Fluorescence line narrowed spectra of Zn and metal-free cytochrome c

Fluorescence line narrowing (FLN) spectroscopy was used to study the role of the polypeptide chain in influencing the spectrum of Zn-substituted cytochrome c (Zn cyt c) and metal-free cyt c (porphyrin cyt c). For both derivatives the spectra show characteristics of relaxed fluorescence from an inhomogeneously broadened sample. Zero phonon lines and phonon wings can be clearly distinguished, and vibrational frequencies of the ground and excited states were identified. The inhomogeneous distribution width for porphyrin cyt c is slightly wider than that of Zn cyt c and a second population of molecules was apparent in the porphyrin cyt c. The phonon coupling was greater for Zn cyt c than for porphyrin cyt c, which may be due to the extra coupling to the polypeptide chain by metal ligation.This work has been done in partial fulfillment of the requirements for the Doctor of Philosophy degree.     

Geometric Algebra in Linear Algebra and Geometry

This article explores the use of geometric algebra in linear and multilinear algebra, and in affine, projective and conformal geometries. Our principal objective is to show how the rich algebraic tools of geometric algebra are fully compatible with and augment the more traditional tools of matrix algebra. The novel concept of an h-twistor makes possible a simple new proof of the striking relationship between conformal transformations in a pseudo-Euclidean space to isometries in a pseudo-Euclidean space of two higher dimensions. The utility of the h-twistor concept, which is a generalization of the idea of a Penrose twistor to a pseudo-Euclidean space of arbitrary signature, is amply demonstrated in a new treatment of the Schwarzian derivative.     

Hydrogen Atoms Are Produced When Tryptophan within a Protein Is Irradiated with Ultraviolet Light

Abstract— The UV photolysis of the aromatic amino acid, tryptophan (Trp), in the Ca²⁺-binding protein, cod paralbumin, type III, was studied using electron paramagnetic resonance (EPR) spectroscopy in the temperature range 4–80 K. For the Ca²⁺-bound protein, irradiation with UV light (250–400 nm) resulted in the generation of atomic hydrogen with a hyperfine splitting of 50.9 mT, whereas in the Ca²⁺-free form, where the Trp is exposed to solvent, the trapped atomic hydrogen was not in evidence. In the same spectra, the radical signal in the g = 2.00 region could be detected. The line shape of the Ca²⁺-bound form is similar to the EPR line shape obtained for Trp in micellar systems. In contrast, the EPR line shape for the Ca²⁺-free form is essentially featureless up to 80 K. The EPR spectra of the photoproducts of Trp and the nature of the photoreactions are therefore sensitive to the environment of Trp within the protein.     

Unitary Geometric Algebra

The geometric significance of the imaginary unit in a complex geometric algebra has troubled the author for 40?years. In the unitary geometric algebra presented here, the imaginary i is a unit (pseudo) vector with square minus one which anti commutes with all of the real vectors. The resulting natural hermitian inner product and hermitian outer product induce a grading of the algebra into complex k-vectors. Basic orthogonality relationships are studied.     

Temperature Dependence for Fluorescence of β-NADH in Glycerol/Water Solution and in Trehalose/Sucrose Glass

Fluorescence imaging of cells and tissue can be used to evaluate β-NADH redox and location. At low temperature, β-NADH fluorescence intensity increases and therefore sensitivity of imaging increases. In this paper, the temperature dependence of fluorescence was evaluated for β-NADH in glycerol/water solution and in trehalose/sucrose glass. The average fluorescence lifetime for NADH in glycerol/water is 0.66 ns, compared with 5.3 ns in trehalose/ sucrose at 20°C. Emission spectra were recorded from 290 to 12 K. The fluorescence of β-NADH in glycerol/water increases ∼16 fold and the emission shifts about 35 nm to the blue as temperature decreases. Much smaller change is seen for fluorescence of β-NADH in sugar glass. Below 77 K, the β-NADH spectral features did not change significantly with temperature change, and so no increase in sensitivity is obtained by going to very low temperatures. It is suggested that the sensitivity of β-NADH fluorescence is related to water relaxation around the excited state molecule. Differences in water in various tissues may contribute to β-NADH fluorescence changes when cells are altered.     

Vibrational Stark Effects on Carbonyl, Nitrile, and Nitrosyl Compounds Including Heme Ligands, CO, CN, and NO, Studied with Density Functional Theory

Changes in the matrix electric field in a protein, due for example to mutations or structural fluctuations, can be correlated with changes in the vibrational transition frequencies of suitable chromophores measured by IR spectroscopy through the Stark tuning rate. To make this correlation, the Stark tuning rate must be known from experiment or theory. In this paper, density functional theory at the B3LYP/TZV level of theory is used to compute the Stark tuning rate of adducts of heme porphyrin, namely, -CO, -CN, and -NO+ compounds. The results are compared with the corresponding vibrational frequencies-field dependencies from vibrational Stark spectroscopy of heme-proteins. The zero-field computed Stark tuning rate of 1.3 cm-1/MV/cm for heme-CO is in agreement with experiment, where typically the rate is 2.4/f cm-1/MV/cm for myoglobin, where f is a local field correction between 1.1 and 1.4. Several small nitrile, carbonyl, and dinitrile molecules were studied to rationalize the findings for the heme-adducted models. Here, the higher B3LYP/6-311++G(2d,2p) level of theory could be used so the agreement with recent experimental results is even better than for heme-adducted groups.     

Solvent effects on the intramolecular charge transfer character of N,N-diaryl dihydrophenazine catalysts for organocatalyzed atom transfer radical polymerization

The nature of intramolecular charge transfer (CT) of N,N-diaryl dihydrophenazine photocatalysts (PCs) in different solvents is explored in context of their performance in organocatalyzed atom transfer radical polymerization (O-ATRP). PCs having a computationally predicted lowest energy excited state exhibiting CT character can operate a highly controlled O-ATRP in a wide range of solvent polarities, from non-polar hexanes to highly polar N,N-dimethylacetamide. For PCs having a computationally predicted lowest energy excited state not possessing CT character, their ability to operate a controlled O-ATRP is decreased. This study confirms the importance of CT character in the excited state for N,N-diaryl dihydrophenazine PCs, and a deeper understanding of the activity of CT PCs has enabled the synthesis of polymers of low dispersity (<1.10) in a controlled fashion. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 3017–3027