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1.2 Previous studies of the green fluorescent protein
chromophore
Unique electronic properties of the green fluorescent protein (GFP) whose natural func-tion
is to convert blue light to green light have motivated a number of experimental and
theoretical studies85, 86 and have been exploited in numerous practical applications87–89.
Due to their fundamental and practical importance, studies of the structure and prop-erties
of photoreceptor proteins and their denatured chromophores constitute an impor-tant
field of modern research. Moreover, GFP can be considered as a model for other
fluorogenic unsymmetric methine dyes90–95, and is of interest to organic photovoltaic
materials. For example, the fluorescent protein motif has already inspired the creation
of new organic phototovoltaic sensitizers96 and other optoelectronic materials97.
From the theoretical perspective, characterization of the electronic structure of iso-lated
chromophores is the first step towards understanding their photochemical and pho-tobiological
properties in realistic environments. Modeling isolated species involves
calculating the molecular parameters of the chromophores in the gas phase and in solu-tion
using quantum chemistry methods. This work presents accurate calculations of
the properties of biological chromophores with ab initio methods using the model GFP
chromophore, 4’-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) anion, as a
benchmark system (Fig. 1.3). We also study the vertical excitation and electron detach-ment
energies, discuss the electronic properties of the excited and detached states, the
cis-trans isomerization of the HBDI anion in the ground electronic state.
19
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 29 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | 1.2 Previous studies of the green fluorescent protein chromophore Unique electronic properties of the green fluorescent protein (GFP) whose natural func-tion is to convert blue light to green light have motivated a number of experimental and theoretical studies85, 86 and have been exploited in numerous practical applications87–89. Due to their fundamental and practical importance, studies of the structure and prop-erties of photoreceptor proteins and their denatured chromophores constitute an impor-tant field of modern research. Moreover, GFP can be considered as a model for other fluorogenic unsymmetric methine dyes90–95, and is of interest to organic photovoltaic materials. For example, the fluorescent protein motif has already inspired the creation of new organic phototovoltaic sensitizers96 and other optoelectronic materials97. From the theoretical perspective, characterization of the electronic structure of iso-lated chromophores is the first step towards understanding their photochemical and pho-tobiological properties in realistic environments. Modeling isolated species involves calculating the molecular parameters of the chromophores in the gas phase and in solu-tion using quantum chemistry methods. This work presents accurate calculations of the properties of biological chromophores with ab initio methods using the model GFP chromophore, 4’-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) anion, as a benchmark system (Fig. 1.3). We also study the vertical excitation and electron detach-ment energies, discuss the electronic properties of the excited and detached states, the cis-trans isomerization of the HBDI anion in the ground electronic state. 19 |
