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clear, as the temperature of the ions in the ring is unknown), one would like the computed
wavelength to fall within 2.47–2.72 eV (456–502 nm). However, due to the resonance
nature of the pp state, calculating the excitation energies and oscillator strengths, as
well as comparing them with the experimental spectrum, are not as straightforward as in
the case of excited states lying below the electron detachment energy. In the following,
we will use the term “detached states” to identify the electronic states that compose the
continuum instead of the usual “ionized states” as the initial species is anionic.
The ground-state equilibrium geometry was optimized with PBE0/cc-pVDZ,
CASSCF/cc-pVDZ, and RI-MP2/cc-pVTZ. Although the differences between the
geometries are small (maximum bond length deviation is 0.03 °A
and angles agree within
2 degrees), the pp excitation energy computed using wavefunction-based methods dif-fers
by about 0.1 eV. This effect of geometry is consistent with previous calculations
by Olsen34 for a similar system (p-hydroxybenzylidene-imidazolin-5-one, HBI). Of the
three structures, the RI-MP2/cc-pVTZ one is the most accurate7. Since most of the
changes in electron density occur in the bridge region, it is interesting to compare the
C1p-C1B and C1B-C1I bond lengths computed by different methods. The RI-MP2 val-ues
are 1.394 °A
and 1.378 ° A, which is very close to the PBE0 values of 1.404 °A
and
1.385 A° . Due to the absence of dynamical correlation, CASSCF exaggerates the bond
alternation giving 1.406 °A
and 1.397 A° .
Calculations in small basis sets create discrete states from the continuum and artifi-cially
exclude the detached states from the picture. Assuming that the character of the
resonance state of interest is well described, such calculations may provide a fairly good
estimate of the position of this state in the continuum, however, it is difficult to predict
how expanding the basis set will affect the resonance state25, 31. Moreover, one should
anticipate broadening of the resonance state due to the interaction with the detached
51
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 61 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | clear, as the temperature of the ions in the ring is unknown), one would like the computed wavelength to fall within 2.47–2.72 eV (456–502 nm). However, due to the resonance nature of the pp state, calculating the excitation energies and oscillator strengths, as well as comparing them with the experimental spectrum, are not as straightforward as in the case of excited states lying below the electron detachment energy. In the following, we will use the term “detached states” to identify the electronic states that compose the continuum instead of the usual “ionized states” as the initial species is anionic. The ground-state equilibrium geometry was optimized with PBE0/cc-pVDZ, CASSCF/cc-pVDZ, and RI-MP2/cc-pVTZ. Although the differences between the geometries are small (maximum bond length deviation is 0.03 °A and angles agree within 2 degrees), the pp excitation energy computed using wavefunction-based methods dif-fers by about 0.1 eV. This effect of geometry is consistent with previous calculations by Olsen34 for a similar system (p-hydroxybenzylidene-imidazolin-5-one, HBI). Of the three structures, the RI-MP2/cc-pVTZ one is the most accurate7. Since most of the changes in electron density occur in the bridge region, it is interesting to compare the C1p-C1B and C1B-C1I bond lengths computed by different methods. The RI-MP2 val-ues are 1.394 °A and 1.378 ° A, which is very close to the PBE0 values of 1.404 °A and 1.385 A° . Due to the absence of dynamical correlation, CASSCF exaggerates the bond alternation giving 1.406 °A and 1.397 A° . Calculations in small basis sets create discrete states from the continuum and artifi-cially exclude the detached states from the picture. Assuming that the character of the resonance state of interest is well described, such calculations may provide a fairly good estimate of the position of this state in the continuum, however, it is difficult to predict how expanding the basis set will affect the resonance state25, 31. Moreover, one should anticipate broadening of the resonance state due to the interaction with the detached 51 |
