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Overall, it is unrealistic to expect accuracy better than 0.1 eV (20 nm) from computa-tional
protocols applicable to a molecule of this size even for non-resonance states, and
the observed discrepancies between different methods confirm that. Moreover, when
assessing the accuracy of computed values, one should keep in mind the finite width of
the experimental absorption band. Thus, more calculations are necessary to provide a
converged theoretical estimate, especially stabilization analysis. For practical applica-tions,
however, it is important that all the reliable theoretical methods agree with each
other in that the origin of the intensity in the resonance state is due to pp excitation.
SOS-CIS(D) offers an inexpensive alternative to more rigorous multireference methods
if single excitations are dominant in the wavefunction.
Changes in electronic density in the singlet pp state
As one may expect from the molecular orbital character (Fig. 2.3) and the large oscil-lator
strength, electronic excitation results in a significant redistribution of electronic
density. A convenient measure of charge distribution is the permanent dipole moment.
Although in charged system it is origin-dependent, the difference between the two dipole
moments, Dμ = μgr μex, is not. At the CIS level of theory, the value of jDμj is 0.6 D,
and its direction is in the molecular plain pointing towards the bridge carbon. This value
can be compared with the experimentally measured Dμ, derived from Stark effect mea-surements
in a buffered at pH=6.5 glycerol solution at 77 K38. This work also reports the
angle between Dμ and Dμtr. Strikingly, the experimental value is 10 times larger than the
computed one. Since Dμ is related to the changes in orbital occupations upon excitation,
it is dominated by contributions from the leading excitation amplitudes, and should be
reproduced fairly accurately at the CIS level. Thus, large discrepancy is likely to be due
to the solvent effect. Indeed, polar solvents result in the increased dipole moment of the
59
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 69 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Overall, it is unrealistic to expect accuracy better than 0.1 eV (20 nm) from computa-tional protocols applicable to a molecule of this size even for non-resonance states, and the observed discrepancies between different methods confirm that. Moreover, when assessing the accuracy of computed values, one should keep in mind the finite width of the experimental absorption band. Thus, more calculations are necessary to provide a converged theoretical estimate, especially stabilization analysis. For practical applica-tions, however, it is important that all the reliable theoretical methods agree with each other in that the origin of the intensity in the resonance state is due to pp excitation. SOS-CIS(D) offers an inexpensive alternative to more rigorous multireference methods if single excitations are dominant in the wavefunction. Changes in electronic density in the singlet pp state As one may expect from the molecular orbital character (Fig. 2.3) and the large oscil-lator strength, electronic excitation results in a significant redistribution of electronic density. A convenient measure of charge distribution is the permanent dipole moment. Although in charged system it is origin-dependent, the difference between the two dipole moments, Dμ = μgr μex, is not. At the CIS level of theory, the value of jDμj is 0.6 D, and its direction is in the molecular plain pointing towards the bridge carbon. This value can be compared with the experimentally measured Dμ, derived from Stark effect mea-surements in a buffered at pH=6.5 glycerol solution at 77 K38. This work also reports the angle between Dμ and Dμtr. Strikingly, the experimental value is 10 times larger than the computed one. Since Dμ is related to the changes in orbital occupations upon excitation, it is dominated by contributions from the leading excitation amplitudes, and should be reproduced fairly accurately at the CIS level. Thus, large discrepancy is likely to be due to the solvent effect. Indeed, polar solvents result in the increased dipole moment of the 59 |
