Efficient correlated electronic structure theory and quantum dynamics for photoactive systems from small molecules to biological macromolecules
Abstract/Contents
- Abstract
- A fundamental understanding of the paradigms of molecular photochemistry underlies the ability to exploit light-sensitivity in modern biophysics. Photochemical processes occur at ultrafast time regimes in which nonequilibrium dynamic effects critically influence the reactions. Due to the involvement of light, classical molecular dynamics simulations are not sufficient for describing photochemistry. Instead, direct simulation of the nonadiabatic dynamics is necessary to understand the photoreactivity of molecular systems. Nonadiabatic dynamics simulations are often paired with solving the electronic Schrödinger equation using approximate electronic structure methods in order to obtain the potential energy surfaces, forces and nonadiabatic couplings that govern the evolution of the dynamics. Unfortunately, doing so entails significant computational expense. Although conventional low-cost methods, such as time-dependent density functional theory (TDDFT) and multiconfigurational self-consistent field (MCSCF) wavefunction techniques, are often used in ab initio molecular dynamics applications, each suffers from shortcomings that limit the accuracy of the insights they provide (more severely in the case of TDDFT). Highly accurate electronic structure methods exist but are often too expensive to be employed alongside dynamics simulations, especially for large systems such as proteins. There thus exists a need for simultaneously efficient and accurate electronic structure methods for photochemical simulations. This dissertation addresses this deficiency through the development of hole-hole Tamm Dancoff approximated density functional theory (hh-TDA) for applications in photochemistry. hh-TDA combines the strengths of density functional theory (DFT) and wavefunction theory while maintaining effective quadratic scaling. The accuracy and utility of hh-TDA paired with nonadiabatic ab initio multiple spawning (AIMS) dynamics simulations is demonstrated here for several model molecular systems. The hh-TDA/AIMS methodology is then employed to study azobenzene, a small photoactive molecule and one of the most ubiquitous photoswitches in photochemistry. This study resolves a decades old controversy: the violation of Kasha's rule by azobenzene. Until this work, the direct nonadiabatic dynamics simulation of photoexcited azobenzene with the requisite accuracy to resolve the Kasha's rule violation phenomenon was computationally intractable. Furthermore, these results predate experimental resolution of the phenomenon and are thus true predictions. These nonadiabatic dynamics techniques are then scaled to the macromolecular level in a study of bacteriorhodopsin using the spin-restricted ensemble Kohn-Sham (REKS) electronic structure method to settle long-standing uncertainties in the dynamics of the ultrafast reactive step of the photocycle, including characterization of the fluorescent excited transient state, the reaction mechanism, and the motion of the chromophore counterion cluster. The results reported here coincide with independent spectroscopic work published at almost the same time. These developments therefore suggest that truly predictive quantum dynamics simulations of photoactive molecular systems from the scale of small molecules to that of macromolecules may be close at hand, if not already available
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2020; ©2020 |
| Publication date | 2020; 2020 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Yu, Jimmy King Zhi |
|---|---|
| Degree supervisor | Martinez, Todd J. (Todd Joseph), 1968- |
| Thesis advisor | Martinez, Todd J. (Todd Joseph), 1968- |
| Thesis advisor | Boxer, Steven G. (Steven George), 1947- |
| Thesis advisor | Markland, Thomas E |
| Degree committee member | Boxer, Steven G. (Steven George), 1947- |
| Degree committee member | Markland, Thomas E |
| Associated with | Stanford University, Biophysics Program |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Jimmy King Zhi Yu |
|---|---|
| Note | Submitted to the Biophysics Program |
| Thesis | Thesis Ph.D. Stanford University 2020 |
| Location | electronic resource |
Access conditions
- Copyright
- © 2020 by Jimmy King Zhi Yu
- License
- This work is licensed under a Creative Commons Attribution 3.0 Unported license (CC BY).
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