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Gate G, Williams A, Boldissar S, Šponer J, Szabla R, de Vries M. The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations. Photochem Photobiol 2024; 100:404-418. [PMID: 38124372 DOI: 10.1111/php.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ann Williams
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc-Holice, Czech Republic
| | - Rafal Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mattanjah de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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2
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Chakraborty R, Boguslawski K, Tecmer P. Static embedding with pair coupled cluster doubles based methods. Phys Chem Chem Phys 2023; 25:25377-25388. [PMID: 37705409 DOI: 10.1039/d3cp02502k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Quantum embedding methods have recently been significantly developed to model large molecular structures. This work proposes a novel wave function theory in a density functional theory (WTF-in-DFT) embedding scheme based on pair-coupled cluster doubles (pCCD)-type methods. While pCCD can reliably describe strongly-correlated systems with mean-field-like computational cost, the large extent of the dynamic correlation can be accounted for by (linearized) coupled-cluster corrections on top of the pCCD wave function. Here we focus on the linearized coupled-cluster singles and doubles (LCCSD) ansatz for electronic ground states and its extension to excited states within the equation of motion (EOM) formalism. We test our EOM-pCCD-LCCSD-in-DFT approach for the vertical excitation energies of the hydrogen-bonded water-ammonia complex, micro-solvated thymine, and uranyl tetrahalides (UO2X42-, X = F, Cl, Br). Furthermore, we assess the quality of the embedding potential using an orbital entanglement and correlation analysis. The approximate embedding models successfully capture changes in the excitation energies going from bare fragments to supramolecular structures and represent a promising computational method for excited states in large molecular systems.
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Affiliation(s)
- Rahul Chakraborty
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
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3
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Usabiaga I, Camiruaga A, Calabrese C, Veloso A, D'mello VC, Wategaonkar S, Fernández JA. Exploration of the theobromine-water dimer: comparison with DNA microhydration. Phys Chem Chem Phys 2020; 22:15759-15768. [PMID: 32627788 DOI: 10.1039/d0cp02397c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Understanding the molecular basis of the appearance of life on Earth is an exciting research field. Many factors may have influenced the election of the molecules used by living beings and evolution may have modified those original compounds. In an attempt to understand the role played by intermolecular interactions in the election of CGAT as the alphabet of life, we present here a thorough experimental and computational study on the interaction of theobromine with water. Theobromine is a xanthine derivative, structurally related to the nucleobases, and also present in many living beings. The experimental results demonstrate that the most stable isomer of theobromine-water was formed and detected in supersonic expansions. This isomer very well resembles the structure of the dimers between nucleobases and water, offering similar values of binding energy. A comparison between the results obtained for theobromine-water with those reported in the literature for monohydrates of nucleobases is also offered.
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Affiliation(s)
- Imanol Usabiaga
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), 48940, Leioa, Spain.
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4
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Lischka H, Barbatti M, Siddique F, Das A, Aquino AJ. The effect of hydrogen bonding on the nonadiabatic dynamics of a thymine-water cluster. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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5
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Milovanović B, Kojić M, Petković M, Etinski M. New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics. J Chem Theory Comput 2018; 14:2621-2632. [DOI: 10.1021/acs.jctc.8b00139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Marko Kojić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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UV fragmentation and ultrafast dynamics of trinuclear silver/1-methylthymine and silver/1-methyluracil metal-base pairs in an ion trap. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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7
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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: 338] [Impact Index Per Article: 42.3] [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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Ligare M, Siouri F, Bludsky O, Nachtigallová D, de Vries MS. Characterizing the dark state in thymine and uracil by double resonant spectroscopy and quantum computation. Phys Chem Chem Phys 2015; 17:24336-41. [DOI: 10.1039/c5cp03516c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double resonant spectroscopy characterizes both grounds state and dark excited state of uracil and thymine.
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Affiliation(s)
- M. Ligare
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - F. Siouri
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - O. Bludsky
- Institute of Organic Chemistry and Biochemistry v.v.i
- AS CR
- 16610 Prague
- Czech Republic
| | - D. Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i
- AS CR
- 16610 Prague
- Czech Republic
| | - M. S. de Vries
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
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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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10
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Ataelahi M, Omidyan R. Microhydration effects on the electronic properties of protonated phenol: a theoretical study. J Phys Chem A 2013; 117:12842-50. [PMID: 24191660 DOI: 10.1021/jp409537s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The CC2 (second-order approximate coupled cluster method) has been employed to investigate microhydration effect on electronic properties of protonated phenol (PhH(+)) According to the CC2 calculation results on electronic excited states of microhydrated PhH(+), for the S1 and S2 electronic states, which are of (1)ππ* nature and belong to the A' representation of molecular Cs point group, a significant blue shift effect on the S1 and S2 electronic states, which are of 1ππ* nature and belong to the A' representation of molecular Cs point group, in comparison to corresponding transitions on bare cation (PhH(+)), has been predicted. Nevertheless, for the S3-S0 (1A'', 1σπ*) transition, a large red shift effect has been predicted. Furthermore, it has been found that the lowest (1)σπ* state plays a prominent role in the photochemistry of these systems. In the bare protonated phenol, the (1)σπ* state is a bound state with a broad potential curve along the OH stretching coordinate, while it is dissociative in microhydrated species. This indicates to a predissociation of the S1((1)ππ*) state by a low-lying (1)σπ* state, which leads the excited system to a concerted proton-transfer reaction from protonated chromophore to the solvent. The dissociative (1)σπ* state in monohydrated PhH(+) has small barrier, while increasing the solvent molecules up to three removes the barrier and consequently expedites the proton-transfer reaction dynamics.
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Affiliation(s)
- Mitra Ataelahi
- Department of Chemistry, University of Isfahan , 81746-73441 Isfahan, Iran
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12
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Improta R. Photophysics and photochemistry of thymine deoxy-dinucleotide in water: a PCM/TD-DFT quantum mechanical study. J Phys Chem B 2012; 116:14261-74. [PMID: 23134336 DOI: 10.1021/jp3093385] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We here report a fully quantum mechanical study of the main photochemical and photophysical decay routes in aqueous solution of thymine deoxy-dinucleotide (TpT(-) and TpTNa) and of its analogue locked in C3-endo puckering, characterizing five different representative backbone conformers and discussing the chemical physical effects modulating the yield of the different photoproducts. Our approach is based on time-dependent DFT calculations, using the last generation M052X functional, whereas solvent effects are included by means of the polarizable continuum model. Especially when at least one of the sugars adopts C3-endo puckering, a barrierless path on the bright ππ* excitons leads to the S(1)/S(0) crossing region corresponding to the formation of cyclobutane pyrimidine dimer. Charge transfer excited states involving the transfer of an electron from the 5' Thy toward the 3' Thy are involved in the formation of the oxetane intermediate in the path leading to 6-4 pyrimidine pyrimidinone adducts. A non-negligible energy barrier is associated with this latter pathway, which is possible only when one of the two nucleotides adopts C2-endo puckering. Monomer-like decay pathways, involving ππ* or nπ* excited states localized on a single base, are shown to be operative also for loosely stacked bases.
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Affiliation(s)
- Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture Biommagini (IBB-CNR), Via Mezzocannone 16, I-80134 Napoli, Italy.
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Pohler L, Kleinschmidt M, Etinski M, Marian CM. In search of the dark state of 5-methyl-2-hydroxypyrimidine using a numerical DFT/MRCI gradient. Mol Phys 2012. [DOI: 10.1080/00268976.2012.695030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Larissa Pohler
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
| | - Martin Kleinschmidt
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
| | - Mihajlo Etinski
- b Faculty of Physical Chemistry , University of Belgrade , Studentski Trg 12-16, 11000 Belgrade , Serbia
| | - Christel M. Marian
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
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Yamazaki S, Taketsugu T. Nonradiative Deactivation Mechanisms of Uracil, Thymine, and 5-Fluorouracil: A Comparative ab Initio Study. J Phys Chem A 2011; 116:491-503. [DOI: 10.1021/jp206546g] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shohei Yamazaki
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Lobsiger S, Frey HM, Leutwyler S, Morgan P, Pratt D. S0 and S1 State Structure, Methyl Torsional Barrier Heights, and Fast Intersystem Crossing Dynamics of 5-Methyl-2-hydroxypyrimidine. J Phys Chem A 2011; 115:13281-90. [DOI: 10.1021/jp207213c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Philip Morgan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - David Pratt
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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González L, Escudero D, Serrano-Andrés L. Progress and Challenges in the Calculation of Electronic Excited States. Chemphyschem 2011; 13:28-51. [DOI: 10.1002/cphc.201100200] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 08/05/2011] [Indexed: 11/09/2022]
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17
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Nosenko Y, Kunitski M, Stark T, Göbel M, Tarakeshwar P, Brutschy B. 4-Aminobenzimidazole–1-Methylthymine: A Model for Investigating Hoogsteen Base-Pairing between Adenine and Thymine. J Phys Chem A 2011; 115:11403-11. [DOI: 10.1021/jp205575w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Pilarisetty Tarakeshwar
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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Nosenko Y, Kunitski M, Brutschy B. Specific photodynamics in thymine clusters: the role of hydrogen bonding. J Phys Chem A 2011; 115:9429-39. [PMID: 21648386 DOI: 10.1021/jp111373t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.
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Affiliation(s)
- Yevgeniy Nosenko
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-str. 7, 60438 Frankfurt/Main, Germany
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Picconi D, Barone V, Lami A, Santoro F, Improta R. The Interplay between ππ*/nπ* Excited States in Gas-Phase Thymine: A Quantum Dynamical Study. Chemphyschem 2011; 12:1957-68. [DOI: 10.1002/cphc.201001080] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/01/2011] [Indexed: 11/10/2022]
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20
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Kunitski M, Nosenko Y, Brutschy B. On the Nature of the Long-Lived “Dark” State of Isolated 1-Methylthymine. Chemphyschem 2011; 12:2024-30. [DOI: 10.1002/cphc.201000985] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 02/16/2011] [Indexed: 11/10/2022]
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Sinha RK, Lobsiger S, Trachsel M, Leutwyler S. Vibronic Spectra of Jet-Cooled 2-Aminopurine·H2O Clusters Studied by UV Resonant Two-Photon Ionization Spectroscopy and Quantum Chemical Calculations. J Phys Chem A 2011; 115:6208-17. [DOI: 10.1021/jp111469n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajeev K. Sinha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Maria Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Bányász Á, Karpati S, Mercier Y, Reguero M, Gustavsson T, Markovitsi D, Improta R. The Peculiar Spectral Properties of Amino-Substituted Uracils: A Combined Theoretical and Experimental Study. J Phys Chem B 2010; 114:12708-19. [DOI: 10.1021/jp105267q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ákos Bányász
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Szilvia Karpati
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Yannick Mercier
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Mar Reguero
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Thomas Gustavsson
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Dimitra Markovitsi
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Roberto Improta
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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Etinski M, Marian CM. Ab initio investigation of the methylation and hydration effects on the electronic spectra of uracil and thymine. Phys Chem Chem Phys 2010; 12:4915-23. [DOI: 10.1039/b925677f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Etinski M, Marian CM. Overruling the energy gap law: fast triplet formation in 6-azauracil. Phys Chem Chem Phys 2010; 12:15665-71. [DOI: 10.1039/c0cp00106f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nosenko Y, Kunitski M, Riehn C, Harbach PHP, Dreuw A, Brutschy B. The structure of adenine monohydrates studied by femtosecond multiphoton ionization detected IR spectroscopy and quantum chemical calculations. Phys Chem Chem Phys 2010; 12:863-70. [DOI: 10.1039/b914236c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Hoshino-Nagasaka M, Suzuki T, Ichimura T, Kasahara S, Baba M, Kawauchi S. Rotationally resolved high-resolution spectrum of the S1–S0 transition of jet-cooled thioanisole. Phys Chem Chem Phys 2010; 12:13243-7. [DOI: 10.1039/c004454g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lobsiger S, Frey HM, Leutwyler S. Supersonic jet UV spectrum and nonradiative processes of the thymine analogue 5-methyl-2-hydroxypyrimidine. Phys Chem Chem Phys 2010; 12:5032-40. [DOI: 10.1039/b924395j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Improta R, Barone V, Lami A, Santoro F. Quantum Dynamics of the Ultrafast ππ*/nπ* Population Transfer in Uracil and 5-Fluoro-Uracil in Water and Acetonitrile. J Phys Chem B 2009; 113:14491-503. [DOI: 10.1021/jp906524p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Vincenzo Barone
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Alessandro Lami
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
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Etinski M, Fleig T, Marian CM. Intersystem Crossing and Characterization of Dark States in the Pyrimidine Nucleobases Uracil, Thymine, and 1-Methylthymine. J Phys Chem A 2009; 113:11809-16. [DOI: 10.1021/jp902944a] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mihajlo Etinski
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Timo Fleig
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christel M. Marian
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Kistler KA, Matsika S. Solvatochromic Shifts of Uracil and Cytosine Using a Combined Multireference Configuration Interaction/Molecular Dynamics Approach and the Fragment Molecular Orbital Method. J Phys Chem A 2009; 113:12396-403. [DOI: 10.1021/jp901601u] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kurt A. Kistler
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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Feng K, Engler G, Seefeld K, Kleinermanns K. Dispersed Fluorescence and Delayed Ionization of Jet-Cooled 2-Aminopurine: Relaxation to a Dark State Causes Weak Fluorescence. Chemphyschem 2009; 10:886-9. [DOI: 10.1002/cphc.200800816] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Sobolewski AL, Shemesh D, Domcke W. Computational studies of the photophysics of neutral and zwitterionic amino acids in an aqueous environment: tyrosine-(H(2)O)(2) and tryptophan-(H(2)O)(2) clusters. J Phys Chem A 2009; 113:542-50. [PMID: 19099467 DOI: 10.1021/jp8091754] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tyrosine-(H(2)O)(2) and tryptophan-(H(2)O)(2) clusters have been considered as models for the study of the photochemistry of neutral and zwitterionic tyrosine and tryptophan in an aqueous environment. It has been found that the detachment of neutral NH(3) in the S(1) state of the zwitterionic clusters leads to a low-lying conical intersection of the S(1) and S(0) energy surfaces. This conical intersection can provide the mechanism for efficient radiationless deactivation of the excited state back to the ground state or, alternatively, deamination (loss of ammonia). These results provide a mechanistic explanation of the efficient fluorescence quenching and the high quantum yield of ammonia in the UV photolysis of tyrosine and tryptophan in aqueous solution.
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