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[128] A.M. Tokmachev, M. Boggio-Pasqua, M.J. Bearpark, and M.A. Robb. Photo-stability
via sloped conical intersections: A computational study of the pyrene
radical cation. J. Phys. Chem. A, 112:10881–10886, 2008.
[129] J.P. Perdew, K. Burke, and M. Ernzerhof. Phys. Rev. B, 77:3865, 1996.
[130] C. Adamo and V. Barone. J. Chem. Phys., 110:6158, 1999.
[131] L.H. Andersen, H. Bluhme, S. Boy´e, T.J.D. Jørgensen, H. Krogh, I.B. Nielsen,
S.B. Nielsen, and A. Svendsen. Experimental studies of the photophysics of
gas-phase fluorescent protein chromophores. Phys. Chem. Chem. Phys., 6:2617–
2627, 2004.
[132] T.M.H. Greemers, A.J. Lock, V. Subramaniam, T.M. Jovin, and S. V¨olker. Pho-tophysics
and optical switching in green fluorescent protein mutants. Proc. Nat.
Acad. Sci., 97:2974, 2000.
[133] G. Jung, C. Br¨auchle, and A. Zumbusch. Two-color fluorescence correlation
spectroscopy of one chromophore: Application to the E222Q mutant of the green
fluorescent protein. J. Chem. Phys., 114:3149–3156, 2001.
[134] D.M. Chudakov, V.V. Belousov, A.G. Zaraisky, V.V. Novoselov, D.B. Staroverov,
D.B. Zorov, S. Lukyanov, and K.A. Lukyanov. Kindling fluorescent proteins for
precise in vivo photolabeling. Nature Biotechnology, 21:191–194, 2003.
[135] D.M. Chudakov, A.V. Feofanov, N.N. Mudrik, S. Lukyanov, and K.A. Lukyanov.
Chromophore environment provides clue to “kindling fluorescent protein” riddle.
J. Biol. Chem., 278:7215–7219, 2003.
[136] X. He, A.F. Bell, and P.J. Tonge. FEBS Letters, 549:35, 2003.
[137] B. Hager, B. Schwarzinger, and H. Falk. Concerning the thermal diastereomer-ization
of the green fluorescent protein chromophore. Monatshefte f¨ur Chemie
(Chemical Monthly), 137:163–168, 2006.
[138] D.C. Loos, S. Habuchi, C. Flors, J. Hotta, J. Wiedenmann, G.U. Nienhaus, and
J. Hofkens. J. Am. Chem. Soc., 128:6270, 2006.
[139] J.-S. Yang, G.-J. Huang, Yi-H. Liu, and S.-M. Peng. Photoisomerization of
the green fluorescence protein chromophore and the meta- and para-amino ana-logues.
Chem. Commun., pages 1344–1346, 2008.
[140] K. Nienhaus, H. Nar, R. Heiker, J. Wiedenmann, and G. U. Nienhaus. J. Am.
Chem. Soc., 130:12578, 2008.
39
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 49 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | [128] A.M. Tokmachev, M. Boggio-Pasqua, M.J. Bearpark, and M.A. Robb. Photo-stability via sloped conical intersections: A computational study of the pyrene radical cation. J. Phys. Chem. A, 112:10881–10886, 2008. [129] J.P. Perdew, K. Burke, and M. Ernzerhof. Phys. Rev. B, 77:3865, 1996. [130] C. Adamo and V. Barone. J. Chem. Phys., 110:6158, 1999. [131] L.H. Andersen, H. Bluhme, S. Boy´e, T.J.D. Jørgensen, H. Krogh, I.B. Nielsen, S.B. Nielsen, and A. Svendsen. Experimental studies of the photophysics of gas-phase fluorescent protein chromophores. Phys. Chem. Chem. Phys., 6:2617– 2627, 2004. [132] T.M.H. Greemers, A.J. Lock, V. Subramaniam, T.M. Jovin, and S. V¨olker. Pho-tophysics and optical switching in green fluorescent protein mutants. Proc. Nat. Acad. Sci., 97:2974, 2000. [133] G. Jung, C. Br¨auchle, and A. Zumbusch. Two-color fluorescence correlation spectroscopy of one chromophore: Application to the E222Q mutant of the green fluorescent protein. J. Chem. Phys., 114:3149–3156, 2001. [134] D.M. Chudakov, V.V. Belousov, A.G. Zaraisky, V.V. Novoselov, D.B. Staroverov, D.B. Zorov, S. Lukyanov, and K.A. Lukyanov. Kindling fluorescent proteins for precise in vivo photolabeling. Nature Biotechnology, 21:191–194, 2003. [135] D.M. Chudakov, A.V. Feofanov, N.N. Mudrik, S. Lukyanov, and K.A. Lukyanov. Chromophore environment provides clue to “kindling fluorescent protein” riddle. J. Biol. Chem., 278:7215–7219, 2003. [136] X. He, A.F. Bell, and P.J. Tonge. FEBS Letters, 549:35, 2003. [137] B. Hager, B. Schwarzinger, and H. Falk. Concerning the thermal diastereomer-ization of the green fluorescent protein chromophore. Monatshefte f¨ur Chemie (Chemical Monthly), 137:163–168, 2006. [138] D.C. Loos, S. Habuchi, C. Flors, J. Hotta, J. Wiedenmann, G.U. Nienhaus, and J. Hofkens. J. Am. Chem. Soc., 128:6270, 2006. [139] J.-S. Yang, G.-J. Huang, Yi-H. Liu, and S.-M. Peng. Photoisomerization of the green fluorescence protein chromophore and the meta- and para-amino ana-logues. Chem. Commun., pages 1344–1346, 2008. [140] K. Nienhaus, H. Nar, R. Heiker, J. Wiedenmann, and G. U. Nienhaus. J. Am. Chem. Soc., 130:12578, 2008. 39 |
