Condensed Phase Water Molecular Multipole Moments from Deep Neural Network Models Trained on Ab Initio Simulation Data

Shi, Yu; Doyle, Carrie C.; Beck, Thomas L.

doi:10.1021/acs.jpclett.1c02328

Title: Condensed Phase Water Molecular Multipole Moments from Deep Neural Network Models Trained on Ab Initio Simulation Data

Journal Article · Mon Oct 18 00:00:00 EDT 2021 · Journal of Physical Chemistry Letters

DOI:https://doi.org/10.1021/acs.jpclett.1c02328· OSTI ID:1958367

^[1]; Doyle, Carrie C. ^[1];

^[1]

Univ. of Cincinnati, OH (United States)

Ionic solvation phenomena in liquids involve intense interactions in the inner solvation shell. For interactions beyond the first shell, the ion–solvent interaction energies result from the sum of many smaller-magnitude contributions that can still include polarization effects. Deep neural network (DNN) methods have recently found wide application in developing efficient molecular models that maintain near-quantum accuracy. In this work, we extend the DeePMD-kit code to produce accurate molecular multipole moments in the bulk and near interfaces. The new method is validated by comparing the DNN moments with those generated by ab initio simulations. The moments are used to compute the electrostatic potential at the center of a molecular-sized hydrophobic cavity in water. The results show that the fields produced by the DNN models are in quantitative agreement with the AIMD-derived values. These efficient methods will open the door to more accurate solvation models for large solutes such as proteins.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF)

Grant/Contract Number:: AC05-00OR22725; CHE-1565632; CHE-1955161

OSTI ID:: 1958367

Journal Information:: Journal of Physical Chemistry Letters, Vol. 12, Issue 42; ISSN 1948-7185

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (46)

Generalized Gradient Approximation Made Simple Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868 https://doi.org/10.1103/PhysRevLett.77.3865	journal	October 1996
Examination of the Electrochemical Interface between Two Immiscible Electrolyte Solutions by Second Harmonic Generation Conboy, John C.; Richmond, Geraldine L. The Journal of Physical Chemistry B, Vol. 101, Issue 6 https://doi.org/10.1021/jp962775t	journal	February 1997
Structural, electronic, and bonding properties of liquid water from first principles Silvestrelli, Pier Luigi; Parrinello, Michele The Journal of Chemical Physics, Vol. 111, Issue 8 https://doi.org/10.1063/1.479638	journal	August 1999
Deep neural network for the dielectric response of insulators Zhang, Linfeng; Chen, Mohan; Wu, Xifan Physical Review B, Vol. 102, Issue 4 https://doi.org/10.1103/PhysRevB.102.041121	journal	July 2020
The present state of affairs with Hofmeister effects Kunz, W.; Lo Nostro, P.; Ninham, B. W. Current Opinion in Colloid & Interface Science, Vol. 9, Issue 1-2 https://doi.org/10.1016/j.cocis.2004.05.004	journal	August 2004
Absolute ion hydration free energy scale and the surface potential of water via quantum simulation Shi, Yu; Beck, Thomas L. Proceedings of the National Academy of Sciences, Vol. 117, Issue 48 https://doi.org/10.1073/pnas.2017214117	journal	November 2020
Quasichemical analysis of the cluster-pair approximation for the thermodynamics of proton hydration Pollard, Travis; Beck, Thomas L. The Journal of Chemical Physics, Vol. 140, Issue 22 https://doi.org/10.1063/1.4881602	journal	June 2014
The Potential Distribution Theorem and Models of Molecular Solutions Beck, Tom L.; Paulaitis, Michael E.; Pratt, Lawrence R. Cambridge University Press https://doi.org/10.1017/CBO9780511536663	book	January 2006
Molecular multipole moments of water molecules in ice Ih Batista, Enrique R.; Xantheas, Sotiris S.; Jónsson, Hannes The Journal of Chemical Physics, Vol. 109, Issue 11 https://doi.org/10.1063/1.477058	journal	September 1998
Pushing the Limit of Molecular Dynamics with Ab Initio Accuracy to 100 Million Atoms with Machine Learning Jia, Weile; Wang, Han; Chen, Mohan SC20: International Conference for High Performance Computing, Networking, Storage and Analysis https://doi.org/10.1109/SC41405.2020.00009	conference	November 2020
Communication: Regularizing binding energy distributions and thermodynamics of hydration: Theory and application to water modeled with classical and ab initio simulations Weber, Valéry; Merchant, Safir; Asthagiri, D. The Journal of Chemical Physics, Vol. 135, Issue 18 https://doi.org/10.1063/1.3660205	journal	November 2011
Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges Ceriotti, Michele; Fang, Wei; Kusalik, Peter G. Chemical Reviews, Vol. 116, Issue 13 https://doi.org/10.1021/acs.chemrev.5b00674	journal	April 2016
DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics Wang, Han; Zhang, Linfeng; Han, Jiequn Computer Physics Communications, Vol. 228 https://doi.org/10.1016/j.cpc.2018.03.016	journal	July 2018
Accurate description of van der Waals complexes by density functional theory including empirical corrections Grimme, Stefan Journal of Computational Chemistry, Vol. 25, Issue 12 https://doi.org/10.1002/jcc.20078	journal	January 2004
Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations Sagui, Celeste; Pomorski, Pawel; Darden, Thomas A. The Journal of Chemical Physics, Vol. 120, Issue 9 https://doi.org/10.1063/1.1644800	journal	March 2004
The Water Dipole Moment in Water Clusters Gregory, J. K. Science, Vol. 275, Issue 5301 https://doi.org/10.1126/science.275.5301.814	journal	February 1997
The vapor-liquid interface potential of (multi)polar fluids and its influence on ion solvation Horváth, Lorand; Beu, Titus; Manghi, Manoel The Journal of Chemical Physics, Vol. 138, Issue 15 https://doi.org/10.1063/1.4799938	journal	April 2013
Dielectric Behavior near a Spherical Ion Lee, Min-Sang; Singer, Sherwin J. The Journal of Physical Chemistry B, Vol. 125, Issue 9 https://doi.org/10.1021/acs.jpcb.0c10760	journal	March 2021
Magnetic Properties and Molecular Quadrupole Tensor of the Water Molecule by Beam‐Maser Zeeman Spectroscopy Verhoeven, J.; Dymanus, A. The Journal of Chemical Physics, Vol. 52, Issue 6 https://doi.org/10.1063/1.1673462	journal	March 1970
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu Grimme, Stefan; Antony, Jens; Ehrlich, Stephan The Journal of Chemical Physics, Vol. 132, Issue 15 https://doi.org/10.1063/1.3382344	journal	April 2010
Single ion hydration free energies: A consistent comparison between experiment and classical molecular simulation Ashbaugh, Henry S.; Asthagiri, D. The Journal of Chemical Physics, Vol. 129, Issue 20 https://doi.org/10.1063/1.3013865	journal	November 2008
The Role of Broken Symmetry in Solvation of a Spherical Cavity in Classical and Quantum Water Models Remsing, Richard C.; Baer, Marcel D.; Schenter, Gregory K. The Journal of Physical Chemistry Letters, Vol. 5, Issue 16 https://doi.org/10.1021/jz501067w	journal	July 2014
The Importance of the Water Molecular Quadrupole for Estimating Interfacial Potential Shifts Acting on Ions Near the Liquid–Vapor Interface Doyle, Carrie C.; Shi, Yu; Beck, Thomas L. The Journal of Physical Chemistry B, Vol. 123, Issue 15 https://doi.org/10.1021/acs.jpcb.9b01289	journal	March 2019
Convergence of Molecular and Macroscopic Continuum Descriptions of Ion Hydration Ashbaugh, Henry S. The Journal of Physical Chemistry B, Vol. 104, Issue 31 https://doi.org/10.1021/jp0015067	journal	August 2000
Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases VandeVondele, Joost; Hutter, Jürg The Journal of Chemical Physics, Vol. 127, Issue 11 https://doi.org/10.1063/1.2770708	journal	September 2007
Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh Brown, W. Michael; Kohlmeyer, Axel; Plimpton, Steven J. Computer Physics Communications, Vol. 183, Issue 3 https://doi.org/10.1016/j.cpc.2011.10.012	journal	March 2012
Comment on ‘‘Study on the liquid–vapor interface of water. I. Simulation results of thermodynamic properties and orientational structure’’ Wilson, Michael A.; Pohorille, Andrew; Pratt, Lawrence R. The Journal of Chemical Physics, Vol. 90, Issue 9 https://doi.org/10.1063/1.456536	journal	May 1989
A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods VandeVondele, Joost; Sprik, Michiel Physical Chemistry Chemical Physics, Vol. 7, Issue 7 https://doi.org/10.1039/b501603g	journal	January 2005
A Local Entropic Signature of Specific Ion Hydration Beck, Thomas L. The Journal of Physical Chemistry B, Vol. 115, Issue 32 https://doi.org/10.1021/jp204883h	journal	August 2011
Bronsted basicity of the air-water interface Mishra, H.; Enami, S.; Nielsen, R. J. Proceedings of the National Academy of Sciences, Vol. 109, Issue 46 https://doi.org/10.1073/pnas.1209307109	journal	October 2012
Nosé–Hoover chains: The canonical ensemble via continuous dynamics Martyna, Glenn J.; Klein, Michael L.; Tuckerman, Mark The Journal of Chemical Physics, Vol. 97, Issue 4 https://doi.org/10.1063/1.463940	journal	August 1992
Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K. The Journal of Chemical Physics, Vol. 147, Issue 16 https://doi.org/10.1063/1.4994912	journal	October 2017
Length scales and interfacial potentials in ion hydration Shi, Yu; Beck, Thomas L. The Journal of Chemical Physics, Vol. 139, Issue 4 https://doi.org/10.1063/1.4814070	journal	July 2013
Water Molecule Dipole in the Gas and in the Liquid Phase Silvestrelli, Pier Luigi; Parrinello, Michele Physical Review Letters, Vol. 82, Issue 16 https://doi.org/10.1103/PhysRevLett.82.3308	journal	April 1999
Charge and Electric Field Fluctuations in Aqueous NaCl Electrolytes Sellner, Bernhard; Valiev, Marat; Kathmann, Shawn M. The Journal of Physical Chemistry B, Vol. 117, Issue 37 https://doi.org/10.1021/jp405578w	journal	August 2013
Ion selectivity from local configurations of ligands in solutions and ion channels Asthagiri, D.; Dixit, P. D.; Merchant, S. Chemical Physics Letters, Vol. 485, Issue 1-3 https://doi.org/10.1016/j.cplett.2009.12.013	journal	January 2010
Toward a quantitative theory of Hofmeister phenomena: From quantum effects to thermodynamics Pollard, Travis P.; Beck, Thomas L. Current Opinion in Colloid & Interface Science, Vol. 23 https://doi.org/10.1016/j.cocis.2016.06.015	journal	June 2016
Spontaneous generation of hydrogen peroxide from aqueous microdroplets Lee, Jae Kyoo; Walker, Katherine L.; Han, Hyun Soo Proceedings of the National Academy of Sciences, Vol. 116, Issue 39 https://doi.org/10.1073/pnas.1911883116	journal	August 2019
Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion–protein interactions Collins, Kim D. Biophysical Chemistry, Vol. 167 https://doi.org/10.1016/j.bpc.2012.04.002	journal	June 2012
Nonlinear dielectric response of polar liquids Matyushov, Dmitry V. The Journal of Chemical Physics, Vol. 142, Issue 24 https://doi.org/10.1063/1.4922933	journal	June 2015
Hofmeister Phenomena: An Update on Ion Specificity in Biology Lo Nostro, Pierandrea; Ninham, Barry W. Chemical Reviews, Vol. 112, Issue 4 https://doi.org/10.1021/cr200271j	journal	January 2012
Quadrupole-mediated dielectric response and the charge-asymmetric solvation of ions in water Cox, Stephen J.; Mandadapu, Kranthi K.; Geissler, Phillip L. The Journal of Chemical Physics, Vol. 154, Issue 24 https://doi.org/10.1063/5.0051399	journal	June 2021
Dipole moment of water from Stark measurements of H ₂ O, HDO, and D ₂ O Clough, Shepard A.; Beers, Yardley; Klein, Gerald P. The Journal of Chemical Physics, Vol. 59, Issue 5 https://doi.org/10.1063/1.1680328	journal	September 1973
Free Energy of Ionic Hydration Hummer, Gerhard; Pratt, Lawrence R.; García, Angel E. The Journal of Physical Chemistry, Vol. 100, Issue 4 https://doi.org/10.1021/jp951011v	journal	January 1996
Active learning of uniformly accurate interatomic potentials for materials simulation Zhang, Linfeng; Lin, De-Ye; Wang, Han Physical Review Materials, Vol. 3, Issue 2 https://doi.org/10.1103/PhysRevMaterials.3.023804	journal	February 2019
The thermodynamics of proton hydration and the electrochemical surface potential of water Pollard, Travis P.; Beck, Thomas L. The Journal of Chemical Physics, Vol. 141, Issue 18 https://doi.org/10.1063/1.4896217	journal	November 2014

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Title: Condensed Phase Water Molecular Multipole Moments from Deep Neural Network Models Trained on Ab Initio Simulation Data

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