Molecular Design for Nonlinear optical Materials and Conformational Dependence of Protein Electron Transfer

Abstract

Four parts are included in this dissertation: Chapter 1 is an introduction and provides background on our research; Chapter 2 is the study of designing porphyrin chromophores with unusually large hyperpolarizability; chapter 3 is the hopping charge recombination in cytochrome c-cytochrome c peroxidase electron transfer; and chapter 4 is the parameterizations of flavin adenine dinucleotide and electron transfer coupling calculations in cryptochrome.A new series of push-pull porphyrin-based chromophores with unusually large static first hyperpolarizabilities are designed based on coupled-perturbed Hartree-Fock and density functional calculations. The combination of critical building blocks, including a ruthenium(II) bisterpyridine complex, proquinoidal thiadiazoloquinoxaline, and (porphinato)zinc(II) units produces large enhancement of the static nonlinear optical (NLO) response, computed to be as large as 11,300  1030 esu, 2 orders of magnitude larger than the benchmark species [5-((4'-(dimethylamino)phenyl)ethynyl)-15- ((4''-nitrophenyl)ethynyl)-porphinato]zinc(II). We also studies the inter-protein ET recombination reaction between cytochrome c peroxidase-cytochrome c complex (i.e., ). ET rates in the wild type (WT) CcP:Cc complex and in four mutants of the Cc protein (i.e., F82S, F82W, F82Y and F82I) measured both in solution and in crystals, vary by no more than three fold despite large difference in the ET distances and protein-protein conformations. This theoretical study examines why large changes at the protein-protein interface and the lengthening of the heme-to-ZnP distances in the Cc F82Y(I) mutants do not slow the ET rate dramatically compared with the WT CcP:Cc and Cc F82S(W) mutants. PATHWAY and quantum chemical analysis, performed on molecular dynamics sampled geometries, indicates that the recombination mechanism for all five protein complexes involves two mechanisms: single step heme-ZnP tunneling and two step heme-Trp191-ZnP hopping. We further predict that back ET rates in double mutants W191F CcP:F82S(W) Cc will be dramatically reduced compared to the rates in the WT CcP:Cc complex. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy would compensate the decreased role of hopping recombination in the F82Y(I) mutants. Finally, we examined the photo-induced tryptophan-to-flavin ET in cryptochrome. The amber force field of FAD was parameterized by antechamber using RESP fitting partial charges. The electronic couplings were calculated by generalized Mulliken-hush (GMH). Validation of GMH approach based on orbitals pictures are discussed in detail compared with many-electron coupling derivation.