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of less than one picosecond, and that is believed to be responsible for the remarkable
photostability of DNA. In a review, Crespo-Hern´andez et al.146 discuss mechanisms,
pathways, and dynamics of the relaxation process.
The mechanism of the excited state population decay varies from nucleobase to
nucleobase and depends on the order of the lowest electronically excited states, which
correspond to a forbidden np and an allowed pp transition. Areas of potential
energy surfaces (PESs) where the ground and the excited states are degenerate or near-degenerate
play a special role in the radiationless relaxation dynamics4, 150, 151. The
mechanism of the efficient radiationless decay through conical intersections in uracil
was initially investigated using the multi-reference configuration interaction (MRCI)
method by Matsika152. Later results obtained with other methods153–158 are in qualita-tive
agreement with MRCI.
The equilibrium structure of uracil is planar and has the Cs point group symmetry.
The first singlet excited state corresponds to the np transition and belongs to the A00
irreducible representation. The second singlet excited state, A0, arises from the pp
transition. Only the second transition has oscillator strength by symmetry. The next two
valence singlet states are also of the np and pp types. A Rydberg A00 state is close in
energy to the second np state.
Absorption spectra of uracil in the gas phase159 and in solution155 show a broad fea-ture
centered at 244 nm (5.08 eV) and 259 nm (4.79 eV), respectively. These values
have been interpreted as the vertical pp excitation energy. The assignment was sup-ported
by complete active space self-consistent field (CASSCF)160 calculations with the
perturbation theory correction (CASPT2) and time-dependent density functional theory
27
Object Description
| Title | Development of predictive electronic structure methods and their application to atmospheric chemistry, combustion, and biologically relevant systems |
| Author | Epifanovskiy, Evgeny |
| Author email | epifanov@usc.edu; epifanov@usc.edu |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Chemistry |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2011-03-21 |
| Date submitted | 2011 |
| Restricted until | Unrestricted |
| Date published | 2011-04-28 |
| Advisor (committee chair) | Krylov, Anna I. |
| Advisor (committee member) |
Wittig, Curt Johnson, Clifford |
| Abstract | This work demonstrates electronic structure techniques that enable predictive modeling of the properties of biologically relevant species. Chapters 2 and 3 present studies of the electronically excited and detached states of the chromophore of the green fluorescent protein, the mechanism of its cis-trans isomerization, and the effect of oxidation. The bright excited ππ∗ state of the chromophore in the gas phase located at 2.6 eV is found to have an autoionizing resonance nature as it lies above the electron detachment level at 2.4 eV. The calculation of the barrier for the ground-state cis-trans isomerization of the chromophore yields 14.8 kcal/mol, which agrees with an experimental value of 15.4 kcal/mol; the electronic correlation and solvent stabilization are shown to have an important effect. In Chapter 3, a one-photon two-electron mechanism is proposed to explain the experimentally observed oxidative reddening of the chromophore. Chapter 4 considers the excited states of uracil. It demonstrates the role of the one-electron basis set and triples excitations in obtaining the converged values of the excitation energies of the nπ∗ and ππ∗ states. The effects of the solvent and protein environment are included in some of the models.; Chapter 5 describes an implementation of the algorithm for locating and exploring intersection seams between potential energy surfaces. The theory is illustrated with examples from atmospheric and combustion chemistry. |
| Keyword | electronic structure theory; coupled clusters theory; equation of motion theory; organic chromophore; green fluorescent protein; uracil |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m3801 |
| Contributing entity | University of Southern California |
| Rights | Epifanovskiy, Evgeny |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | cisadmin@lib.usc.edu |
| Filename | etd-Epifanovskiy-4557 |
| Archival file | uscthesesreloadpub_Volume14/etd-Epifanovskiy-4557.pdf |
Description
| Title | Page 37 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | of less than one picosecond, and that is believed to be responsible for the remarkable photostability of DNA. In a review, Crespo-Hern´andez et al.146 discuss mechanisms, pathways, and dynamics of the relaxation process. The mechanism of the excited state population decay varies from nucleobase to nucleobase and depends on the order of the lowest electronically excited states, which correspond to a forbidden np and an allowed pp transition. Areas of potential energy surfaces (PESs) where the ground and the excited states are degenerate or near-degenerate play a special role in the radiationless relaxation dynamics4, 150, 151. The mechanism of the efficient radiationless decay through conical intersections in uracil was initially investigated using the multi-reference configuration interaction (MRCI) method by Matsika152. Later results obtained with other methods153–158 are in qualita-tive agreement with MRCI. The equilibrium structure of uracil is planar and has the Cs point group symmetry. The first singlet excited state corresponds to the np transition and belongs to the A00 irreducible representation. The second singlet excited state, A0, arises from the pp transition. Only the second transition has oscillator strength by symmetry. The next two valence singlet states are also of the np and pp types. A Rydberg A00 state is close in energy to the second np state. Absorption spectra of uracil in the gas phase159 and in solution155 show a broad fea-ture centered at 244 nm (5.08 eV) and 259 nm (4.79 eV), respectively. These values have been interpreted as the vertical pp excitation energy. The assignment was sup-ported by complete active space self-consistent field (CASSCF)160 calculations with the perturbation theory correction (CASPT2) and time-dependent density functional theory 27 |
