Knowledge of the dissociation constants of the ionizable protons of weak acids in aqueous media is of fundamental importance in many areas of chemistry and biochemistry. The pKa value, or equilibrium dissociation constant, of a molecule determines the relative concentration of its protonated and deprotonated forms at a specified pH and is therefore an important descriptor of its chemical reactivity. Considerable efforts have been devoted to the determination of pKa values by deferent experimental techniques. Although in most cases the determination of pKa values from experimental is straightforward, there are situations where interpretation is difficult and the results ambiguous. It is, therefore, not surprising that the capability to provide accurate estimates of the pKa value has been a central goal in theoretical chemistry and there has been a large effort in developing methodologies for predicting pKa values for a variety of chemical systems by differing quantum chemical techniques. A prediction accuracy within 0.5 pKa units of experiment is the desirable level of accuracy. This is a non-trivial exercise, for an error of 1 kcal/mol in estimates of the free energy value would result in an error of 0.74 pKa units. In this thesis ab initio Car-Parrinello molecular dynamics (CPMD) has been used for investigating the Brϕnsted acid-base chemistry of weak acids in aqueous solution. A key issue in any dissociation event is how the solvating water molecules arrange themselves spatially and dynamically around the neutral and dissociated acid molecule. Ab initio methods have the advantage that all solvent water molecules can, in principle, be con- sidered explicitly. One of the factors that has inhibited the widespread use of ab initio MD methods to study the dissociation reaction is that dissociation of weak acids are rare events that require extremely long simulation times before one is observed. The metady- namics formalism provides a solution to this conundrum by preventing the system from revisiting regions of configuration space where it has been in the past. The formalism allows the system to escape the free-energy minima by biasing the dynamics with a history dependent potential (or force) that acts on select degrees of freedom, referred to as collective variables. The bias potentials, modeled by repulsive inverted Gaussians that are dropped during propagation, drive the system out of any free-energy minima and allow it to explore the configuration space by a relatively quick and efficient sampling. The the- sis deals with a detailed investigation of the Brϕnsted acid-base chemistry of weak acids in aqueous solutions by the CPMD-metadynamics procedure. In Chapter 1, current approaches for the theoretical estimation of pKa values are summarized while in Chapter 2 the simulation methodology and the metadynamics sampling techniques used in thisstudy are described. The potential of the CPMD-metadynamics procedure to provide estimates of the acid dissociation constant (pKa) is explored in Chapter 3, using acetic acid as a test sys- tem. Using the bond-distance dependent coordination number of protons bound to the dissociating carboxylic groups as the collective variable, the free-energy profile for the dissociation reaction of acetic acid in water was computed. Convergence of the free-energy profiles and barriers for the simulations parameters is demonstrated. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid and the deference in their values provides the estimate for pKa. The estimated value of pKa for acetic acid from the simulations, 4.80, is in good agreement with the experiment at value of 4.76. It is shown that the good agreement with experiment is a consequence of the cancellation of errors, as the pKa values are computed as the difference in the free energy values at the minima corresponding to the neutral and dissociated state. The chapter further explores the critical factors required for obtaining accurate estimates of the pKa values by the CPMD-metadynamics procedure. It is shown that having water molecules sufficient to complete three hydration shells as well as maintaining water density in the simulation cell as close to unity is important. In Chapter 4, the CPMD-metadynamics procedure described in Chapter-3 has been used to investigate the dissociation of a series of weak organic acids in aqueous solutions. The acids studied were chosen to highlight some of the major factors that influence the dissociation constant. These include the influence of the inductive effect, the stabilization of the dissociated anion by H-bonding as well as the presence of multiple ionizable groups. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cid and trans-butenedioic, the isomers of hydroxybenzoic acid and phthalic acids and its isomers. It was found that in each of these examples the CPMD-metadynamics procedure correctly estimates the pKa values, indicating that the formulism is capable of capturing these influences and equally importantly indicating that the cancellation of errors is indeed universal. Further, it is shown that the procedure can provide accurate estimates of the successive pKa values of polypro tic acids as well as the subtle deference in their values for deterrent isomers of the acid molecule. Changes in protonation-deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. It is shown that CPMD simulations in conjunction with metadynamics calculations of the free energy profile of the protonation- deprotonation reaction can provide estimates of the multiple pKa values of the 20 canonical α-amino acids in aqueous solutions in good agreement with experiment (Chapter 5). The distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic and the amine groups is used as the collective variable to explore the free energy profiles of the Brϕnsted acid-base chemistry of amino acids in aqueous solutions. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule were included explicitly in the computation procedure. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error with respect to experimental results, of 0.2 pKa units. The tripeptide Glutathione (GSH) is one of the most abundant peptides and the major repository for non-protein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thioldisulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influences the redox couple and hence the pKa value of the cysteine residue of GSH is critical to its functioning. In Chapter 6, it has been reported that ab initio Car-Parrinello Molecular Dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. It is shown that the free-energy landscape for the protonation - deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared to the isolated cysteine amino acid. The dissociation constants of weak acids are commonly determined from pH-titration curves. For simple acids the determination of the pKa from the titration curves using the Henderson-Hasselbalch equation is relatively straightforward. There are situations, however, especially in polypro tic acids with closely spaced dissociation constants, where titration curves do not exhibit clear inflexion and equivalence stages and consequently the estimation of multiple pKa values from a single titration curve is no longer straightfor- ward resulting in uncertainties in the determined pKa values. In Chapter 7, the multiple dissociation constant of the hexapeptide glutathione disulfide (GSSG) with six ionizable groups and six associated dissociation constants has been investigated. The six pKa values of GSSG were estimated using the CPMD-metadynamics procedure from the free-energy profiles for each dissociation reaction computed using the appropriate collective variable. The six pKa values of GSSG were estimated and the theoretical pH-titration curve was then compared with the experimentally measured pH-titration curve and found to be in excellent agreement. The object of the exercise was to establish whether interpretation of pH-titration curves of complex molecules with multiple ionizable groups could be facilitated using results of ab initio molecular dynamics simulations.

D. Tech. (Department of Chemistry, Faculty of Applied and Computer Sciences), Vaal University of Technology / A novel low-cost ternary Mn-Fe-Cu (MFC) metal oxide nanocomposite adsorbent was fabricated using facile co-precipitation method and successfully applied for the sequestration of Cr(VI) and As(III) from simulated aqueous efflent. The central composite design (CCD) of the response surface methodology (RSM) optimization technique determined the optimal working parameters for the preparation of the ternary MFC metal oxide nanocomposite. The spectroscopic microstructural analysis of the ternary MFC metal oxide nanocomposite was performed using fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) spectroscopy. The spectroscopic analyses revealed a rough surface with hydroxyl groups and the presence of mixed metal oxides in different valence states. The BET surface area, pore volume and pore size of the nanostructured MFC ternary metal oxide composite were found to be 77.2427 m2/g, 0.2409 cm3/g and 14.7560 nm, respectively. The pH drift method determined that the pHpzc of the adsorbent was 6.75. The batch technique was employed to investigate the adsorption dynamics (effects of ionic strength, co-existing anions, adsorbent regeneration and reuse) and optimum parameters (solution pH, adsorbent dosage concentration, desorption) of Cr(VI) and As(III) adsorption onto the MFC nanocomposite. The fitting of non-linear kinetic (pseudo-first-order, pseudo-second-order and Elovich), diffusion (intraparticle and Boyd) and isotherm (Langmuir, Freundlich and Dubinin-Radushkevich) models to the Cr(VI) and As(III) experimental adsorption data gave an insight into the adsorption mechanisms. The Langmuir adsorption capacities, qm (mg/g), were 168.71 at solution pH 3 and 35.07 at solution pH 9 for Cr(VI) and As(III) adsorption, respectively. The adsorption of Cr(VI) onto the ternary MFC metal oxide nanocomposite was physical and formed outer-sphere surface complexes through electrostatic interactions, while the removal of As(III) was specific due to inner-sphere surface complexation and ligand/ion exchange reactions. The results from XPS and FTIR analysis after the adsorption of Cr(VI) and As(III) showed that the surface hydroxyl groups on the MFC nanocomposite interacted with the Cr(VI) and As(III) species during the formation of the surface complexes. To facilitate ease of adsorbent removal from the treated simulated aqueous effluent, the ternary MFC metal oxide system was co-precipitated onto biochar support.

Monte-Carlo calculations are used to simulate the stochastic effects of fast neutron-induced chemical changes in the radiolysis of the ferrous sulfate (Fricke) dosimeter. To study the dependence of the yield of ferric ions, G(Fe[superscript 3+]), on fast neutron energy, we have simulated, at 25 [degree centigrade], the oxidation of ferrous ions in aerated aqueous 0.4 M H[subscript 2]SO[subscript 4] (pH 0.46) solutions when subjected to ~0.5-10 MeV incident neutrons, as a function of time up to ~50 s. The radiation effects due to fast neutrons are estimated on the basis of track segment (or"escape") yields calculated for the first four recoil protons with appropriate weighting according to the energy deposited by each of these protons. For example, a 0.8-MeV neutron generates recoil protons of 0.505, 0.186, 0.069, and 0.025 MeV, with linear energy transfer (LET) values of ~41, 69, 82, and 62 keV/[micro]m, respectively. In doing so, we consider that further recoils make only a negligible contribution to radiation processes. Our results show that the radiolysis of dilute aqueous solutions by fast neutrons produces smaller radical yields and larger molecular yields (relative to the corresponding yields for the radiolysis of water by [superscript 60]Co [gamma]-rays or fast electrons) due to the high LET associated to fast neutrons. The effect of recoil ions of oxygen, which is also taken into account in the calculations, is shown to decrease G(Fe[superscript 3+]) by about 10%. Our calculated values of G(Fe[superscript 3+]) are found to increase slightly with increasing neutron energy over the energy range covered in this study, in good agreement with available experimental data. We have also simulated the effect of temperature on the G(Fe[superscript 3+]) values in the fast neutron radiolysis of the Fricke dosimeter from 25 to 300 [degree centigrade]. Our results show an increase of G(Fe[superscript 3+]) with increasing temperature, which is readily explained by an increase in the yields of free radicals and a decrease in those of molecular products. For 0.8-MeV incident neutrons (the only case for which experimental data are available in the literature), there is a ~23% increase in G(Fe[superscript 3+]) on going from 25 to 300 [degree centigrade]. Although these results are in reasonable agreement with experiment, more experimental data, in particular for different incident neutron energies, would be needed to test more rigorously our Fe[superscript 3+] ion yield results at elevated temperatures.