1
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Jaiswal VK, Taddei M, Nascimento DR, Garavelli M, Conti I, Nenov A. Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA. Photochem Photobiol 2024; 100:443-452. [PMID: 38356286 DOI: 10.1111/php.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024]
Abstract
Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain onπ π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained byn π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of theπ π * state leading to a wrongπ π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Mario Taddei
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | | | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
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2
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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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3
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Beal R, Valverde D, Gonçalvez PFB, Borin AC. Photophysics of tz Adenine and tz Guanine fluorescent nucleobases embedded into DNA and RNA. J Comput Chem 2023; 44:2246-2255. [PMID: 37486177 DOI: 10.1002/jcc.27194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
UV-VIS photoinduced events of tz A and tz G embedded into DNA and RNA are described by combining the Extended Multi-State Second-Order Perturbation Theory (XMS-CASPT2) and electrostatic embedding molecular mechanics methods (QM/MM). Our results point out that the S1 1 (ππ* La ) state is the bright state in both environments. After the photoexcitation to the S1 1 (ππ* La ) state, the electronic population evolves barrierless towards its minimum, from where the excess of energy can be dissipated by fluorescence. As the minimum energy crossing point structure between the ground and first bright states lies in a high-energy region, the direct internal conversion to the ground state is an unviable mechanism. Other spectroscopic properties (for instance, absorption and Stokes shifts) and comparisons with photochemical properties of canonical nucleobases are also provided.
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Affiliation(s)
- Roiney Beal
- Grupo de Química Teórica e Computacional, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Danillo Valverde
- Unité de Chimie Physique Théorique et Structurale, Namur Institute of Structured Matter, Université de Namur, Namur, Belgium
| | - Paulo F B Gonçalvez
- Grupo de Química Teórica e Computacional, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
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4
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Ricardi N, González-Espinoza CE, Adam S, Church JR, Schapiro I, Wesołowski TA. Embedding Nonrigid Solutes in an Averaged Environment: A Case Study on Rhodopsins. J Chem Theory Comput 2023; 19:5289-5302. [PMID: 37441785 PMCID: PMC10413860 DOI: 10.1021/acs.jctc.3c00285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Many simulation methods concerning solvated molecules are based on the assumption that the solvated species and the solvent can be characterized by some representative structures of the solute and some embedding potential corresponding to this structure. While the averaging of the solvent configurations to obtain an embedding potential has been studied in great detail, this hinges on a single solute structure representation. This assumption is re-examined and generalized for conformationally flexible solutes and tested on 4 nonrigid systems. In this generalized approach, the solute is characterized by a set of representative structures and the corresponding embedding potentials. The representative structures are identified by means of subdividing the statistical ensemble, which in this work is generated by a constant-temperature molecular dynamics simulation. The embedding potential defined in the Frozen-Density Embedding Theory is used to characterize the average effect of the solvent in each subensemble. The numerical examples concern the vertical excitation energies of protonated retinal Schiff bases in protein environments. It is comprehensively shown that subensemble averaging leads to huge computational savings compared with explicit averaging of the excitation energies in the whole ensemble while introducing only minor errors in the case of the systems examined.
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Affiliation(s)
- Niccolò Ricardi
- Department of Physical Chemistry, University of Geneva, 1205 Geneva, Switzerland
| | | | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem Israel, 91904 Jerusalem, Israel
| | - Jonathan R Church
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem Israel, 91904 Jerusalem, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem Israel, 91904 Jerusalem, Israel
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5
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Krul SE, Costa GJ, Hoehn SJ, Valverde D, Oliveira LMF, Borin AC, Crespo-Hernández CE. Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-Aza-7-Deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet. Photochem Photobiol 2022; 99:693-705. [PMID: 35938218 DOI: 10.1111/php.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The guanine derivative, 5-aza-7-deazaguanine (5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art Extended Multi-State Complete Active Space Second-Order Perturbation Theory. It is demonstrated that excitation to the lowest energy 1 ππ* state of 5N7C G results in complex dynamics leading to ca. 10 to 30-fold slower relaxation (depending on solvent) compared to guanine. A significant conformational change occurs at the S1 minimum, resulting in a 10-fold greater fluorescence quantum yield compared to guanine. The fluorescence quantum yield and S1 decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S1 minimum and the S1 /S0 conical intersection going from water to propanol. The longer lifetimes might make 5N7C G more photochemical active to adjacent nucleobases than guanine or other nucleobases within DNA.
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Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Gustavo J Costa
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Danillo Valverde
- Unité de Chimie Physique Theorique et Structurale, Namur Institute of Structured Matter, Université de Namur, B-5000, Namur, Belgium
| | - Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Carlos E Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
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6
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Valverde D, Georg HC, Canuto S. Free-Energy Landscape of the S N2 Reaction CH 3Br + Cl - → CH 3Cl + Br - in Different Liquid Environments. J Phys Chem B 2022; 126:3685-3692. [PMID: 35543431 DOI: 10.1021/acs.jpcb.1c10282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This work describes in detail the reaction path of the well-known SN2 reaction CH3Br + Cl- → CH3Cl + Br-, whose reaction rate has a huge variation with the solvent in the gas phase and in protic and aprotic liquid environments. We employed the ASEC-FEG method to optimize for minima (reactants and products) and saddle points (transition states) in the in-solution free-energy hypersurface. The method takes atomistic details of the solvent into account. A polarizable continuum model (PCM) has also been employed for comparison. The most perceptive structural changes are noted in aqueous solution by using the ASEC-FEG approach. The activation energies in all solvents, estimated by means of free-energy perturbation calculations, are in good agreement with the experimental data. The total solute-solvent hydrogen bonds play an important role in the increased barrier height observed in water and are therefore crucial to explain the huge decrease in the kinetic constant. It is also found that the hydration shell around the ions breaks itself spontaneously to accommodate the molecule, thus forming minimum energy complexes.
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Affiliation(s)
- Danillo Valverde
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371 Cidade Universitária, CEP 05508-090 São Paulo, São Paulo, Brazil
| | - Herbert C Georg
- Instituto de Física, Universidade Federal de Goiás, Avenida Esperança, Campus Samambaia, CEP 74690-900 Goiânia, Goiás, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371 Cidade Universitária, CEP 05508-090 São Paulo, São Paulo, Brazil
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7
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González-Espinoza CE, Rumble CA, Borgis D, Wesolowski TA. Quantifying Fluctuations of Average Solvent Environments for Embedding Calculations. J Chem Theory Comput 2022; 18:1072-1088. [PMID: 35044168 DOI: 10.1021/acs.jctc.1c01108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The viability and effectiveness of replacing an ensemble of embedded solute calculations by a single calculation using an average description of the solvent environment are evaluated. This work explores the fluctuations of the average description of the system obtained in two ways: from calculations on an ensemble of geometries and from an average environment constructed from the same ensemble. To this end, classical molecular dynamics simulations of a rigid acetone solute in SPCE water are performed in order to generate an ensemble of solvent environments. From this ensemble of solvent configurations, a number of different approaches for constructing an average solvent environment are employed. We perform a thorough numerical analysis of the fluctuations of the electrostatic potential experienced by the solute, as well as the resulting fluctuations of the solute's electronic density, measured through its dipole moment and fitted atomic point charges. At the same time, we inspect the accuracy of the methods used to construct average environments. Finally, the proposed method for generating the embedding potential from an average environment density is applied to estimate the solvatochromic shift of the first excitation of acetone. In order to account for quantum confinement effects, which may be important in certain cases, the fluctuations in the shift due to the interaction with the solvent are evaluated using frozen-density-embedding theory. Our results demonstrate that, for normally distributed environments, the constructed average environment is a reasonably good representation of a fluctuating molecular solvent environment. We then provide guidance for future comparisons between these theoretical treatments of solute/solvent systems to experimental measurements.
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Affiliation(s)
| | - Christopher A Rumble
- Université de Genève, Départment de Chimie Physique 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Daniel Borgis
- Ecole Normale Supérieure, Départment de Chimie, UMR 8640, PSL University, Sorbonne University, CNRS, 75005 Paris, France
| | - Tomasz A Wesolowski
- Université de Genève, Départment de Chimie Physique 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
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8
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Valverde D, de Araújo AVS, Borin AC. Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil. Molecules 2021; 26:5191. [PMID: 34500625 PMCID: PMC8434193 DOI: 10.3390/molecules26175191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning's cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the S11(ππ*) bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the S11(ππ*) bright state to the T23(nπ*) triplet state via an intersystem crossing process involving the (S11(ππ*)/T23(nπ*))STCP singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the S11(ππ*) state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the S11(ππ*) potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent.
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Affiliation(s)
- Danillo Valverde
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
| | | | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
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9
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Nikolaev DM, Manathunga M, Orozco-Gonzalez Y, Shtyrov AA, Guerrero Martínez YO, Gozem S, Ryazantsev MN, Coutinho K, Canuto S, Olivucci M. Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems. J Chem Theory Comput 2021; 17:5885-5895. [PMID: 34379429 DOI: 10.1021/acs.jctc.1c00221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel technique for computing the free energy differences between two chromophore "isomers" hosted in a molecular environment (a generalized solvent). Such an environment may range from a relatively rigid protein cavity to a flexible solvent environment. The technique is characterized by the application of the previously reported "average electrostatic solvent configuration" method, and it is based on the idea of using the free energy perturbation theory along with a chromophore annihilation procedure in thermodynamic cycle calculations. The method is benchmarked by computing the ground-state room-temperature relative stabilities between (i) the cis and trans isomers of prototypal animal and microbial rhodopsins and (ii) the analogue isomers of a rhodopsin-like light-driven molecular switch in methanol. Furthermore, we show that the same technology can be used to estimate the activation free energy for the thermal isomerization of systems i-ii by replacing one isomer with a transition state. The results show that the computed relative stability and isomerization barrier magnitudes for the selected systems are in line with the available experimental observation in spite of their widely diverse complexity.
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Affiliation(s)
- Dmitrii M Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | | | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Mikhail N Ryazantsev
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia.,Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy.,Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg-CNRS, UMR 7504, F-67034 Strasbourg, France
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10
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Manzoni V, Gester R, da Cunha AR, Andrade-Filho T, Gester R. Solvent effects on Stokes shifts, and NLO response of thieno[3,4-b]pyrazine: A comprehensive QM/MM investigation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115996] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Gonçalves A, Raiol A, da Cunha AR, Manzoni V, Andrade-Filho T, Gester R. Insights on the crossing of the two lowest n-π∗ and π-π∗ absorption lines of thieno[3,4-b]pyrazine in an aqueous environment. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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13
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Cornetta LM, Coutinho K, Varella MTDN. Solvent effects on the π* shape resonances of uracil. J Chem Phys 2020; 152:084301. [DOI: 10.1063/1.5139459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- L. M. Cornetta
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
| | - K. Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
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14
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Valverde D, Sanches de Araujo AV, Canuto S, Borin AC. Photophysics of Emissive
tz
C[Isothiazolo‐Cytidine] and
tz
U[Isothiazolo‐Uridine] Pyrimidine Analogues. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Danillo Valverde
- Institute of PhysicsUniversity of São Paulo Rua do Matão 1371 São Paulo, SP 05508-090 Brazil
| | | | - Sylvio Canuto
- Institute of PhysicsUniversity of São Paulo Rua do Matão 1371 São Paulo, SP 05508-090 Brazil
| | - Antonio Carlos Borin
- Department of Fundamental ChemistryInstitute of ChemistryUniversity of São Paulo Avenida Professor Lineu Prestes, 748 São Paulo SP, 05508-000 Brazil
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15
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Ding Y, Wang X, Xie L, Yao X, Xu W. Two-dimensional self-assembled nanostructures of nucleobases and their related derivatives on Au(111). Chem Commun (Camb) 2018; 54:9259-9269. [PMID: 30027963 DOI: 10.1039/c8cc03585g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The construction of two-dimensional (2D) self-assembled nanostructures has been one of the considerably interesting areas of on-surface chemistry in the past few decades, and has benefited from the rapid development and improvement of scanning probe microscopy techniques. In this research field, many attempts have been made in the controllable fabrication of well-ordered and multifunctional surface nanostructures, which attracted interest because of the prospect for artificial design of functional molecular nanodevices. DNA and RNA are considered to be programmable self-assembly systems and it is possible to use their base sequences to encode instructions for assembly in a predetermined fashion at the nanometer scale. As important constituents of nucleic acids, nucleobases, with intrinsic functional groups for hydrogen bonding, coordination bonding, and electrostatic interactions, can be employed as a potential system for the versatile construction of various biomolecular nanostructures, which may be used to structure the self-assembly of DNA-based artificial molecular constructions and play an important role in novel biosensors based on surface functionalization. In this article, we will review the recent progress of on-surface self-assembly of nucleobases and their derivatives together with different reactants (e.g., metals, halogens, salts and water), and as a result, various 2D surface nanostructures are summarized.
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Affiliation(s)
- Yuanqi Ding
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
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16
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First hyperpolarizability of isomers of pyridinium N-phenoxide betaine dye in solution using the ASEC-FEG method. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Gueye M, Manathunga M, Agathangelou D, Orozco Y, Paolino M, Fusi S, Haacke S, Olivucci M, Léonard J. Engineering the vibrational coherence of vision into a synthetic molecular device. Nat Commun 2018; 9:313. [PMID: 29358689 PMCID: PMC5778125 DOI: 10.1038/s41467-017-02668-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/15/2017] [Indexed: 11/09/2022] Open
Abstract
The light-induced double-bond isomerization of the visual pigment rhodopsin operates a molecular-level optomechanical energy transduction, which triggers a crucial protein structure change. In fact, rhodopsin isomerization occurs according to a unique, ultrafast mechanism that preserves mode-specific vibrational coherence all the way from the reactant excited state to the primary photoproduct ground state. The engineering of such an energy-funnelling function in synthetic compounds would pave the way towards biomimetic molecular machines capable of achieving optimum light-to-mechanical energy conversion. Here we use resonance and off-resonance vibrational coherence spectroscopy to demonstrate that a rhodopsin-like isomerization operates in a biomimetic molecular switch in solution. Furthermore, by using quantum chemical simulations, we show why the observed coherent nuclear motion critically depends on minor chemical modifications capable to induce specific geometric and electronic effects. This finding provides a strategy for engineering vibrationally coherent motions in other synthetic systems. The ultrafast, vibrationally coherent photoisomerization of rhodopsin is a model of efficient photomechanical energy conversion at the molecular scale. Here, the authors demonstrate a similar photoreaction in synthetic compounds, unraveling the underlying mechanism and discussing its implications.
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Affiliation(s)
- Moussa Gueye
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France
| | - Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Damianos Agathangelou
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France
| | - Yoelvis Orozco
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France
| | - Marco Paolino
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100, Siena, Italy
| | - Stefania Fusi
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100, Siena, Italy
| | - Stefan Haacke
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France
| | - Massimo Olivucci
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France. .,Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA. .,Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100, Siena, Italy.
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France.
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18
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Valverde D, da Costa Ludwig ZM, da Costa CR, Ludwig V, Georg HC. Zwitterionization of glycine in water environment: Stabilization mechanism and NMR spectral signatures. J Chem Phys 2018; 148:024305. [PMID: 29331136 DOI: 10.1063/1.5006645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
At physiological conditions, myriads of biomolecules (e.g., amino acids, peptides, and proteins) exist predominantly in the zwitterionic structural form and their biological functions will result in these conditions. However these geometrical structures are inaccessible energetically in the gas phase, and at this point, stabilization of amino-acids in physiological conditions is still under debate. In this paper, the electronic properties of a glycine molecule in the liquid environment were studied by performing a relaxation of the glycine geometry in liquid water using the free energy gradient method combined with a sequential quantum mechanics/molecular mechanics approach. A series of Monte Carlo Metropolis simulations of the glycine molecule embedded in liquid water, followed by only a quantum mechanical calculation in each of them were carried out. Both the local and global liquid environments were emphasized to obtain nuclear magnetic resonance (NMR) parameters for the glycine molecule in liquid water. The results of the equilibrium structure in solution and the systematic study of the hydrogen bonds were used to discard the direct proton transfer from the carboxyl group to the ammonium group of the glycine molecule in water solution. The calculations of the Density Functional Theory (DFT) were performed to study the polarization of the solvent in the parameters of nuclear magnetic resonance of the glycine molecule in liquid water. DFT calculations predicted isotropic chemical changes on the H, C, N, and O atoms of glycine in liquid water solution which agree with the available experimental data.
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Affiliation(s)
- Danillo Valverde
- Instituto de Física, Universidade Federal de Goiás, CP 131, 74001-970 Goiânia, GO, Brazil
| | | | | | - Valdemir Ludwig
- Departamento de Física, Universidade Federal de Juiz de Fora, CP 36036-330 Juiz de Fora, MG, Brazil
| | - Herbert C Georg
- Instituto de Física, Universidade Federal de Goiás, CP 131, 74001-970 Goiânia, GO, Brazil
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19
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Cerezo J, Liu Y, Lin N, Zhao X, Improta R, Santoro F. Mixed Quantum/Classical Method for Nonadiabatic Quantum Dynamics in Explicit Solvent Models: The ππ*/nπ* Decay of Thymine in Water as a Test Case. J Chem Theory Comput 2018; 14:820-832. [PMID: 29207245 DOI: 10.1021/acs.jctc.7b01015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mutual coupling of the solute and solvent dynamics is included within a mean-field framework and the quantum and classical equations of motions are solved simultaneously. As a test case we apply our method to the ultrafast ππ* → nπ* decay of thymine in water. Solvent dynamical response modifies IC yield already on the 50 fs time scale. This effect is due to water librational motions that stabilize the most populated state. Pure static disorder, that is, the existence of different solvent configurations when photoexcitation takes place, also has a remarkable impact on the dynamics.
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Affiliation(s)
- Javier Cerezo
- 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.,Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Yanli Liu
- 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.,School of Physics and Optoelectronics Engineering, Ludong University , 264025 Yantai, P. R. China
| | - Na Lin
- State Key Laboratory of Crystal Materials, Shandong University , 250100 Jinan, Shandong, P. R. China
| | - Xian Zhao
- State Key Laboratory of Crystal Materials, Shandong University , 250100 Jinan, Shandong, P. R. China
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR) , via Mezzocannone 16, I-80136 Napoli, Italy.,LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - 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
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20
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Orozco-Gonzalez Y, Manathunga M, Marín MDC, Agathangelou D, Jung KH, Melaccio F, Ferré N, Haacke S, Coutinho K, Canuto S, Olivucci M. An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems. J Chem Theory Comput 2017; 13:6391-6404. [DOI: 10.1021/acs.jctc.7b00860] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoelvis Orozco-Gonzalez
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Madushanka Manathunga
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - María del Carmen Marín
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Damianos Agathangelou
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kwang-Hwan Jung
- Department
of Life Science and Institute of Biological Interfaces, Sogang University 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Korea
| | - Federico Melaccio
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
| | - Stefan Haacke
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Massimo Olivucci
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
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21
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Valverde D, Vasconcelos Sanches de Araujo A, Carlos Borin A, Canuto S. Electronic structure and absorption spectra of fluorescent nucleoside analogues. Phys Chem Chem Phys 2017; 19:29354-29363. [PMID: 29075734 DOI: 10.1039/c7cp04885h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This work presents a systematic investigation of the electronic and conformational properties of five new fluorescent nucleobases belonging to the alphabet based on the isothiazole[4,3-d]pyrimidine molecule, very recently synthesized. This is of particular importance in the characterization of the main electronic aspects of these fluorescent nucleosides. The solvent effects of 1,4-dioxane and water were included combining the Sequential Monte Carlo/CASPT2 and the Free Energy Gradient (FEG) methods. For comparison, the Polarizable Continuum method was also used. The geometries of all compounds were optimized in solvent with the largest effects observed in water using the average solvent electrostatic configuration (ASEC) and the FEG approaches. Statistical analysis of the solute-solvent hydrogen bonds is performed and their effect on the absorption spectra analyzed. The dipole moments were calculated and the value obtained from the ASEC-FEG method in water follows the same trend as the natural canonical bases (adenine → uracil → guanine → cytosine). The theoretical results for the absorption spectra obtained from CASPT2(18,13) calculations using the geometries obtained with the ASEC-FEG procedure are in very good agreement with the experimental data. A detailed elucidation of the main aspects of the absorption spectra of the five new fluorescent nucleoside analogues is successfully attempted.
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Affiliation(s)
- Danillo Valverde
- Universidade de São Paulo, Instituto de Física, Rua do Matão 1371, São Paulo, SP CEP 05508-090, Brazil.
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22
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Brandão I, Franco LR, Fonseca TL, Castro MA, Georg HC. Confirming the relationship between first hyperpolarizability and the bond length alternation coordinate for merocyanine dyes. J Chem Phys 2017; 146:224505. [DOI: 10.1063/1.4985672] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Idney Brandão
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Leandro R. Franco
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Tertius L. Fonseca
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Marcos A. Castro
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Herbert C. Georg
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
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23
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Franco LR, Brandão I, Fonseca TL, Georg HC. Elucidating the structure of merocyanine dyes with the ASEC-FEG method. Phenol blue in solution. J Chem Phys 2016; 145:194301. [DOI: 10.1063/1.4967290] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Leandro R. Franco
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Idney Brandão
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Tertius L. Fonseca
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Herbert C. Georg
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
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24
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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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25
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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: 321] [Impact Index Per Article: 40.1] [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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