1
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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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2
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Arcidiacono A, Cignoni E, Mazzeo P, Cupellini L, Mennucci B. Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning. J Phys Chem A 2024; 128:3646-3658. [PMID: 38683801 PMCID: PMC11089512 DOI: 10.1021/acs.jpca.4c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/03/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024]
Abstract
Solvatochromism occurs in both homogeneous solvents and more complex biological environments, such as proteins. While in both cases the solvatochromic effects report on the surroundings of the chromophore, their interpretation in proteins becomes more complicated not only because of structural effects induced by the protein pocket but also because the protein environment is highly anisotropic. This is particularly evident for highly conjugated and flexible molecules such as carotenoids, whose excitation energy is strongly dependent on both the geometry and the electrostatics of the environment. Here, we introduce a machine learning (ML) strategy trained on quantum mechanics/molecular mechanics calculations of geometrical and electrochromic contributions to carotenoids' excitation energies. We employ this strategy to compare solvatochromism in protein and solvent environments. Despite the important specifities of the protein, ML models trained on solvents can faithfully predict excitation energies in the protein environment, demonstrating the robustness of the chosen descriptors.
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Affiliation(s)
- Amanda Arcidiacono
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Edoardo Cignoni
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial
Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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3
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Sršeň Š, von Lilienfeld OA, Slavíček P. Fast and accurate excited states predictions: machine learning and diabatization. Phys Chem Chem Phys 2024; 26:4306-4319. [PMID: 38234256 PMCID: PMC10829538 DOI: 10.1039/d3cp05685f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
The efficiency of machine learning algorithms for electronically excited states is far behind ground-state applications. One of the underlying problems is the insufficient smoothness of the fitted potential energy surfaces and other properties in the vicinity of state crossings and conical intersections, which is a prerequisite for an efficient regression. Smooth surfaces can be obtained by switching to the diabatic basis. However, diabatization itself is still an outstanding problem. We overcome these limitations by solving both problems at once. We use a machine learning approach combining clustering and regression techniques to correct for the deficiencies of property-based diabatization which, in return, provides us with smooth surfaces that can be easily fitted. Our approach extends the applicability of property-based diabatization to multidimensional systems. We utilize the proposed diabatization scheme to achieve higher prediction accuracy for adiabatic states and we show its performance by reconstructing global potential energy surfaces of excited states of nitrosyl fluoride and formaldehyde. While the proposed methodology is independent of the specific property-based diabatization and regression algorithm, we show its performance for kernel ridge regression and a very simple diabatization based on transition multipoles. Compared to most other algorithms based on machine learning, our approach needs only a small amount of training data.
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Affiliation(s)
- Štěpán Sršeň
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 162 28 Prague, Czech Republic.
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Wien, Austria
| | - O Anatole von Lilienfeld
- Vector Institute for Artificial Intelligence, Toronto, ON, M5S 1M1, Canada
- Departments of Chemistry, Materials Science and Engineering, and Physics, University of Toronto, St. George Campus, Toronto, ON, Canada
- Machine Learning Group, Technische Universität Berlin and Institute for the Foundations of Learning and Data, 10587 Berlin, Germany
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 162 28 Prague, Czech Republic.
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4
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Han S, Xie C, Hu X, Yarkony DR, Guo H, Xie D. Quantum Dynamics of Photodissociation: Recent Advances and Challenges. J Phys Chem Lett 2023; 14:10517-10530. [PMID: 37970789 DOI: 10.1021/acs.jpclett.3c02735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Recent advances in constructing accurate potential energy surfaces and nonadiabatic couplings from high-level ab initio data have revealed detailed potential landscapes in not only the ground electronic state but also excited ones. They enabled quantitatively accurate characterization of photoexcited reactive systems using quantum mechanical methods. In this Perspective, we survey the recent progress in quantum mechanical studies of adiabatic and nonadiabatic photodissociation dynamics, focusing on initial state control and product energy disposal. These new insights helped to understand quantum effects in small prototypical systems, and the results serve as benchmarks for developing more approximate theoretical methods.
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Affiliation(s)
- Shanyu Han
- International Center for Isotope Effects Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Changjian Xie
- Institute of Modern Physics, Shaanxi Key Laboratory for Theoretical Physics Frontiers, Northwest University, Xi'an 710127, China
| | - Xixi Hu
- Kuang Yaming Honors School, Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
| | - David R Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hua Guo
- Department of Chemistry and Chemical Biology, Center for Computational Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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5
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Mutsuji A, Saita K, Maeda S. An energy decomposition and extrapolation scheme for evaluating electron transfer rate constants: a case study on electron self-exchange reactions of transition metal complexes. RSC Adv 2023; 13:32097-32103. [PMID: 37920761 PMCID: PMC10619204 DOI: 10.1039/d3ra05784d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
A simple approach to the analysis of electron transfer (ET) reactions based on energy decomposition and extrapolation schemes is proposed. The present energy decomposition and extrapolation-based electron localization (EDEEL) method represents the diabatic energies for the initial and final states using the adiabatic energies of the donor and acceptor species and their complex. A scheme for the efficient estimation of ET rate constants is also proposed. EDEEL is semi-quantitative by directly evaluating the seam-of-crossing region of two diabatic potentials. In a numerical test, EDEEL successfully provided ET rate constants for electron self-exchange reactions of thirteen transition metal complexes with reasonable accuracy. In addition, its energy decomposition and extrapolation schemes provide all the energy values required for activation-strain model (ASM) analysis. The ASM analysis using EDEEL provided rational interpretations of the variation of the ET rate constants as a function of the transition metal complexes. These results suggest that EDEEL is useful for efficiently evaluating ET rate constants and obtaining a rational understanding of their magnitudes.
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Affiliation(s)
- Akihiro Mutsuji
- Graduate School of Chemical Sciences and Engineering, Hokkaido University Sapporo Hokkaido 060-8628 Japan
| | - Kenichiro Saita
- Department of Chemistry, Graduate School of Science, Hokkaido University Sapporo Hokkaido 060-0810 Japan
| | - Satoshi Maeda
- Department of Chemistry, Graduate School of Science, Hokkaido University Sapporo Hokkaido 060-0810 Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Sapporo Hokkaido 001-0021 Japan
- ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Hokkaido University Sapporo Hokkaido 060-0810 Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS) Tsukuba Ibaraki 305-0044 Japan
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6
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Hennefarth MR, Hermes MR, Truhlar DG, Gagliardi L. Linearized Pair-Density Functional Theory. J Chem Theory Comput 2023. [PMID: 37207365 DOI: 10.1021/acs.jctc.3c00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Multiconfiguration pair-density functional theory (MC-PDFT) is a post-SCF multireference method that has been successful at computing ground- and excited-state energies. However, MC-PDFT is a single-state method in which the final MC-PDFT energies do not come from diagonalization of a model-space Hamiltonian matrix, and this can lead to inaccurate topologies of potential energy surfaces near locally avoided crossings and conical intersections. Therefore, in order to perform physically correct ab initio molecular dynamics with electronically excited states or to treat Jahn-Teller instabilities, it is necessary to develop a PDFT method that recovers the correct topology throughout the entire nuclear configuration space. Here we construct an effective Hamiltonian operator, called the linearized PDFT (L-PDFT) Hamiltonian, by expanding the MC-PDFT energy expression to first order in a Taylor series of the wave function density. Diagonalization of the L-PDFT Hamiltonian gives the correct potential energy surface topology near conical intersections and locally avoided crossings for a variety of challenging cases including phenol, methylamine, and the spiro cation. Furthermore, L-PDFT outperforms MC-PDFT and previous multistate PDFT methods for predicting vertical excitations from a variety of representative organic chromophores.
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Affiliation(s)
- Matthew R Hennefarth
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute, and Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew R Hermes
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute, and Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Laura Gagliardi
- Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
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7
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Zhang J, Tang Z, Zhang X, Zhu H, Zhao R, Lu Y, Gao J. Target State Optimized Density Functional Theory for Electronic Excited and Diabatic States. J Chem Theory Comput 2023; 19:1777-1789. [PMID: 36917687 DOI: 10.1021/acs.jctc.2c01317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
A flexible self-consistent field method, called target state optimization (TSO), is presented for exploring electronic excited configurations and localized diabatic states. The key idea is to partition molecular orbitals into different subspaces according to the excitation or localization pattern for a target state. Because of the orbital-subspace constraint, orbitals belonging to different subspaces do not mix. Furthermore, the determinant wave function for such excited or diabatic configurations can be variationally optimized as a ground state procedure, unlike conventional ΔSCF methods, without the possibility of collapsing back to the ground state or other lower-energy configurations. The TSO method can be applied both in Hartree-Fock theory and in Kohn-Sham density functional theory (DFT). The density projection procedure and the working equations for implementing the TSO method are described along with several illustrative applications. For valence excited states of organic compounds, it was found that the computed excitation energies from TSO-DFT and time-dependent density functional theory (TD-DFT) are of similar quality with average errors of 0.5 and 0.4 eV, respectively. For core excitation, doubly excited states and charge-transfer states, the performance of TSO-DFT is clearly superior to that from conventional TD-DFT calculations. It is shown that variationally optimized charge-localized diabatic states can be defined using TSO-DFT in energy decomposition analysis to gain both qualitative and quantitative insights on intermolecular interactions. Alternatively, the variational diabatic states may be used in molecular dynamics simulation of charge transfer processes. The TSO method can also be used to define basis states in multistate density functional theory for excited states through nonorthogonal state interaction calculations. The software implementing TSO-DFT can be accessed from the authors.
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Affiliation(s)
- Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, P. R. China
| | - Zhen Tang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, P. R. China
| | - Xiaoyong Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, P. R. China
| | - Hong Zhu
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, P. R. China.,School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Ruoqi Zhao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, P. R. China.,Institute of Theoretical Chemistry, Jilin University, Changchun, 130023 Jilin, P. R. China
| | - Yangyi Lu
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, P. R. China
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, P. R. China.,School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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8
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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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9
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Shu Y, Varga Z, Kanchanakungwankul S, Zhang L, Truhlar DG. Diabatic States of Molecules. J Phys Chem A 2022; 126:992-1018. [PMID: 35138102 DOI: 10.1021/acs.jpca.1c10583] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative simulations of electronically nonadiabatic molecular processes require both accurate dynamics algorithms and accurate electronic structure information. Direct semiclassical nonadiabatic dynamics is expensive due to the high cost of electronic structure calculations, and hence it is limited to small systems, limited ensemble averaging, ultrafast processes, and/or electronic structure methods that are only semiquantitatively accurate. The cost of dynamics calculations can be made manageable if analytic fits are made to the electronic structure data, and such fits are most conveniently carried out in a diabatic representation because the surfaces are smooth and the couplings between states are smooth scalar functions. Diabatic representations, unlike the adiabatic ones produced by most electronic structure methods, are not unique, and finding suitable diabatic representations often involves time-consuming nonsystematic diabatization steps. The biggest drawback of using diabatic bases is that it can require large amounts of effort to perform a globally consistent diabatization, and one of our goals has been to develop methods to do this efficiently and automatically. In this Feature Article, we introduce the mathematical framework of diabatic representations, and we discuss diabatization methods, including adiabatic-to-diabatic transformations and recent progress toward the goal of automatization.
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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
| | - Siriluk Kanchanakungwankul
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Linyao Zhang
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States.,School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - 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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10
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Guan Y, Xie C, Yarkony DR, Guo H. High-fidelity first principles nonadiabaticity: diabatization, analytic representation of global diabatic potential energy matrices, and quantum dynamics. Phys Chem Chem Phys 2021; 23:24962-24983. [PMID: 34473156 DOI: 10.1039/d1cp03008f] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nonadiabatic dynamics, which goes beyond the Born-Oppenheimer approximation, has increasingly been shown to play an important role in chemical processes, particularly those involving electronically excited states. Understanding multistate dynamics requires rigorous quantum characterization of both electronic and nuclear motion. However, such first principles treatments of multi-dimensional systems have so far been rather limited due to the lack of accurate coupled potential energy surfaces and difficulties associated with quantum dynamics. In this Perspective, we review recent advances in developing high-fidelity analytical diabatic potential energy matrices for quantum dynamical investigations of polyatomic uni- and bi-molecular nonadiabatic processes, by machine learning of high-level ab initio data. Special attention is paid to methods of diabatization, high fidelity construction of multi-state coupled potential energy surfaces and property surfaces, as well as quantum mechanical characterization of nonadiabatic nuclear dynamics. To illustrate the tremendous progress made by these new developments, several examples are discussed, in which direct comparison with quantum state resolved measurements led to either confirmation of the observation or sometimes reinterpretation of the experimental data. The insights gained in these prototypical systems greatly advance our understanding of nonadiabatic dynamics in chemical systems.
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Affiliation(s)
- Yafu Guan
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA.
| | - Changjian Xie
- Institute of Modern Physics, Northwest University, Xi'an, Shaanxi 710069, China.
| | - David R Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA.
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, 87131, USA.
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11
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Ren M, Zhang L, Jiao Y, Chen Z, Wu W. Extended Mulliken-Hush Method with Applications to the Theoretical Study of Electron Transfer. J Chem Theory Comput 2021; 17:6861-6875. [PMID: 34605634 DOI: 10.1021/acs.jctc.1c00603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel adiabatic-to-diabatic (ATD) transformation strategy, namely, the extended Mulliken-Hush (XMH) method, is proposed to evaluate diabatic properties including electronic couplings, potential energy surfaces, and their crossings. The XMH method is developed by adopting our recently proposed ATD transformation formula of a general vectorial physical observable, in which a useful ATD transformation is further determined by using an auxiliary dipole between localized frontier orbitals as a simple approximation of the diabatic transition dipole. The XMH method is simple and practical that provides a flexible way to construct diabatic states. To some extent, it can be regarded as an extension of the generalized Mulliken-Hush (GMH) method since the latter takes a stronger approximation, in which the diabatic transition dipole is assumed to be vanishing. Test calculations on the HeH2+ system show that the electronic couplings predicted by the XMH method are closer to the ones calculated by the valence bond block-diagonalization approach than the GMH ones since the XMH method takes into account both the magnitude and direction of the diabatic transition dipole, which is consistent with the properties of this molecule. In the study of electron transfer in the two kinds of donor-bridge-acceptor systems, the XMH method maintains the simplicity of the GMH method and gives reasonable results even when the latter fails, wherein the diabatic transition dipole is nearly perpendicular to the difference of the initial and final adiabatic dipoles. More importantly, the XMH method can be easily combined with high-level electronic structure methods, in which the properties of the ground and excited states may be more accurately calculated, and hence, one may expect that further development of the XMH method would result in a general computational model for studying electron transfer reactions.
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Affiliation(s)
- Mingxing Ren
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Lina Zhang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yang Jiao
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhenhua Chen
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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12
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Westermayr J, Marquetand P. Machine Learning for Electronically Excited States of Molecules. Chem Rev 2021; 121:9873-9926. [PMID: 33211478 PMCID: PMC8391943 DOI: 10.1021/acs.chemrev.0c00749] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.
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Affiliation(s)
- Julia Westermayr
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Data
Science @ Uni Vienna, University of Vienna, Währinger Strasse 29, 1090 Vienna, Austria
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13
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Abstract
Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.
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Affiliation(s)
- Julia Westermayr
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Data Science @ Uni Vienna, University of Vienna, Währinger Strasse 29, 1090 Vienna, Austria
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14
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Milovanović B, Novak J, Etinski M, Domcke W, Došlić N. Simulation of UV absorption spectra and relaxation dynamics of uracil and uracil-water clusters. Phys Chem Chem Phys 2021; 23:2594-2604. [PMID: 33475644 DOI: 10.1039/d0cp05618a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Despite many studies, the mechanisms of nonradiative relaxation of uracil in the gas phase and in aqueous solution are still not fully resolved. Here we combine theoretical UV absorption spectroscopy with nonadiabatic dynamics simulations to identify the photophysical mechanisms that can give rise to experimentally observed decay time constants. We first compute and theoretically assign the electronic spectra of uracil using the second-order algebraic-diagrammatic-construction (ADC(2)) method. The obtained electronic states, their energy differences and state-specific solvation effects are the prerequisites for understanding the photodynamics. We then use nonadiabatic trajectory-surface-hopping dynamics simulations to investigate the photoinduced dynamics of uracil and uracil-water clusters. In contrast to previous studies, we found that a single mechanism - the ethylenic twist around the C[double bond, length as m-dash]C bond - is responsible for the ultrafast component of the nonradiative decay, both in the gas phase and in solution. Very good agreement with the experimentally determined ultrashort decay time constants is obtained.
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Affiliation(s)
| | - Jurica Novak
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia. and Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
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15
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Yin Z, Braams BJ, Fu B, Zhang DH. Neural Network Representation of Three-State Quasidiabatic Hamiltonians Based on the Transformation Properties from a Valence Bond Model: Three Singlet States of H3+. J Chem Theory Comput 2021; 17:1678-1690. [DOI: 10.1021/acs.jctc.0c01336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhengxi Yin
- 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, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Bastiaan J. Braams
- Centrum Wiskunde & Informatica (CWI), the Dutch National Center for Mathematics and Computer Science, 1098 XG Amsterdam, Netherlands
| | - 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, P. R. 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, P. R. China
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16
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Wang YC, Feng S, Liang W, Zhao Y. Electronic Couplings for Photoinduced Charge Transfer and Excitation Energy Transfer Based on Fragment Particle-Hole Densities. J Phys Chem Lett 2021; 12:1032-1039. [PMID: 33470827 DOI: 10.1021/acs.jpclett.0c03514] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A new scheme is proposed to calculate the electronic couplings for photoinduced charge transfer and excitation energy transfer for both singlet and triplet states. In this scheme, the locally excited and charge-transfer states are constructed from the adiabatic ones by maximally localizing the particle (i.e., electron) and hole densities in terms of predefined molecular fragments. The construction process, after which the electronic couplings are directly obtained, is highly efficient and can be combined with various kinds of preliminary electronic structure calculations as long as the adiabatic excitation energies and transition densities are available. The method also applies to the systems with multiple charge or excitation centers. Its validity is demonstrated by the applications to the 6,13-dichloropentacene dimer and tetramer and the C60-Zn porphyrin dyad. The results reveal that the environment has a strong impact on the electronic couplings and can even enlarge those for long-range charge transfer by several orders of magnitude.
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Affiliation(s)
- Yu-Chen Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Shishi Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Yi Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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17
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Bao P, Hettich CP, Shi Q, Gao J. Block-Localized Excitation for Excimer Complex and Diabatic Coupling. J Chem Theory Comput 2020; 17:240-254. [PMID: 33370101 DOI: 10.1021/acs.jctc.0c01015] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We describe a block-localized excitation (BLE) method to carry out constrained optimization of block-localized orbitals for constructing valence bond-like, diabatic excited configurations using multistate density functional theory (MSDFT). The method is an extension of the previous block-localized wave function method through a fragment-based ΔSCF approach to optimize excited determinants within a molecular complex. In BLE, both the number of electrons and the electronic spin of different fragments in a whole system can be constrained, whereas electrostatic, exchange, and polarization interactions among different blocks can be fully taken into account of. To avoid optimization collapse to unwanted states, a ΔSCF projection scheme and a maximum overlap of wave function approach have been presented. The method is illustrated by the excimer complex of two naphthalene molecules. With a minimum of eight spin-adapted configurational state functions, it was found that the inversion of La- and Lb- states near the optimal structure of the excimer complex is correctly produced, which is in quantitative agreement with DMRG-CASPT2 calculations and experiments. Trends in the computed transfer integrals associated with excited-state energy transfer both in the singlet and triplet states are discussed. The results suggest that MSDFT may be used as an efficient approach to treat intermolecular interactions in excited states with a minimal active space (MAS) for interpretation of the results and for dynamic simulations, although the selection of a small active space is often system dependent.
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Affiliation(s)
- Peng Bao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Christian P Hettich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.,Beijing University Shenzhen Graduate School, Shenzhen 518055, China
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18
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Han S, Wang Y, Guan Y, Yarkony DR, Guo H. Impact of Diabolical Singular Points on Nonadiabatic Dynamics and a Remedy: Photodissociation of Ammonia in the First Band. J Chem Theory Comput 2020; 16:6776-6784. [DOI: 10.1021/acs.jctc.0c00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shanyu Han
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yucheng Wang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Yafu Guan
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David R. Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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19
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Westermayr J, Marquetand P. Machine learning and excited-state molecular dynamics. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/ab9c3e] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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Hong Y, Yin Z, Guan Y, Zhang Z, Fu B, Zhang DH. Exclusive Neural Network Representation of the Quasi-Diabatic Hamiltonians Including Conical Intersections. J Phys Chem Lett 2020; 11:7552-7558. [PMID: 32835486 DOI: 10.1021/acs.jpclett.0c02173] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We propose a numerically simple and straightforward, yet accurate and efficient neural networks-based fitting strategy to construct coupled potential energy surfaces (PESs) in a quasi-diabatic representation. The fundamental invariants are incorporated to account for the complete nuclear permutation inversion symmetry. Instead of derivative couplings or interstate couplings, a so-called modified derivative coupling term is fitted by neural networks, resulting in accurate description of near degeneracy points, such as the conical intersections. The adiabatic energies, energy gradients, and derivative couplings are well reproduced, and the vanishing of derivative couplings as well as the isotropic topography of adiabatic and diabatic energies in asymptotic regions are automatically satisfied. All of these features of the coupled global PESs are requisite for accurate dynamics simulations. Our approach is expected to be very useful in developing highly accurate coupled PESs in a quasi-diabatic representation in an efficient machine learning-based way.
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Affiliation(s)
- Yingyue Hong
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P.R. China 116023
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhengxi Yin
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P.R. China 116023
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yafu Guan
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P.R. China 116023
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Zhaojun 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, P.R. China 116023
| | - 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, P.R. China 116023
| | - 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, P.R. China 116023
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21
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Parker KA, Truhlar DG. Semiglobal diabatic potential energy matrix for the N–H photodissociation of methylamine. J Chem Phys 2020; 152:244309. [DOI: 10.1063/5.0008647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kelsey A. Parker
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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22
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Abstract
This work explores the reactivity of singlet oxygen with respect to two typical reactions: cycloaddition to anthracene and excitation energy transfer (EET) to a carotenoid using diabatic states with multistate density functional theory (MSDFT). Noticeably, the degenerate state 1Δg has distinct open-shell (OS) and closed-shell (CS) components, and the closed-shell component showed more reactivity than the open-shell one due to the strong diabatic couplings to the product diabatic states. The diabatic perspective presented in this work could also apply to general singlet fission processes.
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Affiliation(s)
- Zexing Qu
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, China.
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23
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Shen Y, Yarkony DR. Construction of Quasi-diabatic Hamiltonians That Accurately Represent ab Initio Determined Adiabatic Electronic States Coupled by Conical Intersections for Systems on the Order of 15 Atoms. Application to Cyclopentoxide Photoelectron Detachment in the Full 39 Degrees of Freedom. J Phys Chem A 2020; 124:4539-4548. [PMID: 32374600 DOI: 10.1021/acs.jpca.0c02763] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present, for systems of moderate dimension, a fitting framework to construct quasi-diabatic Hamiltonians that accurately represent ab initio adiabatic electronic structure data including the effects of conical intersections. The framework introduced here minimizes the difference between the fit prediction and the ab initio data obtained in the adiabatic representation, which is singular at a conical intersection seam. We define a general and flexible merit function to allow arbitrary representations and propose a representation to measure the fit-ab initio difference at geometries near electronic degeneracies. A fit Hamiltonian may behave poorly in insufficiently sampled regions, in which case a machine learning theory analysis of the fit representation suggests a regularization to address the deficiency. Our fitting framework including the regularization is used to construct the full 39-dimensional coupled diabatic potential energy surfaces for cyclopentoxy relevant to cyclopentoxide photoelectron detachment.
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Affiliation(s)
- Yifan Shen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David R Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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24
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Guan Y, Guo H, Yarkony DR. Extending the Representation of Multistate Coupled Potential Energy Surfaces To Include Properties Operators Using Neural Networks: Application to the 1,21A States of Ammonia. J Chem Theory Comput 2019; 16:302-313. [DOI: 10.1021/acs.jctc.9b00898] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yafu Guan
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - David R. Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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25
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Ren M, Ma B, Chen Z, Wu W. Two-Dimensional Analysis of the Diabatic Transition of a General Vectorial Physical Observable Based on Adiabatic-to-Diabatic Transformation. J Phys Chem Lett 2019; 10:5868-5872. [PMID: 31522494 DOI: 10.1021/acs.jpclett.9b01812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a full analysis of the magnitude and orientation of the diabatic transition matrix element of a general vectorial physical observable during the adiabatic-to-diabatic transformation. The diabatic transition is a function of the adiabatic-to-diabatic transformation angle and the two basic vectors of the adiabatic states, which are the off-diagonal matrix element and the difference between the two diagonal matrix elements. To the best of our knowledge, this is the first time that the transformation has been accomplished in a more general two-dimensional scale for a vectorial physical observable. All possible extreme values of a diabatic transition are deduced for systems with different features. By using an approximate diabatic transition dipole, the pilot implementation of the analysis produces an electronic coupling curve nearly identical to that obtained by the generalized Mulliken-Hush method for the testing molecule. Evidently, this complete analysis of a diabatic transition will be very useful in determining the adiabatic-to-diabatic transformation angle by using a physical observable and can also be used to evaluate the quality of various approximations for constructing the diabatic states.
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Affiliation(s)
- Mingxing Ren
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , Fujian 361005 , China
| | - Bo Ma
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , Fujian 361005 , China
| | - Zhenhua Chen
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , Fujian 361005 , China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, iChem, and College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , Fujian 361005 , China
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26
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Shu Y, Kryven J, Sampaio de Oliveira-Filho AG, Zhang L, Song GL, Li SL, Meana-Pañeda R, Fu B, Bowman JM, Truhlar DG. Direct diabatization and analytic representation of coupled potential energy surfaces and couplings for the reactive quenching of the excited 2Σ+ state of OH by molecular hydrogen. J Chem Phys 2019; 151:104311. [DOI: 10.1063/1.5111547] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Yinan Shu
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Joanna Kryven
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Antonio Gustavo Sampaio de Oliveira-Filho
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
- Departamento de Química, Laboratório Computacional de Espectroscopia e Cinética, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto-SP, Brazil
| | - Linyao Zhang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Guo-Liang Song
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Shaohong L. Li
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Rubén Meana-Pañeda
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Bina Fu
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
- 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, People’s Republic of China
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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27
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Abstract
Although the charge flux effect or the geometric dependence of the atomic partial charges have been known for a long time, how it can be effectively handled is not yet established. Here, we present a charge interpolation scheme as a new general tool for representing the charge flux in an analytically well-defined manner. By applying it to the anionic GFP chromophore with the diabatically represented atomic charges, we show that the charge interpolation provides a substantial improvement on the accuracy of the geometry-dependent changes in the molecular dipole moments in the gas phase. We also test the scheme toward describing the electrostatic term in the solvation energy in the aqueous environment and observe that it is also improved but that the extent of the improvement is somewhat limited. We show that the remaining errors can be largely corrected by introducing atomic polarizabilities. Overall, our results show that charge interpolation is an amenable approach for describing the charge flux effect and that its description in the condensed phase should be accompanied by proper treatments of polarization effects.
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Affiliation(s)
- Seung Soo Kim
- Department of Chemistry , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , Korea
| | - Young Min Rhee
- Department of Chemistry , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Korea
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28
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Guan Y, Guo H, Yarkony DR. Neural network based quasi-diabatic Hamiltonians with symmetry adaptation and a correct description of conical intersections. J Chem Phys 2019; 150:214101. [DOI: 10.1063/1.5099106] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yafu Guan
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - David R. Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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29
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Yarkony DR, Xie C, Zhu X, Wang Y, Malbon CL, Guo H. Diabatic and adiabatic representations: Electronic structure caveats. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.01.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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30
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Guan Y, Zhang DH, Guo H, Yarkony DR. Representation of coupled adiabatic potential energy surfaces using neural network based quasi-diabatic Hamiltonians: 1,2 2A′ states of LiFH. Phys Chem Chem Phys 2019; 21:14205-14213. [DOI: 10.1039/c8cp06598e] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general algorithm for determining diabatic representations from adiabatic energies, energy gradients and derivative couplings using neural networks is introduced.
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Affiliation(s)
- Yafu Guan
- Department of Chemistry
- Johns Hopkins University
- Baltimore
- 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
| | - Hua Guo
- Department of Chemistry and Chemical Biology
- University of New Mexico
- Albuquerque
- USA
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31
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Wang Y, Yarkony DR. Determining whether diabolical singularities limit the accuracy of molecular property based diabatic representations: The 1,2 1A states of methylamine. J Chem Phys 2018; 149:154108. [PMID: 30342442 DOI: 10.1063/1.5048312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An efficient, easily implemented method for locating singularities attributable to the failure of the defining equations in a molecular property based diabatization, termed diabolical singular points, is reported. For two state diabatizations, the singular points form a seam of dimension N int - 2, where N int is the number of internal degrees of freedom. The dynamical outcomes of nuclear trajectories that reach the region of this seam are flawed. The algorithm easily identifies these otherwise hard to anticipate regions of fallaciously large derivative coupling. The fact that the algorithm is easily incorporated into a two state diabatization code based on molecular properties makes it a practical tool for determining whether the existence of diabolical singularities is relevant to the problem being considered. The algorithm is illustrated using a multireference single and double excitation configuration interaction description of the 1,21A states of CH3NH2.
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Affiliation(s)
- Yuchen Wang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - David R Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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32
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Akimov AV. A Simple Phase Correction Makes a Big Difference in Nonadiabatic Molecular Dynamics. J Phys Chem Lett 2018; 9:6096-6102. [PMID: 30286602 DOI: 10.1021/acs.jpclett.8b02826] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The outcomes of nonadiabatic molecular dynamics (NA-MD) calculations are modulated by the parameters entering the time-dependent Schrödinger equation (TD-SE). The adiabatic states are commonly used as the basis in which the TD-SE is integrated. However, the phase inconsistencies of such states along the nuclear trajectories obtained in NA-MD simulations may render the wave function and other relevant properties ill-behaving, adversely affecting the dynamics. This work illustrates the consequence of adiabatic state phase inconsistencies in nonadiabatic Ehrenfest dynamics. A simple phase-correction approach is proposed and is demonstrated to alter the dynamics to make it consistent with the reference calculations done in the phase-consistent diabatic representation.
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Affiliation(s)
- Alexey V Akimov
- Department of Chemistry , University at Buffalo, The State University of New York , Buffalo , New York 14260 , United States
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33
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Liu M, Chen X, Grofe A, Gao J. Diabatic States at Construction (DAC) through Generalized Singular Value Decomposition. J Phys Chem Lett 2018; 9:6038-6046. [PMID: 30277783 DOI: 10.1021/acs.jpclett.8b02472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A procedure, called generalized diabatic-at-construction (GDAC), is presented to transform adiabatic potential energy surfaces into a diabatic representation by generalized singular value decomposition. First, we use a set of localized, valence bond-like configuration state functions, called DAC, as the basis states. Then, the adiabatic ground and relevant excited states are determined using multistate density functional theory (MSDFT). GDAC differs in the opposite direction from traditional approaches based on adiabatic-to-diabatic transformation with certain property restraints. The method is illustrated with applications to a model first-order bond dissociation reaction of CH3OCH2Cl polarized by a solvent molecule, the ground- and first-excited-state potential energy surfaces near the minimum conical intersection for the ammonia dimer photodissociation, and the multiple avoided curve crossings in the dissociation of lithium hydride. The GDAC diabatization method may be useful for defining charge-localized states in studies of electron transfer and proton-coupled electron transfer reactions in proteins.
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Affiliation(s)
- Meiyi Liu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun , Jilin Province 130023 , China
| | - Xin Chen
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun , Jilin Province 130023 , China
| | - Adam Grofe
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun , Jilin Province 130023 , China
| | - Jiali Gao
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun , Jilin Province 130023 , China
- Department of Chemistry and Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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34
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Penfold TJ, Gindensperger E, Daniel C, Marian CM. Spin-Vibronic Mechanism for Intersystem Crossing. Chem Rev 2018; 118:6975-7025. [DOI: 10.1021/acs.chemrev.7b00617] [Citation(s) in RCA: 401] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Thomas J. Penfold
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon-Tyne NE1 7RU, United Kingdom
| | - Etienne Gindensperger
- Laboratoire de Chimie Quantique, Institut de Chimie UMR-7177, CNRS - Université de Strasbourg, 1 Rue Blaise Pascal 67008 Strasbourg, France
| | - Chantal Daniel
- Laboratoire de Chimie Quantique, Institut de Chimie UMR-7177, CNRS - Université de Strasbourg, 1 Rue Blaise Pascal 67008 Strasbourg, France
| | - Christel M. Marian
- Institut für Theoretische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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35
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Chwee TS, Wong ZC, Sullivan MB, Fan WY. Photophysical properties of acetylene-linked syn bimane oligomers: a molecular photonic wire. Phys Chem Chem Phys 2018; 20:1150-1163. [PMID: 29239433 DOI: 10.1039/c7cp06673b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational studies using correlated wave function methods and density functional theory were carried out on a series of acetylene-linked bimane oligomers with particular emphasis on their excitonic properties and implications for intra-chain excitation energy transfer (EET). The low energy barriers found for the rotation of bimane subunits about the longitudinal axis are such that the π-conjugation is easily disrupted. Nevertheless, a distinctive feature of the oligomer lies in the parallel alignment of the S1 transition dipole along the longitudinal axis, which sustains electronic coupling between adjacent bimane subunits over a range of torsional angles and is crucial for driving intra-chain EET. Using a model that comprises hexameric donor and acceptor fragments, we evaluated electronic couplings and spectral overlaps, and applied Fermi's golden rule (in the weak electronic coupling regime) to approximate the lower limit of intra-chain EET in an acetylene-linked bimane photonic wire.
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Affiliation(s)
- T S Chwee
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, 138632, Singapore.
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36
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Varga Z, Parker KA, Truhlar DG. Direct diabatization based on nonadiabatic couplings: the N/D method. Phys Chem Chem Phys 2018; 20:26643-26659. [DOI: 10.1039/c8cp03410a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose a new diabatization method that is direct, orbital-free, and adiabatic-equivalent based on directly calculated nonadiabatic couplings of states and the adiabatic energy gradients.
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Affiliation(s)
- Zoltan Varga
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
| | - Kelsey A. Parker
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
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37
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Guan Y, Fu B, Zhang DH. Construction of diabatic energy surfaces for LiFH with artificial neural networks. J Chem Phys 2017; 147:224307. [DOI: 10.1063/1.5007031] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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
| | - Bina Fu
- 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
| | - 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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38
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Xie Y, Jiang S, Zheng J, Lan Z. Construction of Vibronic Diabatic Hamiltonian for Excited-State Electron and Energy Transfer Processes. J Phys Chem A 2017; 121:9567-9578. [DOI: 10.1021/acs.jpca.7b07737] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Xie
- CAS
Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Shengshi Jiang
- CAS
Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Zheng
- Industrial Research Institute of Nonwovens & Technical Textiles, College of Textiles & Clothing, Qingdao University, Qingdao 266071, China
| | - Zhenggang Lan
- CAS
Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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39
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Kowalewski M, Fingerhut BP, Dorfman KE, Bennett K, Mukamel S. Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime. Chem Rev 2017; 117:12165-12226. [DOI: 10.1021/acs.chemrev.7b00081] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Markus Kowalewski
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Konstantin E. Dorfman
- State
Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Kochise Bennett
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
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40
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Affiliation(s)
- Tao Zeng
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S5B6, Canada
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41
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Grofe A, Qu Z, Truhlar DG, Li H, Gao J. Diabatic-At-Construction Method for Diabatic and Adiabatic Ground and Excited States Based on Multistate Density Functional Theory. J Chem Theory Comput 2017; 13:1176-1187. [PMID: 28135420 PMCID: PMC5793876 DOI: 10.1021/acs.jctc.6b01176] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a diabatic-at-construction (DAC) strategy for defining diabatic states to determine the adiabatic ground and excited electronic states and their potential energy surfaces using the multistate density functional theory (MSDFT). The DAC approach differs in two fundamental ways from the adiabatic-to-diabatic (ATD) procedures that transform a set of preselected adiabatic electronic states to a new representation. (1) The DAC states are defined in the first computation step to form an active space, whose configuration interaction produces the adiabatic ground and excited states in the second step of MSDFT. Thus, they do not result from a similarity transformation of the adiabatic states as in the ATD procedure; they are the basis for producing the adiabatic states. The appropriateness and completeness of the DAC active space can be validated by comparison with experimental observables of the ground and excited states. (2) The DAC diabatic states are defined using the valence bond characters of the asymptotic dissociation limits of the adiabatic states of interest, and they are strictly maintained at all molecular geometries. Consequently, DAC diabatic states have specific and well-defined physical and chemical meanings that can be used for understanding the nature of the adiabatic states and their energetic components. Here we present results for the four lowest singlet states of LiH and compare them to a well-tested ATD diabatization method, namely the 3-fold way; the comparison reveals both similarities and differences between the ATD diabatic states and the orthogonalized DAC diabatic states. Furthermore, MSDFT can provide a quantitative description of the ground and excited states for LiH with multiple strongly and weakly avoided curve crossings spanning over 10 Å of interatomic separation.
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Affiliation(s)
- Adam Grofe
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Zexing Qu
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Hui Li
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Jiali Gao
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Abstract
This Perspective addresses the use of coupled diabatic potential energy surfaces (PESs) together with rigorous quantum dynamics in full or reduced dimensional coordinate spaces to obtain accurate solutions to problems in nonadiabatic dynamics.
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Affiliation(s)
- Hua Guo
- Department of Chemistry and Chemical Biology
- University of New Mexico
- Albuquerque
- USA
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