This thesis studies three different types of anhydrous proton conducting electrolytes for use in fuel cells. The proton energy level scheme is used to make the first electrolyte which is a rubbery polymer in which the conductivity reaches values typical of activated Nafion, even though it is completely anhydrous. The protons are introduced into a cross-linked polyphospazene rubber by the superacid HOTf, which is absorbed by partial protonation of the backbone nitrogens. The decoupling of conductivity from segmental relaxation times assessed by comparison with conductivity relaxation times amounts to some 10 orders of magnitude, but it cannot be concluded whether it is purely protonic or due equally to a mobile OTf- or H(OTf)2-; component. The second electrolyte is built on the success of phosphoric acid as a fuel cell electrolyte, by designing a variant of the molecular acid that has increased temperature range without sacrifice of high temperature conductivity or open circuit voltage. The success is achieved by introduction of a hybrid component, based on silicon coordination of phosphate groups, which prevents decomposition or water loss to 250ºC, while enhancing free proton motion. Conductivity studies are reported to 285ºC and full H2/O2 cell polarization curves to 226ºC. The current efficiency reported here (current density per unit of fuel supplied per sec) is the highest on record. A power density of 184 (mW.cm-2) is achieved at 226ºC with hydrogen flow rate of 4.1 ml/minute. The third electrolyte is a novel type of ionic liquids which is made by addition of a super strong Brønsted acid to a super weak Brønsted base. Here it is shown that by allowing the proton of transient HAlCl4, to relocate on a very weak base that is also stable to superacids, we can create an anhydrous ionic liquid, itself a superacid, in which the proton is so loosely bound that at least 50% of the electrical conductivity is due to the motion of free protons. The protic ionic liquids (PILs) described, pentafluoropyridinium tetrachloroaluminate and 5-chloro-2,4,6-trifluoropyrimidinium tetrachloroaluminate, might be the forerunner of a class of materials in which the proton plasma state can be approached.

This thesis describes the studies for two groups of molecules in the gas-phase: (a) copper monofluoride (CuF) and copper hydroxide (CuOH); (b) thorium monoxide (ThO) and tungsten carbide (WC). Copper-containing molecules (Group a) are selected to investigate the ionic bonding in transition metal-containing molecules because they have a relatively simple electronic state distribution due to the nearly filled 3d-orbital. ThO and WC (Group b) are in support of particle physics for the determination of electron electric dipole moment (eEDM), de, the existence of which indicates new physics beyond the Standard Model. The determination of the tiny eEDM requires large electric fields applied to the electron. The 3(Delta)1 states for heavy polar molecules were proposed [E. R. Meyer, J. L. Bohn, and M. P. Deskevich, Phys. Rev. A 73, 062108 (2006)] to determine de with the following attractive features: (1) large electric dipole moments; (2) large internal electric fields, Eeff, experienced by valence electrons; (3) nearly degenerate omega-doublets; (4) extremely small magnetic dipole moments. The H3(Delta)1 state for ThO and the X3(Delta)1 state for WC are both good candidates. Spectroscopic parameters (i.e. molecular electric and magnetic dipole moments, omega-doubling parameters, etc) are required for the 3(Delta)1 states of ThO and WC. High resolution optical spectra (linewidth ~50 MHz) of CuF, CuOH, ThO and WC were recorded field-free and in the presence of a static electric field (or magnetic field) using laser ablation source/supersonic expansion and laser induced fluorescence (LIF) detection. The spectra were modeled by a zero-field effective Hamiltonian operator and a Stark (or Zeeman) Hamiltonian operator with various molecular parameters. The determined molecular parameters are compared to theoretical predictions. The small omega-doubling parameter was well determined using the pump/probe microwave optical double resonance (PPMODR) technique with a much higher resolution (linewidth ~60 kHz) than optical spectroscopy. In addition to the above mentioned studies of the two groups of molecules, a resonance enhanced multi-photon ionization (REMPI) combined with a time-of-flight mass spectrometer (TOFMS) has been developed to identify the molecules responsible for observed LIF signals. The operation of this spectrometer has been tested by recording the mass spectrum of Ti/O2 and the REMPI spectrum for TiO using a two-color excitation scheme.

Carbon lacks an extended polyanionic chemistry which appears restricted to carbides with C4-, C22-, and C34- moieties. The most common dimeric anion of carbon atoms is C22- with a triple bond between the two carbon atoms. Compounds containing the dicarbide anion can be regarded as salts of acetylene C2H2 (ethyne) and hence are also called acetylides or ethynides. Inspired by the fact that molecular acetylene undergoes pressure induced polymerization to polyacetylene above 3.5 GPa, it is of particular interest to study the effect of pressure on the crystal structures of acetylides as well. In this work, pressure induced polymerization was attempted with two simple metal acetylides, Li2C2 and CaC2. Li2C2 and CaC2 have been synthesized by a direct reaction of the elements at 800ºC and 1200ºC, respectively. Initial high pressure investigations were performed inside Diamond anvil cell (DAC) at room temperature and in situ Raman spectroscopic measurement were carried out up to 30 GPa. Near 15 GPa, Li2C2 undergoes a transition into a high pressure acetylide phase and around 25 GPa this phase turns amorphous. CaC2 is polymorphic at ambient pressure. Monoclinic CaC2-II does not show stability at pressures above 1 GPa. Tetragonal CaC2-I is stable up to at least 12 GPa above which possibly a pressure-induced distortion occurs. At around 18 GPa, CaC2 turns amorphous. In a subsequent series of experiments both Li2C2 and CaC2 were compressed to 10 GPa in a multi anvil (MA) device and heated to temperatures between 300 and 1100oC for Li2C2, and 300°C to 900°C for CaC2. The recovered products were analyzed by PXRD and Raman spectroscopy. It has been observed that reactions at temperature higher than 900°C were very difficult to control and hitherto only short reaction times could be applied. For Li2C2, a new phase, free of starting material was found at 1100°C. Both the PXRD patterns and Raman spectra of products at 1100oC could not be matched to known forms of carbon or carbides. For CaC2 new reflections in PXRD were visible at 900ºC with the starting material phase.

The behaviors of various amorphous materials are characterized at high pressures to deduce phase transitions, coordination changes, densification, and other structural or electronic alterations in the system. Alongside, improvements on high pressure techniques are presented to measure equations of state of glassy materials and probe liquids using in-situ high resolution nuclear magnetic resonance (NMR) spectroscopy. 27Al NMR is used to quantify coordination changes in CaAl2O4 glass pressure cycled to 16 GPa. The structure and coordination environments remain unchanged up to 8 GPa at which 93% of the recovered glass exists as 4-fold Al, whereas the remaining population exists as [5,6]Al. Upon densification, [5,6]Al comprise nearly 30% of observed Al, most likely through the generation of 3-coordinated oxygen. A method to determine the volumetric equation of state of amorphous solids using optical microscopy in a diamond anvil cell is also described. The method relies on two dimensional image acquisition and analysis to quantify changes in the projected image area with compression. The area analysis method is used to determine the compression of cubic crystals, yielding results in good agreement with diffraction and volumetric measurements. A NMR probe capable of reaching 3 GPa is built to understand the nature of magnetic field gradients and improve upon the resolution of high pressure studies conducted in a diamond anvil cell. Field gradients in strength up to 6 G/cm are caused largely by mismatches in the magnetic susceptibility between the sample and gasket, which is proven to shift the chemical shift distribution by use of several different metallic gaskets. Polyamorphic behavior in triphenyl phosphite is studied at pressures up to 0.7 GPa to elucidate the formation of the glacial phase at high pressures. A perceived liquid-liquid phase transition is shown to follow a positive Clapeyron slope, and closely follows the predicted glass transition line up to 0.4 GPa and temperatures below 270 K. A drastic change in morphology is indicative of a transformation from liquid I to liquid II and followed by optical microscopy.

Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase.

Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet would bring fully hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses ( 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. At the initial experiments at the AMO beamline using 6.9- Å wavelength, Bragg peaks were recorded to 8.5- Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage. Recently, femtosecond X-ray protein nanocrystallography experiments were done at the CXI beamline of the LCLS using 1.3- Å wavelength, and Bragg reflections were recorded to 3- Å resolution; the data are currently being processed. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.