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Bull GD, Thompson KC. The oxidation of guanine by photoionized 2-aminopurine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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2
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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: 1.0] [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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Siffert L, Blaser S, Ottiger P, Leutwyler S. Transition from Water Wires to Bifurcated H-Bond Networks in 2-Pyridone·(H2O)n, n = 1–4 Clusters. J Phys Chem A 2018; 122:9285-9297. [DOI: 10.1021/acs.jpca.8b09410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Luca Siffert
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Susan Blaser
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Philipp Ottiger
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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4
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Trachsel MA, Lobsiger S, Schär T, Blancafort L, Leutwyler S. Planarizing cytosine: The S 1 state structure, vibrations, and nonradiative dynamics of jet-cooled 5,6-trimethylenecytosine. J Chem Phys 2018; 146:244308. [PMID: 28668059 DOI: 10.1063/1.4989465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We measure the S0 → S1 spectrum and time-resolved S1 state nonradiative dynamics of the "clamped" cytosine derivative 5,6-trimethylenecytosine (TMCyt) in a supersonic jet, using two-color resonant two-photon ionization (R2PI), UV/UV holeburning, and ns time-resolved pump/delayed ionization. The experiments are complemented with spin-component scaled second-order approximate coupled cluster (SCS-CC2), time-dependent density functional theory, and multi-state second-order perturbation-theory (MS-CASPT2) ab initio calculations. While the R2PI spectrum of cytosine breaks off ∼500 cm-1 above its 000 band, that of TMCyt extends up to +4400 cm-1 higher, with over a hundred resolved vibronic bands. Thus, clamping the cytosine C5-C6 bond allows us to explore the S1 state vibrations and S0 → S1 geometry changes in detail. The TMCyt S1 state out-of-plane vibrations ν1', ν3', and ν5' lie below 420 cm-1, and the in-plane ν11', ν12', and ν23' vibrational fundamentals appear at 450, 470, and 944 cm-1. S0 → S1 vibronic simulations based on SCS-CC2 calculations agree well with experiment if the calculated ν1', ν3', and ν5' frequencies are reduced by a factor of 2-3. MS-CASPT2 calculations predict that the ethylene-type S1 ⇝ S0 conical intersection (CI) increases from +366 cm-1 in cytosine to >6000 cm-1 in TMCyt, explaining the long lifetime and extended S0 → S1 spectrum. The lowest-energy S1 ⇝ S0 CI of TMCyt is the "amino out-of-plane" (OPX) intersection, calculated at +4190 cm-1. The experimental S1 ⇝ S0 internal conversion rate constant at the S1(v'=0) level is kIC=0.98-2.2⋅108 s-1, which is ∼10 times smaller than in 1-methylcytosine and cytosine. The S1(v'=0) level relaxes into the T1(3ππ*) state by intersystem crossing with kISC=0.41-1.6⋅108 s-1. The T1 state energy is measured to lie 24 580±560 cm-1 above the S0 state. The S1(v'=0) lifetime is τ=2.9 ns, resulting in an estimated fluorescence quantum yield of Φfl=24%. Intense two-color R2PI spectra of the TMCyt amino-enol tautomers appear above 36 000 cm-1. A sharp S1 ionization threshold is observed for amino-keto TMCyt, yielding an adiabatic ionization energy of 8.114±0.002 eV.
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Affiliation(s)
- Maria A Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Tobias Schär
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Facultat de Ciències, Universitat de Girona, C/M. A. 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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5
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Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Orr-Ewing AJ, Temps F. Efficient intersystem crossing in 2-aminopurine riboside probed by femtosecond time-resolved transient vibrational absorption spectroscopy. Phys Chem Chem Phys 2018; 20:20033-20042. [DOI: 10.1039/c8cp02664e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The photophysical dynamics of 2-aminopurine, a fluorescent analogue of the canonical nucleobase adenine, has been studied by femtosecond transient vibrational absorption spectroscopy.
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Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | - Katharina Röttger
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
- School of Chemistry
| | | | | | - Mats Bohnsack
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | | | - Friedrich Temps
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
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Min A, Ahn A, Moon CJ, Lee JH, Seong YG, Kim SK, Choi MY. Conformational structures of jet-cooled acetaminophen-water clusters: a gas phase spectroscopic and computational study. Phys Chem Chem Phys 2017; 19:4840-4848. [PMID: 28134364 DOI: 10.1039/c6cp06863d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Jet-cooled acetaminophen (AAP)-water clusters, AAP-(H2O)1, were investigated by mass-selected resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole-burning (UV-UV HB), infrared-dip (IR-dip), and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy. Each syn- and anti-AAP rotamer has three distinctive binding sites (-OH, >CO, and >NH) for a water molecule, thus 6 different AAP-(H2O)1 conformers are expected to exist in the molecular beam. The origin bands of the AAP(OH)-(H2O)1 and AAP(CO)-(H2O)1 conformers (including their syn- and anti-conformers) in the R2PI spectrum are shifted to red and blue compared to those of the AAP monomer, respectively. These frequency shifts upon complexation between a water molecule and a specific binding site of AAP are also predicted by theoretical calculations. The spectral assignments of the origin bands in the R2PI spectra and the IR vibrational bands in the IR-dip spectra of the four lowest-energy conformers of AAP-(H2O)1, [syn- and anti-AAP(OH)-(H2O)1 and syn- and anti-AAP(CO)-(H2O)1], are aided by ab initio and time-dependent density functional theory (TDDFT) calculations. Further investigation of the IR-dip spectra has revealed a hydrogen-bonded NH stretching mode, supporting the presence of the syn-AAP(NH)-(H2O)1 conformer. Moreover, by employing IR-UV HB spectroscopy, we have reconfirmed the existence of the syn-AAP(NH)-(H2O)1 conformer, which happened to be buried underneath the broad background contributed by the AAP(OH)-(H2O)1 conformers. These observations have led us to conclude that all of the possible conformers of AAP-(H2O)1 have been found in this study.
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Affiliation(s)
- Ahreum Min
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ahreum Ahn
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Cheol Joo Moon
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ji Hoon Lee
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Yeon Guk Seong
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Myong Yong Choi
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
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7
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2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
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Bhattacherjee A, Wategaonkar S. Conformational preferences of monohydrated clusters of imidazole derivatives revisited. Phys Chem Chem Phys 2015; 17:20080-92. [DOI: 10.1039/c5cp02422f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IR-UV double resonance spectroscopy was used to identify the conformers of monohydrated benzimidazole andN-methylbenzimidazole in a supersonic jet. A new OH–N bound conformer relevant to histidine containing proteins was discovered. The long standing differences in the literature about the relative energies and abundance of the monohydrated imidazole derivatives have also been resolved.
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Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
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9
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Abstract
Depending on where it binds, a water molecule may change the excited-state lifetime of 2-aminopurine by a factor of 100. We explain why?
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim an der Ruhr
- Germany
| | - Hans Lischka
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
- Institute for Theoretical Chemistry
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10
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Switching on the fluorescence of 2-aminopurine by site-selective microhydration. Nat Chem 2014; 6:989-93. [DOI: 10.1038/nchem.2086] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 09/11/2014] [Indexed: 11/08/2022]
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Trachsel MA, Lobsiger S, Schär T, Leutwyler S. Low-lying excited states and nonradiative processes of 9-methyl-2-aminopurine. J Chem Phys 2014; 140:044331. [DOI: 10.1063/1.4862913] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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12
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Reid SA, Nyambo S, Kalume A, Uhler B, Karshenas C, Muzangwa L. Reactive pathways in the chlorobenzene-ammonia dimer cation radical: new insights from experiment and theory. J Phys Chem A 2013; 117:12429-37. [PMID: 24156288 DOI: 10.1021/jp4097315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Building upon our recent studies of noncovalent interactions in chlorobenzene and bromobenzene clusters, in this work we focus on interactions of chlorobenzene (PhCl) with a prototypical N atom donor, ammonia (NH3). Thus, we have obtained electronic spectra of PhCl···(NH3)n (n = 1-3) complexes in the region of the PhCl monomer S0 -S1 (ππ*) transition using resonant 2-photon ionization (R2PI) methods combined with time-of-flight mass analysis. Consistent with previous studies, we find that upon ionization the PhCl···NH3 dimer cation radical reacts primarily via Cl atom loss. A second channel, HCl loss, is identified for the first time in R2PI studies of the 1:1 complex, and a third channel, H atom loss, is identified for the first time. While prior studies have assumed the dominance of a π-type complex, we find that the reactive complex corresponds instead to an in-plane σ-type complex. This is supported by electronic structure calculations using density functional theory and post-Hartree-Fock methods and Franck-Condon analysis. The reactive pathways in this system were extensively characterized computationally, and consistent with results from previous calculations, we find two nearly isoenergetic arenium ions (Wheland intermediates; denoted WH1, WH2), which lie energetically below the initially formed dimer cation radical complex. At the energy of our experiment, intermediate WH1, produced from ipso-addition, is not stable with respect to Cl or HCl loss, and the relative branching between these channels observed in our experiment is well reproduced by microcanonical transition state theory calculations based upon the calculated parameters. Intermediate WH2, where NH3 adds ortho to the halogen, decomposes over a large barrier via H atom loss to form protonated o-chloroaniline. This channel is not open at the (2-photon) energy of our experiments, and it is suggested that photodissociation of a long-lived (i.e., several ns) WH2 intermediate leads to the observed products.
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Affiliation(s)
- Scott A Reid
- Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201-1881, United States
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13
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Lobsiger S, Sinha RK, Leutwyler S. Building Up Water-Wire Clusters: Isomer-Selective Ultraviolet and Infrared Spectra of Jet-Cooled 2-Aminopurine (H2O)n, n = 2 and 3. J Phys Chem B 2013; 117:12410-21. [DOI: 10.1021/jp407127c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Lobsiger
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
| | - Rajeev K. Sinha
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
- Department
of Atomic and Molecular Physics, Manipal University, Manipal-576104, Karnataka, India
| | - Samuel Leutwyler
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
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14
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Abou-Zied OK. Effect of NH2 rotation on the fluorescence of 2-aminopurine in solution. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Reichardt C, Wen C, Vogt RA, Crespo-Hernández CE. Role of intersystem crossing in the fluorescence quenching of 2-aminopurine 2′-deoxyriboside in solution. Photochem Photobiol Sci 2013; 12:1341-50. [DOI: 10.1039/c3pp25437b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Zhao GZ, Lu M. Density Functional Theory Studies on Intermolecular Interactions of 4-Amino-3,5-dinitropyrazole with NH3and H2O. J CHIN CHEM SOC-TAIP 2012. [DOI: 10.1002/jccs.201100378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Sinha RK, Lobsiger S, Leutwyler S. Isomer- and Species-Selective Infrared Spectroscopy of Jet-Cooled 7H- and 9H-2-Aminopurine and 2-Aminopurine·H2O Clusters. J Phys Chem A 2012; 116:1129-36. [DOI: 10.1021/jp2077177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajeev K. Sinha
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
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