1
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Huang H, Peng J, Zhang Y, Gu FL, Lan Z, Xu C. The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications. J Chem Phys 2024; 160:234101. [PMID: 38884395 DOI: 10.1063/5.0215036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Understanding the nonadiabatic dynamics of complex systems is a challenging task in computational photochemistry. Herein, we present an efficient and user-friendly quantum mechanics/molecular mechanics (QM/MM) interface to run on-the-fly nonadiabatic dynamics. Currently, this interface consists of an independent set of codes designed for general-purpose use. Herein, we demonstrate the ability and feasibility of the QM/MM interface by integrating it with our long-term developed JADE package. Tailored to handle nonadiabatic processes in various complex systems, especially condensed phases and protein environments, we delve into the theories, implementations, and applications of on-the-fly QM/MM nonadiabatic dynamics. The QM/MM approach is established within the framework of the additive QM/MM scheme, employing electrostatic embedding, link-atom inclusion, and charge-redistribution schemes to treat the QM/MM boundary. Trajectory surface-hopping dynamics are facilitated using the fewest switches algorithm, encompassing classical and quantum treatments for nuclear and electronic motions, respectively. Finally, we report simulations of nonadiabatic dynamics for two typical systems: azomethane in water and the retinal chromophore PSB3 in a protein environment. Our results not only illustrate the power of the QM/MM program but also reveal the important roles of environmental factors in nonadiabatic processes.
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Affiliation(s)
- Haiyi Huang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- MOE Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiawei Peng
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yulin Zhang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
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2
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Abou-Hatab S, Matsika S. Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes. Phys Chem Chem Phys 2024; 26:4511-4523. [PMID: 38240574 DOI: 10.1039/d3cp04844f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.
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3
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Zhao L, Geng X, Han G, Guo Y, Liu R, Chen J. Revealing the excited-state dynamics of cytidine and the role of excited-state proton transfer process. Phys Chem Chem Phys 2023; 25:32002-32009. [PMID: 37975722 DOI: 10.1039/d3cp03683a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The high photostability of DNAs and RNAs is inextricably related to the photochemical and photophysical properties of their building blocks, nucleobases and nucleosides, which can dissipate the absorbed UV light energy in a harmless manner. The deactivation mechanism of the nucleosides, especially the decay pathways of cytidine (Cyd), has been a matter of intense debate. In the current study, we employ high-level electronic structure calculations combined with excited state non-adiabatic dynamic simulations to provide a clear picture of the excited state deactivation of Cyd in both gas phase and aqueous solution. In both environments, a barrierless decay path driven by the ring-puckering motion and a relaxation channel with a small energy barrier driven by the elongation motion of CO bond are assigned to <200 fs and sub-picosecond decay time component, respectively. The presence of ribose group has a subtle effect on the dynamic behavior of Cyd in gas phase as the ribose-to-base hydrogen/proton transfer process is energetically inaccessible with a sizable energy barrier of about 1.4 eV. However, this energy barrier is significantly reduced in water, especially when an explicit water molecule is present. Therefore, we argue that the long-lived decay channel found in aqueous solution could be assigned to the Cyd-water intermolecular hydrogen/proton transfer process. The present study postulates a novel scenario toward deep understanding the intrinsic photostability of DNAs and RNAs and provides solid evidence to disclose the long history debate of cytidine excited-state decay mechanism, especially for the assignment of experimentally observed time components.
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Affiliation(s)
- Li Zhao
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Xuehui Geng
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Guoxia Han
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Yahui Guo
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Runze Liu
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, P. R. China
| | - Junsheng Chen
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 KøbenhavnØ, Denmark.
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4
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Cuéllar-Zuquin J, Pepino AJ, Fdez. Galván I, Rivalta I, Aquilante F, Garavelli M, Lindh R, Segarra-Martí J. Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size. J Chem Theory Comput 2023; 19:8258-8272. [PMID: 37882796 PMCID: PMC10851440 DOI: 10.1021/acs.jctc.3c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
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Affiliation(s)
- Juliana Cuéllar-Zuquin
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Ana Julieta Pepino
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Ignacio Fdez. Galván
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Francesco Aquilante
- Theory
and Simulation of Materials (THEOS), and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Roland Lindh
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Javier Segarra-Martí
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
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5
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Mandal S, Srinivasan V. Rationalizing the Unexpected Sensitivity in Excited State Lifetimes of Adenine to Tautomerization by Nonadiabatic Molecular Dynamics. J Phys Chem B 2022; 126:7077-7087. [PMID: 36083211 DOI: 10.1021/acs.jpcb.2c03178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The remarkable photostability of canonical nucleobases makes them ideal building blocks for DNA and RNA. Even minor structural changes are expected to lead to drastic alteration of their subpicosecond excited state lifetimes. However, it is interesting to note that while the 9H- and 7H-amino tautomers of adenine possess drastically different lifetimes, 9H- and 7H-keto guanine possess similar excited state lifetimes. With an aim to explain this unexpected difference in sensitivity of lifetimes to tautomerization, we have investigated the excited state relaxation mechanism of UV-excited adenine and guanine tautomers using surface hopping based nonadiabatic molecular dynamics. We find that internal conversion in both guanine tautomers is almost barrierless while both adenine tautomers encounter significant barriers before they can deactivate. Moreover, the major deactivation channel (C2-puckering) in 9H-amino adenine is overall more efficient than the one (C6-puckering) in the 7H-amino form. We trace this difference to the frequent rotation of the amino group which disrupts its conjugation with the heterocyclic ring thereby reducing the strength of nonadiabatic coupling and, hence, delaying internal conversion.
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Affiliation(s)
- Satyajit Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462 066, India
| | - Varadharajan Srinivasan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462 066, India
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6
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Janicki MJ, Szabla R, Šponer J, Góra RW. Photoinduced water-chromophore electron transfer causes formation of guanosine photodamage. Phys Chem Chem Phys 2022; 24:8217-8224. [PMID: 35319053 DOI: 10.1039/d2cp00801g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV-induced photolysis of aqueous guanine nucleosides produces 8-oxo-guanine and Fapy-guanine, which can induce various types of cellular malfunction. The mechanistic rationale underlying photodestructive processes of guanine nucleosides is still largely obscure. Here, we employ accurate quantum chemical calculations and demonstrate that an excited-state non-bonding interaction of guanosine and a water molecule facilitates the electron-driven proton transfer process from water to the chromophore fragment. This subsequently allows for the formation of a crucial intermediate, namely guanosine photohydrate. Further (photo)chemical reactions of this intermediate lead to the known products of guanine photodamage.
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Affiliation(s)
- Mikołaj J Janicki
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Rafał Szabla
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Robert W Góra
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
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7
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Caldero-Rodríguez NE, Crespo-Hernández CE. Excited state dynamics of 2'-deoxyisoguanosine and isoguanosine in aqueous solution. Phys Chem Chem Phys 2022; 24:6769-6781. [PMID: 35244114 DOI: 10.1039/d1cp05795b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photostability is thought to be an inherent property of nucleobases required to survive the extreme ultraviolet radiation conditions of the prebiotic era. Previous studies have shown that absorption of ultraviolet radiation by the canonical nucleosides results in ultrafast internal conversion to the ground state, demonstrating that these nucleosides efficiently dissipate the excess electronic energy to the environment. In recent years, studies on the photophysical and photochemical properties of nucleobase derivatives have revealed that chemical substitution influences the electronic relaxation pathways of purine and pyrimidine nucleobases. It has been suggested that amino or carbonyl substitution at the C6 position could increase the photostability of the purine derivatives more than the substitution at the C2 position. This investigation aims to elucidate the excited state dynamics of 2'-deoxyisoguanosine (dIsoGuo) and isoguanosine (IsoGuo) in aqueous solution at pH 7.4 and 1.4, which contain an amino group at the C6 position and a carbonyl group at the C2 position of the purine chromophore. The study of these derivatives is performed using absorption and emission spectroscopies, broadband transient absorption spectroscopy, and density functional and time-dependent density functional levels of theory. It is shown that the primary relaxation mechanism of dIsoGuo and IsoGuo involves nonradiative decay pathways, where the population decays from the S1(ππ*) state through internal conversion to the ground state via two relaxation pathways with lifetimes of hundreds of femtoseconds and less than 2 ps, making these purine nucleosides photostable in aqueous solution.
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8
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Wang D, Wang X, Jiang Y, Cao S, Jin P, Pan H, Sun H, Sun Z, Chen J. Excited State Dynamics of Methylated Guanosine Derivatives Revealed by Femtosecond Time-resolved Spectroscopy. Photochem Photobiol 2022; 98:1008-1016. [PMID: 35203108 DOI: 10.1111/php.13612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/20/2022] [Indexed: 11/28/2022]
Abstract
Methylated DNA/RNA nucleobases are important epigenetic marks in living species and play an important role for targeted therapies. Moreover, they could bring significant changes to the photo-stability of nucleic acid, leading these sites become mutational hotspots for disease such as skin cancer. While a number of studies have demonstrated the relationship between excited state dynamics and the biological function of methylated cytosine in DNA, investigations aimed at unraveling the excited state dynamics of methylated guanosine in RNA have been largely overlooked. In this work, influence of methylation on the excited state dynamics of guanosine is studied by using femtosecond time-resolved spectroscopy. Our results suggest that the effect of methyl substitution on the photophysical properties of guanosine is position sensitive. N1-methylguanosine shows very similar excited state dynamics as that in guanosine, while almost one order of magnitude longer lifetime of the La state is observed in N2, N2-dimethylguanosine. Notably, N7-methylation can lead to a new minimum on the La state, which shows a two orders of magnitude longer excited state lifetime compared with guanosine. These findings not only help understanding excited state dynamics of methylated guanosines, but also lay the foundation for further studying DNA/RNA strands incorporated with these bases.
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Affiliation(s)
- Danhong Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Yanrong Jiang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Simin Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Peipei Jin
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, China
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9
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Ray J, Ramesh SG. Excited-state proton transfer in the 2-aminopyridine dimer: A surface hopping study. Phys Chem Chem Phys 2022; 24:7274-7292. [DOI: 10.1039/d1cp05517h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a theoretical investigation of the excited-state intermolecular proton transfer process in the 2-aminopyridine dimer. Prior experimental and theoretical studies on this doubly hydrogen bonded system have attributed an...
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10
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Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
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Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
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11
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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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12
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Fang YG, Peng Q, Fang Q, Fang W, Cui G. MS-CASPT2 Studies on the Photophysics of Selenium-Substituted Guanine Nucleobase. ACS OMEGA 2019; 4:9769-9777. [PMID: 31460068 PMCID: PMC6649137 DOI: 10.1021/acsomega.9b01276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 05/30/2023]
Abstract
The MS-CASPT2 method has been employed to optimize minimum-energy structures of 6-selenoguanine (6SeGua) and related two- and three-state intersection structures in and between the lowest five electronic states, i.e., S2(1ππ*), S1(1 nπ*), T2(3 nπ*), T1(3ππ*), and S0. In combination with MS-CASPT2 calculated linearly interpolated internal coordinate paths, the photophysical mechanism of 6SeGua has been proposed. The initially populated S2(1ππ*) state decays to either S1(1 nπ*) or T2(3 nπ*) states through a three-state S2/S1/T2 intersection point. The large S2/T2 spin-orbit coupling of 435 cm-1, according to the classical El-Sayed rule, benefits the S2 → T2 intersystem crossing process. The S1(1 nπ*) state that stems from the S2 → S1 internal conversion process at the S2/S1/T2 intersection point can further jump to the T2(3 nπ*) state through the S1 → T2 intersystem crossing process. This process does not comply with the El-Sayed rule, but it is still related to a comparatively large spin-orbit coupling of 39 cm-1 and is expected to occur relatively fast. Finally, the T2(3 nπ*) state, which is populated from the above S2 → T2 and S1 → T2 intersystem crossing processes, decays to the T1(3ππ*) state via an internal conversion process. Because there is merely a small energy barrier of 0.11 eV separating the T1(3ππ*) minimum and an energetically allowed two-state T1/S0 intersection point, the T1(3ππ*) state still can decay to the S0 state quickly, which is also enhanced by a large T1/S0 spin-orbit coupling of 252 cm-1. Our proposed mechanism explains experimentally observed ultrafast intersystem crossing processes in 6SeGua and its 835-fold acceleration of the T1 state decay to the S0 state compared with 6tGua. Finally, we have found that the ground-state electronic structure of 6SeGua has more apparent multireference character.
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13
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Martinez-Fernandez L, Gavvala K, Sharma R, Didier P, Richert L, Segarra Martì J, Mori M, Mely Y, Improta R. Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine. Chemistry 2019; 25:7375-7386. [PMID: 30882930 DOI: 10.1002/chem.201900677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Indexed: 12/27/2022]
Abstract
Thienoguanosine (th G) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, th G exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto-amino tautomers. We herein investigate the photophysics of th G in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5-20.5 and 7-13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of th G, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias, Modúlo13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Javier Segarra Martì
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK
| | - Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto Biostrutture e Bioimmagini, Via Mezzocannone 16, 80134, Napoli, Italy
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14
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Jankowska J, Sobolewski AL. Efficient Separation of Photogenerated Charges in a Ferroelectric Molecular Wire: Nonadiabatic Dynamics Study on 3,5‐Dicyano‐1,7‐dimethylopyrrolo[3,2‐f]indole Trimer. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Zhou P, Zhao L. How Does the O6-Methylation Regulate the Excited-State Decay of Guanine Monomers. J Phys Chem B 2018; 123:201-206. [DOI: 10.1021/acs.jpcb.8b08606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, Liaoning, China
| | - Li Zhao
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China
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16
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Wang R, Chernyak VY. Dynamical consequences of time-reversal symmetry for systems with odd number of electrons: Conical intersections, semiclassical dynamics, and topology. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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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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18
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Ashwood B, Ortiz-Rodríguez LA, Crespo-Hernández CE. Photochemical relaxation pathways of S 6-methylthioinosine and O 6-methylguanosine in solution. Faraday Discuss 2018; 207:351-374. [PMID: 29372193 DOI: 10.1039/c7fd00193b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
S6-Methylthioinosine and O6-methylguanosine are byproducts resulting from the enzymatic reactions of sulfur-substituted prodrugs in cells and from the interaction of alkylating agents with cellular DNA, respectively. Their photochemistry has not been investigated, and it is currently unknown whether light absorption by these byproducts may pose any threat to the cell. In this contribution, their photoinduced processes upon absorption of UVB radiation are reported using broadband transient absorption spectroscopy. Plausible electronic relaxation mechanisms are proposed for both biological molecules, which are supported by steady-state absorption and emission measurements, and by singlet and triplet vertical excitation energies performed on a large subset of ground-state optimized conformational isomers in solution. The results are compared to the body of knowledge gathered in the scientific literature about the light-induced processes in the sulfur-substituted and canonical purine monomers. In particular, it is shown that S6-methylation decreases the rate to populate the lowest-energy triplet state and blueshifts the ground-state absorption spectrum compared to those for the sulfur-substituted prodrugs and for the 6-thioguanosine metabolite. Similarly, O6-methylation decreases the rate of internal conversion to the ground state observed in the guanine monomers by more than 10-fold in acetonitrile and 40-fold in aqueous solution, while it redshifts the ground-state absorption spectrum. Collectively, this investigation provides relevant new insights about the relationship between structural modifications of the purine chromophore and the electronic relaxation mechanisms in this important group of biological molecules.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
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19
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Pang X, Jiang C, Qi Y, Yuan L, Hu D, Zhang X, Zhao D, Wang D, Lan Z, Li F. Ultrafast unidirectional chiral rotation in the Z–E photoisomerization of two azoheteroarene photoswitches. Phys Chem Chem Phys 2018; 20:25910-25917. [DOI: 10.1039/c8cp04762f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Based on a large number of trajectories starting from the Z-isomer, for both azoheteroarenes, more than 99% of the trajectories decay through conical intersections with the same helicities as their initial geometries.
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Affiliation(s)
- Xiaojuan Pang
- Key Laboratory for Quantum Information and Quantum Optoelectronic Devices Shaanxi, and Department of Applied Physics
- Xi’an Jiaotong University
- Xi’an 710049
- China
| | - Chenwei Jiang
- Key Laboratory for Quantum Information and Quantum Optoelectronic Devices Shaanxi, and Department of Applied Physics
- Xi’an Jiaotong University
- Xi’an 710049
- China
| | - Yongnan Qi
- Key Laboratory for Quantum Information and Quantum Optoelectronic Devices Shaanxi, and Department of Applied Physics
- Xi’an Jiaotong University
- Xi’an 710049
- China
| | - Ling Yuan
- Key Laboratory for Quantum Information and Quantum Optoelectronic Devices Shaanxi, and Department of Applied Physics
- Xi’an Jiaotong University
- Xi’an 710049
- China
| | - Deping Hu
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
- China
| | - Xiuxing Zhang
- Department of Physics
- Weinan Normal University
- Weinan 714000
- China
| | - Di Zhao
- Key Laboratory for Quantum Information and Quantum Optoelectronic Devices Shaanxi, and Department of Applied Physics
- Xi’an Jiaotong University
- Xi’an 710049
- China
| | - Dongdong Wang
- Department of Applied Chemistry
- School of Science
- Xi’an Jiaotong University
- Xi’an 710049
- China
| | - Zhenggang Lan
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
- China
| | - Fuli Li
- Key Laboratory for Quantum Information and Quantum Optoelectronic Devices Shaanxi, and Department of Applied Physics
- Xi’an Jiaotong University
- Xi’an 710049
- China
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20
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Ashwood B, Ortiz-Rodríguez LA, Crespo-Hernández CE. Excited-State Dynamics in O 6-Methylguanosine: Impact of O 6-Methylation on the Relaxation Mechanism of Guanine Monomers. J Phys Chem Lett 2017; 8:4380-4385. [PMID: 28850232 DOI: 10.1021/acs.jpclett.7b02090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Absorption of ultraviolet radiation by DNA bases results in ultrafast internal conversion to the ground state, which minimizes photodamage. However, exogenous and endogenous alkylating agents present in the cellular environment can methylate the nucleobases in DNA. In particular, methylation of guanosine at the O6 position in DNA leads to the formation of the O6-methylguanosine adduct, which may alter the photostability of DNA. This contribution demonstrates that O6-methylation of guanosine red shifts its ground-state absorption spectrum and slows down the rate of internal conversion to the ground state by ∼40-fold in aqueous solution. The 40-fold decrease in the rate of excited-state decay increases the probability of photodamage within cellular DNA. It is proposed that the longer decay lifetime corresponds to relaxation of the excited-state population in O6-methylguanosine along a C6-puckered reaction coordinate in the 1ππ*(La) potential energy surface that runs parallel to an ultrafast internal conversion pathway along a C2-puckered coordinate.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Luis A Ortiz-Rodríguez
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , Cleveland, Ohio 44106, United States
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21
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Mondal S, Puranik M. Ultrafast Nuclear Dynamics of Photoexcited Guanosine-5'-Monophosphate in Three Singlet States. J Phys Chem B 2017; 121:7095-7107. [PMID: 28653848 DOI: 10.1021/acs.jpcb.7b05735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report measurement of resonance Raman (RR) spectra of guanosine-5'-monophosphate (GMP), a DNA nucleotide at excitation wavelengths throughout its ππ* absorption band (Bb) in the 210-230 nm range. From these data, we constructed wavelength-dependent Raman intensity excitation profiles (REPs) for all observed modes. These profiles and the absorption spectrum were then modeled using self-consistent simulations based on the time-dependent wave packet propagation formalism. We inferred the initial structural dynamics of GMP immediately after photoexcitation in terms of dimensionless displacements. The simulations also provide linewidth-broadening parameters that in turn report on the time scale of dynamics. We compared deduced structural changes in the purine ring upon photoabsorption into the Bb state with those deduced for the two lowest lying ππ* (La and Lb at 280 and 248 nm, respectively) excited states of GMP. We find that excitation to the Lb state lengthens C6-N1 and C2═N3 bonds, which lie along the formation coordinate of various oxidative adducts but Bb excitation does not. We also find that photoabsorption by the Bb state weakens the C8-N9 bond and thus might assist imidazole ring opening via cleavage of the same bond. Electronic excitation to different ππ* states of the guanine chromophore results in contrasting structural changes; although absorption by the La and Lb states induces expansion of pyrimidine and contraction of imidazole rings, excitation results in overall shrinkage of both the rings. Computed absolute changes in internal coordinates imply that photoexcitation to any of the three singlet states of GMP does not lead directly to the formation of a cation radical of guanine.
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Affiliation(s)
- Sayan Mondal
- Indian Institute of Science Education and Research , Pune 411008, India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research , Pune 411008, India
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22
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Lee J, Challa JR, McCamant DW. Ultraviolet Light Makes dGMP Floppy: Femtosecond Stimulated Raman Spectroscopy of 2'-Deoxyguanosine 5'-Monophosphate. J Phys Chem B 2017; 121:4722-4732. [PMID: 28412810 DOI: 10.1021/acs.jpcb.7b01694] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ultrafast dynamics of 2'-deoxyguanosine 5'-monophosphate after excitation with ultraviolet light has been studied with femtosecond transient absorption (TA) and femtosecond stimulated Raman spectroscopy (FSRS). TA kinetics and transient anisotropy spectra reveal a rapid relaxation from the Franck-Condon region, producing an extremely red-shifted stimulated emission band at ∼440 nm that is formed after 200 fs and subsequent relaxation for 0.8-1.5 ps, consistent with prior studies. Viscosity dependence shows that the initial relaxation, before 0.5 ps, is the same in water or viscous glycerol/water mixtures, but after 0.5 ps the dynamics significantly slow down in a viscous solution. This indicates that large amplitude structural changes occur after 0.5 ps following photoexcitation. FSRS obtained with both 480 and 600 nm Raman pump pulses observe very broad Raman peaks at 509 and 1530 cm-1, as well as a narrower peak at 1179 cm-1. All of the Raman peaks decay with 0.7-1.3 ps time constants. The 1530 cm-1 peak also shows an increasing inhomogeneous linewidth over the first 0.3 ps. Our TA and FSRS data are consistent with a structurally inhomogeneous population in the S1 (La) state and, in particular, with previous theoretical models in which out-of-plane distortion at C2 and the amine move the molecule toward a conical intersection with the ground state. These FSRS data are the first to directly observe the structural inhomogeneity imparted upon the excited-state population by the broad, flat potential energy surface of the S1 (La) state.
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Affiliation(s)
- Joohyun Lee
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - J Reddy Challa
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - David W McCamant
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
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23
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Pola M, Kochman MA, Picchiotti A, Prokhorenko VI, Miller RJD, Thorwart M. Linear photoabsorption spectra and vertical excitation energies of microsolvated DNA nucleobases in aqueous solution. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Employing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations in combination with the semiclassical nuclear ensemble method, we have simulated the photoabsorption spectra of the four canonical DNA nucleobases in aqueous solution. In order to model the effects of solvation, for each nucleobase, a number of solvating water molecules were explicitly included in the simulations, and additionally, the bulk solvent was represented by a continuous polarizable medium. We find that the effect of the solvation shell in general is significant, and its inclusion improves the realism of the spectral simulations. The involvement of lone electron pairs in the hydrogen bonding with the solvating water molecules has the effect of systematically increasing the energies of vertical excitation into the [Formula: see text]-type states. Apart from a systematic blue shift of around [Formula: see text][Formula: see text]eV observed in the absorption peaks, the calculated photoabsorption spectra reproduce the measured ones with good accuracy. The photoabsorption spectra are dominated by excited states with [Formula: see text] and partial [Formula: see text] character. No low-energy charge transfer states are observed with the use of the CAM-B3LYP and M06-2X functionals.
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Affiliation(s)
- Martina Pola
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michal A. Kochman
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alessandra Picchiotti
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Valentyn I. Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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24
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Pang X, Cui X, Hu D, Jiang C, Zhao D, Lan Z, Li F. “Watching” the Dark State in Ultrafast Nonadiabatic Photoisomerization Process of a Light-Driven Molecular Rotary Motor. J Phys Chem A 2017; 121:1240-1249. [DOI: 10.1021/acs.jpca.6b12253] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaojuan Pang
- Key
Laboratory for Quantum Information and Quantum Optoelectronic Devices,
Shaanxi, and Department of Applied Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xueyan Cui
- Key
Laboratory for Quantum Information and Quantum Optoelectronic Devices,
Shaanxi, and Department of Applied Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Deping Hu
- Qingdao Institute
of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101 Shandong China
| | - Chenwei Jiang
- Key
Laboratory for Quantum Information and Quantum Optoelectronic Devices,
Shaanxi, and Department of Applied Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Di Zhao
- Key
Laboratory for Quantum Information and Quantum Optoelectronic Devices,
Shaanxi, and Department of Applied Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Zhenggang Lan
- Qingdao Institute
of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101 Shandong China
| | - Fuli Li
- Key
Laboratory for Quantum Information and Quantum Optoelectronic Devices,
Shaanxi, and Department of Applied Physics, Xi’an Jiaotong University, Xi’an 710049, China
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25
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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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26
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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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27
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Restoring electronic coherence/decoherence for a trajectory-based nonadiabatic molecular dynamics. Sci Rep 2016; 6:24198. [PMID: 27063337 PMCID: PMC4827081 DOI: 10.1038/srep24198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/22/2016] [Indexed: 11/23/2022] Open
Abstract
By utilizing the time-independent semiclassical phase integral, we obtained modified coupled time-dependent Schrödinger equations that restore coherences and induce decoherences within original simple trajectory-based nonadiabatic molecular dynamic algorithms. Nonadiabatic transition probabilities simulated from both Tully’s fewest switches and semiclassical Ehrenfest algorithms follow exact quantum electronic oscillations and amplitudes for three out of the four well-known model systems. Within the present theory, nonadiabatic transitions estimated from statistical ensemble of trajectories accurately follow those of the modified electronic wave functions. The present theory can be immediately applied to the molecular dynamic simulations of photochemical and photophysical processes involving electronic excited states.
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28
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Stavros VG, Verlet JRR. Gas-Phase Femtosecond Particle Spectroscopy: A Bottom-Up Approach to Nucleotide Dynamics. Annu Rev Phys Chem 2016; 67:211-32. [PMID: 26980306 DOI: 10.1146/annurev-physchem-040215-112428] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We summarize how gas-phase ultrafast charged-particle spectroscopy has been used to provide an understanding of the photophysics of DNA building blocks. We focus on adenine and discuss how, following UV excitation, specific interactions determine the fates of its excited states. The dynamics can be probed using a systematic bottom-up approach that provides control over these interactions and that allows ever-larger complexes to be studied. Starting from a chromophore in adenine, the excited state decay mechanisms of adenine and chemically substituted or clustered adenine are considered and then extended to adenosine mono-, di-, and trinucleotides. We show that the gas-phase approach can offer exquisite insight into the dynamics observed in aqueous solution, but we also highlight stark differences. An outlook is provided that discusses some of the most promising developments in this bottom-up approach.
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Affiliation(s)
- Vasilios G Stavros
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom;
| | - Jan R R Verlet
- Department of Chemistry, University of Durham, Durham, DH1 3LE, United Kingdom;
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29
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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: 332] [Impact Index Per Article: 41.5] [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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30
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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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31
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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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32
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Hu D, Huang J, Xie Y, Yue L, Zhuang X, Lan Z. Nonadiabatic dynamics and photoisomerization of biomimetic photoswitches. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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33
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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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34
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Park JW, Rhee YM. Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore. J Chem Phys 2015; 140:164112. [PMID: 24784258 DOI: 10.1063/1.4872155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Simulating molecular dynamics directly on quantum chemically obtained potential energy surfaces is generally time consuming. The cost becomes overwhelming especially when excited state dynamics is aimed with multiple electronic states. The interpolated potential has been suggested as a remedy for the cost issue in various simulation settings ranging from fast gas phase reactions of small molecules to relatively slow condensed phase dynamics with complex surrounding. Here, we present a scheme for interpolating multiple electronic surfaces of a relatively large molecule, with an intention of applying it to studying nonadiabatic behaviors. The scheme starts with adiabatic potential information and its diabatic transformation, both of which can be readily obtained, in principle, with quantum chemical calculations. The adiabatic energies and their derivatives on each interpolation center are combined with the derivative coupling vectors to generate the corresponding diabatic Hamiltonian and its derivatives, and they are subsequently adopted in producing a globally defined diabatic Hamiltonian function. As a demonstration, we employ the scheme to build an interpolated Hamiltonian of a relatively large chromophore, para-hydroxybenzylidene imidazolinone, in reference to its all-atom analytical surface model. We show that the interpolation is indeed reliable enough to reproduce important features of the reference surface model, such as its adiabatic energies and derivative couplings. In addition, nonadiabatic surface hopping simulations with interpolation yield population transfer dynamics that is well in accord with the result generated with the reference analytic surface. With these, we conclude by suggesting that the interpolation of diabatic Hamiltonians will be applicable for studying nonadiabatic behaviors of sizeable molecules.
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Affiliation(s)
- Jae Woo Park
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784, KoreaDepartment of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
| | - Young Min Rhee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784, KoreaDepartment of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
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35
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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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36
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Crespo-Hernández CE, Martínez-Fernández L, Rauer C, Reichardt C, Mai S, Pollum M, Marquetand P, González L, Corral I. Electronic and structural elements that regulate the excited-state dynamics in purine nucleobase derivatives. J Am Chem Soc 2015; 137:4368-81. [PMID: 25763596 PMCID: PMC4410903 DOI: 10.1021/ja512536c] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 12/20/2022]
Abstract
The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited (1)nπ* state. Following vibrational and conformational relaxation, the (1)nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the (1)nπ* state while simultaneously facilitating access to the (1)ππ*(La)/S0 conical intersection, such that population of the (1)nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position.
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Affiliation(s)
- Carlos E. Crespo-Hernández
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Lara Martínez-Fernández
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
| | - Clemens Rauer
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Christian Reichardt
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Marvin Pollum
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Inés Corral
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
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37
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Changenet-Barret P, Gustavsson T, Improta R, Markovitsi D. Ultrafast Excited-State Deactivation of 8-Hydroxy-2'-deoxyguanosine Studied by Femtosecond Fluorescence Spectroscopy and Quantum-Chemical Calculations. J Phys Chem A 2015; 119:6131-9. [PMID: 25752921 DOI: 10.1021/acs.jpca.5b00688] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The fluorescence properties of the 8-hydroxy-2'-deoxyguanosine (8-oxo-dG) in aqueous solution at pH 6.5 are studied by steady-state spectroscopy and femtosecond fluorescence up-conversion and compared with those of 2'-deoxyguanine (dG) and 2'-deoxyguanine monophosphate (dGMP). The steady-state fluorescence spectrum of 8-oxo-dG is composed of a broad band that peaks at 356 nm and extends over the entire visible spectral region, and its fluorescence quantum yield is twice that of dG/dGMP. After excitation at 267 nm, the initial fluorescence anisotropy at all wavelengths is lower than 0.1, giving evidence of an ultrafast internal conversion (<100 fs) between the two lowest excited ππ* states (Lb and La). The fluorescence decays of 8-oxo-dG are biexponential with an average lifetime of 0.7 ± 0.1 ps, which is about two times longer than that of dGMP. In contrast with dGMP, only a moderate dynamical shift (∼1400 vs 10,000 cm(-1)) of the fluorescence spectra of 8-oxo-dG is observed on the time scale of a few picoseconds without modification of the spectral shape. PCM/TD-DFT calculations, employing either the PBE0 or the M052X functionals, provide absorption spectra in good agreement with the experimental one and show that the deactivation path is similar to that proposed for dGMP, with a fast motion toward an energy plateau, where the purine ring keeps an almost planar geometry, followed by decay to S0, via out-of-the plane motion of amino substituent.
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Affiliation(s)
- Pascale Changenet-Barret
- †CNRS, IRAMIS, LIDyL, Laboratoire Francis Perrin, URA 2453, CEA Saclay, 91191 Gif sur Yvette, France
| | - Thomas Gustavsson
- †CNRS, IRAMIS, LIDyL, Laboratoire Francis Perrin, URA 2453, CEA Saclay, 91191 Gif sur Yvette, France
| | - Roberto Improta
- ‡Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80136 Naples, Italy
| | - Dimitra Markovitsi
- †CNRS, IRAMIS, LIDyL, Laboratoire Francis Perrin, URA 2453, CEA Saclay, 91191 Gif sur Yvette, France
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38
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Buchner F, Heggen B, Ritze HH, Thiel W, Lübcke A. Excited-state dynamics of guanosine in aqueous solution revealed by time-resolved photoelectron spectroscopy: experiment and theory. Phys Chem Chem Phys 2015; 17:31978-87. [DOI: 10.1039/c5cp04394h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved photoelectron spectroscopy is performed on aqueous guanosine solution to study its excited-state relaxation dynamics.
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Affiliation(s)
- Franziska Buchner
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
| | - Berit Heggen
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr
- Germany
| | - Hans-Hermann Ritze
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr
- Germany
| | - Andrea Lübcke
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
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39
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Park JW, Rhee YM. Towards the Realization of Ab Initio Dynamics at the Speed of Molecular Mechanics: Simulations with Interpolated Diabatic Hamiltonian. Chemphyschem 2014; 15:3183-93. [DOI: 10.1002/cphc.201402226] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 12/13/2022]
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40
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Nakayama A, Arai G, Yamazaki S, Taketsugu T. Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: excited-state QM/MM molecular dynamics simulations. J Chem Phys 2014; 139:214304. [PMID: 24320377 DOI: 10.1063/1.4833563] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
On-the-fly excited-state quantum mechanics/molecular mechanics molecular dynamics (QM/MM-MD) simulations of thymine in aqueous solution are performed to investigate the role of solvent water molecules on the nonradiative deactivation process. The complete active space second-order perturbation theory (CASPT2) method is employed for a thymine molecule as the QM part in order to provide a reliable description of the excited-state potential energies. It is found that, in addition to the previously reported deactivation pathway involving the twisting of the C-C double bond in the pyrimidine ring, another efficient deactivation pathway leading to conical intersections that accompanies the out-of-plane displacement of the carbonyl group is observed in aqueous solution. Decay through this pathway is not observed in the gas phase simulations, and our analysis indicates that the hydrogen bonds with solvent water molecules play a key role in stabilizing the potential energies of thymine in this additional decay pathway.
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Affiliation(s)
- Akira Nakayama
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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41
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Guo X, Zhao Y, Cao Z. Ab Initio Study on Ultrafast Excited-State Decay of Allopurinol Keto-N9H Tautomer from Gas Phase to Aqueous Solution. J Phys Chem A 2014; 118:9013-20. [DOI: 10.1021/jp5020115] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xugeng Guo
- State Key Laboratory for
Physical Chemistry of Solid Surfaces and Fujian Provincial Key Lab
of Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, No. 422, South Siming Road, Xiamen 361005, P. R. China
| | - Yuan Zhao
- State Key Laboratory for
Physical Chemistry of Solid Surfaces and Fujian Provincial Key Lab
of Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, No. 422, South Siming Road, Xiamen 361005, P. R. China
| | - Zexing Cao
- State Key Laboratory for
Physical Chemistry of Solid Surfaces and Fujian Provincial Key Lab
of Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, No. 422, South Siming Road, Xiamen 361005, P. R. China
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42
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Cheng CCW, Ma C, Chan CTL, Ho KYF, Kwok WM. The solvent effect and identification of a weakly emissive state in nonradiative dynamics of guanine nucleosides and nucleotides--a combined femtosecond broadband time-resolved fluorescence and transient absorption study. Photochem Photobiol Sci 2014; 12:1351-65. [PMID: 23538894 DOI: 10.1039/c3pp25450j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined method of femtosecond broadband time-resolved fluorescence (fs-TRF) and transient absorption (fs-TA) was employed to investigate the excited state dynamics of 2'-deoxyguanosine (dG) and 2'-deoxyguanosine 5'-monophosphate (dGMP). Comparative fs-TRF and fs-TA measurements were conducted on dG and dGMP in neutral water, deuterated water, and methanol with excitation wavelengths of 245, 267 and 285 nm. Very similar results were observed with dG and dGMP. The data provide compelling evidence for the co-existence of two nonradiative pathways. One is the generally recognized Laππ* mediated channel, the other involves an unprecedented weakly emissive state which plays a significant role in the overall deactivation processes. The Laππ* channel features biphasic dynamics with time constants (τ1/τ2) of ~0.2/0.8 ps in water and ~0.25/1.0 ps in methanol. The biphasic decay arises due to a partial transfer with τ1 of the Laππ* population to the newly identified state followed by conversion in τ2 of the remaining Laππ* molecules into the electronic ground state. The channel mediated by the weakly emissive species shows solvent-dependent dynamics with time constants (τ3) of ~2.0 ps in water, ~2.3 ps in deuterated water, and ~4.1 ps in methanol. The species features absorption at UV wavelengths (~300-400 nm) and exhibits deeply red-shifted fluorescence (λmax ~ 520 nm) with polarization direction varied markedly from that of the Laππ* but close to the Lbππ*. This species acts as an effective quenching state to the radiative decay of the brightly emissive Laππ* and Lbππ*. It sets in promptly (<~50 fs) after the photoexcitation and is further populated through nonadiabatic coupling with the Laππ*. The overall involvement of this state is facilitated with excitation at high energy and is favoured in methanol over water. According to the spectral character and the solvent effect in particular the kinetic isotope effect, the species is tentatively associated to the πσ* state with charge transfer (CT) character which is considered to be preferentially stabilized by hydrogen-bonding between the guanine amino and surrounding solvent molecules. The result of this study leads to a dramatically different picture of guanine deactivation. It demonstrates a crucial role of the solvent in shaping the nonradiative dynamics of guanine nucleosides and nucleotides. The data presented are important for understanding the detailed photophysics of not only the monomeric guanine but also DNA assemblies that contain guanine in base pairs or have a guanine tetrad as the structural motif.
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Affiliation(s)
- Chopen Chan-Wut Cheng
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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43
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Martínez-Fernández L, Corral I, Granucci G, Persico M. Competing ultrafast intersystem crossing and internal conversion: a time resolved picture for the deactivation of 6-thioguanine. Chem Sci 2014. [DOI: 10.1039/c3sc52856a] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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44
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Guo X, Zhao Y, Cao Z. A QM/MM MD insight into photodynamics of hypoxanthine: distinct nonadiabatic decay behaviors between keto-N7H and keto-N9H tautomers in aqueous solution. Phys Chem Chem Phys 2014; 16:15381-8. [DOI: 10.1039/c4cp01928h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM MD simulations reveal different H-bonding networks around DNA base analogues, and the π-electron H-bond in the solvated keto-N7H may facilitate its S1 → S0 nonadiabatic decay.
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Affiliation(s)
- Xugeng Guo
- State Key Laboratory for Physical Chemistry of Solid Surfaces and Fujian Provincial Key Lab of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005, P. R. China
| | - Yuan Zhao
- State Key Laboratory for Physical Chemistry of Solid Surfaces and Fujian Provincial Key Lab of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005, P. R. China
| | - Zexing Cao
- State Key Laboratory for Physical Chemistry of Solid Surfaces and Fujian Provincial Key Lab of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005, P. R. China
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45
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Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:1-37. [DOI: 10.1007/128_2013_517] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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46
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Chatterley AS, West CW, Stavros VG, Verlet JRR. Time-resolved photoelectron imaging of the isolated deprotonated nucleotides. Chem Sci 2014. [DOI: 10.1039/c4sc01493f] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Time-resolved photoelectron spectroscopy of deprotonated nucleotides provides new insights into their relaxation dynamics.
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Affiliation(s)
- Adam S. Chatterley
- Department
- of Chemistry
- University of Durham
- Durham DH1 3LE, United Kingdom
- Department of Chemistry
| | | | - Vasilios G. Stavros
- Department of Chemistry
- University of Warwick
- Coventry CV4 7AL, United Kingdom
| | - Jan R. R. Verlet
- Department
- of Chemistry
- University of Durham
- Durham DH1 3LE, United Kingdom
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47
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Excited States Behavior of Nucleobases in Solution: Insights from Computational Studies. Top Curr Chem (Cham) 2014; 355:329-57. [DOI: 10.1007/128_2013_524] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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48
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Stuhldreier MC, Temps F. Ultrafast photo-initiated molecular quantum dynamics in the DNA dinucleotide d(ApG) revealed by broadband transient absorption spectroscopy. Faraday Discuss 2013; 163:173-88; discussion 243-75. [PMID: 24020202 DOI: 10.1039/c3fd00003f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ultrafast photo-initiated quantum dynamics of the adenine-guanine dinucleotide d(ApG) in aqueous solution (pH 7) has been studied by femtosecond time-resolved spectroscopy after excitation at lambda = 260 nm. The results reveal a hierarchy of processes on time scales from tau < 100 fs to tau > 100 ps. Characteristic spectro-temporal signatures are observed indicating the transformation of the molecules in the electronic relaxation from the photo-excited state to a long-lived exciplex. In particular, broadband UV/VIS excited-state absorption (ESA) measurements detected a distinctive absorption by the excited dinucleotide around lambda = 335 nm, approximately 0.5 eV to the blue compared to the maximum of the broad and unstructured ESA spectrum after excitation of an equimolar mixture of the mononucleotides dAMP and dGMP. A similar feature has been identified as signature of the excimer in the dynamics of the adenine dinucleotide d(ApA). The lifetime of the d(ApG) exciplex was found to be tau = 124 +/- 4 ps both from the ESA decay time and from the ground-state recovery time, far longer than the sub-picosecond lifetimes of excited dAMP or dGMP. Fluorescence-time profiles measured by the up-conversion technique indicate that the exciplex state is reached around approximately 6 ps after excitation. Very weak residual fluorescence at longer times red-shifted to the emission from the photo-excited state shows that the exciplex is almost optically dark, but still has enough oscillator strength to give rise to the dual fluorescence of the dinucleotide in the static fluorescence spectrum.
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Affiliation(s)
- Mayra C Stuhldreier
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
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49
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Thiel W. Semiempirical quantum–chemical methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1161] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Walter Thiel
- Max‐Planck‐Institut für KohlenforschungMülheimGermany
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50
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Röttger K, Sönnichsen FD, Temps F. Ultrafast electronic deactivation dynamics of the inosine dimer--a model case for H-bonded purine bases. Photochem Photobiol Sci 2013; 12:1466-73. [PMID: 23788062 DOI: 10.1039/c3pp50093d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The structural properties and ultrafast electronic deactivation dynamics of the inosine dimer in CHCl3 have been investigated by two-dimensional (1)H NMR and static FTIR spectroscopy and by femtosecond time-resolved transient absorption spectroscopy, respectively. The (1)H NMR and IR spectra show the formation of a well-defined, symmetric dimer with an association equilibrium constant of KI·I = 690 ± 100 M(-1). The excited-state dynamics after photoexcitation at λpump = 260 nm monitored by ultrafast absorption spectroscopy show great similarity with those of the monomer inosine in an aqueous solution and are governed by a decay time of τ = 90 ± 10 fs, which is one of the shortest electronic lifetimes of all nucleobases and nucleobase dimers studied so far. On the basis of these observations, the inosine dimer is expected to follow a similar relaxation pathway as the monomer, involving an out-of-plane deformation of the six-membered ring. The importance of the C(2) position for the electronic deactivation of hypoxanthine and guanine is discussed. The obtained well-determined structure and straightforward dynamics qualify the inosine dimer as an excellent reference case for more complicated systems such as the G·G dimer and the G·C and A·T Watson-Crick pairs.
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Affiliation(s)
- Katharina Röttger
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
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