1
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Horváth K, Tajti V, Papp D, Czakó G. Dynamics of the HCl + C 2H 5 Multichannel Reaction on a Full-Dimensional Ab Initio Potential Energy Surface. J Phys Chem A 2024; 128:4474-4482. [PMID: 38807530 PMCID: PMC11163425 DOI: 10.1021/acs.jpca.4c02042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024]
Abstract
We report a full-dimensional ab initio analytical potential energy surface (PES), which accurately describes the HCl + C2H5 multichannel reaction. The new PES is developed by iteratively adding selected configurations along HCl + C2H5 quasi-classical trajectories (QCTs), thereby improving our previous Cl(2P3/2) + C2H6 PES using the Robosurfer program package. QCT simulations for the H'Cl + C2H5 reaction reveal hydrogen-abstraction, chlorine-abstraction, and hydrogen-exchange channels leading to Cl + C2H5H', H' + C2H5Cl, and HCl + C2H4H', respectively. Hydrogen abstraction dominates in the collision energy (Ecoll) range of 1-80 kcal/mol and proceeds with indirect isotropic scattering at low Ecoll and forward-scattered direct stripping at high Ecoll. Chlorine abstraction opens around 40 kcal/mol collision energy and becomes competitive with hydrogen abstraction at Ecoll = 80 kcal/mol. A restricted opening of the cone of acceptance in the Cl-abstraction reaction is found to result in the preference for a backward-scattering direct-rebound mechanism at all energies studied. Initial attack-angle distributions show mainly side-on collision preference of C2H5 for both abstraction reactions, and in the case of the HCl reactant, H/Cl-side preference for the H/Cl abstraction. For hydrogen abstraction, the collision energy transfer into the product translational and internal energy is almost equally significant, whereas in the case of chlorine abstraction, most of the available energy goes into the internal degrees of freedom. Hydrogen exchange is a minor channel with nearly constant reactivity in the Ecoll range of 10-80 kcal/mol.
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Affiliation(s)
- Kitti Horváth
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Viktor Tajti
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Dóra Papp
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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2
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Czakó G, Gruber B, Papp D, Tajti V, Tasi DA, Yin C. First-principles mode-specific reaction dynamics. Phys Chem Chem Phys 2024; 26:15818-15830. [PMID: 38639072 DOI: 10.1039/d4cp00417e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Controlling the outcome of chemical reactions by exciting specific vibrational and/or rotational modes of the reactants is one of the major goals of modern reaction dynamics studies. In the present Perspective, we focus on first-principles vibrational and rotational mode-specific dynamics computations on reactions of neutral and anionic systems beyond six atoms such as X + C2H6 [X = F, Cl, OH], HX + C2H5 [X = Br, I], OH- + CH3I, and F- + CH3CH2Cl. The dynamics simulations utilize high-level ab initio analytical potential energy surfaces and the quasi-classical trajectory method. Besides initial state specificity and the validity of the Polanyi rules, mode-specific vibrational-state assignment for polyatomic product species using normal-mode analysis and Gaussian binning is also discussed and compared with experiment.
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Affiliation(s)
- Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Balázs Gruber
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Dóra Papp
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Viktor Tajti
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Domonkos A Tasi
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Cangtao Yin
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
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3
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Staub R, Gantzer P, Harabuchi Y, Maeda S, Varnek A. Challenges for Kinetics Predictions via Neural Network Potentials: A Wilkinson's Catalyst Case. Molecules 2023; 28:molecules28114477. [PMID: 37298952 DOI: 10.3390/molecules28114477] [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: 04/02/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Ab initio kinetic studies are important to understand and design novel chemical reactions. While the Artificial Force Induced Reaction (AFIR) method provides a convenient and efficient framework for kinetic studies, accurate explorations of reaction path networks incur high computational costs. In this article, we are investigating the applicability of Neural Network Potentials (NNP) to accelerate such studies. For this purpose, we are reporting a novel theoretical study of ethylene hydrogenation with a transition metal complex inspired by Wilkinson's catalyst, using the AFIR method. The resulting reaction path network was analyzed by the Generative Topographic Mapping method. The network's geometries were then used to train a state-of-the-art NNP model, to replace expensive ab initio calculations with fast NNP predictions during the search. This procedure was applied to run the first NNP-powered reaction path network exploration using the AFIR method. We discovered that such explorations are particularly challenging for general purpose NNP models, and we identified the underlying limitations. In addition, we are proposing to overcome these challenges by complementing NNP models with fast semiempirical predictions. The proposed solution offers a generally applicable framework, laying the foundations to further accelerate ab initio kinetic studies with Machine Learning Force Fields, and ultimately explore larger systems that are currently inaccessible.
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Affiliation(s)
- Ruben Staub
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
| | - Philippe Gantzer
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
- Japan Science and Technology Agency (JST), ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
- Japan Science and Technology Agency (JST), ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Alexandre Varnek
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
- Laboratory of Chemoinformatics, UMR 7140, CNRS, University of Strasbourg, 67081 Strasbourg, France
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4
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Feng C, Xi J, Zhang Y, Jiang B, Zhou Y. Accurate and Interpretable Dipole Interaction Model-Based Machine Learning for Molecular Polarizability. J Chem Theory Comput 2023; 19:1207-1217. [PMID: 36753749 DOI: 10.1021/acs.jctc.2c01094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Polarizabilities play significant roles in describing dispersive and inductive interactions of the atom and molecular systems. However, an accurate prediction of molecular polarizabilities from first principles is computationally prohibitive. Although physical models or statistical machine learning models have been proposed, either a lack of accurate description of local chemical environments or demanding a large number of samples for training has limited their practical applications. In this study, we combine a physically inspired dipole interaction model and an accurate neural network method for predicting the polarizability tensors of molecules. With the local chemical environment precisely described and the requirement of rotational covariance naturally fulfilled, this hybrid model is proven to give an accurate molecular polarizability prediction, essentially reducing the number of training samples. The atomic polarizabilities are physically interpretable and transferable to larger molecules unseen in the training set. This promising method may find its wide range of applications, such as spectroscopic simulations and the construction of polarizable force fields.
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Affiliation(s)
- Chaoqiang Feng
- Anhui Key Laboratory of Optoelectric Materials Science and Technology, Department of Physics, Anhui Normal University, Wuhu, Anhui 241000, China.,Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jin Xi
- Anhui Key Laboratory of Optoelectric Materials Science and Technology, Department of Physics, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Yaolong Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Jiang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yong Zhou
- Anhui Key Laboratory of Optoelectric Materials Science and Technology, Department of Physics, Anhui Normal University, Wuhu, Anhui 241000, China
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5
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Arab F, Nazari F, Illas F. Artificial Neural Network-Derived Unified Six-Dimensional Potential Energy Surface for Tetra Atomic Isomers of the Biogenic [H, C, N, O] System. J Chem Theory Comput 2023; 19:1186-1196. [PMID: 36735891 PMCID: PMC9979606 DOI: 10.1021/acs.jctc.2c00915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recognition of different structural patterns in different potential energy surface regions, such as in isomerizing quasilinear tetra atomic molecules, is important for understanding the details of underlying physics and chemistry. In this respect, using three variants of artificial neural networks (ANNs), we investigated the six-dimensional (6-D) singlet potential energy surfaces (PES) of tetra atomic isomers of the biogenic [H, C, N, O] system. At first, we constructed a separate ANN potential for each of the studied isomers. In the next step, a comparative assessment of the separate ANN models led to the setting up of a unified 6-D singlet PES equally and accurately describing all studied isomers. The constructed unified model yields relative energies comparable to those obtained either from the gold standard CCSD(T) method or from separate ANNs for each of the studied isomers. The accuracy of the unified singlet PES is on the order of 10-4 Hartrees (0.1 kcal/mol). The developed PES in this work captures the main features of nonlinear and quasilinear tetra atomic isomers of this biogenic system.
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Affiliation(s)
- Fatemeh Arab
- Department
of Chemistry, Institute for Advanced Studies
in Basic Sciences, Zanjan45137-66731, Iran
| | - Fariba Nazari
- Department
of Chemistry, Institute for Advanced Studies
in Basic Sciences, Zanjan45137-66731, Iran,Center
of Climate Change and Global Warming, Institute
for Advanced Studies in Basic Sciences, Zanjan45137-66731, Iran,
| | - Francesc Illas
- Departament
de Ciència de Materials i Química Física &
Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/Martí i Franquès 1, 08028Barcelona, Spain,
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6
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Shanavas Rasheeda D, Martín Santa Daría A, Schröder B, Mátyus E, Behler J. High-dimensional neural network potentials for accurate vibrational frequencies: the formic acid dimer benchmark. Phys Chem Chem Phys 2022; 24:29381-29392. [PMID: 36459127 DOI: 10.1039/d2cp03893e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In recent years, machine learning potentials (MLP) for atomistic simulations have attracted a lot of attention in chemistry and materials science. Many new approaches have been developed with the primary aim to transfer the accuracy of electronic structure calculations to large condensed systems containing thousands of atoms. In spite of these advances, the reliability of modern MLPs in reproducing the subtle details of the multi-dimensional potential-energy surface is still difficult to assess for such systems. On the other hand, moderately sized systems enabling the application of tools for thorough and systematic quality-control are nowadays rarely investigated. In this work we use benchmark-quality harmonic and anharmonic vibrational frequencies as a sensitive probe for the validation of high-dimensional neural network potentials. For the case of the formic acid dimer, a frequently studied model system for which stringent spectroscopic data became recently available, we show that high-quality frequencies can be obtained from state-of-the-art calculations in excellent agreement with coupled cluster theory and experimental data.
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Affiliation(s)
- Dilshana Shanavas Rasheeda
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany.
| | - Alberto Martín Santa Daría
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Benjamin Schröder
- Universität Göttingen, Institut für Physikalische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany
| | - Edit Mátyus
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany.
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7
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Ab initio characterization of the potential energy profiles for the multi-channel reactions: H/Cl + CH3OH. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Conte R, Nandi A, Qu C, Yu Q, Houston PL, Bowman JM. Semiclassical and VSCF/VCI Calculations of the Vibrational Energies of trans- and gauche-Ethanol Using a CCSD(T) Potential Energy Surface. J Phys Chem A 2022; 126:7709-7718. [PMID: 36240438 DOI: 10.1021/acs.jpca.2c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recent full-dimensional Δ-Machine learning potential energy surface (PES) for ethanol is employed in semiclassical and vibrational self-consistent field (VSCF) and virtual-state configuration interaction (VCI) calculations, using MULTIMODE, to determine the anharmonic vibrational frequencies of vibration for both the trans and gauche conformers of ethanol. Both semiclassical and VSCF/VCI energies agree well with the experimental data. We find significant mixing between the VSCF basis states due to Fermi resonances between bending and stretching modes. The same effects are also accurately described by the full-dimensional semiclassical calculations. These are the first high-level anharmonic calculations using a PES, in particular a "gold-standard" CCSD(T) one.
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Affiliation(s)
- Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent Researcher, Toronto, Ontario M9B0E3, Canada
| | - Qi Yu
- Department of Chemistry Yale University, New Haven, Connecticut 06520, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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9
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Qin J, Liu Y, Li J. Quantitative Dynamics of Paradigmatic SN2 reaction OH− + CH3F on Accurate Full-Dimensional Potential Energy Surface. J Chem Phys 2022; 157:124301. [DOI: 10.1063/5.0112228] [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 bimolecular reaction between OH− and CH3F is not just a prototypical SN2 process but also has three other product channels. Here, we develop an accurate full-dimensional potential energy surface (PES) based on 191 193 points calculated at the level CCSD(T)-F12a/aug-cc-pVTZ. A detailed dynamics and mechanism analysis were carried out on this PES by using the quasi-classical trajectory approach. It is verified that the trajectories do not follow the minimum energy path (MEP) but directly dissociate to F− and CH3OH. In addition, a new transition state for proton exchange and a new product complex CH2F−‧‧‧H2O for proton abstraction were discovered. The trajectories avoid the transition state or this complex, instead dissociate to H2O and CH2F− directly through the ridge regions of the MEP before the transition state. These non-MEP dynamics become more pronounced at high collision energies. Detailed dynamics simulations provide new insights into the atomic-level mechanisms of the title reaction thanks to the new chemically accurate PES with the aid of the machine learning.
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Affiliation(s)
- Jie Qin
- Chemistry and Chemical Engineering, Chongqing University Department of Chemical Engineering, China
| | | | - Jun Li
- School of Chemistry and Chemical Engineering, Chongqing University, China
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10
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Zhu X, Iyengar SS. Graph Theoretic Molecular Fragmentation for Multidimensional Potential Energy Surfaces Yield an Adaptive and General Transfer Machine Learning Protocol. J Chem Theory Comput 2022; 18:5125-5144. [PMID: 35994592 DOI: 10.1021/acs.jctc.1c01241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over a series of publications we have introduced a graph-theoretic description for molecular fragmentation. Here, a system is divided into a set of nodes, or vertices, that are then connected through edges, faces, and higher-order simplexes to represent a collection of spatially overlapping and locally interacting subsystems. Each such subsystem is treated at two levels of electronic structure theory, and the result is used to construct many-body expansions that are then embedded within an ONIOM-scheme. These expansions converge rapidly with many-body order (or graphical rank) of subsystems and have been previously used for ab initio molecular dynamics (AIMD) calculations and for computing multidimensional potential energy surfaces. Specifically, in all these cases we have shown that CCSD and MP2 level AIMD trajectories and potential surfaces may be obtained at density functional theory cost. The approach has been demonstrated for gas-phase studies, for condensed phase electronic structure, and also for basis set extrapolation-based AIMD. Recently, this approach has also been used to derive new quantum-computing algorithms that enormously reduce the quantum circuit depth in a circuit-based computation of correlated electronic structure. In this publication, we introduce (a) a family of neural networks that act in parallel to represent, efficiently, the post-Hartree-Fock electronic structure energy contributions for all simplexes (fragments), and (b) a new k-means-based tessellation strategy to glean training data for high-dimensional molecular spaces and minimize the extent of training needed to construct this family of neural networks. The approach is particularly useful when coupled cluster accuracy is desired and when fragment sizes grow in order to capture nonlocal interactions accurately. The unique multidimensional k-means tessellation/clustering algorithm used to determine our training data for all fragments is shown to be extremely efficient and reduces the needed training to only 10% of data for all fragments to obtain accurate neural networks for each fragment. These fully connected dense neural networks are then used to extrapolate the potential energy surface for all molecular fragments, and these are then combined as per our graph-theoretic procedure to transfer the learning process to a full system energy for the entire AIMD trajectory at less than one-tenth the cost as compared to a regular fragmentation-based AIMD calculation.
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Affiliation(s)
- Xiao Zhu
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
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11
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Gui X, Fan W, Sun J, Li Y. New Stable and Fast Ring-Polymer Molecular Dynamics for Calculating Bimolecular Rate Coefficients with an Example of OH + CH 4. J Chem Theory Comput 2022; 18:5203-5212. [PMID: 35983956 DOI: 10.1021/acs.jctc.2c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The accurate and efficient calculation of the rate coefficients of chemical reactions is a key issue in the research of chemical dynamics. In this work, by applying the dimension-free ultrastable Cayley propagator, the thermal rate coefficients of a prototypic high dimensional chemical reaction OH + CH4 → H2O + CH3 in the temperature range of 200 to 1500 K are investigated with ring polymer molecular dynamics (RPMD) on a highly accurate full-dimensional potential energy surface. Kinetic isotope effects (KIEs) for three isotopologues of the title reaction are also studied. The results demonstrate excellent agreement with experimental data, even in the deep tunneling region. Especially, the Cayley propagator shows a high calculation efficiency with little loss of accuracy. The present results confirmed the applicability of the RPMD method, particularly the speed-up using a Cayley propagator, in theoretical calculations of bimolecular reaction rates.
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Affiliation(s)
- Xiongfei Gui
- Department of Physics, International Center of Quantum and Molecular Structures, and Shanghai Frontiers Science Center of Quantum and Superconducting Matter States, Shanghai 200444, China
| | - Wenbin Fan
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jiace Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Yongle Li
- Department of Physics, International Center of Quantum and Molecular Structures, and Shanghai Frontiers Science Center of Quantum and Superconducting Matter States, Shanghai 200444, China
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12
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Nandi A, Conte R, Qu C, Houston PL, Yu Q, Bowman JM. Quantum Calculations on a New CCSD(T) Machine-Learned Potential Energy Surface Reveal the Leaky Nature of Gas-Phase Trans and Gauche Ethanol Conformers. J Chem Theory Comput 2022; 18:5527-5538. [PMID: 35951990 PMCID: PMC9476654 DOI: 10.1021/acs.jctc.2c00760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Ethanol is a molecule of fundamental interest in combustion,
astrochemistry,
and condensed phase as a solvent. It is characterized by two methyl
rotors and trans (anti) and gauche conformers, which are known to be very close in energy.
Here we show that based on rigorous quantum calculations of the vibrational
zero-point state, using a new ab initio potential
energy surface (PES), the ground state resembles the trans conformer, but substantial delocalization to the gauche conformer is present. This explains experimental issues about identification
and isolation of the two conformers. This “leak” effect
is partially quenched when deuterating the OH group, which further
demonstrates the need for a quantum mechanical approach. Diffusion
Monte Carlo and full-dimensional semiclassical dynamics calculations
are employed. The new PES is obtained by means of a Δ-machine
learning approach starting from a pre-existing low level density functional
theory surface. This surface is brought to the CCSD(T) level of theory
using a relatively small number of ab initio CCSD(T)
energies. Agreement between the corrected PES and direct ab
initio results for standard tests is excellent. One- and
two-dimensional discrete variable representation calculations focusing
on the trans–gauche torsional
motion are also reported, in reasonable agreement with experiment.
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Affiliation(s)
- Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Chen Qu
- Independent Researcher, Toronto 66777, Canada
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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13
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Gruber B, Tajti V, Czako G. Full-dimensional automated potential energy surface development and dynamics for the OH + C 2H 6 reaction. J Chem Phys 2022; 157:074307. [DOI: 10.1063/5.0104889] [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
We develop a full-dimensional analytical potential energy surface (PES) for the OH + C2H6 reaction using the Robosurfer program system, which automatically (1) selects geometries from quasi-classical trajectories, (2) performs ab initio computations using a CCSD(T)-F12/triple-zeta-quality composite method, (3) fits the energies utilizing the permutationally-invariant monomial symmetrization approach, and iteratively improves the PES via steps (1)−(3). Quasi-classical trajectory simulations on the new PES reveal that hydrogen abstraction leading to H2O + C2H5 dominates in the collision energy range of 10−50 kcal/mol. The abstraction cross sections increase and the dominant mechanism shifts from rebound (small impact parameters and backward scattering) to stripping (larger impact parameters and forward scattering) with increasing collision energy as opacity functions and scattering angle distributions indicate. The abstraction reaction clearly favors side-on OH attack over O-side and the least-preferred H-side approach, whereas C2H6 behaves like a spherical object with only slight C−C-perpendicular side-on preference. Collision energy efficiently flows into the relative translation of the products, whereas product internal energy distributions show only little collision energy dependence. H2O/C2H5 vibrational distributions slightly/significantly violate zero-point energy and are nearly independent of collision energy, whereas the rotational distributions clearly blue-shift as collision energy increases.
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Affiliation(s)
- Balázs Gruber
- University of Szeged Faculty of Science and Informatics, Hungary
| | - Viktor Tajti
- Chemistry, University of Szeged Faculty of Science and Informatics, Hungary
| | - Gabor Czako
- Chemistry, University of Szeged Faculty of Science and Informatics, Hungary
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14
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Liu Y, Li J. Permutation-Invariant-Polynomial Neural-Network-Based Δ-Machine Learning Approach: A Case for the HO 2 Self-Reaction and Its Dynamics Study. J Phys Chem Lett 2022; 13:4729-4738. [PMID: 35609295 DOI: 10.1021/acs.jpclett.2c01064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Δ-machine learning, or the hierarchical construction scheme, is a highly cost-effective method, as only a small number of high-level ab initio energies are required to improve a potential energy surface (PES) fit to a large number of low-level points. However, there is no efficient and systematic way to select as few points as possible from the low-level data set. We here propose a permutation-invariant-polynomial neural-network (PIP-NN)-based Δ-machine learning approach to construct full-dimensional accurate PESs of complicated reactions efficiently. Particularly, the high flexibility of the NN is exploited to efficiently sample points from the low-level data set. This approach is applied to the challenging case of a HO2 self-reaction with a large configuration space. Only 14% of the DFT data set is used to successfully bring a newly fitted DFT PES to the UCCSD(T)-F12a/AVTZ quality. Then, the quasiclassical trajectory (QCT) calculations are performed to study its dynamics, particularly the mode specificity.
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Affiliation(s)
- Yang Liu
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
| | - Jun Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
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15
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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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16
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Tóth P, Szűcs T, Czakó G. Benchmark Ab Initio Characterization of the Abstraction and Substitution Pathways of the Cl + CH 3CN Reaction. J Phys Chem A 2022; 126:2802-2810. [PMID: 35482972 PMCID: PMC9109142 DOI: 10.1021/acs.jpca.2c01376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We investigate the
reaction pathways of the Cl + CH3CN system: hydrogen abstraction,
methyl substitution, hydrogen substitution,
and cyanide substitution, leading to HCl + CH2CN, ClCN/CNCl
+ CH3, ClCH2CN + H, and CH3Cl + CN,
respectively. Hydrogen abstraction is exothermic and has a low barrier,
whereas the other channels are endothermic with high barriers. The
latter two can proceed via a Walden inversion or front-side attack
mechanism, and the front-side attack barriers are always higher. The
C-side methyl substitution has a lower barrier and also a lower endothermicity
than the N-side reaction. The computations utilize an accurate composite
ab initio approach and the explicitly correlated CCSD(T)-F12b method.
The benchmark classical and vibrationally adiabatic energies of the
stationary points are determined with the most accurate CCSD(T)-F12b/aug-cc-pVQZ
energies adding further contributions of the post-(T) and core correlation,
scalar relativistic effects, spin–orbit coupling, and zero-point
energy corrections. These contributions are found to be non-negligible
to reach subchemical accuracy.
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Affiliation(s)
- Petra Tóth
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Tímea Szűcs
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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17
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Song K, Song H, Li J. Validating experiments for the reaction H 2 + NH 2- by dynamical calculations on an accurate full-dimensional potential energy surface. Phys Chem Chem Phys 2022; 24:10160-10167. [PMID: 35420091 DOI: 10.1039/d2cp00870j] [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
Ion-molecule reactions play key roles in the field of ion related chemistry. As a prototypical multi-channel ion-molecule reaction, the reaction H2 + NH2- → NH3 + H- has been studied for decades. In this work, we develop a new globally accurate potential energy surface (PES) for the title system based on hundreds of thousands of sampled points over a wide dynamically relevant region that covers long-range interacting configuration space. The permutational invariant polynomial-neural network (PIP-NN) method is used for fitting and the resulting total root mean squared error (RMSE) is extremely small, 0.026 kcal mol-1. Extensive dynamical and kinetic calculations are carried out on this PIP-NN PES. Impressively, a unique phenomenon of significant reactivity suppression by exciting the rotational mode of H2 is reported, supported by both the quasi-classical trajectory (QCT) and quantum dynamics (QD) calculations. Further analysis uncovers that exciting the H2 rotational mode would prevent the formation of the reactant complex and thus suppress the reactivity. The calculated rate coefficients for H2/D2 + NH2- agree well with the experimental results, which show an inverse temperature dependence from 50 to 300 K, consistent with the capture nature of this barrierless reaction. The significant kinetic isotope effect observed by experiments is well reproduced by the QCT computations as well.
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Affiliation(s)
- Kaisheng Song
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, P. R. China.
| | - Hongwei Song
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Jun Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, P. R. China.
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18
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Peng Y, Zhang H. Mechanism and Kinetics of Methane Combustion. Part II: Potential Energy Surface for Hydrogen-Abstraction Reaction of CH 4 + O( 3P). J Phys Chem A 2022; 126:1946-1959. [PMID: 35298157 DOI: 10.1021/acs.jpca.1c10860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methane combustion plays an important role in various fields such as combustion chemistry and atmospheric chemistry of the stratosphere. Highly accurate study of its initial reaction remains a key challenge. Here, through extensive studies with a state-of-the-art ab initio and neural network method, we present a potential energy surface of the O(3P) + CH4 → OH + CH3 reaction on the ground state 13A and the first excited state 23A. In this work, the energies of 10 167 points covering all important regions are obtained with state-averaged complete active space self-consistent field calculations and then fitted using the Levenberg-Marquardt algorithm with a root-mean-square error of 0.391 and 0.442 kcal/mol for the 13A and 23A states, respectively. This study explores the characteristics of the radical van der Waals (VdW) complex and reveals a detailed mechanism of the methane combustion initial reaction. Within the scope of this mechanism, this surface gives a fairly accurate description of the regions around the saddle point, conical intersection, and vdW wells in the entrance for efficient computational simulations. As a theoretical study on a prototypical polyatomic reaction, it is hopeful that this work will modify our understanding of the primary process in hydrocarbon combustion.
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Affiliation(s)
- Ya Peng
- Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China
| | - Hui Zhang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China
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19
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Khire SS, Gurav ND, Nandi A, Gadre SR. Enabling Rapid and Accurate Construction of CCSD(T)-Level Potential Energy Surface of Large Molecules Using Molecular Tailoring Approach. J Phys Chem A 2022; 126:1458-1464. [PMID: 35170973 DOI: 10.1021/acs.jpca.2c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The construction of a potential energy surface (PES) of even a medium-sized molecule employing correlated theory, such as CCSD(T), is arduous due to the high computational cost involved. The present study reports the possibility of efficiently constructing such a PES of molecules containing up to 15 atoms and 550 basis functions by employing the fragment-based molecular tailoring approach (MTA) on off-the-shelf hardware. The MTA energies at the CCSD(T)/aug-cc-pVTZ level for several geometries of three test molecules, viz., acetylacetone, N-methylacetamide, and tropolone, are reported. These energies are in excellent agreement with their full calculation counterparts with a time advantage factor of 3-5. The energy barrier from the ground to transition state is also accurately captured. Further, we demonstrate the accuracy and efficiency of MTA for estimating the energy gradients at the CCSD(T) level. As a further application of our MTA methodology, the energies of acetylacetone at ∼430 geometries are computed at the CCSD(T)/aug-cc-pVTZ level and used for generating a Δ-machine learning (Δ-ML) PES. This leads to the H-transfer barrier of 3.02 kcal/mol, well in agreement with the benchmarked barrier of 3.19 kcal/mol. The fidelity of this Δ-ML PES is examined by geometry optimization and normal mode frequency calculations of global minima and saddle point geometries. We trust that the present work is a major development for the rapid and accurate construction of PES at the CCSD(T) level for molecules containing up to 20 atoms and 600 basis functions using off-the-shelf hardware.
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Affiliation(s)
- Subodh S Khire
- Department of Scientific Computing, Modelling and Simulation, Savitribai Phule Pune University, Pune 411 007, India
| | - Nalini D Gurav
- Department of Scientific Computing, Modelling and Simulation, Savitribai Phule Pune University, Pune 411 007, India
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Shridhar R Gadre
- Department of Scientific Computing, Modelling and Simulation, Savitribai Phule Pune University, Pune 411 007, India
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20
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Mode Specificity Dynamics of the Prototypical Multi-Channel H+CH 3OH Reaction on a Globally Accurate Potential Energy Surface. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2201018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Han L, Jiang GD, Li XN, He SG. Global optimization of Tan clusters by deep neural network. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139118] [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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22
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Papp D, Czakó G. Vibrational mode-specific dynamics of the F( 2P 3/2) + C 2H 6 → HF + C 2H 5 reaction. J Chem Phys 2021; 155:154302. [PMID: 34686045 DOI: 10.1063/5.0069658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the competing effect of vibrational and translational excitation and the validity of the Polanyi rules in the early- and negative-barrier F(2P3/2) + C2H6 → HF + C2H5 reaction by performing quasi-classical dynamics simulations on a recently developed full-dimensional multi-reference analytical potential energy surface. The effect of five normal-mode excitations of ethane on the reactivity, the mechanism, and the post-reaction energy flow is followed through a wide range of collision energies. Promoting effects of vibrational excitations and interaction time, related to the slightly submerged barrier, are found to be suppressed by the early-barrier-induced translational enhancement, in contrast to the slightly late-barrier Cl + C2H6 reaction. The excess vibrational energy mostly converts into ethyl internal excitation while collision energy is transformed into product separation. The substantial reaction energy excites the HF vibration, which tends to show mode-specificity and translational energy dependence as well. With increasing collision energy, direct stripping becomes dominant over the direct rebound and indirect mechanisms, being basically independent of reactant excitation.
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Affiliation(s)
- Dóra Papp
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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23
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Papp D, Li J, Guo H, Czakó G. Vibrational mode-specificity in the dynamics of the Cl + C 2H 6 → HCl + C 2H 5 reaction. J Chem Phys 2021; 155:114303. [PMID: 34551541 DOI: 10.1063/5.0062677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We report a detailed dynamics study on the mode-specificity of the Cl + C2H6 → HCl + C2H5 H-abstraction reaction. We perform quasi-classical trajectory simulations using a recently developed high-level ab initio full-dimensional potential energy surface by exciting five different vibrational modes of ethane at four collision energies. We find that all the studied vibrational excitations, except that of the CC-stretching mode, clearly promote the title reaction, and the vibrational enhancements are consistent with the predictions of the Sudden Vector Projection (SVP) model, with the largest effect caused by the CH-stretching excitations. Intramolecular vibrational redistribution is also monitored for the differently excited ethane molecule. Our results indicate that the mechanism of the reaction changes with increasing collision energy, with no mode-specificity at high energies. The initial translational energy mostly converts into product recoil, while a significant part of the excess vibrational energy remains in the ethyl radical. An interesting competition between translational and vibrational energies is observed for the HCl vibrational distribution: the effect of exciting the low-frequency ethane modes, having small SVP values, is suppressed by translational excitation, whereas a part of the excess vibrational energy pumped into the CH-stretching modes (larger SVP values) efficiently flows into the HCl vibration.
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Affiliation(s)
- Dóra Papp
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Jun Li
- School of Chemistry and Chemical Engineering and Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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24
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Qu C, Houston PL, Conte R, Nandi A, Bowman JM. Breaking the Coupled Cluster Barrier for Machine-Learned Potentials of Large Molecules: The Case of 15-Atom Acetylacetone. J Phys Chem Lett 2021; 12:4902-4909. [PMID: 34006096 PMCID: PMC8279733 DOI: 10.1021/acs.jpclett.1c01142] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Machine-learned potential energy surfaces (PESs) for molecules with more than 10 atoms are typically forced to use lower-level electronic structure methods such as density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2). While these are efficient and realistic, they fall short of the accuracy of the "gold standard" coupled-cluster method, especially with respect to reaction and isomerization barriers. We report a major step forward in applying a Δ-machine learning method to the challenging case of acetylacetone, whose MP2 barrier height for H-atom transfer is low by roughly 1.1 kcal/mol relative to the benchmark CCSD(T) barrier of 3.2 kcal/mol. From a database of 2151 local CCSD(T) energies and training with as few as 430 energies, we obtain a new PES with a barrier of 3.5 kcal/mol in agreement with the LCCSD(T) barrier of 3.5 kcal/mol and close to the benchmark value. Tunneling splittings due to H-atom transfer are calculated using this new PES, providing improved estimates over previous ones obtained using an MP2-based PES.
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Affiliation(s)
- Chen Qu
- Department
of Chemistry & Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Paul L. Houston
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
- Department
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United
States
| | - Riccardo Conte
- Dipartimento
di Chimica, Università degli Studi
di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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25
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Ferguson AL, Hachmann J, Miller TF, Pfaendtner J. The Journal of Physical Chemistry A/ B/ C Virtual Special Issue on Machine Learning in Physical Chemistry. J Phys Chem A 2021; 124:9113-9118. [PMID: 33147969 DOI: 10.1021/acs.jpca.0c09205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Czakó G, Győri T, Papp D, Tajti V, Tasi DA. First-Principles Reaction Dynamics beyond Six-Atom Systems. J Phys Chem A 2021; 125:2385-2393. [PMID: 33631071 PMCID: PMC8028310 DOI: 10.1021/acs.jpca.0c11531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/05/2021] [Indexed: 11/29/2022]
Abstract
Moving beyond the six-atomic benchmark systems, we discuss the new age and future of first-principles reaction dynamics, which investigates complex, multichannel chemical reactions. We describe the methodology starting from the benchmark ab initio characterization of the stationary points, followed by full-dimensional potential energy surface (PES) developments and reaction dynamics computations. We highlight our composite ab initio approach providing benchmark stationary-point properties with subchemical accuracy, the Robosurfer program system enabling automatic PES development, and applications for the Cl + C2H6, F + C2H6, and OH- + CH3I post-six-atom reactions focusing on ab initio issues and their solutions as well as showing the excellent agreement between theory and experiment.
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Affiliation(s)
- Gábor Czakó
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Tibor Győri
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Dóra Papp
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Viktor Tajti
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Domonkos A. Tasi
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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27
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Affiliation(s)
- Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstraße 6, 37077 Göttingen, Germany
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28
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Li J, Li J. A Full-Dimensional Potential Energy Surface and Dynamics of the Multichannel Reaction between H and HO 2. J Phys Chem A 2021; 125:1540-1552. [PMID: 33591185 DOI: 10.1021/acs.jpca.0c11213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In addition to its vital significance in combustion and atmospheric chemistry, the reaction between H' and HO2 on the ground triplet state represents a prototype with multiple product channels, including H2 + O2, OH + OH, O + H2O, and H + H'O2. In this work, a full-dimensional accurate potential energy surface (PES) for the title reaction was developed to provide reliable descriptions for all dynamically relevant regions. Using this PES, we adopted the quasi-classical trajectory approach to study the corresponding reaction dynamics, including the reactivity of each product channel and the associated product branching ratio, the product energy distributions, product angular distributions, and associated microscopic mechanisms. For representing distributions of the product energies, such as product translational energy as well as product rotational and vibrational energies, both the traditional histogram and the kernel density estimation (KDE) methods were used and compared. It seems that the features of the resulting distributions in this work are very similar to each other among different methods. The KDE method is suggested for statistics, particularly for those populations with small oscillations in the histogram plot.
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Affiliation(s)
- Jia Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
| | - Jun Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
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29
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Ferguson AL, Hachmann J, Miller TF, Pfaendtner J. The Journal of Physical Chemistry A/ B/ C Virtual Special Issue on Machine Learning in Physical Chemistry. J Phys Chem B 2021; 124:9767-9772. [PMID: 33147970 DOI: 10.1021/acs.jpcb.0c09206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Liu Y, Li J, Felker PM, Bačić Z. HCl–H2O dimer: an accurate full-dimensional potential energy surface and fully coupled quantum calculations of intra- and intermolecular vibrational states and frequency shifts. Phys Chem Chem Phys 2021; 23:7101-7114. [DOI: 10.1039/d1cp00865j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The present work reports a new full-dimensional potential energy surface (PES) of the HCl–H2O dimer, and the first fully coupled 9D quantum calculations of the intra- and intermolecular vibrational states of the complex, utilizing this PES.
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Affiliation(s)
- Yang Liu
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing 401331
- China
| | - Jun Li
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing 401331
- China
| | - Peter M. Felker
- Department of Chemistry and Biochemistry
- University of California
- Los Angeles
- USA
| | - Zlatko Bačić
- Department of Chemistry
- New York University
- New York
- USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai
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31
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Qin J, Li J. An accurate full-dimensional potential energy surface for the reaction OH + SO → H + SO2. Phys Chem Chem Phys 2021; 23:487-497. [DOI: 10.1039/d0cp05206j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An accurate full-dimensional PES for the OH + SO ↔ H + SO2 reaction is developed by the permutation invariant polynomial-neural network approach.
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Affiliation(s)
- Jie Qin
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry
- Chongqing University
- Chongqing 401331
- China
| | - Jun Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry
- Chongqing University
- Chongqing 401331
- China
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Qu C, Conte R, Houston PL, Bowman JM. Full-dimensional potential energy surface for acetylacetone and tunneling splittings. Phys Chem Chem Phys 2021; 23:7758-7767. [DOI: 10.1039/d0cp04221h] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New, full-dimensional potential energy surface for acetylacetone allows for description of H-tunneling dynamics and characterization of stationary points.
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Affiliation(s)
- Chen Qu
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
| | - Riccardo Conte
- Dipartimento di Chimica
- Università Degli Studi di Milano
- 20133 Milano
- Italy
| | - Paul L. Houston
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
- Department of Chemistry and Biochemistry
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry
- Atlanta
- USA
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Li J, Zhao B, Xie D, Guo H. Advances and New Challenges to Bimolecular Reaction Dynamics Theory. J Phys Chem Lett 2020; 11:8844-8860. [PMID: 32970441 DOI: 10.1021/acs.jpclett.0c02501] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dynamics of bimolecular reactions in the gas phase are of foundational importance in combustion, atmospheric chemistry, interstellar chemistry, and plasma chemistry. These collision-induced chemical transformations are a sensitive probe of the underlying potential energy surface(s). Despite tremendous progress in past decades, our understanding is still not complete. In this Perspective, we survey the recent advances in theoretical characterization of bimolecular reaction dynamics, stimulated by new experimental observations, and identify key new challenges.
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Affiliation(s)
- Jun Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
| | - Bin Zhao
- Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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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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