[No abstract available] / Science, Faculty of / Chemistry, Department of / Graduate

The mechanisms of permanganate oxidation of two very different substrates have been examined. Firstly, in an attempt to elucidate the mechanism of permanganate oxidation of alcohols, a number of meta and para substituted 2,2,2-trifluoro-1-phenylethanols have been prepared and the kinetics of permanganate oxidation studied over a pH range of 1 to 13.3. Secondly, the reaction between permanganate and cyanide ion has been examined over the pH range 3 to 14.6. The reaction between permanganate and 2,2,2-trifluoro-1-phenylethanol in aqueous alkaline solution was shown to give manganate and trifluoroacetophenone (hydrated form) in almost quantitative yield under kinetic conditions and is therefore represented by the equation, 2MnO⁻₄ + C₆H₅CHOHCF₃ + 20H⁻→ 2Mn0⁼₄ + C₆H₅COCF₃ + 2H₂0 The trifluorophenylethanols are more acidic than the normal hydrogen containing secondary alcohols and their pKas as determined spectrophotometrically showed the following order of decreasing acidity for substitution into the phenyl ring m-NO₂> m-Br > H > p-CH₃ >p-MeO. The rate of reduction of permanganate was followed iodometrically and the rate expression which fits the kinetic data for the alkaline catalyzed oxidation is the following: [formula omitted]. The rate of oxidation of the p-CH₃, m-Br and unsubstituted trifluorophenylethanols-l-d by permanganate was found in each case to be 16 times slower than the rate of oxidation of the corresponding protio compounds in alkaline solution. This latter result, the kinetics, i.e., the close similarity between the ionization type rate curves and the calculated ionization curves for the alcohols, the thermodynamics and positive salt effect indicate a mechanism which involves a primary ionization step to give the anion of the alcohol and then a rate controlling bimolecular step where permanganate abstracts a hydride ion from the anion. This mechanism is somewhat invalidated in view of the observation that the rate constants obtained for oxidation of the various substituted alcohols in alkaline solution are relatively insensitive to nuclear substitution. A plot of Hammett σ values versus the log of the rate constants appears to give a smooth curve. A number of mechanisms involving termolecular steps are considered to account for this latter observation and the large deuterium isotope effect is discussed in the light of present theories. Kinetic and oxygen¹⁸ tracer experiments have been performed in an attempt to elucidate the mechanism(s) of permanganate oxidation of cyanide. A mechanistic interpretation is attempted using the data obtained in basic solution above pH 12 to 14.6 where the oxidation is represented by the equation, 2MnO₄⁻ + CN⁻ + 20H⁻→ 2MnO₄⁼ + NCO⁻ + H₂0 From pH 12 to 6 the reaction was found to be complex and unstoichiometric yielding cyanate, carbon dioxide, cyanide ion and finally cyanogen at pH 9 to 6. The rate of reduction of permanganate as followed iodometrically and spectrophotometrically, is found to be markedly dependent on the pH of the medium and reactant concentration. The observation that the rate is negligible in acid solution but rapid in basic media suggests cyanide ion and not hydrocyanic acid molecule to be the primary reactive species. At pH greater than 12 two parallel processes are indicated which have been designated as Reaction A and Reaction B. Reaction A appears at low reactant concentrations < 0.0004 M cyanide and higher hydroxyl ion concentrations > pH 13. The rate of Reaction A is represented by the kinetic expression [formula omitted] where k₂ is independent of hydroxyl ion concentration and is insensitive to the effect of manganate and barium ions. A positive salt effect is observed and labeling experiments using permanganate enriched in oxygen¹⁸ showed that the oxygen introduced into the product cyanate comes mainly from the oxidant (70%-80% oxygen transferred). These observations suggest a mechanism which involves a rate determining bimolecular reaction between permanganate and cyanide ions to yield a Mn V species and cyanate ion. The possibility that a second parallel process Reaction B was occurring was indicated by the changing kinetics at higher reactant concentrations and lower basicities, by the non-linear Arrhenius plots and the observation that only 15%-25% oxygen¹⁸ transfer from permanganate to substrate had occurred at pH 13. The rate of this latter process can be tentatively represented by the kinetic expression [formula omitted]. A mode of oxidation is suggested which appears to fit these results. Permanganate, cyanide ion and a hydrocyanic acid molecule are reacted to produce a reactive species which undergoes further oxidation by permanganate to yield cyanogen. Cyanogen hydrolysis results in cyanate where oxygen is derived from the solvent. / Science, Faculty of / Chemistry, Department of / Graduate

This work concerns the description of eigenvalue independent: partitioning theory, and its application to quantum mechanical calculations of interest in chemistry. The basic theory for an m-fold partitioning of a hermitian matrix H, (2 < m < n, the dimension of the matrix), is developed in detail, with particular emphasis on the 2x2 partitioning, which is the most' useful. It consists of the partitioning of the basis space into two subspaces — an n[sub A]-dimensional subspace (n[sub A] > 1), and the complementary n-n[sub A] = n[sub B]-dimensional subspace. Various n[sub A]-(or n[sub B]-) dimensional effective operators, and projections onto n[sub A]- (or n[sub B] dimensional eigenspaces of H, are defined in terms of a mapping, f, relating the parts of eigenvectors lying im each of the partitioned subspaces. This mapping is shown to be determined by a simple nonlinear operator equation, which can be solved by iterative methods exactly, or by using a pertur-bation expansion. Properties of approximate solutions, and various alternative formulas for effective operators, are examined. The theory is developed for use with both orthonormal and non-orthonormal bases. Being a generalization of well known one-dimensional partitioning formalisms, this eigenvalue independent partitioning theory has a number of important areas of application. New and efficient methods are developed for the simultaneous determination of several eigenvalues and eigenvectors of a large hermitian matrix, which are based on the construction and diagonalization of an appropriate effective operator. Perturbation formulas are developed both for effective operators defined in terms of f, and for projections onto whole eigen-spaces of H. The usefulness of these formulas, especially when the zero order states of interest are degenerate, is illustrated by a number of examples, including a formal uncoupling of the four component Dirac hamiltonian to obtain a two component hamiltonian for electrons only, the construction of an effective nuclear spim hamiltonian in esr theory, and the derivation of perturbation series for the one-particle density matrix in molecular orbital theory (in both Huckel-type and closed shell self-consistent field contexts). A procedure is developed for the direct minimization of the total electronic energy in closed shell self-consistent field theory in terms of the elements of f, which are unconstrained and contain no redundancies. This formalism is extended straightforwardly to the general multi-shell single determinant case. The resulting formulas, along with refinements of the basic conjugate gradient minimization algorithm* which involve the use of scaled variables and frequent basis modification, lead to efficient, rapidly convergent methods for the determination of stationary values of the electronic energy* This is illustrated by some numerical calculations in the closed shell and unrestricted Hartree-Fock cases. / Science, Faculty of / Chemistry, Department of / Graduate

The highly interdisciplinary study of molecular magnetism spans a wide array of topics, ranging from spintronics and quantum computing to enzyme function and MRI contrast agents. At the core of all these fields is the study of materials whose properties can be controlled through the rational design of molecules. The chemical tailoring of molecular magnetic properties can only be achieved by understanding the relationship between the physical and electronic structures. In this dissertation, the interplay between structure and physical properties is probed using a variety of magnetic resonance techniques. In Chapter 1, we give a succinct overview of the various methods utilized in this dissertation. We first describe the experimental methods including electron paramagnetic resonance (EPR), 57Fe nuclear gamma resonance (Mössbauer) spectroscopy, electron double resonance detected nuclear magnetic resonance (ELDOR-NMR), and Fourier transform far-infrared (FTIR) spectroscopy. In addition to the introduction of each technique, we describe how the data is analyzed and what quantities may be extracted from each method. We also introduce the quantum chemical methods used to rationalize the spectroscopic parameters. In Chapter 2, we investigate a recently reported Fe-V triply bonded species, [V(iPrNPPh2)3FeI], using high frequency EPR (HFEPR), field- and temperature-dependent 57Fe Mössbauer spectroscopy, and high-field ELDOR-NMR. From the use of this suite of physical methods, we probe the electron spin distribution as well as the effects of spin-orbit coupling on the electronic structure. This is accomplished by measuring the effective g – factors as well as the Fe/V electro – nuclear hyperfine interaction tensors of the spin S = ½ ground state. We have rationalized these tensors in the context of ligand field theory supported by quantum chemical calculations. This combined theoretical and experimental analysis suggests that the S = ½ ground state originates from a single unpaired electron predominately localized on the Fe site. Chapter 3 describes a combined HFEPR and variable-field Mössbauer spectroscopic investigation of a pair of bimetallic compounds with Fe-Fe bonds, [Fe(iPrNPPh2)3FeR] (R = ≡NtBu and PMe3). Both of these compounds have high spin ground states, where R= PMe3 (S = 7/2) and the R= ≡NtBu displays (S = 5/2). The ligand set employed in this work encapsulates each Fe site in a different coordination environment. This results in polarized bonding orbitals which engender each nuclear site with unique hyperfine tensors as revealed by Mössbauer spectroscopy. Absent the metal-metal bond, the tris-amide bound site in both compounds is expected to be Fe(II). To gain insight into the local site electronic structure, we have concurrently studied a compound containing a single Fe(II) in a tris-amide site. Our spectroscopic studies have allowed us to assess the electronic structure via the determination of the zero field splitting parameters and 57Fe electronuclear-hyperfine tensors for the entire series. Through the insight gained in this study, we propose some strategies for the design of polymetallic single molecule magnets where the metal-metal interactions are mediated by the formation of covalent bonds between metal centers. Recently, a great deal of the work in molecular magnetism has moved away from polymetallic compounds and towards molecules containing only a single magnetic ion. A critical challenge in this endeavor is to ensure the preservation of orbital angular momentum in the groundstate. The stabilization of the ground state orbital moment generates the strong magnetic anisotropy which is often required for the design of magnetic materials. The presence of unquenched orbital angular momentum can be identified by significant shifts in the g-value away from the free ion value. In an initial report of a Ni(I) coordination complex, which was found to exhibit field-induced slow magnetic relaxation, no EPR signal was observed. Given the expectation that orbital angular momentum can shift the g-values beyond the range expected for a typical S= ½ system, we have reexamined this compound using multi-frequency EPR and field-dependent FTIR spectroscopy. Through a combined spectroscopic and theoretical effort, we have characterized the effect of first order spin-orbit coupling on the electronic structure. The final report, Chapter 5, examines an exciting new class of photomagnetic materials based on bisdithiazolyl radicals. These materials, and others with magnetic properties that can be modulated via optical excitation, offer enticing opportunities for the development of next generation technologies. The dimorphic system in this study crystallizes in two phases, one composed of diamagnetic dimers and the other of paramagnetic radicals. Here we report on the use of high-field electron paramagnetic resonance spectroscopy to characterize both the thermally- and light-induced transitions in the dimer phase. During the course of this study we show that signals originating from residual radical defects in the dimer phase can be differentiated from those arising from the radical phase. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester 2018. / October 15, 2018. / Includes bibliographical references. / Stephen Hill, Professor Co-Directing Dissertation; Michael Shatruk, Professor Co-Directing Dissertation; Peng Xiong, University Representative; A. Eugene DePrince, III, Committee Member; Oliver Steinbock, Committee Member.

This dissertation presents structure-specific descriptions of optical properties and electronic energy relaxation dynamics of structure precise monolayer-protected gold clusters (MPCs) and narrow size distributed semiconductor nanocrystals (NCs). Femtosecond pump-probe transient extinction spectroscopy has been conducted on MPCs to determine the size at which the transition from non-metallic to metallic electronic behavior occurs. Excitation-pulse-energy-dependent measurements confirmed Au144(pMBA)60 (1.8 nm) as the smallest MPC to exhibit metallic behavior, with a quantifiable electron-phonon coupling constant of (1.63 ± 0.25) × 1016 W m-3 K-1 after a series of gold monolayer protected clusters (MPCs) whose sizes ranged from 1.5 nm to 2.4 nm were studied. Smaller, non-metallic MPCs exhibited nanocluster-specific transient extinction spectra characteristic of transitions between discrete quantum-confined electronic states. Volume-dependent electronic relaxation dynamics for < 1.8 nm MPCs were attributed to an electron-phonon bottleneck, which arose from a combination of large energy differences between electronic states and phonon frequencies and spatial separation of photo-excited electrons and holes. Then, electronic energy relaxation of Au144(SR)60q ligand-protected nanoclusters, where SR = SC6H13 and q = -1, 0, +1 and +2, was examined using femtosecond time-resolved transient extinction spectroscopy. The observed differential transient spectra contained three distinct components: 1) transient bleaches at 525 nm and 600 nm, 2) broad visible excited-state absorption (ESA), and 3) stimulated emission (SE) at 670 nm. The bleach recovery kinetics depended upon the excitation pulse energy and were thus attributed to electron-phonon coupling typical of metallic nanostructures. The prominent bleach at 525 nm was assigned to a core-localized plasmon resonance (CLPR). ESA decay kinetics were oxidation-state dependent and could be described using a metal-sphere charging model. The dynamics, emission energy, and intensity of the SE peak exhibited dielectric-dependent responses indicative of Superatom charge transfer states. Based on these data, the Au144(SR)60 system is one of the smallest-known nanocluster to exhibit quantifiable electron dynamics and optical properties characteristic of metals. To understand the origin of near infrared (NIR) photoluminescence (PL) of Superatomic nanoclusters, electronic energy relaxation dynamics of Au25(SR)18-1 were studied. The transient spectra were composed of three distinct components: 1) spectrally broad excited-state absorption (ESA); 2) stimulated emission and 3) ground-state bleaching. Strong solvent dielectric dependencies of the component 2 relaxation rates and photoluminescence emission implicated metal-to-ligand charge transfer mechanisms in mediating electronic energy relaxation dynamics of MPCs. A full picture of electronic relaxation pathways in Au25(SR)18 has been proposed. After initial excitation from ligand bands into high-energy excited states, rapid internal conversion is followed by non-radiative relaxation into charge transfer states localized on MPC protecting ligands. NIR photoluminescence is attributed to the radiative transition from charge transfer states to ground states. All these data suggested that protecting ligand structure and the surrounding environment could modify nanoclusters-to-ligand charge transfer in MPCs. Finally, charge carrier relaxation dynamics of electronically excited CdSe and CdSe/CdS core/shell nanocrystals (NCs) were studied using femtosecond time-resolved transient absorption spectroscopy, employing both visible and NIR probe laser pulses. Following 400-nm excitation, the combination of visible and NIR laser probe pulses were used to determine the influence of surface passivation on electronic relaxation dynamics for nanocrystals overcoated with either organic ligands or inorganic semiconductors. In particular, low-energy NIR photons were used to isolate transient absorption signals due to either electron and hole intraband transitions. Four relaxation components were detected for CdSe NCs passivated by organic molecules: 1) picosecond hole relaxation; 2) electron deep trapping; 3) electron surface trapping; and 4) exciton radiative recombination. Based on TA data collected over a broad energy range, electron deep trapping at Se2- sites was suppressed for CdSe NCs passivated by inorganic (CdS) semiconducting materials. By comparing the time-dependent transient absorption data of a series of CdSe/CdS NCs with different shell thicknesses, evidence for the transition from Type-I to quasi Type-II NCs was obtained. These data illustrate the sensitivity of femtosecond time-resolved transient absorption measurements carried out over visible and near infrared probe energies for determining the influence of nanocrystal structure on electronic relaxation dynamics. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2015. / April 9, 2015. / electron-phonon coupling, nanoclusters, plasmon, quantum dots, ultrafast spectroscopy / Includes bibliographical references. / Kenneth L. Knappenberger, Jr., Professor Directing Dissertation; Peter G. Fajer, University Representative; Hedi Mattoussi, Committee Member; Wei Yang, Committee Member.

Monoclonal antibody (mAb) A20 is the best characterized AAV2 neutralizing mAb [18, 116, 165]. Large quantities of the mAb A20 were obtained from hybridomas cell culture, and A20 Fab fragments were produced and purified by standard methods [289]. Following optimization of the AAV2-A20 Fab ratio, low resolution preliminary images of AAV2-A20 Fab have been obtained. Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of AAV2 with A20. The structure of the AAV2-A20 Fab complex was determined to 28Å resolution using cryo-electron microscopy and image analysis. The known structure of AAV2 [31] and Fab 1CL7 [168] were fitted to the cryo-electron microscope density map. Preliminary results are plausible. Part of the identified A20 footprint is well matched with peptide scanning results (532-541) [116] and mutations at 548, 708 [171]. It is known that A20 is neutralizing, post-attachment, and therefore unlikely to be bound at the primary receptor site. The reconstruction shows mAb A20 binding to the surface off the shoulder of the threefold spike along the twofold axes side, and this region is away from the putative primary receptor binding sites. The reconstruction continues to be improved through addition of EM images, and through improved processing. The crystal structure of heparin-derived hexasaccharides complexed with AAV2 was determined at a resolution of 5.5Å. Here we identify the specific amino acids on the surface of the capsid that facilitate binding to the cell surface receptor heparin sulfate proteoglycan (HSPG). Our data indicate that residues R585 and R588, are primarily responsible for HSPG binding, and therefore for infectivity. They are the minimal necessary and sufficient requirements for HSPG binding. The heparin hexasaccharide also interacts with an additional binding site formed by K-507. No significant conformational change in AAV2 occurred upon heparin oligosaccharide binding, which suggests that heparin primarily serves to juxtapose components of the AAV2 signal transduction pathway. HS might function as an accessory molecule, enhancing the efficiency of a second, internalization receptor. / A Dissertation submitted to the Institute of Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2007. / February 22, 2007. / Adeno-Associated Virus, Receptor, Antibody, X-ray Crystallography, Electron-Micrography, heparin hexsaccharide / Includes bibliographical references. / Michael S. Chapman, Professor Co-Directing Dissertation; Kenneth A. Taylor, Professor Co-Directing Dissertation; Robert H. Reeves, Outside Committee Member; Michael Blaber, Committee Member; Hong Li, Committee Member.

The Adeno-Associated Virus has moved to the forefront as a vector for human gene therapy. Vectors have been constructed with AAV to repair many genetic deficiencies such as cystic fibrosis and hemophilia and have demonstrated remarkable success. For the application of a gene therapy vector, the particle must be afforded maximal capability to deliver the therapeutic gene without immunological elimination. Unfortunately, AAV is endemic in the human population and as a result, a large proportion of individuals harbor immunity to AAV leading to rapid elimination upon subsequent exposure. One of the major obstacles for the development of AAV as a vector is the absence of robust epitope data. If such data was in hand, gene therapy vectors could be constructed with modifications to these highly immunogenic sites on the viral particle. Given the non-cytopathic nature of AAV, the virus does not lend itself well to traditional plaque assays. Without such assays in hand, the ability to isolate and recover viable viral clones is severely limited. We set out to map the viral epitope to monoclonal antibody A20 by generating monoclonal antibody neutralization escape mutants in cell culture. The lack of plaque assays had prompted us to focus on the development of methods that would facilitate these selection experiments. Having successfully developed a robust and reliable method for plaquing AAV we were capable of applying it to the preliminary selection experiments. The initial application of these methods did not yield the desired mutant. Presented here are the methods developed, their preliminary applications, analysis of the results and future prospective for escape mutant production. / A Dissertation Submitted to the Institute of Molecular Biophysics in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy. / Summer Semester, 2008. / April 17, 2008. / Mutants, Parvovirus, Escape, Epitope, Antibody, Aav / Includes bibliographical references. / Hengli Tang, Professor Co-Directing Dissertation; Michael Chapman, Professor Co-Directing Dissertation; Hong Li, Committee Member; Kenneth Roux, Committee Member; Robert Reeves, Outside Committee Member.

The RNA splicing and processing endonuclease from Nanoarchaeum equitans (NEQ) belongs to the recently identified (ab)2 family of splicing endonucleases that require two different subunits for splicing activity. N. Equitans splicing endonuclease consists of the catalytic subunit (NEQ205) and the structural subunit (NEQ261). Here we report the crystal structure of the functional NEQ enzyme at 2.1 Angstroms resolution containing both subunits, as well as that of the NEQ261 subunit alone at 2.2 Angstroms resolution. The functional enzyme resembles previously known a2 and a4 endonucleases but forms a heterotetramer; a dimer of two heterodimers of the catalytic subunit (NEQ205) and the structural subunit (NEQ261). Surprisingly, NEQ261 alone forms a homodimer, similar to the previously known homodimer of the catalytic subunit. The homodimers of isolated subunits are inhibitory to heterodimerization as illustrated by a covalently linked catalytic homodimer that had no RNA cleavage activity upon mixing with the structural subunit. Detailed structural comparison reveals a more favorable hetero- than homo-dimerization interface, thereby suggesting a possible regulation mechanism of enzyme assembly through available subunits. Finally, the uniquely flexible active site of the NEQ endonuclease provides a possible explanation for its broader substrate specificity. / A Dissertation Submitted to the Institute of Molecular Biophysics in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy. / Summer Semester, 2009. / June 26, 2009. / RNA Cleavage, tRNA Splicing Endonuclease, RNA Processing / Includes bibliographical references. / Hong Li, Professor Directing Dissertation; Penny J. Gilmer, Outside Committee Member; Brian Miller, Committee Member; W. Ross Ellington, Committee Member; Branko Stefanovic, Committee Member.

Familial hypertrophic cardiomyopathy (FHC) is the leading cause of sudden cardiac death in both preadolescents and adolescents. The hallmark of the disorder is myocardial hypertrophy of the left ventricle, which results in an obstruction of blood flow through the left ventricular outflow tract. FHC has been associated with well over 100 mutations, primarily in proteins of the contractile apparatus of the heart. The molecular mechanisms involved in the pathogenesis of FHC are not well understood. For this study, in vitro motility assays (IVM) were conducted to assess the relationship between structure and function of cardiac thin filaments and to elucidate the molecular basis for sequelae of FHC caused by point mutations in the human cardiac regulatory proteins. Our research aims to contribute to the study of FHC by the accomplishment of the following innovations: 1) Development of a simple strategy to express recombinant human cardiac regulatory proteins in E. coli for molecular assays of human cardiac contractility. 2) Fabrication of a thermo-electric controller that allows rapid and reversible characterization over a broad temperature range of the effects of FHC mutations in troponin and tropomyosin using IVM assays. My research yielded the following novel physiological findings 1) Ca2+-sensitivity of human cardiac thin filament sliding is affected by some of the FHC mutations in the cardiac regulatory proteins, but not by changes in myosin isoform, indicating that Ca2+-sensitivity does not depend upon the kinetics of cross-bridge cycling. This finding implies that the hypertrophic response is communicated through different pathways depending whether the mutation is in troponin, tropomyosin, or myosin 2) Troponin and tropomyosin affect the temperature sensitivity as well as the maximum speed of unloaded filament sliding by reducing the myosin cross-bridge duty ratio. Our results suggest that the duty ratio also might be affected by clinically relevant mutations in troponin and tropomyosin. Finally, functional characterization of troponin, bearing FHC mutations in subunit I, subunit T, or both subunits, predicts structural relationships of the thin filament. / A Dissertation submitted to the Program in Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2006. / October 25, 2006. / Troponin, Calciun Sensitivity, Temperature, Familial Hypertrophic Cardiomyopathy, Thermal Stability, Cross-Bridge Cycle, Tropomyosin / Includes bibliographical references. / P. Bryant Chase, Professor Directing Dissertation; Peng Xiong, Outside Committee Member; Timothy S. Moerland, Committee Member; Peter G. Fajer, Committee Member; Thomas C. S. Keller, III, Committee Member.

In aqueous solution, solute conformational transitions are governed by intimate interplays of the fluctuations of solute–solute, solute–water, and water–water interactions. To more effectively sample conformational transitions in aqueous solution, we devised a predictive sampling method: the generalized orthogonal space tempering (gOST) algorithm. Specifically, in the Hamiltonian perturbation part, a solvent-accessible-surface-area-dependent term is introduced to implicitly perturb near-solute water–water fluctuations; more importantly in the orthogonal space response part, the generalized force order parameter is generalized as a two-dimension order parameter set, in which essential solute–solvent and solute–solute components are separately treated. The gOST algorithm is evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine peptide. On the basis of a fully automated sampling protocol, the gOST simulation enabled repetitive folding and unfolding of the solvated peptide within a single continuous trajectory and allowed for detailed constructions of deca-alanine folding/unfolding free energy surfaces. In addition, by employing the gOST method we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. Based on the gOST method, we have developed a solvation force orthogonal space tempering (SFOST) algorithm, in which several major changes were made from the original gOST method. Due to compensating fluctuations of essential solute-solvent and solute-solute interactions, only essential solute-solvent interactions are perturbed in the SFOST algorithm. Importantly, the above treatment enabled us to incorporate a high order orthogonal space sampling strategy. Specifically, to enlarge fluctuations of essential solute-solvent interactions, a third order treatment was introduced to accelerate the coupled responses caused by fluctuations of essential solute-solvent interactions, which come from synchronous fluctuations of essential solute-solute interactions and solvent-solvent interactions. The SFOST algorithm was evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine peptide. More importantly, the SFOST simulation explicitly revealed the compensating fluctuations between the essential solute-solvent interactions and the solvent-solvent interactions, suggesting that solvent cooperative fluctuations intimately interplay with deca-alanine conformational transitions. In addition, the SFOST algorithm was also employed to study ion conduction through gramicidin A (gA). By enlarging fluctuations of the ion-environment interactions, the SFOST simulation enabled several round trips of ion permeation through the channel and allowed detailed construction of free energy surfaces along the conduction. The calculated observables agree very well with experiment. We also found that fluctuations of channel orientations play an essential role in ion conduction. Furthermore, by employing the SFOST algorithm we enabled predictive sampling of the conformational ensemble of the p53 transcriptional activation domain 1 (TAD1). Strikingly, a helical structure resembling the MDM2-bound form was found in our SFOST simulation, indicating the pre-existing nature of the structure. Detailed studies of free energy surfaces revealed that the most popular state is not a fully disordered form but a partially helical state. Upon binding to MDM2, the hydrophobic interactions at the interface shift the conformational equilibrium to favor the total helical structure. In addition to the predictive sampling methods, we developed a Gaussian kernel Monte Carlo (GKMC) method to smoothly approximate multidimensional free energy surfaces of biomolecular processes. By taking a discrete probability distribution of sampled collective variables as an input, a biased Monte Carlo simulation is performed to efficiently resample the distribution in the collective variable space, leading to a smooth analytical estimate of the free energy surface. The GKMC method is evaluated by resampling data of a generalized orthogonal space tempering simulation of deca-alanine peptide, aiming to construct smooth one-dimensional and two-dimensional free energy surfaces along certain collective variables. As demonstrated in these model studies, the GKMC method can robustly construct smooth multidimensional free energy surfaces with super resolutions, which preserve probability distributions of target molecular processes. Constructing smooth free energy surfaces plays a vital role in interpreting simulation data to understand molecular processes of interest. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the Doctor of Philosophy. / Fall Semester 2016. / November 22, 2016. / Orthogonal Space Tempering, Predictive Sampling, Protein Dynamics, Solvation Force / Includes bibliographical references. / Wei Yang, Professor Directing Dissertation; Kenneth A. Taylor, University Representative; Oliver Steinbock, Committee Member; Hong Li, Committee Member; Timothy A. Cross, Committee Member.