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2.7 Cis-trans isomerization of the chromophore inside a cluster of water
molecules. Relative energies of the stationary points are computed with
QM(CASSCF(12/11)/cc-pVDZ)/EFP/MM(TIP3P). . . . . . . . . . . . 71
3.1 Structures of deprotonated HBDI (HBDI anion, top) and the cation (bot-tom).
The structure of the radical is similar to that of the cation, with the
unpaired electron being on the carbon that hosts positive charge in the
cation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
3.2 Relevant molecular orbitals of deprotonated HBDI (HF/6-311G*). In
the ground state of the anion, both p1 and p2 are doubly occupied, and
the bright state is derived by the p1!p excitation. Oxidized forms are
derived by removing the electrons from p1. . . . . . . . . . . . . . . . 90
3.3 Energy levels and electronic states of the HBDI anion and radical. The
bright absorbing p1p state at 2.62 eV is a resonance state embedded
in a photodetachment continuum beginning at 2.54 eV. The respective
MOs are shown in Fig. 3.2. . . . . . . . . . . . . . . . . . . . . . . . . 91
3.4 Electronic states of the doublet HBDI radical. The respective MOs are
shown in Fig. 3.2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
3.5 Electronic states of the doubly ionized HBDI anion. The respective MOs
are shown in Fig. 3.2. . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
3.6 Energy diagram of the relevant electronic states of deprotonated HBDI. 93
3.7 Infrared spectra of the anionic and cationic forms of deprotonated HBDI
computed with RI-MP2/cc-pVTZ. . . . . . . . . . . . . . . . . . . . . 99
4.1 Structure of uracil defining atom labels referred to in Table 4.1. . . . . 111
4.2 Frontier molecular orbitals of uracil at the ground state equilibrium geom-etry.
Orbital energies are calculated with RHF/aug-cc-pVDZ. . . . . . . 112
4.3 Excitation energies (upper panel) and oscillator strengths (lower panel)
of the lowest excited states of uracil calculated with EOM-CCSD and
various one-electron basis sets. . . . . . . . . . . . . . . . . . . . . . . 115
4.4 Absorption spectrum of uracil with theoretical estimations of electronic
transitions calculated with EOM-CCSD/aug-ANO-DZ and CR-EOM-CCSD(
T)/aug-ANO-DZ. . . . . . . . . . . . . . . . . . . . . . . . . . 127
viii
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 8 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | 2.7 Cis-trans isomerization of the chromophore inside a cluster of water molecules. Relative energies of the stationary points are computed with QM(CASSCF(12/11)/cc-pVDZ)/EFP/MM(TIP3P). . . . . . . . . . . . 71 3.1 Structures of deprotonated HBDI (HBDI anion, top) and the cation (bot-tom). The structure of the radical is similar to that of the cation, with the unpaired electron being on the carbon that hosts positive charge in the cation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 3.2 Relevant molecular orbitals of deprotonated HBDI (HF/6-311G*). In the ground state of the anion, both p1 and p2 are doubly occupied, and the bright state is derived by the p1!p excitation. Oxidized forms are derived by removing the electrons from p1. . . . . . . . . . . . . . . . 90 3.3 Energy levels and electronic states of the HBDI anion and radical. The bright absorbing p1p state at 2.62 eV is a resonance state embedded in a photodetachment continuum beginning at 2.54 eV. The respective MOs are shown in Fig. 3.2. . . . . . . . . . . . . . . . . . . . . . . . . 91 3.4 Electronic states of the doublet HBDI radical. The respective MOs are shown in Fig. 3.2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 3.5 Electronic states of the doubly ionized HBDI anion. The respective MOs are shown in Fig. 3.2. . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 3.6 Energy diagram of the relevant electronic states of deprotonated HBDI. 93 3.7 Infrared spectra of the anionic and cationic forms of deprotonated HBDI computed with RI-MP2/cc-pVTZ. . . . . . . . . . . . . . . . . . . . . 99 4.1 Structure of uracil defining atom labels referred to in Table 4.1. . . . . 111 4.2 Frontier molecular orbitals of uracil at the ground state equilibrium geom-etry. Orbital energies are calculated with RHF/aug-cc-pVDZ. . . . . . . 112 4.3 Excitation energies (upper panel) and oscillator strengths (lower panel) of the lowest excited states of uracil calculated with EOM-CCSD and various one-electron basis sets. . . . . . . . . . . . . . . . . . . . . . . 115 4.4 Absorption spectrum of uracil with theoretical estimations of electronic transitions calculated with EOM-CCSD/aug-ANO-DZ and CR-EOM-CCSD( T)/aug-ANO-DZ. . . . . . . . . . . . . . . . . . . . . . . . . . 127 viii |
