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Knowledge on cysteine oxidation state and disulfide bond connectivity is of great importance to protein chemistry and 3-D structures. This research is aimed at finding the most relevant features in prediction of cysteines oxidation states and the disulfide bonds connectivity of proteins. Models predicting the oxidation states of cysteines are developed with machine learning techniques such as Support Vector Machines (SVMs) and Associative Neural Networks (ASNNs). A record high prediction accuracy of oxidation state, 95%, is achieved by incorporating the oxidation states of N-terminus cysteines, flanking sequences of cysteines and global information on the protein chain (number of cysteines, length of the chain and amino acids composition of the chain etc.) into the SVM encoding. This is 5% higher than the current methods. This indicates to us that the oxidation states of amino terminal cysteines infer the oxidation states of other cysteines in the same protein chain. Satisfactory prediction results are also obtained with the newer and more inclusive SPX dataset, especially for chains with higher number of cysteines. Compared to literature methods, our approach is a one-step prediction system, which is easier to implement and use. A side by side comparison of SVM and ASNN is conducted. Results indicated that SVM outperform ASNN on this particular problem. For the prediction of correct pairings of cysteines to form disulfide bonds, we first study disulfide connectivity by calculating the local interaction potentials between the flanking sequences of the cysteine pairs. The obtained interaction potential is further adjusted by the coefficients related to the binding motif of enzymes during disulfide formation and also by the linear distance between the cysteine pairs. Finally, maximized weight matching algorithm is applied and performance of the interaction potentials evaluated. Overall prediction accuracy is unsatisfactory compared with the literature. SVM is used to predict the disulfide connectivity with the assumption that oxidation states of cysteines on the protein are known. Information on binding region during disulfide formation, distance between cysteine pairs, global information of the protein chain and the flanking sequences around the cysteine pairs are included in the SVM encoding. Prediction results illustrate the advantage of using possible anchor region information.

Transition metal carbides (TMCs) are of increasing interest for catalytic processes. Their performance and stability under common oxidative conditions in catalytic reactions are crucial for several applications, including catalysis and electrochemical reactions. In this work, we report a detailed XPS study of the interactions of stoichiometric NbC and TaC surfaces with common oxidizing agents like O2 and H2O, which are important media in many chemical processes. Experimental results showed that NbC reacts with O2 to produce Nb sub-oxrides, while TaC is inert to O2 exposure. TaC surfaces are more sensitive to H2O vapor, with a greater surface oxidation and hydroxylation. Atmospheric oxidation of NbC and TaC was also studied, and results showed that both films oxidized yielding to the formation of Nb2O5 and Ta2O5, hydroxylated/ oxide carbon species, and some adventurous carbon build-up. TMCs are catalytically active in many reactions, especially those involving electrochemical nitrogen reduction reactions (NRR) to ammonia. Experimental and DFT calculations were used to provide insight on how carbide surface structures change electrochemically and how that evolution relates to NRR activity. Results showed that NbC has NRR activity at pH 3.2 after immersion in 0.3 M NaOH, leaving niobium suboxides. However, photoemission data showed that the Nb2O5 overlayer is restored after polarization to -1.3 V vs. Ag/AgCl, inhibiting NRR activity. TaC, on the other hand, is inactive for NRR at potentials more positive than -1.0 V, as NaOH treatment fails to remove the Ta2O5 surface layer induced by ambient exposure. The study also found that the formation and stabilization of intermediate oxidation states on the surface of transition metal ions are crucial for N≡N bond activation and NRR activity.

Hydrophobic coatings find application in various sectors of the economy including to electronics, textiles, optical devices, and in scientific and commercial equipment. These different applications demand that different hydrophobic coatings posses a range of properties that may include smoothness or roughness, thicknesses on the order of a monolayer or a micron, robustness or the ability to dissolve quickly, transparency or opacity, water resistance or water permeability, electrical conductivity, oleophobicity, etc. However, whatever the final/desired properties, deposition via dry-deposition processes offers significant advantages, including greater reproducibility, increased environmental friendliness, and cost effectiveness on an industrial scale. Herein I explore the chemical vapor deposition of silanes and the characterization of a commercial, hydrophobic coating to better prepare and understand hydrophobic coatings on different materials. One of the characterization techniques I used frequently in these studies is X-ray photoelectron spectroscopy (XPS). Accordingly, in Chapter 2 of this thesis I discuss this technique vis-à-vis the chemical shifts it detects, which reflect the oxidation states of materials being probed. In particular, I discuss a recommendation made over a decade ago by Gion Calzaferri for 'fixing' the problem of oxidation numbers as applied to organic materials and show how XPS confirms his suggestion. In Chapter 3 I introduce hydrogen as an etch/cleaning gas for silicon wafers. I first show that, like argon and oxygen plasmas, hydrogen plasmas will effectively clean silicon wafers. However, I then show that hydrogen plasma treatment leads to a silicon surface that is chemically different than those prepared with the other plasmas and that undergoes silanization to a greater extent -- the resulting surfaces have higher water contact angles and thicknesses. In Chapter 4 I study the deposition of a potential barrier layer for water, which was prepared from an aza silane: N-n-butyl-aza-2,2-dimethoxysilacyclopentane (1) in a molecular layer deposition (MLD)-like process using either water or ammonium hydroxide as the second half reactant. This molecule has the interesting property of undergoing self-limiting growth, where the termination of this growth is accelerated by use of an ammonium hydroxide catalyst. Interestingly, films of 1 are considerably thicker on nylon than on silicon, which is explained by nylon acting as a water reservoir in the reaction. In Chapter 5 I show the careful characterization of the hydrophobic coating on an Apple iPod nano, which was probed by ToF-SIMS, wetting, and XPS. I could identify that the coating is only applied to the touchscreen of the device. SIMS suggested that the fluorinated coating contains oxygen, which should add to its biodegradability. Finally, in Chapter 6 I make recommendation for future work in these areas.

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This Thesis extends our fundamental knowledge of high-oxidation-state chemistry and in particular compounds of Xe(VIII), Xe(VI), and Ir(V). The crystal structure of XeVIIIO4 was obtained and provides important information on this fundamentally interesting endothermic and shock-sensitive compound. Macroscopic amounts of XeO3F2 have been prepared for the first time. Although the low-temperature Raman spectrum of solid XeO3F2 exhibits some frequency shifts and band splittings of the bending modes, the spectrum is similar to the Raman spectrum of the previously reported matrix-isolated compound. The crystal structures of decomposition and byproducts resulting from the syntheses of XeO3F2 have been obtained for [XeF5][HF2]∙XeOF4 and XeF2∙XeO2F2. The solid-state structure of xenon trioxide, XeO3, was reinvestigated by low-temperature single-crystal X-ray diffraction and shown to exhibit polymorphism that is dependent on crystallization conditions. The previously reported α-phase (orthorhombic, P212121) only forms upon evaporation of aqueous HF solutions of XeO3. In contrast, two new phases, β-XeO3 (rhombohedral, R3) and gamma-XeO3 (rhombohedral, R3c) have been obtained by slow evaporation of aqueous solutions of XeO3. The extended structures of all three phases result from Xe=O----Xe bridge interactions among XeO3 molecules that arise from the amphoteric donor-acceptor nature of XeO3. The Xe atom of the trigonal pyramidal XeO3-unit has three Xe---O secondary bonding interactions. The orthorhombic α-phase displays the greatest degree of variation among the contact distances and has a significantly higher density than the rhombohedral phases. The ambient-temperature Raman spectra of solid α- and gamma-XeO3 have also been obtained and assigned for the first time. Xenon trioxide interacts with CH3CN and CH3CH2CN to form O3XeNCCH3, O3Xe(NCCH3)2, O3XeNCCH2CH3, and O3Xe(NCCH2CH3)2. Their low-temperature single-crystal X-ray structures show that the xenon atoms are consistently coordinated to three electron-donor atoms which result in pseudo-octahedral environments around their xenon atoms. The adduct series provides the first examples of a neutral xenon oxide bound to nitrogen bases. Energy-minimized gas-phase geometries and vibrational frequencies were obtained for the model compounds O3Xe(NCCH3)n (n = 1−3) and O3Xe(NCCH3)n∙[O3Xe(NCCH3)2]2 (n = 1, 2). The natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), electron localization function (ELF), and molecular electrostatic potential surface (MEPS) analyses were carried out to further probe the nature of the bonding in these adducts. Xenon trioxide forms adducts with the polytopic nitrogen base ligands: hexamine, DABCO, 2,2’-bipyridine, 1,10-phenanthroline, and 4,4’-bipyridine. The adducts were conveniently synthesized in aqueous or CH3CN solutions and are stable at room temperature. The crystal structures of hexamine∙2XeO3, hexamine∙XeO3∙H2O, 2,2’-bipyridine∙XeO3, 1,10-phenanthroline∙XeO3, and 4,4’-bipyridine∙XeO3 have been determined by low-temperature single-crystal X-ray diffraction. The structures consist of XeO3 molecules bridged by the ligands to form extended supramolecular networks with Xe---N bonds which range from 2.634(3) to 2.829(2) Å. Raman spectroscopy was used to characterize and probe the room-temperature stabilities of these adducts. The reaction of 1,4-diazabicyclo[2.2.2]octane (DABCO) with XeO3 in aqueous solutions yields thin, plate-shaped crystals which are severely twinned whereas the reaction of DABCO with XeO3 in the presence of HF forms [DABCOH]2[F2(XeO3)2]∙H2O and [DABCOH2][F][H2F3] which were also characterized by low-temperature X-ray crystallography and Raman spectroscopy. A reversible temperature-dependent phase transition occurred for [DABCOH]2[F2(XeO3)2]∙H2O. The structures of 2,2’-bipy∙XeO3 and 1,10-phen∙XeO3 provide the first examples of noble-gas chelates. The structure of hexamine∙XeO3∙H2O provides the first instance in which a noble-gas centre is coordinated by water. These compounds also represent the first examples of sp2- and sp3-hybridized N---Xe(VI) bonds and are rare examples of noble-gas compounds that are air-stable at ambient temperatures. Adducts between XeO3 and three molar equivalents of the nitrogen bases, pyridine and 4-dimethylaminopyridine (4-DMAP), have been synthesized and characterized. The crystal structures of (C5H5N)3XeO3, {(CH3)2)2NC5H4N}3XeO3∙H2O have been determined by low-temperature single-crystal X-ray diffraction. The reaction of hydrolyzed XeF6 in acetonitrile with pyridine or 4-DMAP afforded [C5H5NH]4[HF2]2[F2(XeO3)2] and [(CH3)2NC5H4NH][HF2]∙XeO3 which were characterized by low-temperature X-ray crystallography and Raman spectroscopy. The structures contain pyridinium cations that are hydrogen bonded to the fluoride coordinated to XeO3 and can be viewed as pyridinium fluoroxenates. The structure of (CH3)2NC5H5N∙XeO3∙H2O contains a water molecule that is hydrogen bonded to two oxygen atoms of two adjacent XeO3 molecules. The pyridine adduct, (C5H5N)3XeO3, was found to be relatively insensitive to shock, whereas the 4-DMAP adduct was extremely shock sensitive. The number of isolable compounds which contain different noble-gas−element bonds is limited for xenon and even more so for krypton. Examples of Xe−Cl bonds are rare and prior to this work, no definitive evidence for a Xe−Br bonded compound existed. The syntheses, isolation, and characterization of the first compounds to contain Xe−Br bonds ([N(C2H5)4]3[Br3(XeO3)3] and [N(CH3)4]4[Br4(XeO3)4]) and their chlorine analogues are described. The bromo- and chloroxenate salts are stable in the atmosphere at room temperature and were characterized in the solid state by Raman spectroscopy, low-temperature single-crystal X-ray diffraction, and in the gas phase by quantum-chemical calculations. They are the only known examples of cage anions that contain a noble-gas element. The Xe−Br and Xe−Cl bonds are weakly covalent and can be viewed as σ-hole interactions, similar to halogen bonds. Xenon trioxide reacts with alkali metal fluorides and chlorides to form a variety of room-temperature stable fluoro- and chloroxenate salts. The reaction of XeO3 with various ratios of KF in water afforded three new compounds. The crystal structures of α-K[F(XeO3)2], β-K[F(XeO3)2], α-K[FXeO3], K2[F2(XeO3)] have been determined. The reaction of XeO3 with aqueous CsF resulted in Cs3[F3(XeO3)2]. The XeVI−F bond lengths range from 2.3520(18) to 2.5927(17) Å. No stable product was isolated when [N(CH3)4]F was the fluoride source, but in the presence of HF, crystals of [N(CH3)4]3[HF2]2[H2F3]∙2XeO3 were obtained. The reaction of KCl with XeO3 in equimolar amounts resulted in the formation of K[ClXeO3] whereas the analogous reaction with CsCl yielded Cs3[Cl3(XeO3)4]. Attempts to synthesize Xe–P and Xe–S bonded compounds were unsuccessful and instead resulted in adducts between XeO3 and O-bases such as the phosphine oxide adduct, {(C6H5)3PO}2XeO3 and dimethylsulfoxide (DMSO) adduct {(CH3)2SO}3(XeO3)2. Although DMSO was found to be resistant to oxidation by XeO3, no significant Xe---S bonding interactions were observed. Acetone was found to be highly resistant to oxidation by XeO3 and forms {(CH3)2CO}3XeO3 at low temperatures. The reaction of pyridine-N-oxide yielded large crystals of (C5H5NO)3(XeO3)2 in which the structure contains short chains in contrast with ((CH3)2SO)3(XeO3)2 whose structure consists of discrete dimers. The reaction of XeO3 with the oxidatively resistant main-group oxide anion source, [N(CH3)4][OTeF5] in CH3CN solvent afforded [N(CH3)4][F5TeOXeO3(CH3CN)2]. Xenon trioxide reacts with potassium hydroxide to form the previously known K4[XeO6]∙2XeO3 salt which was characterized by Raman spectroscopy and low-temperature X-ray crystallography. The reaction of MgO with XeO3 yielded single crystals of [Mg(OH2)6]4[XeO6(XeO3)12O2]∙12H2O, which also contains perxenate-XeO3 interactions. Alkali metal carbonates also incorporate XeO3 into their crystal lattices. Raman spectra of M2[CO3(XeO3)n]∙xH2O (M = Na, K, Rb) were recorded and contain intense bands assigned to the XeO3 stretching modes and very weak bands assigned to the [CO3]2− modes. The reaction of dilute aqueous solutions of XeO3 with RbOH and atmospheric CO2 afforded single crystals of Rb2[CO3(XeO3)2]∙2H2O which were characterized by low-temperature X-ray crystallography. Attempts to incorporate XeO3 into other polyatomic anion salts such as KMnO4, NaClO3, and NaNO3 were unsuccessful. The reaction of IrO2 with XeF6 in aHF provided [Xe2F11][IrF6], whereas the reaction of IrO2 with KrF2 with ClF3 in anhydrous HF solvent provided [ClO2][Ir2F11] and [ClO2][(μ-OIrF4)3]. The structure of [(μ-OIrF4)3]− consists of a six membered Ir3O3 ring with four terminal fluorine atoms on each Ir atom. It was also found that ClF3 forms an adduct with [Xe2F11][HF2] in which the structural parameters of ClF3 are very similar to that of solid ClF3. The [ClO2][Ir2F11] salt provides the first structural information on the [Ir2F11]− anion and the [(μ-OIrF4)3]− anion represents the first isolated iridium oxide fluoride species. / Thesis / Doctor of Philosophy (PhD) / Xenon is a noble-gas element which is located in the far right-hand column of the periodic table and was previously thought to be chemically unreactive and incapable of forming compounds. In 1962, it was shown that xenon reacts with the most reactive compounds, such as elemental fluorine, but the resulting xenon compounds are themselves highly reactive. This Thesis extends the chemistry of some of the most unstable and chemically reactive xenon compounds that are currently known. One such compound, xenon trioxide, tends to easily detonate unless carefully handled. Methods of stabilizing xenon trioxide were developed and its behaviour with compounds which resulted in formation of new xenon compounds was studied. The molecular structures of these compounds were investigated in the solid with particular emphases on their chemical bonding. Iridium is one of the most chemically resistant metals known. Highly reactive xenon and krypton compounds were used synthesize new iridium compounds.