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Dataset for Photophysics and photochemistry of DNA molecules : electronic excited states leading to thymine dimerization

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Li, Jian-Hao and Hine, Nicholas (2018) Dataset for Photophysics and photochemistry of DNA molecules : electronic excited states leading to thymine dimerization. [Dataset]

[img] Archive (ZIP) (Structured folders containing input and output files needed to reproduce the results of “Photophysics and Photochemistry of DNA Molecules - Electronic Excited States Leading to Thymine Dimerization”)
Research_data.zip - Published Version
Available under License Creative Commons Attribution 4.0.

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Official URL: http://wrap.warwick.ac.uk/102497

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Abstract

We combine quantified natural transition orbital (QNTO) analysis with large-scale linear response time-dependent DFT (TDDFT) to investigate the concerted [2 + 2] thymine dimerisation reaction. This reaction is a main cause of UV-light induced damage to DNA, but its mechanism has remained poorly understood. QNTO analysis enables the electronic excitations of a molecule to be identified on the basis of their transition origins across a wide range of molecular geometries, allowing the participating excited states to be identified relatively straightforwardly. We identify a barrierless funnel that is responsible for the ultrafast reaction previously indicated in experiments. The reactive state is found to have crossings with several bright excited states, revealing how the initially populated bright states can decay rapidly to the reactive state. We also examine the contribution of environmental factors such as inclusion of the DNA backbone, which can affect the conformation of the potential energy surfaces of the relevant states.

Item Type: Dataset
Subjects: Q Science > QD Chemistry
Divisions: Faculty of Science, Engineering and Medicine > Science > Physics
Type of Data: Experimental
Library of Congress Subject Headings (LCSH): Thymine, DNA damage, DNA -- Analysis, Ultraviolet radiation -- Physiological effect
Publisher: University of Warwick, Department of Physics
Official Date: 23 May 2018
Dates:
DateEvent
23 May 2018Updated
23 May 2018Published
14 May 2018Submitted
Status: Not Peer Reviewed
Publication Status: Published
Media of Output (format): Mostly plain text input and output files in .dat format, plus .pdf (for which Adobe Acrobat reader is required)
Access rights to Published version: Open Access (Creative Commons)
Copyright Holders: University of Warwick
Description:

This file was created by Jian-Hao Li on 19 May 2018.

The folder "di-Thy" contains 7 subfolders (for 7 consecutive steps):

1. LST-CG: Input file for the linear synchronous transit calculation followed by conjugate gradient minimisation (LST-CG) between an ideal-B-DNA extracted di-Thy and a geometrically optimised Th<>Th. The obtained structure is used for subsequent constrained ground state optimisation scans of di-Thy and Th<>Th.

2. Constrained Opt: Input files for the constrained optimisation of (2.6,74)di-Thy and (2.2,74)Th<>Th. Other structures in the optimisation scans can be computed similarly.

3. Singlepoint: Input files for valence calculation of all the optimised structures obtained in the optimisation scans of di-Thy and of Th<>Th. Each di-Thy structure is marked by a number between 01-74 (see Map_cell#.pdf in the di-Thy folder) that is then used as the folder name for the di-Thy structure. For Th<>Th, the name "1866Th=Th" denotes (1.8,66)Th<>Th.

4. Cond: Input file for calculating the conduction orbitals of (2.6,74)di-Thy. Other structures are calculated with the same parameter settings.

5. LR_TDDFT: Input file for calculating the linear response TDDFT/TDA of (2.6,74)di-Thy. Other structures are calculated with the same parameter settings.

6. Sys2Ref Projection: Input file for performing projections of the hole (NTO1-H) and electron (NTO1-E) orbitals of the first 8 excitations of (2.6,50)di-Thy onto the corresponding NTOs (NTO1-H and NTO1-E) of the other structures. The thy_dimer_state_labellings.dat is used (put in the same folder before calculation) to set up the initial label given to each excited state of (2.6,50)di-Thy. (If thy_dimer_state_labellings.dat is absent, no initial labels are assigned.) After calculation, thy_dimer_state_labellings.dat.tmp is produced that records the new label for each excited state (the last line). In the current example, the NTOs of (2.6,50)di-Thy (folder name "24") are compared to those of the following folders: 03-13, 15-28, 30-74, 02, 29, and 01 (by setting up qnto_ref_dir accordingly in the input file). It can be seen that the "Old Sys label" are the same as "Sys label", indicating that a self-consistent labelling has been achieved.

7. Linear Int with 2274Th=Th: Input files for performing singlepoint calculation (same parameters as in 3.) of the interpolated structures between (2.2,74)Th<>Th and all the di-Thy structures. Conduction and LR_TDDFT calculations can be performed with the same parameters used in 4. and 5., followed by excited states labelling calculations as in 6.

The folder "dTpdT" contains the calculation input files for the dTpdT molecules. Some naming examples: 2850TT and 2850TT-c respectively denote (2.8,50)dTpdT without/with a truncated response density kernel being used in the TDDFT calculation. Similarly, 2274T=T-c denotes (2.2,74)T<p>T with a truncated response density kernel being used in TDDFT.

The folder "TTTTAAAA" contains the calculation input files for the TTTT/AAAA molecular segment extracted from B-DNA. All ONETEP calculations were performed using version 4.3.0.7.

Date of first compliant deposit: 23 May 2018
Date of first compliant Open Access: 23 May 2018
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
EP/P02209X/1[EPSRC] Engineering and Physical Sciences Research Councilhttp://dx.doi.org/10.13039/501100000266
EP/J017639/1[EPSRC] Engineering and Physical Sciences Research Councilhttp://dx.doi.org/10.13039/501100000266
Taiwan Cambridge Scholarship[MEPRC] Ministry of Education of the People's Republic of Chinahttp://dx.doi.org/10.13039/501100002338
EP/J017639/1[EPSRC] Engineering and Physical Sciences Research Councilhttp://dx.doi.org/10.13039/501100000266
eCSE programmeARCHERUNSPECIFIED
Winton Programme for the Physics of SustainabilityUniversity of Cambridgehttp://dx.doi.org/10.13039/501100000735
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Contributors:
ContributionNameContributor ID
DepositorHine, Nicholas66474

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