One very critical aspect of cell biology is the cytoskeleton. The cytoskeleton not only provides a strong foundation for the cell (Pegoraro et al., 2017), but it also allows for protein transport on its tracks that span long distances in cells (Löwe & Amos, 2009), specifically in neurons (Dent, 2017). Microtubules have a particular structure as polymers that are part of the cytoskeleton (Dent, 2017). Their components include alpha- and beta-tubulin dimers, and they have dynamic properties, such as polymerization and depolymerization (Dent, 2017). Concerning these dynamic properties and as will be discussed here, specific associated proteins can be useful in electrical signaling, neurodegeneration, and neurogenesis. In this review, I will review relevant findings on microtubule-associated proteins (MAPs), compare these to a prominent drug called taxol, and describe the significance of having a combination of MAPs in the brain. I will suggest that microtubules and their proteins form a critical geometric infrastructure that provides the framework for neuronal structure and function that contributes to more advanced cognitive processes, including consciousness.

A driving force for studies of water, alcohols, and amides is the determination of the role of hydrogen bonding. Hydrogen bonds can break and reform, consequently creating supramolecular structures. Understanding the role supramolecular structures play in the dynamics of monohydroxyl alcohols is important to understanding hydrogen bonding in more complex systems such as proteins. Since many monohydroxyl alcohols are good glass formers, dielectric spectroscopy in the supercooled regime is used to gather information about the dynamics of these liquids. Application of high external fields will reversibly alter the polarization responses of the material from the linear response. This results in nonlinear dielectric effects (NDE) such as field induced suppression (saturation) and enhancement of amplitudes (chemical effects) as well as shifts in the time constants toward slower (entropy) and faster (energy absorption) dynamics.

The first part of this thesis describes the nonlinear dielectric experiments on monohydroxyl alcohols, with an emphasis on the time dependence of NDEs. For the first time, time-dependent experiments on monoalcohols were done, the results showed that NDEs occur on the Debye time scale. Furthermore, physical vapor deposition (PVD) is used to modify the supramolecular structure of 4-methyl-3-heptanol. Upon deposition the film cannot form the ring like structures, which are preferred in the bulk material. The as deposited film shows an enhancement of the dielectric peak by a factor of approximately 11 when compared to the bulk material. The conversion from the as deposited material back to the near bulk material was found to occur on the Debye timescale.

The second part of this thesis focuses on the question of what is governing the field induced changes seen in the liquids studied. Here a complete set of high field experiments on highly polar propylene carbonate derivatives were performed. It was demonstrated that these materials exhibit a Debye-like peak and using a combination of Adam-Gibbs and Fröhlich’s definition of entropy, proposed by Johari [G.P. Johari, J. Chem. Phys 138, 154503 (2013)], cannot solely be used to describe a frustration of dynamics. It is important to note that although these material exhibit a Debye like peak, the behavior is much different than monoalcohols.

In materials science, developing GeSn alloys is major current research interest concerning the production of efficient Group-IV photonics. These alloys are particularly interesting because the development of next-generation semiconductors for ultrafast (terahertz) optoelectronic communication devices could be accomplished through integrating these novel alloys with industry-standard silicon technology. Unfortunately, incorporating a maximal amount of Sn into a Ge lattice has been difficult to achieve experimentally. At ambient conditions, pure Ge and Sn adopt cubic (α) and tetragonal (β) structures, respectively, however, to date the relative stability and structure of α and β phase GeSn alloys versus percent composition Sn has not been thoroughly studied. In this research project, computational tools were used to perform state-of-the-art predictive quantum simulations to study the structural, bonding and energetic trends in GeSn alloys in detail over a range of experimentally accessible compositions. Since recent X-Ray and vibrational studies have raised some controversy about the nanostructure of GeSn alloys, the investigation was conducted with ordered, random and clustered alloy models.
By means of optimized geometry analysis, pure Ge and Sn were found to adopt the alpha and beta structures, respectively, as observed experimentally. For all theoretical alloys, the corresponding αphase structure was found to have the lowest energy, for Sn percent compositions up to 90%. However at 50% Sn, the correspondingβ alloy energies are predicted to be only ~70 meV higher. The formation energy of α-phase alloys was found to be positive for all compositions, whereas only two beta formation energies were negative. Bond length distributions were analyzed and dependence on Sn incorporation was found, perhaps surprisingly, not to be directly correlated with cell volume. It is anticipated that the data collected in this project may help to elucidate observed complex vibrational properties in these systems.

Fluctuations with a power spectral density depending on frequency as $1/f^\alpha$ ($0<\alpha<2$) are found in a wide class of systems. The number of systems exhibiting $1/f$ noise means it has far-reaching practical implications; it also suggests a possibly universal explanation, or at least a set of shared properties. Given this diversity, there are numerous models of $1/f$ noise. In this dissertation, I summarize my research into models based on linking the characteristic times of fluctuations of a quantity to its multiplicity of states. With this condition satisfied, I show that a quantity will undergo $1/f$ fluctuations and exhibit associated properties, such as slow dynamics, divergence of time scales, and ergodicity breaking. I propose that multiplicity-dependent characteristic times come about when a system shares a constant, maximized amount of entropy with a finite bath. This may be the case when systems are imperfectly coupled to their thermal environment and the exchange of conserved quantities is mediated through their local environment. To demonstrate the effects of multiplicity-dependent characteristic times, I present numerical simulations of two models. The first consists of non-interacting spins in $0$-field coupled to an explicit finite bath. This model has the advantage of being degenerate, so that its multiplicity alone determines the dynamics. Fluctuations of the alignment of this model will be compared to voltage fluctuations across a mesoscopic metal-insulator-metal junction. The second model consists of classical, interacting Heisenberg spins with a dynamic constraint that slows fluctuations according to the multiplicity of the system's alignment. Fluctuations in one component of the alignment will be compared to the flux noise in superconducting quantum interference devices (SQUIDs). Finally, I will compare both of these models to each other and some of the most popular models of $1/f$ noise, including those based on a superposition of exponential relaxation processes and those based on power law renewal processes.

Circular Dichroism (CD) and electron paramagnetic resonance (EPR) were used to investigate the metal-binding sites of five different four-helix bundles, which have slight differences in the population of their side chains. Of the four-helix bundles, three have central dinuclear metal binding sites; two of these three also have outer dinuclear metal binding sites. The other two peptides have two identical, non-central, dinuclear metal binding sites. The CD spectra showed changes in the secondary structure of the peptides, and X-band EPR spectra of these peptides revealed the unique four peak signal of Cu(II). These findings improve our understanding of the metal binding environments of these peptides.

Understanding the relationships between chemistry students' motivation, performance, and gender can help identify and inform ways in which chemistry education might be improved. Students from four CHM 101 classes with two different instructors were surveyed using an adapted Science Motivation Questionnaire II, and motivation data was analyzed with respect to final course performance. Gender data was available for two of these classes, and motivation results analyzed by gender for these classes. Exam scores and gender data was obtained from one of the instructors for CHM 101 courses taught over the past five years and were also analyzed. The motivational study involved small sample sizes, especially in the motivation by gender study. Career motivation, grade motivation, self-efficacy, and total motivation declined over the course of the semester in the four classes combined. Self-efficacy and career motivation were found to predict final course performance only at the end of the semester. Self-efficacy strongly predicted performance, and career motivation was negatively correlated with performance. Female students had higher grade motivation at the end of the semester and lost more self-efficacy over the course of the semester than male students. Gender-performance analysis showed that male students scored slightly higher on exams on average, but that female students received a higher percentage of "A"s and a lower percentage of "D"s, "E"s, and "W"s in the majority of the semesters.

This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano- junctions between molecular electronic devices and biological systems.

This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junc- tion significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction.

In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH···O, OH···O, and NH···N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has fo- cused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance de- scriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular descrip- tion of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions.

A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.

A lack of adequate energy storage technologies is arguably the greatest hindrance to a modern sustainable energy infrastructure. Chemical energy storage, in the form of batteries, is an obvious solution to the problem. Unfortunately, today’s state of the art battery technologies fail to meet the desired metrics for full scale electric grid and/or electric vehicle role out. Considerable effort from scientists and engineers has gone into the pursuit of battery chemistries theoretically capable of far outperforming leading technologies like Li-ion cells. For instance, an anode of the relatively abundant and cheap metal, magnesium, would boost the specific energy by over 4.6 times that of the current Li-ion anode (LiC6).

The work presented here explores the compatibility of magnesium electrolytes in TFSI–-based ionic liquids with a Mg anode (TFSI = bis(trifluoromethylsulfonyl)imide). Correlations are made between the Mg2+ speciation conditions in bulk solutions (as determined via Raman spectroscopy) and the corresponding electrochemical behavior of the electrolytes. It was found that by creating specific chelating conditions, with an appropriate Mg salt, the desired electrochemical behavior could be obtained, i.e. reversible electrodeposition and dissolution. Removal of TFSI– contact ion pairs from the Mg2+ solvation shell was found to be essential for reversible electrodeposition. Ionic liquids with polyethylene glycol chains pendent from a parent pyrrolidinium cation were synthesized and used to create the necessary complexes with Mg2+, from Mg(BH4)2, so that reversible electrodeposition from a purely ionic liquid medium was achieved.

The following document discusses findings from several electrochemical experiments on magnesium electrolytes in ionic liquids. Explanations for the failure of many of these systems to produce reversible Mg electrodeposition are provided. The key characteristics of ionic liquid systems that are capable of achieving reversible Mg electrodeposition are also given.

Photosystem II (PSII) is a large protein-cofactor complex. The first step in

photosynthesis involves the harvesting of light energy from the sun by the antenna (made

of pigments) of the PSII trans-membrane complex. The harvested excitation energy is

transferred from the antenna complex to the reaction center of the PSII, which leads to a

light-driven charge separation event, from water to plastoquinone. This phenomenal

process has been producing the oxygen that maintains the oxygenic environment of our

planet for the past 2.5 billion years.

The oxygen molecule formation involves the light-driven extraction of 4 electrons

and protons from two water molecules through a multistep reaction, in which the Oxygen

Evolving Center (OEC) of PSII cycles through 5 different oxidation states, S0 to S4.

Unraveling the water-splitting mechanism remains as a grant challenge in the field of

photosynthesis research. This requires the development of an entirely new capability, the

ability to produce molecular movies. This dissertation advances a novel technique, Serial

Femtosecond X-ray crystallography (SFX), into a new realm whereby such time-resolved

molecular movies may be attained. The ultimate goal is to make a “molecular movie” that

reveals the dynamics of the water splitting mechanism using time-resolved SFX (TRSFX)

experiments and the uniquely enabling features of X-ray Free-Electron Laser

(XFEL) for the study of biological processes.

This thesis presents the development of SFX techniques, including development of

new methods to analyze millions of diffraction patterns (~100 terabytes of data per XFEL

experiment) with the goal of solving the X-ray structures in different transition states.

ii

The research comprises significant advancements to XFEL software packages (e.g.,

Cheetah and CrystFEL). Initially these programs could evaluate only 8-10% of all the

data acquired successfully. This research demonstrates that with manual optimizations,

the evaluation success rate was enhanced to 40-50%. These improvements have enabled

TR-SFX, for the first time, to examine the double excited state (S3) of PSII at 5.5-Å. This

breakthrough demonstrated the first indication of conformational changes between the

ground (S1) and the double-excited (S3) states, a result fully consistent with theoretical

predictions.

The power of the TR-SFX technique was further demonstrated with proof-of principle

experiments on Photoactive Yellow Protein (PYP) micro-crystals that high

temporal (10-ns) and spatial (1.5-Å) resolution structures could be achieved.

In summary, this dissertation research heralds the development of the TR-SFX

technique, protocols, and associated data analysis methods that will usher into practice a

new era in structural biology for the recording of ‘molecular movies’ of any biomolecular

process.

Metal hydride materials have been intensively studied for hydrogen storage applications. In addition to potential hydrogen economy applications, metal hydrides offer a wide variety of other interesting properties. For example, hydrogen-dominant materials, which are hydrides with the highest hydrogen content for a particular metal/semimetal composition, are predicted to display high-temperature superconductivity. On the other side of the spectrum are hydrides with small amounts of hydrogen (0.1 - 1 at.%) that are investigated as viable magnetic, thermoelectric or semiconducting materials. Research of metal hydride materials is generally important to gain fundamental understanding of metal-hydrogen interactions in materials. Hydrogenation of Zintl phases, which are defined as compounds between an active metal (alkali, alkaline earth, rare earth) and a p-block metal/semimetal, were attempted by a hot sintering method utilizing an autoclave loaded with gaseous hydrogen (< 9 MPa). Hydride formation competes with oxidative decomposition of a Zintl phase. The oxidative decomposition, which leads to a mixture of binary active metal hydride and p-block element, was observed for investigated aluminum (Al) and gallium (Ga) containing Zintl phases. However, a new phase Li2Al was discovered when Zintl phase precursors were synthesized. Using the single crystal x-ray diffraction (SCXRD), the Li2Al was found to crystallize in an orthorhombic unit cell (Cmcm) with the lattice parameters a = 4.6404(8) Å, b = 9.719(2) Å, and c = 4.4764(8) Å. Increased demand for materials with improved properties necessitates the exploration of alternative synthesis methods. Conventional metal hydride synthesis methods, like ball-milling and autoclave technique, are not responding to the demands of finding new materials. A viable alternative synthesis method is the application of high pressure for the preparation of hydrogen-dominant materials. Extreme pressures in the gigapascal ranges can open access to new metal hydrides with novel structures and properties, because of the drastically increased chemical potential of hydrogen. Pressures up to 10 GPa can be easily achieved using the multi-anvil (MA) hydrogenations while maintaining sufficient sample volume for structure and property characterization. Gigapascal MA hydrogenations using ammonia borane (BH3NH3) as an internal hydrogen source were employed in the search for new hydrogen-dominant materials. Ammonia borane has high gravimetric volume of hydrogen, and additionally the thermally activated decomposition at high pressures lead to a complete hydrogen release at reasonably low temperature. These properties make ammonia borane a desired hydrogen source material. The missing member Li2PtH6 of the series of A2PtH6 compounds (A = Na to Cs) was accessed by employing MA technique. As the known heavier analogs, the Li2PtH6 also crystallizes in a cubic K2PtCl6-type structure with a cell edge length of 6.7681(3) Å. Further gigapascal hydrogenations afforded the compounds K2SiH6 and Rb2SiH6 which are isostructural to Li2PtH6. The cubic K2SiH6 and Rb2SiH6 are built from unique hypervalent SiH62- entities with the lattice parameters of 7.8425(9) and 8.1572(4) Å, respectively. Spectroscopic analysis of hexasilicides confirmed the presence of hypervalent bonding. The Si-H stretching frequencies at 1550 cm-1 appeared considerably decreased in comparison with a normal-valent (2e2c) Si-H stretching frequencies in SiH4 at around 2200 cm-1. However, the observed stretching modes in hypervalent hexasilicides were in a reasonable agreement with Ph3SiH2- (1520 cm-1) where the hydrogen has the axial (3e4c bonded) position in the trigoal bipyramidal environment.