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Asha H, Green JA, Esposito L, Martinez-Fernandez L, Santoro F, Improta R. Effect of the Thermal Fluctuations of the Photophysics of GC and CG DNA Steps: A Computational Dynamical Study. J Phys Chem B 2022; 126:10608-10621. [PMID: 36508709 DOI: 10.1021/acs.jpcb.2c05688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC)5 sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50-100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.
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Affiliation(s)
- Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438Frankfurt am Main, Germany
| | - Luciana Esposito
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autònoma de Madrid, Campus de Excelencia UAM-CSIC, 28049Madrid, Spain
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800Kongens Lyngby, Denmark
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Vayá I, Gustavsson T, Markovitsi D. High-Energy Long-Lived Emitting Mixed Excitons in Homopolymeric Adenine-Thymine DNA Duplexes. Molecules 2022; 27:molecules27113558. [PMID: 35684495 PMCID: PMC9181881 DOI: 10.3390/molecules27113558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
The publication deals with polymeric pA●pT and oligomeric A20●T20 DNA duplexes whose fluorescence is studied by time-correlated single photon counting. It is shown that their emission on the nanosecond timescale is largely dominated by high-energy components peaking at a wavelength shorter than 305 nm. Because of their anisotropy (0.02) and their sensitivity to base stacking, modulated by the duplex size and the ionic strength of the solution, these components are attributed to mixed ππ*/charge transfer excitons. As high-energy long-lived excited states may be responsible for photochemical reactions, their identification via theoretical studies is an important challenge.
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Affiliation(s)
- Ignacio Vayá
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain;
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
| | - Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Correspondence:
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Ru X, Crane BR, Zhang P, Beratan DN. Why Do Most Aromatics Fail to Support Hole Hopping in the Cytochrome c Peroxidase-Cytochrome c Complex? J Phys Chem B 2021; 125:7763-7773. [PMID: 34235935 DOI: 10.1021/acs.jpcb.1c05064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transport through aromatic species (especially tryptophan and tyrosine) plays a central role in water splitting, redox signaling, oxidative damage protection, and bioenergetics. The cytochrome c peroxidase (CcP)-cytochrome c (Cc) complex (CcP:Cc) is used widely to study interprotein electron transfer (ET) mechanisms. Tryptophan 191 (Trp191) of CcP supports hole hopping charge recombination in the CcP:Cc complex. Experimental studies find that when Trp191 is substituted by tyrosine, phenylalanine, or redox-active aniline derivatives bound in the W191G cavity, enzymatic activity and charge recombination rates both decrease. Theoretical analysis of these CcP:Cc complexes finds that the ET kinetics depend strongly on the chemistry of the modified Trp site. The computed electronic couplings in the W191F and W191G species are orders of magnitude smaller than in the native protein, due largely to the absence of a hopping intermediate and the large tunneling distance. Small molecules bound in the W191G cavity are weakly coupled electronically to the Cc heme, and the structural disorder of the guest molecule in the binding pocket may contribute further to the lack of enzymatic activity. The couplings in W191Y are not substantially weakened compared to the native species, but the redox potential difference for tyrosine vs tryptophan oxidation accounts for the slower rate in the Tyr mutant. Thus, theoretical analysis explains why only the native Trp supports rapid hole hopping in the CcP:Cc complex. Favorable free energies and electronic couplings are essential for establishing an efficient hole hopping relay in this protein-protein complex.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States
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Schwermann C, Doltsinis NL. Exciton transfer free energy from Car-Parrinello molecular dynamics. Phys Chem Chem Phys 2020; 22:10526-10535. [PMID: 31974540 DOI: 10.1039/c9cp06419b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A computational approach is presented which allows the calculation of free energies profiles for exciton transfer processes within the framework of ab initio molecular dynamics (AIMD) simulations, sampling both the electronic and the nuclear degrees of freedom. To achieve this, restraining potentials are imposed on the centres of maximally localized Wannier orbitals. The resulting quantum-mechanical orbital forces are derived analytically and implemented in an AIMD program. In analogy to classical umbrella sampling techniques, these restraints are used to control an exciton transfer by incrementally moving the Wannier centres corresponding to the electron-hole pair along a suitable reaction coordinate. The new method is applied to study exciton transfer between two stacked penta(3-methylthiophene) molecules as a function of intermolecular distance. From the resulting free energy profiles, exciton transfer rates and diffusion constants are estimated, which prove to be in line with experimental results.
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Affiliation(s)
- Christian Schwermann
- Institute of Solid State Theory and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany.
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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Zámečníková M, Nachtigallová D. Photodynamic behavior of electronic coupling in a N-methylformamide dimer. Phys Chem Chem Phys 2015; 17:12356-64. [DOI: 10.1039/c4cp04573d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the bridging water molecules has been studied during the excited state photodynamics of a N-methylformamide dimer in complex with water molecules employing the complete active space self-consistent field (CASSCF) and CAS perturbation theory (CASPT2) methods.
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Voityuk AA. Intermediate neglect of differential overlap for spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1141] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Voityuk AA. Effects of dynamic disorder on exciton delocalization and photoinduced charge separation in DNA. Photochem Photobiol Sci 2013; 12:1303-9. [DOI: 10.1039/c2pp25389e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Szalay PG, Watson T, Perera A, Lotrich V, Fogarasi G, Bartlett RJ. Benchmark Studies on the Building Blocks of DNA. 2. Effect of Biological Environment on the Electronic Excitation Spectrum of Nucleobases. J Phys Chem A 2012; 116:8851-60. [DOI: 10.1021/jp305130q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Péter G. Szalay
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Thomas Watson
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Ajith Perera
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Victor Lotrich
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Géza Fogarasi
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Rodney J. Bartlett
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
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Lu Y, Lan Z, Thiel W. Monomeric adenine decay dynamics influenced by the DNA environment. J Comput Chem 2012; 33:1225-35. [DOI: 10.1002/jcc.22952] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/09/2012] [Accepted: 01/16/2012] [Indexed: 01/25/2023]
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Koyama T, Miyata Y, Asaka K, Shinohara H, Saito Y, Nakamura A. Ultrafast energy transfer of one-dimensional excitons between carbon nanotubes: a femtosecond time-resolved luminescence study. Phys Chem Chem Phys 2012; 14:1070-84. [DOI: 10.1039/c1cp22781e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Effect of introducing thymine spacers into an adenine strand: Electronic decoupling? J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2011.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Curutchet C, Voityuk AA. Triplet-Triplet Energy Transfer in DNA: A Process that Occurs on the Nanosecond Timescale. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201004732] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Curutchet C, Voityuk AA. Triplet-triplet energy transfer in DNA: a process that occurs on the nanosecond timescale. Angew Chem Int Ed Engl 2011; 50:1820-2. [PMID: 21328647 DOI: 10.1002/anie.201004732] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 11/29/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Carles Curutchet
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain.
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