Dynamics of laser-excited stacked adenines: Semiclassical simulations

Dou, Yusheng; Liu, Zhicheng; Yuan, Shuai; Zhang, Wenying; Tang, Hong; Zhao, Jiashe; Fang, Wei‐Hai; Lo, Glenn V.

doi:10.1016/j.ijbiomac.2012.10.006

Cited by 6 publications

(6 citation statements)

References 57 publications

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“…MQC Ehrenfest-type dynamics of stacked dimers of Ade were reported in a series of papers by Dou et al − exploiting the same SERID/DFTB approach also adopted for pyrimidine dimers (see section ). , Though treating the nuclei classically and using an average potential for the ES PESs, this approach considers explicitly all the nuclear DoF and can describe bond formation and decay to the GS.…”

Section: Oligonucleotides: Base Stackingmentioning

confidence: 99%

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

2016

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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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Section: Oligonucleotides: Base Stackingmentioning

confidence: 99%

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

2016

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“…A hierarchy of different methods is available to describe the excited states and potential energy surfaces of interacting nucleobases [ 31 ]. A starting point is given through the usage of effective exciton models [ 32 , 33 , 34 ] or the application of semi-empirical models, either based on wavefunctions [ 35 , 36 , 37 , 38 ] or on density functional tight binding (DFTB) [ 39 , 40 ]. Such approaches allow for an efficient description of large systems and extended dynamics simulations.…”

Section: Potential Energy Surfacesmentioning

confidence: 99%

“…When interacting bases are considered, charge transfer states come into play, which are problematic for TDDFT [ 41 ]. A particularly challenging task is the description of processes where the nucleobases approach each other, such as exciplex formation [ 18 , 38 , 67 , 69 ] and dimerization [ 10 , 70 , 71 ], considering that the evaluation of accurate interaction potentials between nucleobases is already difficult in the ground state [ 15 ]. Aside from the general description of the excited states, it is a particular problem that, when the nucleobases approach each other, there is a strong basis set superposition error [ 59 ] that cannot be remedied by a simple counterpoise correction [ 69 ].…”

Section: Potential Energy Surfacesmentioning

confidence: 99%

Challenges in Simulating Light-Induced Processes in DNA

et al. 2016

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In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.

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“…7) cannot achieve identical geometries without flipping over one of the bases, a motion thought to occur on subnanosecond time scales. This could indicate that the excimer state formed in high yield is not a neutral or bonded excimer [59,107,108,163,164], the energy and lifetime of which might be expected to depend sensitively on geometry. Instead, an excimer which is essentially a contact radical ion pair similar to those observed in d(OA) and other base heterodimers (Sect.…”

Section: Excimer Lifetimes and Stacking Geometrymentioning

confidence: 99%

Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy

Chen

Zhang

Kohler

2014

Topics in Current Chemistry

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Ultrafast laser experiments on carefully selected DNA model compounds probe the effects of base stacking, base pairing, and structural disorder on excited electronic states formed by UV absorption in single and double DNA strands. Direct π-orbital overlap between two stacked bases in a dinucleotide or in a longer single strand creates new excited states that decay orders of magnitude more slowly than the generally subpicosecond excited states of monomeric bases. Half or more of all excited states in single strands decay in this manner. Ultrafast mid-IR transient absorption experiments reveal that the long-lived excited states in a number of model compounds are charge transfer states formed by interbase electron transfer, which subsequently decay by charge recombination. The lifetimes of the charge transfer states are surprisingly independent of how the stacked bases are oriented, but disruption of π-stacking, either by elevating temperature or by adding a denaturing co-solvent, completely eliminates this decay channel. Time-resolved emission measurements support the conclusion that these states are populated very rapidly from initial excitons. These experiments also reveal the existence of populations of emissive excited states that decay on the nanosecond time scale. The quantum yield of these states is very small for UVB/UVC excitation, but increases at UVA wavelengths. In double strands, hydrogen bonding between bases perturbs, but does not quench, the long-lived excited states. Kinetic isotope effects on the excited-state dynamics suggest that intrastrand electron transfer may couple to interstrand proton transfer. By revealing how structure and non-covalent interactions affect excited-state dynamics, on-going experimental and theoretical studies of excited states in DNA strands can advance understanding of fundamental photophysics in other nanoscale systems.

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Dynamics of laser-excited stacked adenines: Semiclassical simulations

Cited by 6 publications

References 57 publications

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

Challenges in Simulating Light-Induced Processes in DNA

Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy

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