201
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Hernández FJ, Bonafé FP, Aradi B, Frauenheim T, Sánchez CG. Simulation of Impulsive Vibrational Spectroscopy. J Phys Chem A 2019; 123:2065-2072. [DOI: 10.1021/acs.jpca.9b00307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Federico J. Hernández
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
| | - Franco P. Bonafé
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universität Bremen, Bremen 28359, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, Universität Bremen, Bremen 28359, Germany
| | - Cristián G. Sánchez
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
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202
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Segarra-Martí J, Tran T, Bearpark MJ. Ultrafast and radiationless electronic excited state decay of uracil and thymine cations: computing the effects of dynamic electron correlation. Phys Chem Chem Phys 2019; 21:14322-14330. [PMID: 30698175 DOI: 10.1039/c8cp07189f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this article we characterise the radiationless decay of the first few electronic excited states of the cations of DNA/RNA nucleobases uracil and thymine, including the effects of dynamic electron correlation on energies and geometries (optimised with XMS-CASPT2). In both systems, we find that one state of 2n and another two of 2π+ character can be populated following photoionisation, and their different minima and interstate crossings are located. We find strong similarities between uracil and thymine cations: with accessible conical intersections suggesting that depopulation of their electronic excited states takes place on ultrafast timescales in both systems, suggesting that they are photostable in agreement with previous theoretical (uracil+) evidence. We find that dynamic electron correlation separates the energy levels of the "3-state" conical intersection (D2/D1/D0)CI previously located with CASSCF for uracil+, which will therefore have a different geometry and higher energy. Simulating the electronic and vibrational absorptions allows us to characterise spectral fingerprints that could be used to monitor these cation photo-processes experimentally.
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Affiliation(s)
- Javier Segarra-Martí
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
| | - Thierry Tran
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
| | - Michael J Bearpark
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
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203
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Iwaura R. Construction of a DNA-Based Supramolecular Nanosheet That Emits Bluish-White Light from Charge-Transfer Excited States of the Nucleobases. Chemistry 2019; 25:2281-2287. [PMID: 30411410 DOI: 10.1002/chem.201804960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/06/2018] [Indexed: 12/26/2022]
Abstract
1,ω-Inosinic acid-bearing bolaamphiphiles dI(18), dI(19), and dI(20) with a 3'-phosphorylated inosine as a universal base connected to each end of an oligomethylene chain were synthesized for the first time. Single-component self-assemblies of these bolaamphiphiles and their binary self-assemblies with salmon sperm DNA were studied by AFM; temperature-dependent UV absorption, fluorescence, and circular dichroism spectroscopy; and gel electrophoresis. The binary self-assembly of dI(20) and salmon sperm DNA (dI(20)-DNA) had a nanosheet structure with a homogeneous thickness of about 6 nm and widths of several micrometers. Interestingly, an aqueous solution of the nanosheets showed a broad absorption band originating from the charge-transfer (CT) states of the nucleobase in the long-wavelength region (>300 nm), and the molar absorptivity per nucleobase was calculated to be approximately 150 times that of single-stranded (dT20 and dA20) and double-stranded (dT20-dA20) oligonucleotides. In addition, a continuous and broad emission band originating from CT excited states of the nucleobases was observed in the visible region. These observations indicate that CT states of the nucleobases were formed and stabilized in the supramolecular nanosheet and that bluish white light was emitted from CT excited states of the nucleobases.
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Affiliation(s)
- Rika Iwaura
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
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204
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Mato J, Gordon MS. Analytic Gradients for the Spin-Flip ORMAS-CI Method: Optimizing Minima, Saddle Points, and Conical Intersections. J Phys Chem A 2019; 123:1260-1272. [DOI: 10.1021/acs.jpca.8b11569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joani Mato
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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205
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Crespo-Otero R, Li Q, Blancafort L. Exploring Potential Energy Surfaces for Aggregation-Induced Emission-From Solution to Crystal. Chem Asian J 2019; 14:700-714. [PMID: 30548109 DOI: 10.1002/asia.201801649] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/07/2018] [Indexed: 11/12/2022]
Abstract
Aggregation-induced emission (AIE) is a phenomenon where non-luminescent compounds in solution become strongly luminescent in aggregate and solid phase. It provides a fertile ground for luminescent applications that has rapidly developed in the last 15 years. In this review, we focus on the contributions of theory and computations to understanding the molecular mechanism behind it. Starting from initial models, such as restriction of intramolecular rotations (RIR), and the calculation of non-radiative rates with Fermi's golden rule (FGR), we center on studies of the global excited-state potential energy surfaces that have provided the basis for the restricted access to a conical intersection (RACI) model. In this model, which has been shown to apply for a diverse group of AIEgens, the lack of fluorescence in solution comes from radiationless decay at a CI in solution that is hindered in the aggregate state. We also highlight how intermolecular interactions modulate the photophysics in the aggregate phase, in terms of fluorescence quantum yield and emission color.
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Affiliation(s)
- Rachel Crespo-Otero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Quansong Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Zhongguancun Street 5, 100081, Beijing, China
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi (IQCC) i Departament de Química, Facultat de Ciències, Universitat de Girona, C/M. A. Capmany 69, 17003, Girona, Spain
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206
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Marchetti B, Karsili TNV, Ashfold MNR. Exploring Norrish type I and type II reactions: an ab initio mechanistic study highlighting singlet-state mediated chemistry. Phys Chem Chem Phys 2019; 21:14418-14428. [DOI: 10.1039/c8cp07292b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Norrish reactions are important photo-induced reactions in mainstream organic chemistry and are implicated in many industrially and biologically relevant processes and in the processing of carbonyl molecules in the atmosphere.
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Affiliation(s)
- Barbara Marchetti
- Department of Chemistry
- University of Louisiana at Lafayette
- Lafayette
- USA
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207
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Parker SM, Roy S, Furche F. Multistate hybrid time-dependent density functional theory with surface hopping accurately captures ultrafast thymine photodeactivation. Phys Chem Chem Phys 2019; 21:18999-19010. [DOI: 10.1039/c9cp03127h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an efficient analytical implementation of first-order nonadiabatic derivative couplings between arbitrary Born–Oppenheimer states in the hybrid time-dependent density functional theory (TDDFT) framework using atom-centered basis functions.
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Affiliation(s)
- Shane M. Parker
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
| | - Saswata Roy
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
| | - Filipp Furche
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
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208
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Borrego-Varillas R, Nenov A, Ganzer L, Oriana A, Manzoni C, Tolomelli A, Rivalta I, Mukamel S, Garavelli M, Cerullo G. Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules. Chem Sci 2019. [DOI: 10.1039/c9sc03871j] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Two-dimensional ultraviolet spectroscopy has the potential to deliver rich structural and dynamical information on biomolecules such as DNA and proteins.
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Affiliation(s)
| | - A. Nenov
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - L. Ganzer
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - A. Oriana
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - C. Manzoni
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - A. Tolomelli
- Dipartimento di Chimica
- Universitá degli Studi di Bologna
- I-40126 Bologna
- Italy
| | - I. Rivalta
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - S. Mukamel
- Department of Chemistry
- Department of Physics and Astronomy
- University of California
- Irvine
- USA
| | - M. Garavelli
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - G. Cerullo
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
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209
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Zou X, Sun Z, Zhao H, Zhang CY. Mechanistic insight into photocrosslinking reaction between triplet state 4-thiopyrimidine and thymine. Phys Chem Chem Phys 2019; 21:21305-21316. [DOI: 10.1039/c9cp04089g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple nonadiabatic pathways greatly facilitate the proceeding of photocrosslinking reactions between 4-thiopyrimidine and thymine.
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Affiliation(s)
- Xiaoran Zou
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Zhonghua Sun
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Science
- Beijing
- P. R. China
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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210
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Pang X, Jiang C, Xie W, Domcke W. Photoinduced electron-driven proton transfer from water to an N-heterocyclic chromophore: nonadiabatic dynamics studies for pyridine–water clusters. Phys Chem Chem Phys 2019; 21:14073-14079. [DOI: 10.1039/c8cp07015f] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We performed the excited-state dynamics simulations for pyridine–water clusters and found the more water molecules involved in the cluster, the higher efficiency the water-splitting reaction has, which is qualitatively in consistent with a recent gas-phase experimental observations.
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Affiliation(s)
- Xiaojuan Pang
- Key Laboratory for Quantum Information and Quantum Optoelectronic Devices
- China
- Department of Applied Physics
- Xi’an Jiaotong University
- Xi’an 710049
| | - Chenwei Jiang
- Key Laboratory for Quantum Information and Quantum Optoelectronic Devices
- China
- Department of Applied Physics
- Xi’an Jiaotong University
- Xi’an 710049
| | - Weiwei Xie
- Department of Chemistry
- Technical University of Munich
- D-85747 Garching
- Germany
- Institute of Physical Chemistry
| | - Wolfgang Domcke
- Department of Chemistry
- Technical University of Munich
- D-85747 Garching
- Germany
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211
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Fu F, Liao K, Ma J, Cheng Z, Zheng D, Gao L, Liu C, Li S, Li W. How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases. Phys Chem Chem Phys 2019; 21:4072-4081. [DOI: 10.1039/c8cp06152a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intermolecular interactions in terms of molecular packing are crucial for the investigation of the absorption spectra of uracil in different environments.
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Affiliation(s)
- Fangjia Fu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Kang Liao
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Jing Ma
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Zheng Cheng
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Dong Zheng
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Liuzhou Gao
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Chungen Liu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Shuhua Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Wei Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
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212
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Wu X, Ehrmaier J, Sobolewski AL, Karsili TNV, Domcke W. Mechanisms of photoreactivity in hydrogen-bonded adenine-H 2O complexes. Phys Chem Chem Phys 2019; 21:14238-14249. [PMID: 30543228 DOI: 10.1039/c8cp05305g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanisms of photoinduced reactions of adenine with water molecules in hydrogen-bonded adenine-water complexes were investigated with ab initio wave-function-based electronic-structure calculations. Two excited-state electron/proton transfer reaction mechanisms have been characterized: H-atom abstraction from water by photoexcited adenine as well as H-atom transfer from photoexcited adenine or the (adenine+H) radical to water. In the water-to-adenine H-atom transfer reaction, an electron from one of the p orbitals of the water molecule fills the hole in the n (π) orbital of the nπ* (ππ*) excited state of adenine, resulting in a charge-separated electronic state. The electronic charge separation is neutralized by the transfer of a proton from the water molecule to adenine, resulting in the (adenine+H)OH biradical in the electronic ground state. In the adenine-to-water H-atom transfer reaction, πσ* states localized at the acidic sites of adenine provide the mechanism for the photoejection of an electron from adenine, which is followed by proton transfer to the hydrogen-bonded water molecule, resulting in the (adenine-H)H3O biradical. The energy profiles of the photoreactions have been computed as relaxed scans with the ADC(2) electronic-structure method. These reactions, which involve the reactivity of adenine with hydrogen-bonded water molecules, compete with the well-established intrinsic excited-state deactivation mechanisms of adenine via ring-puckering or ring-opening conical intersections. By providing additional decay channels, the electron/proton exchange reactions with water can account for the observed significantly shortened excited-state lifetime of adenine in aqueous environments. These findings indicate that adenine possibly was not only a photostabilizer at the beginning of life, but also a primordial photocatalyst for water splitting.
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Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany.
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213
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Daly S, Porrini M, Rosu F, Gabelica V. Electronic spectroscopy of isolated DNA polyanions. Faraday Discuss 2019; 217:361-382. [DOI: 10.1039/c8fd00207j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We address whether action spectroscopy could be used to investigate structural changes in gas-phase biomolecule (e.g. nucleic acid) ions, owing to changes in the environments of their chromophores, while taking advantage of the additional spectrometric separation of complex mixtures.
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Affiliation(s)
- Steven Daly
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
| | - Massimiliano Porrini
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie
- Université de Bordeaux
- CNRS & Inserm (IECB, UMS3033, US001)
- 33607 Pessac
- France
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
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214
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Green JA, Makhov DV, Cole-Filipiak NC, Symonds C, Stavros VG, Shalashilin DV. Ultrafast photodissociation dynamics of 2-ethylpyrrole: adding insight to experiment with ab initio multiple cloning. Phys Chem Chem Phys 2019; 21:3832-3841. [DOI: 10.1039/c8cp06359a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fully quantum nonadiabatic dynamics calculation of 2-ethylpyrrole photodissociation shows the experimentally obtained ultrafast time-constant has two components.
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Affiliation(s)
| | - Dmitry V. Makhov
- School of Chemistry
- University of Leeds
- Leeds
- UK
- School of Mathematics
| | - Neil C. Cole-Filipiak
- Department of Chemistry
- University of Warwick
- Coventry CV4 7AL
- UK
- Combustion Research Facility
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215
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Martínez-Fernández L, Arslancan S, Ivashchenko D, Crespo-Hernández CE, Corral I. Tracking the origin of photostability in purine nucleobases: the photophysics of 2-oxopurine. Phys Chem Chem Phys 2019; 21:13467-13473. [DOI: 10.1039/c9cp00879a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molding purine PES through functionalization: whilst purine C2-substitution maintains the features of the spectroscopic PES of the heterocycle, C6-functionalization reshapes its topography leading to photostable systems.
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Affiliation(s)
| | - Serra Arslancan
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
| | - Dmytro Ivashchenko
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Departamento de Química e Bioquímica
| | | | - Inés Corral
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- IADCHEM
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216
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Pepino AJ, Segarra-Martí J, Nenov A, Rivalta I, Improta R, Garavelli M. UV-induced long-lived decays in solvated pyrimidine nucleosides resolved at the MS-CASPT2/MM level. Phys Chem Chem Phys 2018; 20:6877-6890. [PMID: 29459916 DOI: 10.1039/c7cp08235e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most relevant 'dark' electronic excited states in DNA/RNA pyrimidine nucleosides are mapped in water employing hybrid MS-CASPT2/MM optimisations with explicit solvation and including the sugar. Conical intersections (CIs) between initially accessed bright 1ππ* and the lowest energy dark 1nπ* excited states, involving the lone pair localised on the oxygen and/or nitrogen atoms are characterised. They are found in the vicinities of the Franck-Condon (FC) region and are shown to facilitate non-adiabatic population transfer. The excited state population of the 1nOπ* state, localised in the carbonyl moiety on all pyrimidine nucleosides, is predicted to rapidly evolve to its minimum, displaying non-negligible potential energy barriers along its non-radiative decay, and accounting for the ps signal registered in pump-probe experiments as well as for an efficient population of the triplet state. Cytidine displays an additional 1nNπ* state localised in the N3 atom and that leads to its excited state minimum displaying large potential energy barriers in the pathway connecting to the CI with the ground state. Sugar-to-base hydrogen/proton transfer processes are assessed in solution for the first time, displaying a sizable barrier along its decay and thus being competitive with other slow decay channels in the ps and ns timescales. A unified deactivation scheme for the long-lived channels of pyrimidine nucleosides is delivered, where the 1nOπ* state is found to mediate the long-lived decay in the singlet manifold and act as the doorway for triplet population and thus accounting for the recorded phosphorescence and, more generally, for the transient/photoelectron spectral signals registered up to the ns timescale.
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Affiliation(s)
- Ana Julieta Pepino
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy.
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217
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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: 1.3] [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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218
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Zhou P, Zhao L. How Does the O6-Methylation Regulate the Excited-State Decay of Guanine Monomers. J Phys Chem B 2018; 123:201-206. [DOI: 10.1021/acs.jpcb.8b08606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, Liaoning, China
| | - Li Zhao
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China
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219
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Khani SK, Faber R, Santoro F, Hättig C, Coriani S. UV Absorption and Magnetic Circular Dichroism Spectra of Purine, Adenine, and Guanine: A Coupled Cluster Study in Vacuo and in Aqueous Solution. J Chem Theory Comput 2018; 15:1242-1254. [DOI: 10.1021/acs.jctc.8b00930] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah Karbalaei Khani
- Arbeitsgruppe Quantenchemie, Ruhr-Universität, Bochum D-44780, Germany
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Rasmus Faber
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organo-Metallici, Consiglio Nazionale delle Ricerche (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Christof Hättig
- Arbeitsgruppe Quantenchemie, Ruhr-Universität, Bochum D-44780, Germany
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
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220
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Guo WW, Zhang TS, Fang WH, Cui G. QM/MM studies on the excited-state relaxation mechanism of a semisynthetic dTPT3 base. Phys Chem Chem Phys 2018; 20:5067-5073. [PMID: 29388994 DOI: 10.1039/c7cp08696b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Semisynthetic alphabets can potentially increase the genetic information stored in DNA through the formation of unusual base pairs. Recent experiments have shown that near-visible-light irradiation of the dTPT3 chromophore could lead to the formation of a reactive triplet state and of singlet oxygen in high quantum yields. However, the detailed excited-state relaxation paths that populate the lowest triplet state are unclear. Herein, we have for the first time employed the QM(MS-CASPT2//CASSCF)/MM method to explore the spectroscopic properties and excited-state relaxation mechanism of the aqueous dTPT3 chromophore. On the basis of the results, we have found that (1) the S2(1ππ*) state of dTPT3 is the initially populated excited singlet state upon near-visible light irradiation; and (2) there are two efficient relaxation pathways to populate the lowest triplet state, i.e. T1(3ππ*). In the first one, the S2(1ππ*) system first decays to the S1(1nπ*) state near the S2/S1 conical intersection, which is followed by an efficient S1 → T1 intersystem crossing process at the S1/T1 crossing point; in the second one, an efficient S2 → T2 intersystem crossing takes place first, and then, the T2(3nπ*) system hops to the T1(3ππ*) state through an internal conversion process at the T2/T1 conical intersection. Moreover, an S2/S1/T2 intersection region is found to play a vital role in the excited-state relaxation. These new mechanistic insights help in understanding the photophysics and photochemistry of unusual base pairs.
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Affiliation(s)
- Wei-Wei Guo
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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221
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Francés-Monerris A, Hognon C, Miranda MA, Lhiaubet-Vallet V, Monari A. Triplet photosensitization mechanism of thymine by an oxidized nucleobase: from a dimeric model to DNA environment. Phys Chem Chem Phys 2018; 20:25666-25675. [PMID: 30298156 DOI: 10.1039/c8cp04866e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nucleic acids are constantly exposed to external agents that can induce chemical and photochemical damage. In spite of the great advances achieved in the last years, some molecular mechanisms of DNA damage are not completely understood yet. A recent experimental report (I. Aparici-Espert et al., ACS Chem. Biol. 2018, 13, 542) proved the ability of 5-formyluracil (ForU), a common oxidatively generated product of thymine, to act as an intrinsic sensitizer of nucleic acids, causing single strand breaks and cyclobutane pyrimidine dimers in plasmid DNA. In the present contribution, we use theoretical methodologies to study the triplet photosensitization mechanism of thymine exerted by ForU in a model dimer and in DNA environment. The photochemical pathways in the former system are described combining the CASPT2 and TD-DFT methods, whereas molecular dynamics simulations and QM/MM calculations are employed for the DNA duplex. It is unambiguously shown that the 1n,π* state localised in ForU mediates the population of the triplet manifold, most likely the 3π,π* state centred in ForU, whereas the 3π,π* state localized in thymine can be populated via triplet-triplet energy transfer given the small energy barrier of <0.23 eV determined for this pathway.
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222
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Francés-Monerris A, Gattuso H, Roca-Sanjuán D, Tuñón I, Marazzi M, Dumont E, Monari A. Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA. Chem Sci 2018; 9:7902-7911. [PMID: 30450180 PMCID: PMC6202918 DOI: 10.1039/c8sc03252a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022] Open
Abstract
The intrinsic photostability of nucleic acids is intimately related to evolution of life, while its understanding at the molecular and electronic levels remains a challenge for modern science. Among the different decay pathways proposed in the last two decades, the excited-state hydrogen transfer between guanine-cytosine base pairs has been identified as an efficient non-reactive channel to dissipate the excess of energy provided by light absorption. The present work studies the dynamics of such phenomena taking place in a (dG)·(dC) B-DNA homopolymer in water solution using state-of-the-art molecular modelling and simulation methods. A dynamic effect that boosts the photostability of the inter-strand hydrogen atom transfers, inherent to the Watson-Crick base pairing, is unveiled and ascribed to the energy released during the proton transfer step. Our results also reveal a novel mechanism of DNA decay named four proton transfer (FPT), in which two protons of two adjacent G-C base pairs are transferred to form a biradical zwitterionic intermediate. Decay of the latter intermediate to the ground state triggers the transfer of the protons back to the guanine molecules recovering the Watson-Crick structure of the tetramer. This FPT process is activated by the close interaction of a nearby Na+ counterion with the oxygen atoms of the guanine nucleobases and hence represents a photostable channel operative in natural nucleic acids.
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Affiliation(s)
| | - Hugo Gattuso
- Theoretical Physical Chemistry , Research Unit Molecular Systems (UR MOLSYS) , University of Liège , 4000 Liège , Belgium
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular , Universitat de València , Apartado 22085 , ES-46071 Paterna , Spain
| | - Iñaki Tuñón
- Departamento de Química Física , Universitat de València , 46100 Burjassot , Spain
| | - Marco Marazzi
- Departamento de Química , Centro de Investigación en Síntesis Química (CISQ) , Universidad de La Rioja , 26006 Logroño , Spain
| | - Elise Dumont
- Univ. Lyon , ENS de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F69342 , Lyon , France
| | - Antonio Monari
- Université de Lorraine , CNRS , LPCT , Nancy F-54000 , France . ;
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223
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Segalina A, Francés-Monerris A, Pastore M, Leininger T, Evangelisti S, Monari A. Conical intersection properties unraveled by the position spread tensor. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2377-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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224
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Liu Y, Martínez-Fernández L, Cerezo J, Prampolini G, Improta R, Santoro F. Multistate coupled quantum dynamics of photoexcited cytosine in gas-phase: Nonadiabatic absorption spectrum and ultrafast internal conversions. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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225
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Concerted-asynchronous reaction path of the excited-state double proton transfer in the 7-azaindole homodimer and 6H-indolo[2,3-b]quinoline/7-azaindole heterodimer. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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226
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Mai S, Mohamadzade A, Marquetand P, González L, Ullrich S. Simulated and Experimental Time-Resolved Photoelectron Spectra of the Intersystem Crossing Dynamics in 2-Thiouracil. Molecules 2018; 23:E2836. [PMID: 30388739 PMCID: PMC6278540 DOI: 10.3390/molecules23112836] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 11/16/2022] Open
Abstract
We report time-dependent photoelectron spectra recorded with a single-photon ionization setup and extensive simulations of the same spectra for the excited-state dynamics of 2-thiouracil (2TU) in the gas phase. We find that single-photon ionization produces very similar results as two-photon ionization, showing that the probe process does not have a strong influence on the measured dynamics. The good agreement between the single-photon ionization experiments and the simulations shows that the norms of Dyson orbitals allow for qualitatively describing the ionization probabilities of 2TU. This reasonable performance of Dyson norms is attributed to the particular electronic structure of 2TU, where all important neutral and ionic states involve similar orbital transitions and thus the shape of the Dyson orbitals do not strongly depend on the initial neutral and final ionic state. We argue that similar situations should also occur in other biologically relevant thio-nucleobases, and that the time-resolved photoelectron spectra of these bases could therefore be adequately modeled with the techniques employed here.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Abed Mohamadzade
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Susanne Ullrich
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
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227
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Karsili TN, Marchetti B, Ashfold MN. The role of 1πσ∗ states in the formation of adenine radical-cations in DNA duplexes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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228
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Ingle RA, Roberts GM, Röttger K, Marroux HJ, Sönnichsen FD, Yang M, Szyc Ł, Harabuchi Y, Maeda S, Temps F, Orr-Ewing AJ. Resolving the excited state relaxation dynamics of guanosine monomers and hydrogen-bonded homodimers in chloroform solution. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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229
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Martinez-Fernandez L, Prampolini G, Cerezo J, Liu Y, Santoro F, Improta R. Solvent effect on the energetics of proton coupled electron transfer in guanine-cytosine pair in chloroform by mixed explicit and implicit solvation models. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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230
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231
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Ai Y, Xing J, Zhang A, Zhao C, Liu Y, Xie B, Chen W, Cui G, Lu Z, Wang X. Computational Study on the Excited-State Decay of 5-Methylcytosine and 5-Hydroxymethylcytosine: The Common Form of DNA Methylation and Its Oxidation Product. J Phys Chem B 2018; 122:10424-10434. [DOI: 10.1021/acs.jpcb.8b07830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | | | - Binbin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | | | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | - Xiangke Wang
- NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences, Soochow University, Suzhou 215123, P. R. China
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232
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Marian CM, Heil A, Kleinschmidt M. The DFT/MRCI method. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1394] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Christel M. Marian
- Institute of Theoretical and Computational Chemistry Heinrich Heine Universität Düsseldorf Düsseldorf
| | - Adrian Heil
- Institute of Theoretical and Computational Chemistry Heinrich Heine Universität Düsseldorf Düsseldorf
| | - Martin Kleinschmidt
- Institute of Theoretical and Computational Chemistry Heinrich Heine Universität Düsseldorf Düsseldorf
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233
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Williams HL, Erickson BA, Neumark DM. Time-resolved photoelectron spectroscopy of adenosine and adenosine monophosphate photodeactivation dynamics in water microjets. J Chem Phys 2018; 148:194303. [PMID: 30307253 DOI: 10.1063/1.5027258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The excited state relaxation dynamics of adenosine and adenosine monophosphate were studied at multiple excitation energies using femtosecond time-resolved photoelectron spectroscopy in a liquid water microjet. At pump energies of 4.69-4.97 eV, the lowest ππ* excited state, S1, was accessed and its decay dynamics were probed via ionization at 6.20 eV. By reversing the role of the pump and probe lasers, a higher-lying ππ* state was excited at 6.20 eV and its time-evolving photoelectron spectrum was monitored at probe energies of 4.69-4.97 eV. The S1 ππ* excited state was found to decay with a lifetime ranging from ∼210 to 250 fs in adenosine and ∼220 to 250 fs in adenosine monophosphate. This lifetime drops with increasing pump photon energy. Signal from the higher-lying ππ* excited state decayed on a time scale of ∼320 fs and was measureable only in adenosine monophosphate.
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Affiliation(s)
- Holly L Williams
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Blake A Erickson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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234
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Abstract
In 1998, the first successful quantum control experiment with application to a molecular framework was conducted with a shaped laser pulse, optimizing the branching ratio between different organometallic reaction channels. This work induced a vast activity in quantum control during the next 10 years, and different optimization aims were achieved in the gas phase, liquid phase, and even in biologically relevant molecules like light-harvesting complexes. Accompanying and preceding this development were important advances in theoretical quantum control simulations. They predicted several control scenarios and explained how and why quantum control experiments work. After many successful proofs of concept in molecular science, the big challenge is to expand its huge conceptual potential of directly being able to steer nuclear and/or electronic motion to more applied implementations. In this Account, based on several recent advances, we give a personal evaluation of where the field of molecular quantum control is at the moment and especially where we think promising applications can be in the near future. One of these paths leads to synthetic chemistry. The synthesis of novel pharmaceutical compounds or natural products often involves many synthetic steps, each one devouring resources and lowering the product yield. Shaped laser pulses can possibly act as photonic reagents and shorten the synthetic route toward the desired product. Chemical synthesis usually takes place in solution, and by including explicit solvent molecules in our quantum control simulations, we were able to identify their highly inhomogeneous influence on chemical reactions and how this affects potential quantum control. More important, we demonstrated for a synthetically relevant example that these complications can be overcome in theory, and laser pulses can be optimized to initiate the desired carbon-carbon bond formation. Putting this into context with the recently emerging concept of flow chemistry, which brings several practical advantages to the application of laser pulses, we want to encourage experimental groups to exploit this concept. Another path was opened by several additions to the commonly used laser pulse optimization algorithm (optimal control theory, OCT), several of which were developed in our group. The OCT algorithm as such is a purely mathematical optimization procedure, with no direct relation to experimental requirements. This means that usually the electric fields obtained out of OCT optimizations do not resemble laser pulses that can be achieved experimentally. However, the previously mentioned additions are aimed at closing the gap toward the experiment. In a recent quantum control study of our group, these algorithmic developments came to fruition. We were able to suggest a shaped laser pulse which can induce a long-living wave packet in the excited state of uracil. This might pave the way for novel experiments dedicated to investigating the formation of biological photodamage in DNA and RNA. The pulse we suggest is surprisingly simple because of the extended OCT algorithm and fulfills all criteria to be experimentally accessible.
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Affiliation(s)
- Daniel Keefer
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
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235
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Banyasz A, Martínez-Fernández L, Improta R, Ketola TM, Balty C, Markovitsi D. Radicals generated in alternating guanine-cytosine duplexes by direct absorption of low-energy UV radiation. Phys Chem Chem Phys 2018; 20:21381-21389. [PMID: 30101268 DOI: 10.1039/c8cp02588f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent studies have evidenced that oxidatively damaged DNA, which potentially leads to carcinogenic mutations and aging, may result from the direct absorption of low-energy photons (>250 nm). Herein, the primary species, i.e., ejected electrons and base radicals associated with such damage in duplexes with an alternating guanine-cytosine sequence are quantified by nanosecond transient absorption spectroscopy. The one-photon ionization quantum yield at 266 nm is 1.2 × 10-3, which is similar to those reported previously for adenine-thymine duplexes. This means that the simple presence of guanine, the nucleobase with the lowest ionization potential, does not affect photo-ionization. The transient species detected after 3 μs are identified as deprotonated guanine radicals, which decay with a half-time of 2.5 ms. Spectral assignment is made with the help of quantum chemistry calculations (TD-DFT), which for the first time, provide reference absorption spectra for guanine radicals in duplexes. In addition, our computed spectra predict the changes in transient absorption expected for hole localization as well as deprotonation (to cytosine and bulk water) and hydration of the radical cation.
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Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
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236
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Ashwood B, Pollum M, Crespo-Hernández CE. Photochemical and Photodynamical Properties of Sulfur-Substituted Nucleic Acid Bases. Photochem Photobiol 2018; 95:33-58. [PMID: 29978490 DOI: 10.1111/php.12975] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 06/28/2018] [Indexed: 12/25/2022]
Abstract
Sulfur-substituted nucleobases (a.k.a., thiobases) are among the world's leading prescriptions for chemotherapy and immunosuppression. Long-term treatment with azathioprine, 6-mercaptopurine and 6-thioguanine has been correlated with the photoinduced formation of carcinomas. Establishing an in-depth understanding of the photochemical properties of these prodrugs may provide a route to overcoming these carcinogenic side effects, or, alternatively, a basis for developing effective compounds for targeted phototherapy. In this review, a broad examination is undertaken, surveying the basic photochemical properties and excited-state dynamics of sulfur-substituted analogs of the canonical DNA and RNA nucleobases. A molecular-level understanding of how sulfur substitution so remarkably perturbs the photochemical properties of the nucleobases is presented by combining experimental results with quantum-chemical calculations. Structure-property relationships demonstrate the impact of site-specific sulfur substitution on the photochemical properties, particularly on the population of the reactive triplet state. The value of fundamental photochemical investigations for driving the development of ultraviolet-A chemotherapeutics is showcased. The most promising photodynamic agents identified thus far have been investigated in various carcinoma cell lines and shown to decrease cell proliferation upon exposure to ultraviolet-A radiation. Overarching principles have been elucidated for the impact that sulfur substitution of the carbonyl oxygen has on the photochemical properties of the nucleobases.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, Case Western Reserve University, Cleveland, OH
| | - Marvin Pollum
- Department of Chemistry, Case Western Reserve University, Cleveland, OH
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237
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COBRAMM 2.0 — A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations. J Mol Model 2018; 24:271. [DOI: 10.1007/s00894-018-3769-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/27/2018] [Indexed: 01/04/2023]
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238
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Farrell KM, Brister MM, Pittelkow M, Sølling TI, Crespo-Hernández CE. Heavy-Atom-Substituted Nucleobases in Photodynamic Applications: Substitution of Sulfur with Selenium in 6-Thioguanine Induces a Remarkable Increase in the Rate of Triplet Decay in 6-Selenoguanine. J Am Chem Soc 2018; 140:11214-11218. [DOI: 10.1021/jacs.8b07665] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Kieran M. Farrell
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Matthew M. Brister
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Theis I. Sølling
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Carlos E. Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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239
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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240
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Ghafur O, Crane SW, Ryszka M, Bockova J, Rebelo A, Saalbach L, De Camillis S, Greenwood JB, Eden S, Townsend D. Ultraviolet relaxation dynamics in uracil: Time-resolved photoion yield studies using a laser-based thermal desorption source. J Chem Phys 2018; 149:034301. [DOI: 10.1063/1.5034419] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Omair Ghafur
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Stuart W. Crane
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Michal Ryszka
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Jana Bockova
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Andre Rebelo
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
- CEFITEC, Departamento de Física, FCT–Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal
| | - Lisa Saalbach
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Simone De Camillis
- School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jason B. Greenwood
- School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Samuel Eden
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
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241
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Röttger K, Marroux HJB, Böhnke H, Morris DTJ, Voice AT, Temps F, Roberts GM, Orr-Ewing AJ. Probing the excited state relaxation dynamics of pyrimidine nucleosides in chloroform solution. Faraday Discuss 2018; 194:683-708. [PMID: 27711889 DOI: 10.1039/c6fd00068a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrafast transient electronic and vibrational absorption spectroscopy (TEAS and TVAS) of 2'-deoxy-cytidine (dC) and 2'-deoxy-thymidine (dT) dissolved in chloroform examines their excited-state dynamics and the recovery of ground electronic state molecules following absorption of ultraviolet light. The chloroform serves as a weakly interacting solvent, allowing comparisons to be drawn with prior experimental studies of the photodynamics of these nucleosides in the gas phase and in polar solvents such as water. The pyrimidine base nucleosides have some propensity to dimerize in aprotic solvents, but the monomer photochemistry can be resolved clearly and is the focus of this study. UV absorption at a wavelength of 260 nm excites a 1ππ* ← S0 transition, but prompt crossing of a significant fraction (50% in dC, 17% in dT) of the 1ππ* population into a nearby 1nπ* state is too fast for the experiments to resolve. The remaining flux on the 1ππ* state leaves the vertical Franck-Condon region and encounters a conical intersection with the ground electronic state of ethylenic twist character. In dC, the 1ππ* state decays to the ground state with a time constant of 1.1 ± 0.1 ps. The lifetime of the 1nπ* state is much longer in the canonical forms of both molecules: recovery of the ground state population from these states occurs with time constants of 18.6 ± 1.1 ps in amino-oxo dC and ∼114 ps in dT, indicating potential energy barriers to the 1nπ*/S0 conical intersections. The small fraction of the imino-oxo tautomer of dC present in solution has a longer-lived 1nπ* state with a lifetime for ground state recovery of 193 ± 55 ps. No evidence is found for photo-induced tautomerization of amino-oxo dC to the imino-oxo form, or for population of low lying triplet states of this nucleoside. In contrast, ∼8% of the UV-excited dT molecules access the long-lived T1 (3ππ*) state through the 1nπ* state. The primary influence of the solvent appears to be the degree to which it destabilizes the states of 1nπ* character, with consequences for the lifetimes of these states as well as the triplet state yields.
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Affiliation(s)
- Katharina Röttger
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Hugo J B Marroux
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Hendrik Böhnke
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - David T J Morris
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Angus T Voice
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Friedrich Temps
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Gareth M Roberts
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Andrew J Orr-Ewing
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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242
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Wang X, Zhou Z, Tang Y, Chen J, Zhong D, Jianhua Xu. Excited State Decay Pathways of 2'-Deoxy-5-methylcytidine and Deoxycytidine Revisited in Solution: A Comprehensive Kinetic Study by Femtosecond Transient Absorption. J Phys Chem B 2018; 122:7027-7037. [PMID: 29939745 DOI: 10.1021/acs.jpcb.8b00927] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylated cytosine is proved to have an important role as an epigenetic signal in gene regulation and is often referred to "the fifth base of DNA". A comprehensive understanding of the electronic excited state relaxation in cytosine and its methylated derivatives is crucial for revealing UV-induced photodamage to the biological genome. Because of the existence of multiple closely lying "bright" and "dark" excited states, the decay pathways in these DNA nucleosides are the most complex and the least understood so far. In this study, femtosecond transient absorption with different excitation wavelengths (240-296 nm) was used to study the relaxation of excited electronic states of 5-methylcytosine (5mC) and 2'-deoxy-5-methylcytidine (5mdCyd) in phosphate buffered aqueous solution and in acetonitrile solution. Two distinct nonradiative decay channels were directly observed. The first one is a several picosecond internal conversion channel that involves two bright ππ* states (ππ*2 and ππ*1) when ππ*2 state is initially populated. The second channel contains the lower energy ππ*1 state and a so far experimental unidentified long-lived state which exhibits a several nanosecond lifetime. The long-lived state can only be accessed by the initially excited ππ*1 state. Inspired by this new discovery in 5mC and 5mdCyd, we revisited the decay of excited state of 2'-deoxycytidine (dCyd), revealing very similar decay pathways. Additionally, a well-known dark nOπ* state (carbonyl lone pair) with ∼30 ps lifetime is present in both decay channels in dCyd. With our detailed experimental results, we successfully reconcile the long history debate of cytosine excited state relaxation mechanism by pointing out that the reason for the complex dynamics under traditional 266 nm excitation is mixed signals from the above-mentioned two distinct decay pathways. Our findings lead to a dramatically different and new picture of electronic energy relaxation in 5mdCyd/dCyd and could help to understand photostability as well as UV-induced photodamage of these nucleotides and related DNAs.
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Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China
| | - Yuankai Tang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China.,Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China.,Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
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243
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Liu X, Wei X, Zhou H, Meng S, Zhao Y, Xue J, Zheng X. UV and Resonance Raman Spectroscopic and Theoretical Studies on the Solvent-Dependent Ground and Excited-State Thione → Thiol Tautomerization of 4,6-Dimethyl-2-mercaptopyrimidine (DMMP). J Phys Chem A 2018; 122:5710-5720. [PMID: 29889517 DOI: 10.1021/acs.jpca.8b04525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vibrational spectra of 4,6-dimethyl-2-mercaptopyrimidine (DMMP) in acetonitrile, methanol, and water were assigned by resonance Raman spectroscopy through a combination of Fourier-transform infrared spectroscopy (FT-IR), FT-Raman UV-vis spectroscopy, and density functional theoretical (DFT) calculations. The FT-Raman spectra show that the neat solid DMMP is formed as a dimer due to intermolecular hydrogen bonding. In methanol and water, however, the majority of the Raman spectra were assigned to the vibrational modes of DMMP(solvent) n ( n = 1-4) clusters containing NH···O hydrogen bonds. The intermolecular NH···O hydrogen bond interactions, which are key constituents of the stable DMMP thione structure, revealed significant structural differences in acetonitrile, methanol, and water. In addition, UV-induced hydrogen transfer isomeric reactions between the thione and thiol forms of DMMP were detected in water and acetonitrile. DFT calculations indicate that the observed thione → thiol tautomerization should occur easily in lower excited states in acetonitrile and water.
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244
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Yang W, Chen X, Fang W. Nonadiabatic Curve-Crossing Model for the Visible-Light Photoredox Catalytic Generation of Radical Intermediate via a Concerted Mechanism. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wenjing Yang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
- College of Material Science & Engineering, Taiyuan University of Technology, Shanxi 030024, People’s Republic of China
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
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245
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Matthews E, Cercola R, Mensa-Bonsu G, Neumark DM, Dessent CEH. Photoexcitation of iodide ion-pyrimidine clusters above the electron detachment threshold: Intracluster electron transfer versus nucleobase-centred excitations. J Chem Phys 2018; 148:084304. [PMID: 29495768 DOI: 10.1063/1.5018168] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Laser photodissociation spectroscopy of the I-·thymine (I-·T) and I-·cytosine (I-·C) nucleobase clusters has been conducted for the first time across the regions above the electron detachment thresholds to explore the excited states and photodissociation channels. Although photodepletion is strong, only weak ionic photofragment signals are observed, indicating that the clusters decay predominantly by electron detachment. The photodepletion spectra of the I-·T and I-·C clusters display a prominent dipole-bound excited state (I) in the vicinity of the vertical detachment energy (∼4.0 eV). Like the previously studied I-·uracil (I-·U) cluster [W. L. Li et al., J. Chem. Phys. 145, 044319 (2016)], the I-·T cluster also displays a second excited state (II) centred at 4.8 eV, which we similarly assign to a π-π* nucleobase-localized transition. However, no distinct higher-energy absorption bands are evident in the spectra of the I-·C. Time-dependent density functional theory (TDDFT) calculations are presented, showing that while each of the I-·T and I-·U clusters displays a single dominant π-π* nucleobase-localized transition, the corresponding π-π* nucleobase transitions for I-·C are split across three separate weaker electronic excitations. I- and deprotonated nucleobase anion photofragments are observed upon photoexcitation of both I-·U and I-·T, with the action spectra showing bands (at 4.0 and 4.8 eV) for both the I- and deprotonated nucleobase anion production. The photofragmentation behaviour of the I-·C cluster is distinctive as its I- photofragment displays a relatively flat profile above the expected vertical detachment energy. We discuss the observed photofragmentation profiles of the I-·pyrimidine clusters, in the context of the previous time-resolved measurements, and conclude that the observed photoexcitations are primarily consistent with intracluster electron transfer dominating in the near-threshold region, while nucleobase-centred excitations dominate close to 4.8 eV. TDDFT calculations suggest that charge-transfer transitions [Iodide n (5p6) → Uracil σ*] may contribute to the cluster absorption profile across the scanned spectral region, and the possible role of these states is also discussed.
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Affiliation(s)
- Edward Matthews
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Rosaria Cercola
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Golda Mensa-Bonsu
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Caroline E H Dessent
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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246
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Reiter S, Keefer D, de Vivie-Riedle R. RNA Environment Is Responsible for Decreased Photostability of Uracil. J Am Chem Soc 2018; 140:8714-8720. [DOI: 10.1021/jacs.8b02962] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sebastian Reiter
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Daniel Keefer
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
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247
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Ultraviolet Transient Absorption Spectrometer with Sub-20-fs Time Resolution. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8060989] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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248
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Martínez-Fernández L, Improta R. Sequence dependence on DNA photochemistry: a computational study of photodimerization pathways in TpdC and dCpT dinucleotides. Photochem Photobiol Sci 2018; 17:586-591. [PMID: 29624198 DOI: 10.1039/c8pp00040a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The excited states involved in the main photodimerization paths in TpdC and dCpT are mapped by PCM/TD-M052X calculations, considering different dinucleotide conformers. As for TT steps, a cyclobutane pyrimidine dimer (CPD) is formed on the PES of the lowest energy exciton, delocalized over two stacked pyrimidines; 6-4 pyrimidine-pyrimidone (64-PP) adduct's formation involves instead a 5'-ter → 3'-ter charge transfer state. For dCpT, 64-PP dimerization occurs via a two-step reaction, which proceeds through an oxetane intermediate. For TpdC, instead, the final 64-PP product is obtained in a single step and it is as stable as the CPD photoproduct, explaining the relatively large yield of 64-PP found experimentally for TC steps in DNA.
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Affiliation(s)
- Lara Martínez-Fernández
- Consiglio Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134 Naples, Italy. and LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Roberto Improta
- Consiglio Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134 Naples, Italy. and LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
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249
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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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250
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Pilles BM, Maerz B, Chen J, Bucher DB, Gilch P, Kohler B, Zinth W, Fingerhut BP, Schreier WJ. Decay Pathways of Thymine Revisited. J Phys Chem A 2018; 122:4819-4828. [PMID: 29747505 DOI: 10.1021/acs.jpca.8b02050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The decay of electronically excited states of thymine (Thy) and thymidine 5'-monophosphate (TMP) was studied by time-resolved UV/vis and IR spectroscopy. In addition to the well-established ultrafast internal conversion to the ground state, a so far unidentified UV-induced species is observed. In D2O, this species decays with a time constant of 300 ps for thymine and of 1 ns for TMP. The species coexists with the lowest triplet state and is formed with a comparably high quantum yield of about 10% independent of the solvent. The experimentally determined spectral signatures are discussed in the light of quantum chemical calculations of the singlet and triplet excited states of thymine.
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Affiliation(s)
- Bert M Pilles
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
| | - Benjamin Maerz
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy , East China Normal University , 3663 North Zhongshan Road , Shanghai 200062 , China
| | - Dominik B Bucher
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
| | - Peter Gilch
- Institut für Physikalische Chemie , Heinrich-Heine-Universität Düsseldorf , Universitätsstrasse 1 , Düsseldorf 40225 , Germany
| | - Bern Kohler
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States
| | - Wolfgang Zinth
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Strasse 2A , Berlin D-12489 , Germany
| | - Wolfgang J Schreier
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
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