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Table 2.5: Cumulative natural charges on the fragments of the HBDI molecule:
the phenyl and dimethylimidazolin rings and the CH bridge calculated with
CASSCF(12/11) and DFT (PBE0 functional).
CASSCF(12/11)/cc-pVDZ PBE0/6-31+G(d,p)
cis TS trans cis TS trans
Gas phase
Phenyl 0:61 0:20 0:50 0:59 0:30 0:57
Bridge 0:13 0:13 0:11 0:10 0:20 0:09
Imidazolin 0:52 0:93 0:61 0:51 0:90 0:52
Solutiona
Phenyl 0:85 0:09 0:91 0:63 0:19 0:70
Bridge 0:14 0:08 0:11 0:13 0:16 0:13
Imidazolin 0:29 0:99 0:20 0:50 0:97 0:43
a Calculated with QM/MM: EFP for the solvent-QM part interaction and TIP3P for the
water-water interaction.
for the PBE0 density: the positive charge on the bridge moiety is 0.19, versus 0.13
at the CASSCF level. Because of the large energy penalty due to charge separation
in the gas phase, small differences in ionicity may produce a large effect. Another
notable difference is larger asymmetry in oxygen charges: at the CASSCF level the
imidazolin oxygen is by 0.22e more negative than the phenyl oxygen, whereas at the
DFT level this difference is reduced to 0.15. This suggests larger contribution of the
second resonance structure in the CASSCF wave function, which can also contribute to
the energy difference.
More ionic character of the PBE0 density and the cusp-like shape of the pro-file
(Fig. 2.5) are due to multiconfigurational character of the wave function at the
TS, which is not adequately described by DFT (or MP2). The CASSCF amplitudes
67
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 77 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Table 2.5: Cumulative natural charges on the fragments of the HBDI molecule: the phenyl and dimethylimidazolin rings and the CH bridge calculated with CASSCF(12/11) and DFT (PBE0 functional). CASSCF(12/11)/cc-pVDZ PBE0/6-31+G(d,p) cis TS trans cis TS trans Gas phase Phenyl 0:61 0:20 0:50 0:59 0:30 0:57 Bridge 0:13 0:13 0:11 0:10 0:20 0:09 Imidazolin 0:52 0:93 0:61 0:51 0:90 0:52 Solutiona Phenyl 0:85 0:09 0:91 0:63 0:19 0:70 Bridge 0:14 0:08 0:11 0:13 0:16 0:13 Imidazolin 0:29 0:99 0:20 0:50 0:97 0:43 a Calculated with QM/MM: EFP for the solvent-QM part interaction and TIP3P for the water-water interaction. for the PBE0 density: the positive charge on the bridge moiety is 0.19, versus 0.13 at the CASSCF level. Because of the large energy penalty due to charge separation in the gas phase, small differences in ionicity may produce a large effect. Another notable difference is larger asymmetry in oxygen charges: at the CASSCF level the imidazolin oxygen is by 0.22e more negative than the phenyl oxygen, whereas at the DFT level this difference is reduced to 0.15. This suggests larger contribution of the second resonance structure in the CASSCF wave function, which can also contribute to the energy difference. More ionic character of the PBE0 density and the cusp-like shape of the pro-file (Fig. 2.5) are due to multiconfigurational character of the wave function at the TS, which is not adequately described by DFT (or MP2). The CASSCF amplitudes 67 |
