A semiclassical dynamics simulation for a long-lived excimer state of π-stacked adenines

Zhang, Wenying; Yuan, Shuai; Wang, Zhijin; Qi, Zhiming; Zhao, Jianshe; Dou, Yusheng; Lo, Glenn V.

doi:10.1016/j.cplett.2011.03.024

Cited by 19 publications

(29 citation statements)

References 35 publications

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“…By contrast, these optimizations lead to a decrease of d C6C6 below 2 Å and a subsequent strong destabilization of the ground state with very small S 0 /S 1 gaps and a concomitant failure of the ADC(2) method. These results suggest that a new deactivation channel arises in the adenine dimer, which is accessed through decreasing the intermolecular distance between the respective C6 atoms to below 2.0 Å, similar to results obtained by semi-empirical calculations, 23 only that in those cases the mutual C2 distance was shortened to below 2.0 Å. In ref.…”

Section: Excited State Geometry Relaxationsupporting

confidence: 84%

“…21,22 Aside from their structure, also the fate of such exciplexes is unknown. There was experimental evidence for a decay through charge recombination 19 and computational evidence for deactivation mediated by a shortening of the intermolecular distance, 23 but also a restoration of localized states has been considered. 24 In light of these unknowns, further studies are needed to fully understand this important phenomenon.…”

Section: Introductionmentioning

confidence: 99%

“…A number of computational strategies with different merits and shortcomings in light of these demands are, in principle, applicable and a wide range of types of calculations have been performed. These amount to wavefunction based ab initio calculations, 21 time-dependent density functional theory (TDDFT) using a polarizable continuum model, 22,28,29 semi-empirical methods, 23,30 and model Hamiltonians. 31 For more information about calculations performed on DNA fragments see also ref.…”

Section: Introductionmentioning

confidence: 99%

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Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution

Plasser

Lischka

2013

Photochem Photobiol Sci

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The excited states and potential surfaces of the adenine dinucleotide are analyzed in gas phase and in solution using a correlated ab initio methodology in a QM/MM framework. In agreement with previous studies, a rather flat S1 surface with a number of minima of different character is found. Specifically, our results suggest that exciplexes with remarkably short intermolecular separation down to ~2.0 Å are formed. A detailed analysis shows that due to strong orbital interactions their character differs significantly from any states present in the Franck-Condon region. The lowest S1 energy minimum is a ππ* exciplex with only a small amount of charge transfer. It possesses appreciable oscillator strength with a polarization almost perpendicular to the planes of the two adenine molecules.

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Section: Excited State Geometry Relaxationsupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution

Plasser

Lischka

2013

Photochem Photobiol Sci

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“…Similar structures have also been reported for adenine dimers by other researchers, with the C 2 carbons on each adenine approaching each other, as well as on a dimer of adenine and thymine. 88,89 …”

Section: Resultsmentioning

confidence: 99%

Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases

Liang

Nguyen

Matsika

2013

Photochem Photobiol Sci

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Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids’ structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process.

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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: 94%

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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A semiclassical dynamics simulation for a long-lived excimer state of π-stacked adenines

Cited by 19 publications

References 35 publications

Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution

Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution

Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases

Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy

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