Incorporating Electronic Information into Machine Learning Potential Energy Surfaces via Approaching the Ground-State Electronic Energy as a Function of Atom-Based Electronic Populations.

Machine Learning (ML) approximations to Density Functional Theory (DFT) potential energy surfaces (PESs) are showing great promise for reducing the computational cost of accurate molecular simulations, but at present they are not applicable to varying electronic states, and in particular, they are not well suited for molecular systems in which the local electronic structure is sensitive to the medium to long-range electronic environment. With this issue as the focal point, we present a new Machine Learning approach called "BpopNN" for obtaining efficient approximations to DFT PESs. Conceptually, the methodology is based on approaching the true DFT energy as a function of electron populations on atoms; in practice, this is realized with available density functionals and constrained DFT (CDFT). The new approach creates approximations to this function with neural networks. These approximations thereby incorporate electronic information naturally into a ML approach, and optimizing the model energy with respect to populations allows the electronic terms to self-consistently adapt to the environment, as in DFT. We confirm the effectiveness of this approach with a variety of calculations on LinHn clusters.

[1]  P. Dugourd,et al.  Dissociation pathways and binding energies of (LiH)nLi+ and (LiH)nLi+3 clusters , 1996 .

[2]  Jörg Behler,et al.  A Full-Dimensional Neural Network Potential-Energy Surface for Water Clusters up to the Hexamer , 2013 .

[3]  Martin Winter,et al.  The Solid Electrolyte Interphase – The Most Important and the Least Understood Solid Electrolyte in Rechargeable Li Batteries , 2009 .

[4]  Andrea Grisafi,et al.  Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems. , 2017, Physical review letters.

[5]  Ryo Nagai,et al.  Completing density functional theory by machine learning hidden messages from molecules , 2019, npj Computational Materials.

[6]  E Weinan,et al.  DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics , 2017, Comput. Phys. Commun..

[7]  Nongnuch Artrith,et al.  High-dimensional neural-network potentials for multicomponent systems: Applications to zinc oxide , 2011 .

[8]  M. Galizio JEAB: past, present, and future. , 2019, Journal of the experimental analysis of behavior.

[9]  Sebastian Dick,et al.  Machine learning accurate exchange and correlation functionals of the electronic density , 2020, Nature Communications.

[10]  T. Voorhis,et al.  Direct optimization method to study constrained systems within density-functional theory , 2005 .

[11]  John C. Snyder,et al.  Orbital-free bond breaking via machine learning. , 2013, The Journal of chemical physics.

[12]  P. Balbuena,et al.  Theoretical studies to understand surface chemistry on carbon anodes for lithium-ion batteries: reduction mechanisms of ethylene carbonate. , 2001, Journal of the American Chemical Society.

[13]  Dmitrij Rappoport,et al.  Property-optimized gaussian basis sets for molecular response calculations. , 2010, The Journal of chemical physics.

[14]  Weitao Yang,et al.  Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks. , 2016, Journal of chemical theory and computation.

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

[16]  P. Schleyer,et al.  Lithium chemistry : a theoretical and experimental overview , 1995 .

[17]  Kondo‐François Aguey‐Zinsou,et al.  Direct and reversible hydrogen storage of lithium hydride (LiH) nanoconfined in high surface area graphite , 2016 .

[18]  Volker L. Deringer,et al.  Understanding the thermal properties of amorphous solids using machine-learning-based interatomic potentials , 2018 .

[19]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[20]  Michele Ceriotti,et al.  A Data-Driven Construction of the Periodic Table of the Elements , 2018, 1807.00236.

[21]  T. Morawietz,et al.  A density-functional theory-based neural network potential for water clusters including van der Waals corrections. , 2013, The journal of physical chemistry. A.

[22]  Swapan K. Pati,et al.  Novel properties of graphene nanoribbons: a review , 2010 .

[23]  K-R Müller,et al.  SchNet - A deep learning architecture for molecules and materials. , 2017, The Journal of chemical physics.

[24]  K. Houk,et al.  Oligoacenes: theoretical prediction of open-shell singlet diradical ground states. , 2004, Journal of the American Chemical Society.

[25]  Tristan Bereau,et al.  Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules. , 2015, Journal of chemical theory and computation.

[26]  Johann Gasteiger,et al.  Electronegativity equalization: application and parametrization , 1985 .

[27]  T. Van Voorhis,et al.  Constrained density functional theory. , 2011, Chemical reviews.

[28]  A. Chaffee,et al.  Charge Equilibration Based on Atomic Ionization in Metal–Organic Frameworks , 2015 .

[29]  Wolfram Koch,et al.  A Chemist's Guide to Density Functional Theory , 2000 .

[30]  M. Marques,et al.  Recent advances and applications of machine learning in solid-state materials science , 2019, npj Computational Materials.

[31]  O. Kühn,et al.  Chapter 6. Electron Transfer , 2007 .

[32]  Stefan Blügel,et al.  Ground States of Constrained Systems: Application to Cerium Impurities , 1984 .

[33]  Volker L. Deringer,et al.  Machine learning based interatomic potential for amorphous carbon , 2016, 1611.03277.

[34]  Samuel S. Schoenholz,et al.  Neural Message Passing for Quantum Chemistry , 2017, ICML.

[35]  R. Marcus,et al.  Electron transfers in chemistry and biology , 1985 .

[36]  Jiahao Chen,et al.  QTPIE: Charge transfer with polarization current equalization. A fluctuating charge model with correct asymptotics , 2007, 0807.2068.

[37]  Electronic properties of doped fullerenes , 2001 .

[38]  Kun Yao,et al.  Kinetic Energy of Hydrocarbons as a Function of Electron Density and Convolutional Neural Networks. , 2015, Journal of chemical theory and computation.

[39]  U. Stalmach,et al.  Effective conjugation length and UV/vis spectra of oligomers , 1997 .

[40]  Single-centre expansion of Gaussian basis functions and the angular decomposition of their overlap integrals , 1989 .

[41]  Klaus-Robert Müller,et al.  Finding Density Functionals with Machine Learning , 2011, Physical review letters.

[42]  Alexie M. Kolpak,et al.  Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods , 2017, Scientific Reports.

[43]  Jun Chen,et al.  Communication: Fitting potential energy surfaces with fundamental invariant neural network. , 2016, The Journal of chemical physics.

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

[45]  Alberto Fabrizio,et al.  Transferable Machine-Learning Model of the Electron Density , 2018, ACS central science.

[46]  Stefan Goedecker,et al.  Interatomic potentials for ionic systems with density functional accuracy based on charge densities obtained by a neural network , 2015, 1501.07344.

[47]  Donald G. Truhlar,et al.  Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods , 2010 .

[48]  M. Allendorf,et al.  Tuning metal hydride thermodynamics via size and composition: Li-H, Mg-H, Al-H, and Mg-Al-H nanoclusters for hydrogen storage. , 2012, Physical chemistry chemical physics : PCCP.

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

[50]  Weitao Yang,et al.  Force Field for Water Based on Neural Network. , 2018, The journal of physical chemistry letters.

[51]  Gerbrand Ceder,et al.  Constructing first-principles phase diagrams of amorphous LixSi using machine-learning-assisted sampling with an evolutionary algorithm. , 2018, The Journal of chemical physics.

[52]  Shyue Ping Ong,et al.  An electrostatic spectral neighbor analysis potential for lithium nitride , 2019, npj Computational Materials.

[53]  Volker L. Deringer,et al.  Machine Learning Interatomic Potentials as Emerging Tools for Materials Science , 2019, Advanced materials.

[54]  K. Müller,et al.  Fast and accurate modeling of molecular atomization energies with machine learning. , 2011, Physical review letters.

[55]  B. Rao,et al.  Molecular cluster calculations of the electronic structure of lithium hydride , 1986 .

[56]  Andrea Grisafi,et al.  Incorporating long-range physics in atomic-scale machine learning. , 2019, The Journal of chemical physics.

[57]  K. Sanui,et al.  Estimate of the effective conjugation length of polythiophene from its|χ(3)(ω;ω,ω,−ω)|spectrum at excitonic resonance , 1998 .

[58]  Yuanqing Wang,et al.  Graph Nets for Partial Charge Prediction , 2019, ArXiv.

[59]  R. A. Nistor,et al.  A generalization of the charge equilibration method for nonmetallic materials. , 2006, The Journal of chemical physics.

[60]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[61]  W. Goddard,et al.  Charge equilibration for molecular dynamics simulations , 1991 .

[62]  John E Herr,et al.  Metadynamics for training neural network model chemistries: A competitive assessment. , 2017, The Journal of chemical physics.

[63]  K. Ishikawa,et al.  Time-dependent multiconfiguration self-consistent-field method based on the occupation-restricted multiple-active-space model for multielectron dynamics in intense laser fields , 2014, 1411.3077.

[64]  M. Gillan,et al.  Calculation of properties of crystalline lithium hydride using correlated wave function theory , 2009 .

[65]  T Verstraelen,et al.  ACKS2: atom-condensed Kohn-Sham DFT approximated to second order. , 2013, The Journal of chemical physics.

[66]  David W Toth,et al.  The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics , 2017, Chemical science.

[67]  Adrian E. Roitberg,et al.  Less is more: sampling chemical space with active learning , 2018, The Journal of chemical physics.

[68]  A. Becke A multicenter numerical integration scheme for polyatomic molecules , 1988 .

[69]  Antonio Díaz Pozuelo High-dimensional neural network potentials , 2016 .

[70]  K. Fukui,et al.  Horizons of Quantum Chemistry , 1980 .

[71]  S. Harder Molecular early main group metal hydrides: synthetic challenge, structures and applications. , 2012, Chemical communications.

[72]  Kipton Barros,et al.  Learning molecular energies using localized graph kernels. , 2016, The Journal of chemical physics.

[73]  Markus Meuwly,et al.  PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges. , 2019, Journal of chemical theory and computation.

[74]  Volker L. Deringer,et al.  Growth Mechanism and Origin of High sp^{3} Content in Tetrahedral Amorphous Carbon. , 2018, Physical review letters.

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

[76]  John E. Herr,et al.  Compressing physics with an autoencoder: Creating an atomic species representation to improve machine learning models in the chemical sciences. , 2019, The Journal of chemical physics.

[77]  D. Jérome Organic Conductors: From Charge Density Wave TTF—TCNQ to Superconducting (TMTSF)2PF6 , 2005 .

[78]  D. Banabic,et al.  Recent advances and applications , 2004 .

[79]  B. Tidor Molecular dynamics simulations , 1997, Current Biology.

[80]  Qin Wu,et al.  Direct calculation of electron transfer parameters through constrained density functional theory. , 2006, The journal of physical chemistry. A.

[81]  Liwu Huang,et al.  Synthesis of destabilized nanostructured lithium hydride via hydrogenation of lithium electrochemically inserted into graphite , 2015 .

[82]  Alexandre Tkatchenko,et al.  Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning. , 2017, The Journal of chemical physics.

[83]  A. Stasch Well-defined, nanometer-sized LiH cluster compounds stabilized by pyrazolate ligands. , 2014, Angewandte Chemie.

[84]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[85]  Paul L. A. Popelier,et al.  A polarizable high-rank quantum topological electrostatic potential developed using neural networks: Molecular dynamics simulations on the hydrogen fluoride dimer , 2007 .

[86]  M. Frisch,et al.  Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields , 1994 .

[87]  Anand Chandrasekaran,et al.  Solving the electronic structure problem with machine learning , 2019, npj Computational Materials.

[88]  M. Levy Universal variational functionals of electron densities, first-order density matrices, and natural spin-orbitals and solution of the v-representability problem. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

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

[90]  M. Head‐Gordon,et al.  Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. , 2008, Physical chemistry chemical physics : PCCP.

[91]  Hong Li,et al.  Review on modeling of the anode solid electrolyte interphase (SEI) for lithium-ion batteries , 2018, npj Computational Materials.

[92]  Mengyun Nie,et al.  Lithium Ion Battery Graphite Solid Electrolyte Interphase Revealed by Microscopy and Spectroscopy , 2013 .

[93]  Li Li,et al.  Bypassing the Kohn-Sham equations with machine learning , 2016, Nature Communications.

[94]  Alireza Khorshidi,et al.  Amp: A modular approach to machine learning in atomistic simulations , 2016, Comput. Phys. Commun..

[95]  Christian Trott,et al.  Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials , 2014, J. Comput. Phys..

[96]  Alán Aspuru-Guzik,et al.  Advances in molecular quantum chemistry contained in the Q-Chem 4 program package , 2014, Molecular Physics.

[97]  Wibe A. de Jong,et al.  Prediction of Atomization Energy Using Graph Kernel and Active Learning , 2018, The Journal of chemical physics.

[98]  Cheng Shang,et al.  LASP: Fast global potential energy surface exploration , 2019, WIREs Computational Molecular Science.

[99]  Emanuel Peled,et al.  The Electrochemical Behavior of Alkali and Alkaline Earth Metals in Nonaqueous Battery Systems—The Solid Electrolyte Interphase Model , 1979 .

[100]  Chi Chen,et al.  Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals , 2018, Chemistry of Materials.

[101]  Stefan Grimme,et al.  Effect of the damping function in dispersion corrected density functional theory , 2011, J. Comput. Chem..

[102]  J S Smith,et al.  ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost , 2016, Chemical science.

[103]  Kipton Barros,et al.  Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning , 2019, Nature Communications.

[104]  Anders S. Christensen,et al.  Alchemical and structural distribution based representation for universal quantum machine learning. , 2017, The Journal of chemical physics.

[105]  Gábor Csányi,et al.  Edge-functionalized and substitutionally doped graphene nanoribbons: Electronic and spin properties , 2007, Physical Review B.

[106]  Y. Aso,et al.  Synthesis and spectroscopic properties of a series of beta-blocked long oligothiophenes up to the 96-mer: revaluation of effective conjugation length. , 2003, Journal of the American Chemical Society.

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

[108]  G. R. Schleder,et al.  From DFT to machine learning: recent approaches to materials science–a review , 2019, Journal of Physics: Materials.

[109]  Gerbrand Ceder,et al.  Efficient and accurate machine-learning interpolation of atomic energies in compositions with many species , 2017, 1706.06293.

[110]  K. Müller,et al.  Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space , 2015, The journal of physical chemistry letters.

[111]  Kristof T. Schütt,et al.  Unifying machine learning and quantum chemistry with a deep neural network for molecular wavefunctions , 2019, Nature Communications.

[112]  Michael Gastegger,et al.  Machine learning molecular dynamics for the simulation of infrared spectra† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc02267k , 2017, Chemical science.

[113]  Garnet Kin-Lic Chan,et al.  The radical character of the acenes: a density matrix renormalization group study. , 2007, The Journal of chemical physics.

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

[115]  William A Goddard,et al.  Polarizable charge equilibration model for predicting accurate electrostatic interactions in molecules and solids. , 2017, The Journal of chemical physics.

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

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

[118]  Oded Hod,et al.  Electronic structure and stability of semiconducting graphene nanoribbons. , 2006, Nano letters.

[119]  Li Li,et al.  Understanding Machine-learned Density Functionals , 2014, ArXiv.

[120]  T. Inabe,et al.  What Happens at the Interface between TTF and TCNQ Crystals (TTF = Tetrathiafulvalene and TCNQ = 7,7,8,8-Tetracyanoquinodimethane)? , 2012 .

[121]  Yoshua Bengio,et al.  Deep Sparse Rectifier Neural Networks , 2011, AISTATS.

[122]  Klaus-Robert Müller,et al.  Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies. , 2013, Journal of chemical theory and computation.

[123]  V. Ozoliņš,et al.  First-principles calculated decomposition pathways for LiBH4 nanoclusters , 2016, Scientific Reports.

[124]  Sereina Riniker,et al.  Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations , 2018, J. Chem. Inf. Model..

[125]  Randall Q Snurr,et al.  An Extended Charge Equilibration Method. , 2012, The journal of physical chemistry letters.

[126]  John E. Herr,et al.  Intrinsic Bond Energies from a Bonds-in-Molecules Neural Network. , 2017, The journal of physical chemistry letters.

[127]  Jonathan Schmidt,et al.  Machine Learning the Physical Nonlocal Exchange-Correlation Functional of Density-Functional Theory. , 2019, The journal of physical chemistry letters.