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involves the protein. It is facilitated by a hydrogen bond network26–28 and can be cou-pled
to the decarboxylation of the glutamate 222 residue8, 9. The electrostatic field of the
protein may induce spectral shifts, although gas-phase studies suggested that the effect
of the protein environment on the excited states energies may be relatively small29, 30.
Despite the role of the protein, an important step towards understanding of the function
of GFP is characterization of the intrinsic properties of the isolated chromophore. By
focusing on the electronic properties of the chromophore, we can quantify changes in
absorption and fluorescence due to specific structural changes and to test different mech-anistic
ideas. Our calculations show that the absorption of the singly oxidized species
(radical) is blue shifted with respect to the HBDI anion. However, the doubly oxidized
system (cation), which has a stable closed-shell electronic structure, features red-shifted
absorption at 2.02 eV. The proposed mechanism involves two-step oxidation proceeding
via electronically excited states.
3.2 Computational details
Equilibrium geometries of closed-shell ground-state species (i.e., the HBDI anion and
cation) were optimized by RI-MP2/cc-pVTZ. The ground state structure of the doublet
radical was computed using wB97X/6-311(+,+)G(2df,2pd). The harmonic vibrational
frequencies and IR intensities of the anionic and cationic forms of deprotonated HBDI
were computed with RI-MP2/cc-pVTZ.
Excitation energies of the cation were computed using SOS-CIS(D) and EOM-EE-CCSD.
SOS-CIS(D) calculations employed the cc-pVTZ and cc-pVDZ bases31. EOM-CCSD
calculations used the 6-311G* basis set32, 33. For the anion, SOS-CIS(D) exci-tation
energies are in excellent agreement with more accurate MR-PT. The oscillator
strengths for SOS-CIS(D) were computed using the underlying CIS wave functions,
86
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 96 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | involves the protein. It is facilitated by a hydrogen bond network26–28 and can be cou-pled to the decarboxylation of the glutamate 222 residue8, 9. The electrostatic field of the protein may induce spectral shifts, although gas-phase studies suggested that the effect of the protein environment on the excited states energies may be relatively small29, 30. Despite the role of the protein, an important step towards understanding of the function of GFP is characterization of the intrinsic properties of the isolated chromophore. By focusing on the electronic properties of the chromophore, we can quantify changes in absorption and fluorescence due to specific structural changes and to test different mech-anistic ideas. Our calculations show that the absorption of the singly oxidized species (radical) is blue shifted with respect to the HBDI anion. However, the doubly oxidized system (cation), which has a stable closed-shell electronic structure, features red-shifted absorption at 2.02 eV. The proposed mechanism involves two-step oxidation proceeding via electronically excited states. 3.2 Computational details Equilibrium geometries of closed-shell ground-state species (i.e., the HBDI anion and cation) were optimized by RI-MP2/cc-pVTZ. The ground state structure of the doublet radical was computed using wB97X/6-311(+,+)G(2df,2pd). The harmonic vibrational frequencies and IR intensities of the anionic and cationic forms of deprotonated HBDI were computed with RI-MP2/cc-pVTZ. Excitation energies of the cation were computed using SOS-CIS(D) and EOM-EE-CCSD. SOS-CIS(D) calculations employed the cc-pVTZ and cc-pVDZ bases31. EOM-CCSD calculations used the 6-311G* basis set32, 33. For the anion, SOS-CIS(D) exci-tation energies are in excellent agreement with more accurate MR-PT. The oscillator strengths for SOS-CIS(D) were computed using the underlying CIS wave functions, 86 |
