1
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Fang W, Zhu YC, Cheng Y, Hao YP, Richardson JO. Robust Gaussian Process Regression Method for Efficient Tunneling Pathway Optimization: Application to Surface Processes. J Chem Theory Comput 2024; 20:3766-3778. [PMID: 38708859 PMCID: PMC11099967 DOI: 10.1021/acs.jctc.4c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024]
Abstract
Simulation of surface processes is a key part of computational chemistry that offers atomic-scale insights into mechanisms of heterogeneous catalysis, diffusion dynamics, and quantum tunneling phenomena. The most common theoretical approaches involve optimization of reaction pathways, including semiclassical tunneling pathways (called instantons). The computational effort can be demanding, especially for instanton optimizations with an ab initio electronic structure. Recently, machine learning has been applied to accelerate reaction-pathway optimization, showing great potential for a wide range of applications. However, previous methods still suffer from numerical and efficiency issues and were not designed for condensed-phase reactions. We propose an improved framework based on Gaussian process regression for general transformed coordinates, which has improved efficiency and numerical stability, and we propose a descriptor that combines internal and Cartesian coordinates suitable for modeling surface processes. We demonstrate with 11 instanton optimizations in three representative systems that the improved approach makes ab initio instanton optimization significantly cheaper, such that it becomes not much more expensive than a classical transition-state theory rate calculation.
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Affiliation(s)
- Wei Fang
- Department
of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative
Materials, Fudan University, Shanghai 200438, P. R. China
- Laboratory
of Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
- State
Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical
Computational Chemistry, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yu-Cheng Zhu
- State
Key Laboratory for Artificial Microstructure and Mesoscopic Physics,
Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, China
| | - Yihan Cheng
- State
Key Laboratory for Artificial Microstructure and Mesoscopic Physics,
Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, China
| | - Yi-Ping Hao
- State
Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical
Computational Chemistry, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Jeremy O. Richardson
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Zürich 8093, Switzerland
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2
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Zhang S, Makoś MZ, Jadrich RB, Kraka E, Barros K, Nebgen BT, Tretiak S, Isayev O, Lubbers N, Messerly RA, Smith JS. Exploring the frontiers of condensed-phase chemistry with a general reactive machine learning potential. Nat Chem 2024; 16:727-734. [PMID: 38454071 PMCID: PMC11087274 DOI: 10.1038/s41557-023-01427-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 12/12/2023] [Indexed: 03/09/2024]
Abstract
Atomistic simulation has a broad range of applications from drug design to materials discovery. Machine learning interatomic potentials (MLIPs) have become an efficient alternative to computationally expensive ab initio simulations. For this reason, chemistry and materials science would greatly benefit from a general reactive MLIP, that is, an MLIP that is applicable to a broad range of reactive chemistry without the need for refitting. Here we develop a general reactive MLIP (ANI-1xnr) through automated sampling of condensed-phase reactions. ANI-1xnr is then applied to study five distinct systems: carbon solid-phase nucleation, graphene ring formation from acetylene, biofuel additives, combustion of methane and the spontaneous formation of glycine from early earth small molecules. In all studies, ANI-1xnr closely matches experiment (when available) and/or previous studies using traditional model chemistry methods. As such, ANI-1xnr proves to be a highly general reactive MLIP for C, H, N and O elements in the condensed phase, enabling high-throughput in silico reactive chemistry experimentation.
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Affiliation(s)
- Shuhao Zhang
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Małgorzata Z Makoś
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University, Dallas, TX, USA
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ryan B Jadrich
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Kipton Barros
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Benjamin T Nebgen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Nicholas Lubbers
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Richard A Messerly
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Justin S Smith
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
- NVIDIA Corp., Santa Clara, CA, USA.
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3
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Brezina K, Beck H, Marsalek O. Reducing the Cost of Neural Network Potential Generation for Reactive Molecular Systems. J Chem Theory Comput 2023; 19:6589-6604. [PMID: 37747971 PMCID: PMC10569056 DOI: 10.1021/acs.jctc.3c00391] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 09/27/2023]
Abstract
Although machine learning potentials have recently had a substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio simulation that covers all the relevant geometries of the system. Recognizing that this can be prohibitive for certain systems, we develop the method of transition tube sampling that mitigates the computational cost of training set and model generation. In this approach, we generate classical or quantum thermal geometries around a transition path describing a conformational change or a chemical reaction using only a sparse set of local normal mode expansions along this path and select from these geometries by an active learning protocol. This yields a training set with geometries that characterize the whole transition without the need for a costly reference trajectory. The performance of the method is evaluated on different molecular systems with the complexity of the potential energy landscape increasing from a single minimum to a double proton-transfer reaction with high barriers. Our results show that the method leads to training sets that give rise to models applicable in classical and path integral simulations alike that are on par with those based directly on ab initio calculations while providing the computational speedup we have come to expect from machine learning potentials.
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Affiliation(s)
- Krystof Brezina
- Charles University, Faculty of Mathematics
and Physics, Ke Karlovu
3, 121 16, Prague
2, Czech Republic
| | - Hubert Beck
- Charles University, Faculty of Mathematics
and Physics, Ke Karlovu
3, 121 16, Prague
2, Czech Republic
| | - Ondrej Marsalek
- Charles University, Faculty of Mathematics
and Physics, Ke Karlovu
3, 121 16, Prague
2, Czech Republic
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4
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Artiukhin DG, Godtliebsen IH, Schmitz G, Christiansen O. Gaussian process regression adaptive density-guided approach: Toward calculations of potential energy surfaces for larger molecules. J Chem Phys 2023; 159:024102. [PMID: 37428042 DOI: 10.1063/5.0152367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Abstract
We present a new program implementation of the Gaussian process regression adaptive density-guided approach [Schmitz et al., J. Chem. Phys. 153, 064105 (2020)] for automatic and cost-efficient potential energy surface construction in the MidasCpp program. A number of technical and methodological improvements made allowed us to extend this approach toward calculations of larger molecular systems than those previously accessible and maintain the very high accuracy of constructed potential energy surfaces. On the methodological side, improvements were made by using a Δ-learning approach, predicting the difference against a fully harmonic potential, and employing a computationally more efficient hyperparameter optimization procedure. We demonstrate the performance of this method on a test set of molecules of growing size and show that up to 80% of single point calculations could be avoided, introducing a root mean square deviation in fundamental excitations of about 3 cm-1. A much higher accuracy with errors below 1 cm-1 could be achieved with tighter convergence thresholds still reducing the number of single point computations by up to 68%. We further support our findings with a detailed analysis of wall times measured while employing different electronic structure methods. Our results demonstrate that GPR-ADGA is an effective tool, which could be applied for cost-efficient calculations of potential energy surfaces suitable for highly accurate vibrational spectra simulations.
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Affiliation(s)
- Denis G Artiukhin
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Ian H Godtliebsen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
| | - Gunnar Schmitz
- Lehrstuhl für Theoretische Chemie II, Ruhr-Universität Bochum, Universitätstraße 150, 44801 Bochum, Germany
| | - Ove Christiansen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
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5
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Käser S, Richardson JO, Meuwly M. Transfer Learning for Affordable and High-Quality Tunneling Splittings from Instanton Calculations. J Chem Theory Comput 2022; 18:6840-6850. [DOI: 10.1021/acs.jctc.2c00790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | | | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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6
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Rangel C, Espinosa-García J, Corchado JC. Full-dimensional potential energy surface for the H + CH 3OH reaction. Theoretical kinetics and dynamics study. Phys Chem Chem Phys 2022; 24:12501-12512. [PMID: 35578997 DOI: 10.1039/d2cp00864e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics and kinetics of the abstraction reactions of hydrogen atoms with methanol have been studied using quasi-classical trajectory calculations and variational transition state theory with tunnelling corrections, based on a new analytical potential energy surface (PES). The new PES is a valence-bond/molecular mechanics (VB/MM) expression that provides us with the potential energy for any set of Cartesian coordinates. Two reaction channels are considered: hydrogen abstraction from the methyl group (R1) and hydrogen abstraction from the alcohol group (R2), R1 being much more likely to occur in the wide temperature range under study (250-1000 K), as expected from the lower barrier height. Our dynamic calculations at a collision energy of 20 kcal mol-1 show that the H2 co-product is produced mainly in its vibrational ground-state and little rotation excitation is found. As for our kinetic results, they agree with those from previous theoretical studies as well as with those from kinetic experimental results (rate constants and kinetic isotopic effects), lending confidence to the analytical PES presented here. Thus, we expect this PES to be a simple yet powerful tool to understand such an important reaction in combustion chemistry at very high temperatures and interstellar chemistry at very low temperatures.
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Affiliation(s)
- Cipriano Rangel
- Área de Química Física, Facultad de Ciencias, and Instituto de Computación Científica Avanzada (ICCAEx). Universidad de Extremadura, Avenida de Elvas S/N, 06006 Badajoz, Spain.
| | - Joaquín Espinosa-García
- Área de Química Física, Facultad de Ciencias, and Instituto de Computación Científica Avanzada (ICCAEx). Universidad de Extremadura, Avenida de Elvas S/N, 06006 Badajoz, Spain.
| | - José C Corchado
- Área de Química Física, Facultad de Ciencias, and Instituto de Computación Científica Avanzada (ICCAEx). Universidad de Extremadura, Avenida de Elvas S/N, 06006 Badajoz, Spain.
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7
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Komp E, Janulaitis N, Valleau S. Progress towards machine learning reaction rate constants. Phys Chem Chem Phys 2021; 24:2692-2705. [PMID: 34935798 DOI: 10.1039/d1cp04422b] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Quantum and classical reaction rate constant calculations come at the cost of exploring potential energy surfaces. Due to the "curse of dimensionality", their evaluation quickly becomes unfeasible as the system size grows. Machine learning algorithms can accelerate the calculation of reaction rate constants by predicting them using low cost input features. In this perspective, we briefly introduce supervised machine learning algorithms in the context of reaction rate constant prediction. We discuss existing and recently created kinetic datasets and input feature representations as well as the use and design of machine learning algorithms to predict reaction rate constants or quantities required for their computation. Amongst these, we first describe the use of machine learning to predict activation, reaction, solvation and dissociation energies. We then look at the use of machine learning to predict reactive force field parameters, reaction rate constants as well as to help accelerate the search for minimum energy paths. Lastly, we provide an outlook on areas which have yet to be explored so as to improve and evaluate the use of machine learning algorithms for chemical reaction rate constants.
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Affiliation(s)
- Evan Komp
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Nida Janulaitis
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Stéphanie Valleau
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
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8
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Miksch AM, Morawietz T, Kästner J, Urban A, Artrith N. Strategies for the construction of machine-learning potentials for accurate and efficient atomic-scale simulations. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abfd96] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Recent advances in machine-learning interatomic potentials have enabled the efficient modeling of complex atomistic systems with an accuracy that is comparable to that of conventional quantum-mechanics based methods. At the same time, the construction of new machine-learning potentials can seem a daunting task, as it involves data-science techniques that are not yet common in chemistry and materials science. Here, we provide a tutorial-style overview of strategies and best practices for the construction of artificial neural network (ANN) potentials. We illustrate the most important aspects of (a) data collection, (b) model selection, (c) training and validation, and (d) testing and refinement of ANN potentials on the basis of practical examples. Current research in the areas of active learning and delta learning are also discussed in the context of ANN potentials. This tutorial review aims at equipping computational chemists and materials scientists with the required background knowledge for ANN potential construction and application, with the intention to accelerate the adoption of the method, so that it can facilitate exciting research that would otherwise be challenging with conventional strategies.
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9
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Zhang X, Chen X, Kuroda DG. Computing the frequency fluctuation dynamics of highly coupled vibrational transitions using neural networks. J Chem Phys 2021; 154:164514. [PMID: 33940799 DOI: 10.1063/5.0044911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The description of frequency fluctuations for highly coupled vibrational transitions has been a challenging problem in physical chemistry. In particular, the complexity of their vibrational Hamiltonian does not allow us to directly derive the time evolution of vibrational frequencies for these systems. In this paper, we present a new approach to this problem by exploiting the artificial neural network to describe the vibrational frequencies without relying on the deconstruction of the vibrational Hamiltonian. To this end, we first explored the use of the methodology to predict the frequency fluctuations of the amide I mode of N-methylacetamide in water. The results show good performance compared with the previous experimental and theoretical results. In the second part, the neural network approach is used to investigate the frequency fluctuations of the highly coupled carbonyl stretch modes for the organic carbonates in the solvation shell of the lithium ion. In this case, the frequency fluctuation predicted by the neural networks shows a good agreement with the experimental results, which suggests that this model can be used to describe the dynamics of the frequency in highly coupled transitions.
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Affiliation(s)
- Xiaoliu Zhang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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10
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Han R, Rodríguez-Mayorga M, Luber S. A Machine Learning Approach for MP2 Correlation Energies and Its Application to Organic Compounds. J Chem Theory Comput 2021; 17:777-790. [DOI: 10.1021/acs.jctc.0c00898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruocheng Han
- Department of Chemistry A, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | - Sandra Luber
- Department of Chemistry A, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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11
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Manzhos S, Carrington T. Neural Network Potential Energy Surfaces for Small Molecules and Reactions. Chem Rev 2020; 121:10187-10217. [PMID: 33021368 DOI: 10.1021/acs.chemrev.0c00665] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We review progress in neural network (NN)-based methods for the construction of interatomic potentials from discrete samples (such as ab initio energies) for applications in classical and quantum dynamics including reaction dynamics and computational spectroscopy. The main focus is on methods for building molecular potential energy surfaces (PES) in internal coordinates that explicitly include all many-body contributions, even though some of the methods we review limit the degree of coupling, due either to a desire to limit computational cost or to limited data. Explicit and direct treatment of all many-body contributions is only practical for sufficiently small molecules, which are therefore our primary focus. This includes small molecules on surfaces. We consider direct, single NN PES fitting as well as more complex methods that impose structure (such as a multibody representation) on the PES function, either through the architecture of one NN or by using multiple NNs. We show how NNs are effective in building representations with low-dimensional functions including dimensionality reduction. We consider NN-based approaches to build PESs in the sums-of-product form important for quantum dynamics, ways to treat symmetry, and issues related to sampling data distributions and the relation between PES errors and errors in observables. We highlight combinations of NNs with other ideas such as permutationally invariant polynomials or sums of environment-dependent atomic contributions, which have recently emerged as powerful tools for building highly accurate PESs for relatively large molecular and reactive systems.
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Affiliation(s)
- Sergei Manzhos
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650, Boulevard Lionel-Boulet, Varennes, Québec City, Québec J3X 1S2, Canada
| | - Tucker Carrington
- Chemistry Department, Queen's University, Kingston Ontario K7L 3N6, Canada
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12
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Laude G, Calderini D, Welsch R, Richardson JO. Calculations of quantum tunnelling rates for muonium reactions with methane, ethane and propane. Phys Chem Chem Phys 2020; 22:16843-16854. [PMID: 32666960 DOI: 10.1039/d0cp01346c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermal rate constants for Mu + CH4, Mu + C2H6 and Mu + C3H8 and their equivalent reactions with H were evaluated with ab initio instanton rate theory. The potential-energy surfaces are fitted using Gaussian process regression to high-level electronic-structure calculations evaluated around the tunnelling pathway. This method was able to successfully reproduce various experimental measurements for the rate constant of these reactions. However, it was not able to reproduce the faster-than-expected rate of Mu + C3H8 at 300 K reported by Fleming et al. [Phys. Chem. Chem. Phys., 2015, 17, 19901 and Phys. Chem. Chem. Phys., 2020, 22, 6326]. Analysis of our results indicates that the kinetic isotope effect at this temperature is not significantly influenced by quantum tunnelling. We consider many possible factors for the discrepancy between theory and experiment but conclude that in each case, the instanton approximation is unlikely to be the cause of the error. This is in part based on the good agreement we find between the instanton predictions and new multiconfigurational time-dependent Hartree (MCTDH) calculations for Mu + CH4 using the same potential-energy surface. Further experiments will therefore be needed to resolve this issue.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zürich, Switzerland.
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13
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Meyer R, Hauser AW. Geometry optimization using Gaussian process regression in internal coordinate systems. J Chem Phys 2020; 152:084112. [PMID: 32113346 DOI: 10.1063/1.5144603] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Locating the minimum energy structure of molecules, typically referred to as geometry optimization, is one of the first steps of any computational chemistry calculation. Earlier research was mostly dedicated to finding convenient sets of molecule-specific coordinates for a suitable representation of the potential energy surface, where a faster convergence toward the minimum structure can be achieved. More recent approaches, on the other hand, are based on various machine learning techniques and seem to revert to Cartesian coordinates instead for practical reasons. We show that the combination of Gaussian process regression with those coordinate systems employed by state-of-the-art geometry optimizers can significantly improve the performance of this powerful machine learning technique. This is demonstrated on a benchmark set of 30 small covalently bonded molecules.
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Affiliation(s)
- Ralf Meyer
- Institute of Experimental Physics, Graz University of Technology, Petersgasse 16, 8010 Graz, Austria
| | - Andreas W Hauser
- Institute of Experimental Physics, Graz University of Technology, Petersgasse 16, 8010 Graz, Austria
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14
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Meyer R, Schmuck KS, Hauser AW. Machine Learning in Computational Chemistry: An Evaluation of Method Performance for Nudged Elastic Band Calculations. J Chem Theory Comput 2019; 15:6513-6523. [PMID: 31553610 DOI: 10.1021/acs.jctc.9b00708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The localization of transition states and the calculation of reaction pathways are routine tasks of computational chemists but often very CPU-intense problems, in particular for large systems. The standard algorithm for this purpose is the nudged elastic band method, but it has become obvious that an "intelligent" selection of points to be evaluated on the potential energy surface can improve its convergence significantly. This article summarizes, compares, and extends known strategies that have been heavily inspired by the machine learning developments of recent years. It presents advantages and disadvantages and provides an unbiased comparison of neural network based approaches, Gaussian process regression in Cartesian coordinates, and Gaussian approximation potentials. We test their performance on two example reactions, the ethane rotation and the activation of carbon dioxide on a metal catalyst, and provide a clear ranking in terms of usability for future implementations.
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Affiliation(s)
- Ralf Meyer
- Graz University of Technology , Institute of Experimental Physics , Petersgasse 16 , 8010 Graz , Austria
| | - Klemens S Schmuck
- Graz University of Technology , Institute of Experimental Physics , Petersgasse 16 , 8010 Graz , Austria
| | - Andreas W Hauser
- Graz University of Technology , Institute of Experimental Physics , Petersgasse 16 , 8010 Graz , Austria
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15
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Cooper AM, Kästner J. Low-Temperature Kinetic Isotope Effects in CH3OH + H → CH2OH + H2 Shed Light on the Deuteration of Methanol in Space. J Phys Chem A 2019; 123:9061-9068. [DOI: 10.1021/acs.jpca.9b07013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- April M. Cooper
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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16
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Winter P, Richardson JO. Divide-and-Conquer Method for Instanton Rate Theory. J Chem Theory Comput 2019; 15:2816-2825. [DOI: 10.1021/acs.jctc.8b01267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pierre Winter
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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17
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McConnell SR, Kästner J. Instanton rate constant calculations using interpolated potential energy surfaces in nonredundant, rotationally and translationally invariant coordinates. J Comput Chem 2019; 40:866-874. [PMID: 30677168 DOI: 10.1002/jcc.25770] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/25/2018] [Accepted: 11/27/2018] [Indexed: 11/07/2022]
Abstract
A trivial flaw in the utilization of artificial neural networks in interpolating chemical potential energy surfaces (PES) whose descriptors are Cartesian coordinates is their dependence on simple translations and rotations of the molecule under consideration. A different set of descriptors can be chosen to circumvent this problem, internuclear distances, inverse internuclear distances or z-matrix coordinates are three such descriptors. The objective is to use an interpolated PES in instanton rate constant calculations, hence information on the energy, gradient, and Hessian is required at coordinates in the vicinity of the tunneling path. Instanton theory relies on smoothly fitted Hessians, therefore we use energy, gradients, and Hessians in the training procedure. A major challenge is presented in the proper back-transformation of the output gradients and Hessians from internal coordinates to Cartesian coordinates. We perform comparisons between our method, a previous approach and on-the-fly rate constant calcuations on the hydrogen abstraction from methanol and on the hydrogen addition to isocyanic acid. © 2018Wiley Periodicals, Inc.
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Affiliation(s)
- Sean R McConnell
- Institute for Theoretical Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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18
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19
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Laude G, Calderini D, Tew DP, Richardson JO. Ab initio instanton rate theory made efficient using Gaussian process regression. Faraday Discuss 2018; 212:237-258. [PMID: 30230495 DOI: 10.1039/c8fd00085a] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio instanton rate theory is a computational method for rigorously including tunnelling effects into the calculations of chemical reaction rates based on a potential-energy surface computed on the fly from electronic-structure theory. This approach is necessary to extend conventional transition-state theory into the deep-tunnelling regime, but it is also more computationally expensive as it requires many more ab initio calculations. We propose an approach which uses Gaussian process regression to fit the potential-energy surface locally around the dominant tunnelling pathway. The method can be converged to give the same result as from an on-the-fly ab initio instanton calculation but it requires far fewer electronic-structure calculations. This makes it a practical approach for obtaining accurate rate constants based on high-level electronic-structure methods. We show fast convergence to reproduce benchmark H + CH4 results and evaluate new low-temperature rates of H + C2H6 in full dimensionality at a UCCSD(T)-F12b/cc-pVTZ-F12 level.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland. and On exchange from School of Chemistry, University of Edinburgh, UK
| | | | - David P Tew
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
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