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Theoretical Studies on Kinetics of Molecular Excited States
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
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: urn:nbn:se:kth:diva-11994ISBN: 978-91-7415-551-8 (print)OAI: oai:DiVA.org:kth-11994DiVA: diva2:292616
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
List of papers
1. Nonradiative decay of the lowest excited singlet state of 2-aminopyridine is considerably faster than the radiative decay
Open this publication in new window or tab >>Nonradiative decay of the lowest excited singlet state of 2-aminopyridine is considerably faster than the radiative decay
2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 14, 144315- p.Article in journal (Refereed) Published
Abstract [en]

Ab initio calculations reveal that radiative lifetime of the lowest excited singlet state of 2-aminopyridine (2AP) molecule should be around 20 ns, consistent with the molecules of the same type, but is about one order of magnitude larger than the claimed experimental fluorescent lifetime in recent years. A S1/S0 conical intersection close to the S1 state has been located which could be the possible nonradiative channel that is responsible for the fast decay observed in the experiment.

Place, publisher, year, edition, pages
America: American -institute of Physics, 2009
Keyword
ab initio calculations, excited states, fluorescences, organic compounds, radiative lifetimes
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-11898 (URN)10.1063/1.3113664 (DOI)000265617200033 ()2-s2.0-65249190165 (Scopus ID)
Note
QC20100719 Copyright (2009) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of PhysicsAvailable from: 2010-01-29 Created: 2010-01-21 Last updated: 2017-12-12Bibliographically approved
2. A multidimensional microcanonical Monte Carlo study of S0-T1 intersystem crossing of isocyanic acid
Open this publication in new window or tab >>A multidimensional microcanonical Monte Carlo study of S0-T1 intersystem crossing of isocyanic acid
2009 (English)In: Science in China Series B: Chemistry, ISSN 1006-9291, E-ISSN 1862-2771, Vol. 52, no 11, 1885-1891 p.Article in journal (Refereed) Published
Abstract [en]

A general formula for multi-dimensional Monte Carlo microcanonical nonadiabatic rate constant expressed in configuration space is applied to calculate the rate of intersystem crossing (ISC) between the ground (S0) and first excited triplet (T1) states for isocyanic acid. One-, two- and three-dimensional potential energy surfaces are constructed by the CCSD calculations, which are used for Monte Carlo sampling. The calculated S0→T1 ISC rate is in good agreement with experimental findings, which gives us reason to expect that the multi-dimensional Monte Carlo microcanonical nonadiabatic rate theory is one of very effective methods for calculating nonadiabatic transition rate of a polyatomic molecule.

Place, publisher, year, edition, pages
China: Science in China Press, co-published with Springer-Verlag GmbH, 2009
Keyword
multi-dimensional Monte Carlo, microcanical nondiabatic rate theory, intersystem crossing, isocyanic acid
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-11899 (URN)10.1007/s11426-009-0259-9 (DOI)000272032700021 ()2-s2.0-72149110634 (Scopus ID)
Note
QC20100719Available from: 2010-01-29 Created: 2010-01-21 Last updated: 2017-12-12Bibliographically approved
3. Nonadiabatic histidine dissociation of hexacoordinate heme in neuroglobin protein
Open this publication in new window or tab >>Nonadiabatic histidine dissociation of hexacoordinate heme in neuroglobin protein
2010 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215Article in journal (Refereed) Published
Abstract [en]

In the present work, density functional theory and canonical nonadiabatic Monte Carlo transition state theory have been used to investigate histidine dissociation process from the hexacoordinate heme in Ngb protein. The potential energy surfaces (PES) of the lowest singlet, triplet, and quintet states are calculated by stepwise optimization along with the histidine dissociation pathway. Based on the calculated two-dimensional PES, the histidine dissociation rates for the spin-forbidden processes via singlet to triplet and singlet to quintet transitions have been calculated by the nonadiabatic Monte Carlo transition state theory in canonical ensemble. The present study provides a quantitative description on spin-forbidden histidine dissociation processes.

Place, publisher, year, edition, pages
America: American Chemical Society, 2010
Keyword
density functional theory, canonical nonadiabatic Monte Carlo transition state theory, potential energy surface, heme, neuroglobin
National Category
Physical Chemistry Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-11901 (URN)10.1021/jp909887d (DOI)000273948100047 ()2-s2.0-77249172674 (Scopus ID)
Note
QC 20100719Available from: 2010-01-29 Created: 2010-01-21 Last updated: 2017-12-12Bibliographically approved
4. Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences
Open this publication in new window or tab >>Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences
Show others...
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]

Keyword
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:nbn:se:kth:diva-26848 (URN)10.1063/1.3464485 (DOI)000280941800014 ()2-s2.0-77955754884 (Scopus ID)
Note
QC 20101202. Updated from submitted to published.Available from: 2010-12-02 Created: 2010-11-29 Last updated: 2017-12-12Bibliographically approved
5. Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase
Open this publication in new window or tab >>Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase
Show others...
2010 (English)In: Journal of Physical Chemisty Letters, ISSN 1948-7185, Vol. 1, 743-747 p.Article in journal (Refereed) Published
Abstract [en]

The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this letter that the often used model system, a lumiflavin (7,8-dimethy-10-methyl-isoalloxazine), can not correctly describe geometrical and electronic structures of FADHin DNA photolyase. The intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is found to play a significant role in controlling photochemical properties of FADHin DNA photolyase

Place, publisher, year, edition, pages
U. S. A.: American Chemical Society, 2010
Keyword
flavin, intramolecular hydrogen bonding, excited states
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-11995 (URN)10.1021/jz900434z (DOI)000277040600013 ()2-s2.0-77749242712 (Scopus ID)
Funder
Swedish Research Council
Note
QC 20100719Available from: 2010-02-08 Created: 2010-02-08 Last updated: 2012-02-22Bibliographically approved

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