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The experimental action spectrum of the denatured gas phase anionic GFP chro-mophore
features a broad line (2.4–2.8 eV) with a maximum at 2.59 eV and a minor fea-ture
at 2.3 eV. Wavefunction-based and DFT calculations estimate VDE of 2.4–2.5 eV.
Thus, we assign the minor peak as due to the photodetachment transition. Based on
our estimate of VDE, the absorption band at 2.6 eV corresponds to the transition to the
resonance state embedded in an electron detached continuum, and the broad character
of the spectrum is at least partially due to the interaction with the continuum states.
The resonance nature of the pp state suggest a finite lifetime, and that autoioniza-tion
channel should be considered when modeling the anionic GFP photocycle. The
triplet state is found to be well below the photodetachment threshold (vertical excita-tion
energy 1.86 eV). Thus, the two states are expected to have very different lifetimes,
which makes the suggested3 population trapping in the triplet state even more essential
for explaining slow fragmentation kinetics. The resonance nature of the pp state in
the anionic GFP might be responsible for very different behavior of the photofragment
yield of the anionic and protonated GFP3, however, more detailed electronic structure
calculations are required in order to suggest a viable mechanism. An important question
is how photoinduced isomerization and other structural changes40, 41 affect the relative
states energies.
All wavefunction-based and TD-DFT methods agree on the nature of the transition
lending the intensity to the resonance state, which is a bright pp transition (HOMO-LUMO
in a small basis set), however, quantitative agreement is more difficult to achieve.
Most importantly, small basis set calculations discretize the ionization continuum, and
the results of such calculations provide only a crude estimate of the energy of the res-onance
state. In order to account for basis set effects, the stabilization analysis can be
74
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 84 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | The experimental action spectrum of the denatured gas phase anionic GFP chro-mophore features a broad line (2.4–2.8 eV) with a maximum at 2.59 eV and a minor fea-ture at 2.3 eV. Wavefunction-based and DFT calculations estimate VDE of 2.4–2.5 eV. Thus, we assign the minor peak as due to the photodetachment transition. Based on our estimate of VDE, the absorption band at 2.6 eV corresponds to the transition to the resonance state embedded in an electron detached continuum, and the broad character of the spectrum is at least partially due to the interaction with the continuum states. The resonance nature of the pp state suggest a finite lifetime, and that autoioniza-tion channel should be considered when modeling the anionic GFP photocycle. The triplet state is found to be well below the photodetachment threshold (vertical excita-tion energy 1.86 eV). Thus, the two states are expected to have very different lifetimes, which makes the suggested3 population trapping in the triplet state even more essential for explaining slow fragmentation kinetics. The resonance nature of the pp state in the anionic GFP might be responsible for very different behavior of the photofragment yield of the anionic and protonated GFP3, however, more detailed electronic structure calculations are required in order to suggest a viable mechanism. An important question is how photoinduced isomerization and other structural changes40, 41 affect the relative states energies. All wavefunction-based and TD-DFT methods agree on the nature of the transition lending the intensity to the resonance state, which is a bright pp transition (HOMO-LUMO in a small basis set), however, quantitative agreement is more difficult to achieve. Most importantly, small basis set calculations discretize the ionization continuum, and the results of such calculations provide only a crude estimate of the energy of the res-onance state. In order to account for basis set effects, the stabilization analysis can be 74 |
