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Table 3.4: Selected geometric parameters (bond lengths in A° , angles in degrees) of
the HBDI anion, and its singly and doubly oxidized forms.
Species CP-CB CI-CB CP-CB-CI OP-C OI-C
Aniona 1.393 1.385 134.8 1.248 1.236
Cationa 1.386 1.389 127.8 1.226 1.197
Radicalb 1.413 1.369 129.6 1.228 1.209
a RI-MP2/cc-pVTZ b wB97X/6-311(+,+)G(2df,2pd)
CI–CB and CP–CB bond orders are scrambled. The analysis of the structural param-eters
and the wave functions demonstrated that the phenolic form dominates, i.e., the
CP–CB bond is longer than CI–CB. Double ionization eliminates the phenolic struc-ture
entirely producing the quinoid structure shown in Fig. 3.1 (bottom). The positive
charge located on the imidazolin carbon is stabilized by electron-donating methyl group
(the NBO analysis52 suggests considerable delocalization of the hole over imidazolin
moiety). The structure of the radical can be described as the quinoid structure with the
unpaired electron on the imidazolin’s methyl-substituted carbon.
Table 3.4 summarizes important geometric parameters of the anion, neutral, and
the cation. Consistently with the above analysis, both CO bonds become shorter in the
cation, and the CP–CB bond becomes shorter than CI–CB. However, the bond alternation
remains small due to conjugation. Moreover, because of the two resonance structures
present in the anion, the overall structural differences between the anion and the cation
are less than could be expected by considering only the dominant phenolate structure.
The ionization-induced structural changes strongly affect vibrational frequencies,
which may be exploited in the experimental characterization of the red form of GFP,
e.g., by using IR or Raman spectroscopy as in Refs. 9, 53 (a detailed summary of the
vibrational spectroscopy studies of GFP can be found in Ref. 54). Fig. 3.7 shows the
98
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 108 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Table 3.4: Selected geometric parameters (bond lengths in A° , angles in degrees) of the HBDI anion, and its singly and doubly oxidized forms. Species CP-CB CI-CB CP-CB-CI OP-C OI-C Aniona 1.393 1.385 134.8 1.248 1.236 Cationa 1.386 1.389 127.8 1.226 1.197 Radicalb 1.413 1.369 129.6 1.228 1.209 a RI-MP2/cc-pVTZ b wB97X/6-311(+,+)G(2df,2pd) CI–CB and CP–CB bond orders are scrambled. The analysis of the structural param-eters and the wave functions demonstrated that the phenolic form dominates, i.e., the CP–CB bond is longer than CI–CB. Double ionization eliminates the phenolic struc-ture entirely producing the quinoid structure shown in Fig. 3.1 (bottom). The positive charge located on the imidazolin carbon is stabilized by electron-donating methyl group (the NBO analysis52 suggests considerable delocalization of the hole over imidazolin moiety). The structure of the radical can be described as the quinoid structure with the unpaired electron on the imidazolin’s methyl-substituted carbon. Table 3.4 summarizes important geometric parameters of the anion, neutral, and the cation. Consistently with the above analysis, both CO bonds become shorter in the cation, and the CP–CB bond becomes shorter than CI–CB. However, the bond alternation remains small due to conjugation. Moreover, because of the two resonance structures present in the anion, the overall structural differences between the anion and the cation are less than could be expected by considering only the dominant phenolate structure. The ionization-induced structural changes strongly affect vibrational frequencies, which may be exploited in the experimental characterization of the red form of GFP, e.g., by using IR or Raman spectroscopy as in Refs. 9, 53 (a detailed summary of the vibrational spectroscopy studies of GFP can be found in Ref. 54). Fig. 3.7 shows the 98 |
