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3.3 Standard oxidation potentials corresponding to different one-electron
oxidation transitions computed using gas-phase detachment and ioniza-tion
energies (see text). . . . . . . . . . . . . . . . . . . . . . . . . . . 95
3.4 Selected geometric parameters (bond lengths in A° , angles in degrees) of
the HBDI anion, and its singly and doubly oxidized forms. . . . . . . . 98
4.1 Equilibrium geometry of uracil. The calculated structure is optimized
with B3LYP/6-311G(2df,2pd). Experimental values are obtained by
averaging dimensions found in crystal structuresa. Atomic labels are
defined in Fig. 4.1, distances in A° , angles in degrees. . . . . . . . . . . 113
4.2 Leading electronic configurations in the EOM-CCSD/aug-cc-pVDZ wave
function. r is the weight of a configuration, R21
is the norm of the EOM
singles amplitudes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
4.3 Vertical EOM-CCSD excitation energies of uracil (eV). Ground state
CCSD energies are shown in hartree, oscillator strengths are given in
parentheses. The singlet CCSD reference wave function was used for
both singlet and triplet EOM calculations. . . . . . . . . . . . . . . . . 116
4.4 Effect of triple excitations on vertical excitation energies. Shift in exci-tation
energies due to triple excitations is shown in parentheses. All
energies are in eV. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
4.5 Norms of the amplitudes Rm;k from Eq. (1.15) in the EOM-CC(2,˜3)/6-
31G(d) wave function of uracil. The (10,10) active space is used. Total
norm is not unity in virtue of biorthogonal properties of EOM-CC. . . . 120
4.6 MRCI excitation energies (eV) of the four lowest singlet excited states
of uracil. Oscillator strengths are given in parentheses. . . . . . . . . . 122
4.7 Vertical excitation energies (eV) of uracil in the gas phase and water
solution calculated with QM/MM. Energy shifts due to the solvent are
shown in parentheses. . . . . . . . . . . . . . . . . . . . . . . . . . . 124
4.8 Best estimates of the vertical excitation energies (eV) of the lowest sin-glet
and triplet states compared with previously published results. . . . 126
5.1 Geometries and total energies of the intersection seam minima and points
of triple degeneracy in N+3
calculated by EOM-CCSD/6-31G. All bond
lengths are given in angstroms, all angles are given in degrees, all ener-gies
are given in a.u. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
v
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 5 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | 3.3 Standard oxidation potentials corresponding to different one-electron oxidation transitions computed using gas-phase detachment and ioniza-tion energies (see text). . . . . . . . . . . . . . . . . . . . . . . . . . . 95 3.4 Selected geometric parameters (bond lengths in A° , angles in degrees) of the HBDI anion, and its singly and doubly oxidized forms. . . . . . . . 98 4.1 Equilibrium geometry of uracil. The calculated structure is optimized with B3LYP/6-311G(2df,2pd). Experimental values are obtained by averaging dimensions found in crystal structuresa. Atomic labels are defined in Fig. 4.1, distances in A° , angles in degrees. . . . . . . . . . . 113 4.2 Leading electronic configurations in the EOM-CCSD/aug-cc-pVDZ wave function. r is the weight of a configuration, R21 is the norm of the EOM singles amplitudes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 4.3 Vertical EOM-CCSD excitation energies of uracil (eV). Ground state CCSD energies are shown in hartree, oscillator strengths are given in parentheses. The singlet CCSD reference wave function was used for both singlet and triplet EOM calculations. . . . . . . . . . . . . . . . . 116 4.4 Effect of triple excitations on vertical excitation energies. Shift in exci-tation energies due to triple excitations is shown in parentheses. All energies are in eV. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119 4.5 Norms of the amplitudes Rm;k from Eq. (1.15) in the EOM-CC(2,˜3)/6- 31G(d) wave function of uracil. The (10,10) active space is used. Total norm is not unity in virtue of biorthogonal properties of EOM-CC. . . . 120 4.6 MRCI excitation energies (eV) of the four lowest singlet excited states of uracil. Oscillator strengths are given in parentheses. . . . . . . . . . 122 4.7 Vertical excitation energies (eV) of uracil in the gas phase and water solution calculated with QM/MM. Energy shifts due to the solvent are shown in parentheses. . . . . . . . . . . . . . . . . . . . . . . . . . . 124 4.8 Best estimates of the vertical excitation energies (eV) of the lowest sin-glet and triplet states compared with previously published results. . . . 126 5.1 Geometries and total energies of the intersection seam minima and points of triple degeneracy in N+3 calculated by EOM-CCSD/6-31G. All bond lengths are given in angstroms, all angles are given in degrees, all ener-gies are given in a.u. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 v |
