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yields very accurate structures for well-behaved closed-shell molecules7. MP2 calcula-tions
employed the resolution-of-the-identity (RI) technique. The CASSCF and PBE0
structures are C1, whereas the RI-MP2 optimization produced a Cs minimum.
Vertical excitation energies were computed by MRMP2, TDDFT with the BNL and
wPB97X functionals, CIS, SOS-CIS(D), and EOMEE-CCSD. The VDE was computed
at the CASSCF geometry as the energy of the Hartree–Fock HOMO (Koopmans’ theo-rem),
by EOMIP-CCSD, and by using the BNL HOMO energy (as described below, this
is equivalent to computing VDE as the difference between the total BNL energies of the
anion and the neutral radical). The wPB97X and B3LYP Koopmans’ theorem and DE
values are also given for comparison.
The cis-trans isomerization pathways of the chromophore were studied with the DFT
and CASSCF methods. Solvent effects we estimated using continuum solvation models,
as well as by explicit treatment of water molecules in a QM/MM scheme.
MRMP2 and D-PCM calculations were carried out with the PC GAMESS version8
of the GAMESS(US) quantum chemistry package9. CIS, SOS-MP2, SOS-CIS(D),
EOM-CCSD, and BNL calculations were performed with Q-Chem10. GAMESS(US)9
was employed for C-PCM and SVPE computations. The QM/MM implementation is
based on PC GAMESS8 and the Tinker molecular mechanics package11.
2.2.1 Continuum solvation models
To simulate solvent effects on the chromophore’s cis-trans isomerization energy pro-file
in aqueous solution, we employ three versions of the continuum solvation model12:
D-PCM, C-PCM, and SVPE. In the simplest approach, the dielectric polarizable con-tinuum
model (D-PCM)13, the water solvent is treated as a continuous unstructured
dielectric with a dielectric constant of 78.39. C-PCM14 is a version of PCM that takes
44
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 54 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | yields very accurate structures for well-behaved closed-shell molecules7. MP2 calcula-tions employed the resolution-of-the-identity (RI) technique. The CASSCF and PBE0 structures are C1, whereas the RI-MP2 optimization produced a Cs minimum. Vertical excitation energies were computed by MRMP2, TDDFT with the BNL and wPB97X functionals, CIS, SOS-CIS(D), and EOMEE-CCSD. The VDE was computed at the CASSCF geometry as the energy of the Hartree–Fock HOMO (Koopmans’ theo-rem), by EOMIP-CCSD, and by using the BNL HOMO energy (as described below, this is equivalent to computing VDE as the difference between the total BNL energies of the anion and the neutral radical). The wPB97X and B3LYP Koopmans’ theorem and DE values are also given for comparison. The cis-trans isomerization pathways of the chromophore were studied with the DFT and CASSCF methods. Solvent effects we estimated using continuum solvation models, as well as by explicit treatment of water molecules in a QM/MM scheme. MRMP2 and D-PCM calculations were carried out with the PC GAMESS version8 of the GAMESS(US) quantum chemistry package9. CIS, SOS-MP2, SOS-CIS(D), EOM-CCSD, and BNL calculations were performed with Q-Chem10. GAMESS(US)9 was employed for C-PCM and SVPE computations. The QM/MM implementation is based on PC GAMESS8 and the Tinker molecular mechanics package11. 2.2.1 Continuum solvation models To simulate solvent effects on the chromophore’s cis-trans isomerization energy pro-file in aqueous solution, we employ three versions of the continuum solvation model12: D-PCM, C-PCM, and SVPE. In the simplest approach, the dielectric polarizable con-tinuum model (D-PCM)13, the water solvent is treated as a continuous unstructured dielectric with a dielectric constant of 78.39. C-PCM14 is a version of PCM that takes 44 |
