1
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Chevalier F, Schlathölter T, Poully JC. Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems. Chembiochem 2023; 24:e202300543. [PMID: 37712497 DOI: 10.1002/cbic.202300543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.
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Affiliation(s)
- François Chevalier
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen (The, Netherlands
- University College Groningen, University of Groningen, Groningen (The, Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
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2
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Barone V. DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase. J Chem Theory Comput 2023; 19:4970-4981. [PMID: 37479680 PMCID: PMC10413851 DOI: 10.1021/acs.jctc.3c00465] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Indexed: 07/23/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore
di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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3
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Huang SR, Tureček F. Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization. J Phys Chem A 2022; 126:2480-2497. [PMID: 35439003 DOI: 10.1021/acs.jpca.2c00894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation radicals of DNA nucleosides, 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion-electron recombination energies (REad) for the lowest-energy isomers 2'-deoxy-(N-3H)adenos-1'-yl (4.74 eV), 2'-deoxy-(N-7H)guanos-1'-yl (4.66 eV), 2'-deoxy-(N-3H)cytid-1'-yl (5.12 eV), and 2'-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2'-deoxyadenosine, 2'-deoxy guanosine, 2'-deoxy cytidine, and 2'-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born-Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+· to A in both dAT+· and dA⊂dT+·, leading to charge and radical separation. Noncanonical T+· in dCT+· and dTC+· initiated rapid proton transfer to cytosine, whereas the canonical dCT+· dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+· and dG⊂dC+· containing canonical neutral and noncanonical ionized deoxycytidine.
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Affiliation(s)
- Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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4
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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:1077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
| | | | - Andrea Amadei
- Department of Chemical and Technological Sciences, Tor Vergata University, 00133 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
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5
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Molina F, Dezalay J, Soorkia S, Broquier M, Hochlaf M, Pino GA, Grégoire G. Cryogenic IR and UV spectroscopy of isomer-selected cytosine radical cation. Phys Chem Chem Phys 2022; 24:25182-25190. [DOI: 10.1039/d2cp03953b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The UV photodissociation of cryogenic-cooled isomer-selected cytosine–silver complex leads to the production of cytosine radical cation without isomerization.
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Affiliation(s)
- Franco Molina
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Jordan Dezalay
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Satchin Soorkia
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Michel Broquier
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes 77454, Champs sur Marne, France
| | - Gustavo Ariel Pino
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Gilles Grégoire
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
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6
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Savee J, Sztáray B, Hemberger P, Zádor J, Bodi A, Osborn DL. Unimolecular isomerisation of 1,5-hexadiyne observed by threshold photoelectron photoion coincidence spectroscopy. Faraday Discuss 2022; 238:645-664. [DOI: 10.1039/d2fd00028h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unimolecular isomerisation of the prompt propargyl + propargyl "head-to-head" adduct, 1,5- hexadiyne, to fulvene and benzene by the 3,4-dimethylenecyclobut-1-ene (DMCB) intermediate (all C6H6) was studied in the high-pressure limit...
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7
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Ho J, Cheng P. Ultrafast excited‐state dynamics of gas‐phase 5‐methylcytosine tautomers. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jr‐Wei Ho
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Po‐Yuan Cheng
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
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8
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Ahmed M, Kostko O. From atoms to aerosols: probing clusters and nanoparticles with synchrotron based mass spectrometry and X-ray spectroscopy. Phys Chem Chem Phys 2020; 22:2713-2737. [DOI: 10.1039/c9cp05802h] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Synchrotron radiation provides insight into spectroscopy and dynamics in clusters and nanoparticles.
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Affiliation(s)
- Musahid Ahmed
- Chemical Sciences Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - Oleg Kostko
- Chemical Sciences Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
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9
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Trachsel MA, Blaser S, Siffert L, Wiedmer T, Leutwyler S. Excited-state vibrations, lifetimes, and nonradiative dynamics of jet-cooled 1-ethylcytosine. J Chem Phys 2019; 151:124301. [PMID: 31575195 DOI: 10.1063/1.5116911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The S1 excited-state lifetime of jet-cooled 1-ethylcytosine (1ECyt) is ∼1 ns, one of the longest lifetimes for cytosine derivatives to date. Here, we analyze its S0 → S1 vibronic spectrum using two-color resonant two-photon ionization and UV/UV holeburning spectroscopy. Compared to cytosine and 1-methylcytosine, the S0 → S1 spectrum of 1ECyt shows a progression in the out-of-plane "butterfly" mode ν1 ', identified by spin-component scaled-second-order coupled-cluster method ab initio calculations. We also report time-resolved S1 state nonradiative dynamics at ∼20 ps resolution by the pump/delayed ionization technique. The S1 lifetime increases with the number of ν1 ' quanta from τ = 930 ps at v1 '=0 to 1030 ps at v1 '=2, decreasing to 14 ps at 710 cm-1 vibrational energy. We measured the rate constants for S1 ⇝ S0 internal conversion and S1 ⇝ T1 intersystem crossing (ISC): At the v' = 0 level, kIC is 8 × 108 s-1 or three times smaller than 1-methylcytosine. The ISC rate constant from v' = 0 to the T1(3ππ*) state is kISC = 2.4 × 108 s-1, 10 times smaller than the ISC rate constants of cytosine, but similar to that of 1-methylcytosine. Based on the calculated S1(1ππ*) state radiative lifetime τrad = 12 ns, the fluorescence quantum yield of 1ECyt is Φfl ∼ 7% and the intersystem crossing yield is ΦISC ∼ 20%. We measured the adiabatic ionization energy of 1-ethylcytosine via excitation of the S1 state as 8.353 ± 0.008 eV, which is 0.38 eV lower than that of amino-keto cytosine. Measurement of the ionization energy of the long-lived T1(ππ*) state formed via ISC reveals that it lies 3.2-3.4 eV above the S0 ground state.
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Affiliation(s)
- Maria A Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Susan Blaser
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Luca Siffert
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Timo Wiedmer
- 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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10
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Wu XK, Tang XF, Zhou XG, Liu SL. Dissociation dynamics of energy-selected ions using threshold photoelectron-photoion coincidence velocity imaging. CHINESE J CHEM PHYS 2019. [DOI: 10.1063/1674-0068/cjcp1811257] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xiang-kun Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xiao-feng Tang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031, China
| | - Xiao-guo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Shi-lin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
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11
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Zhang Y, Xie P, Yang S, Han K. Ionization and Electron Attachment for Nucleobases in Water. J Phys Chem B 2019; 123:1237-1247. [DOI: 10.1021/acs.jpcb.8b09435] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yan Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao, Binhai Road 72, Qingdao 266237, China
| | - Peng Xie
- School of Chemistry & Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
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12
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Wei SC, Ho JW, Yen HC, Shi HQ, Cheng LH, Weng CN, Chou WK, Chiu CC, Cheng PY. Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents. J Phys Chem A 2018; 122:9412-9425. [PMID: 30452255 DOI: 10.1021/acs.jpca.8b09526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microsolvation effects on the ultrafast excited-state deactivation dynamics of cytosine (Cy) were studied in hydrogen-bonded Cy clusters with protic and aprotic solvents using mass-resolved femtosecond pump-probe ionization spectroscopy. Two protic solvents, water (H2O) and methanol (MeOH), and one aprotic solvent, tetrahydrofuran (THF), were investigated, and transients of Cy·(H2O)1-6, Cy·(MeOH)1-3, and Cy·THF microsolvated clusters produced in supersonic expansions were measured. With the aid of electronic structure calculations, we assigned the observed dynamics to the low-energy isomers of various Cy clusters and discussed the microsolvation effect on the excited-state deactivation dynamics. With the protic solvents only the microsolvated clusters of Cy keto tautomer were observed. The observed decay time constants of Cy·(H2O) n are 0.5 ps for n = 1 and ∼0.2-0.25 ps for n = 2-6. For Cy·(MeOH) n clusters, the decay time constant for n = 1 cluster is similar to that of the Cy monohydrate, but for n = 2 and 3 the decays are about a factor of 2 slower than the corresponding microhydrates. With the aprotic solvent, THF, hydrogen-bonded complexes of both keto and enol tautomers are present in the beam. The keto-Cy·THF shows a decay similar to that of the keto-Cy monomer, whereas the enol-Cy·THF exhibits a 2-fold slower decay than the enol-Cy monomer, suggesting an increase in the barrier to excited-state deactivation upon binding of one THF molecule to the enol form of Cy.
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Affiliation(s)
- Shih-Chun Wei
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Jr-Wei Ho
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Hung-Chien Yen
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Hui-Qi Shi
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Li-Hao Cheng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Chih-Nan Weng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Wei-Kuang Chou
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Chih-Chung Chiu
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Po-Yuan Cheng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
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13
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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14
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Krylov AI. The Quantum Chemistry of Open-Shell Species. REVIEWS IN COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1002/9781119356059.ch4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anna I. Krylov
- Department of Chemistry; University of Southern California; Los Angeles CA United States
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15
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González J, Usabiaga I, Arnaiz PF, León I, Martínez R, Millán J, Fernández JA. Competition between stacked and hydrogen bonded structures of cytosine aggregates. Phys Chem Chem Phys 2017; 19:8826-8834. [DOI: 10.1039/c6cp08476a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The four bases of DNA constitute what is known as the “alphabet of life”.
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Affiliation(s)
- Jorge González
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Imanol Usabiaga
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Pedro F. Arnaiz
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Iker León
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Rodrigo Martínez
- Department of Chemistry
- Faculty of Science and Technology
- University of La Rioja
- Logroño
- Spain
| | - Judith Millán
- Department of Chemistry
- Faculty of Science and Technology
- University of La Rioja
- Logroño
- Spain
| | - José A. Fernández
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
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16
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Hochlaf M. Advances in spectroscopy and dynamics of small and medium sized molecules and clusters. Phys Chem Chem Phys 2017; 19:21236-21261. [DOI: 10.1039/c7cp01980g] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Investigations of the spectroscopy and dynamics of small- and medium-sized molecules and clusters represent a hot topic in atmospheric chemistry, biology, physics, atto- and femto-chemistry and astrophysics.
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Affiliation(s)
- Majdi Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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17
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Chen Z, Lau KC, Garcia GA, Nahon L, Božanić DK, Poisson L, Al-Mogren MM, Schwell M, Francisco JS, Bellili A, Hochlaf M. Identifying Cytosine-Specific Isomers via High-Accuracy Single Photon Ionization. J Am Chem Soc 2016; 138:16596-16599. [DOI: 10.1021/jacs.6b10413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Ziyong Chen
- Department
of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Kai-Chung Lau
- Department
of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Gustavo A. Garcia
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Dušan K. Božanić
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Lionel Poisson
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, F-91191 Gif-sur-Yvette, France
| | - Muneerah Mogren Al-Mogren
- Chemistry
Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Martin Schwell
- Laboratoire
Interuniversitaire des Systèmes Atmosphériques (LISA),
UMR 7583 CNRS, Universités Paris-Est Créteil et Paris Diderot, 61 Avenue du Général de Gaulle, 94010 Créteil, France
| | - Joseph S. Francisco
- Department
of Chemistry, University of Nebraska-Lincoln. 433 Hamilton Hall, Lincoln, Nebraska 68588-0304, United States
| | - Ayad Bellili
- Laboratoire
Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est. 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Majdi Hochlaf
- Laboratoire
Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est. 5 bd Descartes, 77454 Marne-la-Vallée, France
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18
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Ruckenbauer M, Mai S, Marquetand P, González L. Revealing Deactivation Pathways Hidden in Time-Resolved Photoelectron Spectra. Sci Rep 2016; 6:35522. [PMID: 27762396 PMCID: PMC5071879 DOI: 10.1038/srep35522] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/27/2016] [Indexed: 11/09/2022] Open
Abstract
Time-resolved photoelectron spectroscopy is commonly employed with the intention to monitor electronic excited-state dynamics occurring in a neutral molecule. With the help of theory, we show that when excited-state processes occur on similar time scales the different relaxation pathways are completely obscured in the total photoionization signal recorded in the experiment. Using non-adiabatic molecular dynamics and Dyson norms, we calculate the photoionization signal of cytosine and disentangle the transient contributions originating from the different deactivation pathways of its tautomers. In the simulations, the total signal from the relevant keto and enol tautomers can be decomposed into contributions either from the neutral electronic state populations or from the distinct mechanistic pathways across the multiple potential surfaces. The lifetimes corresponding to these contributions cannot be extracted from the experiment, thereby illustrating that new experimental setups are necessary to unravel the intricate non-adiabatic pathways occurring in polyatomic molecules after irradiation by light.
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Affiliation(s)
- Matthias Ruckenbauer
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
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19
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Trachsel MA, Wiedmer T, Blaser S, Frey HM, Li Q, Ruiz-Barragan S, Blancafort L, Leutwyler S. The excited-state structure, vibrations, lifetimes, and nonradiative dynamics of jet-cooled 1-methylcytosine. J Chem Phys 2016; 145:134307. [DOI: 10.1063/1.4964091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Maria A. Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Timo Wiedmer
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Susan Blaser
- 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
| | - Quansong Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, 100081 Beijing, China
| | - Sergi Ruiz-Barragan
- Lehrstuhl für Theoretische Chemie, Ruhr-Universitat Bochum, 44780 Bochum, Germany
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Facultat de Ciències, C/ M. Aurèlia Campmany 69, 17003 Girona, Spain
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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20
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Rubovič P, Pysanenko A, Lengyel J, Nachtigallová D, Fárník M. Biomolecule Analogues 2-Hydroxypyridine and 2-Pyridone Base Pairing on Ice Nanoparticles. J Phys Chem A 2016; 120:4720-30. [PMID: 26785038 DOI: 10.1021/acs.jpca.5b11359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters.
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Affiliation(s)
- Peter Rubovič
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Andriy Pysanenko
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Jozef Lengyel
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
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21
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Nguyen NL, Borghi G, Ferretti A, Marzari N. First-Principles Photoemission Spectroscopy of DNA and RNA Nucleobases from Koopmans-Compliant Functionals. J Chem Theory Comput 2016; 12:3948-58. [DOI: 10.1021/acs.jctc.6b00145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ngoc Linh Nguyen
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giovanni Borghi
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Centro
S3, CNR−Istituto Nanoscienze, 41125 Modena, Italy
| | | | - Nicola Marzari
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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22
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Kostko O, Bandyopadhyay B, Ahmed M. Vacuum Ultraviolet Photoionization of Complex Chemical Systems. Annu Rev Phys Chem 2016; 67:19-40. [DOI: 10.1146/annurev-physchem-040215-112553] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Oleg Kostko
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Biswajit Bandyopadhyay
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
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23
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Lobsiger S, Etinski M, Blaser S, Frey HM, Marian C, Leutwyler S. Intersystem crossing rates of S1 state keto-amino cytosine at low excess energy. J Chem Phys 2016; 143:234301. [PMID: 26696056 DOI: 10.1063/1.4937375] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The amino-keto tautomer of supersonic jet-cooled cytosine undergoes intersystem crossing (ISC) from the v = 0 and low-lying vibronic levels of its S1((1)ππ(∗)) state. We investigate these ISC rates experimentally and theoretically as a function of S1 state vibrational excess energy Eexc. The S1 vibronic levels are pumped with a ∼5 ns UV laser, the S1 and triplet state ion signals are separated by prompt or delayed ionization with a second UV laser pulse. After correcting the raw ISC yields for the relative S1 and T1 ionization cross sections, we obtain energy dependent ISC quantum yields QISC (corr)=1%-5%. These are combined with previously measured vibronic state-specific decay rates, giving ISC rates kISC = 0.4-1.5 ⋅ 10(9) s(-1), the corresponding S1⇝S0 internal conversion (IC) rates are 30-100 times larger. Theoretical ISC rates are computed using SCS-CC2 methods, which predict rapid ISC from the S1; v = 0 state with kISC = 3 ⋅ 10(9) s(-1) to the T1((3)ππ(∗)) triplet state. The surprisingly high rate of this El Sayed-forbidden transition is caused by a substantial admixture of (1)nOπ(∗) character into the S1((1)ππ(∗)) wave function at its non-planar minimum geometry. The combination of experiment and theory implies that (1) below Eexc = 550 cm(-1) in the S1 state, S1⇝S0 internal conversion dominates the nonradiative decay with kIC ≥ 2 ⋅ 10(10) s(-1), (2) the calculated S1⇝T1 ((1)ππ(∗)⇝(3)ππ(∗)) ISC rate is in good agreement with experiment, (3) being El-Sayed forbidden, the S1⇝T1 ISC is moderately fast (kISC = 3 ⋅ 10(9) s(-1)), and not ultrafast, as claimed by other calculations, and (4) at Eexc ∼ 550 cm(-1) the IC rate increases by ∼50 times, probably by accessing the lowest conical intersection (the C5-twist CI) and thereby effectively switching off the ISC decay channels.
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Affiliation(s)
- Simon Lobsiger
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Mihajlo Etinski
- Fakultet za Fizičku Hemiju, Univerzitet u Beogradu, Studentski Trg 12-16, SRB-11000 Beograd, Serbia
| | - Susan Blaser
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Christel Marian
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine Universität, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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24
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Fulfer KD, Hardy D, Aguilar AA, Poliakoff ED. High-resolution photoelectron spectra of the pyrimidine-type nucleobases. J Chem Phys 2015; 142:224310. [DOI: 10.1063/1.4922310] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- K. D. Fulfer
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - D. Hardy
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - A. A. Aguilar
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - E. D. Poliakoff
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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25
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Riml C, Glasner H, Rodgers MT, Micura R, Breuker K. On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent. Nucleic Acids Res 2015; 43:5171-81. [PMID: 25904631 PMCID: PMC4446422 DOI: 10.1093/nar/gkv288] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/14/2015] [Accepted: 03/24/2015] [Indexed: 12/18/2022] Open
Abstract
Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in 'top-down' strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)(n+) and (M-nH)(n-) ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into C: and Y: ions from phosphodiester bond cleavage.
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Affiliation(s)
- Christian Riml
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Heidelinde Glasner
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - M T Rodgers
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202-3489, United States
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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26
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Bull JN, Lee JWL, Vallance C. Absolute electron total ionization cross-sections: molecular analogues of DNA and RNA nucleobase and sugar constituents. Phys Chem Chem Phys 2015; 16:10743-52. [PMID: 24756123 DOI: 10.1039/c4cp00490f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Accurate ionization cross-sections for DNA and RNA constituents in the condensed or aqueous phase are important parameters for models simulating radiation damage to genetic material in living cells. In this work, absolute gas-phase electron total ionization cross-sections (TICSs) have been measured for a series of six aromatic and eight non-aromatic cyclic species that can be considered as prototype functional group analogues for the nucleobases and sugar backbone constituents of DNA and RNA. TICSs for water, hexane, and ethylacetamide (a peptide bond analogue) are also reported. The experimental apparatus utilizes a cylindrical ion collector that surrounds the ionization region, providing essentially unit detection efficiency. Two theoretical models, the polarizability-correlation method and binary-encounter Bethe theory, are able to reproduce the measured maximum TICS well for all species studied. An empirical energy-dependent correction is found to yield improvement in the agreement between experimental energy-dependent cross sections and the predictions of the BEB model. Having characterised and optimised the performance of both models, they are then used to predict TICSs for gas-phase DNA and RNA nucleobases and sugars. Direct experimental determinations of TICSs for these species are difficult because of their low volatility, which makes it difficult to prepare suitable gas-phase samples for measurement.
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Affiliation(s)
- James N Bull
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
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27
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Nakayama A, Yamazaki S, Taketsugu T. Quantum Chemical Investigations on the Nonradiative Deactivation Pathways of Cytosine Derivatives. J Phys Chem A 2014; 118:9429-37. [DOI: 10.1021/jp506740r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akira Nakayama
- Catalysis
Research Center, Hokkaido University, Sapporo 001-0021, Japan
| | - 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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28
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Das T, Ghosh D. Ionization-Induced Tautomerization in Cytosine and Effect of Solvation. J Phys Chem A 2014; 118:5323-32. [DOI: 10.1021/jp503947d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tamal Das
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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29
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Frey JA, Ottiger P, Leutwyler S. Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone. J Phys Chem B 2014; 118:682-91. [DOI: 10.1021/jp409660b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jann A. Frey
- Department
of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Philipp Ottiger
- 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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30
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Schwell M, Hochlaf M. Photoionization Spectroscopy of Nucleobases and Analogues in the Gas Phase Using Synchrotron Radiation as Excitation Light Source. Top Curr Chem (Cham) 2014; 355:155-208. [DOI: 10.1007/128_2014_550] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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31
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Khistyaev K, Golan A, Bravaya KB, Orms N, Krylov AI, Ahmed M. Proton Transfer in Nucleobases is Mediated by Water. J Phys Chem A 2013; 117:6789-97. [DOI: 10.1021/jp406029p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Amir Golan
- Chemical Sciences
Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Natalie Orms
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Musahid Ahmed
- Chemical Sciences
Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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32
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Li W, Hu Y, Guan J, Liu F, Shan X, Sheng L. Site-selective ionization of ethanol dimer under the tunable synchrotron VUV radiation and its subsequent fragmentation. J Chem Phys 2013; 139:024307. [DOI: 10.1063/1.4812780] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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33
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Touboul D, Gaie-Levrel F, Garcia GA, Nahon L, Poisson L, Schwell M, Hochlaf M. VUV photoionization of gas phase adenine and cytosine: A comparison between oven and aerosol vaporization. J Chem Phys 2013; 138:094203. [DOI: 10.1063/1.4793734] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Nakayama A, Harabuchi Y, Yamazaki S, Taketsugu T. Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:12322-39. [DOI: 10.1039/c3cp51617b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Lobsiger S, Leutwyler S. The Adiabatic Ionization Energy and Triplet T1 Energy of Jet-Cooled Keto-Amino Cytosine. J Phys Chem Lett 2012; 3:3576-3580. [PMID: 26290991 DOI: 10.1021/jz301719h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Gas-phase cytosine exists in five different tautomer/rotamer forms 1, 2a, 2b, 3a, and 3b. We determine the threshold ionization energy (IE) of the keto-amino tautomer 1 as 8.73 ± 0.02 eV, using resonant two-photon ionization mass spectrometry in a supersonic molecular beam via the (1)ππ* excited state. This is the first IE threshold measurement for the biologically relevant tautomer 1. The IE of the thermal gas-phase mixture of cytosine has been measured as 8.60 ± 0.05 eV by Kostko et al. using single-photon VUV photoionization [Phys. Chem. Chem. Phys., 2010, 12, 2860]. Given the tautomer distribution and ionization energies calculated in that work, our determination of the keto-amino tautomer IE implies that the IE measured by Kostko et al. is dominated by the enol-amino tautomers 2a and 2b. Upon excitation of keto-amino cytosine to its (1)ππ* state, relaxation occurs to a lower-lying long-lived state. The IE threshold measured via this state places its energy about 0.69 eV below the (1)ππ* state, in good agreement with the triplet T1 energy of keto-amino cytosine calculated by several high-level ab initio methods. The identification of keto-amino cytosine T1 is the basis for characterizing the intersystem crossing rates into and the photochemical reactions of this long-lived state.
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Affiliation(s)
- Simon Lobsiger
- 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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36
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Gozem S, Krylov AI, Olivucci M. Conical Intersection and Potential Energy Surface Features of a Model Retinal Chromophore: Comparison of EOM-CC and Multireference Methods. J Chem Theory Comput 2012; 9:284-92. [DOI: 10.1021/ct300759z] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samer Gozem
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
| | - Anna I. Krylov
- Department of Chemistry, University
of Southern California, Los Angeles, California 90089-0482, United
States
| | - Massimo Olivucci
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Chimica,
Università
di Siena, via De Gasperi 2, I-53100 Siena, Italy
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37
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Golan A, Ahmed M. Molecular beam mass spectrometry with tunable vacuum ultraviolet (VUV) synchrotron radiation. J Vis Exp 2012:50164. [PMID: 23149375 DOI: 10.3791/50164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Tunable soft ionization coupled to mass spectroscopy is a powerful method to investigate isolated molecules, complexes and clusters and their spectroscopy and dynamics(1-4). Fundamental studies of photoionization processes of biomolecules provide information about the electronic structure of these systems. Furthermore determinations of ionization energies and other properties of biomolecules in the gas phase are not trivial, and these experiments provide a platform to generate these data. We have developed a thermal vaporization technique coupled with supersonic molecular beams that provides a gentle way to transport these species into the gas phase. Judicious combination of source gas and temperature allows for formation of dimers and higher clusters of the DNA bases. The focus of this particular work is on the effects of non-covalent interactions, i.e., hydrogen bonding, stacking, and electrostatic interactions, on the ionization energies and proton transfer of individual biomolecules, their complexes and upon micro-hydration by water(1, 5-9). We have performed experimental and theoretical characterization of the photoionization dynamics of gas-phase uracil and 1,3-dimethyluracil dimers using molecular beams coupled with synchrotron radiation at the Chemical Dynamics Beamline(10) located at the Advanced Light Source and the experimental details are visualized here. This allowed us to observe the proton transfer in 1,3-dimethyluracil dimers, a system with pi stacking geometry and with no hydrogen bonds(1). Molecular beams provide a very convenient and efficient way to isolate the sample of interest from environmental perturbations which in return allows accurate comparison with electronic structure calculations(11, 12). By tuning the photon energy from the synchrotron, a photoionization efficiency (PIE) curve can be plotted which informs us about the cationic electronic states. These values can then be compared to theoretical models and calculations and in turn, explain in detail the electronic structure and dynamics of the investigated species (1, 3).
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Affiliation(s)
- Amir Golan
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
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38
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Guan J, Hu Y, Zou H, Cao L, Liu F, Shan X, Sheng L. Competitive fragmentation pathways of acetic acid dimer explored by synchrotron VUV photoionization mass spectrometry and electronic structure calculations. J Chem Phys 2012; 137:124308. [DOI: 10.1063/1.4754273] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Bravaya KB, Epifanovsky E, Krylov AI. Four Bases Score a Run: Ab Initio Calculations Quantify a Cooperative Effect of H-Bonding and π-Stacking on the Ionization Energy of Adenine in the AATT Tetramer. J Phys Chem Lett 2012; 3:2726-2732. [PMID: 26295899 DOI: 10.1021/jz3011139] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Benchmark calculations of the lowest ionized state of the (A:T)2 (mixed adenine-thymine) cluster at the geometry taken from the DNA X-ray structure are presented. Vertical ionization energies (IEs) computed by the equation-of-motion coupled-cluster method with single and double substitutions are reported and analyzed. The shift in IE relative to the monomer (A) is -0.7 eV. The performance of the widely used B3LYP, ωB97X-D, and M06-2X functionals with respect to their ability to describe energetics and the character (localization versus delocalization) of the ionized states is also investigated. The shifts in IEs caused by H-bonding and stacking interactions are analyzed in terms of additive versus cooperative effects. It is found that the cooperative effect accounts for more than 20% of the shift in IE relative to the monomer. The cooperative effect and, consequently, the magnitude of the shift are well reproduced by the hybrid quantum mechanics/molecular mechanics scheme in which neutral thymine bases are represented by point charges.
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Affiliation(s)
- Ksenia B Bravaya
- †Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Evgeny Epifanovsky
- †Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
- ‡Department of Chemistry, University of California, Berkeley, California 94720, United States and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Anna I Krylov
- †Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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40
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Cauët E, Carette T, Lauzin C, Li JG, Loreau J, Delsaut M, Nazé C, Verdebout S, Vranckx S, Godefroid M, Liévin J, Vaeck N. From atoms to biomolecules: a fruitful perspective. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1254-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Ghosh D, Roy A, Seidel R, Winter B, Bradforth S, Krylov AI. First-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: theory and application to aqueous phenol and phenolate. J Phys Chem B 2012; 116:7269-80. [PMID: 22497288 PMCID: PMC3381078 DOI: 10.1021/jp301925k] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP) and determined experimentally by valence photoemission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (ΔVIEs) are -0.66 and +5.72 eV for phenol and phenolate, respectively. Our best estimates of the absolute values of VIEs (7.9 and 7.7 eV for phenol and phenolate) agree reasonably well with the respective experimental values (7.8 ± 0.1 and 7.1 ± 0.1 eV). The EOM/EFP scheme was benchmarked against full EOM-IP-CCSD using microsolvated phenol and phenolate clusters. A protocol for calculating redox potentials with EOM/EFP was developed based on linear response approximation (LRA) of free energy determination. The oxidation potentials of phenol and phenolate calculated using LRA and EOM/EFP are 1.32 and 0.89 V, respectively; they agree well with experimental values.
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Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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42
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Reva I, Nowak MJ, Lapinski L, Fausto R. Spontaneous tunneling and near-infrared-induced interconversion between the amino-hydroxy conformers of cytosine. J Chem Phys 2012; 136:064511. [DOI: 10.1063/1.3683217] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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43
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Zhang J, Valeev EF. Hybrid one-electron/many-electron methods for ionized states of molecular clusters. Phys Chem Chem Phys 2012; 14:7863-71. [DOI: 10.1039/c2cp40222j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Domingo A, Rodríguez-Fortea A, de Graaf C. The Absorption Spectrum of Cytosine Tautomers: Beyond the Static Approach. J Chem Theory Comput 2011; 8:235-44. [DOI: 10.1021/ct2007023] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alex Domingo
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Antonio Rodríguez-Fortea
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Coen de Graaf
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, 43007 Tarragona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Kostko O, Takahashi LK, Ahmed M. Desorption dynamics, internal energies, and imaging of organic molecules from surfaces with laser desorption and vacuum ultraviolet (VUV) photoionization. Chem Asian J 2011; 6:3066-76. [PMID: 21976383 DOI: 10.1002/asia.201100419] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Indexed: 11/11/2022]
Abstract
There is enormous interest in visualizing the chemical composition of organic material that comprises our world. A convenient method to obtain molecular information with high spatial resolution is imaging mass spectrometry. However, the internal energy deposited within molecules upon transfer to the gas phase from a surface can lead to increased fragmentation and to complications in analysis of mass spectra. Here it is shown that in laser desorption with postionization by tunable vacuum ultraviolet (VUV) radiation, the internal energy gained during laser desorption leads to minimal fragmentation of DNA bases. The internal temperature of laser-desorbed triacontane molecules approaches 670 K, whereas the internal temperature of thymine is 800 K. A synchrotron-based VUV postionization technique for determining translational temperatures reveals that biomolecules have translational temperatures in the range of 216-346 K. The observed low translational temperatures as well as their decrease with increased desorption laser power is explained by collisional cooling. An example of imaging mass spectrometry on an organic polymer by using laser-desorption VUV postionization shows 5 μm feature details while using a 30 μm laser spot size and 7 ns pulse duration. Applications of laser-desorption postionization to the analysis of cellulose, lignin, and humic acids are briefly discussed.
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Affiliation(s)
- Oleg Kostko
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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46
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Ho JW, Yen HC, Chou WK, Weng CN, Cheng LH, Shi HQ, Lai SH, Cheng PY. Disentangling Intrinsic Ultrafast Excited-State Dynamics of Cytosine Tautomers. J Phys Chem A 2011; 115:8406-18. [DOI: 10.1021/jp205603w] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ghosh D, Isayev O, Slipchenko LV, Krylov AI. Effect of solvation on the vertical ionization energy of thymine: from microhydration to bulk. J Phys Chem A 2011; 115:6028-38. [PMID: 21500795 PMCID: PMC3116069 DOI: 10.1021/jp110438c] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent-solute configurations obtained from equilibrium molecular dynamics trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule, while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine's VIE is approximately -0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute-solvent interactions, which were investigated using model structures. The convergence of IE to the bulk value requires the hydration sphere of approximately 13.5 Å radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01-0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated.
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Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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Melvin Blaze M, Takahashi LK, Zhou J, Ahmed M, Gasper GL, Pleticha FD, Hanley L. Brominated tyrosine and polyelectrolyte multilayer analysis by laser desorption vacuum ultraviolet postionization and secondary ion mass spectrometry. Anal Chem 2011; 83:4962-9. [PMID: 21548612 PMCID: PMC3115520 DOI: 10.1021/ac200693h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The small molecular analyte 3,5-dibromotyrosine (Br(2)Y) and chitosan-alginate polyelectrolyte multilayers (PEM) with and without adsorbed Br(2)Y were analyzed by laser desorption postionization-mass spectrometry (LDPI-MS). LDPI-MS using a 7.87 eV laser and tunable 8-12.5 eV synchrotron vacuum ultraviolet (VUV) radiation found that desorption of clusters from Br(2)Y films allowed detection by ≤8 eV single photon ionization. Thermal desorption and electronic structure calculations determined the ionization energy of Br(2)Y to be ~8.3 ± 0.1 eV and further indicated that the lower ionization energies of clusters permitted their detection at ≤8 eV photon energies. However, single photon ionization could only detect Br(2)Y adsorbed within PEMs when using either higher photon energies or matrix addition to the sample. All samples were also analyzed by 25 keV Bi(3)(+) secondary ion mass spectrometry (SIMS), with the negative ion spectra showing strong parent ion signal which complemented that observed by LDPI-MS. However, the negative ion SIMS appeared strongly dependent on the high electron affinity of this specific analyte and the analyte's condensed phase environment.
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Affiliation(s)
- M.T. Melvin Blaze
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607
| | - Lynelle K. Takahashi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Jia Zhou
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Gerald L. Gasper
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607
| | - F. Douglas Pleticha
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607
| | - Luke Hanley
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607
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Abstract
Abstract
The threshold photoelectron spectrum of NTCDA (1,4,5,8-naphthalene-tetracarboxylic dianhydride) has been recorded using synchrotron radiation. An ionization energy of 9.66 eV was observed. The experiments are supported by DFT computations that yield a value of 9.51 eV, in good agreement with the measured value. Several bands corresponding to excited electronic states of the cation are also visible and can be assigned with the aid of computations.
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Affiliation(s)
- Kathrin H. Fischer
- Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Würzburg, Deutschland
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50
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Khistyaev K, Bravaya KB, Kamarchik E, Kostko O, Ahmed M, Krylov AI. The effect of microhydration on ionization energies of thymine. Faraday Discuss 2011; 150:313-30; discussion 391-418. [DOI: 10.1039/c0fd00002g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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