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and the activation energies using the NMR technique. The authors stressed that the
activation energy of 15.4 kcal/mol derived from their measurements in aqueous solu-tion
is in distinct disagreement with the results of calculations,103, 104 which estimated
that the barrier is above 21 kcal/mol. The relatively low value of the barrier (as com-pared
to other isomerization reactions involving exocyclic double bonds) has also been
emphasized in subsequent studies of the isomerization and several explanations have
been suggested137, 141. For example, thermal isomerization studies of model GFP-like
compounds137 suggested that different substituent groups may have a significant effect
on the activation energy by changing the interaction between two resonance structures
of the chromophore. Tolbert and coworkers considered mechanisms involving changes
in chemical structure of the chromophore, e.g., addition/elimination pathway141. No
ab initio calculations have been reported so far to resolve this disagreement between
experimental measurements and theoretical estimates and explain the low value of the
barrier.
1.3 Previous studies of the excited states of uracil
Natural nucleobases—adenine, guanine, thymine, cytosine, and uracil—combine with
residues of phosphoric acid and sugars to form nucleotides, the monomers of nucleic
acids. Being UV chromophores, the nucleobases define a large portion of the RNA
and DNA photochemistry and are used as model systems to study the properties of the
polymers146–149.
UV radiation is harmful to living organisms: when absorbed by the nucleic acid, it
initiates excited-state dynamics that can result in structural damage. The process, which
starts with an electronic excitation of a UV chromophore, can be quenched by radia-tionless
relaxation to the ground state. Photoexcited natural nucleobases have lifetimes
26
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 36 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | and the activation energies using the NMR technique. The authors stressed that the activation energy of 15.4 kcal/mol derived from their measurements in aqueous solu-tion is in distinct disagreement with the results of calculations,103, 104 which estimated that the barrier is above 21 kcal/mol. The relatively low value of the barrier (as com-pared to other isomerization reactions involving exocyclic double bonds) has also been emphasized in subsequent studies of the isomerization and several explanations have been suggested137, 141. For example, thermal isomerization studies of model GFP-like compounds137 suggested that different substituent groups may have a significant effect on the activation energy by changing the interaction between two resonance structures of the chromophore. Tolbert and coworkers considered mechanisms involving changes in chemical structure of the chromophore, e.g., addition/elimination pathway141. No ab initio calculations have been reported so far to resolve this disagreement between experimental measurements and theoretical estimates and explain the low value of the barrier. 1.3 Previous studies of the excited states of uracil Natural nucleobases—adenine, guanine, thymine, cytosine, and uracil—combine with residues of phosphoric acid and sugars to form nucleotides, the monomers of nucleic acids. Being UV chromophores, the nucleobases define a large portion of the RNA and DNA photochemistry and are used as model systems to study the properties of the polymers146–149. UV radiation is harmful to living organisms: when absorbed by the nucleic acid, it initiates excited-state dynamics that can result in structural damage. The process, which starts with an electronic excitation of a UV chromophore, can be quenched by radia-tionless relaxation to the ground state. Photoexcited natural nucleobases have lifetimes 26 |
