Editorial Dynamics in Photoexcited DNA Bases and Related ...downloads.hindawi.com/journals/ijp/2015/501028.pdf · Editorial Dynamics in Photoexcited DNA Bases and Related Molecules

EditorialDynamics in Photoexcited DNA Bases and Related Molecules

Yusheng Dou,1,2 Zhisong Wang,3 Fuli Li,4 and Roland E. Allen5

1 Institute of Computational Chemistry, Chongqing University of Posts and Telecommunications, Chongqing 400065, China2Department of Physical Sciences, Nicholls State University, P.O. Box 2022, Thibodaux, LA 70310, USA3Department of Physics, National University of Singapore, Singapore 1175424Department of Applied Physics, Xi’an Jiaotong University, Xi’an 710049, China5Department of Physics and Astronomy, Texas A&M University, College Station, TX 77843-4242, USA

Correspondence should be addressed to Yusheng Dou; [email protected]

Received 15 September 2014; Accepted 15 September 2014

Copyright © 2015 Yusheng Dou et al. 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.

Deoxyribonucleic acid (DNA), the hereditary basis of life’sgenetic identity, has been of enormous interest for more thana century and particularly since its structure was determinedin 1953. Nucleobases are primary building blocks and UVchromophores in DNA. Exposing DNA to radiation in the200–300 nm range results in strong UV absorption by thesebases, which could lead to photochemical reactions caus-ing DNA damage. Fortunately, highly efficient nonradiativedecay pathways exist in DNA bases, assuring that mostexcited molecules quickly relax to the electronic ground statewithout leading to harmful reactions. The electron dynamicsfollowing photoexcitation plays an important role in thisdeactivation, which is clearly essential for life. Since thedevelopment of ultrafast laser pulses and high performancecomputers, there has been tremendous progress in under-standing the electron dynamics of DNA bases, but it is farfrom complete.

In this special issue, we selected six peer-reviewedresearch articles which present recent progress in under-standing the electronic response of DNA bases excited bylaser pulses, mostly through semiclassical dynamical simu-lations. There is also a brief review of deactivation processesin DNA bases studied with this approach. In the paragraphsbelow, we provide a brief overview of the key results in eachpaper.

In “Detailed Photoisomerization Dynamics of a GreenFluorescent Protein Chromophore Based Molecular Switch,”quantum yields were found to be 32% for the trans-to-cisphotoisomerization of BMH and 33% for cis-to-trans. Thesesimulations indicate that the average excited state lifetime of

trans-BMH is about 1460 fs, which is shorter than that foundfor cis-BMH (3100 fs). For both the trans-to-cis and cis-to-trans reactions, rotation around the central C2=C3 bond isthe dominant reactionmechanism. Deexcitation occurs at anavoided crossing near a conical intersection which is close tothe midpoint of the rotation.

Thepaper “CompetingDeactivationChannels for Excited𝜋-Stacked Cytosines” suggests that the deactivation channelleading to the electronic ground state of stacked basescompetes with the path that leads to dimerization. For bothpathways, the initial excited state was found to lead to acharge-separated neutral excimer state by charge transfer.Vibrational energy distribution determines the fate of theexcimer at the avoided crossing.

The paper “Electron Correlation Effects on the Longi-tudinal Polarizabilities and Second Hyperpolarizabilities ofPolyenes: A Finite Field Study” reports finite-field-based abinitio calculations of the longitudinal polarizabilities (𝛼L) andsecond hyperpolarizabilities (𝛾L) of conjugated polyenes andproposes that electron correlation reduces linear longitudinalpolarizability and enhances longitudinal second hyperpolar-izability for short polyenes, with the effects decreasing as thechain length increases.

The paper “Constraint Trajectory Surface-HoppingMolecular Dynamics Simulation of the Photoisomerizationof Stilbene” extends the trajectory surface hopping (TSH)method from full to flexible dimensional potential energysurfaces by combining the TSH method with constrainedmolecular dynamics. In this approach, classical trajectoriesare followed in Cartesian coordinates with constraints in

Hindawi Publishing CorporationInternational Journal of PhotoenergyVolume 2015, Article ID 501028, 2 pageshttp://dx.doi.org/10.1155/2015/501028

2 International Journal of Photoenergy

internal coordinates, while nonadiabatic switching probabil-ities are calculated separately in free internal coordinates byLandau-Zener and Zhu-Nakamura formulas along the seam.

The paper “Detailed Molecular Dynamics of the Pho-tochromic Reaction of Spiropyran: A Semiclassical DynamicsStudy” reports a realistic simulation study for the photoin-duced ring-opening reaction of spiropyran. The main resultsshow two different pathways: one involves hydrogen out-of-plane (HOOP) torsion of the phenyl ring nearby the Natom, and the other dominant pathway corresponds to thering-opening reaction of trans-SP to form the most stablemerocyanine (MC) product.

In the paper “Bonded Excimer in Stacked Cytosines: ASemiclassical Simulation Study,” the formation of a covalentbond between two stacked cytosines is found to facilitatethe deactivation of the electronically excited DNA bases bylowering the energy gap between the LUMO and HOMO.

We believe that the papers published in this special issuerepresent a significant positive contribution to this generalfield.

Acknowledgments

We would like to express our sincere appreciation to all theauthors for submitting their exciting scientific results to thisspecial issue. We are also grateful to all the reviewers aroundthe world, whose dedicated efforts and high-quality workhave made this issue possible. Last but not least, we wouldlike to thank the editorial board of the International Journalof Photoenergy for giving us the opportunity to publish thisspecial issue.

Yusheng DouZhisong Wang

Fuli LiRoland E. Allen

Submit your manuscripts athttp://www.hindawi.com

Hindawi Publishing Corporationhttp://www.hindawi.com Volume 2014

Inorganic ChemistryInternational Journal of

Hindawi Publishing Corporation http://www.hindawi.com Volume 2014

International Journal ofPhotoenergy


Carbohydrate Chemistry

International Journal of


Journal of

Chemistry


Advances in

Physical Chemistry

Hindawi Publishing Corporationhttp://www.hindawi.com

Analytical Methods in Chemistry

Journal of

Volume 2014

Bioinorganic Chemistry and ApplicationsHindawi Publishing Corporationhttp://www.hindawi.com Volume 2014

SpectroscopyInternational Journal of


The Scientific World JournalHindawi Publishing Corporation http://www.hindawi.com Volume 2014

Medicinal ChemistryInternational Journal of


Chromatography Research International


Applied ChemistryJournal of



Theoretical ChemistryJournal of


Journal of

Spectroscopy

Analytical ChemistryInternational Journal of


Journal of


Quantum Chemistry


Organic Chemistry International

ElectrochemistryInternational Journal of

Hindawi Publishing Corporation http://www.hindawi.com Volume 2014


CatalystsJournal of

Documents

Editorial Dynamics in Photoexcited DNA Bases and Related ...downloads.hindawi.com/journals/ijp/2015/501028.pdf · Editorial Dynamics in Photoexcited DNA Bases and Related Molecules