1
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Hartweg S, Hochlaf M, Garcia GA, Nahon L. Photoionization Dynamics and Proton Transfer within the Adenine-Thymine Nucleobase Pair. J Phys Chem Lett 2023; 14:3698-3705. [PMID: 37040591 DOI: 10.1021/acs.jpclett.3c00564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Studying the stability of hydrogen-bonded nucleobase pairs, at the heart of the genetic code, is of utmost importance for an in-depth understanding of basic mechanisms of life and biomolecular evolution. We present here a VUV single photon ionization dynamic study of the nucleobase pair adenine-thymine (AT), revealing its ionization and dissociative ionization thresholds via double imaging electron/ion coincidence spectroscopy. The experimental data, consisting of cluster mass-resolved threshold photoelectron spectra and photon energy-dependent ion kinetic energy release distributions, allow the unambiguous distinction of the dissociation of AT into protonated adenine AH+ and a dehydrogenated thymine radical T(-H) from dissociative ionization processes of other nucleobase clusters. Comparison to high-level ab initio calculations indicates that our experimental observations can be explained by a single hydrogen-bonded conformer present in our molecular beam and allows the estimation of an upper limit of the barrier of the proton transfer in the ionized AT pair.
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Affiliation(s)
- Sebastian Hartweg
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
- University of Freiburg, Institute of Physics, Hermann-Herder-Straße 3, 79104 Freiburg, Germany
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454 Champs sur Marne, France
| | - Gustavo A Garcia
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
| | - Laurent Nahon
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
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2
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Cabezas C, Peña I, Caminati W. Rotational spectrum and internal dynamics of the hydrogen-bonded pyrrole-pyridine aromatic pair. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119320. [PMID: 33360563 PMCID: PMC7610520 DOI: 10.1016/j.saa.2020.119320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/29/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Non-covalent interactions determine the three-dimensional structure and activity of biological molecules. In this work, the pyrrole-pyridine complex considered as a model of the NH⋯N hydrogen-bonded Watson-Crick base pairs has been generated in a supersonic expansion and characterized by chirped pulse Fourier transform microwave spectroscopy. The analysis of the unconventional spectral pattern of the 1:1 pyrrole-pyridine adduct and its 13C and 15N isotopologues reveal a non-planar complex, with a bent NH⋯N hydrogen bond and large amplitude motion of the pyrrole subunit. The bent structure is likely to arise from the stablishment of the secondary CH⋯N interaction between pyridine and pyrrole moieties.
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Affiliation(s)
- Carlos Cabezas
- Instituto de Física Fundamental (IFF-CSIC), Group of Molecular Astrophysics, C/Serrano 121, 28006 Madrid, Spain.
| | - Isabel Peña
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid, Spain.
| | - Walther Caminati
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, Bologna 40126, Italy
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3
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Sarkar S, Sruthi P, Ramanathan N, Sundararajan K. Experimental evidence of N–H⋯N hydrogen bonding in the heterodimers of pyrrole with nitrogen bases. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Abedini F, Omidyan R. Excited-State Proton Transfer in Thiazolo-[4, 5-d]thiazo Heterocyclic Systems and the Geometry Alterations' Effect on Photophysical Characters: A Theoretical Study. J Phys Chem A 2018; 122:2653-2662. [PMID: 29489372 DOI: 10.1021/acs.jpca.7b09593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiazolo-[4,5- d]-thiazo-frame (tztz) compounds are important heteroaromatic organic systems, which recently became a subject of several studies in the field of organic electronics and organic photovoltaics. The most important physical nature of these systems is reported to be an equilibrium between enol and keto forms following excited-state proton transfer. This process originates from a flat trend of the S1 PE (potential energy) profile along the proton transfer coordinate. In the present work, we determined and interpreted the excited-state proton transfer and photophysical nature of these systems extensively by means of the MP2/CC2 and CASSCF theoretical approaches. Also, the effects of amine (-NH2) and cyano (-CN) substitutions were taken into account comprehensively by considering the transition energies and proton transfer pathways of the resulting tztz derivatives. It has been predicted that the physical nature of the excited-state intramolecular proton transfer, as the main character of these systems, is being affected significantly by substitutions. For all of the considered tztz derivatives, a conical intersection (CI) between ground and the S1 excited state was predicted. This CI makes the considered species capable to be responsible for photochromism and photoswitching as well.
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Affiliation(s)
- Fatemeh Abedini
- Department of Chemistry , University of Isfahan , 81746-73441 Isfahan , Iran
| | - Reza Omidyan
- Department of Chemistry , University of Isfahan , 81746-73441 Isfahan , Iran
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5
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Yu XF, Yamazaki S, Taketsugu T. Solvent effects on the excited-state double proton transfer mechanism in the 7-azaindole dimer: a TDDFT study with the polarizable continuum model. Phys Chem Chem Phys 2017; 19:23289-23301. [DOI: 10.1039/c7cp04942k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvent effects on the excited-state double proton transfer (ESDPT) mechanism in the 7-azaindole (7AI) dimer were investigated using the time-dependent density functional theory (TDDFT) method.
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Affiliation(s)
- Xue-fang Yu
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Shohei Yamazaki
- Department of Frontier Materials Chemistry
- Graduate School of Science and Technology
- Hirosaki University
- Hirosaki 036-8561
- Japan
| | - Tetsuya Taketsugu
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
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6
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Esboui M, Jaidane N. Non-radiative deactivation in phenol–pyridine complex: theoretical study. Photochem Photobiol Sci 2015; 14:1127-37. [DOI: 10.1039/c4pp00199k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparative theoretical study of the nonradiative decay mechanisms to the ground state of phenol-pyridine complex under Cs symmetry (Pl and Pe conformers) and without symmetry constraints has been performed by ab initio calculations.
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Affiliation(s)
- Mounir Esboui
- Laboratoire de Spectroscopie Atomique
- Moléculaire et Applications
- Département de Physique
- Faculté des Sciences de Tunis
- 2092 Tunis
| | - Nejmeddine Jaidane
- Laboratoire de Spectroscopie Atomique
- Moléculaire et Applications
- Département de Physique
- Faculté des Sciences de Tunis
- 2092 Tunis
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7
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Chen JS, Zhao FJ, Yang Y, Chu TS. Hydrogen bond effect on the photophysical properties of 2-ureido-4[1H]-pyrimidinone quadruple hydrogen bonded systems. RSC Adv 2015. [DOI: 10.1039/c5ra04005a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two different hydrogen bond effects on the photophysical properties of UPy systems in different solutions have been studied.
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Affiliation(s)
- Jun-Sheng Chen
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- People's Republic of China
| | - Feng-Jiao Zhao
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- People's Republic of China
| | - Yang Yang
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- People's Republic of China
| | - Tian-Shu Chu
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- People's Republic of China
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8
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Omidyan R, Salehi M, Azimi G. A theoretical exploration of the nonradiative deactivation of hydrogen-bond complexes: isoindole–pyridine and quinoline–pyrrole. RSC Adv 2015. [DOI: 10.1039/c5ra18950k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CC2 potential energy profiles of the ground and excited states of the isoindole–pyridine complex along the proton transfer reaction coordinate are studied.
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Affiliation(s)
- Reza Omidyan
- Department of Chemistry
- University of Isfahan
- 81746-73441 Isfahan
- Iran
| | - Mohammad Salehi
- Department of Chemistry
- University of Isfahan
- 81746-73441 Isfahan
- Iran
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9
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Han S, You HS, Kim SY, Kim SK. Dynamic Role of the Intramolecular Hydrogen Bonding in Nonadiabatic Chemistry Revealed in the UV Photodissociation Reactions of 2-Fluorothiophenol and 2-Chlorothiophenol. J Phys Chem A 2014; 118:6940-9. [DOI: 10.1021/jp505699w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Songhee Han
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - Hyun Sik You
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - So-Yeon Kim
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
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10
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Sauri V, Gobbo JP, Serrano-Pérez JJ, Lundberg M, Coto PB, Serrano-Andrés L, Borin AC, Lindh R, Merchán M, Roca-Sanjuán D. Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism. J Chem Theory Comput 2012; 9:481-96. [DOI: 10.1021/ct3006166] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vicenta Sauri
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - João P. Gobbo
- Instituto de Química,
Universidade de São Paulo and NAP-PhotoTech, the USP Consortium
for Photochemical Technology, Av. Prof. Lineu Prestes, 748, 05508-900,
São Paulo, SP, Brazil
| | - Juan J. Serrano-Pérez
- Department of Chemistry, Imperial
College London, Exhibition Road, London, SW7 2AZ, United Kingdom
| | - Marcus Lundberg
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
| | - Pedro B. Coto
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
- Institut
für Theoretische
Physik, Friedrich-Alexander-Universität Erlangen-Nürnberg,
Staudtstraβe 7, 91058 Erlangen, Germany
- Departamento de Química-Física,
Universidad de Alcalá de Henares, Ctra. Madrid-Barcelona (Autovía
A2) Km. 33.600, 28871 Alcalá de Henares, Spain
| | - Luis Serrano-Andrés
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - Antonio C. Borin
- Instituto de Química,
Universidade de São Paulo and NAP-PhotoTech, the USP Consortium
for Photochemical Technology, Av. Prof. Lineu Prestes, 748, 05508-900,
São Paulo, SP, Brazil
| | - Roland Lindh
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
| | - Manuela Merchán
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - Daniel Roca-Sanjuán
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
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11
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Weinberg DR, Gagliardi CJ, Hull JF, Murphy CF, Kent CA, Westlake BC, Paul A, Ess DH, McCafferty DG, Meyer TJ. Proton-Coupled Electron Transfer. Chem Rev 2012; 112:4016-93. [DOI: 10.1021/cr200177j] [Citation(s) in RCA: 1125] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David R. Weinberg
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
- Department of Physical and Environmental
Sciences, Colorado Mesa University, 1100 North Avenue, Grand Junction,
Colorado 81501-3122, United States
| | - Christopher J. Gagliardi
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Jonathan F. Hull
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Christine Fecenko Murphy
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Caleb A. Kent
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Brittany C. Westlake
- The American Chemical Society,
1155 Sixteenth Street NW, Washington, District of Columbia 20036,
United States
| | - Amit Paul
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Daniel H. Ess
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Dewey Granville McCafferty
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Thomas J. Meyer
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
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12
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Marazzi M, Navizet I, Lindh R, Frutos LM. Photostability Mechanisms in Human γB-Crystallin: Role of the Tyrosine Corner Unveiled by Quantum Mechanics and Hybrid Quantum Mechanics/Molecular Mechanics Methodologies. J Chem Theory Comput 2012; 8:1351-9. [DOI: 10.1021/ct300114w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Marazzi
- Departamento de Química
Física, Universidad de Alcalá, E-28871 Alcalá de Henares (Madrid), Spain
| | - Isabelle Navizet
- School of Chemistry, University of the Witwatersrand, ZA-2050 Johannesburg,
South Africa
| | - Roland Lindh
- Department of Chemistry, Ångström, The Theoretical Chemistry Programme, Uppsala University, SE-75120 Uppsala, Sweden
| | - Luis Manuel Frutos
- Departamento de Química
Física, Universidad de Alcalá, E-28871 Alcalá de Henares (Madrid), Spain
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13
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Lan Z, Nonell S, Barbatti M. Theoretical Characterization of Absorption and Emission Spectra of an Asymmetric Porphycene. J Phys Chem A 2012; 116:3366-76. [DOI: 10.1021/jp300888a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zhenggang Lan
- Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People’s Republic of China
| | - Santi Nonell
- Grup d’Enginyeria Molecular,
Institut Quimic de Sarria, Universitat Ramon Llull, Via Augusta 390, E-08017, Barcelona, Spain
| | - Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
D-45470 Mülheim, Germany
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14
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Roca-Sanjuán D, Aquilante F, Lindh R. Multiconfiguration second-order perturbation theory approach to strong electron correlation in chemistry and photochemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.97] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Marazzi M, Sancho U, Castaño O, Frutos LM. First principles study of photostability within hydrogen-bonded amino acids. Phys Chem Chem Phys 2011; 13:7805-11. [PMID: 21403960 DOI: 10.1039/c0cp02554b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photochemistry and photophysics of a two-glycine minimal model is studied at the CASPT2//CASSCF level of theory. Different photoinduced processes are discussed, on the basis of the calculated minimum energy paths and the characterization of the electronic state crossings. Two main processes could provide UV-photostability to the hydrogen-bonded peptide system: (i) forward-backward photoinduced electron/proton transfer involving the H in the hydrogen bond, (ii) singlet-singlet energy transfer between two amino acids, providing ultrafast population of the low-energy n,π* state.
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Affiliation(s)
- Marco Marazzi
- Departamento de Química Física, Universidad de Alcalá, 28871 Alcalá de Henares (Madrid), Spain.
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16
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Udvarhelyi A, Domratcheva T. Photoreaction in BLUF Receptors: Proton-coupled Electron Transfer in the Flavin-Gln-Tyr System†. Photochem Photobiol 2011; 87:554-63. [DOI: 10.1111/j.1751-1097.2010.00884.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Slavíček P, Fárník M. Photochemistry of hydrogen bonded heterocycles probed by photodissociation experiments and ab initio methods. Phys Chem Chem Phys 2011; 13:12123-37. [DOI: 10.1039/c1cp20674e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Nenov A, Cordes T, Herzog TT, Zinth W, de Vivie-Riedle R. Molecular Driving Forces for Z/E Isomerization Mediated by Heteroatoms: The Example Hemithioindigo. J Phys Chem A 2010; 114:13016-30. [DOI: 10.1021/jp107899g] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Artur Nenov
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Thorben Cordes
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Teja T. Herzog
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Wolfgang Zinth
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Regina de Vivie-Riedle
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
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19
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Conti I, Altoè P, Stenta M, Garavelli M, Orlandi G. Adenine deactivation in DNA resolved at the CASPT2//CASSCF/AMBER level. Phys Chem Chem Phys 2010; 12:5016-23. [DOI: 10.1039/b926608a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Mulkidjanian AY. On the origin of life in the zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth. Biol Direct 2009; 4:26. [PMID: 19703272 PMCID: PMC3152778 DOI: 10.1186/1745-6150-4-26] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 08/24/2009] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The complexity of the problem of the origin of life has spawned a large number of possible evolutionary scenarios. Their number, however, can be dramatically reduced by the simultaneous consideration of various bioenergetic, physical, and geological constraints. RESULTS This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27). CONCLUSION The suggested "Zn world" scenario identifies the geological conditions under which photosynthesizing ZnS edifices of hydrothermal origin could emerge and persist on primordial Earth, includes a mechanism of the transient storage and utilization of solar light for the production of diverse organic compounds, and identifies the driving forces and selective factors that could have promoted the transition from the first simple, photostable polymers to more complex living organisms.
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21
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Mandal TK, Pati SK, Datta A. Degenerate intermolecular and intramolecular proton-transfer reactions: electronic structure of the transition states. J Phys Chem A 2009; 113:8147-51. [PMID: 19606892 DOI: 10.1021/jp9044513] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Density functional theory (DFT) calculations are performed on a series of double and single proton-transfer reactions to study the variation in polarizations in complexes during the dynamics of proton transfer from one isoenergetic, hydrogen-bonded ground-state structure to the other. The isotropic average polarizability (alpha(av)) shows an interesting single-humped profile with a maxima coinciding with the transition state of the reaction. Similar profiles are also computed at Nd:YaG frequencies. The origin of the maximal polarizability at the transition state is traced to maximal charge separation and large D (donor)-A (acceptor) distances. Maximal polarizability for the transition state suggests an interesting, novel, and less memory extensive computational tool to locate the transition state for hydrogen-transfer reactions in hydrogen-bonded complexes.
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22
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Poterya V, Profant V, Fárník M, Šištík L, Slavíček P, Buck U. Photoinduced Processes in Hydrogen Bonded System: Photodissociation of Imidazole Clusters. J Phys Chem A 2009; 113:14583-90. [DOI: 10.1021/jp904145q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | - Udo Buck
- Max-Planck Institut für Dynamik und Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany
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Photochemistry of hydrogen-bonded aromatic pairs: Quantum dynamical calculations for the pyrrole-pyridine complex. Proc Natl Acad Sci U S A 2008; 105:12707-12. [PMID: 18663223 DOI: 10.1073/pnas.0801062105] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The photochemical dynamics of the pyrrole-pyridine hydrogen-bonded complex has been investigated with computational methods. In this system, a highly polar charge-transfer state of (1)pipi* character drives the proton transfer from pyrrole to pyridine, leading to a conical intersection of S(1) and S(0) energy surfaces. A two-sheeted potential-energy surface including 39 in-plane nuclear degrees of freedom has been constructed on the basis of ab initio multiconfiguration electronic-structure data. The non-Born-Oppenheimer nuclear dynamics has been treated with time-dependent quantum wave-packet methods, including the two or three most relevant nuclear degrees of freedom. The effect of the numerous weakly coupled vibrational modes has been taken into account with reduced-density-matrix methods (multilevel Redfield theory). The results provide insight into the mechanisms of excited-state deactivation of hydrogen-bonded aromatic systems via the electron-driven proton-transfer process. This process is believed to be of relevance for the ultrafast excited-state deactivation of DNA base pairs and may contribute to the photostability of the molecular encoding of the genetic information.
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Kryachko ES, Scheiner S. Bonding rearrangements of hydrogen-bonded complexes involving alkynes. J Phys Chem A 2008; 112:1940-5. [PMID: 18266343 DOI: 10.1021/jp076795e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecules containing a C-C triple bond, such as HC[triple bond]CH, FC[triple bond]CF, and the C[triple bond]CH radical, are allowed to interact with a partner molecule of H2O, NH3, or HF. Quantum chemical calculations show that these C[triple bond]CH...X H-bonded complexes are bound by up to 4 kcal x mol(-1). More importantly, they can rearrange in such a way that the partner molecule adds to the triple bond so as to form a double C=C bond. Whereas this process is strongly exoergic, there is a high-energy barrier to this rearrangement process. On the other hand, when a second water molecule is added to the complex, it can shuttle protons from the donor part of the complex to the acceptor, and thereby greatly reduce the rearrangement energy barrier. In the case of CCH + 2H2O, this barrier is computed to be less than 4 kcal x mol(-1).
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Affiliation(s)
- Eugene S Kryachko
- Department of Chemistry, Bat. B6c, University of Liege, Sart-Tilman, B-4000 Liege 1, Belgium.
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Affiliation(s)
- My Hang V Huynh
- DE-1: High Explosive Science and Technology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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