1
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Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024; 161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.
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Affiliation(s)
- John P Pederson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Jesse G McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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2
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Yan S, Wang B, Lin H. Reshaping the QM Region On-the-Fly: Adaptive-Shape QM/MM Dynamic Simulations of a Hydrated Proton in Bulk Water. J Chem Theory Comput 2024; 20:3462-3472. [PMID: 38671391 DOI: 10.1021/acs.jctc.4c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Adaptive quantum mechanics/molecular mechanics (QM/MM) reclassifies on-the-fly a molecule or molecular fragment as QM or MM during dynamics simulations without abrupt changes in the energy or forces. Notably, the permuted adaptive-partitioning (PAP) algorithms have been applied to simulate a hydrated proton, with a mobile QM zone anchored at a pseudoatom called a proton indicator. The position of the proton indicator approximates the location of the delocalized excess proton, yielding a smooth trajectory of the proton diffusing via the Grotthuss mechanism in aqueous solutions. The mobile QM zone, which has been taken to be a sphere with a preset radius, follows the proton wherever it goes. Although the simulations are successful, the use of a spherical QM zone has one disadvantage: A large preset radius must be utilized to minimize the chance of missing water molecules that are important to proton translocation. A large radius leads to a large QM zone, which is computationally expensive. In this work, we report a new way to set up the QM zone, where one includes only the water molecules important to proton transfer. The importance of a given water molecule is quantified by its "weight" that depends on its relation to the reaction path of proton transfer. The weight varies smoothly, ensuring that a water molecule gradually appears in or disappears from the QM zone without abrupt changes, as required by the PAP method. Consequently, the shape of the QM zone evolves on-the-fly, keeping the QM zone as small as possible and as large as necessary. Test simulations demonstrate that the new algorithm significantly improves the computation efficiency while maintaining the proper descriptions of proton transfer in bulk water.
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Affiliation(s)
- Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Hai Lin
- Department of Chemistry, CB 194, University of Colorado Denver, Denver, P.O. Box 173364, Colorado 80217, United States
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3
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Bruch N, Binninger T, Huang J, Eikerling M. Incorporating Electrolyte Correlation Effects into Variational Models of Electrochemical Interfaces. J Phys Chem Lett 2024; 15:2015-2022. [PMID: 38349906 PMCID: PMC10895655 DOI: 10.1021/acs.jpclett.3c03295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/15/2024]
Abstract
We propose a way for obtaining a classical free energy density functional for electrolytes based on a first-principle many-body partition function. Via a one-loop expansion, we include coulombic correlations beyond the conventional mean-field approximation. To examine electrochemical interfaces, we integrate the electrolyte free energy functional into a hybrid quantum-classical model. This scheme self-consistently couples electronic, ionic, and solvent degrees of freedom and incorporates electrolyte correlation effects. The derived free energy functional causes a correlation-induced enhancement in interfacial counterion density and leads to an overall increase in capacitance. This effect is partially compensated by a reduction of the dielectric permittivity of interfacial water. At larger surface charge densities, ion crowding at the interface stifles these correlation effects. While scientifically intriguing already at planar interfaces, we anticipate these correlation effects to play an essential role for electrolytes in nanoconfinement.
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Affiliation(s)
- Nils Bruch
- Theory
and Computation of Energy Materials (IEK-13), Institute of Energy
and Climate Research, Forschungszentrum
Jülich GmbH, 52425, Jülich, Germany
- Chair
of Theory and Computation of Energy Materials, Faculty of Georesources
and Materials Engineering, RWTH Aachen University, 52062, Aachen Germany
| | - Tobias Binninger
- Theory
and Computation of Energy Materials (IEK-13), Institute of Energy
and Climate Research, Forschungszentrum
Jülich GmbH, 52425, Jülich, Germany
| | - Jun Huang
- Theory
and Computation of Energy Materials (IEK-13), Institute of Energy
and Climate Research, Forschungszentrum
Jülich GmbH, 52425, Jülich, Germany
- Chair
of Theory and Computation of Energy Materials, Faculty of Georesources
and Materials Engineering, RWTH Aachen University, 52062, Aachen Germany
| | - Michael Eikerling
- Theory
and Computation of Energy Materials (IEK-13), Institute of Energy
and Climate Research, Forschungszentrum
Jülich GmbH, 52425, Jülich, Germany
- Chair
of Theory and Computation of Energy Materials, Faculty of Georesources
and Materials Engineering, RWTH Aachen University, 52062, Aachen Germany
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4
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Tran AL, Guidez EB, Lin H. Adaptive-Partitioning Multilayer Dynamics Simulations: 2. Implementations of the Permuted and Interpolated Adaptive-Partitioning Gradients. J Phys Chem A 2023; 127:10320-10333. [PMID: 38058156 PMCID: PMC10712430 DOI: 10.1021/acs.jpca.3c05600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 12/08/2023]
Abstract
Recently, an adaptive-partitioning multilayer Q1/Q2/MM method was proposed, where Q1 and Q2 denote, respectively, two distinct quantum-mechanical levels of theory and MM, the molecular-mechanical force fields. Such a multilayer model resembles the ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) model by Morokuma and co-workers, but it is distinguished by on-the-fly reclassifying atoms to be Q1, Q2, or MM in dynamics simulations. To smoothly blend the levels of descriptions of the atoms, buffer zones are introduced between adjacent layers, and the energy is smoothly interpolated. In particular, the Q1/Q2 interaction energy was expressed in two different formalisms: permuted and interpolated adaptive-partitioning (PAP and IAP), respectively. While the PAP energy is based on a weighted many-body expansion, the IAP energy is derived via alchemical quantum calculations with interpolated Fock and overlap matrices. In this article, we examine in-depth the irregularities in the IAP energy near the boundary between the buffer and Q2 zones, which were found prominent in some calculations. These irregularities are due to basis-set linear dependencies, which can be effectively suppressed using a cutoff for the weighted atomic orbital coefficients. Furthermore, we derived and implemented the gradients for both PAP and IAP. Test calculations on a series of water cluster models show perfectly smooth gradients in PAP, while a minor discontinuity occurs in IAP gradients at the buffer/Q2 boundary. The energy and gradient discontinuities in IAP become smaller when moving the buffer/Q2 boundary further away from the Q1 center and when increasing the size of the basis sets used. Overall, those discontinuities are controllable, and possible ways to further diminish them are discussed.
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Affiliation(s)
- Anh L. Tran
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
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5
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Csizi K, Reiher M. Universal
QM
/
MM
approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Zürich Switzerland
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6
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Yan S, Wang B, Lin H. Tracking the Delocalized Proton in Concerted Proton Transfer in Bulk Water. J Chem Theory Comput 2023; 19:448-459. [PMID: 36630655 DOI: 10.1021/acs.jctc.2c01097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A solvated proton in water is often characterized as a charge or structural defect, and it is important to track its evolution on-the-fly in certain dynamics simulations. Previously, we introduced the proton indicator, a pseudo-atom, whose position approximates the location of the excess proton modeled as a structural defect. The proton indicator generally yields a smooth trajectory of a hydrated proton diffusing in aqueous solutions, including in the events of stepwise proton transfer via the Grotthuss mechanism; however, the proton indicator did not perform well in the events of concerted proton transfer, for which it occasionally yielded large position displacements between two successive time steps. To overcome this hurdle, we develop a new algorithm of a proton indicator with greatly enhanced performance for concerted proton transfer in bulk water. A protocol is proposed to exhaustively explore the hydrogen-bonding network of the water wires over which the excess proton is delocalized and to properly account for the contributions of the water molecules in this network as the geometry evolves. The new proton indicator (called Indicator 2.0) is assessed in dynamics simulations of an excess proton in bulk water and in specially constructed model systems of more complex architectures. The results demonstrate that the new indicator yields a smooth trajectory in both stepwise and concerted proton transfers.
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Affiliation(s)
- Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen360015P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen360015P. R. China
| | - Hai Lin
- Department of Chemistry, CB 194, University of Colorado Denver, P.O. Box 173364, Denver, Colorado80217, United States
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7
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Pederson JP, McDaniel J. DFT-based QM/MM with Particle-Mesh Ewald for Direct, Long-Range Electrostatic Embedding. J Chem Phys 2022; 156:174105. [DOI: 10.1063/5.0087386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a DFT-based, QM/MM implementation with long-range electrostatic embedding achieved by direct real-space integration of the particle mesh Ewald (PME) computed electrostatic potential. The key transformation is the interpolation of the electrostatic potential from the PME grid to the DFT quadrature grid, from which integrals are easily evaluated utilizing standard DFT machinery. We provide benchmarks of the numerical accuracy with choice of grid size and real-space corrections, and demonstrate that good convergence is achieved while introducing nominal computational overhead. Furthermore, the approach requires only small modification to existing software packages, as is demonstrated with our implementation in the OpenMM and Psi4 software. After presenting convergence benchmarks, we evaluate the importance of long-range electrostatic embedding in three solute/solvent systems modeled with QM/MM. Water and BMIM/BF4 ionic liquid were considered as ``simple' and ``complex' solvents respectively, with water and p-phenylenediamine (PPD) solute molecules treated at QM level of theory. While electrostatic embedding with standard real-space truncation may introduce negligible error for simple systems such as water solute in water solvent, errors become more significant when QM/MM is applied to complex solvents such as ionic liquids. An extreme example is the electrostatic embedding energy for oxidized PPD in BMIM/BF4 for which real-space truncation produces severe error even at 2-3 nm cutoff distances. This latter example illustrates that utilization of QM/MM to compute redox potentials within concentrated electrolytes/ionic media requires carefully chosen long-range electrostatic embedding algorithms, with our presented algorithm providing a general and robust approach.
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Affiliation(s)
| | - Jesse McDaniel
- Chemistry, Georgia Institute of Technology, United States of America
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8
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Wu R, Matta M, Paulsen BD, Rivnay J. Operando Characterization of Organic Mixed Ionic/Electronic Conducting Materials. Chem Rev 2022; 122:4493-4551. [PMID: 35026108 DOI: 10.1021/acs.chemrev.1c00597] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Operando characterization plays an important role in revealing the structure-property relationships of organic mixed ionic/electronic conductors (OMIECs), enabling the direct observation of dynamic changes during device operation and thus guiding the development of new materials. This review focuses on the application of different operando characterization techniques in the study of OMIECs, highlighting the time-dependent and bias-dependent structure, composition, and morphology information extracted from these techniques. We first illustrate the needs, requirements, and challenges of operando characterization then provide an overview of relevant experimental techniques, including spectroscopy, scattering, microbalance, microprobe, and electron microscopy. We also compare different in silico methods and discuss the interplay of these computational methods with experimental techniques. Finally, we provide an outlook on the future development of operando for OMIEC-based devices and look toward multimodal operando techniques for more comprehensive and accurate description of OMIECs.
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Affiliation(s)
- Ruiheng Wu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Micaela Matta
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Bryan D Paulsen
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Jonathan Rivnay
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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9
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Mato J, Duster AW, Guidez EB, Lin H. Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory. J Chem Theory Comput 2021; 17:5456-5465. [PMID: 34448578 PMCID: PMC8979635 DOI: 10.1021/acs.jctc.1c00556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We propose to generalize the previously developed two-layer permuted adaptive-partitioning quantum-mechanics/molecular-mechanics (QM/MM), which reclassifies atoms as QM or MM on-the-fly in dynamics simulations, to multilayer adaptive-partitioning algorithms that enable multiple levels of theory. In this work, we formulate two new algorithms that smoothly interpolate the energy between two QM (Q1 and Q2) levels of theory. The first "permuted adaptive-partitioning" scheme is based on the weighted many-body expansion of the potential, as in the adaptive-partitioning QM/MM. Unconventional and potentially more efficient, the second "interpolated adaptive-partitioning" method employs alchemical QM calculations with Q1/Q2-mixed basis sets, Fock matrices, and overlap matrices. To our knowledge, this is the first time that such alchemical calculations are performed in QM, although they are routinely done in MM. Test calculations on water-cluster models show that both new algorithms indeed yield smooth energy curves when water molecules shift between Q1 and Q2.
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Affiliation(s)
- Joani Mato
- Department of Chemistry, University of Colorado Denver, Denver, Colorado, 80217 USA
| | - Adam W. Duster
- Department of Chemistry, University of Colorado Denver, Denver, Colorado, 80217 USA
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado, 80217 USA
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, Colorado, 80217 USA
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10
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Lambros E, Dasgupta S, Palos E, Swee S, Hu J, Paesani F. General Many-Body Framework for Data-Driven Potentials with Arbitrary Quantum Mechanical Accuracy: Water as a Case Study. J Chem Theory Comput 2021; 17:5635-5650. [PMID: 34370954 DOI: 10.1021/acs.jctc.1c00541] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general framework for the development of data-driven many-body (MB) potential energy functions (MB-QM PEFs) that represent the interactions between small molecules at an arbitrary quantum-mechanical (QM) level of theory. As a demonstration, a family of MB-QM PEFs for water is rigorously derived from density functionals belonging to different rungs across Jacob's ladder of approximations within density functional theory (MB-DFT) and from Møller-Plesset perturbation theory (MB-MP2). Through a systematic analysis of individual MB contributions to the interaction energies of water clusters, we demonstrate that all MB-QM PEFs preserve the same accuracy as the corresponding ab initio calculations, with the exception of those derived from density functionals within the generalized gradient approximation (GGA). The differences between the DFT and MB-DFT results are traced back to density-driven errors that prevent GGA functionals from accurately representing the underlying molecular interactions for different cluster sizes and hydrogen-bonding arrangements. We show that this shortcoming may be overcome, within the MB formalism, by using density-corrected functionals (DC-DFT) that provide a more consistent representation of each individual MB contribution. This is demonstrated through the development of a MB-DFT PEF derived from DC-PBE-D3 data, which more accurately reproduce the corresponding ab initio results.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Steven Swee
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jie Hu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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11
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Tesch R, Kowalski PM, Eikerling MH. Properties of the Pt(111)/electrolyte electrochemical interface studied with a hybrid DFT-solvation approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:444004. [PMID: 34348250 DOI: 10.1088/1361-648x/ac1aa2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Self-consistent modeling of the interface between solid metal electrode and liquid electrolyte is a crucial challenge in computational electrochemistry. In this contribution, we adopt the effective screening medium reference interaction site method (ESM-RISM) to study the charged interface between a Pt(111) surface that is partially covered with chemisorbed oxygen and an aqueous acidic electrolyte. This method proves to be well suited to describe the chemisorption and charging state of the interface at controlled electrode potential. We present an in-depth assessment of the ESM-RISM parameterization and of the importance of computing near-surface water molecules explicitly at the quantum mechanical level. We found that ESM-RISM is able to reproduce some key interface properties, including the peculiar, non-monotonic charging relation of the Pt(111)/electrolyte interface. The comparison with independent theoretical models and explicit simulations of the interface reveals strengths and limitations of ESM-RISM for modeling electrochemical interfaces.
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Affiliation(s)
- Rebekka Tesch
- Institute of Energy and Climate Research, Theory and Computation of Energy Materials (IEK-13), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Chair of Theory and Computation of Energy Materials, Faculty of Georesources and Materials Engineering, RWTH Aachen University, 52062 Aachen, Germany
- Jülich Aachen Research Alliance, JARA-CSD and JARA-ENERGY, 52425 Jülich, Germany
| | - Piotr M Kowalski
- Institute of Energy and Climate Research, Theory and Computation of Energy Materials (IEK-13), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Jülich Aachen Research Alliance, JARA-CSD and JARA-ENERGY, 52425 Jülich, Germany
| | - Michael H Eikerling
- Institute of Energy and Climate Research, Theory and Computation of Energy Materials (IEK-13), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Chair of Theory and Computation of Energy Materials, Faculty of Georesources and Materials Engineering, RWTH Aachen University, 52062 Aachen, Germany
- Jülich Aachen Research Alliance, JARA-CSD and JARA-ENERGY, 52425 Jülich, Germany
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12
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Lambros E, Lipparini F, Cisneros GA, Paesani F. A Many-Body, Fully Polarizable Approach to QM/MM Simulations. J Chem Theory Comput 2020; 16:7462-7472. [PMID: 33213149 PMCID: PMC8131112 DOI: 10.1021/acs.jctc.0c00932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum-mechanical contributions (e.g., exchange-repulsion and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Using the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit two-body and three-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 two-body and three-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | | | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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13
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Schwarz K, Sundararaman R. The electrochemical interface in first-principles calculations. SURFACE SCIENCE REPORTS 2020; 75:10.1016/j.surfrep.2020.100492. [PMID: 34194128 PMCID: PMC8240516 DOI: 10.1016/j.surfrep.2020.100492] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
First-principles predictions play an important role in understanding chemistry at the electrochemical interface. Electronic structure calculations are straightforward for vacuum interfaces, but do not easily account for the interfacial fields and solvation that fundamentally change the nature of electrochemical reactions. Prevalent techniques for first-principles prediction of electrochemical processes range from expensive explicit solvation using ab initio molecular dynamics, through a hierarchy of continuum solvation techniques, to neglecting solvation and interfacial field effects entirely. Currently, no single approach reliably captures all relevant effects of the electrochemical double layer in first-principles calculations. This review systematically lays out the relation between all major approaches to first-principles electrochemistry, including the key approximations and their consequences for accuracy and computational cost. Focusing on ab initio methods for thermodynamic properties of aqueous interfaces, we first outline general considerations for modeling electrochemical interfaces, including solvent and electrolyte dynamics and electrification. We then present the specifics of various explicit and implicit models of the solvent and electrolyte. Finally, we discuss the compromise between computational efficiency and accuracy, and identify key outstanding challenges and future opportunities in the wide range of techniques for first-principles electrochemistry.
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Affiliation(s)
- Kathleen Schwarz
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, Maryland 20899, USA
| | - Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th St., Troy, New York 12180, USA
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14
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Cruzeiro VWD, Feliciano GT, Roitberg AE. Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems. J Am Chem Soc 2020; 142:3823-3835. [PMID: 32011132 DOI: 10.1021/jacs.9b11433] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Coupled redox and pH-driven processes are at the core of many important biological mechanisms. As the distribution of protonation and redox states in a system is associated with the pH and redox potential of the solution, having efficient computational tools that can simulate under these conditions becomes very important. Such tools have the potential to provide information that complement and drive experiments. In previous publications we have presented the implementation of the constant pH and redox potential molecular dynamics (C(pH,E)MD) method in AMBER and we have shown how multidimensional replica exchange can be used to significantly enhance the convergence efficiency of our simulations. In the current work, after an improvement in our C(pH,E)MD approach that allows a given residue to be simultaneously pH- and redox-active, we have employed our methodologies to study five different systems of interest in the literature. We present results for capped tyrosine dipeptide, two maquette systems containing one pH- and redox-active tyrosine (α3Y and peptide A), and two proteins that contain multiple heme groups (diheme cytochrome c from Rhodobacter sphaeroides and Desulfovibrio vulgaris Hildenborough cytochrome c3). We show that our results can provide new insights into previous theoretical and experimental findings by using a fully force-field-based and GPU-accelerated approach, which allows the simulations to be executed with high computational performance.
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Affiliation(s)
| | - Gustavo Troiano Feliciano
- Departamento de Físico-Química, Instituto de Química , Universidade Estadual Paulista (Unesp) , Araraquara , Brazil
| | - Adrian E Roitberg
- Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
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15
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Leung K. DFT modelling of explicit solid–solid interfaces in batteries: methods and challenges. Phys Chem Chem Phys 2020; 22:10412-10425. [DOI: 10.1039/c9cp06485k] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density Functional Theory (DFT) calculations of electrode material properties in high energy density storage devices like lithium batteries have been standard practice for decades.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories
- MS 1415
- Albuquerque
- USA
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Kim J, Kim H, Lee WJ, Ruqia B, Baik H, Oh HS, Paek SM, Lim HK, Choi CH, Choi SI. Theoretical and Experimental Understanding of Hydrogen Evolution Reaction Kinetics in Alkaline Electrolytes with Pt-Based Core–Shell Nanocrystals. J Am Chem Soc 2019; 141:18256-18263. [DOI: 10.1021/jacs.9b09229] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeonghyeon Kim
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
| | - Haesol Kim
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Won-Jae Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
| | - Bibi Ruqia
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
| | - Hionsuck Baik
- Korea Basic Science Institute (KBSI), Seoul 02841, Korea
| | - Hyung-Suk Oh
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
| | - Seung-Min Paek
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
| | - Hyung-Kyu Lim
- Division of Chemical Engineering and Bioengineering, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Chang Hyuck Choi
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sang-Il Choi
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
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17
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Duster AW, Lin H. Tracking Proton Transfer through Titratable Amino Acid Side Chains in Adaptive QM/MM Simulations. J Chem Theory Comput 2019; 15:5794-5809. [DOI: 10.1021/acs.jctc.9b00649] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adam W. Duster
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Hai Lin
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
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Zhang B, Altarawy D, Barnes T, Turney JM, Schaefer HF. Janus: An Extensible Open-Source Software Package for Adaptive QM/MM Methods. J Chem Theory Comput 2019; 15:4362-4373. [DOI: 10.1021/acs.jctc.9b00182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Boyi Zhang
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Doaa Altarawy
- The Molecular Sciences Software Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
- Department of Computer and Systems Engineering, Alexandria University, Alexandria 21544, Egypt
| | - Taylor Barnes
- The Molecular Sciences Software Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Justin M. Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
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Exner KS. Recent Advancements Towards Closing the Gap between Electrocatalysis and Battery Science Communities: The Computational Lithium Electrode and Activity-Stability Volcano Plots. CHEMSUSCHEM 2019; 12:2330-2344. [PMID: 30861313 DOI: 10.1002/cssc.201900298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Despite of the fact that the underlying processes are of electrochemical nature, electrocatalysis and battery research are commonly perceived as two disjointed research fields. Herein, recent advancements towards closing this apparent community gap by discussing the concepts of the constrained ab initio thermodynamics approach and the volcano relationship, which were originally introduced for studying heterogeneously catalyzed reactions by first-principles methods at the beginning of the 21st century, are summarized. The translation of the computational hydrogen electrode (CHE) approach or activity-based volcano plots to a computational lithium electrode (CLiE) or activity-stability volcano plots, respectively, for the investigation of electrode surfaces in batteries may refine theoretical modeling with the aim that enhancements of the underlying concepts are transferred between the research communities. The presented strategy of developing novel approaches by interdisciplinary research activities may trigger further progress of improved theoretical concepts in the near future.
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Affiliation(s)
- Kai S Exner
- Faculty of Chemistry and Pharmacy, Department of Physical Chemistry, Sofia University, 1 James Bourchier Avenue, 1164, Sofia, Bulgaria
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Duster AW, Garza CM, Aydintug BO, Negussie MB, Lin H. Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel. J Chem Theory Comput 2019; 15:892-905. [DOI: 10.1021/acs.jctc.8b01128] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adam W. Duster
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Christina M. Garza
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Baris O. Aydintug
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Mikias B. Negussie
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Hai Lin
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
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21
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Duster AW, Wang CH, Lin H. Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes. Molecules 2018; 23:E2170. [PMID: 30154373 PMCID: PMC6225285 DOI: 10.3390/molecules23092170] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 11/16/2022] Open
Abstract
In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput.2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of "water-in-water" model system.
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Affiliation(s)
- Adam W Duster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA.
| | - Chun-Hung Wang
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA.
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA.
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Zheng M, Waller MP. Yoink:An interaction-based partitioning API. J Comput Chem 2018; 39:799-806. [DOI: 10.1002/jcc.25146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Min Zheng
- Department of Physics and International Centre for Quantum and Molecular Structures; Shanghai University; Shanghai 200444 China
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40; Münster 48149 Germany
| | - Mark P. Waller
- Department of Physics and International Centre for Quantum and Molecular Structures; Shanghai University; Shanghai 200444 China
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Dohm S, Spohr E, Korth M. Merging Empirical Valence Bond Theory with Quantum Chemistry to Model Proton Transfer Processes in Water. Electrocatalysis (N Y) 2017. [DOI: 10.1007/s12678-017-0396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Duster AW, Wang C, Garza CM, Miller DE, Lin H. Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here? WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1310] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Adam W. Duster
- Chemistry Department University of Colorado Denver Denver CO USA
| | - Chun‐Hung Wang
- Chemistry Department University of Colorado Denver Denver CO USA
| | | | | | - Hai Lin
- Chemistry Department University of Colorado Denver Denver CO USA
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26
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Balducci A. Ionic Liquids in Lithium-Ion Batteries. Top Curr Chem (Cham) 2017; 375:20. [DOI: 10.1007/s41061-017-0109-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/18/2017] [Indexed: 11/25/2022]
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