Siu Chi-kit. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1999. / Includes bibliographical references (leaves 48-52). / Abstracts in English and Chinese. / TITLE PAGE --- p.i / THESIS COMMITTEE --- p.ii / ABSTRACT (ENGLISH) --- p.iii / (CHINESE) --- p.iv / ACKNOWLEDGEMENTS --- p.v / TABLE OF CONTENTS --- p.vi / LIST OF TABLES --- p.viii / LIST OF FIGURES --- p.ix / Chapter CHAPTER 1 --- Introduction --- p.1 / Chapter Section 1.1 --- Introduction --- p.1 / Chapter Section 1.2 --- Reaction of Chlorine Hydrolysis and Its Reverse Reaction --- p.2 / Chapter 1.2.1 --- Reaction in the Gas Phase --- p.2 / Chapter 1.2.2 --- Reaction in Aqueous Solution --- p.4 / Chapter 1.2.3 --- Reaction on Ice Surface --- p.5 / Chapter Section 1.3 --- Computational Method --- p.6 / Chapter Section 1.4 --- Study of Chemical Reaction by Constraint Molecular Dynamics --- p.8 / Chapter 1.4.1 --- Constraint Molecular Dynamics --- p.8 / Chapter 1.4.2 --- RATTLE Constraint Dynamics --- p.9 / Chapter 1.4.3 --- Free Energy of Chemical Reaction --- p.10 / Chapter 1.4.4 --- Radial Distribution Function --- p.11 / Chapter CHAPTER 2 --- "Ab initio Molecular Dynamics Study of the Reaction Between HC1 and HOC1 in Gas Phase, in Aqueous Solution and on Ice Surface" --- p.12 / Chapter Section 2.1 --- Structure of the Isolated Molecules --- p.13 / Chapter Section 2.2 --- Chlorine Hydrolysis in Aqueous Solution --- p.17 / Chapter 2.2.1 --- Model --- p.17 / Chapter 2.2.2 --- Results and Discussion --- p.18 / Chapter 2.2.3 --- Conclusion --- p.31 / Chapter Section 2.3 --- Heterogeneous Reaction of HC1 and HOC1 on Ice Surface --- p.32 / Chapter 2.3.1 --- Model --- p.32 / Chapter 2.3.2 --- Results and Discussion --- p.36 / Chapter 2.3.3 --- Conclusion --- p.45 / Chapter Section 2.4 --- "Comparison of the Reaction between HC1 and HOC1 in Gas Phase, in Aqueous Solution and on Ice Surface" --- p.46 / REFERENCES --- p.48

Predicting and quantifying solvent effects on non-covalent interactions is often very challenging, as they are influenced and modulated by multiple factors. In this thesis, a series of molecular torsion balances is used as a tool to tackle the complexities of noncovalent interactions in solution. Chapter 1 presents an up-to-date literature review on solvent effects on non-covalent interactions, with a particular focus on solvent effects on conformational equilibria and molecular torsion balances. Chapter 2 demonstrates the use of molecular torsion balances and a simple explicit solvation computational model to show that the electrostatic potential of the substituted aromatic rings is largely dependent on the explicit solvation of the substituent. The contribution of both bond polarisation and through-space field effects is also covered. Chapter 3 provides a literature review on the deuterium isotope effects on non-covalent interactions, presenting a range of contradictory findings. Molecular torsion balances are used here as a probe of H/D isotope effects on the conformational equilibria, solvent isotope effects and the solvophobic effect in aqueous mixtures. The balances are studied from thermodynamic and kinetic viewpoints, through which both intra- and intermolecular interactions are examined. It is shown here that H/D isotope effects on the presented system are either non-existent or negligibly small. Chapter 4 presents the use of molecular torsion balances to investigate carbonylcarbonyl interactions, taking into account steric and solvent effects. This is compared experimentally and computationally against two existing theories rationalising these interactions. In Chapter 5, a background of metal-ligand interactions is outlined, along the most widely utilised theories rationalising them. The electronic effects of Pt complexation by a pyridyl-substituted molecular torsion balance is analysed both experimentally and computationally, and the arising discrepancies are addressed. The applicability limits of the previously presented simple solvation models are determined using systems displaying extreme electronic effects.

Além do interesse intrínseco pelos seus aspectos mecanísticos, as reações de hidrólise de compostos carbonílicos apresentam também a interessante particularidade da reação pelo próprio solvente, a água. Dentre estas reações, conhecidas como \"reações de água\" (Robertson, 1967; Johnson, 1967), estudou-se neste trabalho a hidrólise de carbonatos, através do cálculo das energias de transferência da fase gasosa para o solvente, de reagentes (R), estado de transição (ET) e produtos (P). O estudo da solvatação de modelos moleculares para R e ET indica uma correlação entre reatividade e estrutura molecular. Os resultados usando o enfoque de \"super-molécula\" mostram maior concordância com os dados experimentais do que o cálculo de solvatação da molécula simples e indicam que a solvatação dos modelos de ET é mais eficiente que para R e, portanto, há um aumento da reatividade. O estudo mais detalhado das estruturas de R, ET e P, em misturas água/acetonitrila para carbonatos de difenila e bis(2,4-dinitrofenila), sugere a existência de duas ligações de hidrogênio: entre o oxigênio da água do \"cluster\" e um dos hidrogênios dos anéis aromáticos (CF e CDNF), e entre o hidrogênio da água e o oxigênio do grupo nitro do outro anel aromático (CDNF). A consequente diminuição da liberdade conformacional em relação à fase gasosa, provocada por estas ligações de hidrogênio (CF e CDNF), expõe um dos hemisférios da carbonila ao ataque da água, provocando então uma aceleração entrópica do processo. Os efeitos eletrônicos, devidos às ligações de hidrogênio, estão de acordo com a maior acidez esperada dos hidrogênios dos anéis do CDNF em relação ao CF. Também mostram uma compensação no CDNF, pouco contribuindo para alterar a densidade eletrônica no seu carbono carbonílico, enquanto que indica uma soma de efeitos no CF, contribuindo então para um aumento desta densidade eletrônica no CF, de acordo com sua conhecida baixa reatividade. O trabalho permite ainda concluir sobre o relativo sucesso do uso de método semi-empírico PM3 e modelo relativamente simples de solvatação (Cramer & Truhlar, 1991), para o cálculo de energia de transferência em misturas de água/acetonitrila, na faixa de fração molar da água (0,40 a 1,00) onde o método apresenta resultados concordantes com os valores experimentais. / In addition to their intrinsic mechanistic interest, hydrolysis reactions of carbonyl compounds in aqueous media exhibit the interesting peculiarity of direct reaction with the solvent itself, i.e., water. In the present work, we have investigated a representative example of one of these \"water reactions\" (Robertson, 1967; Johnson, 1967), the hydrolysis of carbonates, via quantum chemical ca1culation of the free energies of transfer of the reagents (R), the transition state (TS) and the products (P) from the gas phase to water. A model study of the solvation of R and TS points to a correlation between reactivity and molecular structure. Results using the \"super-molecule\" approach show greater agreement with experiment than solvation ca1culations on the isolated molecule and imply that the solvation of the TS is more effective than that of R in increasing reactivity. A more detailed study of the structures of R, TS and P for diphenyl- (DPC) and bis(2,4-dinitrophenyl)carbonates (DNPC) in acetonitrile/water mixtures suggests the existence of two possible types of hydrogen bonds, i.e., between oxygen of the water c1uster and an aromatic ring hydrogen (DPC and DNPC) or, in the case of DNPC, between the protons of water and the oxygens of the nitro group of the second aromatic ring. The decrease in conformational degrees of freedom reI ative to the gas phase provoked by these hydrogen bonds exposes one of the hemispheres of the carbonyl group to attack by water, resulting in an entropic acceleration of the reaction. The electronic effects on the hydrogen bonds are in line with the greater acidity of the aromatic ring hydrogens of DNPC relative to those of DNP. In DNPC, there is a compensation effect, with very little alteration of the electron density on the carbonyl carbon, while in DPC a sum of effects increases the electron density on the carbonyl carbon, in line with the known lower reactivity of the latter. This work points to the relative success of the semi-empirical PM3 method combined with relatively simple solvation models (Cramer & Truhlar, 1991) for ca1culating free energies of transfer involving acetonitrile/water mixtures in the water mole fraction range from 0.40-1.00.

Photolysis of nitrate ion in the natural environment produces NO, NO2, and O3, releasing these toxic gases into the atmosphere. Work done by other groups has shown ionic strength dependence of the ratio of products from photolysis of aqueous nitrate ion. To better understand the kinetic mechanisms of nitrate photolysis, the effects that ionic strength in solution have on nitrate ion symmetry breaking are needed. Different solvation environments induce nitrate bonding motifs that may be correlated to the product ratio. Fourier-transform infrared spectra of aqueous nitrate–ion solutions were obtained over a range of temperatures for several total electrolyte concentrations. The electric fields (arising from water molecules and ions in solution) in aqueous potassium nitrate solution distort the trigonal planar shape of the nitrate ion, which may favor a specific initial path of the decomposition of nitrate during photolysis. Van’t Hoff plots of the relative peak areas corresponding to the formally-degenerate asymmetric stretching mode reveal the relative energies of the two solvation geometries. The difference in energy between the two geometries is linearly proportional to the ionic strength of the solution. Electronic structure calculations suggest that the more symmetric geometry has an increased stability relative to the less-symmetric geometry in high ionic strength solutions. Thus, the relative amounts of the nitrate ion solvation geometries can be correlated to the amount of products produced during photolysis to help explain the ionic-strength dependence of the product yields. Nitrate geometries at the water—CCl4 interface and aqueous carbonate ion bonding motifs are being investigated to identify pure-water effects. Preliminary results suggest that the more symmetric geometry nitrate is stabilized at the water—CCl4 interface and the lesssymmetric carbonate solvation geometry has an increased stability relative to the more symmetric geometry in high ionic strength solutions.

Thesis (M.Ch.E.)--University of Delaware, 2006. / Principal faculty advisor: Annette D.Shine, Dept. of Chemical Engineering. Includes bibliographical references.

Thesis (Ph. D.)--University of Chicago, Dept. of Chemistry, December 1997. / Includes bibliographical references. Also available on the Internet.

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2000. / Thesis based on five papers, which are included. Includes bibliographical references.

Free energy simulations have been widely employed to compute the thermodynamic properties of many important biochemical processes. In the first part of this dissertation, two important biochemical processes, protonation/deprotonation of acid in solution and solvation of small organic molecules, are investigated using free energy simulations. Accurate computation of the pKa value of a compound in solution is important and challenging. To efficiently simulate the free energy change associated with the protonation/deprotonation processes in solution, a new method of mixing Hamiltonian, implemented as an approach using a fractional protonin the hybrid quantum mechanics/molecular mechanics (QM/MM) scheme, is developed. This method is a combination of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theoretical and technical details of this method, along with the calculation results of the pKa value of methanol and methanethiol molecules in aqueous solution, are discussed. The simulation results show satisfactory agreement with experimental data. Though the QM/MM method is one of the most useful methods in the modeling of biochemical processes, little attention has been paid to the accuracy of QM/MM methods as an integrated unit. Therefore, the solvation free energies of a set of small organic molecules are simulated as an assessment of ab initio QM/MM methods. It shows that the solvation free energy from QM/MM simulations can vary over a broad range depending on the level of QM theory / basis sets employed. Diffuse functions tend to over-stabilize the solute molecules in aqueous solution. The deviations pose a pressing challenge to the future development of new generation of MM force fields and QM/MM methods if consistency with QM methods becomes a natural requirement. In the second part of the dissertation, the dynamic and energetic properties of two molten globule (MG) protein molecules, α-lactalbumin(α-LA) and monomeric chorismate mutase (mCM) are investigated using molecular dynamics simulations. The exploring of the molecular mechanism of protein folding is a never-settled battle while the properties of MG states and their roles in protein folding become an important question. The MGs show increased side chain flexibility while maintain comparable side-chain coupling compared to the native state, which partially explains the preserving of native-like overall conformation. The enhanced sampling method, temperature-accelerated molecular dynamics (TAMD), is used for the study of the hydrophobic interactions inside both biomolecules. The results suggest that these hydrophobic cores could overcome energy barriers and repack into new conformation states with even lower energies. The repacking of the hydrophobic cores in MGs might be served as a criterion for recognizing the MGs in large class of biomolecules. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Temperature, pressure, and length scale dependence of the solvation of simple solvophobic solutes is investigated in the Jagla liquid, a simple liquid consisting of particles that interact via a spherically symmetric potential combining hard and soft core interactions. The results are compared with identical calculations for a model of a typical atomic liquid, the Lennard-Jones (LJ) potential, and with predictions for hydrophobic solvation in water using the recently developed cavity equation of state and the extended simple point charge model. We find that the Jagla liquid captures the qualitative thermodynamic behavior of hydrophobic hydration as a function of temperature and pressure for both small and large length scale solutes. In particular, for both the Jagla liquid and water, we observe temperature-dependent enthalpy and entropy of solvation for all solute sizes as well as a negative solvation entropy for sufficiently small solutes at low temperature. This feature of water-like solvation is distinct from the strictly positive and temperature independent enthalpy and entropy of cavity solvation observed in the Lennard-Jones fluid. The results suggest that a competition between two energy scales that favors low-density, open structures as temperature is decreased is an essential interaction of a liquid that models hydrophobic hydration. In addition the Jagla liquid dewets surfaces of large radii of curvature less readily than the Lennard-Jones liquid, and the so-called ``length scale crossover'' in solvation, whereby solvation free energies change from scaling with the solute volume to scaling with the solute surface area, occurs at length scales that are larger relative to the solvent size. Both features reflect a greater flexibility or elasticity in the Jagla liquid structure than that of a typical liquid, similar to water's ability to maintain its hydrogen bond network. The implications of the differences in crossover behavior between water-like and typical liquids are examined in the context of a simple thought experiment on the aggregation of solvophobic solutes that builds on ideas from Chandler and Rajamani et al. We find that water-like crossover behavior exposes a size range of solvophobic aggregates to destabilization upon cooling and pressurizing, which may thereby precipitate phenomena such as cold and pressure denaturation of proteins. Statistics of density fluctuations, void space, and pair distributions are analyzed for molecular-scale volumes. The pair distribution functions are used to provide an estimate of the size of the Jagla particle with a physical basis. The void distributions are observed to be distinct in the three liquids, with low temperature distributions in the LJ and Jagla liquids demonstrating a high degree of skewness. The void distributions observed in LJ liquid are hard sphere-like, while those of water and the Jagla liquid exhibit a higher degree of density inhomogeneity relative to a hard sphere system. The well-known Gaussian behavior of density fluctuations in molecular volumes in water is not generally observed in other liquids, as evidenced by the fact that this behavior is not consistently observed in either the LJ or the Jagla liquids. An exploratory study of the effects of explicit solvent on the sequence energy landscape of model heteropolymers has been performed. For a fixed set of configurations, the energy landscape of all possible sequences taken from a two letter alphabet consisting of only solvophilic and solvophobic monomers is characterized at different solvent temperatures. Non-trivial solvent and temperature effects are manifest in the distribution of sequences, confirming that the negation of these effects may have profound consequences on designability. / text

Thesis (M.Sc.)--Memorial University of Newfoundland, 1999. / Restricted until November 2000. Bibliography: leaves 132-140.