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set of diffuse functions is required to describe it correctly, and with a second set of dif-fuse
functions its excitation energy drops by 0.15 eV. Fleig et al.27 report similar effects
of improving the basis set. They also show that the CC2 excitation energies for the
four lowest valence singlet states of uracil change by 0.01 eV by extending the basis
set from aug-cc-pVTZ to aug-cc-pVQZ, whereas the energy of the lowest Rydberg state
changes by 0.05 eV. Thus, we consider our aug-cc-pVTZ energies of the valence states
converged within approximately 0.01 eV with respect to the one-electron basis set.
The oscillator strength of the allowed pp transitions changes very slightly as the
basis set is expanded. In the case of the dark np transitions, the oscillator strength
drops by an order of magnitude upon addition of a set of diffuse functions on heavy
atoms.
We also note the excellent performance of the augmented ANO double-zeta and
aug-cc-pVDZ bases, which produce excitation energies for the two lowest states within
0.02 eV from aug-cc-pVTZ (see Table 4.3), whereas the CC2 energies from Ref. 27
change by 0.08–0.11 eV between the aug-cc-pVDZ and aug-cc-pVTZ bases.
Overall, both polarization and diffuse functions are required to obtain the correct
order and converged energy of the excited states. The basis set effects can account for as
much as 0.25 eV for the pp state, while the np state is less sensitive. We will use the
aug-ANO-DZ and aug-cc-pVTZ basis sets in the best estimations of excitation energies.
As summarized in Table 4.3, EOM-CCSD calculations with the 6-311(2+)G(df)/6-
31G(d,p), aug-ANO-DZ, and aug-cc-pVTZ bases give excitation energies of 5.21–
5.25 eV for the lowest np state and 5.59–5.71 eV for the pp transition.
117
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 127 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | set of diffuse functions is required to describe it correctly, and with a second set of dif-fuse functions its excitation energy drops by 0.15 eV. Fleig et al.27 report similar effects of improving the basis set. They also show that the CC2 excitation energies for the four lowest valence singlet states of uracil change by 0.01 eV by extending the basis set from aug-cc-pVTZ to aug-cc-pVQZ, whereas the energy of the lowest Rydberg state changes by 0.05 eV. Thus, we consider our aug-cc-pVTZ energies of the valence states converged within approximately 0.01 eV with respect to the one-electron basis set. The oscillator strength of the allowed pp transitions changes very slightly as the basis set is expanded. In the case of the dark np transitions, the oscillator strength drops by an order of magnitude upon addition of a set of diffuse functions on heavy atoms. We also note the excellent performance of the augmented ANO double-zeta and aug-cc-pVDZ bases, which produce excitation energies for the two lowest states within 0.02 eV from aug-cc-pVTZ (see Table 4.3), whereas the CC2 energies from Ref. 27 change by 0.08–0.11 eV between the aug-cc-pVDZ and aug-cc-pVTZ bases. Overall, both polarization and diffuse functions are required to obtain the correct order and converged energy of the excited states. The basis set effects can account for as much as 0.25 eV for the pp state, while the np state is less sensitive. We will use the aug-ANO-DZ and aug-cc-pVTZ basis sets in the best estimations of excitation energies. As summarized in Table 4.3, EOM-CCSD calculations with the 6-311(2+)G(df)/6- 31G(d,p), aug-ANO-DZ, and aug-cc-pVTZ bases give excitation energies of 5.21– 5.25 eV for the lowest np state and 5.59–5.71 eV for the pp transition. 117 |
