he interactions of the chemical warfare agent sulfur mustard with amorphous silica were investigated using electronic structure calculations. In this thesis, the binding energies of sulfur mustard and mimic species used in the laboratory were calculated using density functional theory and fully ab initio calculations. The wB97XD and B97D functionals, which include functions to account for long-range dispersion interactions, were compared to experimental trends. The hydroxylated amorphous silica surface was approximated using a gas-phase silanol molecule and clusters containing a single hydroxyl moiety. Recent temperature programmed desorption experiments performed in UHV concluded that sulfur mustard and its less toxic mimics undergo molecular adsorption to amorphous silica. Hydrogen bonding can occur between surface silanol groups and either the sulfur or chlorine atom of the adsorbates, and the calculations indicate that the binding energies for the two hydrogen bond acceptors are similar. The adsorption of sulfur mustard and its mimics on silica also exhibits the presence of significant van der Waals interactions between alkyl of the adsorbates and the surface. These interactions, in combination with the formation of a hydrogen bond between a surface silanol group and the Cl or S atoms of the adsorbates, provide remarkably large binding energies. / Master of Science

Yes / The creation of multi-component crystals between chiral and achiral components has gained increased interest in recent years. In many cases the overall crystal structure is similar with the creation of a pseudo-inversion centre in the enantiopure case. This allows for the formation of solid solutions between the two extremes, which may have applications within chiral resolution. Utilising a combination of database mining, computational prediction and experimental screening, the frequency of formation for such materials has been investigated showing that for co-crystals this occurs more frequently than for salts, though there is a limited number of samples to draw structural conclusions. Computational modelling indicates the prediction of such systems can be challenging due to the similarities in energy of many crystal structures, so development of tools to design such systems is required to fully utilise these concepts. / The Deanship of Scientific Research at Princess Nourah bint Abdulrahman University through the Fast-track Research Funding Program.

The amino acid sequence of a protein encodes its folding, the reaction by which a peptide self-assembles into its native functional shape. A folded protein will then go on to carry on biological functions such as ligand binding, signaling, mechanical functions, or biomolecular catalysis. While much experimental work has been done to elucidate protein structure and conformational dynamics, Molecular Dynamics (MD) simulations have been necessary to provide atomic-level details of biomolecular dynamics. A challenge in using MD is the the large computational cost required to reach biologically relevant timescales when integration steps are typically limited to a few femtoseconds. To address this challenge, specialized hardware such as the ANTON supercomputer or distributed computing platforms like Folding@home can be used to collect milliseconds of aggregate trajectory data. From these datasets, kinetic network models called Markov state models (MSMs) can be constructed to infer long timescale dynamics from ensembles of short trajectories. These models can be analyzed in a human interpretable way and make physics-based connections to experimental observables. This dissertation describes how we have used MD simulations and MSMs to model protein folding reactions and protein-protein binding reactions to better understand mutation effects on our systems of interest. The first chapter of this dissertation describes MD simulations FOXO1 FKH domain folding, which we used MSMs to characterize at atomic resolution. To predict how mutations found in diffuse large B-cell lymphoma (DLBCL) cell lines effect protein stability, we developed an MSM-based hydrophobic free energy of transfer (HT) model to estimate mutation effects. Our HT model results agree better with experiment than other state-of-the-art computational methods. Chapter two describes how we have used approximately 43000 relative binding free energy calculations via the expanded ensemble (EE) method to perform in silico site saturation mutagenesis on miniprotein binders to the highly conserved influenza A H1 hemagglutinin stem region (HA2) de novo designed by the Baker [66]. These miniproteins were selected through an exhaustive design process with iterations of computational design, high throughput affinity screens, and site saturation mutagenesis. We compare our EE SSM method with inferred relative affinities from Chevalier et al.[66], as well as with the state-of-the-art Rosetta method Flex ddG. While Flex ddG predictions are more accurate on average, they are highly conservative. In contrast, EE predictions can better classify stabilizing and destabilizing mutations. We also use a Shannon entropy based method to identify residue positions that are more susceptible to mutation. This work suggests that simulation-based free energy methods can provide predictive information for in silico affinity maturation of designed miniproteins, with many feasible improvements to the efficiency and accuracy within reach. In the final chapter, we atttempt to model the complete binding reactions of the 6 miniproteins mentioned above. We used unbiased simulations to build standard msms and , in combination with biased simulations, multiensemble markov models (MEMMs) of binding for each wild type and affinity matured pair. The unbiased MSMs show that the affinity matured miniproteins prefer different bound states than the wild type miniproteins. Additionally, they provide physically realistic k_on_s and a macroscopic 3 state pathway through an encounter complex. We characterize each of those states and use an contact map based structural similarity index measure (SSIM) and residue-wise Kullback-Leibler divergence method to better understand the differences in the bound states between affinity matured and wild type construct. Interestingly, while our biased simulations do see unbinding transitions, in estimating the MEMM, they overweight the unbinding reaction and unbound state, leading to models that do not make physical sense. This demonstrates that more sensitive enhances sampling techniques may be necessary for building MEMMs. The final two chapters of this dissertation present new methodologies for computational protein design, making great strides towards a dynamic understanding of how proteins bind their targets and how mutations effect those reactions. / Chemistry

Hydrogen storage in lightweight hydrides continues to attract significant interest as the lack of a safe and efficient storage of hydrogen remains the major technological barrier to the widespread use of hydrogen as a fuel. The metal borohydrides Ca(BH₄)₂ and LiBH₄ form the subject of this thesis; three aspects of considerable academic interest were investigated by density functional theory (DFT) and molecular dynamics (MD) modelling. (i) High-pressure crystal structures of Ca(BH₄)₂ were predicted from a structural analogy between metal borohydrides and isoelectronic metal oxides. The structural stability of hydrogen storage materials under high pressure is an important aspect, as high-pressure polymorphs may provide structures with better hydrogen desorption properties. The isoelectronic analogue of Ca(BH₄)₂ is TiO₂, and structural equivalents of Ca(BH₄)₂ in the baddeleyite, columbite and cotunnite structures of TiO₂ were found to be stable at elevated pressure. Thermodynamic stability was evaluated by computing the Gibbs energy with respect to pressure and temperature. The pressure-dependence of the Helmholtz energy was determined to described a third-order Birch-Murnaghan equation of state, and the harmonic approximation was used to compute the vibrational energy levels and the Helmholtz energy as a function of temperature. The proposed structures are consistent with reports of two hitherto unidentified high-pressure phases observed experimentally. (ii) The disordered structure of the high-temperature phase of LiBH4 was studied by ab initio molecular dynamics (MD) at temperatures ranging from 200-535 K. It was found that the model emerging from analysis of the MD simulations properly accounts for dynamical disorder and fundamentally differs from the published experimental and theoretical structures. The validity of the MD model was corroborated by comparison of calculated pair distribution functions, vibrational spectra and a crystallographic model with neutron diffraction data; good agreement was found. A reassignment of the space group from P63mc to P63/mmc is proposed based on evidence for additional symmetry from MD simulations. (iii) Finally, a new MD-based method was developed to simulate fast ionic diffusion in LiBH₄. The colour diffusion algorithm - a nonequilibrium molecular dynamics method originally developed for the study of model fluids - was adapted and applied to self-diffusion of atoms in a solid for the first time. Calculated diffusion coefficients agreed very well with published measurements, and diffusion pathways that include collective particle effects were determined directly from the simulation results, thereby opening up a promising and efficient new method for the study of phenomena such as superionic conduction.

In this thesis, mathematical modelling is used to theoretically investigate the electrochemical behaviour of surfaces which can be broadly classified as being ‘electrochemically heterogeneous’. Simulated voltammetry is used in the exploration of a number of specific systems as listed below. The cyclic voltammetry of electrodes composed of two different electroactive materials that differ in terms of their electrochemical rate constants towards any given redox couple. The effect of the distribution of the two materials was investigated and the occurrence of split peak cyclic voltammetry where two peaks are observed in the forward sweep, was studied. The technique was specifically applied to the modelling of highly-ordered pyrolytic graphite (HOPG). The steady-state voltammetry of a conducting spherical particle resting on an insulating supporting surface. An algebraic expression that completely describes the voltammetric waveform in the limit of irreversible kinetics was developed. The cyclic voltammetry of the EC′ (catalytic) mechanism at a regularly distributed array of hemispherical particles on an insulating supporting surface. Particular attention was paid to the ‘split-wave’ phenomenon, where two peaks are observed in the forward scan of a cyclic voltammogram and the conditions under which these peaks are resolvable were elucidated. The linear sweep voltammetry of micro- and nano-particle modified electrodes and other electrodes of partially covered and non-planar geometry. It was demonstrated that the apparent electrochemical rate constant of the reaction and thus the peak position of the voltammetry is dependent only on the relative electroactive surface area of the particles on the surface and not upon their shape or distribution. This has wide reaching implications as it can be used to explain some instances of a purported nano-catalytic effect without appeal to altered properties at the nanoscale. The linear sweep voltammetry of the interior of a partially electroactive cylindrical pore. Four limiting cases were observed and fully characterised. The linear sweep voltammetry of porous surfaces. It was established that if the pores are less than a certain threshold depth, then a porous surface will also display an apparent catalytic effect that is dependent on the relative electroactive surface area (including the area in the interior of the pores).

Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: A theoretical and experimental study was performed in order to identify factors that influence the propensity of compounds containing anionic functional groups that are commonly found on pharmaceutical drug compounds to form hydrates. A Cambridge Structural Database (CSD) survey was initially undertaken to determine the propensity of different pharmaceutically acceptable anions to form hydrates. The results showed that hydrate formation will take place more regularly when the polarity of the functional group increases. Furthermore, if the charge distribution is very concentrated over the polar groups, hydrate formation will occur more readily. This observation was further investigated by performing a series of potential energy surface (PES) scans for the hydrogen bond (H-bond) in the structure of N-(aminoiminomethyl)-N-methylglycine monohydrate (creatine monohydrate) with various Density Functional Theory (DFT) and Wave Functional Theory (WFT) methods. WFT is often also referred to as ab initio, which refers to the construction of the wave function from first principles when this theory is applied. The scans revealed that several strong and directional H-bonds with different geometrical parameters between the carboxylate group and the water molecule are possible, which suggests that the H-bond plays an important role in driving the formation of pharmaceutical hydrates. A total of 44 hydrate structures were identified that have pharmaceutically acceptable functional groups. Optimisations in the gas phase and in an implicit solvent polarisable continuum solvent model with a variety of solvents showed that there is a significant dependence of the H-bond interaction energy on the anionic group as well as the steric density of surrounding substituents. It was found that the M06-2X method utilising the 6-311++G(d,p) basis set outperformed the other methods that were tested when compared to optimisations performed with the benchmark MP2/aug-cc-pVTZ level of theory. Furthermore, the strength of the H-bond was measured in the 44 experimentally determined structures by using a total of five generalized gradient approximation (GGA) methods, of which two methods contained the DFT-D3 correction. The results of these DFT methods were subsequently compared to results obtained at the benchmark MP2/aug-cc-pVTZ level of theory. The M06-2X method was identified as the most economical method to calculate H-bond energies. It was also found that the H-bond interaction energy shows a substantial dependence on the electrostatic environment. This was observed by a significant decrease in H-bond strength as the relative permittivity of the solvent increases. The effect of steric density on the H-bond interaction energy was investigated by performing hydrogen bond propensity calculations. These values were then compared to the interaction energies of each structure and the results showed that the presence of large bulky substituents can lead to an increase in bond energy by forcing the anionic functional group closer to the water molecule. Contrastingly, the bulky group can also push the anionic group away from the water molecule and result in a decrease in bond energy. Approximate values for the amount of stabilisation offered to the H-bonding system by the surrounding crystalline environment were calculated by optimising the H-bond geometrical parameters of selected compounds with a combination of the M06-2X and MP2 methods utilising the 6-311++G(d,p) basis set. The H-bond interaction energies were then calculated at the M06-2X/6-311++G(d,p) level of theory and compared to the H-bond interaction energies in geometries that have been fully optimised. After these energies were compared and the crystal packing of each structure was investigated, it was found that the packing of some structures within the crystalline environment limits the number of H-bonds that can be formed between the water and the compound of interest. Full optimisation calculations result in structures with cooperative stabilisation, such that more than one H-bond is found between the two fragments. The effect of substituents on H-bond interaction energy was investigated by the addition of six electron-donating and electron-withdrawing groups on four aromatic compounds with different anionic functional groups, namely carboxylate, nitrogen dioxide, sulfonate and phosphonate. It should also be mentioned that the nitrogen dioxide is not an anionic functional group, but it was included as it is a neutral radical that often forms hydrogen bonds. A total of 80 structures were optimised with a combination of the M06-2X and MP2 methods utilising the 6-311++G(d,p) basis set. This was followed by counterpoise corrected single point calculations at the M06-2X/6-311++G(d,p) level of theory. The results showed that the H-bond interaction energy bears no relationship to the inductive strength or the inductive ability of the substituents, but rather the ability of these substituents to rotate the anionic functional group and allow cooperative stabilisation of the H-bond. Furthermore, AIM analysis was performed for the substituted H-bonded aromatic structure. The results showed that electron-donating groups that are placed at the para position yield stronger H-bonds, which is once again accompanied by cooperative stabilisation. Electron-withdrawing groups with sufficient inductive effects can result in a weaker H-bond when placed at the meta position. The effect of water activity (aw) on the hydrate crystal formation was investigated experimentally by performing a series of crystallisations in various solvent mixtures. These mixtures consisted of water mixed with acetone, ethanol and ethyl acetate. A total of three organic acids were used in crystal formation, namely pyridine-4-carboxylic acid (isonicotinic acid), N-amino-iminomethyl-N-methylglycine (creatine) and benzene-1,3,5-tricarboxylic acid. It was found that water activity affects the formation of the hydrate as well as the anhydrous product. Additionally, nucleation and super saturation plays a large role in crystal formation and can serve as an effective technique when the formation of crystals of an appropriate shape and size is required for further analysis. / AFRIKAANSE OPSOMMING: 'n Teoretiese en eksperimentele studie was uitgevoer om faktore te identifiseer wat die geneigdheid van verbindings met anioniese funksionele groepe wat algemeen gevind word op farmaseutiese dwelm verbindings om die hidraat produk te vorm, affekteer. 'n Opname van strukture in die Cambridge Strukturele Databasis (CSD) is onderneem om die geneigdheid van verskillende farmaseutiese aanvaarbare anione om hidrate te vorm te bepaal. Die resultate het getoon dat hidraatvorming meer gereeld plaasvind indien die polariteit van die funksionele groepe toeneem. Verder is daar ook opgemerk dat 'n gekonsentreerde ladingsverspreiding op die polêre groepe ook tot 'n toename in hidraat vorming sal lei. Hierdie waarneming is verder ondersoek deur 'n reeks potensiële energie oppervlak (PES) skanderings van die waterstof binding (H-binding) vir die struktuur van N-amino-iminometiel-N-metielglisien monohidraat (kreatien monohidraat) met verskeie Digtheids-Funksionele Teorie (DFT) en Golffunksie Teorie (WFT) metodes uit te voer. Die skanderings het getoon dat verskeie sterk, gerigte H-bindings met verskillende geometriese parameters tussen die karboksilaatgroep en die watermolekule kan vorm. Hierdie bevindinge lê klem op die belangrike rol wat H-bindings in die vorming van farmaseutiese koolhidrate speel. 'n Totaal van 44 hidraat strukture met farmaseutiese aanvaarbare funksionele groepe was geïdentifiseer. Optimaliserings is in die gas fase asook in 'n implisiete kontinuum polariseerbare oplosmiddel model met 'n verskeidenheid oplosmiddels uitgevoer. Die resultate het 'n beduidende afhanklikheid van die H-binding interaksie-energie op die anioniese groep asook die steriese afkskerming van omringende groepe getoon. Daar is bepaal dat die M06-2X metode wat saam met die 6-311++G(d,p) basisstel die mees akkuraatste resultate gelewer het in vergelyking met die ander DFT metodes asook die MP2/aug-cc-pVTZ maatstaf. Die H-binding se sterkte is vir hierdie strukture bereken deur vyf GGA metodes te gebruik, waarvan twee metodes van die DFT-D3 korreksie gebruik maak. Die resultate van die berekeninge met hierdie DFT metodes is daarna vergelyk met resultate verkry met die MP2/aug-cc-pVTZ maatstaf. Daar is gevolglik bepaal dat die M06-2X metode die mees ekonomiese metode is om H-binding energië te bereken. Die H-binding interaksie energie toon 'n aansienlike afhanklikheid op die diëlektriese konstante van die oplosmiddel aan. Hierdie waarneming is op grond van 'n beduidende afname in die H-binding interaksie-energie indien die relatiewe permittiwiteit van die oplosmiddel verhoog word gemaak. Die effek van steriese digtheid is ondersoek deur waterstofbindinggeneigdheid waardes te bereken. Hierdie waardes is met die interaksie-energië van elke struktuur vergelyk. Die resultate dui daarop dat steries digte groepe tot 'n toename in interaksie energie kan lei wanneer die anioniese funksionele groep nader aan die water molekule gestoot word. Verder is dit ook moontlik vir hierdie steries digte groepe om die anioniese groep weg van die water molekule te stoot en gevolglik 'n afname in interaksie energie te veroorsaak. Benaderde waardes vir die hoeveelheid stabilisering wat die omringende kristallyne omgewing aan die H-binding bied is bereken deur die H-binding geometriese parameters van geselekteerde verbindings met die M06-2X en MP2 metodes en die 6-311++G (d,p) basisstel te optimaliseer. Die H-binding interaksie-energië is gevolglik by die M06-2X/6-311++G(d,p) vlak van teorie bereken en met die H-binding energië in strukture wat volledige optimaliseer is vergelyk. Nadat hierdie waardes vergelyk is, is daar gevind dat die pakking van strukture in the kristallyne omgewing verhoed dat sekere H-bindings tussen die water molekule en die verbinding van belang kan vorm. Strukture wat volledig optimaliseer is, lei tot strukture wat in staat is om koöperatiewe stabilisering te ondergaan. Koöperatiewe stabilisering word gekenmerk deur die vorming van meer as een H-binding tussen twee fragmente. Die effek van substituente op die H-binding interaksie energie is ondersoek deur die bevoeging van ses elektrondonor- en elektronontrekkendegroepe op vier aromatiese verbindings, naamlike die karboksilaatgroep , stikstofdioksied , sulfonaat en fosfonaat. Dit moet ook genoem word dat stikstofdioksied nie 'n anioniese funksionele groep is nie, maar dit was wel ingesluit omdat dit ‘n neutrale radikaal groep is wat dikwels waterstofbindings vorm. 'n Totaal van 80 strukture optimiserings was uitgevoer met 'n kombinasie van die M06-2X en MP2 metodes wat gebruik maak van die 6-311++G(d,p) basisstel. Dit is gevolg deur interaksie-energie berekeninge op die M06-2X/6-311++G(d,p) vlak van teorie. Die resultate het getoon dat daar geen verband tussen die induktiewe vermoë van die substituente en die sterkte van die H-binding is nie, dit is eerder die vermoë van hierdie substituente om die anioniese funksionele groep te laat roteer wat toelaat dat koöperatiewe stabilisering van die H-binding kan geskied. Die AIM analise is op 'n gesubstitueerde H-binding struktuur toegepas. Die resultate het getoon dat elektrondonorgroepe wat by die para posisie geplaas word tot sterker H-bindings sal lei, wat weereens met koöperatiewe stabilisering vergesel word. Elektrononttrekkendegroepe met sterk induktiewe effekte kan tot 'n swakker H-binding lei indien hulle by die meta posisie geplaas word. Die effek van water aktiwiteit (𝑎w) op hidraatkristalvorming is deur die uitvoering van 'n reeks kristallisasies in verskeie oplosmiddelmengsels ondersoek. Hierdie oplosmiddel mengsels bestaan uit water met asetoon, etanol of etielasetaat gemeng. Kristallisasies is vir drie organiese sure, naamlik piridien-4-karboksielsuur, N-amino-iminometiel-N-metielglisien monohidraat en 1,3,5-benseen tri-karboksielsuur uitgevoer. Daar is gevind dat water aktiwiteit 'n invloed op die vorming van die hidraat en watervrye produkte kan hê. Daarbenewens, speel water aktiwiteit 'n belangrike rol in die nukleasie fase van kristalvorming en kan as 'n effektiewe tegniek dien om kristalle van 'n toepaslike vorm en grootte vir verdere analise te verkry.

This thesis presents electronic structure calculations on problems related to the bonding in inorganic coordination compounds and clusters. A wide range of molecules with the ability to exist in different structural forms or electronic states has been selected and density functional theory is systematically applied in order to gain detailed insight into their characteristics and reactivity at the electronic level. First, we address the question of redox non-innocent behaviour of bipyridine in a series of 1st row transition metal complexes. Complexes of the type [M(2,2'-bipyridine)(mes)₂]⁰ (M = Cr, Mn, Fe, Co, Ni; mes = 2,4,6-Me₃C6H₂) and their one-electron reduced forms have been explored. The results clearly show that the anions are best described as complexes of the monoanionic bipyridine radical (S_bpy = 1/2), giving a rationale for the observed structural changes within the ligand. Likewise, we have identified dianionic bipyridine in both the complexes [Zn2(4,4'-bpy)(mes)₄]²⁻ and [Fe(2,2'-bpy)₂]²⁻. In no case have we found evidence for significant metal-to-ligand backbonding. The subject of redox-noninnocence is further revisited in a comparative study of the two complexes [M(o-Clpap)₃] (M = Cr, Mo; o-Clpap = 2-[(2-chloro-phenyl)azo]-pyridine), and their associated electron transfer series. The results indicate that all electron transfer processes are primarily ligand-based, although in the case of the Mo analogue these are coupled to substantial electron density changes at the metal. The ability of pap to form radical anions finds a contrasting case in the di- nuclear Rh complex [Rh₂(μ-p-Clpap)₂ (cod)Cl₂], where the two ligand bridges act as acceptors of strong dπ∗ backbonding from a formally Rh^–I centre. We then direct our attention to the endohedral Zintl clusters [Fe@Ge₁₀]³⁻ and [Mn@Pb₁₂]³⁻, which reveal peculiar topologies. We have probed the electronic factors that influence their geometric preferences, and propose a model based on the shift of electron density from the endo- hedral metal to the cage to account for the observed geometries. Subsequently, we reassess the electronic structure of the xenophilic clusters Mn₂(thf)₄(Fe(CO)₄)₂ and [Mn(Mn(thf)₂)₃(Mn(CO)₄)₃]^–. We conclude that these are best viewed as exchange coupled Mn^II centres bridged by closed- shell carbonylate fragments. In the closing chapter the reduction of NO₂^– to NO by the complex [Cu(tct)(NO₂)]⁺ (tct = cis,cis-1,3,5-tris(cinnamylideneamino)cyclohexane) is studied, a process that mimics the enzyme-catalysed reaction. Two viable pathways for the reaction have been traced and key inter-mediates identified. Both direct release of NO or via decomposition of a Cu-NO complex are kinetically and thermodynamically feasible.

Radiation chemistry is concerned with understanding the chemical kinetics following the application of ionising radiation. There are two main methods for modelling recom- bination and spin dynamics in radiation chemical systems: The Monte Carlo random flights algorithm, in which the trajectories of the diffusing species are followed ex- plicitly and the Independent Reaction Times (IRT) algorithm, where reaction times are sampled from appropriate marginal distribution functions. This thesis reports develop- ments to both methods, and applies them to better understand experimental findings, particularly spin relaxation effects. Chapter 4 introduces current simulation techniques and presents newly developed algorithms and simulation programs (namely Hybrid and Slice) for modelling spatially dependent spin effects. A new analytical approximation for accurately treating ion-pair recombination in low-permittivity solvents in also presented in this chapter. Chapter 5 explores the photodissociation of H₂O₂, where there is some controversy in the literature on the spin state of the precursor. This chapter explores the possibility of reproducing the observed spin polarisation phase using the Radical Pair Mechanism. Chapter 6 presents two new algorithms for treating reactive products in the IRT framework. These have been tested for two chemical systems: (i) photodissociation of H₂O₂ where the ·OH are scavengeable; (ii) water photolysis which produces H⁺, ·OH and e⁻__aq. In the latter case a careful handling of three body correlations is required. Chapter 7 presents simulation results which suggest a strong correlation between scavenging and ion recombination in low permittivity solvents. A path decomposition method has been devised that allows IRT simulations to be corrected for this effect. Chapter 8 presents evidence for spin-entanglement and cross-recombination to act as an extra source of relaxation for ion-recombination in low permittivity solvents. It is hypothesised this effect contributes to the anomalous relaxation times observed for certain cyclic hydrocarbons. Chapter 9 presents an extension of the IRT simulation method to micelles. The kinetics are shown to be accurately described using the mean reaction time and the exponential approximation.

Reductive functionalization of methyl ligands by 3d metal catalysts and two possible side reactions has been studied. Selective oxidation of methane, which is the primary component of natural gas, to methanol (a more easily transportable liquid) using organometallic catalysis, has become more important due to the abundance of domestic natural gas. In this regard, reductive functionalization (RF) of methyl ligands in [M(diimine)2(CH3)(Cl)] (M: VII (d3) through CuII (d9)) complexes, has been studied computationally using density functional techniques. A SN2 mechanism for the nucleophilic attack of hydroxide on the metal-methyl bond, resulting in the formation of methanol, was studied. Similar highly exergonic pathways with very low energy SN2 barriers were observed for the proposed RF mechanism for all complexes studied. To modulate RF pathways closer to thermoneutral for catalytic purposes, a future challenge, paradoxically, requires finding a way to strengthen the metal-methyl bond. Furthermore, DFT calculations suggest that for 3d metals, ligand properties will be of greater importance than metal identity in isolating suitable catalysts for alkane hydroxylation in which reductive functionalization is used to form the C—O bond. Two possible competitive reactions for RF of metal-methyl complexes were studied to understand the factors that lower the selectivity of C—O bond forming reactions. One of them was deprotonation of the methyl group, which leads to formation of a methylene complex and water. The other side reaction was metal-methyl bond dissociation, which was assessed by calculating the bond dissociation free energies of M3d—CH3 bonds. Deprotonation was found to be competitive kinetically for most of the 1st row transition metal-methyl complexes (except for CrII, MnII and CuII), but less favorable thermodynamically as compared to reductive functionalization for all of the studied 1st row transition metal complexes. Metal-carbon bond dissociation was found to be less favorable than the RF reactions for most 3d transition metal complexes studied. The first dinitrogen dicopper (I) complex has been characterized using computational and experimental methods. Low temperature reaction of the tris(pyrazolyl)borate copper(II) hydroxide {iPr2TpCu}2(µ-OH)2 with triphenylsilane under a dinitrogen atmosphere gives the µ -N2 complex, {iPr2TpCu}2(µ -N2). X-ray crystallography reveals an only slightly activated N2 ligand (N-N: 1.111(6) Å) that bridges between two iPr2TpCuI fragments. While DFT studies of mono- and dinuclear copper dinitrogen complexes suggest a weak µ-backbonding between the d10 CuI centers and the N2 ligand, they reveal a degree of cooperativity in the dinuclear Cu-N2-Cu interaction.

Submitted by Angela Maria de Oliveira (amolivei@uepg.br) on 2017-10-25T13:39:14Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Januario Kordiak.pdf: 1907122 bytes, checksum: a65c6272637170bbfa2b17ce2175c777 (MD5) / Made available in DSpace on 2017-10-25T13:39:14Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Januario Kordiak.pdf: 1907122 bytes, checksum: a65c6272637170bbfa2b17ce2175c777 (MD5) Previous issue date: 2017-08-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O ensino de ligações químicas é uma das fases mais importantes no processo de ensino-aprendizagem da Química. Todavia, existe uma grande necessidade de introduzir aos educandos do Ensino Médio a conexão entre a ligação química e a sua natureza quântica. Para alcançar esse objetivo utilizou-se o método de Hückel, um método simples desenvolvido em pesquisas em Química Teórica, antes do início da química computacional. Como metodologia avaliativa o método foi contraposto com as concepções prévias e posteriores dos educandos e, separadamente, com as concepções de educandos ensinados pelo método tradicional, ou seja, quadro, giz e livro. Foi observado que o uso de conceitos atuais, principalmente com o uso do computador, melhorou as argumentações por parte dos educandos ao definirem as ligações químicas, indicando que as aplicações da química quântica aliada a programas computacionais contribuem para resultados expressivos no processo de ensino-aprendizagem da Química. / The nature of chemical bond is essential to understand chemistry concepts, mainly, at initial process in high school. From quantum mechanics concepts was possible describe the chemical bond basing in electronic density, which around the nucleus between two atoms. Hückel method was the first method presented to solve the Schrodinger Equation in approximate level and it reached good qualitative results for aromatic compounds indicating the feasibility of the computational chemistry. However, the Hückel method based on matrix is in accordance with molecular geometry proposed; then, the resolution of such method is possible for students in high level. From this idea, we presented the Hückel method as fundamental to understand the chemical bond for students in the first and second years of high school and we applied questions to evaluate the chemical bond knowledge before/after the Hückel method. We observed that there was increase and reinforce of the chemical bond concept for students.