Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions.

The accurate representation of multidimensional potential energy surfaces is a necessary requirement for realistic computer simulations of molecular systems. The continued increase in computer power accompanied by advances in correlated electronic structure methods nowadays enables routine calculations of accurate interaction energies for small systems, which can then be used as references for the development of analytical potential energy functions (PEFs) rigorously derived from many-body (MB) expansions. Building on the accuracy of the MB-pol many-body PEF, we investigate here the performance of permutationally invariant polynomials (PIPs), neural networks, and Gaussian approximation potentials (GAPs) in representing water two-body and three-body interaction energies, denoting the resulting potentials PIP-MB-pol, Behler-Parrinello neural network-MB-pol, and GAP-MB-pol, respectively. Our analysis shows that all three analytical representations exhibit similar levels of accuracy in reproducing both two-body and three-body reference data as well as interaction energies of small water clusters obtained from calculations carried out at the coupled cluster level of theory, the current gold standard for chemical accuracy. These results demonstrate the synergy between interatomic potentials formulated in terms of a many-body expansion, such as MB-pol, that are physically sound and transferable, and machine-learning techniques that provide a flexible framework to approximate the short-range interaction energy terms.

[1]  F. R. Parker,et al.  Monte Carlo Equation of State of Molecules Interacting with the Lennard‐Jones Potential. I. A Supercritical Isotherm at about Twice the Critical Temperature , 1957 .

[2]  Francesco Paesani,et al.  Exploring Electrostatic Effects on the Hydrogen Bond Network of Liquid Water through Many-Body Molecular Dynamics. , 2016, The journal of physical chemistry. B.

[3]  R. Kondor,et al.  On representing chemical environments , 2012, 1209.3140.

[4]  P. Mankoo,et al.  The vibrational proton potential in bulk liquid water and ice. , 2008, The Journal of chemical physics.

[5]  Michele Parrinello,et al.  Simplifying the representation of complex free-energy landscapes using sketch-map , 2011, Proceedings of the National Academy of Sciences.

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

[7]  Petros Drineas,et al.  CUR matrix decompositions for improved data analysis , 2009, Proceedings of the National Academy of Sciences.

[8]  Gábor Csányi,et al.  Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions , 2016, Chemical reviews.

[9]  Berhane Temelso,et al.  Benchmark structures and binding energies of small water clusters with anharmonicity corrections. , 2011, The journal of physical chemistry. A.

[10]  Francesco Paesani,et al.  Getting the Right Answers for the Right Reasons: Toward Predictive Molecular Simulations of Water with Many-Body Potential Energy Functions. , 2016, Accounts of chemical research.

[11]  Sotiris S. Xantheas,et al.  Development of transferable interaction models for water. III. Reparametrization of an all-atom polarizable rigid model (TTM2–R) from first principles , 2002 .

[12]  Jörg Behler,et al.  Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link Between Experiments. , 2016, The journal of physical chemistry letters.

[13]  Volodymyr Babin,et al.  Development of a "First-Principles" Water Potential with Flexible Monomers. III. Liquid Phase Properties. , 2014, Journal of chemical theory and computation.

[14]  J. Pablo.,et al.  Dinámica del volteo de bloques en taludes rocosos , 2020 .

[15]  Gregory S. Tschumper,et al.  CCSD(T) complete basis set limit relative energies for low-lying water hexamer structures. , 2009, The journal of physical chemistry. A.

[16]  Giorgina Corongiu,et al.  Molecular dynamics simulations of liquid water using the NCC ab initio potential , 1990 .

[17]  E. Clementi,et al.  Preliminary observations on a new water–water potential , 2009 .

[18]  V. Babin,et al.  Development of a "First Principles" Water Potential with Flexible Monomers. II: Trimer Potential Energy Surface, Third Virial Coefficient, and Small Clusters. , 2014, Journal of chemical theory and computation.

[19]  Francesco Paesani,et al.  Dissecting the Molecular Structure of the Air/Water Interface from Quantum Simulations of the Sum-Frequency Generation Spectrum. , 2016, Journal of the American Chemical Society.

[20]  Lie,et al.  Molecular-dynamics simulation of liquid water with an ab initio flexible water-water interaction potential. , 1986, Physical review. A, General physics.

[21]  Bertrand Guillot,et al.  A reappraisal of what we have learnt during three decades of computer simulations on water , 2002 .

[22]  Joel M. Bowman,et al.  Permutationally invariant potential energy surfaces in high dimensionality , 2009 .

[23]  Thomas E. Markland,et al.  Competing quantum effects in the dynamics of a flexible water model. , 2009, The Journal of chemical physics.

[24]  Hans-Joachim Werner,et al.  A simple and efficient CCSD(T)-F12 approximation. , 2007, The Journal of chemical physics.

[25]  Joel M. Bowman,et al.  Flexible, ab initio potential, and dipole moment surfaces for water. I. Tests and applications for clusters up to the 22-mer. , 2011, The Journal of chemical physics.

[26]  Michele Ceriotti,et al.  Mapping and classifying molecules from a high-throughput structural database , 2016, Journal of Cheminformatics.

[27]  Volodymyr Babin,et al.  A Critical Assessment of Two-Body and Three-Body Interactions in Water. , 2012, Journal of chemical theory and computation.

[28]  L. Dang,et al.  MOLECULAR DYNAMICS STUDY OF WATER CLUSTERS, LIQUID, AND LIQUID-VAPOR INTERFACE OF WATER WITH MANY-BODY POTENTIALS , 1997 .

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

[30]  Noam Bernstein,et al.  Machine learning unifies the modeling of materials and molecules , 2017, Science Advances.

[31]  Volodymyr Babin,et al.  Toward a Universal Water Model: First Principles Simulations from the Dimer to the Liquid Phase. , 2012, The journal of physical chemistry letters.

[32]  S. Xantheas,et al.  Development of transferable interaction models for water. I. Prominent features of the water dimer potential energy surface , 2002 .

[33]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[34]  Harry Partridge,et al.  The determination of an accurate isotope dependent potential energy surface for water from extensive ab initio calculations and experimental data , 1997 .

[35]  P. Kollman,et al.  Water–water and water–ion potential functions including terms for many body effects , 1985 .

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

[37]  Sandra E Brown,et al.  Monitoring Water Clusters "Melt" Through Vibrational Spectroscopy. , 2017, Journal of the American Chemical Society.

[38]  Robert J. Harrison,et al.  Development of transferable interaction models for water. II. Accurate energetics of the first few water clusters from first principles , 2002 .

[39]  Volodymyr Babin,et al.  Development of a "First Principles" Water Potential with Flexible Monomers: Dimer Potential Energy Surface, VRT Spectrum, and Second Virial Coefficient. , 2014, Journal of chemical theory and computation.

[40]  T. Morawietz,et al.  How van der Waals interactions determine the unique properties of water , 2016, Proceedings of the National Academy of Sciences.

[41]  Francesco Paesani,et al.  Molecular Origin of the Vibrational Structure of Ice Ih. , 2017, The journal of physical chemistry letters.

[42]  B. Alder,et al.  Studies in Molecular Dynamics. II. Behavior of a Small Number of Elastic Spheres , 1960 .

[43]  Gábor Csányi,et al.  Comparing molecules and solids across structural and alchemical space. , 2015, Physical chemistry chemical physics : PCCP.

[44]  Wei Zhang,et al.  An accurate and simple quantum model for liquid water. , 2006, The Journal of chemical physics.

[45]  Frederick R. Manby,et al.  Machine-learning approach for one- and two-body corrections to density functional theory: Applications to molecular and condensed water , 2013 .

[46]  Michele Parrinello,et al.  Generalized neural-network representation of high-dimensional potential-energy surfaces. , 2007, Physical review letters.

[47]  John E Herr,et al.  The many-body expansion combined with neural networks. , 2016, The Journal of chemical physics.

[48]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[49]  T. Cheatham,et al.  Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations , 2008, The journal of physical chemistry. B.

[50]  D. Wales,et al.  Structure and torsional dynamics of the water octamer from THz laser spectroscopy near 215 μm , 2016, Science.

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

[52]  F. Stillinger,et al.  Molecular Dynamics Study of Liquid Water , 1971 .

[53]  O. Matsuoka,et al.  CI study of the water dimer potential surface , 1976 .

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

[55]  K. Kitaura,et al.  A new form for intermolecular potential energy functions , 1987 .

[56]  Alexander P. Lyubartsev,et al.  Determination of effective pair potentials from ab initio simulations: application to liquid water , 2000 .

[57]  B. Montgomery Pettitt,et al.  Simple intramolecular model potentials for water , 1987 .

[58]  J. Behler First Principles Neural Network Potentials for Reactive Simulations of Large Molecular and Condensed Systems. , 2017, Angewandte Chemie.

[59]  Krzysztof Szalewicz,et al.  Predictions of the Properties of Water from First Principles , 2007, Science.

[60]  Aditya Kamath,et al.  Neural networks vs Gaussian process regression for representing potential energy surfaces: A comparative study of fit quality and vibrational spectrum accuracy. , 2018, The Journal of chemical physics.

[61]  F. Paesani,et al.  A refined MS-EVB model for proton transport in aqueous environments. , 2012, The journal of physical chemistry. B.

[62]  Andreas W Götz,et al.  On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice. , 2016, The Journal of chemical physics.

[63]  Josh E. Campbell,et al.  Machine learning for the structure–energy–property landscapes of molecular crystals† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04665k , 2017, Chemical science.

[64]  I. Shvab,et al.  Atomistic water models: Aqueous thermodynamic properties from ambient to supercritical conditions , 2016 .

[65]  Pengyu Y. Ren,et al.  Systematic improvement of a classical molecular model of water. , 2013, The journal of physical chemistry. B.

[66]  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 .

[67]  Carlos Vega,et al.  Simulating water with rigid non-polarizable models: a general perspective. , 2011, Physical chemistry chemical physics : PCCP.

[68]  Jörg Behler,et al.  Constructing high‐dimensional neural network potentials: A tutorial review , 2015 .

[69]  Sotiris S Xantheas,et al.  Development of transferable interaction potentials for water. V. Extension of the flexible, polarizable, Thole-type model potential (TTM3-F, v. 3.0) to describe the vibrational spectra of water clusters and liquid water. , 2008, The Journal of chemical physics.

[70]  Wojciech Cencek,et al.  Interaction energies of large clusters from many-body expansion. , 2011, The Journal of chemical physics.

[71]  J. A. Barker,et al.  Structure of water; A Monte Carlo calculation , 1969 .

[72]  Zhen Xie,et al.  Permutationally Invariant Polynomial Basis for Molecular Energy Surface Fitting via Monomial Symmetrization. , 2010, Journal of chemical theory and computation.

[73]  Brooks H. Pate,et al.  Concerted hydrogen-bond breaking by quantum tunneling in the water hexamer prism , 2016, Science.

[74]  Francesco Paesani,et al.  Infrared and Raman Spectroscopy of Liquid Water through "First-Principles" Many-Body Molecular Dynamics. , 2015, Journal of chemical theory and computation.

[75]  Sotiris S. Xantheas,et al.  Development of transferable interaction models for water. IV. A flexible, all-atom polarizable potential (TTM2-F) based on geometry dependent charges derived from an ab initio monomer dipole moment surface , 2002 .

[76]  Andreas W Götz,et al.  On the representation of many-body interactions in water. , 2015, The Journal of chemical physics.

[77]  Gábor Csányi,et al.  Gaussian approximation potentials: A brief tutorial introduction , 2015, 1502.01366.

[78]  P. Ball Water as an active constituent in cell biology. , 2008, Chemical reviews.

[79]  Christopher Knight,et al.  Many-Body Interactions in Ice. , 2017, Journal of chemical theory and computation.

[80]  Greg L. Hura,et al.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. , 2004, The Journal of chemical physics.

[81]  J. Behler Atom-centered symmetry functions for constructing high-dimensional neural network potentials. , 2011, The Journal of chemical physics.

[82]  DAVID M. FERGUSON,et al.  Parameterization and evaluation of a flexible water model , 1995, J. Comput. Chem..

[83]  Michele Parrinello,et al.  Demonstrating the Transferability and the Descriptive Power of Sketch-Map. , 2013, Journal of chemical theory and computation.

[84]  Hans-Joachim Werner,et al.  Systematically convergent basis sets for explicitly correlated wavefunctions: the atoms H, He, B-Ne, and Al-Ar. , 2008, The Journal of chemical physics.

[85]  Daniel J. Rosenkrantz,et al.  An Analysis of Several Heuristics for the Traveling Salesman Problem , 1977, SIAM J. Comput..

[86]  R. Kondor,et al.  Gaussian approximation potentials: the accuracy of quantum mechanics, without the electrons. , 2009, Physical review letters.

[87]  Henry S. Frank,et al.  Ion-solvent interaction. Structural aspects of ion-solvent interaction in aqueous solutions: a suggested picture of water structure , 1957 .