1
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Gutierrez-Cardenas J, Gibbas BD, Whitaker K, Kaledin M, Kaledin AL. A Low-Order Permutationally Invariant Polynomial Approach to Learning Potential Energy Surfaces Using the Bond-Order Charge-Density Matrix: Application to C n Clusters for n = 3-10, 20. J Phys Chem A 2024; 128:7703-7713. [PMID: 39205486 PMCID: PMC11407436 DOI: 10.1021/acs.jpca.4c04281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
A representation for learning potential energy surfaces (PESs) in terms of permutationally invariant polynomials (PIPs) using the Hartree-Fock expression for electronic energy is proposed. Our approach is based on the one-electron core Hamiltonian weighted by the configuration-dependent elements of the bond-order charge density matrix (CDM). While the previously reported model used an s-function Gaussian basis for the CDM, the present formulation is expanded with p-functions, which are crucial for describing chemical bonding. Detailed results are demonstrated on linear and cyclic Cn clusters (n = 3-10) trained on extensive B3LYP/aug-cc-pVTZ data. The described method facilitates PES learning by reducing the root mean squared error (RMSE) by a factor of 5 relative to the s-function formulation and by a factor of 20 relative to the conventional PIP approach. This is equivalent to using CDM and an sp basis with a PIP of order M to achieve the same RMSE as with the conventional method with a PIP of order M + 2. Implications for large-scale problems are discussed using the case of the PES of the C20 fullerene in full permutational symmetry.
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Affiliation(s)
- Jose Gutierrez-Cardenas
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW ,Box#1203,Kennesaw 30144, Georgia
| | - Benjamin D Gibbas
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW ,Box#1203,Kennesaw 30144, Georgia
| | - Kyle Whitaker
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW ,Box#1203,Kennesaw 30144, Georgia
| | - Martina Kaledin
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW ,Box#1203,Kennesaw 30144, Georgia
| | - Alexey L Kaledin
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, 1515 Dickey Drive ,Atlanta 30322, Georgia
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2
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Li W, Dong B, Niu X, Wang M, Zhang Y. Non-adiabatic dynamics studies of the C+(2P1/2, 3/2) + H2 reaction: Based on global diabatic potential energy surfaces of CH2. J Chem Phys 2024; 161:074302. [PMID: 39145555 DOI: 10.1063/5.0223199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024] Open
Abstract
Global diabatic potential energy surfaces (PESs) of CH2+ are constructed using the neural network method with a specific function based on 18 213 ab initio points. The multi-reference configuration interaction method with the aug-cc-pVQZ basis set is adopted to perform the ab initio calculations. The topographical properties of the diabatic PESs are examined in detail. In general, the diabatic PESs provide an accurate quasi-diabatic representation. To validate the diabatic PESs, the dynamics studies of the C+(2P1/2, 3/2) + H2 (v0 = 0, j0 = 0) → H + CH+(X1Σ+) reaction are performed using the time-dependent wave packet method. The reaction probabilities, integral cross sections, differential cross sections, and rate constants are calculated and compared with the experimental and theoretical results. Non-adiabatic dynamics results are in good agreement with experimental data. In addition, the non-adiabatic effect in the C+(2P1/2, 3/2) + H2 reaction is significant due to the non-adiabatic results being obviously larger than adiabatic values. The reasonable non-adiabatic dynamics results indicate that present diabatic PESs can be recommended for any type of dynamics study.
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Affiliation(s)
- Wentao Li
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Bin Dong
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Xianghong Niu
- School of Science, Nanjing University of Posts and Telecommunications, Nanjing 210003, China
| | - Meishan Wang
- College of Integrated Ciruits, Ludong University, Yantai 264025, People's Republic of China
| | - Yong Zhang
- Department of Physics, Tonghua Normal University, Tonghua, Jilin 134002, China
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3
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Li W, Zhang Z, Niu X, He D, Xing W, Zhang Y. Diabatic Potential Energy Surfaces of SrH 2+ and Dynamics Studies of the Sr +(5s 2S) + H 2 Reaction. J Phys Chem A 2024; 128:6677-6684. [PMID: 39093206 DOI: 10.1021/acs.jpca.4c03648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Based on the ab initio energy points of both ground and excited states, a neural network fitting method combined with a specific function was successfully used to construct the diabatic potential energy surfaces (PESs) of the SrH2+ system. The topographical features of the diabatic PESs were examined in detail. The results indicate that the nonadiabatic transition characteristics between ground and excited states are accurately described by the newly constructed diabatic PESs. To verify the validity and applicability of the diabatic PESs, as well as the nonadiabatic effects during the reaction process, the quantum dynamics studies of the Sr+(5s2S) + H2 reaction were performed based on both adiabatic and diabatic PESs. The dynamics results indicate that adiabatic dynamics results are dozens of times larger than those of nonadiabatic. This illustrates the significant effect of nonadiabaticity, indicating that adiabatic dynamics results often overestimate the actual values. The integral cross sections (ICSs) were calculated and compared with the experimental data. The diabatic ICSs are in good agreement with the experimental results. The reasonable dynamics results indicate that the newly constructed diabatic PESs are suitable for the relevant dynamics studies.
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Affiliation(s)
- Wentao Li
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Zhijun Zhang
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Xianghong Niu
- School of Science, Nanjing University of Posts and Telecommunications, Nanjing 210003, China
| | - Di He
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Wei Xing
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Yong Zhang
- Department of Physics, Tonghua Normal University, Tonghua ,Jilin134002, China
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4
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Song K, Li J. Fundamental Invariant Neural Network (FI-NN) Potential Energy Surface for the OH + CH 3OH Reaction with Analytical Forces. J Phys Chem A 2024; 128:6636-6647. [PMID: 39096277 DOI: 10.1021/acs.jpca.4c02432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
The hydrogen abstraction reaction of OH + CH3OH plays a great role in combustion and atmospheric and interstellar chemistry and has been extensively studied theoretically and experimentally. Theoretically, the numerical gradients with respect to the Cartesian coordinates of atoms in molecular simulations on our recent potential energy surface (PES) for the title reaction trained using the permutationally invariant polynomial neural network (PIP-NN) approach hinder the extensive calculation because of the unaffordable computation cost. To address this issue, we in this work report a new full-dimensional accurate analytical PES for the title reaction using the fundamental invariant neural network (FI-NN) approach based on 140,192 points of the quality UCCSD(T)-F12a/AVTZ. Besides, the spin-orbit (SO) corrections of OH in the entrance channel were determined at the level of complete active space self-consistent field with the AVTZ basis set. As a compromise between computational cost and efficiency, the Δ-machine learning approach was employed to construct the SO-corrected PES. Based on this new FI-NN PES with analytical forces, thermal rate coefficients and various dynamic properties, including the integral cross sections, the differential cross sections, and the product energy partitioning, were determined by running a total of 5.5 million trajectories. The use of analytical gradients of the FI-NN PES accelerated simulations and about 99% of computation cost was saved, compared to that for the PIP-NN PES with numerical gradients. Such a significant acceleration is achieved mainly by replacing PIPs with FIs.
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Affiliation(s)
- Kaisheng Song
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Chemical Theory and Mechanism, Chongqing University, Chongqing 401331, P.R. China
| | - Jun Li
- School of Chemistry and Chemical Engineering & Chongqing Key Laboratory of Chemical Theory and Mechanism, Chongqing University, Chongqing 401331, P.R. China
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Shu Y, Varga Z, Parameswaran AM, Truhlar DG. Fitting of Coupled Potential Energy Surfaces via Discovery of Companion Matrices by Machine Intelligence. J Chem Theory Comput 2024. [PMID: 39106186 DOI: 10.1021/acs.jctc.4c00716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Fitting coupled potential energy surfaces is a critical step in simulating electronically nonadiabatic chemical reactions and energy transfer processes. Analytic representation of coupled potential energy surfaces enables one to perform detailed dynamics calculations. Traditionally, fitting is performed in a diabatic representation to avoid fitting the cuspidal ridges of coupled adiabatic potential energy surfaces at conical intersection seams. In this work, we provide an alternative approach by carrying out fitting in the adiabatic representation using a modified version of the Frobenius companion matrices, whose usage was first proposed by Opalka and Domcke. Their work involved minimizing the errors in fits of the characteristic polynomial coefficients (CPCs) and diagonalizing the resulting companion matrix, whose eigenvalues are adiabatic potential energies. We show, however, that this may lead to complex eigenvalues and spurious discontinuities. To alleviate this problem, we provide a new procedure for the automatic discovery of CPCs and the diagonalization of a companion matrix by using a special neural network architecture. The method effectively allows analytic representation of global coupled adiabatic potential energy surfaces and their gradients with only adiabatic energy input and without experience-based selection of a diabatization scheme. We demonstrate that the new procedure, called the companion matrix neural network (CMNN), is successful by showing applications to LiH, H3, phenol, and thiophenol.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Zoltan Varga
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Aiswarya M Parameswaran
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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Li W, Liang Y, Niu X, He D, Xing W, Zhang Y. Construction of diabatic potential energy surfaces for the SiH2+ system and dynamics studies of the Si+(2P1/2, 3/2) + H2 reaction. J Chem Phys 2024; 161:044310. [PMID: 39051835 DOI: 10.1063/5.0219621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024] Open
Abstract
The construction of diabatic potential energy surfaces (PESs) for the SiH2+ system, related to the ground (12A') and excited states (22A'), has been successfully achieved. This was accomplished by utilizing high-level ab initio energy points, employing a neural network fitting method in conjunction with a specifically designed function. The newly constructed diabatic PESs are carefully examined for dynamics calculations of the Si+(2P1/2, 3/2) + H2 reaction. Through time-dependent quantum wave packet calculations, the reaction probabilities, integral cross sections (ICSs), and differential cross sections (DCSs) of the Si+(2P1/2, 3/2) + H2 reaction were reported. The dynamics results indicate that the total ICS is in excellent agreement with experimental data within the collision energy range studied. The results also indicate that the SiH+ ion is hardly formed via the Si+(2P3/2) + H2 reaction. The results from the DCSs suggest that the "complex-forming" reaction mechanism predominates in the low collision energy region. Conversely, the forward abstraction reaction mechanism is dominant in the high collision energy region.
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Affiliation(s)
- Wentao Li
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Yongping Liang
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Xianghong Niu
- School of Science, Nanjing University of Posts and Telecommunications, Nanjing 210003, China
| | - Di He
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Wei Xing
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang 464000, People's Republic of China
| | - Yong Zhang
- Department of Physics, Tonghua Normal University, Tonghua, Jilin 134002, China
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7
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Tu Z, Li J, Yang M, Chen Y, Wang Y, Song H. Accurate ab initio based potential energy surface and kinetics of the Cl + NH3 → HCl + NH2 reaction. J Chem Phys 2024; 161:034304. [PMID: 39007384 DOI: 10.1063/5.0216562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
The gas-phase reaction Cl + NH3 → HCl + NH2 is a prototypical hydrogen abstraction reaction, whose minimum energy path involves several intermediate complexes. In this work, a full-dimensional, spin-orbit corrected potential energy surface (SOC PES) is constructed for the ground electronic state of the Cl + NH3 reaction. About 52 000 energy points are sampled and calculated at the UCCSD(T)-F12a/aug-cc-pVTZ level, in which the data points located in the entrance channel are spin-orbit corrected. The spin-orbit corrections are predicted by a fitted three-dimensional energy surface from about 7520 energy points in the entrance channel at the level of CASSCF (15e, 11o)/aug-cc-pVTZ. The fundamental-invariant neural network method is utilized to fit the SOC PES, resulting in a total root mean square error of 0.12 kcal mol-1. The calculated thermal rate constants of the Cl + NH3 → HCl + NH2 reaction on the SOC PES with the soft-zero-point energy constraint agree reasonably well with the available experimental values.
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Affiliation(s)
- Zhao Tu
- School of Chemical and Environmental Engineering, Hubei Minzu University, Enshi 445000, China
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jiaqi Li
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- College of Physical Science and Technology, Huazhong Normal University, Wuhan 430079, China
| | - Mingjuan Yang
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yizhuo Chen
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- College of Physical Science and Technology, Huazhong Normal University, Wuhan 430079, China
| | - Yan Wang
- School of Chemical and Environmental Engineering, Hubei Minzu University, Enshi 445000, China
| | - Hongwei Song
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
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8
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Buren B, Zhang J, Li Y. Quantum Dynamics Studies of the Li + Na 2 ( V = 0, j = 0) → Na + NaLi Reaction on a New Neural Network Potential Energy Surface. J Phys Chem A 2024; 128:5115-5127. [PMID: 38889710 DOI: 10.1021/acs.jpca.4c01891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The ultracold reaction offers a unique opportunity to elucidate the intricate microscopic mechanism of chemical reactions, and the Na2Li system serves as a pivotal reaction system in the investigation of ultracold reactions. In this work, a high-precision potential energy surface (PES) of the Na2Li system is constructed based on high-level ab initio energy points and the neural network (NN) method, and a proper asymptotic functional form is adopted for the long-range interaction, which is suitable for the study of cold or ultracold collisions. Based on the new NN PES, the dynamics of the Li + Na2 (v = 0, j = 0) → Na + NaLi reaction are studied in the collision energy range of 10-7 to 80 cm-1. In the high collision energy range of 8 to 80 cm-1, the dynamics of the reaction is studied using the time-dependent wave packet method and the statistical quantum mechanical (SQM) method. Comparing the results of the two methods, it is found that the SQM method provides a rough description of the product ro-vibrational state distribution but overestimates the integral cross-section values. With the decrease of collision energy, the reaction differential cross section gradually changes from forward-backward symmetric scattering to predominant forward scattering. In the low collision energy range from 10-7 to 8 cm-1, the SQM method is used to study the reaction dynamics, and the rate constant in the Wigner threshold region is estimated to be 2.87 × 10-10 cm3/s.
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Affiliation(s)
- Bayaer Buren
- School of Science, Shenyang University of Technology, Shenyang 110870, China
| | - Jiapeng Zhang
- Department of Physics, Liaoning University, Shenyang 110036, China
| | - Yongqing Li
- Department of Physics, Liaoning University, Shenyang 110036, China
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9
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Chang H, Li W, Sun Z. New Diabatic Potential Energy Surfaces for the Li + H 2 Reaction and Time-Dependent Quantum Wave Packet Studies. J Phys Chem A 2024; 128:4412-4424. [PMID: 38787593 DOI: 10.1021/acs.jpca.4c00539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
New global diabatic potential energy surfaces (DPESs) for the ground (12A') and first excited (22A') states for the Li + H2 system were developed, with more than 30,000 energy points at the IC-MRCI+Q level of theory, utilizing the aug-cc-pV5Z basis set for the H atoms and the cc-pCV5Z basis set for the Li atom, fitted by a single neural network (NN) with symmetry. Product state-resolved quantum dynamics calculations of the nonadiabatic reaction Li (2P) + H2 (X 1 ∑g+, v0 = 0, j0 = 0) → LiH (X 1∑+) + H(2S) were carried out using these new DPESs and also the previous HYLC-DPESs. The numerical results suggested that our newly constructed DPESs provided an accurate description of the LiH2 system.
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Affiliation(s)
- Hanwen Chang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wentao Li
- Weifang University of Science and Technology, Shouguang 262700, China
| | - Zhigang Sun
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Yang Y, Zhang S, Ranasinghe KD, Isayev O, Roitberg AE. Machine Learning of Reactive Potentials. Annu Rev Phys Chem 2024; 75:371-395. [PMID: 38941524 DOI: 10.1146/annurev-physchem-062123-024417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
In the past two decades, machine learning potentials (MLPs) have driven significant developments in chemical, biological, and material sciences. The construction and training of MLPs enable fast and accurate simulations and analysis of thermodynamic and kinetic properties. This review focuses on the application of MLPs to reaction systems with consideration of bond breaking and formation. We review the development of MLP models, primarily with neural network and kernel-based algorithms, and recent applications of reactive MLPs (RMLPs) to systems at different scales. We show how RMLPs are constructed, how they speed up the calculation of reactive dynamics, and how they facilitate the study of reaction trajectories, reaction rates, free energy calculations, and many other calculations. Different data sampling strategies applied in building RMLPs are also discussed with a focus on how to collect structures for rare events and how to further improve their performance with active learning.
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Affiliation(s)
- Yinuo Yang
- Department of Chemistry, University of Florida, Gainesville, Florida;
| | - Shuhao Zhang
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania;
| | | | - Olexandr Isayev
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania;
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida;
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Mazo-Sevillano PD, Aguado A, Goicoechea JR, Roncero O. Quantum study of the CH3+ photodissociation in full-dimensional neural network potential energy surfaces. J Chem Phys 2024; 160:184307. [PMID: 38738612 DOI: 10.1063/5.0206895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
C H 3 + , a cornerstone intermediate in interstellar chemistry, has recently been detected for the first time by using the James Webb Space Telescope. The photodissociation of this ion is studied here. Accurate explicitly correlated multi-reference configuration interaction ab initio calculations are done, and full-dimensional potential energy surfaces are developed for the three lower electronic states, with a fundamental invariant neural network method. The photodissociation cross section is calculated using a full-dimensional quantum wave packet method in heliocentric Radau coordinates. The wave packet is represented in angular and radial grids, allowing us to reduce the number of points physically accessible, requiring to push up the spurious states appearing when evaluating the angular kinetic terms, through projection technique. The photodissociation spectra, when employed in astrochemical models to simulate the conditions of the Orion bar, result in a lesser destruction of CH3+ compared to that obtained when utilizing the recommended values in the kinetic database for astrochemistry.
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Affiliation(s)
- Pablo Del Mazo-Sevillano
- Unidad Asociada UAM-IFF-CSIC, Departamento de Química Física Aplicada, Facultad de Ciencias M-14, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alfredo Aguado
- Unidad Asociada UAM-IFF-CSIC, Departamento de Química Física Aplicada, Facultad de Ciencias M-14, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Javier R Goicoechea
- Instituto de Física Fundamental (IFF-CSIC), C.S.I.C., Serrano 123, 28006 Madrid, Spain
| | - Octavio Roncero
- Instituto de Física Fundamental (IFF-CSIC), C.S.I.C., Serrano 123, 28006 Madrid, Spain
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Laskar MR, Bhattacharya A, Dasgputa K. Efficient simulation of potential energy operators on quantum hardware: a study on sodium iodide (NaI). Sci Rep 2024; 14:10831. [PMID: 38734700 DOI: 10.1038/s41598-024-60605-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
This study introduces a conceptually novel polynomial encoding algorithm for simulating potential energy operators encoded in diagonal unitary forms in a quantum computing machine. The current trend in quantum computational chemistry is effective experimentation to achieve high-precision quantum computational advantage. However, high computational gate complexity and fidelity loss are some of the impediments to the realization of this advantage in a real quantum hardware. In this study, we address the challenges of building a diagonal Hamiltonian operator having exponential functional form, and its implementation in the context of the time evolution problem (Hamiltonian simulation and encoding). Potential energy operators when represented in the first quantization form is an example of such types of operators. Through systematic decomposition and construction, we demonstrate the efficacy of the proposed polynomial encoding method in reducing gate complexity from O ( 2 n ) to O ∑ i = 1 r n C r (for some r ≪ n ). This offers a solution with lower complexity in comparison to the conventional Hadamard basis encoding approach. The effectiveness of the proposed algorithm was validated with its implementation in the IBM quantum simulator and IBM quantum hardware. This study demonstrates the proposed approach by taking the example of the potential energy operator of the sodium iodide molecule (NaI) in the first quantization form. The numerical results demonstrate the potential applicability of the proposed method in quantum chemistry problems, while the analytical bound for error analysis and computational gate complexity discussed, throw light on issues regarding its implementation.
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Affiliation(s)
- Mostafizur Rahaman Laskar
- IBM Research, Bangalore, India.
- G. S. Sanyal School of Telecommunications, Indian Institute of Technology Kharagpur, Kharagpur, India.
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Zhang R, Yan S, Song H, Guo H, Ning C. Probing the activated complex of the F + NH 3 reaction via a dipole-bound state. Nat Commun 2024; 15:3858. [PMID: 38719855 PMCID: PMC11079065 DOI: 10.1038/s41467-024-48202-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Experimental characterization of the transition state poses a significant challenge due to its fleeting nature. Negative ion photodetachment offers a unique tool for probing transition states and their vicinity. However, this approach is usually limited to Franck-Condon regions. For example, high-lying Feshbach resonances with an excited HF stretching mode (vHF = 2-4) were recently identified in the transition-state region of the F + NH3 → HF + NH2 reaction through photo-detaching FNH3- anions, but the direct photodetachment failed to observe the lower-lying vHF = 0,1 resonances and bound states due apparently to negligible Franck-Condon factors. Indeed, these weak transitions can be resonantly enhanced via a dipole-bound state (DBS) formed between an electron and the polar FNH3 species. In this study, we unveil a series of Feshbach resonances and bound states along the F + NH3 reaction path via a DBS by combining high-resolution photoelectron spectroscopy with high-level quantum dynamical computations. This study presents an approach for probing the activated complex in a reaction by negative ion photodetachment through a DBS.
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Affiliation(s)
- Rui Zhang
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, 100084, Beijing, China
| | - Shuaiting Yan
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, 100084, Beijing, China
| | - Hongwei Song
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Hua Guo
- Department of Chemistry and Chemical Biology, Center for Computational Chemistry, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Chuangang Ning
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, 100084, Beijing, China.
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Pandey P, Arandhara M, Houston PL, Qu C, Conte R, Bowman JM, Ramesh SG. Assessing Permutationally Invariant Polynomial and Symmetric Gradient Domain Machine Learning Potential Energy Surfaces for H 3O 2. J Phys Chem A 2024; 128:3212-3219. [PMID: 38624168 PMCID: PMC11056970 DOI: 10.1021/acs.jpca.4c01044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
The singly hydrated hydroxide anion OH-(H2O) is of central importance to a detailed molecular understanding of water; therefore, there is strong motivation to develop a highly accurate potential to describe this anion. While this is a small molecule, it is necessary to have an extensive data set of energies and, if possible, forces to span several important stationary points. Here, we assess two machine-learned potentials, one using the symmetric gradient domain machine learning (sGDML) method and one based on permutationally invariant polynomials (PIPs). These are successors to a PIP potential energy surface (PES) reported in 2004. We describe the details of both fitting methods and then compare the two PESs with respect to precision, properties, and speed of evaluation. While the precision of the potentials is similar, the PIP PES is much faster to evaluate for energies and energies plus gradient than the sGDML one. Diffusion Monte Carlo calculations of the ground vibrational state, using both potentials, produce similar large anharmonic downshift of the zero-point energy compared to the harmonic approximation of the PIP and sGDML potentials. The computational time for these calculations using the sGDML PES is roughly 300 times greater than using the PIP one.
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Affiliation(s)
- Priyanka Pandey
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Mrinal Arandhara
- Department
of Inorganic and Physical Chemistry, Indian
Institute of Science, Bangalore 560012, India
| | - 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
| | - Chen Qu
- Independent
Researcher, Toronto, Ontario M9B0E3, Canada
| | - Riccardo Conte
- Dipartimento
di Chimica, Università degli Studi
di Milano, Milano 20133, Italy
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Sai G. Ramesh
- Department
of Inorganic and Physical Chemistry, Indian
Institute of Science, Bangalore 560012, India
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15
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Shu Y, Akher FB, Guo H, Truhlar DG. Parametrically Managed Activation Functions for Improved Global Potential Energy Surfaces for Six Coupled 5A' States and Fourteen Coupled 3A' States of O + O 2. J Phys Chem A 2024; 128:1207-1217. [PMID: 38349764 DOI: 10.1021/acs.jpca.3c06823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
We report new potential energy surfaces for six coupled 5A' states and 14 coupled 3A' states of O3. The new surfaces are created by parametrically managed diabatization by deep neural network (PM-DDNN). The PM-DDNN method uses calculated adiabatic potential energy surfaces to discover and fit an underlying adiabatic-equivalent set of diabatic surfaces and their couplings and obtains the fit to the adiabatic surfaces by diagonalization of the diabatic potential energy matrix (DPEM). The procedure yields the adiabatic surfaces and their gradients, as well as the DPEM and its gradient. If desired one can also compute the nonadiabatic coupling due to the transformation. The present work improves on previous work by using a new coordinate to guide the decay of the neural network contribution to the many-body fit to the whole DPEM. The main objective was to obtain smoother potentials than the previous ones with better suitability for dynamics calculations, and this was achieved. Furthermore, we obtained suitably small deviations from the input reference data. For the six coupled 5A' surfaces, the 60,366 data below 10 eV are fit with a mean unsigned error (MUE) of 49 meV, and for the 14 coupled 3A' surfaces, the 76,733 data below 10 eV are fit with an MUE of 28 meV. The data below 5 eV fit even more accurately with MUEs of 37 meV (5A') and 20 meV (3A').
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Affiliation(s)
- Yinan Shu
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Farideh Badichi Akher
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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16
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Miao Z, Zhang X, Zhang Y, Wang L, Meng Q. Chemistry-Informed Generative Model for Classical Dynamics Simulations. J Phys Chem Lett 2024; 15:532-539. [PMID: 38194494 DOI: 10.1021/acs.jpclett.3c03114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
In this work, a chemistry-informed generative model was proposed, leading to the chemistry-informed generative adversarial network (CI-GAN) approach. To easily build the input database for complex molecular systems, an image-input algorithm is also implemented, leading to the capability to directly recognize the molecular image. Extensive test calculations and analysis on typical examples, H + H2, OH + HO2, and H2O/TiO2(110), find that the present CI-GAN approach generates distributions of geometry and energy. Calculations on the above examples show that the present CI-GAN approach is able to generate 50%-80% meaningful results among all of the generated data with chemistry constraints. Thus, it has the potential capability to predict classical dynamics simulations as well as ab initio calculations avoiding expensive calculations. These results and the power of CI-GANs in generating ab initio energies and MD trajectories are deeply discussed.
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Affiliation(s)
- Zekai Miao
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
| | - Xingyu Zhang
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
| | - Yuyuan Zhang
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
| | - Lemei Wang
- Ministry-of-Education Engineering Center for Embedded System Integration, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
| | - Qingyong Meng
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
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17
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Yu Y, Yang D, Zhou Y, Xie D. A New Full-Dimensional Ab Initio Intermolecular Potential Energy Surface and Rovibrational Energies of the H 2O-H 2 Complex. J Phys Chem A 2024; 128:170-181. [PMID: 38109882 DOI: 10.1021/acs.jpca.3c06805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
H2O-H2 is a prototypical five-atom van der Waals system, and the interaction between H2O and H2 plays an important role in many physical and chemical environments. However, previous full-dimensional intermolecular potential energy surfaces (IPESs) cannot accurately describe the H2O-H2 interaction in the repulsive or van der Waals minimum region. In this work, we constructed a full-dimensional IPES for the title system with a small root-mean-square error of 0.252 cm-1 by using the permutation invariant polynomial neural network method. The ab initio calculations were performed by employing the explicitly corrected coupled cluster [CCSD(T)-F12a] method with the augmented correlation-consistent polarized valence quintuple-ζ basis set. Based on the newly developed IPES, the bound states of the H2O-H2 complex were calculated within the rigid-rotor approximation. The transition frequencies and band origins agreed well with the experimental values [Weida, M. J.; Nesbitt, D. J. J. Chem. Phys. 1999, 110, 156-167] with errors less than 0.1 cm-1 for most transitions. Those results demonstrate the high accuracy of our new IPES, which would build a solid foundation for the collisional dynamics of H2O-H2 at low temperatures.
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Affiliation(s)
- Yipeng Yu
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dongzheng Yang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yanzi Zhou
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Hefei National Laboratory, Hefei 230088, China
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18
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Stark W, Westermayr J, Douglas-Gallardo OA, Gardner J, Habershon S, Maurer RJ. Machine Learning Interatomic Potentials for Reactive Hydrogen Dynamics at Metal Surfaces Based on Iterative Refinement of Reaction Probabilities. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:24168-24182. [PMID: 38148847 PMCID: PMC10749455 DOI: 10.1021/acs.jpcc.3c06648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/28/2023]
Abstract
The reactive chemistry of molecular hydrogen at surfaces, notably dissociative sticking and hydrogen evolution, plays a crucial role in energy storage and fuel cells. Theoretical studies can help to decipher underlying mechanisms and reaction design, but studying dynamics at surfaces is computationally challenging due to the complex electronic structure at interfaces and the high sensitivity of dynamics to reaction barriers. In addition, ab initio molecular dynamics, based on density functional theory, is too computationally demanding to accurately predict reactive sticking or desorption probabilities, as it requires averaging over tens of thousands of initial conditions. High-dimensional machine learning-based interatomic potentials are starting to be more commonly used in gas-surface dynamics, yet robust approaches to generate reliable training data and assess how model uncertainty affects the prediction of dynamic observables are not well established. Here, we employ ensemble learning to adaptively generate training data while assessing model performance with full uncertainty quantification (UQ) for reaction probabilities of hydrogen scattering on different copper facets. We use this approach to investigate the performance of two message-passing neural networks, SchNet and PaiNN. Ensemble-based UQ and iterative refinement allow us to expose the shortcomings of the invariant pairwise-distance-based feature representation in the SchNet model for gas-surface dynamics.
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Affiliation(s)
- Wojciech
G. Stark
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Julia Westermayr
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | | | - James Gardner
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Scott Habershon
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Reinhard J. Maurer
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
- Department
of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
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19
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Teng C, Huang D, Donahue E, Bao JL. Exploring torsional conformer space with physical prior mean function-driven meta-Gaussian processes. J Chem Phys 2023; 159:214111. [PMID: 38051097 DOI: 10.1063/5.0176709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/12/2023] [Indexed: 12/07/2023] Open
Abstract
We present a novel approach for systematically exploring the conformational space of small molecules with multiple internal torsions. Identifying unique conformers through a systematic conformational search is important for obtaining accurate thermodynamic functions (e.g., free energy), encompassing contributions from the ensemble of all local minima. Traditional geometry optimizers focus on one structure at a time, lacking transferability from the local potential-energy surface (PES) around a specific minimum to optimize other conformers. In this work, we introduce a physics-driven meta-Gaussian processes (meta-GPs) method that not only enables efficient exploration of target PES for locating local minima but, critically, incorporates physical surrogates that can be applied universally across the optimization of all conformers of the same molecule. Meta-GPs construct surrogate PESs based on the optimization history of prior conformers, dynamically selecting the most suitable prior mean function (representing prior knowledge in Bayesian learning) as a function of the optimization progress. We systematically benchmarked the performance of multiple GP variants for brute-force conformational search of amino acids. Our findings highlight the superior performance of meta-GPs in terms of efficiency, comprehensiveness of conformer discovery, and the distribution of conformers compared to conventional non-surrogate optimizers and other non-meta-GPs. Furthermore, we demonstrate that by concurrently optimizing, training GPs on the fly, and learning PESs, meta-GPs exhibit the capacity to generate high-quality PESs in the torsional space without extensive training data. This represents a promising avenue for physics-based transfer learning via meta-GPs with adaptive priors in exploring torsional conformer space.
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Affiliation(s)
- Chong Teng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Daniel Huang
- Department of Computer Science, San Francisco State University, San Francisco, California 94132, USA
| | - Elizabeth Donahue
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Junwei Lucas Bao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
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20
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Fu B, Zhang DH. Accurate fundamental invariant-neural network representation of ab initio potential energy surfaces. Natl Sci Rev 2023; 10:nwad321. [PMID: 38274241 PMCID: PMC10808953 DOI: 10.1093/nsr/nwad321] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 01/27/2024] Open
Abstract
Highly accurate potential energy surfaces are critically important for chemical reaction dynamics. The large number of degrees of freedom and the intricate symmetry adaption pose a big challenge to accurately representing potential energy surfaces (PESs) for polyatomic reactions. Recently, our group has made substantial progress in this direction by developing the fundamental invariant-neural network (FI-NN) approach. Here, we review these advances, demonstrating that the FI-NN approach can represent highly accurate, global, full-dimensional PESs for reactive systems with even more than 10 atoms. These multi-channel reactions typically involve many intermediates, transition states, and products. The complexity and ruggedness of this potential energy landscape present even greater challenges for full-dimensional PES representation. These PESs exhibit a high level of complexity, molecular size, and accuracy of fit. Dynamics simulations based on these PESs have unveiled intriguing and novel reaction mechanisms, providing deep insights into the intricate dynamics involved in combustion, atmospheric, and organic chemistry.
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Affiliation(s)
- Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Hefei National Laboratory, Hefei 230088, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Hefei National Laboratory, Hefei 230088, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Xia J, Zhang Y, Jiang B. Accuracy Assessment of Atomistic Neural Network Potentials: The Impact of Cutoff Radius and Message Passing. J Phys Chem A 2023; 127:9874-9883. [PMID: 37943102 DOI: 10.1021/acs.jpca.3c06024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Atomistic neural network potentials have achieved great success in accelerating atomistic simulations in complicated systems in recent years. They are typically based on the atomic decomposition of total properties, truncating the interatomic correlations to a local environment within a given cutoff radius. A more recently developed message passing (MP) neural network framework can, in principle, incorporate nonlocal effects through iteratively correlating some atoms outside the cutoff sphere with atoms inside, a process referred to as MP. However, how the model accuracy depends on the cutoff radius and the MP process has rarely been discussed. In this work, we investigate this dependence using a recursively embedded atom neural network method that possesses both local and MP features, in two representative systems: liquid H2O and solid Al2O3. We focus on how these settings influence predictions for structural and vibrational properties, namely, radial distribution functions (RDFs) and vibrational density of states (VDOSs). We find that while MP lowers test errors of energy and forces in general, it may not improve the prediction for RDFs and/or VDOSs if direct interatomic correlations in the local environment are insufficiently described. A cutoff radius exceeding the first neighbor shell is necessary, beyond which involving MP quickly enhances the model accuracy until convergence. This is a potentially more efficient way to increase the model accuracy than directly increasing the cutoff radius, especially with more memory savings in the GPU implementation. Our findings also suggest that using the mean test error as the measure of the model accuracy alone is inadequate.
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Affiliation(s)
- Junfan Xia
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yaolong Zhang
- École Polytechnique FFlytech de Lausanne, 1015 Lausanne, Switzerland
| | - Bin Jiang
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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22
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Shu Y, Varga Z, Zhang D, Truhlar DG. ChemPotPy: A Python Library for Analytic Representations of Potential Energy Surfaces and Diabatic Potential Energy Matrices. J Phys Chem A 2023; 127:9635-9640. [PMID: 37916790 DOI: 10.1021/acs.jpca.3c05899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Constructing analytic representations of global and semiglobal potential energy surfaces is difficult and can be laborious, and it is even harder when one needs coupled potential energy surfaces and their electronically nonadiabatic couplings. When accomplished, however, the resulting potential functions are a valuable resource. To facilitate the convenient use of potentials that have been developed, we provide a collection of existing surfaces in a library with consistent units and formats. A potential energy surface library of this type, namely PotLib, was built more than 20 years ago. However, that library only provided pristine Fortran subroutines for each potential energy surface, and therefore, it is not as user-friendly as would be desirable. Here, we report the creation of ChemPotPy, a CHEMical library of POTential energy surfaces in PYthon. ChemPotPy is a user-friendly library for analytic representation of single-state and multistate potential energy surfaces and couplings. A given entry in the library contains an analytic potential energy function or analytic functions for a set of coupled potential energy surfaces, and depending on the case, it may also include analytic or numerical gradients, nonadiabatic coupling vectors, and/or diabatic potential energy matrices and their gradients. Only three inputs, namely, the chemical formula of the system, the name of the potential energy surface or surface set, and the Cartesian geometry, are required. ChemPotPy uses the same units for input and output quantities of all surfaces and surface sets to facilitate general interfaces with the dynamics programs. The initial version of the library contains 338 entries, and we anticipate that more will be added in the future.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Zoltan Varga
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Dayou Zhang
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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23
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Wu H, Fu Y, Fu B, Zhang DH. Roaming Dynamics in Hydroxymethyl Hydroperoxide Decomposition Revealed by the Full-Dimensional Potential Energy Surface of the CH 2OO + H 2O Reaction. J Phys Chem A 2023; 127:9098-9105. [PMID: 37870501 DOI: 10.1021/acs.jpca.3c05818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The CH2OO + H2O reaction is an important atmospheric process that leads to the formation of formic acid (HCOOH) and water via the intermediate hydroxymethyl hydroperoxide (HOCH2OOH, HMHP). We investigated the intricacies of this process by employing quasiclassical trajectory calculations on an accurate, full-dimensional ab initio potential energy surface (PES). In addition to the direct mechanism via the transition state (TS), an interesting roaming mechanism was found to play the predominant role in producing H2O and HCOOH. This roaming pathway is featured as the near direct dissociation of HMHP into OH and hydroxymethoxy radical, followed by the retraction of OH and abstraction of the H atom, culminating in the formation of H2O. Due to the longer interaction time of the roaming mechanism, less product translational energy was released, but more internal energies of HCOOH were obtained, as compared with the direct TS mechanism. The enhanced yield of H2O and formic acid achieved through roaming dynamics underscores the significance of dynamics simulations based on an accurate full-dimensional PES. This work provides new insights into the dynamics of the CH2OO + H2O reaction and its implications for atmospheric chemistry.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanlin Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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24
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Zhang Z, Wu H, Chen Z, Fu Y, Fu B, Zhang DH, Yang X, Yuan K. Multiple Dissociation Pathways in HNCO Decomposition Governed by Potential Energy Surface Topography. JACS AU 2023; 3:2855-2861. [PMID: 37885590 PMCID: PMC10598830 DOI: 10.1021/jacsau.3c00414] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/24/2023] [Accepted: 08/31/2023] [Indexed: 10/28/2023]
Abstract
The exquisite features of molecular photochemistry are key to any complete understanding of the chemical processes governed by potential energy surfaces (PESs). It is well established that multiple dissociation pathways relate to nonadiabatic transitions between multiple coupled PESs. However, little detail is known about how the single PES determines reaction outcomes. Here we perform detailed experiments on HNCO photodissociation, acquiring the state-specific correlations of the NH (a1Δ) and CO (X1Σ+) products. The experiments reveal a trimodal CO rotational distribution. Dynamics simulations based on a full-dimensional machine-learning-based PES of HNCO unveil three dissociation pathways exclusively occurring on the S1 excited electronic state. One pathway, following the minimum energy path (MEP) via the transition state, contributes to mild rotational excitation in CO, while the other two pathways deviating substantially from the MEP account for relatively cold and hot CO rotational state populations. These peculiar dynamics are unambiguously governed by the S1 state PES topography, i.e., a narrow acceptance cone in the vicinity of the transition state region. The dynamical picture shown in this work will serve as a textbook example illustrating the importance of the PES topography in molecular photochemistry.
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Affiliation(s)
- Zhiguo Zhang
- State
Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent
Light Source, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- Key
Laboratory of Functional Materials and Devices for Informatics of
Anhui Educational Institutions and School of Physics and Electronic
Engineering, Fuyang Normal University, Fuyang, Anhui 236041, China
| | - Hao Wu
- State
Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent
Light Source, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhichao Chen
- State
Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent
Light Source, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yanlin Fu
- State
Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent
Light Source, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Bina Fu
- State
Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent
Light Source, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Hefei
National Laboratory, Hefei 230088, China
| | - Dong H. Zhang
- State
Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent
Light Source, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Hefei
National Laboratory, Hefei 230088, China
| | - Xueming Yang
- State
Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent
Light Source, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Hefei
National Laboratory, Hefei 230088, China
- Department
of Chemistry and Center for Advanced Light Source Research, College
of Science, Southern University of Science
and Technology, Shenzhen 518055, China
| | - Kaijun Yuan
- State
Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent
Light Source, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Hefei
National Laboratory, Hefei 230088, China
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25
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Liu X, Wang W, Pérez-Ríos J. Molecular dynamics-driven global potential energy surfaces: Application to the AlF dimer. J Chem Phys 2023; 159:144103. [PMID: 37811831 DOI: 10.1063/5.0169080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
In this work, we present a full-dimensional potential energy surface for AlF-AlF. We apply a general machine learning approach for full-dimensional potential energy surfaces, employing an active learning scheme trained on ab initio points, whose size grows based on the accuracy required. The training points are selected based on molecular dynamics simulations, choosing the most suitable configurations for different collision energy and mapping the most relevant part of the potential energy landscape of the system. The present approach does not require long-range information and is entirely general. As a result, it is possible to provide the full-dimensional AlF-AlF potential energy surface, requiring ≲0.01% of the configurations to be calculated ab initio. Furthermore, we analyze the general properties of the AlF-AlF system, finding critical differences with other reported results on CaF or bi-alkali dimers.
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Affiliation(s)
- Xiangyue Liu
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Weiqi Wang
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Jesús Pérez-Ríos
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-3800, USA
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26
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Zhang Y, Jiang B. Universal machine learning for the response of atomistic systems to external fields. Nat Commun 2023; 14:6424. [PMID: 37827998 PMCID: PMC10570356 DOI: 10.1038/s41467-023-42148-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/01/2023] [Indexed: 10/14/2023] Open
Abstract
Machine learned interatomic interaction potentials have enabled efficient and accurate molecular simulations of closed systems. However, external fields, which can greatly change the chemical structure and/or reactivity, have been seldom included in current machine learning models. This work proposes a universal field-induced recursively embedded atom neural network (FIREANN) model, which integrates a pseudo field vector-dependent feature into atomic descriptors to represent system-field interactions with rigorous rotational equivariance. This "all-in-one" approach correlates various response properties like dipole moment and polarizability with the field-dependent potential energy in a single model, very suitable for spectroscopic and dynamics simulations in molecular and periodic systems in the presence of electric fields. Especially for periodic systems, we find that FIREANN can overcome the intrinsic multiple-value issue of the polarization by training atomic forces only. These results validate the universality and capability of the FIREANN method for efficient first-principles modeling of complicated systems in strong external fields.
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Affiliation(s)
- Yaolong Zhang
- Key Laboratory of Precision and Intelligent Chemistry, 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
- École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Bin Jiang
- Key Laboratory of Precision and Intelligent Chemistry, 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.
- Hefei National Laboratory, University of Science and Technology of China, Hefei, 230088, China.
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27
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Yu Q, Qu C, Houston PL, Nandi A, Pandey P, Conte R, Bowman JM. A Status Report on "Gold Standard" Machine-Learned Potentials for Water. J Phys Chem Lett 2023; 14:8077-8087. [PMID: 37656898 PMCID: PMC10510435 DOI: 10.1021/acs.jpclett.3c01791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Owing to the central importance of water to life as well as its unusual properties, potentials for water have been the subject of extensive research over the past 50 years. Recently, five potentials based on different machine learning approaches have been reported that are at or near the "gold standard" CCSD(T) level of theory. The development of such high-level potentials enables efficient and accurate simulations of water systems using classical and quantum dynamical approaches. This Perspective serves as a status report of these potentials, focusing on their methodology and applications to water systems across different phases. Their performances on the energies of gas phase water clusters, as well as condensed phase structural and dynamical properties, are discussed.
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Affiliation(s)
- Qi Yu
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent
Researcher, Toronto, Ontario M9B 0E3, 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
| | - Apurba Nandi
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Priyanka Pandey
- 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
| | - 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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28
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Hashem Y, Foust K, Kaledin M, Kaledin AL. Fitting Potential Energy Surfaces by Learning the Charge Density Matrix with Permutationally Invariant Polynomials. J Chem Theory Comput 2023; 19:5690-5700. [PMID: 37561135 PMCID: PMC10501011 DOI: 10.1021/acs.jctc.3c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Indexed: 08/11/2023]
Abstract
The electronic energy in the Hartree-Fock (HF) theory is the trace of the product of the charge density matrix (CDM) with the one-electron and two-electron matrices represented in an atomic orbital basis, where the two-electron matrix is also a function of the same CDM. In this work, we examine a formalism of analytic representation of a generic molecular potential energy surface (PES) as a sum of a linearly parameterized HF and a correction term, the latter formally representing the electron correlation energy, also linearly parameterized, by expressing the elements of CDM using permutationally invariant polynomials (PIPs). We show on a variety of numerical examples, ranging from exemplary two-electron systems HeH+ and H3+ to the more challenging cases of methanium (CH5+) fragmentation and high-energy tautomerization of formamide to formimidic acid that such a formulation requires significantly fewer, 10-20% of PIPs, to accomplish the same accuracy of the fit as the conventional representation at practically the same computational cost.
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Affiliation(s)
- Younos Hashem
- Department
of Chemistry & Biochemistry, Kennesaw
State University, 370 Paulding Ave NW, Box # 1203, Kennesaw 30144, Georgia
| | - Katheryn Foust
- Department
of Chemistry & Biochemistry, Kennesaw
State University, 370 Paulding Ave NW, Box # 1203, Kennesaw 30144, Georgia
| | - Martina Kaledin
- Department
of Chemistry & Biochemistry, Kennesaw
State University, 370 Paulding Ave NW, Box # 1203, Kennesaw 30144, Georgia
| | - Alexey L. Kaledin
- Cherry
L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta 30322, Georgia
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29
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Fu L, Yang S, Zhang DH. Neural network potential energy surfaces and dipole moment surfaces for SO 2(H 2O) and SO 2(H 2O) 2 complexes. Phys Chem Chem Phys 2023; 25:22804-22812. [PMID: 37584113 DOI: 10.1039/d3cp03113f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Full-dimensional, ab initio-based many-body potential energy surfaces and dipole moment surfaces constructed using the neural network method for SO2(H2O)n (n = 1,2) complexes are reported. The database of the SO2 1-body PES, SO2(H2O) 2-body PES and SO2(H2O)2 3-body PES consists of 11 952, 79 882 and 84 159 ab initio energies, respectively. All 1-body energies were calculated at the CCSD(T)/CBS(AVTZ:AVQZ) level and all 2,3-body energies were calculated at the DSD-PBEP86/AVTZ level. The database of DMSs is the same as that of PESs and all dipole moments were calculated at the MP2/AVTZ level. Harmonic frequencies and dissociation energies of SO2(H2O) and SO2(H2O)2 were calculated on these PESs and compared with ab initio results to examine the fidelity of these PESs.
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Affiliation(s)
- Liangfei Fu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shuo Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.
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30
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Tkachenko NV, Tkachenko AA, Nebgen B, Tretiak S, Boldyrev AI. Neural network atomistic potentials for global energy minima search in carbon clusters. Phys Chem Chem Phys 2023; 25:21173-21182. [PMID: 37490276 DOI: 10.1039/d3cp02317f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The global energy optimization problem is an acute and important problem in chemistry. It is crucial to know the geometry of the lowest energy isomer (global minimum, GM) of a given compound for the evaluation of its chemical and physical properties. This problem is especially relevant for atomic clusters. Due to the exponential growth of the number of local minima geometries with the increase of the number of atoms in the cluster, it is important to find a computationally efficient and reliable method to navigate the energy landscape and locate a true global minima structure. Newly developed neural network (NN) atomistic potentials offer a numerically efficient and relatively accurate approach for molecular structure optimization. An important question that needs to be answered is "Can NN potentials, trained on a given set, represent the potential energy surface (PES) of a neighboring domain?". In this work, we tested the applicability of ANI-1ccx and ANI-nr NN atomistic potentials for the global minima optimization of carbon clusters Cn (n = 3-10). We showed that with the introduction of the cluster connectivity restriction and consequent DFT or ab initio calculations, ANI-1ccx and ANI-nr can be considered as robust PES pre-samplers that can capture the GM structure even for large clusters such as C20.
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Affiliation(s)
- Nikolay V Tkachenko
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
| | | | - Benjamin Nebgen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Alexander I Boldyrev
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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31
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Li J, Tu Z, Xiang H, Li Y, Song H. Theoretical studies on the kinetics and dynamics of the BeH + + H 2O reaction: comparison with the experiment. Phys Chem Chem Phys 2023; 25:20997-21005. [PMID: 37503894 DOI: 10.1039/d3cp02322b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The reaction of BeH+ with background gaseous H2O may play a role in qubit loss for quantum information processing with Be+ as trapped ions, and yet its reaction mechanism has not been well understood until now. In this work, a globally accurate, full-dimensional ground-state potential energy surface (PES) for the BeH+ + H2O reaction was constructed by fitting a total of 170 438 ab initio energy points at the level of RCCSD(T)-F12/aug-cc-pVTZ using the fundamental invariant-neural network method. The total root-mean-square error of the final PES was 0.178 kcal mol-1. For comparison, quasi-classical trajectory calculations were carried out on the PES at an experimental temperature of 150 K. The obtained thermal rate constant and product branching ratio of the BeD+ + H2O reaction agreed quite well with experimental results. In addition, the vibrational state distributions and energy disposals of the products were calculated and rationalized using the sudden vector projection model.
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Affiliation(s)
- Jiaqi Li
- College of Physical Science and Technology, Huazhong Normal University, Wuhan 430079, China.
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Zhao Tu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- School of Chemical and Environmental Engineering, Hubei Minzu University, Enshi 445000, China
| | - Haipan Xiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- School of Physics and Electronics, Hunan University, Changsha 410082, China
| | - Yong Li
- College of Physical Science and Technology, Huazhong Normal University, Wuhan 430079, China.
| | - Hongwei Song
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
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32
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Akher FB, Shu Y, Varga Z, Bhaumik S, Truhlar DG. Parametrically Managed Activation Function for Fitting a Neural Network Potential with Physical Behavior Enforced by a Low-Dimensional Potential. J Phys Chem A 2023. [PMID: 37307218 DOI: 10.1021/acs.jpca.3c02627] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Machine-learned representations of potential energy surfaces generated in the output layer of a feedforward neural network are becoming increasingly popular. One difficulty with neural network output is that it is often unreliable in regions where training data is missing or sparse. Human-designed potentials often build in proper extrapolation behavior by choice of functional form. Because machine learning is very efficient, it is desirable to learn how to add human intelligence to machine-learned potentials in a convenient way. One example is the well-understood feature of interaction potentials that they vanish when subsystems are too far separated to interact. In this article, we present a way to add a new kind of activation function to a neural network to enforce low-dimensional constraints. In particular, the activation function depends parametrically on all of the input variables. We illustrate the use of this step by showing how it can force an interaction potential to go to zero at large subsystem separations without either inputting a specific functional form for the potential or adding data to the training set in the asymptotic region of geometries where the subsystems are separated. In the process of illustrating this, we present an improved set of potential energy surfaces for the 14 lowest 3A' states of O3. The method is more general than this example, and it may be used to add other low-dimensional knowledge or lower-level knowledge to machine-learned potentials. In addition to the O3 example, we present a greater-generality method called parametrically managed diabatization by deep neural network (PM-DDNN) that is an improvement on our previously presented permutationally restrained diabatization by deep neural network (PR-DDNN).
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Affiliation(s)
- Farideh Badichi Akher
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Yinan Shu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Zoltan Varga
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Suman Bhaumik
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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33
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Li C, Hou S, Xie C. Constructing Diabatic Potential Energy Matrices with Neural Networks Based on Adiabatic Energies and Physical Considerations: Toward Quantum Dynamic Accuracy. J Chem Theory Comput 2023. [PMID: 37216273 DOI: 10.1021/acs.jctc.2c01074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A permutation invariant polynomial-neural network (PIP-NN) approach for constructing the global diabatic potential energy matrices (PEMs) of the coupled states of molecules is proposed. Specifically, the diabatization scheme is based merely on the adiabatic energy data of the system, which is ideally a most convenient way due to not requiring additional ab initio calculations for the data of the derivative coupling or any other physical properties of the molecule. Considering the permutation and coupling characteristics of the system, particularly in the presence of conical intersections, some vital treatments for the off-diagonal terms in diabatic PEM are essentially needed. Taking the photodissociation of H2O(X~/B~)/NH3(X~/A~) and nonadiabatic reaction Na(3p) + H2 → NaH(Σ+) + H for example, this PIP-NN method is shown to build up the global diabatic PEMs effectively and accurately. The root-mean-square errors of the adiabatic potential energies in the fitting for three different systems are all small (<10 meV). Further quantum dynamic calculations show that the absorption spectra and product branching ratios in both H2O(X~/B~) and NH3(X~/A~) nonadiabatic photodissociation are well reproduced on the new diabatic PEMs, and the nonadiabatic reaction probability of Na(3p) + H2 → NaH(Σ+) + H obtained on the new diabatic PEMs of the 12A1 and 12B2 states is in reasonably good agreement with previous theoretical result as well, validating this new PIP-NN method.
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Affiliation(s)
- Chaofan Li
- Institute of Modern Physics, Shaanxi Key Laboratory for Theoretical Physics Frontiers, Northwest University, Xi'an 710127, China
| | - Siting Hou
- Institute of Modern Physics, Shaanxi Key Laboratory for Theoretical Physics Frontiers, Northwest University, Xi'an 710127, China
| | - Changjian Xie
- Institute of Modern Physics, Shaanxi Key Laboratory for Theoretical Physics Frontiers, Northwest University, Xi'an 710127, China
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34
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Wu H, Fu Y, Dong W, Fu B, Zhang DH. Full-dimensional neural network potential energy surface and dynamics of the CH 2OO + H 2O reaction. RSC Adv 2023; 13:13397-13404. [PMID: 37143908 PMCID: PMC10153484 DOI: 10.1039/d3ra02069j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/16/2023] [Indexed: 05/06/2023] Open
Abstract
An accurate global full-dimensional machine learning-based potential energy surface (PES) of the simplest Criegee intermediate (CH2OO) reaction with water monomer was developed based on the high level of extensive CCSD(T)-F12a/aug-cc-pVTZ calculations. This analytical global PES not only covers the regions of reactants to hydroxymethyl hydroperoxide (HMHP) intermediates, but also different end product channels, which facilities both the reliable and efficient kinetics and dynamics calculations. The rate coefficients calculated by the transition state theory with the interface to the full-dimensional PES agree well with the experimental results, indicating the accuracy of the current PES. Extensive quasi-classical trajectory (QCT) calculations were performed both from the bimolecular reaction CH2OO + H2O and from HMHP intermediate on the new PES. The product branching ratios of hydroxymethoxy radical (HOCH2O, HMO) + OH radical, formaldehyde (CH2O) + H2O2 and formic acid (HCOOH) + H2O were calculated. The reaction yields dominantly HMO + OH, because of the barrierless pathway from HMHP to this channel. The computed dynamical results for this product channel show the total available energy was deposited into the internal rovibrational excitation of HMO, and the energy release in OH and translational energy is limited. The large amount of OH radical found in the current study implies that the CH2OO + H2O reaction can provide crucially OH yield in Earth's atmosphere.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yanlin Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Wenrui Dong
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Hefei National Laboratory Hefei 230088 China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Hefei National Laboratory Hefei 230088 China
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35
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Wang HD, Fu YL, Fu B, Fang W, Zhang DH. A highly accurate full-dimensional ab initio potential surface for the rearrangement of methylhydroxycarbene (H 3C-C-OH). Phys Chem Chem Phys 2023; 25:8117-8127. [PMID: 36876923 DOI: 10.1039/d3cp00312d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
We report here a full-dimensional machine learning global potential surface (PES) for the rearrangement of methylhydroxycarbene (H3C-C-OH, 1t). The PES is trained with the fundamental invariant neural network (FI-NN) method on 91 564 ab initio energies calculated at the UCCSD(T)-F12a/cc-pVTZ level of theory, covering three possible product channels. FI-NN PES has the correct symmetry properties with respect to permutation of four identical hydrogen atoms and is suitable for dynamics studies of the 1t rearrangement. The averaged root mean square error (RMSE) is 11.4 meV. Six important reaction pathways, as well as the energies and vibrational frequencies at the stationary geometries on these pathways are accurately preproduced by our FI-NN PES. To demonstrate the capacity of the PES, we calculated the rate coefficient of hydrogen migration in -CH3 (path A) and hydrogen migration of -OH (path B) with instanton theory on this PES. Our calculations predicted the half-life of 1t to be 95 min, which is excellent in agreement with experimental observations.
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Affiliation(s)
- Heng-Ding Wang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yan-Lin Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Wei Fang
- Fudan University, Shanghai, 200032, China.
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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36
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Li Y, Zhai Y, Li H. MLRNet: Combining the Physics-Motivated Potential Models with Neural Networks for Intermolecular Potential Energy Surface Construction. J Chem Theory Comput 2023; 19:1421-1431. [PMID: 36826225 DOI: 10.1021/acs.jctc.2c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
A physics-based machine learning model called MLRNet has been developed to construct the high-accuracy two-body intermolecular potential energy surface (IPES). The outputs of the neural network are integrated into the physically realistic Morse/long-range (MLR) function, which ensures that the MLRNet has meaningful extrapolation at both short and long ranges and solves the asymptotic problem in common neural network potential (NNP) models. The neural network representation of the MLR parameters is more flexible and more efficient than the polynomial expansion in the conventional mdMLR model, especially for systems containing nonrigid monomer(s). The present work illustrates the basic framework of the current MLRNet model, including (i) how to combine the physically meaningful MLR function with different possible NN structures, (ii) the preservation of permutation symmetry, and (iii) the predetermination of the long-range function uLR. We choose two realistic systems to demonstrate the performance of MLRNet: the three-dimensional IPES of CO2-He including the CO2 antisymmetric vibration Q3 and the six-dimensional IPES of the H2O-Ar system. In both cases, the fitting errors of the MLRNet are several times smaller than those of the conventional mdMLR model. Both short-range and long-range extrapolation tests were performed to illustrate the extrapolation ability of the MLRNet and its damping function version. Moreover, for the 6-D H2O-Ar system, the MLRNet only needs 1596 trainable parameters, which is almost equal to the number needed for the 5-D mdMLR model (1509) and half that needed for the PIP-NN model (3501) within similar accuracy, which illustrates the model efficiency in high-dimensional IPES fitting.
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Affiliation(s)
- You Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Yu Zhai
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Hui Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
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37
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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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38
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Käser S, Vazquez-Salazar LI, Meuwly M, Töpfer K. Neural network potentials for chemistry: concepts, applications and prospects. DIGITAL DISCOVERY 2023; 2:28-58. [PMID: 36798879 PMCID: PMC9923808 DOI: 10.1039/d2dd00102k] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Artificial Neural Networks (NN) are already heavily involved in methods and applications for frequent tasks in the field of computational chemistry such as representation of potential energy surfaces (PES) and spectroscopic predictions. This perspective provides an overview of the foundations of neural network-based full-dimensional potential energy surfaces, their architectures, underlying concepts, their representation and applications to chemical systems. Methods for data generation and training procedures for PES construction are discussed and means for error assessment and refinement through transfer learning are presented. A selection of recent results illustrates the latest improvements regarding accuracy of PES representations and system size limitations in dynamics simulations, but also NN application enabling direct prediction of physical results without dynamics simulations. The aim is to provide an overview for the current state-of-the-art NN approaches in computational chemistry and also to point out the current challenges in enhancing reliability and applicability of NN methods on a larger scale.
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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
| | - Kai Töpfer
- Department of Chemistry, University of Basel Klingelbergstrasse 80 CH-4056 Basel Switzerland
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39
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Observation of resonances in the transition state region of the F + NH 3 reaction using anion photoelectron spectroscopy. Nat Chem 2023; 15:194-199. [PMID: 36509851 DOI: 10.1038/s41557-022-01100-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/24/2022] [Indexed: 12/14/2022]
Abstract
The transition state of a chemical reaction is a dividing surface on the reaction potential energy surface (PES) between reactants and products and is thus of fundamental interest in understanding chemical reactivity. The transient nature of the transition state presents challenges to its experimental characterization. Transition-state spectroscopy experiments based on negative-ion photodetachment can provide a direct probe of this region of the PES, revealing the detailed vibrational structure associated with the transition state. Here we study the F + NH3 → HF + NH2 reaction using slow photoelectron velocity-map imaging spectroscopy of cryogenically cooled FNH3- anions. Reduced-dimensionality quantum dynamical simulations performed on a global PES show excellent agreement with the experimental results, enabling the assignment of spectral structure. Our combined experimental-theoretical study reveals a manifold of vibrational Feshbach resonances in the product well of the F + NH3 PES. At higher energies, the spectra identify features attributed to resonances localized across the transition state and into the reactant complex that may impact the bimolecular reaction dynamics.
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40
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Jiang T, Fang W, Alavi A, Chen J. General Analytical Nuclear Forces and Molecular Potential Energy Surface from Full Configuration Interaction Quantum Monte Carlo. J Chem Theory Comput 2022; 18:7233-7242. [PMID: 36326847 DOI: 10.1021/acs.jctc.2c00440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The full configuration interaction quantum Monte Carlo (FCIQMC) is a state-of-the-art stochastic electronic structure method, providing a methodology to compute FCI-level state energies of molecular systems within a quantum chemical basis. However, especially to probe dynamics at the FCIQMC level, it is necessary to devise more efficient schemes to produce nuclear forces and potential energy surfaces (PES) from FCIQMC. In this work, we derive the general formula for nuclear forces from FCIQMC, and clarify different contributions of the total force. This method to obtain FCIQMC forces eliminates previous restrictions and can be used with frozen core approximation and free selection of orbitals, making it promising for more efficient nuclear forces calculations. After some numerical checks of this procedure on the binding curve of N2 molecule, we use the FCIQMC energy and force to obtain the full-dimensional ground state PES of the water molecule via Gaussian processes regression. The new water FCIQMC PES can be used as the basis for H2O ground state nuclear dynamics, structure optimization, and rotation-vibrational spectrum calculation.
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Affiliation(s)
- Tonghuan Jiang
- School of Physics, Peking University, Beijing100871, P. R. China
| | - Wei Fang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China.,Department of Chemistry, Fudan University, Shanghai200438, P. R. China
| | - Ali Alavi
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569Stuttgart, Germany.,University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Ji Chen
- School of Physics, Peking University, Beijing100871, P. R. China.,Collaborative Innovation Center of Quantum Matter, Beijing100871, P. R. China.,Interdisciplinary Institute of Light-Element Quantum Materials and Research Center for Light-Element Advanced Materials, Peking University, Beijing100871, P. R. China.,Frontiers Science Center for Nano-Optoelectronics, Peking University, Beijing100871, P. R. China
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41
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Zhang Y, Lin Q, Jiang B. Atomistic neural network representations for chemical dynamics simulations of molecular, condensed phase, and interfacial systems: Efficiency, representability, and generalization. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yaolong Zhang
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
| | - Qidong Lin
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
| | - Bin Jiang
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
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42
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Luan Z, Fu Y, Tan Y, Wang Y, Shan B, Li J, Zhou X, Chen W, Liu L, Fu B, Zhang DH, Yang X, Wang X. Observation of Competitive Nonadiabatic Photodissociation Dynamics of H 2S + Cations. J Phys Chem Lett 2022; 13:8157-8162. [PMID: 36001649 DOI: 10.1021/acs.jpclett.2c01892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A comprehensive understanding of dissociation mechanisms is of fundamental importance in the photochemistry of small molecules. Here, we investigated the detailed photodissociation dynamics of H2S+ near 337 nm by using the velocity map ion imaging technique together with the theoretical characterizations by developing global full-dimensional potential energy surfaces (PESs). Rotational state resolved images were acquired for the S+(4S) + H2 product channel. Significant changes in product total kinetic energy release distributions and angular distributions have been observed within a small excitation photon energy range of 5 wavenumbers. Analysis based on the full-dimensional PESs reveals that two nonadiabatic pathways determined by the transition state connecting two minima on the 12A' state are responsible for the dramatic variation of observed product distributions. The current study has directly witnessed the competitive photodissociation mechanisms controlled by a critical energy point on the PES, thereby providing in-depth insight into the nonadiabatic dynamics in photochemistry.
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Affiliation(s)
- Zhiwen Luan
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Yanlin Fu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yuxin Tan
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Yaling Wang
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Baokun Shan
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Jie Li
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xiaoguo Zhou
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Wentao Chen
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Lijie Liu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xingan Wang
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
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43
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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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44
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Unexpected steric hindrance failure in the gas phase F - + (CH 3) 3CI S N2 reaction. Nat Commun 2022; 13:4427. [PMID: 35907925 PMCID: PMC9338938 DOI: 10.1038/s41467-022-32191-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) reactions are of significant importance in physical organic chemistry. The textbook example of the retardation of SN2 reactivity by bulky alkyl substitution is widely accepted based on the static analysis of molecular structure and steric environment. However, the direct dynamical evidence of the steric hindrance of SN2 from experiment or theory remains rare. Here, we report an unprecedented full-dimensional (39-dimensional) machine learning-based potential energy surface for the 15-atom F− + (CH3)3CI reaction, facilitating the reliable and efficient reaction dynamics simulations that can reproduce well the experimental outcomes and examine associated atomic-molecular level mechanisms. Moreover, we found surprisingly high “intrinsic” reactivity of SN2 when the E2 pathway is completely blocked, indicating the reaction that intends to proceed via E2 transits to SN2 instead, due to a shared pre-reaction minimum. This finding indicates that the competing factor of E2 but not the steric hindrance determines the small reactivity of SN2 for the F− + (CH3)3CI reaction. Our study provides new insight into the dynamical origin that determines the intrinsic reactivity in gas-phase organic chemistry. Base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) are of significant importance in physical organic chemistry. Here, the authors show that the competing factor of E2 as opposed to steric hindrance determines the low reactivity of SN2 in the F− + (CH3)3CI reaction.
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45
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Guan Y, Yarkony DR, Zhang DH. Permutation invariant polynomial neural network based diabatic ansatz for the (E + A) × (e + a) Jahn-Teller and Pseudo-Jahn-Teller systems. J Chem Phys 2022; 157:014110. [PMID: 35803819 DOI: 10.1063/5.0096912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, the permutation invariant polynomial neural network (PIP-NN) approach is employed to construct a quasi-diabatic Hamiltonian for system with non-Abelian symmetries. It provides a flexible and compact NN-based diabatic ansatz from the related approach of Williams, Eisfeld, and co-workers. The example of H3 + is studied, which is an (E + A) × (e + a) Jahn-Teller and Pseudo-Jahn-Teller system. The PIP-NN diabatic ansatz is based on the symmetric polynomial expansion of Viel and Eisfeld, the coefficients of which are expressed with neural network functions that take permutation-invariant polynomials as input. This PIP-NN-based diabatic ansatz not only preserves the correct symmetry but also provides functional flexibility to accurately reproduce ab initio electronic structure data, thus resulting in excellent fits. The adiabatic energies, energy gradients, and derivative couplings are well reproduced. A good description of the local topology of the conical intersection seam is also achieved. Therefore, this diabatic ansatz completes the PIP-NN based representation of DPEM with correct symmetries and will enable us to diabatize even more complicated systems with complex symmetries.
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Affiliation(s)
- Yafu Guan
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
| | - David R Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
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46
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Meng Q, Chen J, Ma J, Zhang X, Chen J. Adiabatic models for the quantum dynamics of surface scattering with lattice effects. Phys Chem Chem Phys 2022; 24:16415-16436. [PMID: 35766107 DOI: 10.1039/d2cp01560a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this contribution, we review models for the lattice effects in quantum dynamics calculations on surface scattering, which is important to modeling heterogeneous catalysis for achieving an interpretation of experimental measurements. Unlike dynamics models for reactions in the gas phase, those for heterogeneous reactions have to include the effects of the surface. For manageable computational costs in calculations, the effects of static surface (SS) are firstly modeled as this is simply and easily implemented. Then, the SS model has to be improved to include the effects of the flexible surface, that is the lattice effects. To do this, various surface models have been designed where the coordinates of the surface atoms are introduced in the Hamiltonian operator, especially those of the top surface atom. Based on this model Hamiltonian operator, extensive multi-dimension quantum dynamics calculations can be performed to recover the lattice effects. Here, we first review an overview of the techniques in constructing the Hamiltonian operator, which is a sum of the kinetic energy operator (KEO) and potential energy surface (PES). Since the PES containing the coordinates of the surface atoms in a cell is still expensive, the SS model is often accepted. We consider a mathematical model, called the coupled harmonic oscillator (CHO) model, to introduce the concepts of adiabatic and diabatic representations for separating the molecule and surface. Under the adiabatic model, we further introduce the expansion model where the potential function is Taylor expanded around the optimized geometry of the surface. By an expansion model truncated at the first and second order, various coupling surface models between the molecule and surface are derived. Moreover, by further and deeply understanding the adiabatic representation, an effective Hamiltonian operator is obtained by optimizing the total wave function in factorized form. By this factorized form of wave function and effective Hamiltonian operator, the geometry phase of the surface wave function is theoretically found. This theoretical prediction may be measured by carefully designing experiments. Finally, discussions on the adiabatic representation, the PES construction, and possibility of the classical-dynamics solutions are given. Based on these discussions, a simple outlook on the dynamics of photocatalytics is finally given.
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Affiliation(s)
- Qingyong Meng
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China.
| | - Junbo Chen
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China. .,Xi'an Modern Chemistry Research Institute, China North Industries Group Corp., Ltd., East Zhangba Road 168, 710065 Xi'an, China
| | - Jianxing Ma
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China.
| | - Xingyu Zhang
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China.
| | - Jun Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Yangqiao Road West 155, 350002 Fuzhou, China.,Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Optoelectronic Industry Base at High-tech Zone, 350108 Fuzhou, China
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47
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Liu J, Lan J, He X. Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks. J Phys Chem A 2022; 126:3926-3936. [PMID: 35679610 DOI: 10.1021/acs.jpca.2c00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jinggang Lan
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
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48
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Espinosa-Garcia J, Rangel C, Corchado JC. Current Status of the X + C 2H 6 [X ≡ H, F( 2P), Cl( 2P), O( 3P), OH] Hydrogen Abstraction Reactions: A Theoretical Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123773. [PMID: 35744901 PMCID: PMC9228020 DOI: 10.3390/molecules27123773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022]
Abstract
This paper is a detailed review of the chemistry of medium-size reactive systems using the following hydrogen abstraction reactions with ethane, X + C2H6 → HX + C2H5; X ≡ H, F(2P), Cl(2P), O(3P) and OH, and focusing attention mainly on the theoretical developments. These bimolecular reactions range from exothermic to endothermic systems and from barrierless to high classical barriers of activation. Thus, the topography of the reactive systems changes from reaction to reaction with the presence or not of stabilized intermediate complexes in the entrance and exit channels. The review begins with some reflections on the inherent problems in the theory/experiment comparison. When one compares kinetics or dynamics theoretical results with experimental measures, one is testing both the potential energy surface describing the nuclei motion and the kinetics or dynamics method used. Discrepancies in the comparison may be due to inaccuracies of the surface, limitations of the kinetics or dynamics methods, and experimental uncertainties that also cannot be ruled out. The paper continues with a detailed review of some bimolecular reactions with ethane, beginning with the reactions with hydrogen atoms. The reactions with halogens present a challenge owing to the presence of stabilized intermediate complexes in the entrance and exit channels and the influence of the spin-orbit states on reactivity. Reactions with O(3P) atoms lead to three surfaces, which is an additional difficulty in the theoretical study. Finally, the reactions with the hydroxyl radical correspond to a reactive system with ten atoms and twenty-four degrees of freedom. Throughout this review, different strategies in the development of analytical potential energy surfaces describing these bimolecular reactions have been critically analyzed, showing their advantages and limitations. These surfaces are fitted to a large number of ab initio calculations, and we found that a huge number of calculations leads to accurate surfaces, but this information does not guarantee that the kinetics and dynamics results match the experimental measurements.
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49
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Lu X, Li L, Zhang X, Fu B, Xu X, Zhang DH. Dynamical Effects of S N2 Reactivity Suppression by Microsolvation: Dynamics Simulations of the F -(H 2O) + CH 3I Reaction on a 21-Dimensional Potential Energy Surface. J Phys Chem Lett 2022; 13:5253-5259. [PMID: 35674277 DOI: 10.1021/acs.jpclett.2c01323] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A comparison of atomistic dynamics between microsolvated and unsolvated reactions can expose the precise role of solvent molecules and thus provide deep insight into how solvation influences chemical reactions. Here we developed the first full-dimensional analytical potential energy surface of the F-(H2O) + CH3I reaction, which facilitates the efficient dynamics simulations on a quantitatively accurate level. The computed SN2 reactivity suppression ratio of the monosolvated F-(H2O) + CH3I reaction relative to the unsolvated F- + CH3I reaction as a function of collision energy first increases and then decreases steadily, forming an inverted-V shape, due to the combined dynamical effects of interaction time, steric hindrance, and collision-induced dehydration. Moreover, further analysis reveals that the steric effect of the F-(H2O) + CH3I reaction resulting from the single water molecule is manifested mainly in dragging the F- anion away from the central C atom, rather than shielding F- from C. Our study shows there is great potential in rigorously studying the role of the solvent in more complicated reactions.
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Affiliation(s)
- Xiaoxiao Lu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lulu Li
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaoren Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xin Xu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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50
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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: 12] [Impact Index Per Article: 6.0] [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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