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[74] S. Coussan, Y. Ferro, A. Trivella, M. Rajzmann, P. Roubin, R. Wieczorek,
C. Manca, P. Piecuch, K. Kowalski, M. Włoch, S.A. Kucharski, and M. Musiał.
Experimental and theoretical UV characterizations of acetylacetone and its iso-mers.
J. Phys. Chem. A, 110(11):3920–3926, 2006.
[75] M. Valiev and K. Kowalski. Hybrid coupled cluster and molecular dynamics
approach: Application to the excitation spectrum of cytosine in the native DNA
environment. J. Chem. Phys., 125:211101, 2006.
[76] P.U. Manohar and A.I. Krylov. A non-iterative perturbative triples correction for
the spin-flipping and spin-conserving equation-of-motion coupled-cluster meth-ods
with single and double substitutions. J. Chem. Phys., 129:194105, 2008.
[77] I. Shavitt. In H.F. Schaefer III, editor, Methods of Electronic Structure Theory,
volume 4 of Modern Theoretical Chemistry, pages 189–275. Plenum Press: New
York, 1977.
[78] S.R. Langhoff and E.R. Davidson. Configuration interaction calculations on the
nitrogen molecule. Int. J. Quant. Chem., 8:61–72, 1974.
[79] Y.M. Rhee and M. Head-Gordon. Scaled second order perturbation corrections to
configuration interaction singles: efficient and reliable excitation energy methods.
J. Phys. Chem. A, 111:5314–5326, 2007.
[80] H. Iikura, T. Tsuneda, T. Yanai, and K. Hirao. A long-range correction scheme
for generalized-gradient-approximation exchange functionals. J. Chem. Phys.,
115:3540, 2001.
[81] R. Baer and D. Neuhauser. Density functional theory with correct long-range
asymptotic behavior. Phys. Rev. Lett., 94:043002, 2005.
[82] E. Livshits and R. Baer. A well-tempered density functional theory of electrons
in molecules. Phys. Chem. Chem. Phys., 9:2932–2941, 2007.
[83] T. Stein, L. Kronik, and R. Baer. Reliable prediction of charge transfer excitations
in molecular complexes using time-dependent density functional theory. J. Am.
Chem. Soc., 131:28182820, 2009.
[84] J.-D. Chai and M. Head-Gordon. Systematic optimization of long-range corrected
hybrid density functionals. J. Chem. Phys., 128:084106, 2008.
[85] S.R. Meech. Excited state reactions in fluorescent proteins. Chem. Soc. Rev.,
38:2922–2934, 2009.
[86] V. Sample, R.H. Newman, and J. Zhang. The structure and function of fluorescent
proteins. Chem. Soc. Rev., 38:2852–2864, 2009.
35
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 45 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | [74] S. Coussan, Y. Ferro, A. Trivella, M. Rajzmann, P. Roubin, R. Wieczorek, C. Manca, P. Piecuch, K. Kowalski, M. Włoch, S.A. Kucharski, and M. Musiał. Experimental and theoretical UV characterizations of acetylacetone and its iso-mers. J. Phys. Chem. A, 110(11):3920–3926, 2006. [75] M. Valiev and K. Kowalski. Hybrid coupled cluster and molecular dynamics approach: Application to the excitation spectrum of cytosine in the native DNA environment. J. Chem. Phys., 125:211101, 2006. [76] P.U. Manohar and A.I. Krylov. A non-iterative perturbative triples correction for the spin-flipping and spin-conserving equation-of-motion coupled-cluster meth-ods with single and double substitutions. J. Chem. Phys., 129:194105, 2008. [77] I. Shavitt. In H.F. Schaefer III, editor, Methods of Electronic Structure Theory, volume 4 of Modern Theoretical Chemistry, pages 189–275. Plenum Press: New York, 1977. [78] S.R. Langhoff and E.R. Davidson. Configuration interaction calculations on the nitrogen molecule. Int. J. Quant. Chem., 8:61–72, 1974. [79] Y.M. Rhee and M. Head-Gordon. Scaled second order perturbation corrections to configuration interaction singles: efficient and reliable excitation energy methods. J. Phys. Chem. A, 111:5314–5326, 2007. [80] H. Iikura, T. Tsuneda, T. Yanai, and K. Hirao. A long-range correction scheme for generalized-gradient-approximation exchange functionals. J. Chem. Phys., 115:3540, 2001. [81] R. Baer and D. Neuhauser. Density functional theory with correct long-range asymptotic behavior. Phys. Rev. Lett., 94:043002, 2005. [82] E. Livshits and R. Baer. A well-tempered density functional theory of electrons in molecules. Phys. Chem. Chem. Phys., 9:2932–2941, 2007. [83] T. Stein, L. Kronik, and R. Baer. Reliable prediction of charge transfer excitations in molecular complexes using time-dependent density functional theory. J. Am. Chem. Soc., 131:28182820, 2009. [84] J.-D. Chai and M. Head-Gordon. Systematic optimization of long-range corrected hybrid density functionals. J. Chem. Phys., 128:084106, 2008. [85] S.R. Meech. Excited state reactions in fluorescent proteins. Chem. Soc. Rev., 38:2922–2934, 2009. [86] V. Sample, R.H. Newman, and J. Zhang. The structure and function of fluorescent proteins. Chem. Soc. Rev., 38:2852–2864, 2009. 35 |
