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for the GFP chromophore. Bravaya et al.109 performed calculations of the vertical
pp transition energies for various forms of HBDI using a very expensive and highly
correlated approach, i.e. state-averaged CASSCF(16/14) wave functions constructed
in the full p-orbital active space augmented by perturbative corrections: multireference
second-order Møller-Plesset perturbation theory (MRMP2)15 and an extended version of
the multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2)16, 24, 25
(using ground-state equilibrium geometries optimized using DFT with the PBE0 func-tional129,
130 and the (aug)-cc-pVDZ basis set:10 aug-cc-pVDZ on oxygen atoms and
cc-pVDZ on all other atoms). The MRMP2 and aug-MCQDPT2 results are within 0.12
and only 0.05 eV from the experimental value, respectively (Table 1.1). These data sug-gest
that one can compute the positions of absorption bands of biological chromophores
with an accuracy of 10–20 nm (less than 0.1 eV) by applying perturbatively corrected
CASSCF-based approaches. These techniques, however, are computationally demand-ing,
and their execution requires advanced skills and extreme care, as the application of
the method involves: (i) a careful selection of a large number of active space orbitals
in fairly large basis sets; (ii) converging the state averaged CASSCF solutions corre-sponding
to the pp transition, especially in realistic basis sets; (iii) a careful and often
ambiguous treatment of perturbative corrections to the reference CASSCF solutions.
Moreover, gradient calculations are only available for bare CASSCF wave functions.
Thus, it is desirable to find a more robust approach of a comparable accuracy for wider
applications in modeling the properties of biological chromophores.
Contrarily to the bright singlet pp state, little is known about the triplet states of
the GFP chromophore. The fluorescence properties of GFP suggest that the intersystem
crossing is not efficient, at least in the chromophore in the native protein environment. In
24
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 34 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | for the GFP chromophore. Bravaya et al.109 performed calculations of the vertical pp transition energies for various forms of HBDI using a very expensive and highly correlated approach, i.e. state-averaged CASSCF(16/14) wave functions constructed in the full p-orbital active space augmented by perturbative corrections: multireference second-order Møller-Plesset perturbation theory (MRMP2)15 and an extended version of the multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2)16, 24, 25 (using ground-state equilibrium geometries optimized using DFT with the PBE0 func-tional129, 130 and the (aug)-cc-pVDZ basis set:10 aug-cc-pVDZ on oxygen atoms and cc-pVDZ on all other atoms). The MRMP2 and aug-MCQDPT2 results are within 0.12 and only 0.05 eV from the experimental value, respectively (Table 1.1). These data sug-gest that one can compute the positions of absorption bands of biological chromophores with an accuracy of 10–20 nm (less than 0.1 eV) by applying perturbatively corrected CASSCF-based approaches. These techniques, however, are computationally demand-ing, and their execution requires advanced skills and extreme care, as the application of the method involves: (i) a careful selection of a large number of active space orbitals in fairly large basis sets; (ii) converging the state averaged CASSCF solutions corre-sponding to the pp transition, especially in realistic basis sets; (iii) a careful and often ambiguous treatment of perturbative corrections to the reference CASSCF solutions. Moreover, gradient calculations are only available for bare CASSCF wave functions. Thus, it is desirable to find a more robust approach of a comparable accuracy for wider applications in modeling the properties of biological chromophores. Contrarily to the bright singlet pp state, little is known about the triplet states of the GFP chromophore. The fluorescence properties of GFP suggest that the intersystem crossing is not efficient, at least in the chromophore in the native protein environment. In 24 |
