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Recently, a gas-phase action spectrum of anionic HBDI (as well as other protonated
forms) using photodestruction spectroscopy of mass-selected ions injected into an elec-trostatic
ion-storage ring was reported providing an important reference for theory99, 100.
The spectrum shows an absorption band centered at 2.59 eV (479 nm), which extends
from 2.4–2.8 eV (440–520 nm), as well as a minor peak around 2.3 eV (540 nm). The
authors emphasized a striking similarity between the absorption bands in the gas phase
and in the protein and suggested that the protein environment shields the chromophore
from water and that the absorption in the protein is an intrinsic property of HBDI. While
the role of the protein still needs to be investigated, this measurement facilitates more
direct comparison between the gas-phase calculations of vertical excitation energies and
the experimental absorption for benchmarking theoretical methods.
The large absorption band in the gas phase spectrum of the HBDI anion has been
assigned as the pp transition, however, the nature of the minor feature at 2.3 eV has not
been discussed.
A variety of electronic structure techniques ranging from simple semiempirical
approximations to high-level ab initio methods have been applied to simulate the prop-erties
of the cis-anionic form of HBDI103–109. Selected representative results are sum-marized
in Table 1.1.
These studies have identified the absorbing state of the HBDI anion as the S1 state
derived from a HOMO-LUMO excitation of the pp character. LUMO, however, is a
valence p -like orbital only in relatively small basis sets; including diffuse functions
increases the number of molecular orbitals between the HOMO and the lowest p -like
orbital. Though the bright state retains its pp character, it is not, strictly speaking, a
HOMO-LUMO transition in a realistic basis set.
21
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 31 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Recently, a gas-phase action spectrum of anionic HBDI (as well as other protonated forms) using photodestruction spectroscopy of mass-selected ions injected into an elec-trostatic ion-storage ring was reported providing an important reference for theory99, 100. The spectrum shows an absorption band centered at 2.59 eV (479 nm), which extends from 2.4–2.8 eV (440–520 nm), as well as a minor peak around 2.3 eV (540 nm). The authors emphasized a striking similarity between the absorption bands in the gas phase and in the protein and suggested that the protein environment shields the chromophore from water and that the absorption in the protein is an intrinsic property of HBDI. While the role of the protein still needs to be investigated, this measurement facilitates more direct comparison between the gas-phase calculations of vertical excitation energies and the experimental absorption for benchmarking theoretical methods. The large absorption band in the gas phase spectrum of the HBDI anion has been assigned as the pp transition, however, the nature of the minor feature at 2.3 eV has not been discussed. A variety of electronic structure techniques ranging from simple semiempirical approximations to high-level ab initio methods have been applied to simulate the prop-erties of the cis-anionic form of HBDI103–109. Selected representative results are sum-marized in Table 1.1. These studies have identified the absorbing state of the HBDI anion as the S1 state derived from a HOMO-LUMO excitation of the pp character. LUMO, however, is a valence p -like orbital only in relatively small basis sets; including diffuse functions increases the number of molecular orbitals between the HOMO and the lowest p -like orbital. Though the bright state retains its pp character, it is not, strictly speaking, a HOMO-LUMO transition in a realistic basis set. 21 |
