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comparing electronic configurations of the doublet states (see Fig. 3.4) and the S1 state
(Fig. 3.3), we note that these transitions include significant one-electron character.
Thus, a possible mechanism of the oxidative redding emerging from the present
study is
The first step involves photoexcitation, and blue light is sufficient to generate this tran-sition.
The second and third steps are one-electron oxidation steps with E = 0:88 V,
which is within the reach of the oxidizing agents employed in Ref. 13. The two-electron
oxidation is consistent with the stoichiometric results from Ref. 13. Moreover, the
closed-shell character of the cation is consistent with the chemically stable nature of
the red form of GFP. Moreover, the closed-shell character of the cation is consistent
with the relatively chemically stable nature of the red form of GFP. Although the chem-ical
structure of the cation suggests high reactivity with respect to nucleophilic agents
such as water, the protein may be sufficiently effective in shielding this fragile species.
Finally, the absorption of the cationic form is red-shifted by 0.6 eV, and the resulting
value of 2.02 eV is in a good agreement with the experimental excitation energy of
2.12 eV. The structural differences between the chromophores of the FPs that undergo
oxidative redding (AcGFP1, TagGFP, zFP506, amFP486, and ppuGFP2), and those that
do not (EBFP and ECFP) provide additional support to the proposed mechanism. The
chromophores in the former group contain a phenolic moiety that can be easily con-verted
to the anionic deprotonated form and thus oxidized, whereas in EBFP and ECFP
the imidazolin moiety is connected to nitrogen-containing aromatic fragments that are
expected to be basic rather than acidic.
96
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 106 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | comparing electronic configurations of the doublet states (see Fig. 3.4) and the S1 state (Fig. 3.3), we note that these transitions include significant one-electron character. Thus, a possible mechanism of the oxidative redding emerging from the present study is The first step involves photoexcitation, and blue light is sufficient to generate this tran-sition. The second and third steps are one-electron oxidation steps with E = 0:88 V, which is within the reach of the oxidizing agents employed in Ref. 13. The two-electron oxidation is consistent with the stoichiometric results from Ref. 13. Moreover, the closed-shell character of the cation is consistent with the chemically stable nature of the red form of GFP. Moreover, the closed-shell character of the cation is consistent with the relatively chemically stable nature of the red form of GFP. Although the chem-ical structure of the cation suggests high reactivity with respect to nucleophilic agents such as water, the protein may be sufficiently effective in shielding this fragile species. Finally, the absorption of the cationic form is red-shifted by 0.6 eV, and the resulting value of 2.02 eV is in a good agreement with the experimental excitation energy of 2.12 eV. The structural differences between the chromophores of the FPs that undergo oxidative redding (AcGFP1, TagGFP, zFP506, amFP486, and ppuGFP2), and those that do not (EBFP and ECFP) provide additional support to the proposed mechanism. The chromophores in the former group contain a phenolic moiety that can be easily con-verted to the anionic deprotonated form and thus oxidized, whereas in EBFP and ECFP the imidazolin moiety is connected to nitrogen-containing aromatic fragments that are expected to be basic rather than acidic. 96 |
