Calculations of the exciton coupling elements between the DNA bases using the transition density cube method

The Journal of Chemical Physics
Arkadiusz Czader, Eric R Bittner

Abstract

Excited states of the double-stranded DNA model (A)12.(T)12 were calculated in the framework of the Frenkel exciton theory. The off-diagonal elements of the exciton matrix were calculated using the transition densities and ideal dipole approximation associated with the lowest energy pipi* excitations of the individual nucleobases as obtained from time-dependent density functional theory calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal dipole approximation (IDA) methods were found to be significantly different for the small interchromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of structural fluctuations of the DNA chain on the magnitude of dipolar coupling were also found to be very significant. The difference between the maximum and minimum values was as large as 1000 and 300 cm(-1) for the IDA and TDC methods, respectively. To account for these effects, the properties of the excited states were averaged over a large number of conformations obtained from the molecular dynamics simulations. Our calculations using the TDC method indicate that the absorption of the UV light creates exciton states carrying the majority of the ...Continue Reading

References

Mar 1, 1975·Biopolymers·W C Brunner, M F Maestre
Oct 1, 1977·Biopolymers·C A Sprecher, W C Johnson
Jun 8, 1977·Journal of the American Chemical Society·L B Clark
Jul 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·S E FreemanB M Sutherland
Oct 23, 1968·Journal of the American Chemical Society·W VoelterC Djerassi
Feb 12, 1969·Journal of the American Chemical Society·D W MilesH Eyring
Jan 15, 1999·Science·S O Kelley, J K Barton
Oct 18, 2001·Journal of the American Chemical Society·J M PecourtB Kohler
Mar 29, 2003·Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology·Rajeshwar P Sinha, Donat P Häder
Feb 24, 2004·Journal of Computational Chemistry·M K Shukla, Jerzy Leszczynski
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Mar 4, 2005·The Journal of Chemical Physics·Clélia CanuelMohamed Elhanine
Jun 9, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Emanuela EmanueleKrystyna Zakrzewska
Jul 13, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ahmad BesaratiniaGerd P Pfeifer
Aug 27, 2005·Nature·Carlos E Crespo-HernándezBern Kohler
Dec 8, 2005·Journal of the American Chemical Society·Dimitra MarkovitsiElodie Lazzarotto
Jun 9, 2006·Nature·Dimitra MarkovitsiSylvie Marguet
Jul 21, 2006·The Journal of Physical Chemistry. B·Emanuela EmanuelePhilippe Millié
Sep 7, 2006·Proceedings of the National Academy of Sciences of the United States of America·Stéphane MouretThierry Douki
Sep 13, 2006·The Journal of Chemical Physics·Eric R Bittner
Dec 19, 2006·Inorganic Chemistry·Jakub ChalupskýLubomír Rulísek
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Ivan BuchvarovTorsten Fiebig
Mar 31, 2007·Physical Chemistry Chemical Physics : PCCP·Hans-Hermann RitzeDana Nachtigallová
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

❮ Previous
Next ❯

Citations

Apr 10, 2008·The Journal of Chemical Physics·Kim Hyeon-DeukMinhaeng Cho
Dec 15, 2015·The Journal of Physical Chemistry. B·Elise P Kenny, Ivan Kassal
Mar 18, 2009·Chemistry : a European Journal·Anthony HarrimanRaymond Ziessel
Apr 3, 2013·Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology·Lisbeth Munksgaard NielsenSteen Brøndsted Nielsen
Jul 8, 2017·Journal of Chemical Theory and Computation·Aleksey A KocherzhenkoChristine M Isborn
Dec 1, 2017·Nucleic Acids Research·Ivan L VolkovAlexei I Kononov
Jun 10, 2010·Physical Chemistry Chemical Physics : PCCP·Alexander A Voityuk
Jun 10, 2020·Physical Chemistry Chemical Physics : PCCP·Matthias Wohlgemuth, Roland Mitrić
Oct 29, 2008·Physical Chemistry Chemical Physics : PCCP·Dana NachtigallováHans-Hermann Ritze
Aug 16, 2017·The Journal of Chemical Physics·Arend G Dijkstra, Valentyn I Prokhorenko
Jul 4, 2009·The Journal of Physical Chemistry. B·E B StarikovShigenori Tanaka
Sep 2, 2009·The Journal of Physical Chemistry. B·Wai-Ming KwokDavid Lee Phillips
Jan 12, 2010·The Journal of Physical Chemistry. B·Christopher R KozakSpiridoula Matsika
Aug 28, 2010·The Journal of Physical Chemistry. B·Anastassia N AlexandrovaGiovanni Granucci
Dec 24, 2010·Journal of the American Chemical Society·Theodore LazaridesRichard Eisenberg
Aug 14, 2012·Journal of Chemical Theory and Computation·Felix Plasser, Hans Lischka
Nov 18, 2015·Journal of Chemical Theory and Computation·Bartosz BłasiakRobert W Góra
Oct 23, 2020·The Journal of Physical Chemistry. a·Viviana PiccinniRegina de Vivie-Riedle
Jul 13, 2012·The Journal of Physical Chemistry. a·Felix PlasserHans Lischka
Jul 6, 2019·Chemical Reviews·Francesco SegattaBenedetta Mennucci
Sep 9, 2021·The Journal of Physical Chemistry. a·Mohammed I SorourSpiridoula Matsika

❮ Previous
Next ❯

Software Mentioned

CHIMERA
GAUSSIAN03
3DNA
IDA
ORCA
TDDFT
TDC

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
Emanuela EmanueleKrystyna Zakrzewska
Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
Dimitra MarkovitsiThomas Gustavsson
© 2021 Meta ULC. All rights reserved