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5.1 The potential energy surface slices for the ground and the first excited
states of a substituted ethylene. There is an energy barrier that prevents
the molecule from rotating freely around the double bond. The top of
the barrier on the ground state PES corresponds to the minimum on the
excited state PES. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
5.2 D3h-constrained scans of adiabatic PESs of N+3
around the points of
intersections calculated by EOM-CCSD/6-31G. . . . . . . . . . . . . . 147
5.3 The seam of the X2A1/A2B2 intersection in nitrogen dioxide. At every
N–O distance, the PESs of both states were scanned to find the O–N–O
angle at which the states are degenerate. . . . . . . . . . . . . . . . . . 148
5.4 The singlet and the Ms=0 triplet target states of the para-benzyne dirad-ical
derived from the high-spin triplet reference by spin-flip. . . . . . . 150
5.5 Geometrical parameters used to describe the para-benzyne diradical in
Table 5.5. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
5.6 Convergence of the 1Ag/3B1u intersection optimization in the para-benzyne
diradical by EOMSF-CCSD/6-31G*. In the upper part, the relative ener-gies
of both states are plotted for each iteration. The corresponding
energy gaps are shown in the lower part. Convergence is achieved in
about 50 iterations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
5.7 Relative energies of the 1Ag and 3B1u states of para-benzyne diradical
at their equilibrium structures and MECP. Both at the singlet and triplet
equilibrium geometry, the singlet is below the triplet. The two states
intersect 0.65 eV above the ground state minimum. . . . . . . . . . . . 153
6.1 Large biological systems such as this active center of GFP require treat-ment
of the QM core and the MM environment using hybrid QM/MM
methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
A.1 Components of the tensor algebra library. . . . . . . . . . . . . . . . . 189
ix
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 9 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | 5.1 The potential energy surface slices for the ground and the first excited states of a substituted ethylene. There is an energy barrier that prevents the molecule from rotating freely around the double bond. The top of the barrier on the ground state PES corresponds to the minimum on the excited state PES. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 5.2 D3h-constrained scans of adiabatic PESs of N+3 around the points of intersections calculated by EOM-CCSD/6-31G. . . . . . . . . . . . . . 147 5.3 The seam of the X2A1/A2B2 intersection in nitrogen dioxide. At every N–O distance, the PESs of both states were scanned to find the O–N–O angle at which the states are degenerate. . . . . . . . . . . . . . . . . . 148 5.4 The singlet and the Ms=0 triplet target states of the para-benzyne dirad-ical derived from the high-spin triplet reference by spin-flip. . . . . . . 150 5.5 Geometrical parameters used to describe the para-benzyne diradical in Table 5.5. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 5.6 Convergence of the 1Ag/3B1u intersection optimization in the para-benzyne diradical by EOMSF-CCSD/6-31G*. In the upper part, the relative ener-gies of both states are plotted for each iteration. The corresponding energy gaps are shown in the lower part. Convergence is achieved in about 50 iterations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 5.7 Relative energies of the 1Ag and 3B1u states of para-benzyne diradical at their equilibrium structures and MECP. Both at the singlet and triplet equilibrium geometry, the singlet is below the triplet. The two states intersect 0.65 eV above the ground state minimum. . . . . . . . . . . . 153 6.1 Large biological systems such as this active center of GFP require treat-ment of the QM core and the MM environment using hybrid QM/MM methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 A.1 Components of the tensor algebra library. . . . . . . . . . . . . . . . . 189 ix |
