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Bezabih MS, Kaliakin DS, Blanco-González A, Barneschi L, Tarnovsky AN, Olivucci M. Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories. J Phys Chem B 2023; 127:10871-10879. [PMID: 38055701 DOI: 10.1021/acs.jpcb.3c06433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.
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Affiliation(s)
- Meseret Simachew Bezabih
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Danil S Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Leonardo Barneschi
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Alexander N Tarnovsky
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
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Romeo-Gella F, Arpa EM, Corral I. A molecular insight into the photophysics of barbituric acid, a candidate for canonical nucleobases' ancestor. Phys Chem Chem Phys 2022; 24:1405-1414. [PMID: 34982082 DOI: 10.1039/d1cp04987a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This work investigates the photophysics of barbituric acid at different pH conditions using ab initio methods. Our calculations ascribe the most intense bands at ca. 260 nm at neutral pH and 210 nm at acidic pH conditions in the absorption spectra of this chromophore to the lowest lying ππ* transitions. Consistently with the ultrashort excited state lifetimes experimentally registered, the potential energy landscapes of both the neutral and deprotonated forms of barbituric acid combined with the interpretation of their transient absorption spectra suggest the deactivation of these systems along the singlet manifold. Compared to uracil, its closest natural nucleobase, barbituric acid presents a red shifted absorption spectrum, due to the lowering by more than 0.5 eV of the lowest-energy ππ* excited state, and a much more complex topography of the S1 potential energy surface, with several energetically accessible local minima. This fact, however, does not affect the excited state lifetimes, which for barbituric acid were experimentally registered in the sub-ps time scale.
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Affiliation(s)
- Fernando Romeo-Gella
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Enrique M Arpa
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Inés Corral
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
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Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
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Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
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Effects of hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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Sun S, Brown A. Simulation of the Resonance Raman Spectra for 5-Halogenated (F, Cl, and Br) Uracils. J Phys Chem A 2015; 119:3961-71. [DOI: 10.1021/acs.jpca.5b01052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuai Sun
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Excited States Behavior of Nucleobases in Solution: Insights from Computational Studies. Top Curr Chem (Cham) 2014; 355:329-57. [DOI: 10.1007/128_2013_524] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Picconi D, Avila Ferrer FJ, Improta R, Lami A, Santoro F. Quantum-classical effective-modes dynamics of the ππ* → nπ* decay in 9H-adenine. A quadratic vibronic coupling model. Faraday Discuss 2013; 163:223-42; discussion 243-75. [DOI: 10.1039/c3fd20147c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Barbatti M, Lan Z, Crespo-Otero R, Szymczak JJ, Lischka H, Thiel W. Critical appraisal of excited state nonadiabatic dynamics simulations of 9H-adenine. J Chem Phys 2012; 137:22A503. [DOI: 10.1063/1.4731649] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Picconi D, Lami A, Santoro F. Hierarchical transformation of Hamiltonians with linear and quadratic couplings for nonadiabatic quantum dynamics: Application to the ππ*/nπ* internal conversion in thymine. J Chem Phys 2012; 136:244104. [DOI: 10.1063/1.4729049] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Yamazaki S, Taketsugu T. Nonradiative Deactivation Mechanisms of Uracil, Thymine, and 5-Fluorouracil: A Comparative ab Initio Study. J Phys Chem A 2011; 116:491-503. [DOI: 10.1021/jp206546g] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shohei Yamazaki
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Picconi D, Barone V, Lami A, Santoro F, Improta R. The Interplay between ππ*/nπ* Excited States in Gas-Phase Thymine: A Quantum Dynamical Study. Chemphyschem 2011; 12:1957-68. [DOI: 10.1002/cphc.201001080] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/01/2011] [Indexed: 11/10/2022]
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DeFusco A, Ivanic J, Schmidt MW, Gordon MS. Solvent-Induced Shifts in Electronic Spectra of Uracil. J Phys Chem A 2011; 115:4574-82. [DOI: 10.1021/jp112230f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Albert DeFusco
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Joseph Ivanic
- Advanced Biomedical Computing Center, Information Systems Program, SAIC—Frederick, Inc., National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Michael W. Schmidt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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Gustavsson T, Banyasz A, Improta R, Markovitsi D. Femtosecond fluorescence studies of DNA/RNA constituents. ACTA ACUST UNITED AC 2011. [DOI: 10.1088/1742-6596/261/1/012009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Improta R, Barone V. PCM/TD-DFT study of the two lowest excited states of uracil derivatives in solution: The effect of the functional and of the cavity model. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.02.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Improta R, Barone V, Lami A, Santoro F. Quantum Dynamics of the Ultrafast ππ*/nπ* Population Transfer in Uracil and 5-Fluoro-Uracil in Water and Acetonitrile. J Phys Chem B 2009; 113:14491-503. [DOI: 10.1021/jp906524p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Vincenzo Barone
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Alessandro Lami
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
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