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Zhang L, Pios SV, Martyka M, Ge F, Hou YF, Chen Y, Chen L, Jankowska J, Barbatti M, Dral PO. MLatom Software Ecosystem for Surface Hopping Dynamics in Python with Quantum Mechanical and Machine Learning Methods. J Chem Theory Comput 2024; 20:5043-5057. [PMID: 38836623 DOI: 10.1021/acs.jctc.4c00468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
We present an open-source MLatom@XACS software ecosystem for on-the-fly surface hopping nonadiabatic dynamics based on the Landau-Zener-Belyaev-Lebedev algorithm. The dynamics can be performed via Python API with a wide range of quantum mechanical (QM) and machine learning (ML) methods, including ab initio QM (CASSCF and ADC(2)), semiempirical QM methods (e.g., AM1, PM3, OMx, and ODMx), and many types of ML potentials (e.g., KREG, ANI, and MACE). Combinations of QM and ML methods can also be used. While the user can build their own combinations, we provide AIQM1, which is based on Δ-learning and can be used out-of-the-box. We showcase how AIQM1 reproduces the isomerization quantum yield of trans-azobenzene at a low cost. We provide example scripts that, in dozens of lines, enable the user to obtain the final population plots by simply providing the initial geometry of a molecule. Thus, those scripts perform geometry optimization, normal mode calculations, initial condition sampling, parallel trajectories propagation, population analysis, and final result plotting. Given the capabilities of MLatom to be used for training different ML models, this ecosystem can be seamlessly integrated into the protocols building ML models for nonadiabatic dynamics. In the future, a deeper and more efficient integration of MLatom with Newton-X will enable a vast range of functionalities for surface hopping dynamics, such as fewest-switches surface hopping, to facilitate similar workflows via the Python API.
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Affiliation(s)
- Lina Zhang
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Sebastian V Pios
- Zhejiang Laboratory, Hangzhou, Zhejiang 311100, People's Republic of China
| | - Mikołaj Martyka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Fuchun Ge
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yi-Fan Hou
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuxinxin Chen
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Lipeng Chen
- Zhejiang Laboratory, Hangzhou, Zhejiang 311100, People's Republic of China
| | - Joanna Jankowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Mario Barbatti
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
- Institut Universitaire de France, Paris 75231, France
| | - Pavlo O Dral
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, Fujian 361005, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, China
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Athavale V, Teh HH, Shao Y, Subotnik J. Analytical gradients and derivative couplings for the TDDFT-1D method. J Chem Phys 2022; 157:244110. [PMID: 36586994 DOI: 10.1063/5.0130404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We derive and implement analytic gradients and derivative couplings for time-dependent density functional theory plus one double (TDDFT-1D) which is a semiempirical configuration interaction method whereby the Hamiltonian is diagonalized in a basis of all singly excited configurations and one doubly excited configuration as constructed from a set of reference Kohn-Sham orbitals. We validate the implementation by comparing against finite difference values. Furthermore, we show that our implementation can locate both optimized geometries and minimum-energy crossing points along conical seams of S1/S0 surfaces for a set of test cases.
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Affiliation(s)
- Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hung-Hsuan Teh
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Joseph Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Liu J, Lan Z, Yang J. An efficient implementation of spin-orbit coupling within the framework of semiempirical orthogonalization-corrected methods for ultrafast intersystem crossing dynamics. Phys Chem Chem Phys 2021; 23:22313-22323. [PMID: 34591049 DOI: 10.1039/d1cp03477d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We implement spin-orbit coupling (SOC) within the framework of semiempirical orthogonalization-corrected methods (OMx). The excited-state wavefunction is generated from configuration interaction with single excitations (CIS). The SOC Hamiltonian in terms of the one-electron Breit-Pauli operator with effective nuclear charges is adopted in this work. Benchmark calculations show that SOCs evaluated using the OMx/CIS method agree very well with those obtained from time-dependent density functional theory. As a particularly attractive application, we incorporate SOCs between singlet and triplet states into Tully's fewest switches surface hopping algorithm to enable excited-state nonadiabatic dynamics simulations, treating internal conversion and intersystem crossing on an equal footing. This semiempirical dynamics simulation approach is applied to investigate ultrafast intersystem crossing processes in core-substituted naphthalenediimides.
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Affiliation(s)
- Jie Liu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Jinlong Yang
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China.
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Matsika S. Electronic Structure Methods for the Description of Nonadiabatic Effects and Conical Intersections. Chem Rev 2021; 121:9407-9449. [PMID: 34156838 DOI: 10.1021/acs.chemrev.1c00074] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonadiabatic effects are ubiquitous in photophysics and photochemistry, and therefore, many theoretical developments have been made to properly describe them. Conical intersections are central in nonadiabatic processes, as they promote efficient and ultrafast nonadiabatic transitions between electronic states. A proper theoretical description requires developments in electronic structure and specifically in methods that describe conical intersections between states and nonadiabatic coupling terms. This review focuses on the electronic structure aspects of nonadiabatic processes. We discuss the requirements of electronic structure methods to describe conical intersections and nonadiabatic couplings, how the most common excited state methods perform in describing these effects, and what the recent developments are in expanding the methodology and implementing nonadiabatic couplings.
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Affiliation(s)
- Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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Uratani H, Morioka T, Yoshikawa T, Nakai H. Fast Nonadiabatic Molecular Dynamics via Spin-Flip Time-Dependent Density-Functional Tight-Binding Approach: Application to Nonradiative Relaxation of Tetraphenylethylene with Locked Aromatic Rings. J Chem Theory Comput 2020; 16:7299-7313. [PMID: 33197192 DOI: 10.1021/acs.jctc.0c00936] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nonadiabatic dynamics around conical intersections between ground and excited states are crucial to understand excited-state phenomena in complex chemical systems. With this background in mind, we present an approach combining fewest-switches trajectory surface hopping and spin-flip (SF) time-dependent (TD) density-functional tight binding (DFTB), which is a simplified version of SF-TD density functional theory (DFT) with semiempirical parametrizations, for computationally efficient nonadiabatic molecular dynamics simulations. The estimated computational time of the SF-TD-DFTB approach is several orders of magnitude lower than that of SF-TD-DFT. In addition, the proposed method reproduces the time scales and quantum yields in photoisomerization reactions of azobenzene at a level comparable with conventional ab initio approaches, demonstrating reasonable accuracy. Finally, we report a practical application of the developed technique to explore the nonradiative relaxation processes of tetraphenylethylene and its derivative with torsionally locked aromatic rings and discuss the effect of locking the rings on the excited-state lifetime.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Toshiki Morioka
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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Wang Z, Li Z, Zhang Y, Liu W. Analytic energy gradients of spin-adapted open-shell time-dependent density functional theory. J Chem Phys 2020; 153:164109. [DOI: 10.1063/5.0025428] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Zikuan Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Zhendong Li
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Yong Zhang
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
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Czernel G, Budziak I, Oniszczuk A, Karcz D, Pustuła K, Górecki A, Matwijczuk A, Gładyszewska B, Gagoś M, Niewiadomy A, Matwijczuk A. ESIPT-Related Origin of Dual Fluorescence in the Selected Model 1,3,4-Thiadiazole Derivatives. Molecules 2020; 25:molecules25184168. [PMID: 32933032 PMCID: PMC7570705 DOI: 10.3390/molecules25184168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022] Open
Abstract
In our previous work, we discussed the emergence of the dual fluorescence phenomenon in selected compounds from the group of 1,3,4-thiadiazoles. The results obtained in a number of experimental studies, supported by [TD]DFT calculations, clearly indicated that the phenomenon of dual fluorescence stemmed from an overlap of several factors, including the correct conformation of the analyzed molecule and, very significantly in this context, aggregation effects. Where those two conditions were met, we could observe the phenomenon of intermolecular charge transfer (CT) and the emergence of electronic states responsible for long wave emissions. However, in light of the new studies presented in this paper, we were able, for the first time, to provide a specific theory for the effect of dual fluorescence observed in the analyzed group of 1,3,4-thiadiazoles. We present the results of spectroscopic measurements conducted for two selected analogues from the 1,3,4-thiadiazole group, both in polar and non-polar solvents, which clearly evidence (as we have already suspected in the past, albeit have not shown in publications to date) the possibility of processes related to emission from the tautomer formed in the process of excited state intramolecular proton transfer, which is responsible for the long-wavelength emissions observed in the selected analogues. The presented results obtained with the use of UV-Vis, fluorescence (stationary and time-resolved), FTIR, and Raman spectroscopy, as well as from calculations of dipole moment changes between the ground and excited state with the use of two derivatives with different structures of the resorcylic system, corroborated our standing hypothesis. At the same time, they excluded the presence of ground state keto forms of the analyzed analogues unless necessitated by the structure of the molecule itself. In this case, aggregation factors enhance the observed effects related to the dual fluorescence of the analyzed compounds (by way of AIE-aggregated induced emissions).
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Affiliation(s)
- Grzegorz Czernel
- Department of Biophysics, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland; (G.C.); (A.M.); (B.G.)
| | - Iwona Budziak
- Department of Chemistry, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland;
| | - Anna Oniszczuk
- Department of Inorganic Chemistry, Medical University in Lublin, 20-059 Lublin, Poland
- Correspondence: (A.O.); (D.K.); (A.M.); Tel.: +48-814-456-937 (A.M.); Fax: +48-814-456-684 (A.M.)
| | - Dariusz Karcz
- Department of Analytical Chemistry (C1), Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Cracow, Poland
- Correspondence: (A.O.); (D.K.); (A.M.); Tel.: +48-814-456-937 (A.M.); Fax: +48-814-456-684 (A.M.)
| | - Katarzyna Pustuła
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland;
| | - Andrzej Górecki
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology of the Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland;
| | - Alicja Matwijczuk
- Department of Biophysics, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland; (G.C.); (A.M.); (B.G.)
| | - Bożena Gładyszewska
- Department of Biophysics, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland; (G.C.); (A.M.); (B.G.)
| | - Mariusz Gagoś
- Department of Cell Biology, Institute of Biology and Biochemistry, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Andrzej Niewiadomy
- Institute of Industrial Organic Chemistry, Annopol 6, 03-236 Warsaw, Poland;
| | - Arkadiusz Matwijczuk
- Department of Biophysics, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland; (G.C.); (A.M.); (B.G.)
- Correspondence: (A.O.); (D.K.); (A.M.); Tel.: +48-814-456-937 (A.M.); Fax: +48-814-456-684 (A.M.)
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Minezawa N, Nakajima T. Quantum mechanical/molecular mechanical trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory. J Chem Phys 2020; 152:024119. [DOI: 10.1063/1.5132879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Noriyuki Minezawa
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takahito Nakajima
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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9
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Minezawa N, Nakajima T. Trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory. J Chem Phys 2019; 150:204120. [DOI: 10.1063/1.5096217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Noriyuki Minezawa
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takahito Nakajima
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Dral PO, Wu X, Thiel W. Semiempirical Quantum-Chemical Methods with Orthogonalization and Dispersion Corrections. J Chem Theory Comput 2019; 15:1743-1760. [PMID: 30735388 PMCID: PMC6416713 DOI: 10.1021/acs.jctc.8b01265] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/31/2022]
Abstract
We present two new semiempirical quantum-chemical methods with orthogonalization and dispersion corrections: ODM2 and ODM3 (ODM x). They employ the same electronic structure model as the OM2 and OM3 (OM x) methods, respectively. In addition, they include Grimme's dispersion correction D3 with Becke-Johnson damping and three-body corrections E ABC for Axilrod-Teller-Muto dispersion interactions as integral parts. Heats of formation are determined by adding explicitly computed zero-point vibrational energy and thermal corrections, in contrast to standard MNDO-type and OM x methods. We report ODM x parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine that are optimized with regard to a wide range of carefully chosen state-of-the-art reference data. Extensive benchmarks show that the ODM x methods generally perform better than the available MNDO-type and OM x methods for ground-state and excited-state properties, while they describe noncovalent interactions with similar accuracy as OM x methods with a posteriori dispersion corrections.
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Affiliation(s)
- Pavlo O. Dral
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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