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Symons BCB, Bane MK, Popelier PLA. DL_FFLUX: A Parallel, Quantum Chemical Topology Force Field. J Chem Theory Comput 2021; 17:7043-7055. [PMID: 34617748 PMCID: PMC8582247 DOI: 10.1021/acs.jctc.1c00595] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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DL_FFLUX is a force
field based on quantum chemical topology that
can perform molecular dynamics for flexible molecules endowed with
polarizable atomic multipole moments (up to hexadecapole). Using the
machine learning method kriging (aka Gaussian process regression),
DL_FFLUX has access to atomic properties (energy, charge, dipole moment,
etc.) with quantum mechanical accuracy. Newly optimized and parallelized
using domain decomposition Message Passing Interface (MPI), DL_FFLUX
is now able to deliver this rigorous methodology at scale while still
in reasonable time frames. DL_FFLUX is delivered as an add-on to the
widely distributed molecular dynamics code DL_POLY 4.08. For the systems
studied here (103–105 atoms), DL_FFLUX
is shown to add minimal computational cost to the standard DL_POLY
package. In fact, the optimization of the electrostatics in DL_FFLUX
means that, when high-rank multipole moments are enabled, DL_FFLUX
is up to 1.25× faster than standard DL_POLY. The parallel DL_FFLUX
preserves the quality of the scaling of MPI implementation in standard
DL_POLY. For the first time, it is feasible to use the full capability
of DL_FFLUX to study systems that are large enough to be of real-world
interest. For example, a fully flexible, high-rank polarized (up to
and including quadrupole moments) 1 ns simulation of a system of 10 125
atoms (3375 water molecules) takes 30 h (wall time) on 18 cores.
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Affiliation(s)
- Benjamin C B Symons
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain.,Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| | - Michael K Bane
- High End Compute LTD, 23 Welby Street, Manchester M13 0EL, Great Britainhttps://highendcompute.co.uk.,Department of Computing and Mathematics, Manchester Metropolitan University, Manchester M15 6BH, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain.,Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
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Di Pasquale N, Elliott JD, Hadjidoukas P, Carbone P. Dynamically Polarizable Force Fields for Surface Simulations via Multi-output Classification Neural Networks. J Chem Theory Comput 2021; 17:4477-4485. [PMID: 34197102 DOI: 10.1021/acs.jctc.1c00360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general procedure to introduce electronic polarization into classical Molecular Dynamics (MD) force fields using a Neural Network (NN) model. We apply this framework to the simulation of a solid-liquid interface where the polarization of the surface is essential to correctly capture the main features of the system. By introducing a multi-input, multi-output NN and treating the surface polarization as a discrete classification problem, we are able to obtain very good accuracy in terms of quality of predictions. Through the definition of a custom loss function we are able to impose a physically motivated constraint within the NN itself making this model extremely versatile, especially in the modeling of different surface charge states. The NN is validated considering the redistribution of electronic charge density within a graphene based electrode in contact with an aqueous electrolyte solution, a system highly relevant to the development of next generation low-cost supercapacitors. We compare the performances of our NN/MD model against Quantum Mechanics/Molecular Dynamics simulations where we obtain a most satisfactory agreement.
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Affiliation(s)
- Nicodemo Di Pasquale
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9AL, United Kingdom
| | - Joshua D Elliott
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9AL, United Kingdom
| | | | - Paola Carbone
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9AL, United Kingdom
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Sauza-de la Vega A, Rocha-Rinza T, Guevara-Vela JM. Cooperativity and Anticooperativity in Ion-Water Interactions: Implications for the Aqueous Solvation of Ions. Chemphyschem 2021; 22:1269-1285. [PMID: 33635563 DOI: 10.1002/cphc.202000981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/24/2021] [Indexed: 01/03/2023]
Abstract
Non-additive effects in hydrogen bonds (HB) take place as a consequence of electronic charge transfers. Therefore, it is natural to expect cooperativity and anticooperativity in ion-water interactions. Nevertheless, investigations on this matter are scarce. This paper addresses the interactions of (i) the cations Li+ , Na+ , K+ , Be2+ , Mg2+ , and Ca2+ together with (ii) the anions F- , Cl- , Br- , NO3 - and SO4 2- with water clusters (H2 O)n , n=1-8, and the effects of these ions on the HBs within the complete molecular adducts. We used quantum chemical topology tools, specifically the quantum theory of atoms in molecules and the interacting quantum atoms energy partition to investigate non-additive effects among the interactions studied herein. Our results show a decrease on the interaction energy between ions and the first neighbouring water molecules with an increment of the coordination number. We also found strong cooperative effects in the interplay between HBs and ion-dipole interactions within the studied systems. Such cooperativity affects considerably the interactions among ions with their first and second solvation shells in aqueous environments. Overall, we believe this article provides valuable information about how ion-dipole contacts interact with each other and how they relate to other interactions, such as HBs, in the framework of non-additive effects in aqueous media.
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Affiliation(s)
- Arturo Sauza-de la Vega
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., 04510, CDMX, México
| | - Tomás Rocha-Rinza
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., 04510, CDMX, México
| | - José Manuel Guevara-Vela
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., 04510, CDMX, México
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Guevara-Vela JM, Francisco E, Rocha-Rinza T, Martín Pendás Á. Interacting Quantum Atoms-A Review. Molecules 2020; 25:E4028. [PMID: 32899346 PMCID: PMC7504790 DOI: 10.3390/molecules25174028] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
The aim of this review is threefold. On the one hand, we intend it to serve as a gentle introduction to the Interacting Quantum Atoms (IQA) methodology for those unfamiliar with it. Second, we expect it to act as an up-to-date reference of recent developments related to IQA. Finally, we want it to highlight a non-exhaustive, yet representative set of showcase examples about how to use IQA to shed light in different chemical problems. To accomplish this, we start by providing a brief context to justify the development of IQA as a real space alternative to other existent energy partition schemes of the non-relativistic energy of molecules. We then introduce a self-contained algebraic derivation of the methodological IQA ecosystem as well as an overview of how these formulations vary with the level of theory employed to obtain the molecular wavefunction upon which the IQA procedure relies. Finally, we review the several applications of IQA as examined by different research groups worldwide to investigate a wide variety of chemical problems.
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Affiliation(s)
- José Manuel Guevara-Vela
- Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., Mexico City 04510, Mexico; (J.M.G.-V.); (T.R.-R.)
| | - Evelio Francisco
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006 Oviedo, Spain;
| | - Tomás Rocha-Rinza
- Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., Mexico City 04510, Mexico; (J.M.G.-V.); (T.R.-R.)
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006 Oviedo, Spain;
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Silva AF, Duarte LJ, Popelier PLA. Contributions of IQA electron correlation in understanding the chemical bond and non-covalent interactions. Struct Chem 2020. [DOI: 10.1007/s11224-020-01495-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractThe quantum topological energy partitioning method Interacting Quantum Atoms (IQA) has been applied for over a decade resulting in an enlightening analysis of a variety of systems. In the last three years we have enriched this analysis by incorporating into IQA the two-particle density matrix obtained from Møller–Plesset (MP) perturbation theory. This work led to a new computational and interpretational tool to generate atomistic electron correlation and thus topologically based dispersion energies. Such an analysis determines the effects of electron correlation within atoms and between atoms, which covers both bonded and non-bonded “through -space” atom–atom interactions within a molecule or molecular complex. A series of papers published by us and other groups shows that the behavior of electron correlation is deeply ingrained in structural chemistry. Some concepts that were shown to be connected to bond correlation are bond order, multiplicity, aromaticity, and hydrogen bonding. Moreover, the concepts of covalency and ionicity were shown not to be mutually excluding but to both contribute to the stability of polar bonds. The correlation energy is considerably easier to predict by machine learning (kriging) than other IQA terms. Regarding the nature of the hydrogen bond, correlation energy presents itself in an almost contradicting way: there is much localized correlation energy in a hydrogen bond system, but its overall effect is null due to internal cancelation. Furthermore, the QTAIM delocalization index has a connection with correlation energy. We also explore the role of electron correlation in protobranching, which provides an explanation for the extra stabilization present in branched alkanes compared to their linear counterparts. We hope to show the importance of understanding the true nature of the correlation energy as the foundation of a modern representation of dispersion forces for ab initio, DFT, and force field calculations.
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Rupp M, von Lilienfeld OA, Burke K. Guest Editorial: Special Topic on Data-Enabled Theoretical Chemistry. J Chem Phys 2018; 148:241401. [DOI: 10.1063/1.5043213] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Matthias Rupp
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - O. Anatole von Lilienfeld
- Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel, 4056 Basel, Switzerland
| | - Kieron Burke
- Departments of Chemistry and Physics, University of California, Irvine, California 92697, USA
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