Graduation date: 1994

Linear dichroism in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy has been used to determine molecular orientation at surfaces and in microscopic domains. However, the molecular orientation of n-alkanes cannot be derived unambiguously from their NEXAFS spectra due to the inadequate understanding of the character of the relevant spectroscopic features in the NEXAFS spectra of n-alkanes (i.e. C 1s to sigma*C-H, C 1s to sigma*C-C transitions).<p>We have studied the linear dichroism in the NEXAFS spectra of n-alkane thin films by using angular dependent NEXAFS spectroscopy to explore the molecular orientation of hexacontane (HC, n-C60H122). The HC thin films were epitaxially grown onto the cleaved NaCl (001) surfaces by physical vapor deposition. NEXAFS spectra of the HC thin film were acquired at different angles using STXM microscopy. A detailed analysis of the angular dependence of the NEXAFS spectra of the HC thin film helps to understand the relationship between the linear dichroism and the molecular orientation in n-alkane molecules. This linear dichroism in the NEXAFS spectroscopy of n-alkanes is relevant for quantitative measurements of molecular orientation, such as for the microanalysis of crystalline organic materials. <p>The linear dichroism of the NEXAFS resonances for n-alkanes has also been studied by ab initio calculations. These calculations were carried out on an isolated n-alkane molecule and a cluster of n-alkane molecules. The calculations on an isolated n-alkane molecule are used to study the linear dichroism for the NEXAFS resonances above the C 1s IP. The cluster calculations account for matrix effects in the NEXAFS features of condensed n-alkanes. A comparison of calculations on an isolated molecule and on a cluster of molecules provides information on how the NEXAFS spectra change from gas phase to condensed phase and determines the linear dichroism of each NEXAFS feature below the C 1s IP.<p>In the process of preparing n-alkane thin films for the study of linear dichroism, the morphology and molecular orientation of n-alkane thin films with different chain length (n-C36H74 and n-C60H122) have also been investigated by the NEXAFS spectroscopy and microscopy. These thin films were epitaxially grown onto cleaved NaCl (001) surfaces by physical vapor deposition. The results revealed that the morphology and molecular orientation of n-alkane thin films depend on the chain length and deposition parameters, such as substrate temperature. These observations have been rationalized by the thermodynamics of nucleation and the kinetics of growth.

Linear dichroism in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy has been used to determine molecular orientation at surfaces and in microscopic domains. However, the molecular orientation of n-alkanes cannot be derived unambiguously from their NEXAFS spectra due to the inadequate understanding of the character of the relevant spectroscopic features in the NEXAFS spectra of n-alkanes (i.e. C 1s to sigma*C-H, C 1s to sigma*C-C transitions).<p>We have studied the linear dichroism in the NEXAFS spectra of n-alkane thin films by using angular dependent NEXAFS spectroscopy to explore the molecular orientation of hexacontane (HC, n-C60H122). The HC thin films were epitaxially grown onto the cleaved NaCl (001) surfaces by physical vapor deposition. NEXAFS spectra of the HC thin film were acquired at different angles using STXM microscopy. A detailed analysis of the angular dependence of the NEXAFS spectra of the HC thin film helps to understand the relationship between the linear dichroism and the molecular orientation in n-alkane molecules. This linear dichroism in the NEXAFS spectroscopy of n-alkanes is relevant for quantitative measurements of molecular orientation, such as for the microanalysis of crystalline organic materials. <p>The linear dichroism of the NEXAFS resonances for n-alkanes has also been studied by ab initio calculations. These calculations were carried out on an isolated n-alkane molecule and a cluster of n-alkane molecules. The calculations on an isolated n-alkane molecule are used to study the linear dichroism for the NEXAFS resonances above the C 1s IP. The cluster calculations account for matrix effects in the NEXAFS features of condensed n-alkanes. A comparison of calculations on an isolated molecule and on a cluster of molecules provides information on how the NEXAFS spectra change from gas phase to condensed phase and determines the linear dichroism of each NEXAFS feature below the C 1s IP.<p>In the process of preparing n-alkane thin films for the study of linear dichroism, the morphology and molecular orientation of n-alkane thin films with different chain length (n-C36H74 and n-C60H122) have also been investigated by the NEXAFS spectroscopy and microscopy. These thin films were epitaxially grown onto cleaved NaCl (001) surfaces by physical vapor deposition. The results revealed that the morphology and molecular orientation of n-alkane thin films depend on the chain length and deposition parameters, such as substrate temperature. These observations have been rationalized by the thermodynamics of nucleation and the kinetics of growth.

Graduation date: 1994

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 227-246).

All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.

All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.

Probing orientations of fluorescent molecules embedded in or attached to cell membranes has a great potential to reveal information on membrane structure and processes occurring in living cells. In this thesis, we first describe one- and two-photon linear dichroism measurements on a fluorescent probe embedded in a phospholipid membrane with a well- defined lipid composition. On the basis of experimental data, we determine the distribution of the angle between the one-photon transition dipole moment of the probe and the membrane normal. At the same time, we perform molecular dynamics simulations of the fluorescent probe and quantum calculations of its one-photon and two-photon absorption properties. By comparing the orientational distribution gained from experiments with that predicted by simulations, we test the ability of linear dichroism measurements to report on the orientation of a fluorescent molecule in a lipid membrane. We also examine the applicability of molecular simulations as a basis for the interpretation of experimental data.

In this work we study thin epilayers of new antiferromagnetic semimetal CuMnAs by time- resolved magneto-optical experiments. In 10 nm layers of CuMnAs, we observed a harmonic dependence of the dynamical magneto-optical signal on the orientation of probe pulse linear polarization. This shows that in this 10 nm layer there is an in-plane uniaxial magnetic anisotropy which can be detected due to a quadratic magneto-optical effect - magnetic linear dichroism. From the measured data we also estimated the Néel temperature and the spectral variation of the magneto-optical coefficient describing the magnitude of the magnetic linear dichroism in this sample.

<p>This thesis focuses on peptides derived from the Prion, Doppel and Influenza haemagglutinin proteins in the context of bilayer interactions with model membranes and live cells. The studies involve spectroscopic techniques like fluorescence, fluorescence correlation spectroscopy (FCS), circular and linear dichroism (CD and LD), confocal fluorescence microscopy and NMR.</p><p>The peptides derived from the Prion and Doppel proteins combined with their subsequent nuclear localization-like sequences, makes them resemble cell-penetrating peptides (CPPs). mPrPp(1-28), corresponding to the first 28 amino acids of the mouse PrP, was shown to translocate across cell membranes, concomitantly causing cell toxicity. Its bovine counterpart bPrPp(1-30) was demonstrated to enter live cells, with and without cargo, mainly via macropinocytosis. The mPrPp(23-50) peptide sequence overlaps with mPrPp(1-28) sharing the KKRPKP sequence believed to encompass the driving force behind translocation. mPrPp(23-50) was however found unable to cross over cell membranes and had virtually no perturbing effects on membranes.</p><p>mDplp(1-30), corresponding of the first 30 N-terminal amino acids of the Doppel protein, was demonstrated to be almost as membrane perturbing as melittin. NMR experiments in bicelles implied a transmembrane configuration of its alpha-helix, which was corroborated by LD in vesicle bilayers. The positioning of the induced alpha-helix in transportan was found to be more parallel to the bilayer surface in the same model system.</p><p>Positioning of the native Influenza derived fusion peptide in bilayers showed no pH dependence. The glutamic acid enriched variant however, changed its insertion angle from 70 deg to a magic angle alignment relative the membrane normal upon a pH drop from 7.4 to 5.0. Concomitantly, the alpha-helical content dramatically rose from 18% to 52% in partly anionic membranes, while the native peptide’s helicity increased only from 39% to 44% in the same conditions.</p>