151
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Janicki MJ, Szabla R, Šponer J, Góra RW. Electron-driven proton transfer enables nonradiative photodeactivation in microhydrated 2-aminoimidazole. Faraday Discuss 2018; 212:345-358. [DOI: 10.1039/c8fd00086g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prebiotically credible activator of non-enzymatic RNA template-copying, 2-aminoimidazole, is protected from destructive photochemistry by photoacidity.
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Affiliation(s)
- Mikołaj J. Janicki
- Department of Physical and Quantum Chemistry
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Rafał Szabla
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
- Institute of Biophysics of the Czech Academy of Sciences
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences
- Brno
- Czech Republic
| | - Robert W. Góra
- Department of Physical and Quantum Chemistry
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
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152
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Dommett M, Rivera M, Crespo-Otero R. How Inter- and Intramolecular Processes Dictate Aggregation-Induced Emission in Crystals Undergoing Excited-State Proton Transfer. J Phys Chem Lett 2017; 8:6148-6153. [PMID: 29219318 DOI: 10.1021/acs.jpclett.7b02893] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Aggregation-induced emission (AIE) offers a route for the development of luminescent technologies with high quantum efficiencies. Excited-state intramolecular proton transfer (ESIPT) coupled to AIE can produce devices with emission across the visible spectrum. We use a combination of theoretical models to determine the factors that mediate fluorescence in molecular crystals undergoing ESIPT. Using two materials based on 2'-hydroxychalcone as exemplar cases, we analyze how inter- and intramolecular processes determine the emissive properties in the crystal environment. This systematic investigation extends the current interpretation of AIE to polar chromophores with multiple decay pathways. We find that population of nonradiative pathways is dictated by the electronic effects of the substituents and the degree of distortion allowed in the crystal environment. Localization of the electron density is crucial to maximize fluorescence via ESIPT. Our conclusions offer design strategies for the development of luminescent molecular crystals.
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Affiliation(s)
- Michael Dommett
- School of Biological and Chemical Sciences, Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Miguel Rivera
- School of Biological and Chemical Sciences, Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Rachel Crespo-Otero
- School of Biological and Chemical Sciences, Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
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153
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Shu Y, Parker KA, Truhlar DG. Dual-Functional Tamm–Dancoff Approximation with Self-Interaction-Free Orbitals: Vertical Excitation Energies and Potential Energy Surfaces near an Intersection Seam. J Phys Chem A 2017; 121:9728-9735. [DOI: 10.1021/acs.jpca.7b11400] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yinan Shu
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Kelsey A. Parker
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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154
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Kjønstad EF, Koch H. Resolving the Notorious Case of Conical Intersections for Coupled Cluster Dynamics. J Phys Chem Lett 2017; 8:4801-4807. [PMID: 28927266 DOI: 10.1021/acs.jpclett.7b02118] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The motion of electrons and nuclei in photochemical events often involves conical intersections, or degeneracies between electronic states. They serve as funnels in nuclear relaxation processes where the electrons and nuclei couple nonadiabatically. Accurate ab initio quantum chemical models are essential for interpreting experimental measurements of such phenomena. In this Letter, we resolve a long-standing problem in coupled cluster theory, presenting the first formulation of the theory that correctly describes conical intersections between excited electronic states of the same symmetry. This new development demonstrates that the highly accurate coupled cluster theory can be applied to describe dynamics on excited electronic states involving conical intersections.
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Affiliation(s)
- Eirik F Kjønstad
- Department of Chemistry, Norwegian University of Science and Technology , 7491 Trondheim, Norway
- Department of Chemistry and the PULSE Institute, Stanford University , Stanford, California 94305, United States
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology , 7491 Trondheim, Norway
- Department of Chemistry and the PULSE Institute, Stanford University , Stanford, California 94305, United States
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155
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Isomerization of the RPSB chromophore in the gas phase along the torsional pathways using QTAIM. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.07.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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156
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Lefrancois D, Tuna D, Martínez TJ, Dreuw A. The Spin-Flip Variant of the Algebraic-Diagrammatic Construction Yields the Correct Topology of S1/S0 Conical Intersections. J Chem Theory Comput 2017; 13:4436-4441. [DOI: 10.1021/acs.jctc.7b00634] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Lefrancois
- Interdisciplinary
Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer
Feld 205, 69120 Heidelberg, Germany
| | - Deniz Tuna
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Todd J. Martínez
- Department
of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Andreas Dreuw
- Interdisciplinary
Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer
Feld 205, 69120 Heidelberg, Germany
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157
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Snyder JW, Parrish RM, Martínez TJ. α-CASSCF: An Efficient, Empirical Correction for SA-CASSCF To Closely Approximate MS-CASPT2 Potential Energy Surfaces. J Phys Chem Lett 2017; 8:2432-2437. [PMID: 28513165 DOI: 10.1021/acs.jpclett.7b00940] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Because of its computational efficiency, the state-averaged complete active-space self-consistent field (SA-CASSCF) method is commonly employed in nonadiabatic ab initio molecular dynamics. However, SA-CASSCF does not effectively recover dynamical correlation. As a result, there can be qualitative differences between SA-CASSCF potential energy surfaces (PESs) and more accurate reference surfaces computed using multistate complete active space second-order perturbation theory (MS-CASPT2). Here we introduce an empirical correction to SA-CASSCF that scales the splitting between individual states and the state-averaged energy. We call this the α-CASSCF method, and we show here that it significantly improves the accuracy of relative energies and PESs compared with MS-CASPT2 for the chromophores of green fluorescent and photoactive yellow proteins. As such, this method may prove to be quite valuable for nonadiabatic dynamics.
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Affiliation(s)
- James W Snyder
- Department of Chemistry and The PULSE Institute, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Robert M Parrish
- Department of Chemistry and The PULSE Institute, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
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158
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Prlj A, Vannay L, Corminboeuf C. Fluorescence Quenching in BODIPY Dyes: The Role of Intramolecular Interactions and Charge Transfer. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201700093] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Antonio Prlj
- Institut des Sciences et Ingénierie Chimiques; École polytechnique fédérale de Lausanne; CH-1015 Lausanne
| | - Laurent Vannay
- Institut des Sciences et Ingénierie Chimiques; École polytechnique fédérale de Lausanne; CH-1015 Lausanne
| | - Clemence Corminboeuf
- Institut des Sciences et Ingénierie Chimiques; École polytechnique fédérale de Lausanne; CH-1015 Lausanne
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159
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Novak J, Prlj A, Basarić N, Corminboeuf C, Došlić N. Photochemistry of 1- and 2-Naphthols and Their Water Clusters: The Role of1ππ*(La) Mediated Hydrogen Transfer to Carbon Atoms. Chemistry 2017; 23:8244-8251. [DOI: 10.1002/chem.201700691] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jurica Novak
- Department of Physical Chemistry; Ruđer Bošković Institute; Bijenička cesta 54 10000 Zagreb Croatia
| | - Antonio Prlj
- Institut des Sciences et Ingénierie Chimiques; Ecole Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry; Ruđer Bošković Institute; Bijenička cesta 54 10000 Zagreb Croatia
| | - Clémence Corminboeuf
- Institut des Sciences et Ingénierie Chimiques; Ecole Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Nađa Došlić
- Department of Physical Chemistry; Ruđer Bošković Institute; Bijenička cesta 54 10000 Zagreb Croatia
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160
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Shu Y, Parker KA, Truhlar DG. Dual-Functional Tamm-Dancoff Approximation: A Convenient Density Functional Method that Correctly Describes S 1/S 0 Conical Intersections. J Phys Chem Lett 2017; 8:2107-2112. [PMID: 28418680 DOI: 10.1021/acs.jpclett.7b00594] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Time-dependent Kohn-Sham density functional theory has been used successfully to compute vertical excitation energies, especially for large molecular systems. However, the lack of double excitation character in the excited amplitudes produced by linear response in the adiabatic approximation holds it back from broader applications in photochemistry; for example, it shows (3N - 7)-dimensional conical intersection seams (where N is the number of atoms) between ground and excited states, although the correct dimensionality is 3N - 8. In this letter, we present a new, conceptually simple, easy-to-implement, and easy-to-use way to employ time-dependent Kohn-Sham density functional theory that has global accuracy comparable with the conventional single-functional version and that recovers the double cone topology of the potential energy surfaces at S1/S0 conical intersection seams. The new method is called the dual-functional Tamm-Dancoff approximation (DF-TDA).
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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
| | - Kelsey A Parker
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
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161
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Peccati F, Mai S, González L. Insights into the deactivation of 5-bromouracil after ultraviolet excitation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20160202. [PMID: 28320905 PMCID: PMC5360901 DOI: 10.1098/rsta.2016.0202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Francesca Peccati
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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162
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Harabuchi Y, Taketsugu T, Maeda S. Combined gradient projection/single component artificial force induced reaction (GP/SC-AFIR) method for an efficient search of minimum energy conical intersection (MECI) geometries. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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163
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Mališ M, Došlić N. Nonradiative Relaxation Mechanisms of UV Excited Phenylalanine Residues: A Comparative Computational Study. Molecules 2017; 22:E493. [PMID: 28335582 PMCID: PMC6155328 DOI: 10.3390/molecules22030493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/09/2017] [Accepted: 03/16/2017] [Indexed: 11/17/2022] Open
Abstract
The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory. The work emphasizes the role that excitation transfer from the phenylππ*to amidenπ*state plays in the deactivation of the three systems and shows how the ease of out-of-plane distortions of the amide group determines the rate of population transfer between the two electronic states. The subsequent dynamics on thenπ*state is barrierless along several pathways and leads to fast deactivation to the ground electronic state.
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Affiliation(s)
- Momir Mališ
- Ruđer Bošković Institute, HR-10000 Zagreb, Croatia.
- Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Nađa Došlić
- Ruđer Bošković Institute, HR-10000 Zagreb, Croatia.
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164
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Sinha Ray S, Ghosh P, Chaudhuri RK, Chattopadhyay S. Improved virtual orbitals in state specific multireference perturbation theory for prototypes of quasidegenerate electronic structure. J Chem Phys 2017; 146:064111. [DOI: 10.1063/1.4975322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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165
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García-Prieto FF, Muñoz-Losa A, Fdez Galván I, Sánchez ML, Aguilar MA, Martín ME. QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore. J Chem Theory Comput 2017; 13:737-748. [PMID: 28072537 DOI: 10.1021/acs.jctc.6b01069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.
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Affiliation(s)
- Francisco F García-Prieto
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Aurora Muñoz-Losa
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Ignacio Fdez Galván
- Department of Chemistry-Ångström, The Theoretical Chemistry Programme, Uppsala University , Box 518, 751 20 Uppsala, Sweden
| | - M Luz Sánchez
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Manuel A Aguilar
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - M Elena Martín
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
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166
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Pijeau S, Hohenstein EG. Improved Complete Active Space Configuration Interaction Energies with a Simple Correction from Density Functional Theory. J Chem Theory Comput 2017; 13:1130-1146. [DOI: 10.1021/acs.jctc.6b00893] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shiela Pijeau
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Edward G. Hohenstein
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- Ph.D.
Program in Chemistry, The City University of New York, New York, New York 10016, United States
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167
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Bai S, Barbatti M. On the decay of the triplet state of thionucleobases. Phys Chem Chem Phys 2017; 19:12674-12682. [DOI: 10.1039/c7cp02050c] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The double-well triplet state of thionucleobases allows for a two-step mechanistic control of their triplet decay lifetime.
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168
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Mališ M, Novak J, Zgrablić G, Parmigiani F, Došlić N. Mechanism of ultrafast non-reactive deactivation of the retinal chromophore in non-polar solvents. Phys Chem Chem Phys 2017; 19:25970-25978. [DOI: 10.1039/c7cp03293e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Counterion sensitive photodynamics of the retinal chromophore in solution.
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Affiliation(s)
- M. Mališ
- Department of Physical Chemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
- Centre Européen de Calcul Atomique et Moléculaire
| | - J. Novak
- Department of Physical Chemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - G. Zgrablić
- Elettra-Sincrotrone Treste
- T-ReX Laboratory
- Trieste
- Italy
- Politehnika Pula
| | - F. Parmigiani
- Elettra-Sincrotrone Treste
- T-ReX Laboratory
- Trieste
- Italy
- Department of Physics
| | - N. Došlić
- Department of Physical Chemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
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169
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Carlos Borin A, Mai S, Marquetand P, González L. Ab initio molecular dynamics relaxation and intersystem crossing mechanisms of 5-azacytosine. Phys Chem Chem Phys 2017; 19:5888-5894. [DOI: 10.1039/c6cp07919a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nonadiabatic SHARC dynamics simulations reveal the molecular deformations involved in the photodeactivation pathways of 5-azacytosine.
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Affiliation(s)
- Antonio Carlos Borin
- Department of Fundamental Chemistry
- Institute of Chemistry
- University of São Paulo
- NAP-PhotoTech the USP Consortium for Photochemical Technology
- São Paulo
| | - Sebastian Mai
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
| | - Leticia González
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
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170
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Kammeraad JA, Zimmerman PM. Estimating the Derivative Coupling Vector Using Gradients. J Phys Chem Lett 2016; 7:5074-5079. [PMID: 27973885 DOI: 10.1021/acs.jpclett.6b02501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The difference gradient and derivative coupling vectors span the branching planes of conical intersections between electronic states. While gradients are commonly available in many electronic structure methods, the derivative coupling vectors are not always implemented and ready for use in characterizing conical intersections. This Letter shows how the derivative coupling vectors can be computed to high accuracy (direction and magnitude) using energy and gradient information. The new method is based on the combination of a linear-coupling two-state Hamiltonian and a finite-difference Davidson approach for computing the branching plane. Benchmark cases are provided showing these vectors can be efficiently computed near conical intersections.
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Affiliation(s)
- Joshua A Kammeraad
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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171
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Three-state conical intersection optimization methods: development and implementation at QM/MM level. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2029-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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172
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Mavros MG, Hait D, Van Voorhis T. Condensed phase electron transfer beyond the Condon approximation. J Chem Phys 2016; 145:214105. [DOI: 10.1063/1.4971166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael G. Mavros
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Diptarka Hait
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
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173
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Stojanović L, Bai S, Nagesh J, Izmaylov AF, Crespo-Otero R, Lischka H, Barbatti M. New Insights into the State Trapping of UV-Excited Thymine. Molecules 2016; 21:E1603. [PMID: 27886099 PMCID: PMC6273395 DOI: 10.3390/molecules21111603] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 11/23/2022] Open
Abstract
After UV excitation, gas phase thymine returns to a ground state in 5 to 7 ps, showing multiple time constants. There is no consensus on the assignment of these processes, with a dispute between models claiming that thymine is trapped either in the first (S₁) or in the second (S₂) excited states. In the present study, a nonadiabatic dynamics simulation of thymine is performed on the basis of ADC(2) surfaces, to understand the role of dynamic electron correlation on the deactivation pathways. The results show that trapping in S₂ is strongly reduced in comparison to previous simulations considering only non-dynamic electron correlation on CASSCF surfaces. The reason for the difference is traced back to the energetic cost for formation of a CO π bond in S₂.
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Affiliation(s)
| | - Shuming Bai
- Aix Marseille Univ., CNRS, ICR, Marseille, France.
| | - Jayashree Nagesh
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Artur F Izmaylov
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Rachel Crespo-Otero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA.
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174
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Mai S, Pollum M, Martínez-Fernández L, Dunn N, Marquetand P, Corral I, Crespo-Hernández CE, González L. The origin of efficient triplet state population in sulfur-substituted nucleobases. Nat Commun 2016; 7:13077. [PMID: 27703148 PMCID: PMC5059480 DOI: 10.1038/ncomms13077] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/01/2016] [Indexed: 12/19/2022] Open
Abstract
Elucidating the photophysical mechanisms in sulfur-substituted nucleobases (thiobases) is essential for designing prospective drugs for photo- and chemotherapeutic applications. Although it has long been established that the phototherapeutic activity of thiobases is intimately linked to efficient intersystem crossing into reactive triplet states, the molecular factors underlying this efficiency are poorly understood. Herein we combine femtosecond transient absorption experiments with quantum chemistry and nonadiabatic dynamics simulations to investigate 2-thiocytosine as a necessary step to unravel the electronic and structural elements that lead to ultrafast and near-unity triplet-state population in thiobases in general. We show that different parts of the potential energy surfaces are stabilized to different extents via thionation, quenching the intrinsic photostability of canonical DNA and RNA nucleobases. These findings satisfactorily explain why thiobases exhibit the fastest intersystem crossing lifetimes measured to date among bio-organic molecules and have near-unity triplet yields, whereas the triplet yields of canonical nucleobases are nearly zero.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Marvin Pollum
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | | | - Nicholas Dunn
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Inés Corral
- Universidad Autónoma de Madrid, Departamento de Química, Cantoblanco, Madrid 28049, Spain
| | - Carlos E. Crespo-Hernández
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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175
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Yost SR, Head-Gordon M. Size consistent formulations of the perturb-then-diagonalize Møller-Plesset perturbation theory correction to non-orthogonal configuration interaction. J Chem Phys 2016; 145:054105. [DOI: 10.1063/1.4959794] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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176
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Harabuchi Y, Taketsugu T, Maeda S. Nonadiabatic Pathways of Furan and Dibenzofuran: What Makes Dibenzofuran Fluorescent? CHEM LETT 2016. [DOI: 10.1246/cl.160398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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177
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Watanabe KJ, Nakatani N, Nakayama A, Higashi M, Hasegawa JY. Spin-Blocking Effect in CO and H2 Binding Reactions to Molybdenocene and Tungstenocene: A Theoretical Study on the Reaction Mechanism via the Minimum Energy Intersystem Crossing Point. Inorg Chem 2016; 55:8082-90. [DOI: 10.1021/acs.inorgchem.6b01187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K-jiro Watanabe
- Institute for Catalysis, Hokkaido University, N21 W10 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Department of Chemistry, Biology and Marine Science,
Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Naoki Nakatani
- Institute for Catalysis, Hokkaido University, N21 W10 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Akira Nakayama
- Institute for Catalysis, Hokkaido University, N21 W10 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science,
Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Jun-ya Hasegawa
- Institute for Catalysis, Hokkaido University, N21 W10 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
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178
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Fdez. Galván I, Delcey MG, Pedersen TB, Aquilante F, Lindh R. Analytical State-Average Complete-Active-Space Self-Consistent Field Nonadiabatic Coupling Vectors: Implementation with Density-Fitted Two-Electron Integrals and Application to Conical Intersections. J Chem Theory Comput 2016; 12:3636-53. [DOI: 10.1021/acs.jctc.6b00384] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Mickaël G. Delcey
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kenneth
S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Thomas Bondo Pedersen
- Centre
for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O.
Box 1033 Blindern, 0315 Oslo, Norway
| | - Francesco Aquilante
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, IT-40126 Bologna, Italy
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179
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Sasaki S, Suzuki S, Sameera WMC, Igawa K, Morokuma K, Konishi GI. Highly Twisted N,N-Dialkylamines as a Design Strategy to Tune Simple Aromatic Hydrocarbons as Steric Environment-Sensitive Fluorophores. J Am Chem Soc 2016; 138:8194-206. [DOI: 10.1021/jacs.6b03749] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Shunsuke Sasaki
- Department
of Organic and Polymeric Materials, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Satoshi Suzuki
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - W. M. C. Sameera
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Kazunobu Igawa
- Institute
for Materials Chemistry and Engineering, Kyushu University, Fukuoka 816-8580, Japan
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Gen-ichi Konishi
- Department
of Organic and Polymeric Materials, Tokyo Institute of Technology, Tokyo 152-8552, Japan
- PRESTO, Japan Science and Technology Agency (JST), Tokyo 102-0076, Japan
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180
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Affiliation(s)
- Xiaolei Zhu
- Department of Chemistry, Johns Hopkins University Baltimore, MD, USA
| | - David R. Yarkony
- Department of Chemistry, Johns Hopkins University Baltimore, MD, USA
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181
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Barbatti M, Sen K. Effects of different initial condition samplings on photodynamics and spectrum of pyrrole. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2016; 116:762-771. [DOI: 10.1002/qua.25049] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
- Mario Barbatti
- Aix Marseille Université, CNRS, ICR UMR7273; Marseille 13397 France
| | - Kakali Sen
- Department of Chemistry; École Normale Supérieure, UMR ENS-CNRS-UPMC 8640; Paris 75005 France
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182
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Dobryakov A, Quick M, Lenoir D, Detert H, Ernsting N, Kovalenko S. Time-resolved photoisomerization of 1,1′-di-tert-butylstilbene and 1,1′-dicyanostilbene. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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183
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Kunitsa AA, Bravaya KB. Electronic structure of the para-benzoquinone radical anion revisited. Phys Chem Chem Phys 2016; 18:3454-62. [DOI: 10.1039/c5cp06476g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Photoinduced processes in para-benzoquinone anion are studied with multistate multireference perturbation theory: an interplay between autodetachment and internal conversion.
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Affiliation(s)
- Alexander A. Kunitsa
- Department of Chemistry
- Boston University
- Boston
- USA
- Institute of Problems of Chemical Physics
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184
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Prlj A, Fabrizio A, Corminboeuf C. Rationalizing fluorescence quenching in meso-BODIPY dyes. Phys Chem Chem Phys 2016; 18:32668-32672. [DOI: 10.1039/c6cp06799a] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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185
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García-Prieto FF, Muñoz-Losa A, Luz Sánchez M, Elena Martín M, Aguilar MA. Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore. Phys Chem Chem Phys 2016; 18:27476-27485. [DOI: 10.1039/c6cp03541h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Environmental effects on the deactivation channels of the PYP chromophore in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level.
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Affiliation(s)
| | - Aurora Muñoz-Losa
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - M. Luz Sánchez
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
| | - M. Elena Martín
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
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186
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Liu X, Karsili TN, Sobolewski AL, Domcke W. Photocatalytic water splitting with acridine dyes: Guidelines from computational chemistry. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2015.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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187
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Szabla R, Góra RW, Janicki M, Šponer J. Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires. Faraday Discuss 2016; 195:237-251. [DOI: 10.1039/c6fd00131a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H2O)5 cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S0 state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H2O)5 cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.
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Affiliation(s)
- Rafał Szabla
- Institute of Biophysics
- Academy of Sciences of the Czech Republic
- Brno
- Czech Republic
| | - Robert W. Góra
- Department of Physical and Quantum Chemistry
- Faculty of Chemistry
- Wrocław University of Technology
- 50-370 Wrocław
- Poland
| | - Mikołaj Janicki
- Department of Physical and Quantum Chemistry
- Faculty of Chemistry
- Wrocław University of Technology
- 50-370 Wrocław
- Poland
| | - Jiří Šponer
- Institute of Biophysics
- Academy of Sciences of the Czech Republic
- Brno
- Czech Republic
- CEITEC–Central European Institute of Technology
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188
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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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189
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Kitagawa Y, Chen Y, Nakatani N, Nakayama A, Hasegawa J. A DFT and multi-configurational perturbation theory study on O2 binding to a model heme compound via the spin-change barrier. Phys Chem Chem Phys 2016; 18:18137-44. [DOI: 10.1039/c6cp02329k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potential energy surface of the O2 binding to a model heme compound via minimum energy intersystem crossing point (MEISCP) was investigated with DFT and MS-CASPT2. The porphyrin's symmetric shrinking vibration mode contributes to reach the MESICP from the T1 minimum.
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Affiliation(s)
- Y. Kitagawa
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - Y. Chen
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - N. Nakatani
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - A. Nakayama
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - J. Hasegawa
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
- JST-CREST
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190
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Tuna D, Domcke W. Excited-state deactivation in 8-oxo-deoxyguanosine: comparison between anionic and neutral forms. Phys Chem Chem Phys 2016; 18:947-55. [DOI: 10.1039/c5cp05804j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ab initio explorations of excited-state potential-energy surfaces show that a radiationless deactivation mechanism via intramolecular excited-state proton transfer is available in neutral 8-oxo-deoxyguanosine, whereas it is not available in the anionic form.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim an der Ruhr
- Germany
| | - Wolfgang Domcke
- Department of Chemistry
- Technische Universität München
- 85747 Garching
- Germany
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191
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Zhang X, Herbert JM. Spin-flip, tensor equation-of-motion configuration interaction with a density-functional correction: A spin-complete method for exploring excited-state potential energy surfaces. J Chem Phys 2015; 143:234107. [DOI: 10.1063/1.4937571] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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192
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Hansen JA, Bauman NP, Shen J, Borden WT, Piecuch P. Ab initiocoupled-cluster and multi-reference configuration interaction studies of the low-lying electronic states of 1,2,3,4-cyclobutanetetraone. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1112926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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193
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Tuna D, Lefrancois D, Wolański Ł, Gozem S, Schapiro I, Andruniów T, Dreuw A, Olivucci M. Assessment of Approximate Coupled-Cluster and Algebraic-Diagrammatic-Construction Methods for Ground- and Excited-State Reaction Paths and the Conical-Intersection Seam of a Retinal-Chromophore Model. J Chem Theory Comput 2015; 11:5758-81. [PMID: 26642989 DOI: 10.1021/acs.jctc.5b00022] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As a minimal model of the chromophore of rhodopsin proteins, the penta-2,4-dieniminium cation (PSB3) poses a challenging test system for the assessment of electronic-structure methods for the exploration of ground- and excited-state potential-energy surfaces, the topography of conical intersections, and the dimensionality (topology) of the branching space. Herein, we report on the performance of the approximate linear-response coupled-cluster method of second order (CC2) and the algebraic-diagrammatic-construction scheme of the polarization propagator of second and third orders (ADC(2) and ADC(3)). For the ADC(2) method, we considered both the strict and extended variants (ADC(2)-s and ADC(2)-x). For both CC2 and ADC methods, we also tested the spin-component-scaled (SCS) and spin-opposite-scaled (SOS) variants. We have explored several ground- and excited-state reaction paths, a circular path centered around the S1/S0 surface crossing, and a 2D scan of the potential-energy surfaces along the branching space. We find that the CC2 and ADC methods yield a different dimensionality of the intersection space. While the ADC methods yield a linear intersection topology, we find a conical intersection topology for the CC2 method. We present computational evidence showing that the linear-response CC2 method yields a surface crossing between the reference state and the first response state featuring characteristics that are expected for a true conical intersection. Finally, we test the performance of these methods for the approximate geometry optimization of the S1/S0 minimum-energy conical intersection and compare the geometries with available data from multireference methods. The present study provides new insight into the performance of linear-response CC2 and polarization-propagator ADC methods for molecular electronic spectroscopy and applications in computational photochemistry.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, University of Heidelberg , 69120 Heidelberg, Germany
| | - Łukasz Wolański
- Department of Chemistry, Wrocław University of Technology , 50370 Wrocław, Poland
| | - Samer Gozem
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Igor Schapiro
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504 , Strasbourg 67034, France
| | - Tadeusz Andruniów
- Department of Chemistry, Wrocław University of Technology , 50370 Wrocław, Poland
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, University of Heidelberg , 69120 Heidelberg, Germany
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Universitá de Siena , 53100 Siena, Italy
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194
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Snyder JW, Hohenstein EG, Luehr N, Martínez TJ. An atomic orbital-based formulation of analytical gradients and nonadiabatic coupling vector elements for the state-averaged complete active space self-consistent field method on graphical processing units. J Chem Phys 2015; 143:154107. [DOI: 10.1063/1.4932613] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- James W. Snyder
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Nathan Luehr
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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195
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Chaiwongwattana S, Sapunar M, Ponzi A, Decleva P, Došlić N. Exploration of Excited State Deactivation Pathways of Adenine Monohydrates. J Phys Chem A 2015; 119:10637-44. [DOI: 10.1021/acs.jpca.5b07496] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Marin Sapunar
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Aurora Ponzi
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Piero Decleva
- Dipartimento di
Scienze Chimiche, Università di Trieste, 34127 Trieste, Italy
| | - Nađa Došlić
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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196
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Li Z, Vendrell O, Santra R. Ultrafast Charge Transfer of a Valence Double Hole in Glycine Driven Exclusively by Nuclear Motion. PHYSICAL REVIEW LETTERS 2015; 115:143002. [PMID: 26551809 DOI: 10.1103/physrevlett.115.143002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Indexed: 06/05/2023]
Abstract
We explore theoretically the ultrafast transfer of a double electron hole between the functional groups of glycine after K-shell ionization and subsequent Auger decay. Although a large energy gap of about 15 eV initially exists between the two electronic states involved and coherent electronic dynamics play no role in the hole transfer, we find that the double hole is transferred within 3 to 4 fs between both functional ends of the glycine molecule driven solely by specific nuclear displacements and non-Born-Oppenheimer effects. The nuclear displacements along specific vibrational modes are of the order of 15% of a typical chemical bond between carbon, oxygen, and nitrogen atoms and about 30% for bonds involving hydrogen atoms. The time required for the hole transfer corresponds to less than half a vibrational period of the involved nuclear modes. This finding challenges the common wisdom that nuclear dynamics of the molecular skeleton are unimportant for charge transfer processes at the few-femtosecond time scale and shows that they can even play a prominent role. It also indicates that in x-ray imaging experiments, in which ionization is unavoidable, valence electron redistribution caused by nuclear dynamics might be much faster than previously anticipated. Thus, non-Born-Oppenheimer effects may affect the apparent electron densities extracted from such measurements.
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Affiliation(s)
- Zheng Li
- Center for Free-Electron Laser Science, DESY, Notkestraß e 85, D-22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Oriol Vendrell
- Center for Free-Electron Laser Science, DESY, Notkestraß e 85, D-22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestraß e 85, D-22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstraße 9, D-20355 Hamburg, Germany
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197
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Arulmozhiraja S, Nakatani N, Nakayama A, Hasegawa JY. Energy dissipative photoprotective mechanism of carotenoid spheroidene from the photoreaction center of purple bacteria Rhodobacter sphaeroides. Phys Chem Chem Phys 2015; 17:23468-80. [PMID: 26292635 DOI: 10.1039/c5cp03089g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carotenoid spheroidene (SPO) functions for photoprotection in the photosynthetic reaction centers (RCs) and effectively dissipates its triplet excitation energy. Sensitized cis-to-trans isomerization was proposed as a possible mechanism for a singlet-triplet energy crossing for the 15,15'-cis-SPO; however, it has been questioned recently. To understand the dissipative photoprotective mechanism of this important SPO and to overcome the existing controversies on this issue, we carried out a theoretical investigation using density functional theory on the possible triplet energy relaxation mechanism through the cis-to-trans isomerization. Together with the earlier experimental observations, the possible mechanism was discussed for the triplet energy relaxation of the 15,15'-cis-SPO. The result shows that complete cis-to-trans isomerization is not necessary. Twisting the C15-C15' bond leads to singlet-triplet energy crossing at ϕ(14,15,15',14') = 77° with an energy 32.5 kJ mol(-1) (7.7 kcal mol(-1)) higher than that of the T1 15,15'-cis minimum. Further exploration of the minimum-energy intersystem crossing (MEISC) point shows that triplet relaxation could occur at a less distorted structure (ϕ = 58.4°) with the energy height of 26.5 KJ mol(-1) (6.3 kcal mol(-1)). Another important reaction coordinate to reach the MEISC point is the bond-length alternation. The model truncation effect, solvent effect, and spin-orbit coupling were also investigated. The singlet-triplet crossing was also investigated for the 13,14-cis stereoisomer and locked-13,14-cis-SPO. We also discussed the origin of the natural selection of the cis over trans isomer in the RC.
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Affiliation(s)
- Sundaram Arulmozhiraja
- Catalysis Research Center, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan.
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198
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Piecuch P, Hansen JA, Ajala AO. Benchmarking the completely renormalised equation-of-motion coupled-cluster approaches for vertical excitation energies. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1076901] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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199
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Shu Y, Fales BS, Levine BG. Defect-Induced Conical Intersections Promote Nonradiative Recombination. NANO LETTERS 2015; 15:6247-6253. [PMID: 26291975 DOI: 10.1021/acs.nanolett.5b02848] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We apply multireference electronic structure calculations to demonstrate the presence of conical intersections between the ground and the first excited electronic states of three silicon nanocrystals containing defects characteristic of the oxidized silicon surface. These intersections are accessible upon excitation at visible wavelengths and are predicted to facilitate nonradiative recombination with a rate that increases with decreasing particle size. This work illustrates a new framework for identifying defects responsible for nonradiative recombination.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - B Scott Fales
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Benjamin G Levine
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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200
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Liu X, Karsili TNV, Sobolewski AL, Domcke W. Photocatalytic Water Splitting with the Acridine Chromophore: A Computational Study. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04833] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaojun Liu
- Department
of Chemistry, Technische Universität München, D-85747 Garching, Germany
- Key
Laboratory of Luminescence and Optical Information, Institute of Optoelectronic
Technology, Beijing Jiaotong University, 100044 Beijing, China
| | - Tolga N. V. Karsili
- Department
of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | | | - Wolfgang Domcke
- Department
of Chemistry, Technische Universität München, D-85747 Garching, Germany
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