1
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Ghosh P. Investigation of the Nonradiative Photoprocesses of Unnatural DNA Base: 7-(2-Thienyl)-imidazo[4,5- b]pyridine (Ds)─A Computational Study. J Phys Chem A 2024; 128:8065-8071. [PMID: 39279655 PMCID: PMC11440586 DOI: 10.1021/acs.jpca.4c04070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
7-(2-Thienyl)-imidazo[4,5-b]pyridine (Ds) is an unnatural nucleic acid that forms a stable pair with pyrrole-2-carbaldehyde (Pa) in DNA. This Ds-Pa pair gets stabilized via van der Waals interaction and shape fitting. In our previous study [Ghosh, P. J. Phys. Chem. A 2021, 125, 5556-5561], we investigated the nonradiative photoprocesses of the unnatural DNA base Pa, and also there are some studies on its stability and reactivity in the ground state. But, to consider it as a good unnatural base pair, one has to understand its stability not only in the ground state but also in the excited states after absorbing ultraviolet (UV) radiation. Therefore, in this study, the excited-state photoprocesses of Ds on UV irradiation and its nonradiative decay channels have been investigated using state-of-the-art multireference methods, and this investigation finally leads the molecule to access the minimum energy crossing point (MECP) via a downhill pathway.
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Affiliation(s)
- Paulami Ghosh
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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2
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Sarkar R, Loos PF, Boggio-Pasqua M, Jacquemin D. Assessing the Performances of CASPT2 and NEVPT2 for Vertical Excitation Energies. J Chem Theory Comput 2022; 18:2418-2436. [PMID: 35333060 DOI: 10.1021/acs.jctc.1c01197] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Methods able to simultaneously account for both static and dynamic electron correlations have often been employed, not only to model photochemical events but also to provide reference values for vertical transition energies, hence allowing benchmarking of lower-order models. In this category, both the complete-active-space second-order perturbation theory (CASPT2) and the N-electron valence state second-order perturbation theory (NEVPT2) are certainly popular, the latter presenting the advantage of not requiring the application of the empirical ionization-potential-electron-affinity (IPEA) and level shifts. However, the actual accuracy of these multiconfigurational approaches is not settled yet. In this context, to assess the performances of these approaches, the present work relies on highly accurate (±0.03 eV) aug-cc-pVTZ vertical transition energies for 284 excited states of diverse character (174 singlet, 110 triplet, 206 valence, 78 Rydberg, 78 n → π*, 119 π → π*, and 9 double excitations) determined in 35 small- to medium-sized organic molecules containing from three to six non-hydrogen atoms. The CASPT2 calculations are performed with and without IPEA shift and compared to the partially contracted (PC) and strongly contracted (SC) variants of NEVPT2. We find that both CASPT2 with IPEA shift and PC-NEVPT2 provide fairly reliable vertical transition energy estimates, with slight overestimations and mean absolute errors of 0.11 and 0.13 eV, respectively. These values are found to be rather uniform for the various subgroups of transitions. The present work completes our previous benchmarks focused on single-reference wave function methods ( J. Chem. Theory Comput. 2018, 14, 4360; J. Chem. Theory Comput. 2020, 16, 1711), hence allowing for a fair comparison between various families of electronic structure methods. In particular, we show that ADC(2), CCSD, and CASPT2 deliver similar accuracies for excited states with a dominant single-excitation character.
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Affiliation(s)
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, CNRS, UPS, Université de Toulouse, Toulouse 31062, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques, CNRS, UPS, Université de Toulouse, Toulouse 31062, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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3
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Huang X, Xie W, Došlić N, Gelin MF, Domcke W. Ab Initio Quasiclassical Simulation of Femtosecond Time-Resolved Two-Dimensional Electronic Spectra of Pyrazine. J Phys Chem Lett 2021; 12:11736-11744. [PMID: 34851116 DOI: 10.1021/acs.jpclett.1c03589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Two-dimensional (2D) electronic spectroscopy is a powerful nonlinear technique which provides spectroscopic information on two frequency axes as well as dynamical information as a function of the so-called waiting time. Herein, an ab initio theoretical framework for the simulation of electronic 2D spectra has been developed. The method is based on the classical approximation to the doorway-window representation of three-pulse photon-echo signals and the description of nuclear motion by classical trajectories. Nonadiabatic effects are taken into account by a trajectory surface-hopping algorithm. 2D electronic spectra were simulated with ab initio on-the-fly trajectory calculations using the ADC(2) electronic-structure method for the pyrazine molecule, which is a benchmark system for ultrafast radiationless decay through conical intersections. It is demonstrated that 2D spectroscopy with subfemtosecond UV pulses can provide unprecedented detailed information on the ultrafast photodynamics of polyatomic molecules.
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Affiliation(s)
- Xiang Huang
- Department of Chemistry, Technical University of Munich, Garching, D-85747, Germany
| | - Weiwei Xie
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruder Boscovic Institute, Zagreb, HR-10000, Croatia
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, D-85747, Germany
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4
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Chen Q, Kwok YH, Zhou W, Chen G, Mukamel S. Time-dependent simulation of photocurrent-detected two-dimensional spectroscopy of open systems. J Chem Phys 2021; 155:194113. [PMID: 34800940 DOI: 10.1063/5.0067362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new time-domain simulation protocol of two-dimensional electronic spectra with photocurrent detection is presented. Time-dependent density functional theory for open systems at finite temperature is applied to evaluate the photocurrent response to four laser pulses, and a non-perturbative phase-matching approach is implemented to extract the fourth-order photocurrent signal with a desired phase-matching condition. Simulations for an open three-level model indicates that transition dipoles interact resonantly with the incident pulses and that different sample-electrode couplings may be identified by appearance of different peaks/valleys in photocurrent spectra from different electrodes. Moreover, qualitative reproduction of experimental spectra of a PbS quantum dot photocell [Karki et al., Nat. Commun. 5(1), 5869 (2014)] reveals the stimulated electron dynamics.
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Affiliation(s)
- Qizhou Chen
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Yan Ho Kwok
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Weijun Zhou
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Guanhua Chen
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Shaul Mukamel
- Department of Chemistry, Department of Physics and Astronomy, University of California, Irvine, California 92617, USA
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5
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Conti I, Cerullo G, Nenov A, Garavelli M. Ultrafast Spectroscopy of Photoactive Molecular Systems from First Principles: Where We Stand Today and Where We Are Going. J Am Chem Soc 2020; 142:16117-16139. [PMID: 32841559 PMCID: PMC7901644 DOI: 10.1021/jacs.0c04952] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Computational spectroscopy is becoming a mandatory tool for the interpretation of the
complex, and often congested, spectral maps delivered by modern non-linear multi-pulse
techniques. The fields of Electronic Structure Methods,
Non-Adiabatic Molecular Dynamics, and Theoretical
Spectroscopy represent the three pillars of the virtual ultrafast
optical spectrometer, able to deliver transient spectra in
silico from first principles. A successful simulation strategy requires a
synergistic approach that balances between the three fields, each one having its very
own challenges and bottlenecks. The aim of this Perspective is to demonstrate that,
despite these challenges, an impressive agreement between theory and experiment is
achievable now regarding the modeling of ultrafast photoinduced processes in complex
molecular architectures. Beyond that, some key recent developments in the three fields
are presented that we believe will have major impacts on spectroscopic simulations in
the very near future. Potential directions of development, pending challenges, and
rising opportunities are illustrated.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
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6
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Teles‐Ferreira DC, Conti I, Borrego‐Varillas R, Nenov A, Van Stokkum IHM, Ganzer L, Manzoni C, Paula AM, Cerullo G, Garavelli M. A Unified Experimental/Theoretical Description of the Ultrafast Photophysics of Single and Double Thionated Uracils. Chemistry 2019; 26:336-343. [DOI: 10.1002/chem.201904541] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Danielle Cristina Teles‐Ferreira
- Departamento de Física Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil
- Electrical Engineering Department Federal Institute of Minas Gerais Formiga MG Brazil
| | - Irene Conti
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
| | - Rocío Borrego‐Varillas
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
| | - Ivo H. M. Van Stokkum
- Department of Physics and Astronomy Faculty of Sciences Vrije Universiteit Amsterdam De Boelelaan 1081 1081HV Amsterdam The Netherlands
| | - Lucia Ganzer
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Cristian Manzoni
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Ana Maria Paula
- Departamento de Física Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil
| | - Giulio Cerullo
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
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7
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Abstract
After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Lausanne Centre for Ultrafast Science (LACUS), FSB, Station 6, CH-1015 Lausanne, Switzerland.
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8
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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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9
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Towards Accurate Simulation of Two-Dimensional Electronic Spectroscopy. Top Curr Chem (Cham) 2018; 376:24. [DOI: 10.1007/s41061-018-0201-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/24/2018] [Indexed: 10/14/2022]
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10
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Segarra-Martí J, Zvereva E, Marazzi M, Brazard J, Dumont E, Assfeld X, Haacke S, Garavelli M, Monari A, Léonard J, Rivalta I. Resolving the Singlet Excited State Manifold of Benzophenone by First-Principles Simulations and Ultrafast Spectroscopy. J Chem Theory Comput 2018; 14:2570-2585. [DOI: 10.1021/acs.jctc.7b01208] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Javier Segarra-Martí
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
| | - Elena Zvereva
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific CentreRussian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
| | - Marco Marazzi
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Johanna Brazard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Elise Dumont
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
| | - Xavier Assfeld
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Stefan Haacke
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
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11
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The highly excited-state manifold of guanine: calibration for nonlinear electronic spectroscopy simulations. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2225-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Zvereva E, Segarra-Martí J, Marazzi M, Brazard J, Nenov A, Weingart O, Léonard J, Garavelli M, Rivalta I, Dumont E, Assfeld X, Haacke S, Monari A. The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone. Photochem Photobiol Sci 2018; 17:323-331. [DOI: 10.1039/c7pp00439g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Modeling time-resolved spectra to unravel ultra fast solvent reorganization.
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13
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Segarra-Martí J, Jaiswal VK, Pepino AJ, Giussani A, Nenov A, Mukamel S, Garavelli M, Rivalta I. Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates. Faraday Discuss 2018; 207:233-250. [DOI: 10.1039/c7fd00201g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry.
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Affiliation(s)
- Javier Segarra-Martí
- Univ Lyon, Ens de Lyon, CNRS
- Université Claude Bernard Lyon 1
- Laboratoire de Chimie UMR 5182
- Lyon
- France
| | - Vishal K. Jaiswal
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Ana Julieta Pepino
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Angelo Giussani
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Shaul Mukamel
- Department of Chemistry
- University of California
- Irvine
- USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Ivan Rivalta
- Univ Lyon, Ens de Lyon, CNRS
- Université Claude Bernard Lyon 1
- Laboratoire de Chimie UMR 5182
- Lyon
- France
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14
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Dijkstra AG, Prokhorenko VI. Simulation of photo-excited adenine in water with a hierarchy of equations of motion approach. J Chem Phys 2017; 147:064102. [DOI: 10.1063/1.4997433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Arend G. Dijkstra
- University of Leeds, School of Chemistry and School of Physics and Astronomy, Leeds LS2 9JT, United Kingdom
| | - Valentyn I. Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
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15
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Giussani A, Marcheselli J, Mukamel S, Garavelli M, Nenov A. On the Simulation of Two-dimensional Electronic Spectroscopy of Indole-containing Peptides. Photochem Photobiol 2017; 93:1368-1380. [PMID: 28380692 DOI: 10.1111/php.12770] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/27/2017] [Indexed: 01/27/2023]
Abstract
A benchmark study of low-cost multiconfigurational CASSCF/CASPT2 schemes for computing the electronic structure of indole is presented. This facilitates the simulation of near-ultraviolet (UV) pump visible (VIS) probe (i.e. two-color) two-dimensional electronic spectra (2DES) of homo- and hetero-aggregates as well as for processing of multiple snapshots from molecular dynamics simulations. Fingerprint excited-state absorption signatures of indole are identified in a broad spectral window between 10 and 25 k cm-1 . The 18-24 k cm-1 spectral window which has no absorption of the monomer and noninteracting aggregates is ideally suited to embed charge-transfer signatures in stacked aggregates. The small peptide Trp-cage, containing a tryptophan and a tyrosine amino acids, having indole and phenol as side chains, respectively, serves to prove the concept. Clear charge-transfer signatures are found in the proposed spectral window for an interchromophore distance of 5 Å making near-UV pump VIS probe 2DES a suitable technique for resolving closely packed aggregates. We demonstrate that 2DES utilizing ultra-short pulses has the potential to resolve the nature of the spectroscopically resolved electronic states and that the line shapes of the excited-state absorption signals can be correlated to the polarity of the relevant states.
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Affiliation(s)
- Angelo Giussani
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy
| | | | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, CA
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy.,Dipartimento di Chimica Industriale "Toso Montanari", Universita degli Studi di Bologna, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy.,Dipartimento di Chimica Industriale "Toso Montanari", Universita degli Studi di Bologna, Bologna, Italy
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16
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Zobel JP, Nogueira JJ, González L. The IPEA dilemma in CASPT2. Chem Sci 2017; 8:1482-1499. [PMID: 28572908 PMCID: PMC5452265 DOI: 10.1039/c6sc03759c] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/23/2016] [Indexed: 12/22/2022] Open
Abstract
Multi-configurational second order perturbation theory (CASPT2) has become a very popular method for describing excited-state properties since its development in 1990. To account for systematic errors found in the calculation of dissociation energies, an empirical correction applied to the zeroth-order Hamiltonian, called the IPEA shift, was introduced in 2004. The errors were attributed to an unbalanced description of open-shell versus closed-shell electronic states and is believed to also lead to an underestimation of excitation energies. Here we show that the use of the IPEA shift is not justified and the IPEA should not be used to calculate excited states, at least for organic chromophores. This conclusion is the result of three extensive analyses. Firstly, we survey the literature for excitation energies of organic molecules that have been calculated with the unmodified CASPT2 method. We find that the excitation energies of 356 reference values are negligibly underestimated by 0.02 eV. This value is an order of magnitude smaller than the expected error based on the calculation of dissociation energies. Secondly, we perform benchmark full configuration interaction calculations on 137 states of 13 di- and triatomic molecules and compare the results with CASPT2. Also in this case, the excited states are underestimated by only 0.05 eV. Finally, we perform CASPT2 calculations with different IPEA shift values on 309 excited states of 28 organic small and medium-sized organic chromophores. We demonstrate that the size of the IPEA correction scales with the amount of dynamical correlation energy (and thus with the size of the system), and gets immoderate already for the molecules considered here, leading to an overestimation of the excitation energies. It is also found that the IPEA correction strongly depends on the size of the basis set. The dependency on both the size of the system and of the basis set, contradicts the idea of a universal IPEA shift which is able to compensate for systematic CASPT2 errors in the calculation of excited states.
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Affiliation(s)
- J Patrick Zobel
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ;
| | - Juan J Nogueira
- 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 . ;
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17
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Segarra-Martí J, Francés-Monerris A, Roca-Sanjuán D, Merchán M. Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2. Molecules 2016; 21:molecules21121666. [PMID: 27918489 PMCID: PMC6274573 DOI: 10.3390/molecules21121666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/16/2022] Open
Abstract
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.
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Affiliation(s)
- Javier Segarra-Martí
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
- Present Address: Laboratoire de Chimie UMR 5182, École Normale Supérieure de Lyon, CNRS, Université de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France.
| | - Antonio Francés-Monerris
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Manuela Merchán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
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Gattuso H, Besancenot V, Grandemange S, Marazzi M, Monari A. From non-covalent binding to irreversible DNA lesions: nile blue and nile red as photosensitizing agents. Sci Rep 2016; 6:28480. [PMID: 27329409 PMCID: PMC4916457 DOI: 10.1038/srep28480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/03/2016] [Indexed: 12/15/2022] Open
Abstract
We report a molecular modeling study, coupled with spectroscopy experiments, on the behavior of two well known organic dyes, nile blue and nile red, when interacting with B-DNA. In particular, we evidence the presence of two competitive binding modes, for both drugs. However their subsequent photophysical behavior is different and only nile blue is able to induce DNA photosensitization via an electron transfer mechanism. Most notably, even in the case of nile blue, its sensitization capabilities strongly depend on the environment resulting in a single active binding mode: the minor groove. Fluorescence spectroscopy confirms the presence of competitive interaction modes for both sensitizers, while the sensitization via electron transfer, is possible only in the case of nile blue.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
| | - Vanessa Besancenot
- Université de Lorraine – Nancy Santé, Biologie, Signal - CRAN, Vandoeuvre-lès-Nancy, France
- CNRS, Santé, Biologie, Signal, CRAN, Vandoeuvre-lès-Nancy, France
| | - Stéphanie Grandemange
- Université de Lorraine – Nancy Santé, Biologie, Signal - CRAN, Vandoeuvre-lès-Nancy, France
- CNRS, Santé, Biologie, Signal, CRAN, Vandoeuvre-lès-Nancy, France
| | - Marco Marazzi
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
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19
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Li Q, Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Voityuk AA, Mukamel S, Roca-Sanjuán D, Garavelli M, Blancafort L. Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate. Chemistry 2016; 22:7497-507. [PMID: 27113273 PMCID: PMC5021121 DOI: 10.1002/chem.201505086] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 02/04/2023]
Abstract
The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.
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Affiliation(s)
- Quansong Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, 100081, Beijing, P.R. China
| | - Angelo Giussani
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Ivan Rivalta
- Univ Lyon, >Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 69342, Lyon, France
| | - Alexander A Voityuk
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilvi, 17071, Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California, 92697-2025, USA
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, 46071, Valencia, Spain
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Univ Lyon, >Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 69342, Lyon, France.
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilvi, 17071, Girona, Spain.
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Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Tolomelli A, Mukamel S, Garavelli M. Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1867-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Nenov A, Giussani A, Fingerhut BP, Rivalta I, Dumont E, Mukamel S, Garavelli M. Spectral lineshapes in nonlinear electronic spectroscopy. Phys Chem Chem Phys 2016; 17:30925-36. [PMID: 26084213 DOI: 10.1039/c5cp01167a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We outline a computational approach for nonlinear electronic spectra, which accounts for the electronic energy fluctuations due to nuclear degrees of freedom and explicitly incorporates the fluctuations of higher excited states, induced by the dynamics in the photoactive state(s). This approach is based on mixed quantum-classical dynamics simulations. Tedious averaging over multiple trajectories is avoided by employing the linearly displaced Brownian harmonic oscillator to model the correlation functions. The present strategy couples accurate computations of the high-lying excited state manifold with dynamics simulations. The application is made to the two-dimensional electronic spectra of pyrene, a polycyclic aromatic hydrocarbon characterized by an ultrafast (few tens of femtoseconds) decay from the bright S2 state to the dark S1 state. The spectra for waiting times t2 = 0 and t2 = 1 ps demonstrate the ability of this approach to model electronic state fluctuations and realistic lineshapes. Comparison with experimental spectra [Krebs et al., New Journal of Physics, 2013, 15, 085016] shows excellent agreement and allows us to unambiguously assign the excited state absorption features.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica G. Ciamician, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy.
| | - Angelo Giussani
- Dipartimento di Chimica G. Ciamician, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy.
| | - Benjamin P Fingerhut
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Strasse 2A, Berlin, 12489, Germany
| | - Ivan Rivalta
- Laboratoire de Chimie, Ecole Normale Suprieure de Lyon, 46, allée d'Italie, 69364 Lyon, France
| | - Elise Dumont
- Laboratoire de Chimie, Ecole Normale Suprieure de Lyon, 46, allée d'Italie, 69364 Lyon, France
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | - Marco Garavelli
- Dipartimento di Chimica G. Ciamician, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy. and Laboratoire de Chimie, Ecole Normale Suprieure de Lyon, 46, allée d'Italie, 69364 Lyon, France
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22
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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: 341] [Impact Index Per Article: 42.6] [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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23
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Theoretical study on the excited-state π-stacking versus intermolecular hydrogen-transfer processes in the guanine–cytosine/cytosine trimer. Theor Chem Acc 2016. [DOI: 10.1007/s00214-015-1762-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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24
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Nenov A, Giussani A, Segarra-Martí J, Jaiswal VK, Rivalta I, Cerullo G, Mukamel S, Garavelli M. Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy. J Chem Phys 2015; 142:212443. [PMID: 26049463 DOI: 10.1063/1.4921016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pump-probe electronic spectroscopy using femtosecond laser pulses has evolved into a standard tool for tracking ultrafast excited state dynamics. Its two-dimensional (2D) counterpart is becoming an increasingly available and promising technique for resolving many of the limitations of pump-probe caused by spectral congestion. The ability to simulate pump-probe and 2D spectra from ab initio computations would allow one to link mechanistic observables like molecular motions and the making/breaking of chemical bonds to experimental observables like excited state lifetimes and quantum yields. From a theoretical standpoint, the characterization of the electronic transitions in the visible (Vis)/ultraviolet (UV), which are excited via the interaction of a molecular system with the incoming pump/probe pulses, translates into the determination of a computationally challenging number of excited states (going over 100) even for small/medium sized systems. A protocol is therefore required to evaluate the fluctuations of spectral properties like transition energies and dipole moments as a function of the computational parameters and to estimate the effect of these fluctuations on the transient spectral appearance. In the present contribution such a protocol is presented within the framework of complete and restricted active space self-consistent field theory and its second-order perturbation theory extensions. The electronic excited states of adenine have been carefully characterized through a previously presented computational recipe [Nenov et al., Comput. Theor. Chem. 1040-1041, 295-303 (2014)]. A wise reduction of the level of theory has then been performed in order to obtain a computationally less demanding approach that is still able to reproduce the characteristic features of the reference data. Foreseeing the potentiality of 2D electronic spectroscopy to track polynucleotide ground and excited state dynamics, and in particular its expected ability to provide conformational dependent fingerprints in dimeric systems, the performances of the selected reduced level of calculations have been tested in the construction of 2D electronic spectra for the in vacuo adenine monomer and the unstacked adenine homodimer, thereby exciting the Lb/La transitions with the pump pulse pair and probing in the Vis to near ultraviolet spectral window.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Angelo Giussani
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Vishal K Jaiswal
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Ivan Rivalta
- Université de Lyon, CNRS, Institut de Chimie de Lyon, École Normale Supérieure de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo Da Vinci 32, IT-20133 Milano, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
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25
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Dumont E, Monari A. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front Chem 2015; 3:43. [PMID: 26236706 PMCID: PMC4500984 DOI: 10.3389/fchem.2015.00043] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.
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Affiliation(s)
- Elise Dumont
- Laboratoire de Chimie, UMR 5182 Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon Lyon, France
| | - Antonio Monari
- Université de Lorraine - Nancy, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France ; Centre National de la Recherche Scientifique, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France
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Altavilla SF, Segarra-Martí J, Nenov A, Conti I, Rivalta I, Garavelli M. Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate. Front Chem 2015; 3:29. [PMID: 25941671 PMCID: PMC4403598 DOI: 10.3389/fchem.2015.00029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/30/2015] [Indexed: 01/17/2023] Open
Abstract
The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.
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Affiliation(s)
| | | | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Irene Conti
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
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