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Molecules 2017, 22(1), 49;

Challenges in Simulating Light-Induced Processes in DNA

Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
Author to whom correspondence should be addressed.
Academic Editor: Carlos E. Crespo-Hernández
Received: 18 November 2016 / Revised: 14 December 2016 / Accepted: 21 December 2016 / Published: 29 December 2016
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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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. View Full-Text
Keywords: DNA; photochemistry; excited states; simulation; electronic structure; ab initio molecular dynamics; QM/MM; theoretical chemistry DNA; photochemistry; excited states; simulation; electronic structure; ab initio molecular dynamics; QM/MM; theoretical chemistry
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Marquetand, P.; Nogueira, J.J.; Mai, S.; Plasser, F.; González, L. Challenges in Simulating Light-Induced Processes in DNA. Molecules 2017, 22, 49.

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