Journal Article10.1021/JA7103894
Electronic Excitations and Spectra in Single-Stranded DNA
Stefano Tonzani,George C. Schatz +1 more
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TL;DR: It is shown that delocalized states extending over three bases can be directly excited in single-stranded poly(A) DNA, suggesting that the short delocalization in ssDNA arises in spite of strong stacking.
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Abstract: Using density functional theory and molecular dynamics simulations, we show that delocalized states extending over three bases can be directly excited in single-stranded poly(A) DNA. The results are in semiquantitative agreement with recent experimental results for the delocalization length of these states in single- and double-stranded DNA. The structures used in these molecular dynamics calculations are validated by comparing calculated circular dichroic spectra for d(A)2 and d(A)4 with experiment. These spectra, which arise from highly stacked structures, are in good agreement with experiment, suggesting that the short delocalization in ssDNA arises in spite of strong stacking.
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Citations
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References
Chemistry with ADF
G. te Velde,F.M. Bickelhaupt,Evert Jan Baerends,C. Fonseca Guerra,S. J. A. van Gisbergen,J.G. Snijders,T. Ziegler +6 more
TL;DR: The “Activation‐strain TS interaction” (ATS) model of chemical reactivity is reviewed as a conceptual framework for understanding how activation barriers of various types of reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis.
9.6K
How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules
TL;DR: In this paper, the authors present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges.
DNA in a material world
TL;DR: The specific bonding of DNA base pairs provides the chemical foundation for genetics and this powerful molecular recognition system can be used in nanotechnology to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information.
Ultraviolet radiation-mediated damage to cellular DNA
TL;DR: Each of the twelve possible dimeric photoproducts that are produced at the four main bipyrimidine sites can now be singled out as dinucleoside monophosphates that are enzymatically released from UV-irradiated DNA.
954
Trajectory Surface Hopping in the Time-Dependent Kohn-Sham Approach for Electron-Nuclear Dynamics
TL;DR: The mean-field treatment of electron-nuclear interaction results in many qualitative breakdowns in the time-dependent Kohn-Sham (TDKS) density functional theory, but this problem is resolved by the trajectory surface-hopping TDKS approach, illustrated by the photoinduced electron injection from a molecular chromophore into TiO2, and the excited-state relaxation of the green fluorescent protein chromophores.
704