51
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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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52
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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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53
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Ponzi A, Sapunar M, Angeli C, Cimiraglia R, Došlić N, Decleva P. Photoionization of furan from the ground and excited electronic states. J Chem Phys 2016; 144:084307. [DOI: 10.1063/1.4941608] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Aurora Ponzi
- Department of Physical Chemistry, R. Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Marin Sapunar
- Department of Physical Chemistry, R. Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Celestino Angeli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Renzo Cimiraglia
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Nađa Došlić
- Department of Physical Chemistry, R. Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Piero Decleva
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
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54
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Wu X, Karsili TNV, Domcke W. Excited-State Deactivation of Adenine by Electron-Driven Proton-Transfer Reactions in Adenine-Water Clusters: A Computational Study. Chemphyschem 2016; 17:1298-304. [DOI: 10.1002/cphc.201501154] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry; Technische Universität München; 85747 Garching Germany
| | - Tolga N. V. Karsili
- Department of Chemistry; Technische Universität München; 85747 Garching Germany
| | - Wolfgang Domcke
- Department of Chemistry; Technische Universität München; 85747 Garching Germany
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55
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Szabla R, Góra RW, Janicki M, Šponer J. Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires. Faraday Discuss 2016; 195:237-251. [DOI: 10.1039/c6fd00131a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H2O)5 cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S0 state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H2O)5 cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.
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Affiliation(s)
- Rafał Szabla
- Institute of Biophysics
- Academy of Sciences of the Czech Republic
- Brno
- Czech Republic
| | - Robert W. Góra
- Department of Physical and Quantum Chemistry
- Faculty of Chemistry
- Wrocław University of Technology
- 50-370 Wrocław
- Poland
| | - Mikołaj Janicki
- Department of Physical and Quantum Chemistry
- Faculty of Chemistry
- Wrocław University of Technology
- 50-370 Wrocław
- Poland
| | - Jiří Šponer
- Institute of Biophysics
- Academy of Sciences of the Czech Republic
- Brno
- Czech Republic
- CEITEC–Central European Institute of Technology
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56
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Chaiwongwattana S, Sapunar M, Ponzi A, Decleva P, Došlić N. Exploration of Excited State Deactivation Pathways of Adenine Monohydrates. J Phys Chem A 2015; 119:10637-44. [DOI: 10.1021/acs.jpca.5b07496] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Marin Sapunar
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Aurora Ponzi
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Piero Decleva
- Dipartimento di
Scienze Chimiche, Università di Trieste, 34127 Trieste, Italy
| | - Nađa Došlić
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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57
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Nikiforov A, Gamez JA, Thiel W, Huix-Rotllant M, Filatov M. Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules. J Chem Phys 2015; 141:124122. [PMID: 25273427 DOI: 10.1063/1.4896372] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 Å or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems.
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Affiliation(s)
- Alexander Nikiforov
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Jose A Gamez
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Miquel Huix-Rotllant
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Michael Filatov
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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58
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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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59
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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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60
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Das S, Samanta PK, Pati SK. Watson–Crick base pairing, electronic and photophysical properties of triazole modified adenine analogues: a computational study. NEW J CHEM 2015. [DOI: 10.1039/c5nj01566a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Triazole adenine nucleobase analogues show fluorescence in the UV-Vis region and form Watson–Crick base pairing with thymine nucleobases.
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Affiliation(s)
- Shubhajit Das
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Pralok K Samanta
- Theoretical Sciences Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Swapan K Pati
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
- Theoretical Sciences Unit
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61
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Kánnár D, Szalay PG. Benchmarking coupled cluster methods on singlet excited states of nucleobases. J Mol Model 2014; 20:2503. [DOI: 10.1007/s00894-014-2503-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/13/2014] [Indexed: 11/30/2022]
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62
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Roberts GM, Marroux HJB, Grubb MP, Ashfold MNR, Orr-Ewing AJ. On the Participation of Photoinduced N–H Bond Fission in Aqueous Adenine at 266 and 220 nm: A Combined Ultrafast Transient Electronic and Vibrational Absorption Spectroscopy Study. J Phys Chem A 2014; 118:11211-25. [DOI: 10.1021/jp508501w] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gareth M. Roberts
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Hugo J. B. Marroux
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Michael P. Grubb
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Michael N. R. Ashfold
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Andrew J. Orr-Ewing
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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63
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Blancafort L. Photochemistry and photophysics at extended seams of conical intersection. Chemphyschem 2014; 15:3166-81. [PMID: 25157686 DOI: 10.1002/cphc.201402359] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Indexed: 11/07/2022]
Abstract
The role of extended seams of conical intersection in excited-state mechanisms is reviewed. Seams are crossings of the potential energy surface in many dimensions where the decay from the excited to the ground state can occur, and the extended seam is composed of different segments lying along a reaction coordinate. Every segment is associated with a different primary photoproduct, which gives rise to competing pathways. This idea is first illustrated for fulvene and ethylene, and then it is used to explain more complex cases such as the dependence of the isomerisation of retinal chromophore isomers on the protein environment, the dependence of the efficiency of the azobenzene photochemical switch on the wavelength of irradiation and the direction of the isomerisation, and the coexistence of different mechanisms in the photo-induced Wolff rearrangement of diazonaphthoquinone. The role of extended seams in the photophysics of the DNA nucleobases and the relationship between two-state seams and three-state crossings is also discussed. As an outlook, the design of optical control strategies based on the passage of the excited molecule through the seam is considered, and it is shown how the excited-state lifetime of fulvene can be modulated by shaping the energy of the seam.
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Affiliation(s)
- 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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64
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Benda Z, Szalay PG. Details of the Excited-State Potential Energy Surfaces of Adenine by Coupled Cluster Techniques. J Phys Chem A 2014; 118:6197-207. [DOI: 10.1021/jp505331s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Zsuzsanna Benda
- Laboratory of Theoretical Chemistry, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest, Hungary
| | - Péter G. Szalay
- Laboratory of Theoretical Chemistry, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest, Hungary
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65
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Ou Q, Fatehi S, Alguire E, Shao Y, Subotnik JE. Derivative couplings between TDDFT excited states obtained by direct differentiation in the Tamm-Dancoff approximation. J Chem Phys 2014; 141:024114. [DOI: 10.1063/1.4887256] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qi Ou
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Shervin Fatehi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yihan Shao
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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66
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Barbatti M. Photorelaxation Induced by Water–Chromophore Electron Transfer. J Am Chem Soc 2014; 136:10246-9. [DOI: 10.1021/ja505387c] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, D-45470 Mülheim
an der Ruhr, Germany
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67
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An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1526-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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68
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69
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Santoro F, Improta R, Fahleson T, Kauczor J, Norman P, Coriani S. Relative Stability of the La and Lb Excited States in Adenine and Guanine: Direct Evidence from TD-DFT Calculations of MCD Spectra. J Phys Chem Lett 2014; 5:1806-1811. [PMID: 26273857 DOI: 10.1021/jz500633t] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The relative position of La and Lb ππ* electronic states in purine nucleobases is a much debated topic, since it can strongly affect our understanding of their photoexcited dynamics. To assess this point, we calculated the absorption and magnetic circular dichroism (MCD) spectra of adenine, guanine, and their nucleosides in gas-phase and aqueous solution, exploiting recent developments in MCD computational technology within time-dependent density functional theory. MCD spectroscopy allows us to resolve the intense S0→ La transition from the weak S0→ Lb transition. The spectra obtained in water solution, by using B3LYP and CAM-B3LYP functionals and describing solvent effect by cluster models and by the polarizable continuum model (PCM), are in very good agreement with the experimental counterparts, thus providing direct and unambiguous evidence that the energy ordering predicted by TD-DFT, La < Lb, is the correct one.
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Affiliation(s)
- Fabrizio Santoro
- †Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, via Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- ‡Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 6, I-80134 Napoli, Italy
| | - Tobias Fahleson
- ¶Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Joanna Kauczor
- ¶Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Patrick Norman
- ¶Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Sonia Coriani
- §Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
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70
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Ouyang W, Subotnik JE. Estimating the entropy and quantifying the impurity of a swarm of surface-hopping trajectories: A new perspective on decoherence. J Chem Phys 2014; 140:204102. [DOI: 10.1063/1.4876491] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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71
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Plasser F, Crespo-Otero R, Pederzoli M, Pittner J, Lischka H, Barbatti M. Surface Hopping Dynamics with Correlated Single-Reference Methods: 9H-Adenine as a Case Study. J Chem Theory Comput 2014; 10:1395-405. [PMID: 26580359 DOI: 10.1021/ct4011079] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface hopping dynamics methods using the coupled cluster to approximated second order (CC2), the algebraic diagrammatic construction scheme to second order (ADC(2)), and the time-dependent density functional theory (TDDFT) were developed and implemented into the program system Newton-X. These procedures are especially well-suited to simulate nonadiabatic processes involving various excited states of the same multiplicity and the dynamics in the first excited state toward an energetic minimum or up to the region where a crossing with the ground state is found. 9H-adenine in the gas phase was selected as the test case. The results showed that dynamics with ADC(2) is very stable, whereas CC2 dynamics fails within 100 fs, because of numerical instabilities present in the case of quasi-degenerate excited states. ADC(2) dynamics correctly predicts the ultrafast character of the deactivation process. It predicts that C2-puckered conical intersections should be the preferential pathway for internal conversion for low-energy excitation. C6-puckered conical intersection also contributes appreciably to internal conversion, becoming as important as C2-puckered for high-energy excitations. In any case, H-elimination plays only a minor role. TDDFT based on a long-range corrected functional fails to predict the ultrafast deactivation. In the comparison with several other methods previously used for dynamics simulations of adenine, ADC(2) has the best performance, providing the most consistent results so far.
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Affiliation(s)
- Felix Plasser
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls-University , Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Rachel Crespo-Otero
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Marek Pederzoli
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Jiri Pittner
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States.,Institute for Theoretical Chemistry, University of Vienna , Währingerstr. 17, A-1090 Vienna, Austria
| | - Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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72
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Chatterley AS, West CW, Roberts GM, Stavros VG, Verlet JRR. Mapping the Ultrafast Dynamics of Adenine onto Its Nucleotide and Oligonucleotides by Time-Resolved Photoelectron Imaging. J Phys Chem Lett 2014; 5:843-848. [PMID: 26274076 DOI: 10.1021/jz500264c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The intrinsic photophysics of nucleobases and nucleotides following UV absorption presents a key reductionist step toward understanding the complex photodamage mechanisms occurring in DNA. The decay mechanism of adenine in particular has been the focus of intense investigation, as has how these correlate to those of its more biologically relevant nucleotide and oligonucleotides in aqueous solution. Here, we report on time-resolved photoelectron imaging of the deprotonated 3'-deoxy-adenosine-5'-monophosphate nucleotide and the adenosine di- and trinucleotides. Through a comparison of gas- and solution-phase experiments and available theoretical studies, the dynamics of the base are shown to be relatively insensitive to the surrounding environment. The decay mechanism primarily involves internal conversion from the initially populated (1)ππ* states to the ground state. The relaxation dynamics of the adenosine oligonucleotides are similar to those of the nucleobase, in contrast to the aqueous oligonucleotides, where a fraction of the ensemble forms long-lived excimer states.
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Affiliation(s)
- Adam S Chatterley
- †Department of Chemistry, University of Durham, Durham DH1 3LE, United Kingdom
- ‡Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christopher W West
- †Department of Chemistry, University of Durham, Durham DH1 3LE, United Kingdom
| | - Gareth M Roberts
- ‡Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - 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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73
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Modeling processes of non-radiative relaxation of electronically excited states of fluorescent probe 4-dimethylaminochalcone and its complexes with water using non-adiabatic molecular dynamics. J Photochem Photobiol A Chem 2014. [DOI: 10.1016/j.jphotochem.2014.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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74
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Plasser F, Lischka H. Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution. Photochem Photobiol Sci 2014; 12:1440-52. [PMID: 23737069 DOI: 10.1039/c3pp50032b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The excited states and potential surfaces of the adenine dinucleotide are analyzed in gas phase and in solution using a correlated ab initio methodology in a QM/MM framework. In agreement with previous studies, a rather flat S1 surface with a number of minima of different character is found. Specifically, our results suggest that exciplexes with remarkably short intermolecular separation down to ~2.0 Å are formed. A detailed analysis shows that due to strong orbital interactions their character differs significantly from any states present in the Franck-Condon region. The lowest S1 energy minimum is a ππ* exciplex with only a small amount of charge transfer. It possesses appreciable oscillator strength with a polarization almost perpendicular to the planes of the two adenine molecules.
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Affiliation(s)
- Felix Plasser
- Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna, Austria.
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75
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Nachtigallová D, Aquino AJA, Horn S, Lischka H. The effect of dimerization on the excited state behavior of methylated xanthine derivatives: a computational study. Photochem Photobiol Sci 2014; 12:1496-508. [PMID: 23824308 DOI: 10.1039/c3pp50077b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The behavior of monomers and dimers of methylated xanthine derivatives in their excited states is investigated by means of the ADC(2), CASSCF, and CASPT2 methods. The results of the calculations of stationary points in the ground and excited states, minima on the S0/S1 crossing seams and the relaxation pathways are used to provide the interpretation of experimental observations of the monomer xanthine derivatives. The effect of dimerization on the excited state properties is studied for various relative orientations of the monomers in the dimer complexes in comparison with the relevant monomer species. A significant stabilization in the excited state minima of dimers is observed. These can act as trapping sites. Various types of conical intersections, with both localized and delocalized characters of wavefunctions, have been found, mainly energetically above the lowest bright excited state in the FC region. In addition, structures with the bonds formed between the two monomers were also found on the crossing seams. The possibility of ultrafast relaxation via these conical intersections is discussed.
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Affiliation(s)
- Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
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76
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Zhu X, Yarkony DR. Fitting coupled potential energy surfaces for large systems: Method and construction of a 3-state representation for phenol photodissociation in the full 33 internal degrees of freedom using multireference configuration interaction determined data. J Chem Phys 2014; 140:024112. [DOI: 10.1063/1.4857335] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xiaolei Zhu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - David R. Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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77
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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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78
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Mai S, Richter M, Marquetand P, González L. Excitation of Nucleobases from a Computational Perspective II: Dynamics. Top Curr Chem (Cham) 2014; 355:99-153. [DOI: 10.1007/128_2014_549] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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79
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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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80
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Tuna D, Sobolewski AL, Domcke W. Electronically excited states and photochemical reaction mechanisms of β-glucose. Phys Chem Chem Phys 2014; 16:38-47. [DOI: 10.1039/c3cp52359d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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81
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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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82
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Aquino AAJ, Borges I, Nieman R, Köhn A, Lischka H. Intermolecular interactions and charge transfer transitions in aromatic hydrocarbon–tetracyanoethylene complexes. Phys Chem Chem Phys 2014; 16:20586-97. [DOI: 10.1039/c4cp02900c] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ADC(2) calculations accurately describe charge transfer transitions in complexes of the tetracyanoethylene electron acceptor and three distinct aromatic donors.
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Affiliation(s)
- Adélia A. J. Aquino
- Dep. of Chemistry and Biochemistry
- Texas Tech University
- Lubbock, USA
- Institute for Soil Research
- University of Natural Resources and Life Sciences Vienna
| | - Itamar Borges
- Departamento de Química
- Instituto Militar de Engenharia
- Rio de Janeiro 22290-270, Brazil
| | - Reed Nieman
- Dep. of Chemistry and Biochemistry
- Texas Tech University
- Lubbock, USA
| | - Andreas Köhn
- Institute of Theoretical Chemistry
- Stuttgart University
- 70569 Stuttgart, Germany
| | - Hans Lischka
- Dep. of Chemistry and Biochemistry
- Texas Tech University
- Lubbock, USA
- Institute for Theoretical Chemistry
- University of Vienna
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83
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Abstract
Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany,
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84
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Barbatti M, Crespo-Otero R. Surface Hopping Dynamics with DFT Excited States. DENSITY-FUNCTIONAL METHODS FOR EXCITED STATES 2014; 368:415-44. [DOI: 10.1007/128_2014_605] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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85
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Tuna D, Sobolewski AL, Domcke W. Mechanisms of Ultrafast Excited-State Deactivation in Adenosine. J Phys Chem A 2013; 118:122-7. [DOI: 10.1021/jp410121h] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Deniz Tuna
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
| | | | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
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86
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Zhuang X, Wang J, Lan Z. Tracking of the Molecular Motion in the Primary Event of Photoinduced Reactions of a Phytochromobilin Model. J Phys Chem B 2013; 117:15976-86. [DOI: 10.1021/jp408799b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xuhui Zhuang
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
| | - Jun Wang
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
| | - Zhenggang Lan
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
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87
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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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88
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Nelson T, Fernandez-Alberti S, Roitberg AE, Tretiak S. Nonadiabatic excited-state molecular dynamics: Treatment of electronic decoherence. J Chem Phys 2013; 138:224111. [DOI: 10.1063/1.4809568] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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89
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Zhuang X, Wang J, Lan Z. Photoinduced Nonadiabatic Decay and Dissociation Dynamics of Dimethylnitramine. J Phys Chem A 2013; 117:4785-93. [DOI: 10.1021/jp402180p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xuhui Zhuang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, 189 Songling Road, Qingdao, 266101 Shandong, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jun Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, 189 Songling Road, Qingdao, 266101 Shandong, P. R. China
| | - Zhenggang Lan
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, 189 Songling Road, Qingdao, 266101 Shandong, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao, 266101 Shandong, P. R. China
- Qingdao Key Laboratory of Solar
Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese
Academy of Sciences, Qingdao, 266101, Shandong, P. R. China
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90
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Szalay PG, Watson T, Perera A, Lotrich V, Bartlett RJ. Benchmark Studies on the Building Blocks of DNA. 3. Watson–Crick and Stacked Base Pairs. J Phys Chem A 2013; 117:3149-57. [DOI: 10.1021/jp3100975] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Péter G. Szalay
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Thomas Watson
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Ajith Perera
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Victor Lotrich
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Rodney J. Bartlett
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
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91
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Janeček I, Janča T, Naar P, Kalus R, Gadea FX. Multiscale approach combining nonadiabatic dynamics with long-time radiative and non-radiative decay: Dissociative ionization of heavy rare-gas tetramers revisited. J Chem Phys 2013; 138:044303. [DOI: 10.1063/1.4775804] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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92
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Gustavsson T, Sarkar N, Vayá I, Jiménez MC, Markovitsi D, Improta R. A joint experimental/theoretical study of the ultrafast excited state deactivation of deoxyadenosine and 9-methyladenine in water and acetonitrile. Photochem Photobiol Sci 2013; 12:1375-86. [DOI: 10.1039/c3pp50060h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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93
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Picconi D, Avila Ferrer FJ, Improta R, Lami A, Santoro F. Quantum-classical effective-modes dynamics of the ππ* → nπ* decay in 9H-adenine. A quadratic vibronic coupling model. Faraday Discuss 2013; 163:223-42; discussion 243-75. [DOI: 10.1039/c3fd20147c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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94
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Excitation of Nucleobases from a Computational Perspective I: Reaction Paths. Top Curr Chem (Cham) 2013; 355:57-97. [DOI: 10.1007/128_2013_501] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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95
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Hua Y, Changenet-Barret P, Gustavsson T, Markovitsi D. The effect of size on the optical properties of guanine nanostructures: a femtosecond to nanosecond study. Phys Chem Chem Phys 2013; 15:7396-402. [DOI: 10.1039/c3cp00060e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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96
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Buchner F, Ritze HH, Lahl J, Lübcke A. Time-resolved photoelectron spectroscopy of adenine and adenosine in aqueous solution. Phys Chem Chem Phys 2013; 15:11402-8. [DOI: 10.1039/c3cp51057c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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97
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Filatov M. Understanding the dynamics behind photoisomerization of light-driven molecular rotary motors. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1135] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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