Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisors: Keith P. Johnston and William J. Koros. Vita. Includes bibliographical references.

In this work, we wish to determine the free energy landscape and the nucleation rate associated with the process of homogeneous ice nucleation. To do this, we simulate the homogeneous nucleation of ice with the mW monatomic model of water and with all-atom models of water using primarily the umbrella sampling rare event method. We find that the use of the mW model of water, which has simpler dynamics compared to all-atom models of water, but is nevertheless surprisingly good at reproducing experimental data, results in very reasonable agreement with classical nucleation theory, in contrast to some previous simulations of homogeneous ice nucleation. We suggest that previous simulations did not observe the lowest free energy pathway in order parameter space because of their use of global order parameters, leading to a deviation from classical nucleation theory predictions. Whilst monatomic water can nucleate reasonably quickly, all-atom models of water are considerably more difficult to simulate, primarily because of their slow dynamics of ice growth and the fact that standard order parameters do not work well in driving nucleation when such models are being used. In this thesis, we describe a local, rotationally invariant order parameter that is capable of growing ice homogeneously in a biassed simulation without the unnatural effects introduced by global order parameters, and without leading to non-physical chain-like growth of 'ice' clusters that results from a naïve implementation of the standard Steinhardt-Ten Wolde order parameter. We have successfully used this order parameter to force the growth of ice clusters in simulations of all-atom models of water. However, although ice growth can be achieved, equilibrating simulations with all-atom models of water is extremely difficult. We describe several approaches to speeding up the equilibration in all-atom models of water to enable the computation of free energy profiles for homogeneous ice nucleation.

Nuclear magnetic resonance (NMR) is a powerful experimental technique for probing the local environment of nuclei in materials. However, it can be difficult to separate the large number of interactions that are recorded in the resulting spectra. First-principles calculations based on quantum mechanics therefore provide much-needed support for interpreting experimental spectra. In this way, the underlying mechanisms recorded in experimental spectra can be investigated on an atomic level, and trends can be noted with which to guide the direction of future experiments. This thesis presents two cases in which first-principles calculations do just that. The first is an investigation of the perovskite structures of NaNbO₃, KNbO₃, LiNbO₃ and the related solid solutions of Na_xK_1-xNbO₃, K_xNa_1-xNbO₃ and Li_xNa_1-xNbO₃ in order to study how structural disorder affects their NMR parameters. The second investigation involves the calculation of the Knight shift in platinum, palladium and rhodium---in their elemental bulk forms and in a set of surface structures. The Knight shift is a systematic shift in the NMR frequencies of metallic systems. It arises from the hyperfine interaction between the nuclear spins and the spins of the unpaired conduction electrons. When calculating the Knight shift, it is found that the Brillouin zone must be very finely sampled. A discussion of core polarisation is also presented. This is the polarisation of core electrons as a result of their interaction with valence electrons. In the case of Curie paramagnets, core polarisation can have a significant effect on the calculation of hyperfine parameters.

The development of interatomic potentials for magnetic transition metals, and particularly for iron, is difficult, yet it is also necessary for large-scale atomistic simulations of industrially important iron and steel alloys. The magnetism of iron is especially important as it is responsible for many of the element's unique physical properties -- its bcc ground state structure, its high-temperature phase transitions, and the mobility of its self-interstitial atom (SIA) defects. Yet an accurate description of itinerant magnetism within a real-space formalism is particularly challenging and existing interatomic potentials based on the Embedded Atom Method are suited only for studies of near-equilibrium ferritic iron, due to their restricted functional forms. For this work, the magnetic analytic Bond-Order Potential (BOP) method has been implemented in full to test the convergence properties in both collinear and non-collinear magnetic iron. The known problems with negative densities of states (DOS) are addressed by assessing various possible definitions for the bandwidth and by including the damping factors adapted from the Kernel Polynomial Method. A 9-moment approximation is found to be sufficient to reproduce the major structural energy differences observed in Density Functional Theory (DFT) and Tight Binding (TB) reference calculations, as well as the volume dependence of the atomic magnetic moments. The Bain path connecting bcc and fcc structures and the formation energy of mono- and divacancies are also described well at this level of approximation. Other quantities such as the high-spin/low-spin transition in fcc iron, the bcc elastic constants and the SIA formation energies converge more slowly towards the TB reference data. The theory of non-collinear magnetism within analytic BOP is extended as required for a practical implementation. The spin-rotational behaviour of the energy is shown to converge more slowly than the collinear bulk energy differences, and there are specific problems at low angles of rotation where the magnitude of the magnetic moment depends sensitively on the detailed structure of the local DOS. Issues of charge transfer in relation to magnetic defects are discussed, as well as inadequacies in the underlying d-electron TB model.

There is currently a need for vaccine adjuvants that are effective for eliciting Th1-type CD4 and CD8 T cell responses when formulated with protein and peptide-based subunit vaccines. Some of the most promising adjuvants in this regard are combined small molecule Toll-like receptor-7/8 agonists (TLR-7/8a). However, poor pharmacokinetic properties have precluded TLR-7/8a for use in vaccines. In this thesis, polymer carriers were used to control pharmacokinetics and to modulate activity of TLR-7/8a for use as vaccine adjuvants. Combinatorial synthesis and in vivo structure-activity studies were used to evaluate how properties of Polymer-TLR-7/8a conjugates (Poly-7/8a) influence innate immune activation in lymph nodes that drain the site of vaccine administration. The most striking finding was that particle formation by Poly-7/8a strongly enhances the magnitude and duration (>14 days) of innate immune activation in lymph nodes by restricting agonist biodistribution and promoting uptake by dendritic cells. Particle-forming Poly-7/8a optimized for activity were found to induce only local innate immune activation (not systemic) and were effective for eliciting Th1-type CD4 and CD8 T cells that mediated protection against infectious challenge. Based on the importance of particle formation for activity of Poly-7/8a, thermo-responsive Poly-7/8a were developed that exist as single water-soluble macromolecules in solution but undergo temperature-driven particle formation in vivo. In conclusion, polymer carriers of TLR-7/8a represent a versatile and effective platform for modulating innate immune activity and warrant further investigation as a class of adjuvants for vaccines.

The development of a clean hydrogen economy will aid a smooth transition from fossil fuels which is required to stem the environmental impact and economic instability caused by oil dependency. For vehicular application, in addition to being cheap and safe, a commercial hydrogen store must contain a certain weight percentage of hydrogen to provide a reasonable range (~300 miles). It must also be able to release hydrogen under near-ambient conditions (80-120°C) and have a reasonable cycling capacity (~1000 cycles). The primary motivation of this thesis is to gain a fundamental understanding into the sorption processes of hydrogen on carbon- and aluminium-based materials to improve their hydrogen storage capacity. The sorption processes of hydrogen on mechanically milled graphite have been investigated, primarily using Electron Spin Resonance Spectroscopy and Inelastic Neutron Scattering. An investigation into the storage properties of tetrahydroaluminates, primarily NaAlH₄ and LiAlH₄, is performed in the presence and absence of a catalyst, and a new phase of NaAlH₄ is observed prior to its decomposition. Variable temperature neutron and synchrotron diffraction, in conjunction with gravimetric and mass spectroscopy data were obtained for several mixtures of tetrahydroaluminates and alkali amides and the hydrogen desorption processes are shown to be quite different from the constituent materials. The structure of Ca(AlH₄)₂ has been experimentally determined for the first time and a complete set of equations describing its decomposition pathway is given.

The photocatalytic approach is known to be one of the most promising advanced oxidation processes for the tertiary treatment of polluted water. In this paper, β-NaYF4/TiO2 composite films have been synthetized through a novel sol–gel/spin-coating approach using a mixture of β-diketonate complexes of Na and Y, and Yb3+, Tm3+, Gd3+, Eu3+ as doping ions, together with the TiO2 P25 nanoparticles. The herein pioneering approach represents an easy, straightforward and industrially appealing method for the fabrication of doped β-NaYF4/TiO2 composites. The effect of the doped β-NaYF4 phase on the photocatalytic activity of TiO2 for the degradation of methylene blue (MB) has been deeply investigated. In particular, the upconverting TiO2/β-NaYF4: 20%Yb, 2% Gd, x% Tm (x = 0.5 and 1%) and the downshifting TiO2/β-NaYF4: 10% Eu composite films have been tested on MB degradation both under UV and visible light irradiation. An improvement up to 42.4% in the degradation of MB has been observed for the TiO2/β-NaYF4: 10% Eu system after 240 min of UV irradiation.

The synthesis and properties of metal phosphonates prepared using piperazine-based bisphosphonic acids have been investigated. The ligands N,N’-piperazinebis(methylenephosphonic acid) (H₄L), and the 2-methyl (H₄L-Me) and 2,5-dimethyl (H₄L 2,5-diMe) derivatives have been prepared using a modified Mannich reaction. Hydrothermal reaction of gels prepared from metal (II) acetates and the bisphosphonic acids results in the synthesis of four structures: STA-12, Ni VSB-5, Co H₂L.H₂O and Mg H₂L. STA-12, synthesised by reaction of Mn, Fe, Co or Ni acetate with H₄L or H₄L-Me, has been investigated further. STA-12 crystallises in the space group R⁻₃, and Ni STA-12 is the most crystalline version. Its structure was solved from synchrotron data (a = b = 27.8342(1) Å, c = 6.2421(3) Å, α = β = 90°, γ = 120°), and it has large 10 Å hexagonal shaped pores. Helical chains of Ni octahedra are coordinated by the ligands, resulting in phosphonate tetrahedra pointing towards the pore space. Water is present, both coordinated to the Ni²⁺ cations and physically adsorbed in the pores. Mixed metal structures based on Ni STA-12, where some Ni is replaced in the gel by another divalent metal (Mg, Mn, Fe or Co) can also be synthesised. Dehydration of STA-12 results in two types of behaviour, depending on the metal present. Rhombohedral symmetry is retained on dehydration of Mn and Fe STA-12, the a cell parameter decreasing compared to the as-prepared structures by 2.42 Å and 1.64 Å respectively. Structure solution of dehydrated Mn STA-12 indicates changes in the torsion angles of the piperazine ring bring the inorganic chains closer together. Fe and Mn STA-12 do not adsorb N₂, which is thought to be due to the formation of an amorphous surface layer. Dehydration of Ni and Co STA-12 causes crystallographic distortion. Three phases were isolated for Ni STA-12: removal of physically adsorbed water results in retention of rhombohedral symmetry, while dehydration at 323 K removes some coordinated water forming a triclinic structure. A fully dehydrated structure (dehydrated at 423 K) was solved from synchrotron data (a = 6.03475(5) Å, b = 14.9156(2) Å, c = 16.1572(7) Å, α = 112.5721(7)°, β = 95.7025(11)°, γ = 96.4950(11)°). The dehydration mechanism, followed by UV-vis and Infra-red spectroscopy, involves removal of water from the Ni²⁺ cations and full coordination of two out of three of the phosphonate tetrahedra forming three crystallographically distinct Ni and P atoms. No structural distortion takes place on dehydration of Ni and Co STA-12 prepared using the methylated bisphosphonate, and the solids give a higher N₂ uptake as a result. Dehydrated Ni and Co STA-12 were tested for adsorption performance for fuel related gases and probe molecules. Investigations were undertaken at low temperature with H₂, CO and CO₂, and ambient temperature with CO₂, CH₄, CH₃CN, CH₃OH and large hydrocarbons. Due to the presence of lower crystallinity, Co STA-12 has an inferior adsorption performance to Ni STA-12, although it has similar adsorption enthalpies for CO₂ at ambient temperature (-30 to -35 kJ mol⁻¹). Ni STA-12 adsorbs similar amounts of CO₂ and N₂ at low temperature, indicating the adsorption mechanisms are similar. Also, it adsorbs 10 × more CO₂ than CH₄ at low pressure, meaning it could be used for separation applications. Ni STA-12 adsorbs 2 mmol g⁻¹ H₂ with an enthalpy of -7.5 kJ mol⁻¹, the uptake being due to adsorption on only one-third of the Ni²⁺ cations. The uptake for CO is 6 mmol g⁻¹, with adsorption enthalpies ranging from -24 to -14 kJ mol⁻¹. This uptake is due to adsorption on all the Ni²⁺, meaning the adsorption enthalpies are high enough to allow the structure to relax. This is also observed for adsorption of CH₃CN and CH₃OH, where there is a return to rhombohedral symmetry after uptake. The adsorption sites in dehydrated Ni and Co STA-12 were investigated via Infra-red spectroscopic analysis of adsorbed probe molecules (H₂, CO, CO₂, CH₃CN and CH₃OH). The results indicate the adsorption sites at both low and ambient temperature are the metal cations and the P=O groups. The metal cation sites are also characterised as Lewis acids with reasonable strength. STA-12 was shown to have acidic activity for the liquid phase selective oxidations of 1-hexene and cyclohexene, although there is evidence active sites are coordinated by products and/or solvents during the reaction. STA-12 also demonstrates basic activity for the Knoevenagel condensation of ethyl cyanoacetate and benzaldehyde. Modification of STA-12 by adsorption of diamine molecules causes a slight increase in the basicity, and the highest conversions are where water and diamine molecules are both present.

Nanomaterials have attracted great interest due to the unique physical properties and great potential in the applications of nanoscale devices. Two dimensional atomic crystals, which are atomic thickness, especially graphene, have triggered the gold rush recently due to the fascinating high mobility at room temperature for future electronics. The crystal structure of nanomaterials will have great influence on their physical properties. Thus, this thesis is focused on developing the methods to control the crystal structure of nanomaterials, namely quantum dots as semiconductor, boron nitride (BN) as insulator, graphene as semimetal, with low cost for their applications in photonics, structural support and electronics. In this thesis, firstly, Mn doped ZnSe quantum dots have been synthesized using colloidal synthesis. The shape control of Mn doped ZnSe quantum dots has been achieved from branched to spherical by switching the injection temperature from kinetics to thermodynamics region. Injection rates have been found to have effect on controlling the crystal phase from zinc blende to wurtzite. The structural-property relationship has been investigated. It is found that the spherical wurtzite Mn doped ZnSe quantum dots have the highest quantum yield comparing with other shape or crystal phase of the dots. Then, the Mn doped ZnSe quantum dots were deposited onto the BN sheets, which were micron-sized and fabricated by chemical exfoliation, for high resolution imaging. It is the first demonstration of utilizing ultrathin carbon free 2D atomic crystal as support for high resolution imaging. Phase contrast images reveal moiré interference patterns between nanocrystals and BN substrate that are used to determine the relative orientation of the nanocrystals with respect to the BN sheets and interference lattice planes using a newly developed equation method. Double diffraction is observed and has been analyzed using a vector method. As only a few microns sized 2D atomic crystal, like BN, can be fabricated by the chemical exfoliation. Chemical vapour deposition (CVD) is as used as an alternative to fabricate large area graphene. The mechanism and growth dynamics of graphene domains have been investigated using Cu catalyzed atmospheric pressure CVD. Rectangular few layer graphene domains were synthesized for the first time. It only grows on the Cu grains with (111) orientation due to the interplay between atomic structure of Cu lattice and graphene domains. Hexagonal graphene domains can form on nearly all non-(111) Cu surfaces. The few layer hexagonal single crystal graphene domains were aligned in their crystallographic orientation over millimetre scale. In order to improve the alignment and reduce the layer of graphene domains, a novel method is invented to perform the CVD reaction above the melting point of copper (1090 ºC) and using molybdenum or tungsten to prevent the balling of the copper from dewetting. By controlling the amount of hydrogen during the growth, individual single crystal domains of monolayer over 200 µm are produced determined by electron diffraction mapping. Raman mapping shows the monolayer nature of graphene grown by this method. This graphene exhibits a linear dispersion relationship and no sign of doping. The large scale alignment of monolayer hexagonal graphene domains with epitaxial relationship on Cu is the key to get wafer-sized single crystal monolayer graphene films. This paves the way for industry scale production of 2D single crystal graphene.

Lithium-ion batteries have transformed energy storage and technological applications. They stand poised to convert transportation from combustion to electric engines. The discharge/charge rate is a key parameter that determines battery power output and recharge time; typically, operation is on the timescale of hours but reducing this would improve existing applications and open up new possibilities. Conventionally, the rate at which a battery can operate has been improved by synthetic strategies to decrease the solid-state diffusion length of lithium ions by decreasing particle sizes down to the nanoscale. In this work, a different approach is taken toward next-generation high-power and fast charging lithium-ion battery electrode materials. The phenomenon of high-rate charge storage without nanostructuring is discovered in niobium oxide and the mechanism is explained in the context of the structure–property relationships of Nb2O5. Three polymorphs, T-Nb2O5, B-Nb2O5, and H-Nb2O5, take bronze-like, rutile-like, and crystallographic shear structures, respectively. The bronze and crystallographic shear compounds, with unique electrochemical properties, can be described as ordered, anion-deficient nonstoichiometric defect structures derived from ReO3. The lessons learned in niobia serve as a platform to identify other compounds with related structural motifs that apparently facilitate high-rate lithium insertion and extraction. This leads to the synthesis, characterisation, and electrochemical evaluation of the even more complicated composition–structure–property relationships in ternary TiO2–Nb2O5 and Nb2O5–WO3 phases. Advanced structural characterisation including multinuclear solid-state nuclear magnetic resonance spectroscopy, density functional theory, X-ray absorption spectroscopy, operando high-rate X-ray diffraction, and neutron diffraction is conducted throughout to understand the evolution of local and long-range atomic structure and changes in electronic states.