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Table 2.2: Vertical pp electronic excitation energies (DE, in eV), corresponding wavelengths (nm) and oscillator strength
( fL) for the gas phase GFP chromophore (Fig. 1). The reference experimental value is 2.59 eV (479 nm).
Method Ground-state geometry optimized with
PBE0/cc-pVDZ CASSCF(14/12)/cc-pVDZ RI-MP2/cc-pVTZ
DE fL nm DE fL nm DE fL nm
MRMP2 based on sa-CASSCF(14/12)/cc-pVDZ 2.52b 491b 2.61c 476c
EOM-CCSD/6-31G(d) 3.08 1.26 402 3.16 1.27 392 3.12 398
EOM-CCSD/6-31+G(d) 2.97 1.24 418 3.04 1.25 408
SOS-CIS(D)/cc-pVDZ 2.71 1.59a 457 2.81 1.61a 441 2.75 1.60a 451
SOS-CIS(D)/aug-cc-pVDZ 2.57 1.45a 482 2.67 1.45a 464 2.61 1.45a 475
SOS-CIS(D)/cc-pVTZ 2.58 1.54a 480 2.68 1.56a 463 2.62 1.54a 473
SOS-CIS(D)/aug-cc-pVTZ 2.58 1.37a 480 2.90 1.04a 427
TD-DFT/BNL/cc-pVDZ 3.44 1.51 360 3.50 1.51 354 3.59 1.55 346
TD-DFT/BNL/6-311(+,+)G(2df,2pd) 3.22 1.38 385 3.27 1.38 379
TD-DFT/wWB97x/cc-pVDZ 3.52 1.52 352 3.59 1.53 346 3.55 1.53 349
TD-DFT/wWB97x/6-311(+,+)G(2df,2pd) 3.38 1.45 367 3.44 1.46 360
a Oscillator strength calculated with CIS. b At the equilibrium geometry computed with PBE0/(aug)-cc-pVDZ (diffuse functions
only on oxygen atoms). c At the equilibrium geometry computed with CASSCF(12/11)/(aug)-cc-pVDZ (diffuse functions only
on oxygen atoms).
57
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 67 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Table 2.2: Vertical pp electronic excitation energies (DE, in eV), corresponding wavelengths (nm) and oscillator strength ( fL) for the gas phase GFP chromophore (Fig. 1). The reference experimental value is 2.59 eV (479 nm). Method Ground-state geometry optimized with PBE0/cc-pVDZ CASSCF(14/12)/cc-pVDZ RI-MP2/cc-pVTZ DE fL nm DE fL nm DE fL nm MRMP2 based on sa-CASSCF(14/12)/cc-pVDZ 2.52b 491b 2.61c 476c EOM-CCSD/6-31G(d) 3.08 1.26 402 3.16 1.27 392 3.12 398 EOM-CCSD/6-31+G(d) 2.97 1.24 418 3.04 1.25 408 SOS-CIS(D)/cc-pVDZ 2.71 1.59a 457 2.81 1.61a 441 2.75 1.60a 451 SOS-CIS(D)/aug-cc-pVDZ 2.57 1.45a 482 2.67 1.45a 464 2.61 1.45a 475 SOS-CIS(D)/cc-pVTZ 2.58 1.54a 480 2.68 1.56a 463 2.62 1.54a 473 SOS-CIS(D)/aug-cc-pVTZ 2.58 1.37a 480 2.90 1.04a 427 TD-DFT/BNL/cc-pVDZ 3.44 1.51 360 3.50 1.51 354 3.59 1.55 346 TD-DFT/BNL/6-311(+,+)G(2df,2pd) 3.22 1.38 385 3.27 1.38 379 TD-DFT/wWB97x/cc-pVDZ 3.52 1.52 352 3.59 1.53 346 3.55 1.53 349 TD-DFT/wWB97x/6-311(+,+)G(2df,2pd) 3.38 1.45 367 3.44 1.46 360 a Oscillator strength calculated with CIS. b At the equilibrium geometry computed with PBE0/(aug)-cc-pVDZ (diffuse functions only on oxygen atoms). c At the equilibrium geometry computed with CASSCF(12/11)/(aug)-cc-pVDZ (diffuse functions only on oxygen atoms). 57 |
