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Martyka M, Jankowska J. New insights into the photocyclization reaction of a popular diarylethene switch: a nonadiabatic molecular dynamics study. Phys Chem Chem Phys 2024; 26:13383-13394. [PMID: 38646878 DOI: 10.1039/d3cp06256b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Diarylethene (DAE) molecular switches have continued to attract the attention of researchers for over 20 years. Their remarkable photophysical properties endow them with countless applications in photonics and molecular technologies. However, despite extensive experimental and theoretical research, the mechanism of DAE photoswitching is not yet fully rationalized. In this work, we investigate the ring closure dynamics of a popular DAE switch, 1,2-bis(3-methyl-5-phenyl-2 thienyl)perfluorocyclopentene (PT), using nonadiabatic molecular dynamics (NAMD) simulations. Employing the fewest switches surface hopping protocol, along with the semi-empirical multireference ODM2/MRCI-SD method, we investigate possible reaction pathways for this photoprocess, as well as their timescales and resulting photoproducts. Furthermore, using a dynamic configuration-space sampling procedure, we elucidate the role of triplet states in the photocyclization of PT, supporting available experimental data for the closely related DMPT molecule, which indicate an ultrafast intersystem crossing (ISC) transition competing with the singlet-driven photoswitching reaction. Our findings not only corroborate experimental studies on DAE switches, but also provide new mechanistic insights into the potential use in the rational design of DAE switches tailored for specific technological applications.
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Affiliation(s)
- Mikołaj Martyka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland.
- Interdisciplinary Doctoral School, University of Warsaw, Dobra 56/66, Warsaw, 00-312, Poland
| | - Joanna Jankowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland.
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2
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Martyka M, Jankowska J. Nonadiabatic molecular dynamics study of a complete photoswitching cycle for a full-size diarylethene system. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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3
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Xie RF, Zhang JB, Wu Y, Li L, Liu XY, Cui G. Non-negligible roles of charge transfer excitons in ultrafast excitation energy transfer dynamics of a double-walled carbon nanotube. J Chem Phys 2023; 158:054108. [PMID: 36754819 DOI: 10.1063/5.0134353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Herein, we employed a developed linear response time dependent density functional theory-based nonadiabatic dynamics simulation method that explicitly takes into account the excitonic effects to investigate photoinduced excitation energy transfer dynamics of a double-walled carbon nanotube (CNT) model with different excitation energies. The E11 excitation of the outer CNT will generate a local excitation (LE) |out*〉 exciton due to its low energy, which does not induce any charge separation. In contrast, the E11 excitation of the inner CNT can generate four kinds of excitons with the LE exciton |in*〉 dominates. In the 500-fs dynamics simulation, the LE exciton |in*〉 and charge transfer (CT) excitons |out-in+〉 and |out+in-〉 are all gradually converted to the |out*〉 exciton, corresponding to a photoinduced excitation energy transfer, which is consistent with experimental studies. Finally, when the excitation energy is close to the E22 state of the outer CNT (∼1.05 eV), a mixed population of different excitons, with the |out*〉 exciton dominated, is generated. Then, photoinduced energy transfer from the outer to inner CNTs occurs in the first 50 fs, which is followed by an inner to outer excitation energy transfer that is completed in 400 fs. The present work not only sheds important light on the mechanistic details of wavelength-dependent excitation energy transfer of a double-walled CNT model but also demonstrates the roles and importance of CT excitons in photoinduced excitation energy transfer. It also emphasized that explicitly including the excitonic effects in electronic structure calculations and nonadiabatic dynamics simulations is significant for correct understanding/rational design of optoelectronic properties of periodically extended systems.
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Affiliation(s)
- Rui-Fang Xie
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Jing-Bin Zhang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Yang Wu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Laicai Li
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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4
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Jankowska J, Martyka M, Michalski M. Photo-cycloreversion mechanism in diarylethenes revisited: A multireference quantum-chemical study at the ODM2/MRCI level. J Chem Phys 2021; 154:204305. [PMID: 34241185 DOI: 10.1063/5.0045830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photoswitchable diarylethenes (DAEs), over years of intense fundamental and applied research, have been established among the most commonly chosen molecular photoswitches, often employed as controlling units in molecular devices and smart materials. At the same time, providing reliable explanation for their photophysical behavior, especially the mechanism of the photo-cycloreversion transformation, turned out to be a highly challenging task. Herein, we investigate this mechanism in detail by means of multireference semi-empirical quantum chemistry calculations, allowing, for the first time, for a balanced treatment of the static and dynamic correlation effects, both playing a crucial role in DAE photochemistry. In the course of our study, we find the second singlet excited state of double electronic-excitation character to be the key to understanding the nature of the photo-cycloreversion transformation in DAE molecular photoswitches.
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Affiliation(s)
- J Jankowska
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland
| | - M Martyka
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland
| | - M Michalski
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland
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"On-The-Fly" Non-Adiabatic Dynamics Simulations on Photoinduced Ring-Closing Reaction of a Nucleoside-Based Diarylethene Photoswitch. Molecules 2021; 26:molecules26092724. [PMID: 34066431 PMCID: PMC8125013 DOI: 10.3390/molecules26092724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 11/17/2022] Open
Abstract
Nucleoside-based diarylethenes are emerging as an especial class of photochromic compounds that have potential applications in regulating biological systems using noninvasive light with high spatio-temporal resolution. However, relevant microscopic photochromic mechanisms at atomic level of these novel diarylethenes remain to be explored. Herein, we have employed static electronic structure calculations (MS-CASPT2//M06-2X, MS-CASPT2//SA-CASSCF) in combination with non-adiabatic dynamics simulations to explore the related photoinduced ring-closing reaction of a typical nucleoside-based diarylethene photoswitch, namely, PS-IV. Upon excitation with UV light, the open form PS-IV can be excited to a spectroscopically bright S1 state. After that, the molecule relaxes to the conical intersection region within 150 fs according to the barrierless relaxed scan of the C1–C6 bond, which is followed by an immediate deactivation to the ground state. The conical intersection structure is very similar to the ground state transition state structure which connects the open and closed forms of PS-IV, and therefore plays a crucial role in the photochromism of PS-IV. Besides, after analyzing the hopping structures, we conclude that the ring closing reaction cannot complete in the S1 state alone since all the C1–C6 distances of the hopping structures are larger than 2.00 Å. Once hopping to the ground state, the molecules either return to the original open form of PS-IV or produce the closed form of PS-IV within 100 fs, and the ring closing quantum yield is estimated to be 56%. Our present work not only elucidates the ultrafast photoinduced pericyclic reaction of the nucleoside-based diarylethene PS-IV, but can also be helpful for the future design of novel nucleoside-based diarylethenes with better performance.
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Gheorghiu A, Coveney PV, Arabi AA. The influence of base pair tautomerism on single point mutations in aqueous DNA. Interface Focus 2020; 10:20190120. [PMID: 33178413 PMCID: PMC7653342 DOI: 10.1098/rsfs.2019.0120] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.
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Affiliation(s)
- A Gheorghiu
- Centre for Computational Science, University College London, London, UK
| | - P V Coveney
- Centre for Computational Science, University College London, London, UK.,Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - A A Arabi
- Centre for Computational Science, University College London, London, UK.,College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates
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Mai S, González L. Molecular Photochemistry: Recent Developments in Theory. Angew Chem Int Ed Engl 2020; 59:16832-16846. [PMID: 32052547 PMCID: PMC7540682 DOI: 10.1002/anie.201916381] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/12/2020] [Indexed: 12/16/2022]
Abstract
Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light-induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non-adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.
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Affiliation(s)
- Sebastian Mai
- Photonics InstituteVienna University of TechnologyGusshausstrasse 27–291040ViennaAustria
| | - Leticia González
- Institute of Theoretical ChemistryFaculty of ChemistryUniversity of ViennaWähringer Strasse 171090ViennaAustria
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8
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Liu XY, Li ZW, Fang WH, Cui G. Nonadiabatic Exciton and Charge Separation Dynamics at Interfaces of Zinc Phthalocyanine and Fullerene: Orientation Does Matter. J Phys Chem A 2020; 124:7388-7398. [DOI: 10.1021/acs.jpca.0c05865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, P. R. China
| | - Zi-Wen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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9
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Mai S, González L. Molekulare Photochemie: Moderne Entwicklungen in der theoretischen Chemie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sebastian Mai
- Institut für Photonik Technische Universität Wien Gußhausstraße 27–29 1040 Wien Österreich
| | - Leticia González
- Institut für theoretische Chemie Fakultät für Chemie Universität Wien Währinger Straße 17 1090 Wien Österreich
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10
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Francés‐Monerris A, Carmona‐García J, Acuña AU, Dávalos JZ, Cuevas CA, Kinnison DE, Francisco JS, Saiz‐Lopez A, Roca‐Sanjuán D. Photodissociation Mechanisms of Major Mercury(II) Species in the Atmospheric Chemical Cycle of Mercury. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Antonio Francés‐Monerris
- Université de LorraineCNRS, LPCT 54000 Nancy France
- Departamento de Química FísicaUniversitat de València 46100 Burjassot Spain
| | | | - A. Ulises Acuña
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Juan Z. Dávalos
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Carlos A. Cuevas
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | | | - Joseph S. Francisco
- Department of Earth and Environmental Sciences and Department of ChemistryUniversity of Pennsylvania Philadelphia PA 19104 USA
| | - Alfonso Saiz‐Lopez
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
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11
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Francés‐Monerris A, Carmona‐García J, Acuña AU, Dávalos JZ, Cuevas CA, Kinnison DE, Francisco JS, Saiz‐Lopez A, Roca‐Sanjuán D. Photodissociation Mechanisms of Major Mercury(II) Species in the Atmospheric Chemical Cycle of Mercury. Angew Chem Int Ed Engl 2020; 59:7605-7610. [DOI: 10.1002/anie.201915656] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Antonio Francés‐Monerris
- Université de LorraineCNRS, LPCT 54000 Nancy France
- Departamento de Química FísicaUniversitat de València 46100 Burjassot Spain
| | | | - A. Ulises Acuña
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Juan Z. Dávalos
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Carlos A. Cuevas
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | | | - Joseph S. Francisco
- Department of Earth and Environmental Sciences and Department of ChemistryUniversity of Pennsylvania Philadelphia PA 19104 USA
| | - Alfonso Saiz‐Lopez
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
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12
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Wohlgemuth M, Mitrić R. Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping. Phys Chem Chem Phys 2020; 22:16536-16551. [DOI: 10.1039/d0cp02255a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Revealing the extended excited state lifetime due to excitation energy transport in DNA by multi-chromophoric field-induced surface-hopping (McFISH).
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Affiliation(s)
- Matthias Wohlgemuth
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
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Snyder JA, Charnay AP, Kohl FR, Zhang Y, Kohler B. DNA-like Photophysics in Self-Assembled Silver(I)–Nucleobase Nanofibers. J Phys Chem B 2019; 123:5985-5994. [PMID: 31283245 DOI: 10.1021/acs.jpcb.9b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Joshua A. Snyder
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Aaron P. Charnay
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Forrest R. Kohl
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Fang YG, Peng LY, Liu XY, Fang WH, Cui G. QM/MM nonadiabatic dynamics simulation on ultrafast excited-state relaxation in osmium(II) compounds in solution. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Liu XY, Li ZW, Fang WH, Cui G. Nonadiabatic dynamics simulations on internal conversion and intersystem crossing processes in gold(i) compounds. J Chem Phys 2018; 149:044301. [PMID: 30068207 DOI: 10.1063/1.5029991] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The position at which the second gold(i)-phosphine group is attached was experimentally found to play a noticeable role in intersystem crossing rates of gold(i) naphthalene derivatives. However, the physical origin is ambiguous. Herein we have employed generalized trajectory-based surface-hopping dynamics simulations to simulate the excited-state relaxation dynamics of these gold(i) naphthalene compounds including both the intersystem crossing process from the initially populated first excited singlet states S1 to triplet manifolds and internal conversion processes within these triplet states. Our predicted intersystem crossing rates are consistent with experiments very well. On the basis of the present results, we have found that (1) ultrafast and subpicosecond intersystem crossing processes are mainly caused by small energy gaps and large spin-orbit couplings between S1 and Tn; (2) adding the second gold(i)-phosphine group does not increase spin-orbit couplings between S1 and Tn but decrease their values remarkably, which implies that heavy-atom effects are state-specific, not state-universal; (3) the position at which the second gold(i)-phosphine group is attached has a remarkable influence on the electronic structures of S1 and Tn and their relative energies, which affect energy gaps and spin-orbit couplings between S1 and Tn and eventually modulate intersystem crossing rates from S1 to Tn. These new insights are very useful for the design of gold-containing compounds with excellent photoluminescence properties. Finally, this work also exemplifies that different isomers of a compound could have distinct excited-state relaxation dynamics.
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Affiliation(s)
- Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zi-Wen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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Liu J, Koslowski A, Thiel W. Analytic gradient and derivative couplings for the spin-flip extended configuration interaction singles method: Theory, implementation, and application to proton transfer. J Chem Phys 2018; 148:244108. [DOI: 10.1063/1.5037081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Jie Liu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- 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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Nogueira JJ, Roßbach S, Ochsenfeld C, González L. Effect of DNA Environment on Electronically Excited States of Methylene Blue Evaluated by a Three-Layered QM/QM/MM ONIOM Scheme. J Chem Theory Comput 2018; 14:4298-4308. [DOI: 10.1021/acs.jctc.8b00185] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan J. Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, A-1090 Wien, Austria
| | - Sven Roßbach
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 Munich, Germany
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, A-1090 Wien, Austria
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Liu XY, Zhang YH, Fang WH, Cui G. Early-Time Excited-State Relaxation Dynamics of Iridium Compounds: Distinct Roles of Electron and Hole Transfer. J Phys Chem A 2018; 122:5518-5532. [PMID: 29874071 DOI: 10.1021/acs.jpca.8b04392] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ya-Hui Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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20
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Hu Y, Gao X, Li X, Liang H, Zhang D, Liu C. The application of flavonoid derivatives as redox-responsive fluorescent probes in hydrophobic microenvironment. SENSORS AND ACTUATORS B: CHEMICAL 2018; 262:144-152. [DOI: 10.1016/j.snb.2018.01.184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2024]
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21
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Armengol P, Spörkel L, Gelabert R, Moreno M, Thiel W, Lluch JM. Ultrafast action chemistry in slow motion: atomistic description of the excitation and fluorescence processes in an archetypal fluorescent protein. Phys Chem Chem Phys 2018; 20:11067-11080. [PMID: 29620123 DOI: 10.1039/c8cp00371h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report quantum mechanical/molecular mechanical non-adiabatic molecular dynamics simulations on the electronically excited state of green fluorescent protein mutant S65T/H148D. We examine the driving force of the ultrafast (τ < 50 fs) excited-state proton transfer unleashed by absorption in the A band at 415 nm and propose an atomistic description of the two dynamical regimes experimentally observed [Stoner Ma et al., J. Am. Chem. Soc., 2008, 130, 1227]. These regimes are explained in terms of two sets of successive dynamical events: first the proton transfers quickly from the chromophore to the acceptor Asp148. Thereafter, on a slower time scale, there are geometrical changes in the cavity of the chromophore that involve the distance between the chromophore and Asp148, the planarity of the excited-state chromophore, and the distance between the chromophore and Tyr145. We find two different non-radiative relaxation channels that are operative for structures in the reactant region and that can explain the mismatch between the decay of the emission of A* and the rise of the emission of I*, as well as the temperature dependence of the non-radiative decay rate.
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Affiliation(s)
- Pau Armengol
- Departament de Qímica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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22
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Liu J, Thiel W. An efficient implementation of semiempirical quantum-chemical orthogonalization-corrected methods for excited-state dynamics. J Chem Phys 2018; 148:154103. [DOI: 10.1063/1.5022466] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jie Liu
- 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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23
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Liu XY, Xie XY, Fang WH, Cui G. Photoinduced relaxation dynamics of nitrogen-capped silicon nanoclusters: a TD-DFT study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1433335] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Xiao-Ying Xie
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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24
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Xu C, Gu FL, Zhu C. Ultrafast intersystem crossing for nitrophenols: ab initio nonadiabatic molecular dynamics simulation. Phys Chem Chem Phys 2018; 20:5606-5616. [DOI: 10.1039/c7cp08601f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast intersystem crossing mechanisms for two p- and m-nitrophenol groups (PNP and MNP) have been investigated using ab initio nonadiabatic molecular dynamics simulations at the 6SA-CASSCF level of theory.
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Affiliation(s)
- Chao Xu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry & Environment of South China Normal University
- Guangzhou 51006
- P. R. China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry & Environment of South China Normal University
- Guangzhou 51006
- P. R. China
| | - Chaoyuan Zhu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry & Environment of South China Normal University
- Guangzhou 51006
- P. R. China
- Department of Applied Chemistry, Institute of Molecular Science and Center for Interdisciplinary Molecular Science, National Chiao-Tung University
- Hsinchu 30010
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25
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Gao YJ, Chang XP, Liu XY, Li QS, Cui G, Thiel W. Excited-State Decay Paths in Tetraphenylethene Derivatives. J Phys Chem A 2017; 121:2572-2579. [PMID: 28318255 PMCID: PMC5385518 DOI: 10.1021/acs.jpca.7b00197] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photophysical properties of tetraphenylethene (TPE) compounds may differ widely depending on the substitution pattern, for example, with regard to the fluorescence quantum yield ϕf and the propensity to exhibit aggregation-induced emission (AIE). We report combined electronic structure calculations and nonadiabatic dynamics simulations to study the excited-state decay mechanisms of two TPE derivatives with four methyl substituents, either in the meta position (TPE-4mM, ϕf = 0.1%) or in the ortho position (TPE-4oM, ϕf = 64.3%). In both cases, two excited-state decay pathways may be relevant, namely, photoisomerization around the central ethylenic double bond and photocyclization involving two adjacent phenyl rings. In TPE-4mM, the barrierless S1 cyclization is favored; it is responsible for the ultralow fluorescence quantum yield observed experimentally. In TPE-4oM, both the S1 photocyclization and photoisomerization paths are blocked by non-negligible barriers, and fluorescence is thus feasible. Nonadiabatic dynamics simulations with more than 1000 surface hopping trajectories show ultrafast cyclization upon photoexcitation of TPE-4mM, whereas TPE-4oM remains unreactive during the 1 ps simulations. We discuss the chances for spectroscopic detection of the postulated cyclic photoproduct of TPE-4mM and the relevance of our findings for the AIE process.
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Affiliation(s)
- Yuan-Jun Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University Beijing 100875, China
| | - Xue-Ping Chang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University Beijing 100875, China
| | - Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University Beijing 100875, China
| | - Quan-Song Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology , Beijing 100081, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University Beijing 100875, China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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26
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Pratihar S, Ma X, Homayoon Z, Barnes GL, Hase WL. Direct Chemical Dynamics Simulations. J Am Chem Soc 2017; 139:3570-3590. [DOI: 10.1021/jacs.6b12017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Xinyou Ma
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Zahra Homayoon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - George L. Barnes
- Department
of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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27
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Marquetand P, Nogueira JJ, Mai S, Plasser F, González L. Challenges in Simulating Light-Induced Processes in DNA. Molecules 2016. [PMCID: PMC6155660 DOI: 10.3390/molecules22010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.
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28
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Lin H, Chang X, Yan D, Fang WH, Cui G. Tuning excited-state-intramolecular-proton-transfer (ESIPT) process and emission by cocrystal formation: a combined experimental and theoretical study. Chem Sci 2016; 8:2086-2090. [PMID: 28451328 PMCID: PMC5399640 DOI: 10.1039/c6sc04354b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/14/2016] [Indexed: 12/16/2022] Open
Abstract
The formation of two-component molecular cocrystals can lead to the tunable excited state intramolecular proton transfer (ESIPT) process and emission, as first confirmed by both experimental and computational studies.
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Affiliation(s)
- Heyang Lin
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , Beijing 100029 , P. R. China
| | - Xueping Chang
- Key Laboratory of Theoretical and Computational Photochemistry , Ministry of Education , College of Chemistry , Beijing Normal University , Beijing 100875 , P. R. China . ; ; ; Tel: +86-10-64412131
| | - Dongpeng Yan
- Key Laboratory of Theoretical and Computational Photochemistry , Ministry of Education , College of Chemistry , Beijing Normal University , Beijing 100875 , P. R. China . ; ; ; Tel: +86-10-64412131.,State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , Beijing 100029 , P. R. China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry , Ministry of Education , College of Chemistry , Beijing Normal University , Beijing 100875 , P. R. China . ; ; ; Tel: +86-10-64412131
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry , Ministry of Education , College of Chemistry , Beijing Normal University , Beijing 100875 , P. R. China . ; ; ; Tel: +86-10-64412131
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29
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Spata VA, Matsika S. Photophysical deactivation pathways in adenine oligonucleotides. Phys Chem Chem Phys 2016; 17:31073-83. [PMID: 26536353 DOI: 10.1039/c5cp04254b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this work we study deactivation processes in adenine oligomers after absorption of UV radiation using Quantum Mechanics combined with Molecular Mechanics (QM/MM). Correlated electronic structure methods appropriate for describing the excited states are used to describe a π-stacked dimer of adenine bases incorporated into (dA)20(dT)20. The results of these calculations reveal three different types of excited state minima which play a role in deactivation processes. Within this set of minima there are minima where the excited state is localized on one adenine (monomer-like) as well as minima where the excited state is delocalized on two adenines, forming different types of excimers and bonded excimers of varying but inter-related character. The proximity of their energies reveals that the minima can decay into one another along a flat potential energy surface dependent on the interbase separation. Additionally, analysis of the emissive energies and other physical properties, including theoretical anisotropy calculations, and comparison with fluorescence experiments, provides evidence that excimers play an important role in long-lived signals in adenine oligonucleotides while the subpicosecond decay is attributed to monomer-like minima. The necessity for a close approach of the nucleobases reveals that the deactivation mechanism is tied to macro-molecular motion.
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Affiliation(s)
- Vincent A Spata
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
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30
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Beckstead AA, Zhang Y, de Vries MS, Kohler B. Life in the light: nucleic acid photoproperties as a legacy of chemical evolution. Phys Chem Chem Phys 2016; 18:24228-38. [PMID: 27539809 DOI: 10.1039/c6cp04230a] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Photophysical investigations of the canonical nucleobases that make up DNA and RNA during the past 15 years have revealed that excited states formed by the absorption of UV radiation decay with subpicosecond lifetimes (i.e., <10(-12) s). Ultrashort lifetimes are a general property of absorbing sunscreen molecules, suggesting that the nucleobases are molecular survivors of a harsh UV environment. Encoding the genome using photostable building blocks is an elegant solution to the threat of photochemical damage. Ultrafast excited-state deactivation strongly supports the hypothesis that UV radiation played a major role in shaping molecular inventories on the early Earth before the emergence of life and the subsequent development of a protective ozone shield. Here, we review the general physical and chemical principles that underlie the photostability, or "UV hardiness", of modern nucleic acids and discuss the possible implications of these findings for prebiotic chemical evolution. In RNA and DNA strands, much longer-lived excited states are observed, which at first glance appear to increase the risk of photochemistry. It is proposed that the dramatically different photoproperties that emerge from assemblies of photostable building blocks may explain the transition from a world of molecular survival to a world in which energy-rich excited electronic states were eventually tamed for biological purposes such as energy transduction, signaling, and repair of the genetic machinery.
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Affiliation(s)
- Ashley A Beckstead
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400, USA.
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31
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Tuna D, Lu Y, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks of Electronically Excited States. J Chem Theory Comput 2016; 12:4400-22. [DOI: 10.1021/acs.jctc.6b00403] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - You Lu
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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32
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Li Q, Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Voityuk AA, Mukamel S, Roca-Sanjuán D, Garavelli M, Blancafort L. Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate. Chemistry 2016; 22:7497-507. [PMID: 27113273 PMCID: PMC5021121 DOI: 10.1002/chem.201505086] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 02/04/2023]
Abstract
The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.
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Affiliation(s)
- Quansong Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, 100081, Beijing, P.R. China
| | - Angelo Giussani
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Ivan Rivalta
- Univ Lyon, >Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 69342, Lyon, France
| | - Alexander A Voityuk
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilvi, 17071, Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California, 92697-2025, USA
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, 46071, Valencia, Spain
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Univ Lyon, >Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 69342, Lyon, France.
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilvi, 17071, Girona, Spain.
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33
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Wu D, Guo WW, Liu XY, Cui G. Excited-State Intramolecular Proton Transfer in a Blue Fluorescence Chromophore Induces Dual Emission. Chemphyschem 2016; 17:2340-7. [DOI: 10.1002/cphc.201600386] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Dan Wu
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Wei-Wei Guo
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
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34
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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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35
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 341] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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36
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Dral PO, Wu X, Spörkel L, Koslowski A, Weber W, Steiger R, Scholten M, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters. J Chem Theory Comput 2016; 12:1082-96. [PMID: 26771204 PMCID: PMC4785507 DOI: 10.1021/acs.jctc.5b01046] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Semiempirical orthogonalization-corrected
methods (OM1, OM2, and
OM3) go beyond the standard MNDO model by explicitly including additional
interactions into the Fock matrix in an approximate manner (Pauli
repulsion, penetration effects, and core–valence interactions),
which yields systematic improvements both for ground-state and excited-state
properties. In this Article, we describe the underlying theoretical
formalism of the OMx methods and their implementation
in full detail, and we report all relevant OMx parameters
for hydrogen, carbon, nitrogen, oxygen, and fluorine. For a standard
set of mostly organic molecules commonly used in semiempirical method
development, the OMx results are found to be superior
to those from standard MNDO-type methods. Parametrized Grimme-type
dispersion corrections can be added to OM2 and OM3 energies to provide
a realistic treatment of noncovalent interaction energies, as demonstrated
for the complexes in the S22 and S66×8 test sets.
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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
| | - Lasse Spörkel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Weber
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rainer Steiger
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Mirjam Scholten
- 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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37
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Xie BB, Xia SH, Chang XP, Cui G. Photophysics of Auramine-O: electronic structure calculations and nonadiabatic dynamics simulations. Phys Chem Chem Phys 2016; 18:403-413. [DOI: 10.1039/c5cp05312a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Sequential vs. concerted S1 relaxation pathways.
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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
| | - Shu-Hua Xia
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Xue-Ping Chang
- 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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38
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Cui G, Thiel W. Generalized trajectory surface-hopping method for internal conversion and intersystem crossing. J Chem Phys 2015; 141:124101. [PMID: 25273406 DOI: 10.1063/1.4894849] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Trajectory-based fewest-switches surface-hopping (FSSH) dynamics simulations have become a popular and reliable theoretical tool to simulate nonadiabatic photophysical and photochemical processes. Most available FSSH methods model internal conversion. We present a generalized trajectory surface-hopping (GTSH) method for simulating both internal conversion and intersystem crossing processes on an equal footing. We consider hops between adiabatic eigenstates of the non-relativistic electronic Hamiltonian (pure spin states), which is appropriate for sufficiently small spin-orbit coupling. This choice allows us to make maximum use of existing electronic structure programs and to minimize the changes to available implementations of the traditional FSSH method. The GTSH method is formulated within the quantum mechanics (QM)/molecular mechanics framework, but can of course also be applied at the pure QM level. The algorithm implemented in the GTSH code is specified step by step. As an initial GTSH application, we report simulations of the nonadiabatic processes in the lowest four electronic states (S0, S1, T1, and T2) of acrolein both in vacuo and in acetonitrile solution, in which the acrolein molecule is treated at the ab initio complete-active-space self-consistent-field level. These dynamics simulations provide detailed mechanistic insight by identifying and characterizing two nonadiabatic routes to the lowest triplet state, namely, direct S1 → T1 hopping as major pathway and sequential S1 → T2 → T1 hopping as minor pathway, with the T2 state acting as a relay state. They illustrate the potential of the GTSH approach to explore photoinduced processes in complex systems, in which intersystem crossing plays an important role.
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Affiliation(s)
- Ganglong Cui
- 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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Nikiforov A, Gamez JA, Thiel W, Huix-Rotllant M, Filatov M. Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules. J Chem Phys 2015; 141:124122. [PMID: 25273427 DOI: 10.1063/1.4896372] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 Å or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems.
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Affiliation(s)
- Alexander Nikiforov
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Jose A Gamez
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Miquel Huix-Rotllant
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Michael Filatov
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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40
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Huix-Rotllant M, Brazard J, Improta R, Burghardt I, Markovitsi D. Stabilization of Mixed Frenkel-Charge Transfer Excitons Extended Across Both Strands of Guanine-Cytosine DNA Duplexes. J Phys Chem Lett 2015; 6:2247-2251. [PMID: 26266599 DOI: 10.1021/acs.jpclett.5b00813] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The photoreactive pathways that may lead to DNA damage depend crucially upon the nature of the excited electronic states. The study of alternating guanine-cytosine duplexes by fluorescence spectroscopy and quantum mechanical calculations identifies a novel type of excited states that can be populated following UVB excitation. These states, denoted High-energy Emitting Long-lived Mixed (HELM) states, extend across both strands and arise from mixing between cytosine Frenkel excitons and guanine-to-cytosine charge transfer states. They emit at energies higher than ππ* states localized on single bases, survive for several nanoseconds, are sensitive to the ionic strength of the solution, and are strongly affected by the structural transition from the B form to the Z form. Their impact on the formation of lesions of the genetic code needs to be assessed.
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Affiliation(s)
- Miquel Huix-Rotllant
- †CNRS, IRAMIS, LIDYL, Laboratoire Francis Perrin, URA 2453, F-91191 Gif-sur-Yvette, France
- §Institut für Physikalische u. Theoretische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Johanna Brazard
- †CNRS, IRAMIS, LIDYL, Laboratoire Francis Perrin, URA 2453, F-91191 Gif-sur-Yvette, France
| | - Roberto Improta
- ‡Istituto Biostrutture e Bioimmagini- Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80136 Napoli, Italy
| | - Irene Burghardt
- §Institut für Physikalische u. Theoretische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Dimitra Markovitsi
- †CNRS, IRAMIS, LIDYL, Laboratoire Francis Perrin, URA 2453, F-91191 Gif-sur-Yvette, France
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41
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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42
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 760] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Conti I, Nenov A, Höfinger S, Flavio Altavilla S, Rivalta I, Dumont E, Orlandi G, Garavelli M. Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back. Phys Chem Chem Phys 2015; 17:7291-302. [DOI: 10.1039/c4cp05546b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
La and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Siegfried Höfinger
- Zentraler Informatikdienst
- Technische Universität Wien
- 1040 Wien, Austria
- Department of Physics
- Michigan Technological University
| | | | - Ivan Rivalta
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07, France
| | - Elise Dumont
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
- Lyon, France
| | - Giorgio Orlandi
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
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Spörkel L, Jankowska J, Thiel W. Photoswitching of salicylidene methylamine: a theoretical photodynamics study. J Phys Chem B 2014; 119:2702-10. [PMID: 25341075 PMCID: PMC4479613 DOI: 10.1021/jp5095678] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Photoswitching
of simple photochromic molecules attracts substantial
attention because of its possible role in future photon-driven molecular
electronics. Here we model the full photoswitching cycle of a minimal
photochromic Schiff base–salicylidene methylamine (SMA). We
perform semiempirical nonadiabatic on-the-fly photodynamics simulations
at the OM2/MRCI level and thoroughly analyze the structural time evolution
and switching efficiency of the system. We also identify and examine
in detail the crucial steps in the SMA photochemistry ruled by excited-state
intramolecular proton transfer. The results place the investigated
model aromatic Schiff base among the promising candidates for novel
photoswitching molecular materials. Our study also shows the potential
of the semiempirical multireference photodynamics simulations as a
tool for early stage molecular photodevice design.
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Affiliation(s)
- Lasse Spörkel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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45
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Chen X, Fang W, Wang H. Slow deactivation channels in UV-photoexcited adenine DNA. Phys Chem Chem Phys 2014; 16:4210-9. [PMID: 24452764 DOI: 10.1039/c3cp55020f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular mechanism for removing the excess energy in DNA bases is responsible for the high photostability of DNA and is thus the subject of intense theoretical/computational investigation. To understand why the excited state decay of the stacked bases is significantly longer than that of the monomers, we carried out electronic structure calculations on an adenine monomer and an aqueous (dA)5 oligonucleotide employing the CASPT2//CASSCF and CASPT2//CASSCF/AMBER levels of theory. The newly-found bright excited state pair Sstack1((1)ππ*) and Sstack2((1)ππ*) of d(A)5, originated from base stacking, is of intra-base charge transfer nature and occurs in different stacked bases with charge transfer along opposite directions. Two slow deactivation channels of d(A)5 were proposed as a result of the sizable barriers along the relaxation paths starting from the FC point of the Sstack1((1)ππ*) state. The SN1P((1)nπ*) state of d(A)5 serves as an intermediate state in one relaxation channel, to which a nonadiabatic decay from the Sstack1((1)ππ*) state occurs in an energy degeneracy region. A relatively high barrier in this state is found and attributed to the steric hindrance of the DNA environment due to the large NH2 group twisting, which gives a weak and red-shifted fluorescence. Another direct relaxation channel, induced by the C2-H2 bond twisting motion, is found to go through a conical intersection between the Sstack1((1)ππ*) and the ground state. The barrier found here enables fluorescence from the Sstack1((1)ππ*) state and may explain the bright state emission observed in the fluorescence upconversion measurements. The inter-molecular SCT((1)ππ*) state may be involved in the slow relaxation process of the photoexcited adenine oligomers through efficient internal conversion to the intra-base Sstack1((1)ππ*) state.
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Affiliation(s)
- Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, China.
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46
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Spata VA, Matsika S. Role of excitonic coupling and charge-transfer states in the absorption and CD spectra of adenine-based oligonucleotides investigated through QM/MM simulations. J Phys Chem A 2014; 118:12021-30. [PMID: 25184994 DOI: 10.1021/jp507520c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this work, we study the photophysical properties of an adenine-based oligonucleotide using an ensemble of about 200 configurations obtained from molecular dynamics simulations. Specifically, a QM/MM approach is used to obtain the excited-state energies and properties of (dA)20(dT)20 with a dimer of π-stacked adenine bases included in the quantum region. The absorption and circular dichroism spectra are computed and analyzed using the algebraic diagrammatic construction through second order level of theory method (ADC(2)) combined with classical mechanics. We find that the experimentally observed red-shifted shoulder in the absorption spectrum is due to excitonic interactions, while charge-transfer states are present within the absorption band at the higher-energy end of the spectrum. More importantly, low-energy states with charge-transfer mixing exist, which could lead to excimers and bonded excimers. These observations suggest that mixing between charge-transfer and excitonic states plays an important role in the photophysics of oligonucleotides. They also highlight the importance of taking into account the conformational flexibility of the oligonucleotide when investigating photophysical properties.
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Affiliation(s)
- Vincent A Spata
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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47
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Zhang Q, Chen X, Cui G, Fang WH, Thiel W. Concerted Asynchronous Hula-Twist Photoisomerization in the S65T/H148D Mutant of Green Fluorescent Protein. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405303] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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48
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Zhang Q, Chen X, Cui G, Fang WH, Thiel W. Concerted Asynchronous Hula-Twist Photoisomerization in the S65T/H148D Mutant of Green Fluorescent Protein. Angew Chem Int Ed Engl 2014; 53:8649-53. [DOI: 10.1002/anie.201405303] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Indexed: 01/24/2023]
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49
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An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1526-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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50
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Reetz MT. One Hundred Years of the Max-Planck-Institut für Kohlenforschung. Angew Chem Int Ed Engl 2014; 53:8562-86. [DOI: 10.1002/anie.201403217] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 12/27/2022]
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