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a fluctuating environment17–19. In the present work, a similar approach is employed to
compute the excitation energies of uracil in the aqueous solution.
Solvent effects are evaluated by the QM/MM approach20 as implemented in
NWChem. The uracil molecule at the equilibrium ground-state geometry is embedded
in a 30 A° -wide cubic box containing 887 water molecules. The QM region consists of
the uracil molecule, and the rest of the system is treated at theMMlevel using the SPC/E
water model21. To ensure proper solvent structure around uracil, the solvent part of the
system is first optimized, equilibrated over the course of 50 ps of molecular dynamics
simulations, and then re-optimized again. During this simulation, the electrostatic field
of uracil is represented by a set of fixed effective charges obtained from an electrostatic
potential (ESP) fitting using B3LYP calculations with the 6-31G(d) basis set. Molecu-lar
dynamics equilibration is performed at the constant temperature of 298.15 K with a
15 °A
cutoff. The resulting configuration is then used to calculate the vertical excitation
energies using the B3LYP and EOM-CCSDt levels of theory with the 6-31G(d) basis
set. The (10,10) active space is used in the QM part.
EOM-CCSD and EOM-CC(2,3) calculations are performed with Q-Chem22, CR-EOM-
CCSD(T), EOM-CCSDt, and some EOM-CCSD computations are carried out
with NWChem16, 23. The COLUMBUS24, 25 suite of programs is used for MRCI calcu-lations.
4.3 Results and discussion
4.3.1 Structure and electronic states of uracil
In the ground electronic state, uracil is a planar molecule. Fig. 4.1 defines atomic labels
in its diketo tautomer. Table 4.1 gives equilibrium geometrical parameters optimized
110
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 120 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | a fluctuating environment17–19. In the present work, a similar approach is employed to compute the excitation energies of uracil in the aqueous solution. Solvent effects are evaluated by the QM/MM approach20 as implemented in NWChem. The uracil molecule at the equilibrium ground-state geometry is embedded in a 30 A° -wide cubic box containing 887 water molecules. The QM region consists of the uracil molecule, and the rest of the system is treated at theMMlevel using the SPC/E water model21. To ensure proper solvent structure around uracil, the solvent part of the system is first optimized, equilibrated over the course of 50 ps of molecular dynamics simulations, and then re-optimized again. During this simulation, the electrostatic field of uracil is represented by a set of fixed effective charges obtained from an electrostatic potential (ESP) fitting using B3LYP calculations with the 6-31G(d) basis set. Molecu-lar dynamics equilibration is performed at the constant temperature of 298.15 K with a 15 °A cutoff. The resulting configuration is then used to calculate the vertical excitation energies using the B3LYP and EOM-CCSDt levels of theory with the 6-31G(d) basis set. The (10,10) active space is used in the QM part. EOM-CCSD and EOM-CC(2,3) calculations are performed with Q-Chem22, CR-EOM- CCSD(T), EOM-CCSDt, and some EOM-CCSD computations are carried out with NWChem16, 23. The COLUMBUS24, 25 suite of programs is used for MRCI calcu-lations. 4.3 Results and discussion 4.3.1 Structure and electronic states of uracil In the ground electronic state, uracil is a planar molecule. Fig. 4.1 defines atomic labels in its diketo tautomer. Table 4.1 gives equilibrium geometrical parameters optimized 110 |
