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Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).ORCID iD: 0000-0003-0007-0394
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2010 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 6, 064302- p.Article in journal (Refereed) Published
Abstract [en]

2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized (1)pi pi(*) excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3464485]

Place, publisher, year, edition, pages
2010. Vol. 133, no 6, 064302- p.
Keyword [en]
density functional theory, DNA, exchange interactions (electron), excited states, Monte Carlo methods, photochemistry, potential energy surfaces, reaction kinetics theory
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-26848DOI: 10.1063/1.3464485ISI: 000280941800014Scopus ID: 2-s2.0-77955754884OAI: oai:DiVA.org:kth-26848DiVA: diva2:374038
Note
QC 20101202. Updated from submitted to published.Available from: 2010-12-02 Created: 2010-11-29 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Theoretical studies on photophysics and photochemistry of DNA
Open this publication in new window or tab >>Theoretical studies on photophysics and photochemistry of DNA
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels.

Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments.

We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2010. 76 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2011:15
National Category
Theoretical Chemistry
Research subject
SRA - Molecular Bioscience
Identifiers
urn:nbn:se:kth:diva-33531 (URN)978-91-7415-977-6 (ISBN)
Public defence
2011-06-14, FA32, AlbaNova University Center, Roslagstullsbacken 21,, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20110530Available from: 2011-05-30 Created: 2011-05-09 Last updated: 2011-05-30Bibliographically approved
2. Theoretical Studies on Kinetics of Molecular Excited States
Open this publication in new window or tab >>Theoretical Studies on Kinetics of Molecular Excited States
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

HTML clipboardKinetics on molecular excited states is a challenging subject in the field of theoretical chemistry. This thesis pays attention to theoretical studies on kinetics of photo-induced processes, including photo-chemical reactions, radiative and non-radiative transitions (intersystem crossing and internal conversion) in molecular and bio-related systems.

One- or multi- dimensional potential energy surfaces (PESs) not only provide qualitative mechanistic explanation for excited state decay, but also make it possible to perform kinetic simulations. We have constructed several types of PESs by using computational methods of high-accuracy for a variety of systems of interest. In particular, density functional theory (DFT) and couple cluster singles and doubles (CCSD) method are employed to build PESs of the ground and lowest triple states. For medium-sized molecules, the complete active space self-consistent (CASSCF) method is used for constructing the PESs of excited states.

Various kinetic theories for the decay processes of excite states are briefly introduced, in particularly adiabatic and nonadiabatic Rice–Ramsperger–Kassel -Marcus (RRKM) approaches for the kinetics of nonradiative decay of excited 2-aminopridine molecule. Special attention has been devoted to Monte Carlo transition state theory which can provide an efficient way to predict the rate of nonradiative transitions of polyatomic molecules on multi-dimensional PESs. Examples of Monte Carlo simulations on the intersystem crossing of isocyanic acid and a model molecule of hexacoordinate heme, as well as internal conversion process for 2-amininopyridine dimer and the adenine-thymine base pair are presented.

Place, publisher, year, edition, pages
Stockholm: KTH, 2010. 62 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2010:2
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-11994 (URN)978-91-7415-551-8 (ISBN)
Public defence
2010-03-05, FB 53 Svedbergssalen, Roslagstullsbacken 21, AlbaNova, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC20100720Available from: 2010-02-09 Created: 2010-02-08 Last updated: 2012-03-28Bibliographically approved

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