Symposium‐in‐Print: DNA Photodynamics Introduction

Kohler, Bern

doi:10.1111/j.1751-1097.2007.00131.x

Cited by 7 publications

(4 citation statements)

References 19 publications

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“…Time variation of characteristic geometrical parameters is given in Figure 5(b), and as seen the dihedral angle of d(N1-C6-C5-C9) representing the twisting of the C5-C6 double bond gradually increases as the molecule moves toward this CI. The C5-C6 bond is elongated right after the excitation at t = 0, which is consistent with the excitation character involving a transition of π (C5-C6) → π *(C5-C6), and then it oscillates around 1.47 Å The CASPT2(12,9) energies of the 1 ππ* state along the trajectory show very good agreement with those of CASPT2 (2,2). When the molecule is photo-excited at t = 0, the 1 ππ* and 1 nπ * states are close in energy, which is reflected in the absorption spectrum shown above.…”

Section: Qm-md Simulations In the Gas Phasesupporting

confidence: 74%

“…[1][2][3][4] It is now well-known that the conical intersection (CI) points between the ground-and excited-state potential energy surfaces play a crucial role in dissipating the energy attained by photo-excitation 5,6 and that this process occurs very fast ranging from the subpicosecond to picosecond timescale. The interplay between experiments and theoretical calculations continues to aid in the elucidation of the decay mechanisms, and the intricate dynamics of DNA bases are being rapidly unraveled.…”

Section: Introductionmentioning

confidence: 99%

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Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: Excited-state QM/MM molecular dynamics simulations

Nakayama

Arai

Yamazaki

et al. 2013

The Journal of Chemical Physics

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On-the-fly excited-state quantum mechanics/molecular mechanics molecular dynamics (QM/MM-MD) simulations of thymine in aqueous solution are performed to investigate the role of solvent water molecules on the nonradiative deactivation process. The complete active space second-order perturbation theory (CASPT2) method is employed for a thymine molecule as the QM part in order to provide a reliable description of the excited-state potential energies. It is found that, in addition to the previously reported deactivation pathway involving the twisting of the C-C double bond in the pyrimidine ring, another efficient deactivation pathway leading to conical intersections that accompanies the out-of-plane displacement of the carbonyl group is observed in aqueous solution. Decay through this pathway is not observed in the gas phase simulations, and our analysis indicates that the hydrogen bonds with solvent water molecules play a key role in stabilizing the potential energies of thymine in this additional decay pathway. © 2013 AIP Publishing LLC.

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Section: Qm-md Simulations In the Gas Phasesupporting

confidence: 74%

Section: Introductionmentioning

confidence: 99%

Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: Excited-state QM/MM molecular dynamics simulations

Nakayama

Arai

Yamazaki

et al. 2013

The Journal of Chemical Physics

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“…As most of the biomolecular recognition processes involving proteins and enzymes utilize various noncovalent interactions, several attempts have been made to mimic nature's design and architecture through the synthesis of molecules that can selectively interact with DNA (6)(7)(8)(9)(10). The essence of these efforts is to develop molecules, which can be used in various DNA-mediated applications ranging from the design of effective drugs to probes useful in studying the electron transfer properties of DNA (11)(12)(13)(14)(15).…”

Section: Introductionmentioning

confidence: 99%

Effect of Bridging Units on Photophysical and DNA Binding Properties of a Few Cyclophanes

Neelakandan¹,

Sanju²,

Ramaiah³

2010

Photochem & Photobiology

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A few novel anthracene-based cyclophanes CP-1, CP-2 and CP-3 were synthesized and their interactions with DNA were investigated employing photophysical and biophysical techniques. In methanol and acetonitrile, these systems exhibited optical properties characteristic of the anthracene chromophore. However, in the aqueous medium, the symmetric cyclophane CP-1 showed a dual emission having lambda(max) at 430 and 550 nm, due to the monomer and excimer, respectively. In contrast, the cyclophanes CP-2 and CP-3 in the aqueous medium showed structured anthracene absorption and emission spectra similar to those obtained in methanol and acetonitrile. DNA binding studies indicate that CP-1 undergoes efficient nonclassical partial intercalative interactions with DNA resulting in the exclusive formation of a sandwich-type excimer having enhanced emission intensity and lifetimes. The cyclophane CP-2 having one anthracene moiety exhibited nonclassical intercalative binding with DNA, albeit with less efficiency compared with CP-1. In contrast, CP-3, having sterically bulky viologen bridging group showed DNA electrostatic as well as groove binding interactions. These results demonstrate that the nature of the bridging unit plays an important role in the binding mode of the cyclophanes with DNA and in the formation of the novel sandwich-type excimer.

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“…

Ultraviolet (UV) photodamage of biological chromophores, such as nucleic acid bases and amino acids, is critically controlled by the relaxation pathways following the initial excitation. [1][2][3][4][5][6][7][8][9][10][11][12] Photostability as a concept involves "dark structures", [13] which undergo photophysical and/or photochemical pathways. [14] Of major relevance is the time scale of structural change, since long-lived species would not be desirable for the photostability.

…”

mentioning

confidence: 99%

Ultrafast Electron Diffraction Reveals Dark Structures of the Biological Chromophore Indole

Park

Gahlmann

et al. 2008

Angewandte Chemie

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Symposium‐in‐Print: DNA Photodynamics Introduction

Cited by 7 publications

References 19 publications

Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: Excited-state QM/MM molecular dynamics simulations

Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: Excited-state QM/MM molecular dynamics simulations

Effect of Bridging Units on Photophysical and DNA Binding Properties of a Few Cyclophanes

Ultrafast Electron Diffraction Reveals Dark Structures of the Biological Chromophore Indole

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