. Halgren,et al.  Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 , 1996, J. Comput. Chem..

[9]  Thomas A. Halgren,et al.  Merck molecular force field. IV. conformational energies and geometries for MMFF94 , 1996 .

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

[11]  Hui Li,et al.  Note: FixSol solvation model and FIXPVA2 tessellation scheme. , 2012, The Journal of chemical physics.

[12]  G. Torrie,et al.  Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid , 1974 .

[13]  Jean-Joseph Max,et al.  Infrared Spectroscopy of Aqueous Carboxylic Acids: Comparison between Different Acids and Their Salts , 2004 .

[14]  Dennis R. Salahub,et al.  Molecular excitation energies to high-lying bound states from time-dependent density-functional response theory: Characterization and correction of the time-dependent local density approximation ionization threshold , 1998 .

[15]  M. Plesset,et al.  Note on an Approximation Treatment for Many-Electron Systems , 1934 .

[16]  R. Zwanzig.  High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .

[17]  B. Roos,et al.  The complete active space SCF (CASSCF) method in a Newton–Raphson formulation with application to the HNO molecule , 1981 .

[18]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[19]  G. Voth,et al.  Flexible simple point-charge water model with improved liquid-state properties. , 2006, The Journal of chemical physics.

[20]  Hui Li,et al.  Analytic energy gradient in combined time-dependent density functional theory and polarizable force field calculation. , 2010, The Journal of chemical physics.

[21]  Tjerk P. Straatsma,et al.  NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations , 2010, Comput. Phys. Commun..

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

[23]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[24]  J Andrew McCammon,et al.  Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method. , 2008, The Journal of chemical physics.

[25]  Hui Li,et al.  Analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculation. , 2011, The Journal of chemical physics.

[26]  Jiali Gao,et al.  Solvatochromic Shifts of the n → π* Transition of Acetone from Steam Vapor to Ambient Aqueous Solution:  A Combined Configuration Interaction QM/MM Simulation Study Incorporating Solvent Polarization. , 2007, Journal of chemical theory and computation.

[27]  Jan H. Jensen,et al.  Continuum solvation of large molecules described by QM/MM: a semi-iterative implementation of the PCM/EFP interface , 2003 .

[28]  Weitao Yang,et al.  QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase. , 2007, Journal of chemical theory and computation.

[29]  T. Halgren,et al.  Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules , 1996 .

[30]  Jiali Gao,et al.  Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model , 1997, J. Comput. Chem..

[31]  Hui Li,et al.  Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation , 2004, J. Comput. Chem..

[32]  S. Grzesiek,et al.  Determination of a high‐precision NMR structure of the minicollagen cysteine rich domain from Hydra and characterization of its disulfide bond formation , 2004, FEBS letters.

[33]  F. Jensen.  Locating transition structures by mode following: A comparison of six methods on the Ar8 Lennard‐Jones potential , 1995 .

[34]  T. Halgren.  Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions , 1996 .

[35]  Manuel F. Ruiz-López,et al.  A QM/MM/continuum model for computations in solution: Comparison with QM/MM molecular dynamics simulations , 2001 .

[36]  J. A. V. BUTLER,et al.  Advances in Protein Chemistry , 1946, Nature.

[37]  Roland H. Hertwig,et al.  On the parameterization of the local correlation functional. What is Becke-3-LYP? , 1997 .

[38]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[39]  P. Kollman,et al.  Encyclopedia of computational chemistry , 1998 .

[40]  Hui Li,et al.  Excited state geometry of photoactive yellow protein chromophore: a combined conductorlike polarizable continuum model and time-dependent density functional study. , 2010, The Journal of chemical physics.

[41]  Ranbir Singh,et al.  J. Mol. Struct. (Theochem) , 1996 .

[42]  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.

[43]  Jiali Gao.  Monte Carlo Quantum Mechanical-Configuration Interaction and Molecular Mechanics Simulation of Solvent Effects on the n .fwdarw. .pi.* Blue Shift of Acetone , 1994 .

[44]  Arieh Warshel,et al.  Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event , 2001 .

[45]  Julian Tirado-Rives,et al.  Molecular modeling of organic and biomolecular systems using BOSS and MCPRO , 2005, J. Comput. Chem..

[46]  D. Vernon.  Inform , 1995, Encyclopedia of the UN Sustainable Development Goals.

[47]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

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

[49]  U. Singh,et al.  Development of a quantum mechanics-based free-energy perturbation method: use in the calculation of relative solvation free energies. , 2004, Journal of the American Chemical Society.

[50]  Arieh Warshel,et al.  Calculations of chemical processes in solutions , 1979 .

[51]  M. E. Casida.  Time-Dependent Density Functional Response Theory for Molecules , 1995 .

[52]  M. Gordon,et al.  A systematic multireference perturbation-theory study of the low-lying states of SiC3. , 2006, The Journal of chemical physics.

[53]  David Beeman,et al.  Some Multistep Methods for Use in Molecular Dynamics Calculations , 1976 .

[54]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[55]  Hui Li.  Analytic energy gradient in combined second-order Møller-Plesset perturbation theory and polarizable force field calculation. , 2011, The journal of physical chemistry. A.

[56]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[57]  Solvation of large dipoles A molecular dynamics study II. , 1978 .

[58]  Wei Zhang,et al.  Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides , 2006, J. Comput. Chem..

[59]  M. A. Aguilar,et al.  Study of solvent effects by means of averaged solvent electrostatic potentials obtained from molecular dynamics data , 1997 .

[60]  R. McKay,et al.  Solution structure of Cu6 metallothionein from the fungus Neurospora crassa. , 2004, European journal of biochemistry.

[61]  Mark S. Gordon,et al.  Parallel Unrestricted MP2 Analytic Gradients Using the Distributed Data Interface , 2004 .

[62]  P. P. Ewald.  Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .

[63]  Bobby G. Sumpter,et al.  Efficient computation of potential energy first and second derivatives for molecular dynamics, normal coordinate analysis, and molecular mechanics calculations† , 1996 .

[64]  G. Torrie,et al.  Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .

[65]  Walter Thiel,et al.  QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.

[66]  V. Barone,et al.  Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model , 1998 .

[67]  Ian J. Bush,et al.  The GAMESS-UK electronic structure package: algorithms, developments and applications , 2005 .

[68]  Mark S. Gordon,et al.  An effective fragment method for modeling solvent effects in quantum mechanical calculations , 1996 .

[69]  Bernard R. Brooks,et al.  CHARMMing: A New, Flexible Web Portal for CHARMM , 2008, J. Chem. Inf. Model..

[70]  Mark S. Gordon,et al.  A derivation of the frozen-orbital unrestricted open-shell and restricted closed-shell second-order perturbation theory analytic gradient expressions , 2003 .

[71]  J. Ponder,et al.  An efficient newton‐like method for molecular mechanics energy minimization of large molecules , 1987 .

[72]  Frank H. Stillinger,et al.  Polarization model for water and its ionic dissociation products , 1978 .

[73]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[74]  Klaus Ruedenberg,et al.  Identification of deadwood in configuration spaces through general direct configuration interaction , 2001 .

[75]  Steven G. Johnson,et al.  The Design and Implementation of FFTW3 , 2005, Proceedings of the IEEE.

[76]  H. Nakano,et al.  Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent. , 2012, The Journal of chemical physics.

[77]  Joseph Ivanic,et al.  A MCSCF method for ground and excited states based on full optimizations of successive Jacobi rotations , 2003, J. Comput. Chem..

[78]  Gregory K. Schenter,et al.  Excited States of the Bacteriochlorophyll b Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization , 1995 .

[79]  Hui Li,et al.  Mean field QM/MM method: average position approximation. , 2013, The Journal of chemical physics.

[80]  W. Goddard,et al.  Generalized valence bond description of bonding in low-lying states of molecules , 1973 .

[81]  Alexander D. MacKerell,et al.  Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations , 2004, J. Comput. Chem..

[82]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[83]  Kazuya Ishimura,et al.  New parallel algorithm for MP2 energy gradient calculations , 2007, J. Comput. Chem..

[84]  M. Delepierre,et al.  Pharmacological and structural characterization of long-sarafotoxins, a new family of endothelin-like peptides: Role of the C-terminus extension. , 2012, Biochimie.

[85]  Mark Earl Casida,et al.  In Recent Advances in Density-Functional Methods , 1995 .

[86]  Y. Maréchal.  IR spectra of carboxylic acids in the gas phase: A quantitative reinvestigation , 1987 .

[87]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[88]  A. Warshel,et al.  Microscopic Calculations of Solvent Effects on Absorption Spectra of Conjugated Molecules , 1991 .

[89]  Arieh Warshel,et al.  Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution. , 2008, The journal of physical chemistry. B.

[90]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

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

[92]  Franz J. Vesely,et al.  N-particle dynamics of polarizable Stockmayer-type molecules , 1977 .

[93]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[94]  Kimihiko Hirao,et al.  An efficient state-specific scheme of time-dependent density functional theory , 2006 .

[95]  Hui Li,et al.  Quantum mechanical/molecular mechanical/continuum style solvation model: linear response theory, variational treatment, and nuclear gradients. , 2009, The Journal of chemical physics.

[96]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[97]  Mark S. Gordon,et al.  A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO) , 2004, J. Comput. Chem..

[98]  M. Aguilar,et al.  A mean field approach that combines quantum mechanics and molecular dynamics simulation: the water molecule in liquid water , 1998 .

[99]  Stefan Boresch,et al.  The Role of Bonded Terms in Free Energy Simulations. 2. Calculation of Their Influence on Free Energy Differences of Solvation , 1999 .

[100]  H. C. Andersen.  Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations , 1983 .

[101]  F. Matthias Bickelhaupt,et al.  Chemistry with ADF , 2001, J. Comput. Chem..

[102]  Jiali Gao,et al.  Solvent effects on the nπ* transition of pyrimidine in aqueous solution , 1997 .

[103]  S. Rick.  A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums. , 2004, The Journal of chemical physics.

[104]  Kurt V. Mikkelsen,et al.  The combined multiconfigurational self-consistent-field/molecular mechanics wave function approach , 2001 .

[105]  D. Chong.  Recent Advances in Density Functional Methods Part III , 2002 .

[106]  Qiang Cui,et al.  Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical methods: A critical test with glycine , 2002 .

[107]  S. C. Rogers,et al.  QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis , 2003 .

[108]  J. W. Neidigh,et al.  Designing a 20-residue protein , 2002, Nature Structural Biology.

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

[110]  Jacob Kongsted,et al.  Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde. , 2007, The Journal of chemical physics.

[111]  David Fincham,et al.  Molecular dynamics simulation using the cray-1 vector processing computer , 1981 .

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

[113]  Wei Yang,et al.  Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials. , 2004, The Journal of chemical physics.

[114]  T. Cheatham,et al.  Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise * , 2000, Biopolymers.

[115]  Alexander D. MacKerell,et al.  CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields , 2009, J. Comput. Chem..

[116]  Michael J. Frisch,et al.  A direct MP2 gradient method , 1990 .

[117]  Michael W. Mahoney,et al.  A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions , 2000 .

[118]  Mark S. Gordon,et al.  The Distributed Data Interface in GAMESS , 2000 .

[119]  Kimihiko Hirao,et al.  Excited state geometry optimizations by analytical energy gradient of long-range corrected time-dependent density functional theory. , 2006, The Journal of chemical physics.

[120]  J. E. Quinn,et al.  Cooperative effects in simulated water , 1979, Nature.

[121]  J. Kästner.  Umbrella sampling , 2011 .

[122]  A. Klamt,et al.  COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient , 1993 .

[123]  Jacopo Tomasi,et al.  An Integrated Effective Fragment—Polarizable Continuum Approach to Solvation: Theory and Application to Glycine , 2002 .

[124]  Shawn T. Brown,et al.  Advances in methods and algorithms in a modern quantum chemistry program package. , 2006, Physical chemistry chemical physics : PCCP.

[125]  Yaoqi Zhou,et al.  Protein motions at zero-total angular momentum: the importance of long-range correlations. , 2000, Biophysical journal.

[126]  Bernard R. Brooks,et al.  Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method , 2002 .

[127]  Mark S. Gordon,et al.  Gradient of the ZAPT2 energy , 2002 .

[128]  David A. Pearlman,et al.  A Comparison of Alternative Approaches to Free Energy Calculations , 1994 .

[129]  Greg L. Hura,et al.  Water structure from scattering experiments and simulation. , 2002, Chemical reviews.

[130]  Kazuya Ishimura,et al.  A new parallel algorithm of MP2 energy calculations , 2006, J. Comput. Chem..

[131]  M. Thompson,et al.  QM/MMpol: A Consistent Model for Solute/Solvent Polarization. Application to the Aqueous Solvation and Spectroscopy of Formaldehyde, Acetaldehyde, and Acetone , 1996 .

[132]  L. Verlet.  Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[133]  H. C. Andersen.  Molecular dynamics simulations at constant pressure and/or temperature , 1980 .

[134]  Mark S. Gordon,et al.  DEVELOPMENTS IN PARALLEL ELECTRONIC STRUCTURE THEORY , 2007 .

[135]  M. Gordon,et al.  Solvent effects on optical properties of molecules: a combined time-dependent density functional theory/effective fragment potential approach. , 2008, The Journal of chemical physics.

[136]  Yingkai Zhang,et al.  Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods. , 2005, The Journal of chemical physics.