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Figure 4.1: Structure of uracil defining atom labels referred to in Table 4.1.
by DFT and compares them to experimental values26 obtained by averaging 32 uracil
residue structures found in a crystallographic database. The standard deviation of the
experimental data is about 0.01 °A
for distances and about 1:0 for angles. The differ-ences
between the calculated and experimental parameters do not exceed 0.03 °A
for
bond lengths and 2:5 for angles. The equilibrium structure also agrees well with the
CC2/aug-cc-pVQZ optimized geometry reported by Fleig et al.27: the maximum differ-ence
between the bond lengths is 0.015 A° .
Frontier MOs calculated with RHF/aug-cc-pVDZ are depicted in Fig. 4.2. 26 a0 and
27 a0 are occupied in-plane lone pairs on oxygen atoms. They lie below 28 a00 and 29 a00,
two occupied p orbitals. Two virtual p orbitals, 34 a00 and 35 a00, contain contributions
from orbitals on all the heavy atoms. There are two low-lying diffuse orbitals: the lowest
unoccupied MO 30 a0 and a higher orbital 38 a0.
The pp states correspond to transitions from the p orbitals 28 a00 and 29 a00 to the p
orbitals 34 a00 and 35 a00 (Table 4.2). Transitions originating from the lone pair orbitals
26 a0 and 27 a0 form the np states. The transition from HOMO to the lowest diffuse
orbital gives rise to a low-lying Rydberg state.
111
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 121 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Figure 4.1: Structure of uracil defining atom labels referred to in Table 4.1. by DFT and compares them to experimental values26 obtained by averaging 32 uracil residue structures found in a crystallographic database. The standard deviation of the experimental data is about 0.01 °A for distances and about 1:0 for angles. The differ-ences between the calculated and experimental parameters do not exceed 0.03 °A for bond lengths and 2:5 for angles. The equilibrium structure also agrees well with the CC2/aug-cc-pVQZ optimized geometry reported by Fleig et al.27: the maximum differ-ence between the bond lengths is 0.015 A° . Frontier MOs calculated with RHF/aug-cc-pVDZ are depicted in Fig. 4.2. 26 a0 and 27 a0 are occupied in-plane lone pairs on oxygen atoms. They lie below 28 a00 and 29 a00, two occupied p orbitals. Two virtual p orbitals, 34 a00 and 35 a00, contain contributions from orbitals on all the heavy atoms. There are two low-lying diffuse orbitals: the lowest unoccupied MO 30 a0 and a higher orbital 38 a0. The pp states correspond to transitions from the p orbitals 28 a00 and 29 a00 to the p orbitals 34 a00 and 35 a00 (Table 4.2). Transitions originating from the lone pair orbitals 26 a0 and 27 a0 form the np states. The transition from HOMO to the lowest diffuse orbital gives rise to a low-lying Rydberg state. 111 |
