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Table 4.1: Equilibrium geometry of uracil. The calculated structure is optimized
with B3LYP/6-311G(2df,2pd). Experimental values are obtained by averaging
dimensions found in crystal structuresa. Atomic labels are defined in Fig. 4.1, dis-tances
in A° , angles in degrees.
Bond Calc.b Exp. Angle Calc.b Exp.
N1–C2 1.3908 1.379 C6–N1–C2 123.57 121.3
C2–N3 1.3801 1.373 N1–C2–N3 112.92 114.8
N3–C4 1.4092 1.383 C2–N3–C4 128.15 127.0
C4–C5 1.4559 1.440 N3–C4–C5 113.40 114.7
C5–C6 1.3426 1.338 C4–C5–C6 119.97 119.2
C6–N1 1.3706 1.380 C5–C6–N1 121.99 122.8
C2–O2 1.2084 1.218 O2–C2–N3 124.43 122.0
C4–O4 1.2110 1.227 O4–C4–C5 126.18 125.4
N1–H1 1.0060 H1–N1–C2 115.03
N3–H3 1.0112 H3–N3–C4 116.20
C5–H5 1.0769 H5–C5–C6 121.92
C6–H6 1.0808 H6–C6–N1 115.42
a Ref. 26. b Nuclear repulsion energy Enuc = 357:159959 hartree.
Table 4.2 lists leading electronic configurations as well as EOM singles amplitudes
obtained in an EOM-CCSD/aug-cc-pVDZ calculation. The total norm of singly excited
amplitudes R21
is about 0.9 for all the excited states, which suggests that they do not
carry a significant doubly excited character. This conclusion is also supported by small
weight of triple excitations in the EOM-CCSD(2,3) wave function, as discussed below.
113
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 123 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Table 4.1: Equilibrium geometry of uracil. The calculated structure is optimized with B3LYP/6-311G(2df,2pd). Experimental values are obtained by averaging dimensions found in crystal structuresa. Atomic labels are defined in Fig. 4.1, dis-tances in A° , angles in degrees. Bond Calc.b Exp. Angle Calc.b Exp. N1–C2 1.3908 1.379 C6–N1–C2 123.57 121.3 C2–N3 1.3801 1.373 N1–C2–N3 112.92 114.8 N3–C4 1.4092 1.383 C2–N3–C4 128.15 127.0 C4–C5 1.4559 1.440 N3–C4–C5 113.40 114.7 C5–C6 1.3426 1.338 C4–C5–C6 119.97 119.2 C6–N1 1.3706 1.380 C5–C6–N1 121.99 122.8 C2–O2 1.2084 1.218 O2–C2–N3 124.43 122.0 C4–O4 1.2110 1.227 O4–C4–C5 126.18 125.4 N1–H1 1.0060 H1–N1–C2 115.03 N3–H3 1.0112 H3–N3–C4 116.20 C5–H5 1.0769 H5–C5–C6 121.92 C6–H6 1.0808 H6–C6–N1 115.42 a Ref. 26. b Nuclear repulsion energy Enuc = 357:159959 hartree. Table 4.2 lists leading electronic configurations as well as EOM singles amplitudes obtained in an EOM-CCSD/aug-cc-pVDZ calculation. The total norm of singly excited amplitudes R21 is about 0.9 for all the excited states, which suggests that they do not carry a significant doubly excited character. This conclusion is also supported by small weight of triple excitations in the EOM-CCSD(2,3) wave function, as discussed below. 113 |
