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Table 5.2: Results of energy minimization of the 21A2/11B1 intersection seam in
N+3
calculated by EOM-CCSD/6-31G. All bond lengths are given in angstroms, all
angles are given in degrees.
Starting geometry Iterations Final geometry
R(NN) a(NNN) R(NN) a(NNN)
Tolerancea Dg = 3 104 (Q-Chem default)
1.2000 60.00 6 1.4553 60.00
1.4200 60.00 4 1.4555 60.00
1.4600 70.00 16 1.4556 59.99
1.5400 50.00 5 1.4557 60.00
1.6000 90.00 8 1.4475 60.79
Tolerance Dg = 3 105
1.2000 60.00 7 1.4556 60.00
1.4200 60.00 5 1.4556 60.00
1.4600 70.00 16 1.4556 59.99
1.5400 50.00 6 1.4556 60.00
1.6000 90.00 9 1.4476 60.78
Tolerance Dg = 1 105
1.2000 60.00 7 1.4556 60.00b
1.4200 60.00 5 1.4556 60.00
1.4600 70.00 17 1.4556 60.00
1.5400 50.00 6 1.4556 60.00
1.6000 90.00 9 1.4476 60.78c
aTolerance on the maximum gradient component. The optimization procedure con-verges
if this and one of the two criteria — energy change DE = 106 a.u. and max-imum
displacement Dq = 1:2 103 °A
— are satisfied. bNuclear repulsion energy
Enr = 53:441794 a.u., total energy Etot = 162:822635 a.u. cNuclear repulsion energy
Enr = 53:528406 a.u., total energy Etot = 162:821900 a.u.
5.4.2 Nitrogen dioxide
The PESs of the ground and first excited states of the NO2 molecule, X2A1 and A2B2,
form an intersection35. Crossing points have been located for different N–O bond dis-tances
with the O–N–O angle between 107 and 108 36. 146
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 156 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Table 5.2: Results of energy minimization of the 21A2/11B1 intersection seam in N+3 calculated by EOM-CCSD/6-31G. All bond lengths are given in angstroms, all angles are given in degrees. Starting geometry Iterations Final geometry R(NN) a(NNN) R(NN) a(NNN) Tolerancea Dg = 3 104 (Q-Chem default) 1.2000 60.00 6 1.4553 60.00 1.4200 60.00 4 1.4555 60.00 1.4600 70.00 16 1.4556 59.99 1.5400 50.00 5 1.4557 60.00 1.6000 90.00 8 1.4475 60.79 Tolerance Dg = 3 105 1.2000 60.00 7 1.4556 60.00 1.4200 60.00 5 1.4556 60.00 1.4600 70.00 16 1.4556 59.99 1.5400 50.00 6 1.4556 60.00 1.6000 90.00 9 1.4476 60.78 Tolerance Dg = 1 105 1.2000 60.00 7 1.4556 60.00b 1.4200 60.00 5 1.4556 60.00 1.4600 70.00 17 1.4556 60.00 1.5400 50.00 6 1.4556 60.00 1.6000 90.00 9 1.4476 60.78c aTolerance on the maximum gradient component. The optimization procedure con-verges if this and one of the two criteria — energy change DE = 106 a.u. and max-imum displacement Dq = 1:2 103 °A — are satisfied. bNuclear repulsion energy Enr = 53:441794 a.u., total energy Etot = 162:822635 a.u. cNuclear repulsion energy Enr = 53:528406 a.u., total energy Etot = 162:821900 a.u. 5.4.2 Nitrogen dioxide The PESs of the ground and first excited states of the NO2 molecule, X2A1 and A2B2, form an intersection35. Crossing points have been located for different N–O bond dis-tances with the O–N–O angle between 107 and 108 36. 146 |
