Page 171 |
Save page Remove page | Previous | 171 of 200 | Next |
|
small (250x250 max)
medium (500x500 max)
Large (1000x1000 max)
Extra Large
large ( > 500x500)
Full Resolution
All (PDF)
|
This page
All
|
Figure 6.1: Large biological systems such as this active center of GFP require treat-ment
of the QM core and the MM environment using hybrid QM/MM methods.
Using CC and EOM methods for the quantum subsystem in QM/MM for the purpose
of sampling PES has a prohibitive cost. Because we desire to keep the attractive proper-ties
of the methods, rather than substituting them with cheaper methods, we propose to
increase their efficiency to the extent where direct AIMD calculations on multiple PES
become feasible.
The most challenging problem of CC and EOM theories is their computational com-plexity.
CCSD and EOMEE-CCSD scale as N6, where N is the size of the molecule.
That means that a dimer requires roughly 64 times more computation effort than the
original system. Our approach is to attack the scaling by performing CC and EOM
calculations using reduced-rank (compressed) tensors.
161
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 171 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | Figure 6.1: Large biological systems such as this active center of GFP require treat-ment of the QM core and the MM environment using hybrid QM/MM methods. Using CC and EOM methods for the quantum subsystem in QM/MM for the purpose of sampling PES has a prohibitive cost. Because we desire to keep the attractive proper-ties of the methods, rather than substituting them with cheaper methods, we propose to increase their efficiency to the extent where direct AIMD calculations on multiple PES become feasible. The most challenging problem of CC and EOM theories is their computational com-plexity. CCSD and EOMEE-CCSD scale as N6, where N is the size of the molecule. That means that a dimer requires roughly 64 times more computation effort than the original system. Our approach is to attack the scaling by performing CC and EOM calculations using reduced-rank (compressed) tensors. 161 |
