No description available.

Thesis (Ph. D.)--University of Texas at Austin, 1998. / Vita. Includes bibliographical references (leaves 267-277). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--Earth and Atmospheric Sciences, Georgia Institute of Technology, 2006. / Michael Bergin, Committee Member ; E. Michael Perdue, Committee Chair ; Ching-Hua Huang, Committee Member ; Ellery Ingall, Committee Member ; Martial Taillefert, Committee Member. Vita. Includes bibliographical references.

Thesis (Ph. D.)--Miami University, Dept. of Chemistry and Biochemistry, 2004. / Title from second page of PDF document. Includes bibliographical references.

No description available.

The literature review shows that student alternative conceptions or misconceptions are important for teaching and learning. Causes of such student difficulties may include the counter-intuitive nature of some chemistry concepts or to instruction itself. However, over 30 years research into student conceptual difficulties has had little impact on teaching and learning chemistry. In this study, a critical analysis and synthesis of published research into student conceptions in acid-base chemistry was carried out in the naturalist nomothetic paradigm using a constructivist framework. Historical models which were included were an operational macroscopic model and the theoretical Arrhenius and Brønsted models. Firstly, a comprehensive search strategy with defined inclusion/exclusion criteria identified 42 suitable reports which were mostly peer-reviewed. The identified research was not limited to Anglophone countries although Africa and South America were underrepresented and research among secondary students predominated. Then a critique of the research showed it was of variable quality and often poorly reported. An outcome was a set of guidelines for research into student conceptions. The variable quality and reporting of research then also necessitated a four-level framework to reflect the stability of descriptions of student difficulties. A new method for synthesis of descriptions of student conceptual difficulties was developed which entailed mapping qualitative data on the difficulties, which had been extracted from research publications, to propositional knowledge statements derived in this study. This was an iterative process which simultaneously honed descriptions of difficulties and illuminated propositional knowledge implicated in them. The second major outcome was synthesized descriptions of 10 student difficulties with acid-base species, 26 difficulties with acid-base properties and 17 difficulties concerning terminology and symbolism particular to acid-base chemistry. Some conceptions were also found to have been mis-reported as ‘misconceptions’. The difficulties could be broadly due to student conceptions concerning acid-base models, or students not relating empirical observations to theoretical models or their poor understanding of underlying chemical principles. Some difficulties were found to have been over-researched, while further work was needed to clarify the nature some difficulties with conceptions of bases, acid-base reactions, and symbolism used in acid-base chemistry. The third major outcome from the synthesis was 218 propositional knowledge statements which were shown to be suitable for teaching high-school students, avoided hybrid historical models and were acceptable to expert chemists. These propositional statements were integrated as a set of 11 concept maps. The maps showed the hierarchy and interconnectedness of concepts as well as the propositional links which had been implicated in the difficulties. Furthermore the concept maps indicated critical concepts where teaching in each topic should focus as well as cross-linked concepts that can be used to integrate different aspects of the topic. Accordingly they contribute to PCK in the acidbase topic as they represent the fine-grained yet well integrated conceptual knowledge characteristic of a teacher with highly developed PCK. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2009.

Acid-base equilibria in organic particulate matter (PM) are poorly understood, but have important implications for air quality and public health. First, acid-base reactions in organic particulate matter affect the gas/particle partitioning of organic compounds in the atmosphere, and these processes are not currently represented in atmospheric and climate change models. Second, the acid-base balance of tobacco smoke affects the amount of nicotine absorbed by the smoker, and a greater understanding of this balance would help to relate cigarette smoke composition to the addictive properties of cigarettes. This work presents data related to both air quality and tobacco smoke modeling. The gas/particle partitioning behavior of organic acids and bases is highly dependent on acid-base equilibria and speciation between neutral and ionic forms, because ionic compounds do not volatilize. Descriptions of acid dissociation behavior in atmospheric PM have, to date, focused primarily on phases in which the solvent is water; however, atmospheric PM may include up to 90% organic matter. Data is presented here describing the acid dissociation behavior of organic acids and protonated amines in organic/aqueous mixtures (chosen to approximate the characteristics of organic PM) with varying levels of water content. In such mixtures, the preferential solvation of ions and neutral molecules (by the aqueous portion or the organic portion, respectively) affects the acid-base equilibria of the solutes. It is demonstrated that neutralization reactions between acids and bases that create ions are likely to have non-negligible effects on gas/particle partitioning under certain atmospheric conditions. Thus, including acid-base reactions in organic gas/particle partitioning models could result in a greater proportion of acidic and basic compounds partitioning to the particulate phase. In addition, the acid dissociation constants (pKa values) of atmospherically-relevant acids and bases vary with water content. Specifically, as water content increases, the pKa values of organic acids decrease dramatically, while the pKa values of protonated amines changes only slightly. This situation can result in drastically different speciations and partitioning behavior depending on water content. This second part of this work reports some of the data needed to develop an acid-base balance for tobacco smoke PM using electroneutrality as a governing principle. Five brands of cigarettes were sampled and the smoke PM extracted. Cations (sodium, potassium, and ammonia) and anions (organic acids, nitrate, nitrite, and chloride) were measured using ion chromatography. Ammonia and organic acids were also re-measured after the acidification of the sample in order to determine whether "bound" forms of these compounds exist in cigarette PM. Weak acids were determined by acid-base titration to determine whether or not all of the weak acids (including organic acids) had been accounted for by the ion chromatography. Weak bases were also determined by acid-base titration, and the majority of weak base is expected to be accounted for by total nicotine (to be measured in a separate analysis). In terms of total acidic species and total basic species, two of the five cigarette brands measured were relatively basic, and three were relatively acidic. Between 50% and 89% of the titrated acids were accounted for by the anionic species measured in ion chromatography. Based on samples tested after sample acidification, about half of the potential ammonia in tobacco smoke PM exists in "bound" form. The speciation of weak acids and bases in tobacco smoke PM cannot be determined from this data alone, because the equilibrium constants of acid-base reactions are not understood in complex organic media. The data presented here, when combined with data from free-base and total nicotine analyses, represent a first step toward a predictive model of acid-base behavior in tobacco smoke PM.

The Suwannee River natural organic matter (SRNOM) was fractionated by preparative size-exclusion chromatography (SEC) into seven molecular weight (MW) fractions. The SRNOM and its MW fractions were subsequently analyzed for their concentrations of acidic functional groups by direct titrations, average MWs and MW distributions by semi-analytical SEC, and charge-to-MW distributions by capillary electrophoresis. Carboxyl concentrations in the MW fractions were inversely proportional to their average MWs. Conversely, the phenolic concentrations, though smaller than the carboxyl concentrations, were proportional to average MWs. Hysteresisthe non-overlap between sequential forward and reverse titrationswas observed for the SRNOM and its MW fractions, where the reverse titrations predicted a greater concentration of carboxylic acid groups than the forward titration. Because hysteresis is thought to be caused by the base-catalyzed hydrolysis of esters, this suggests that ester groups in the SRNOM are distributed over all MWs. Data for direct titrations, MW distributions, and capillary electrophoresis were evaluated by a computational scheme that solves for the most probable distribution of acidic functional groups and charges on solutes in the SRNOM and the MW fractions as a function of pH. Depending on the MW ranges of the samples, solutes in the SRNOM and the MW fractions are predicted to have from one to a maximum of 25 carboxyl groups per solute. Most phenolic groups are predicted to be on solutes that have a minimum of two carboxyl groups. At low pH, all samples have high relative abundances of solutes with the lowest charges. The charges of solutes are predicted to increase with increasing pH due to the sequential ionization of acidic functional groups. Depending on the MW ranges of the samples, the maximum probable charges of solutes in the SRNOM and the fractions at high pH are -12 to -30. By knowing the most probable distribution of charge and abundances of acidic functional groups, researchers will make better estimates of thermodynamic parameters and models that describe equilibria between metals and natural organic matter in the environment.

In spite of their high abundance and importance, aqueous systems are enigmatic on the microscopic scale. In order to obtain information about their geometrical and electronic structure, simple aqueous solutions have been studied experimentally by photo- and Auger electron spectroscopy using the novel liquid micro-jet technique in conjunction with synchrotron radiation. The thesis is thematically divided into three parts. In the first part we utilize the surface sensitivity of photoelectron spectroscopy to probe the distributions of solutes near the water surface. In agreement with recent theoretical predictions we find that large polarizable anions, such as I- and ClO4-, display enhanced surface propensities compared to smaller rigid ions. Surface effects arising from ion-ion interactions at higher electrolyte concentrations and as function of pH are investigated. Studies of linear mono-carboxylic acids and benzoic acid show that the neutral molecular forms of such weak acids are better stabilized at the water surface than their respective conjugate base forms. The second part examines what type of information core-electron spectra can yield about the chemical state and hydration structure of small organic molecules in water. We demonstrate that the method is sensitive to the protonation state of titratable functional groups and that core-level lineshapes are dependent on local water hydration configurations. Using a combination of photoelectron and X-ray absorption spectroscopy we also show that the electronic re-arrangement upon hydrolysis of aldehydes yields characteristic fingerprints in core-level spectra. In the last part of this thesis we study ultrafast charge delocalization dynamics in aqueous solutions using resonant and off-resonant Auger spectroscopy. Intermolecular Coulombic decay (ICD) is found to occur in a number of core-excited solutions where excess energy is transferred between the solvent and the solute. The rate of ultrafast electron delocalization between hydrogen bonded water molecules upon oxygen 1s resonant core-excitation is found to decrease upon solvation of inorganic ions. The presented work is illustrative of how core-level photoelectron spectroscopy can be valuable in the study of fundamental phenomena in aqueous solutions.

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.