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Gómez S, Cappelli C. When Tautomers Matter: UV-Vis Absorption Spectra of Hypoxanthine in Aqueous Solution from Fully Atomistic Simulations. Chemphyschem 2024:e202400107. [PMID: 38747323 DOI: 10.1002/cphc.202400107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/13/2024] [Indexed: 07/03/2024]
Abstract
The UV-Vis spectrum of the solvated purine derivative Hypoxanthine (HYX) is investigated using the Quantum Mechanics/Fluctuating Charges (QM/FQ) multiscale approach combined with a sampling of configurations through atomistic Molecular Dynamics (MD) simulations. Keto 1H7H and 1H9H tautomeric forms of HYX are the most stable in aqueous solution and form different stable complexes with the surrounding water molecules, ultimately affecting the electronic absorption spectra. The final simulated spectrum resulting from the combination of the individual spectra of tautomers agrees very well with most of the characteristics in the measured spectrum. The importance of considering the effect of the solute tautomers and, in parallel, the contribution of the different solvent arrangements around the solute when modeling spectral properties, is highlighted. In addition, the high quality of the computed spectra leads to suggesting an alternative way for acquiring tautomeric populations from combined computational/experimental spectra.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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2
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Valverde D, Mai S, Canuto S, Borin AC, González L. Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water. JACS AU 2022; 2:1699-1711. [PMID: 35911449 PMCID: PMC9327080 DOI: 10.1021/jacsau.2c00250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S2 state that converts internally to the dark S1 state, from which the population is transferred to the triplet T2 state via intersystem crossing and finally to the lowest T1 state. This S2 → S1 → T2 → T1 deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T1 lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T1/S0 crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ1 = 131 fs and τ2 = 191 fs) that are in excellent agreement with the experimentally reported value (τexp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.
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Affiliation(s)
- Danillo Valverde
- Department
of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, São Paulo CEP 05508-000, Brazil
- Institute
of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo CEP 05508-090, Brazil
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Sylvio Canuto
- Institute
of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo CEP 05508-090, Brazil
| | - Antonio Carlos Borin
- Department
of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, São Paulo CEP 05508-000, Brazil
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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3
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Vandaele E, Mališ M, Luber S. The ΔSCF method for non-adiabatic dynamics of systems in the liquid phase. J Chem Phys 2022; 156:130901. [PMID: 35395890 DOI: 10.1063/5.0083340] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Computational studies of ultrafast photoinduced processes give valuable insights into the photochemical mechanisms of a broad range of compounds. In order to accurately reproduce, interpret, and predict experimental results, which are typically obtained in a condensed phase, it is indispensable to include the condensed phase environment in the computational model. However, most studies are still performed in vacuum due to the high computational cost of state-of-the-art non-adiabatic molecular dynamics (NAMD) simulations. The quantum mechanical/molecular mechanical (QM/MM) solvation method has been a popular model to perform photodynamics in the liquid phase. Nevertheless, the currently used QM/MM embedding techniques cannot sufficiently capture all solute-solvent interactions. In this Perspective, we will discuss the efficient ΔSCF electronic structure method and its applications with respect to the NAMD of solvated compounds, with a particular focus on explicit quantum mechanical solvation. As more research is required for this method to reach its full potential, some challenges and possible directions for future research are presented as well.
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Affiliation(s)
- Eva Vandaele
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Momir Mališ
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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4
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Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
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Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
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5
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Gómez S, Giovannini T, Cappelli C. Absorption spectra of xanthines in aqueous solution: a computational study. Phys Chem Chem Phys 2020; 22:5929-5941. [PMID: 32115599 DOI: 10.1039/c9cp05420k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a detailed computational analysis of the UV/Vis spectra of caffeine, paraxanthine and theophylline in aqueous solution. A hierarchy of solvation approaches for modeling the aqueous environment have been tested, ranging from the continuum model to the non-polarizable and polarizable quantum mechanical (QM)/molecular mechanics (MM) models, with and without the explicit inclusion of water molecules in the QM portion. The computed results are directly compared with the experimental data, thus highlighting the role of electrostatic, polarization and hydrogen boding solute-solvent interactions.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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6
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Paulikat M, Mata RA, Gelabert R. A high-throughput computational approach to UV-Vis spectra in protein mutants. Phys Chem Chem Phys 2019; 21:20678-20692. [PMID: 31508628 DOI: 10.1039/c9cp03908b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work we present a high-throughput approach to the computation of absorption UV-Vis spectra tailored to mutagenesis studies. The scheme makes use of a single molecular dynamics trajectory of a reference (non-mutated) species. The shifts in absorption energy caused by a residue mutation are evaluated by building an effective potential of the environment and computing a correction term based on perturbation theory. The sampling is only performed in the phase space of the initial protein. We analyze the robustness of the method by comparing different approximations for the effective potential, the sampling of mutant residue geometries and observing the impact in the prediction of both bathocromic and hypsochromic shifts. As a test subject, we consider a red fluorescent protein variant with potential biotechnological applications.
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Affiliation(s)
- Mirko Paulikat
- Institute of Physical Chemistry, University of Goettingen, Tammannstraße 6, D-37077 Göttingen, Germany.
| | - Ricardo A Mata
- Institute of Physical Chemistry, University of Goettingen, Tammannstraße 6, D-37077 Göttingen, Germany.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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7
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Martínez-Fernández L, Arslancan S, Ivashchenko D, Crespo-Hernández CE, Corral I. Tracking the origin of photostability in purine nucleobases: the photophysics of 2-oxopurine. Phys Chem Chem Phys 2019; 21:13467-13473. [DOI: 10.1039/c9cp00879a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molding purine PES through functionalization: whilst purine C2-substitution maintains the features of the spectroscopic PES of the heterocycle, C6-functionalization reshapes its topography leading to photostable systems.
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Affiliation(s)
| | - Serra Arslancan
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
| | - Dmytro Ivashchenko
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Departamento de Química e Bioquímica
| | | | - Inés Corral
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- IADCHEM
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8
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Masoodi HR, Bagheri S, Ghaderi Z. The influence of Cu + binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study. J Biomol Struct Dyn 2018; 37:1923-1934. [PMID: 29757083 DOI: 10.1080/07391102.2018.1475256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the present work, the influence of Cu+ binding to N3- and N7-positions of hypoxanthine on energetic, geometrical and topological properties of hypoxanthine-guanine, hypoxanthine-adenine, hypoxanthine-cytosine, hypoxanthine-thymine and hypoxanthine-hypoxanthine mismatches is theoretically investigated. The calculations, in gas phase, are performed at B3LYP/6-311++G(3df,3pd) level of theory. Unlike the other mispairs, Cu+ binding to N3-position of hypoxanthine causes the proton transfer process from enol form of hypoxanthine to imino forms of adenine and cytosine. This process also occurs in all mismatches having enol form of hypoxanthine when Cu+ binds to N7-position of hypoxanthine. The mismatches are stabilized by hydrogen bonds. The influence of Cu+ on hydrogen bonds is also examined by atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamid Reza Masoodi
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , Rafsanjan , Iran
| | - Sotoodeh Bagheri
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , Rafsanjan , Iran
| | - Zahra Ghaderi
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , Rafsanjan , Iran
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9
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Liu F, Du L, Lan Z, Gao J. Hydrogen bond dynamics governs the effective photoprotection mechanism of plant phenolic sunscreens. Photochem Photobiol Sci 2017; 16:211-219. [PMID: 27982141 DOI: 10.1039/c6pp00367b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sinapic acid derivatives are important sunscreen species in natural plants, which could provide protection from solar UV radiation. Using a combination of ultrafast excited state dynamics, together with classical molecular dynamics studies, we demonstrate that there is direct coupling of hydrogen bond motion with excited state photoprotection dynamics as part of the basic mechanism in solution. Beyond the intra-molecular degree of freedom, the inter-molecular motions on all timescales are potentially important for the photochemical or photophysical events, ranging from the ultrafast hydrogen bond motion to solvent rearrangements. This provides not only an enhanced understanding of the anomalous experimental spectroscopic results, but also the key idea in the development of sunscreen agents with improved photo-chemical properties. We suggest that the hydrogen bond dynamics coupled excited state photoprotection mechanism may also be possible in a broad range of bio-related molecules in the condensed phase.
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Affiliation(s)
- Fang Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
| | - Likai Du
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
| | - Zhenggang Lan
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
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10
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Gutiérrez-Arzaluz L, Ramírez-Palma D, Buitrón-Cabrera F, Rocha-Rinza T, Cortés-Guzmán F, Peon J. Evolution of electron density towards the conical intersection of a nucleic acid purine. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Xie BB, Wang Q, Guo WW, Cui G. The excited-state decay mechanism of 2,4-dithiothymine in the gas phase, microsolvated surroundings, and aqueous solution. Phys Chem Chem Phys 2017; 19:7689-7698. [DOI: 10.1039/c7cp00478h] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
We have employed computational methods to systematically explore the excited-state decay mechanism of 2,4-dithiothymine.
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Affiliation(s)
- Bin-Bin Xie
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Qian Wang
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Wei-Wei Guo
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
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12
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Guo X, Yuan H, Zhu Q, An B, Zhang J. Ab initioinsights on photophysics of 9-methylhypoxanthine. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1164348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Guo X, Yuan H, An B, Zhu Q, Zhang J. Ultrafast excited-state deactivation of 9-methylhypoxanthine in aqueous solution: A QM/MM MD study. J Chem Phys 2016; 144:154306. [DOI: 10.1063/1.4946103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xugeng Guo
- Institute of Environmental and Analytical Sciences, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Huijuan Yuan
- Institute of Environmental and Analytical Sciences, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Beibei An
- Institute of Environmental and Analytical Sciences, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Qiuling Zhu
- Institute of Environmental and Analytical Sciences, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Jinglai Zhang
- Institute of Environmental and Analytical Sciences, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, People’s Republic of China
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14
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Restoring electronic coherence/decoherence for a trajectory-based nonadiabatic molecular dynamics. Sci Rep 2016; 6:24198. [PMID: 27063337 PMCID: PMC4827081 DOI: 10.1038/srep24198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/22/2016] [Indexed: 11/23/2022] Open
Abstract
By utilizing the time-independent semiclassical phase integral, we obtained modified coupled time-dependent Schrödinger equations that restore coherences and induce decoherences within original simple trajectory-based nonadiabatic molecular dynamic algorithms. Nonadiabatic transition probabilities simulated from both Tully’s fewest switches and semiclassical Ehrenfest algorithms follow exact quantum electronic oscillations and amplitudes for three out of the four well-known model systems. Within the present theory, nonadiabatic transitions estimated from statistical ensemble of trajectories accurately follow those of the modified electronic wave functions. The present theory can be immediately applied to the molecular dynamic simulations of photochemical and photophysical processes involving electronic excited states.
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