In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

<p>Lithium ion insertion into electrode materials is commonly used in rechargeable battery technology. The insertion implies changes in both the crystal structure and the electronic structure of the electrode material. Side-reactions may occur on the surface of the electrode, which is exposed to the electrolyte and form a solid electrolyte interface (SEI). The understanding of these processes is of great importance for improving battery performance. The chemical and physical properties of water and alcohols are complicated by the presence of strong hydrogen bonding. Various experimental techniques have been used to study geometrical structures and different models have been proposed to view the details of how these liquids are geometrically organized by hydrogen bonding. However, very little is known about the electronic structure of these liquids, mainly due to the lack of suitable experimental tools.</p><p>This thesis addresses the electronic structure of liquids and lithium battery materials using resonant inelastic X-ray scattering (RIXS) at high brightness synchrotron radiation sources. The electronic structure of battery electrodes has been probed, before and after lithiation, studying the doping of electrons into the host material. The chemical composition of the SEI on cycled graphite electrodes was determined. The local electronic structure of water, methanol and mixtures of the two have been examined using a special liquid cell. Results from the study of liquid water showed a strong influence on the 3a₁ molecular orbital and orbital mixing between molecules upon hydrogen bonding. The study of methanol showed the existence of ring and chain formations in the liquid phase and the dominating structures are formed of 6 and 8 molecules. Upon mixing of the two liquids, a segregation at the molecular level was found and the formation of new structures, which could explain the unexpected low increase of the entropy.</p>

Lithium ion insertion into electrode materials is commonly used in rechargeable battery technology. The insertion implies changes in both the crystal structure and the electronic structure of the electrode material. Side-reactions may occur on the surface of the electrode, which is exposed to the electrolyte and form a solid electrolyte interface (SEI). The understanding of these processes is of great importance for improving battery performance. The chemical and physical properties of water and alcohols are complicated by the presence of strong hydrogen bonding. Various experimental techniques have been used to study geometrical structures and different models have been proposed to view the details of how these liquids are geometrically organized by hydrogen bonding. However, very little is known about the electronic structure of these liquids, mainly due to the lack of suitable experimental tools. This thesis addresses the electronic structure of liquids and lithium battery materials using resonant inelastic X-ray scattering (RIXS) at high brightness synchrotron radiation sources. The electronic structure of battery electrodes has been probed, before and after lithiation, studying the doping of electrons into the host material. The chemical composition of the SEI on cycled graphite electrodes was determined. The local electronic structure of water, methanol and mixtures of the two have been examined using a special liquid cell. Results from the study of liquid water showed a strong influence on the 3a1 molecular orbital and orbital mixing between molecules upon hydrogen bonding. The study of methanol showed the existence of ring and chain formations in the liquid phase and the dominating structures are formed of 6 and 8 molecules. Upon mixing of the two liquids, a segregation at the molecular level was found and the formation of new structures, which could explain the unexpected low increase of the entropy.

This thesis reports on the setup of a new ion trap apparatus designed for experiments with single ⁴⁰Ca⁺ ions to perform molecular spectroscopy. The calcium ion is laser cooled, allowing for sympathetic cooling of the nonfluorescing molecular ion. The aim of these experiments is to explore loading and identifying molecular ions in RF-Paul traps, as well as developing new spectroscopic tools to measure transitions of molecular ions via the fluorescence of co-trapped ⁴⁰Ca⁺ ions. Ground state cooling of a mixed ion pair is implemented as a first step towards increasing the sensitivity of our technique to the level necessary to measure transitions with low scattering rates (like those present in molecular ions). Doppler cooling on the S(1/2)->P(1/2) transition of the calcium ion results in the formation of a Coulomb crystal, the behavior of which may be used to infer properties of the molecular ion. Following cooling, sideband spectroscopy on the narrow S(1/2)->D(5/2) quadrupole transition of calcium may be used to identify the mass of single molecular ions. This method is verified via a non-destructive measurement on ⁴⁰CaH⁺ and ⁴⁰Ca¹⁶O⁺. The normal modes of the Coulomb crystal can also be used to extract information from the target ion to the control ion. By driving the blue side of a transition, laser induced heating can be put into the two ion system, which leads to changes in fluorescence of the ⁴⁰Ca⁺ ion, first demonstrated with two Ca⁺ isotopes. Increasing the sensitivity of this technique requires ground state cooling of both the ⁴⁰Ca⁺ ion and the ion of interest, enabling the transfer of the ion's motional state into the ground state with high probability. This thesis demonstrates ground state cooling of the atomic ion and sympathetic cooling of a second ion (⁴⁴Ca⁺). Once in the ground state, heating of the Coulomb crystal by scattering photons off of the spectroscopy ion can be measured by monitoring the resolved motional sidebands of the S(1/2)->D(5/2) transition of ⁴⁰Ca⁺, allowing for spectral lines to be inferred. Future experiments will investigate this technique with molecular ions.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.