Page 97 |
Save page Remove page | Previous | 97 of 200 | Next |
|
small (250x250 max)
medium (500x500 max)
Large (1000x1000 max)
Extra Large
large ( > 500x500)
Full Resolution
All (PDF)
|
This page
All
|
whereas for EOMEE-CCSD, the transition density matrices computed using EOMEE
wavefunctions were employed.
Electronic structure calculations for the open-shell radical species are more chal-lenging
due to spin contamination of the doublet reference. This effect can be mitigated
by using better reference orbitals, e.g., those optimized for the MP2 wave functions, i.e.,
O2 method. We employed O2 orbitals in the SOS-CIS(D) calculations of the doublet
states. Moreover, excited states in doublet radicals can also develop a notable doubly
excited character causing poor performance of single-reference methods using the dou-blet
reference34–37. This can be avoided by employing the spin-flip (SF) methods38–40
utilizing a high-spin quartet reference, i.e., (p2)1(p1)1(p )1. The SF approach mitigates
spin contamination and provides more balanced description of the ground and relevant
excited states. Our EOMSF-CCSD calculations (which employed B3LYP orbitals to
control spin-contamination of the quartet reference) showed that the wave functions of
the excited states are of singly-excited character (with respect to the doublet reference)
thus validating the SOS-CIS(D) results. The hS2i values for the three lowest states of
the doublet are 0.78. 0.79, and 0.81. The EOMSF-CCSD and SOS-CIS(D) calculations
are in quantitative agreement. Finally, MR-PT calculations on the doublet states are also
in agreement with EOMSF-CCSD and SOS-CIS(D).
MR-PT calculations employed a modified version of second-order multiconfigura-tional
quasidegenerate perturbation theory (MCQDPT2)41. Originally, the correspond-ing
programs were implemented in GAMESS (US)42 and PC GAMESS43. Recently,
serious bugs in the MCQDPT2 algorithm were noticed44 and resolved in the new vari-ant
called XMCQDPT2 as implemented in PC GAMESS/Firefly44.
The XMCQDPT2 calculations used the complete active space self-consistent field
(CASSCF) state-averaged (SA) electron density over several lowest-lying states. As
87
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 97 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | whereas for EOMEE-CCSD, the transition density matrices computed using EOMEE wavefunctions were employed. Electronic structure calculations for the open-shell radical species are more chal-lenging due to spin contamination of the doublet reference. This effect can be mitigated by using better reference orbitals, e.g., those optimized for the MP2 wave functions, i.e., O2 method. We employed O2 orbitals in the SOS-CIS(D) calculations of the doublet states. Moreover, excited states in doublet radicals can also develop a notable doubly excited character causing poor performance of single-reference methods using the dou-blet reference34–37. This can be avoided by employing the spin-flip (SF) methods38–40 utilizing a high-spin quartet reference, i.e., (p2)1(p1)1(p )1. The SF approach mitigates spin contamination and provides more balanced description of the ground and relevant excited states. Our EOMSF-CCSD calculations (which employed B3LYP orbitals to control spin-contamination of the quartet reference) showed that the wave functions of the excited states are of singly-excited character (with respect to the doublet reference) thus validating the SOS-CIS(D) results. The hS2i values for the three lowest states of the doublet are 0.78. 0.79, and 0.81. The EOMSF-CCSD and SOS-CIS(D) calculations are in quantitative agreement. Finally, MR-PT calculations on the doublet states are also in agreement with EOMSF-CCSD and SOS-CIS(D). MR-PT calculations employed a modified version of second-order multiconfigura-tional quasidegenerate perturbation theory (MCQDPT2)41. Originally, the correspond-ing programs were implemented in GAMESS (US)42 and PC GAMESS43. Recently, serious bugs in the MCQDPT2 algorithm were noticed44 and resolved in the new vari-ant called XMCQDPT2 as implemented in PC GAMESS/Firefly44. The XMCQDPT2 calculations used the complete active space self-consistent field (CASSCF) state-averaged (SA) electron density over several lowest-lying states. As 87 |
