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Boulatov A, Burin AL. Crucial effect of transverse vibrations on the transport through polymer chains. J Chem Phys 2020; 153:134102. [PMID: 33032425 DOI: 10.1063/5.0018591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The low temperature transport of electron, or vibrational or electronic exciton toward polymer chains, turns out to be dramatically sensitive to its interaction with transverse acoustic vibrations. We show that this interaction leads to a substantial polaron effect and decoherence, which are generally stronger than those associated with longitudinal vibrations. For site-dependent interactions, transverse phonons form subohmic bath leading to the quantum phase transition accompanied by full suppression of the transport at zero temperature and fast decoherence characterized by temperature dependent rate k2 ∝ T3/4 at low temperature, while k2 ∝ T2 for site-independent interactions. The latter dependence was used to interpret recent measurements of temperature dependent vibrational energy transport in polyethylene glycol oligomers.
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Affiliation(s)
- Alexei Boulatov
- National Research University Higher School of Economics, 11 Pokrovsky Blvd., Moscow 101000, Russia
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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Woźniak AP, Leś A, Adamowicz L. Theoretical modeling of DNA electron hole transport through polypyrimidine sequences: a QM/MM study. J Mol Model 2019; 25:97. [PMID: 30874898 DOI: 10.1007/s00894-019-3976-9] [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: 12/23/2018] [Accepted: 02/20/2019] [Indexed: 11/25/2022]
Abstract
The phenomenon of DNA hole transport (HT) has attracted of scientists for several decades, mainly due to its potential application in molecular electronics. As electron holes mostly localize on purine bases in DNA, the majority of scientific effort has been invested into chemically modifying the structures of adenine and guanine in order to increase their HT-mediating properties. In this work we examine an alternative, never yet explored, way of affecting the HT efficiency by forcing electron holes to localize on pyrimidine bases and move between them. Using an enhanced and revised version of our previously developed QM/MM model, we perform simulations of HT through polyadenine, polycytosine, polyguanine, and polythymine stacks according to a multistep hopping mechanism. From these simulations, kinetic parameters for HT are obtained. The results indicate a particularly high efficiency of cytosine→cytosine hopping, which is about ten times higher than the G → G hopping. We also discuss possible improvement of cytosine HT by modifying the oxidoreductive properties of complementary guanine residues.
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Affiliation(s)
| | - Andrzej Leś
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
- Pharmaceutical Research Institute, Rydygiera 8, 01-793, Warsaw, Poland
| | - Ludwik Adamowicz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, AZ, 85721, USA.
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Toruń, Poland.
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Kubař T, Elstner M. A hybrid approach to simulation of electron transfer in complex molecular systems. J R Soc Interface 2013; 10:20130415. [PMID: 23883952 DOI: 10.1098/rsif.2013.0415] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors.
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Affiliation(s)
- Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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Kubař T, Elstner M. Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA. Phys Chem Chem Phys 2013; 15:5794-813. [PMID: 23493847 DOI: 10.1039/c3cp44619k] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In this work, a fragment-orbital density functional theory-based method is combined with two different non-adiabatic schemes for the propagation of the electronic degrees of freedom. This allows us to perform unbiased simulations of electron transfer processes in complex media, and the computational scheme is applied to the transfer of a hole in solvated DNA. It turns out that the mean-field approach, where the wave function of the hole is driven into a superposition of adiabatic states, leads to over-delocalization of the hole charge. This problem is avoided using a surface hopping scheme, resulting in a smaller rate of hole transfer. The method is highly efficient due to the on-the-fly computation of the coarse-grained DFT Hamiltonian for the nucleobases, which is coupled to the environment using a QM/MM approach. The computational efficiency and partial parallel character of the methodology make it possible to simulate electron transfer in systems of relevant biochemical size on a nanosecond time scale. Since standard non-polarizable force fields are applied in the molecular-mechanics part of the calculation, a simple scaling scheme was introduced into the electrostatic potential in order to simulate the effect of electronic polarization. It is shown that electronic polarization has an important effect on the features of charge transfer. The methodology is applied to two kinds of DNA sequences, illustrating the features of transfer along a flat energy landscape as well as over an energy barrier. The performance and relative merit of the mean-field scheme and the surface hopping for this application are discussed.
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Affiliation(s)
- Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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Barnett RN, Joseph J, Landman U, Schuster GB. Oxidative Thymine Mutation in DNA: Water-Wire-Mediated Proton-Coupled Electron Transfer. J Am Chem Soc 2013; 135:3904-14. [DOI: 10.1021/ja311282k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Robert N. Barnett
- School of Physics, Georgia Institute of Technology, Atlanta,
Georgia 30332-0430, United States
| | - Joshy Joseph
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Uzi Landman
- School of Physics, Georgia Institute of Technology, Atlanta,
Georgia 30332-0430, United States
| | - Gary B. Schuster
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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Tesar SL, Leveritt JM, Kurnosov AA, Burin AL. Temperature dependence for the rate of hole transfer in DNA: Nonadiabatic regime. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Pavanello M, Neugebauer J. Modelling charge transfer reactions with the frozen density embedding formalism. J Chem Phys 2011; 135:234103. [DOI: 10.1063/1.3666005] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Venkatramani R, Keinan S, Balaeff A, Beratan DN. Nucleic Acid Charge Transfer: Black, White and Gray. Coord Chem Rev 2011; 255:635-648. [PMID: 21528017 PMCID: PMC3081592 DOI: 10.1016/j.ccr.2010.12.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Theoretical studies of charge transport in deoxyribonucleic acid (DNA) and peptide nucleic acid (PNA) indicate that structure and dynamics modulate the charge transfer rates, and that different members of a structural ensemble support different charge transport mechanisms. Here, we review the influences of nucleobase geometry, electronic structure, solvent environment, and thermal conformational fluctuations on the charge transfer mechanism. We describe an emerging framework for understanding the diversity of charge transport mechanisms seen in nucleic acids.
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Affiliation(s)
| | - Shahar Keinan
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Alexander Balaeff
- Department of Chemistry, Duke University, Durham, North Carolina 27708
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Conron SMM, Thazhathveetil AK, Wasielewski MR, Burin AL, Lewis FD. Direct Measurement of the Dynamics of Hole Hopping in Extended DNA G-Tracts. An Unbiased Random Walk. J Am Chem Soc 2010; 132:14388-90. [DOI: 10.1021/ja106991f] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Blaustein GS, Lewis FD, Burin AL. Kinetics of Charge Separation in Poly(A)−Poly(T) DNA Hairpins. J Phys Chem B 2010; 114:6732-9. [DOI: 10.1021/jp101328t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Gail S. Blaustein
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, and Department of Northwestern University, Evanston, Illinois 60208
| | - Frederick D. Lewis
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, and Department of Northwestern University, Evanston, Illinois 60208
| | - Alexander L. Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, and Department of Northwestern University, Evanston, Illinois 60208
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Pavanello M, Adamowicz L, Volobuyev M, Mennucci B. Modeling Hole Transport in Wet and Dry DNA. J Phys Chem B 2010; 114:4416-23. [DOI: 10.1021/jp9099094] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Michele Pavanello
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Ludwik Adamowicz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Maksym Volobuyev
- Department of Chemistry, Kharkiv Polytechnical Institute, Kharkiv, Ukraine
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy
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Vladimirov E, Ivanova A, Rösch N. Solvent Reorganization Energies in A-DNA, B-DNA, and Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations with a Polarizable Force Field. J Phys Chem B 2009; 113:4425-34. [DOI: 10.1021/jp809774q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Egor Vladimirov
- Theoretische Chemie, Department Chemie, Technische Universität München, 85748 Garching, Germany, and Department of Physical Chemistry, Faculty of Chemistry, University of Sofia, 1 J. Bourchier Ave., 1164 Sofia, Bulgaria
| | - Anela Ivanova
- Theoretische Chemie, Department Chemie, Technische Universität München, 85748 Garching, Germany, and Department of Physical Chemistry, Faculty of Chemistry, University of Sofia, 1 J. Bourchier Ave., 1164 Sofia, Bulgaria
| | - Notker Rösch
- Theoretische Chemie, Department Chemie, Technische Universität München, 85748 Garching, Germany, and Department of Physical Chemistry, Faculty of Chemistry, University of Sofia, 1 J. Bourchier Ave., 1164 Sofia, Bulgaria
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Burin AL, Dickman JA, Uskov DB, Hebbard CFF, Schatz GC. Optical absorption spectra and monomer interaction in polymers: Investigation of exciton coupling in DNA hairpins. J Chem Phys 2008; 129:091102. [DOI: 10.1063/1.2977727] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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