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Figure 1.3: The chemical structure and atomic labels of the anionic form of
the model GFP chromophore, 4’-hydroxybenzylidene-2,3-dimethylimidazolinone
(HBDI) in the cis-conformation.
Studies of excited states of HBDI
Earlier experimental studies have characterized the absorption of HBDI in the native
protein environment98. The spectrum of the wild-type GFP has two broad absorp-tion
bands at 396 nm (3.13 eV) and 476 nm (2.60 eV) assigned to the neutral and
anionic forms of the chromophore, respectively. The spectra in aqueous solution99, 100
reveal strong pH sensitivity: the absorption maximum at neutral pH is at 370 nm
(3.35 eV), whereas at pH=13 and pH=1 it is shifted to 426 nm (2.91 eV) and 396 nm
(3.13 eV), respectively. The absorption of denatured wild-type proteins exhibit similar
pH-dependence101. The shifts were attributed to different protonation and deprotona-tion
forms, as well as strong interaction with water. The latter is consistent with a large
change (about 7 D) of the dipole moment upon excitation determined in Stark effect
measurements taken in a buffered at pH=6.5 glycerol solution at 77 K102. Therefore,
the protonation and deprotonation of HBDI and solvent effects, which strongly affect
its electronic properties, need to be accounted for in theoretical models. However, it is
important to characterize the chromophore in the gas phase first in order to quantify the
solvent effect separately.
20
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 30 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Figure 1.3: The chemical structure and atomic labels of the anionic form of the model GFP chromophore, 4’-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) in the cis-conformation. Studies of excited states of HBDI Earlier experimental studies have characterized the absorption of HBDI in the native protein environment98. The spectrum of the wild-type GFP has two broad absorp-tion bands at 396 nm (3.13 eV) and 476 nm (2.60 eV) assigned to the neutral and anionic forms of the chromophore, respectively. The spectra in aqueous solution99, 100 reveal strong pH sensitivity: the absorption maximum at neutral pH is at 370 nm (3.35 eV), whereas at pH=13 and pH=1 it is shifted to 426 nm (2.91 eV) and 396 nm (3.13 eV), respectively. The absorption of denatured wild-type proteins exhibit similar pH-dependence101. The shifts were attributed to different protonation and deprotona-tion forms, as well as strong interaction with water. The latter is consistent with a large change (about 7 D) of the dipole moment upon excitation determined in Stark effect measurements taken in a buffered at pH=6.5 glycerol solution at 77 K102. Therefore, the protonation and deprotonation of HBDI and solvent effects, which strongly affect its electronic properties, need to be accounted for in theoretical models. However, it is important to characterize the chromophore in the gas phase first in order to quantify the solvent effect separately. 20 |
