The conformational preferences of several oligosaccharides are investigated herein using a combination of NMR spectroscopy and molecular dynamics (MD) simulations, focusing on the torsion angles associated with the glycosidic linkages. Strategies for obtaining usable J-HMBC spectra for carbons with an adjacent 13C label are described. By employing a selective pulse or a constant time modification, spectra free from interferences are obtained for site-specifically 13C labeled oligosaccharides. Intermolecular hydrogen bonding in sucrose is investigated using MD simulations performed at different concentrations. One of the most frequent intermolecular hydrogen bonds in the simulations, O3f∙∙∙HO3g, was detected using the HSQC-TOCSY NMR experiment. Based on MD simulations and NMR spectroscopy, the conformational ensemble for a trisaccharide segment of the LeaLex hexasaccharide is proposed to feature conformational exchange between conformations with positive and negative values for the ψ3 torsion angle in the β-D-GlcpNAc-(1→3)-β-D-Galp linkage. Using MD simulations, the conformation of the N-acetyl group is shown to influence the glycosidic conformation at a nearby linkage in two oligosaccharides. Short (1→6)-linked oligosaccharides are shown to exhibit conformational exchange at the ω and ψ torsion angles. Notably, the former torsion angle populates states with ψ ≈ ±90°. Conformationally sensitive homo- and heteronuclear coupling constants are determined using various NMR experiments. The experimental data, including effective distances from NOESY obtained for two of the compounds, is used to improve the representation of the ω torsion angle in the CHARMM36 force field. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 5: Accepted. Paper 6: Manuscript.</p>

Indiana University-Purdue University Indianapolis (IUPUI) / Bacterial endospores have been a topic of research interest over the last several decades given their high resistance to ultraviolet (UV) damage. Unlike vegetative bacterial cells, which form cyclobutane pyrimidine dimers (CPD) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs) as the major product upon UV irradiation, endospore bacteria form a spore photoproduct (5-(R-thyminyl)-5,6-dihydrothymine or SP) as the major product. Vegetative bacteria cells are subject to regular cell activities and processes such as division and deoxyribonucleic acid (DNA) replication, which are prone to damage from UV exposure. However, in endospores, which have a largely anhydrous inner environment, the DNA remains dormant when bound to spore-specific small acid-soluble proteins (SASP) and dipicolinic acid, making spores highly resistant to radiation, heat, desiccation, and chemical harm. During spore germination, SP lesions in DNA are repaired by a distinctive repair enzyme, spore photoproduct lyase (SPL). In this thesis, molecular dynamics (MD) simulations were carried out to (i) examine how the formation of the SP lesion in DNA affects the global and local structural properties of duplex DNA and (ii) study how this lesion is recognized and repaired in endospore. The first part of this work was focused on designing and developing a structurally and dynamically stable model for dinucleotide SP molecule (TpT), which was subsequently used as an SP patch incorporated into duplex DNA. Computationally, this requires modifications of the bond and nonbonded force field parameters. The stability of the patch and developed parameters was tested via solution-phase MD simulations for the SP lesion incorporated within the B-DNA dodecamer duplex (PDB 463B). The second part involved applying the new SP patch to simulate the crystallographic structure of the DNA oligomer containing SP lesions. Solution-phase MD simulations were performed for the SP-containing DNA oligomers (modeled based on PDB 4M94) and compared to the simulations of the native structure (PDB 4M95). Our analysis of the MD trajectories revealed a range of SP-induced structural and dynamical changes, including the weakened hydrogen bonds at the SP sites, increased DNA bending, and distinct conformational stability and distribution. In the third part of this thesis project, we carried out MD simulations of SP-containing DNA bound with SASPs to examine how the DNA interacts differently with SASP in the presence and absence of the SP lesion. The simulation results suggested decreased electrostatic and hydrogen bonding interactions between SASP and the damaged DNA at the SP site compared to the undamaged DNA-protein complex. In addition, decreased helicity percentage was observed in the SASPs that directly interact with the SP lesion. The last part of this this thesis work focused on the SP-dimer flipping mechanism, as the lesion is likely flipped out to its extrahelical state to be recognized and repaired by SPL. Using steered molecular dynamic (SMD) simulations and a pseudo-dihedral angle reaction coordinate, we obtained possible SP flipping pathways both in the presence and absence of SASP. Collectively, these simulation results lend new perspectives toward understanding the unique behavior of the SP lesion within the DNA duplex and the nucleoprotein complex. They also provide new insights into how the SP lesion is efficiently recognized and repaired during spore germination.

Rare earth ion doped glasses find applications in optical and photonic devices such as optical windows, laser, and optical amplifiers, and as model systems for immobilization of nuclear waste. Macroscopic properties of these materials, such as luminescence efficiency and phase stability, depend strongly on the atomic structure of these glasses. In this thesis, I have studied the atomic level structure of rare earth doped silicate and aluminophosphate glasses by using molecular dynamics simulations. Extensive comparisons with experimental diffraction and NMR data were made to validate the structure models. Insights on the local environments of rare earth ions and their clustering behaviors and their dependence on glass compositions have been obtained. In this thesis, MD simulations have been used to investigate the structure of Eu2O3-doped silica and sodium silicate glasses to understand the glass composition effect on the rare earth ions local environment and their clustering behaviors in the glass matrix, for compositions with low rare earth oxide concentration (~1mol%). It was found that Eu–O distances and coordination numbers were different in silica (2.19-2.22 Å and 4.6-4.8) from those in sodium silicate (2.32 Å and 5.8). High tendencies of Eu clustering and short Eu-Eu distances in the range 3.40-3.90 Å were observed in pure silica glasses as compared to those of silicate glasses with much better dispersed Eu3+ ions and lower probability to form clusters. The results show Eu3+ clustering behavior dependence on the system size and suggest for low doping levels, over 12,000 atoms to obtain statistical meaningful results on the local environment and clustering for rigid silica-based glasses. The structures of four cerium aluminophosphate glasses have also been studied using MD simulations for systems of about 13,000 atoms to investigate aluminum and cerium ion environment and their distribution. P5+ and Al3+ local structures were found stable while those of Ce3+ and Ce4+ ions, through their coordination numbers and bond lengths, are glass composition-dependence. Cerium clusters were found in the high cerium glasses.P5+ coordination numbers around cerium revealed the preference of phosphorus ions in the second coordination shell. Total structure factors from MD simulations and experimental diffraction results show a general agreement from comparison for all the cerium aluminophosphate glasses and with compositional changes up to 25 Å-1. Aluminum enters the phosphate glass network mainly as AlO4 and AlO5 polyhedra only connected through corner sharing to PO4 tetrahedra identified by Q11(1 AlOx), Q12(2 AlOx), Q21(1 AlOx), and Q22(2 AlOx) species.

The number of three-dimensional structures of potential protein targets available in several platforms such as the Protein Data Bank is subjected to a constant increase over the last decades. This observation should be an additional motivation to use structure-based methodologies in drug discovery. In the recent years, different success stories of Structure Based Drug Design approach have been reported. However, it has also been shown that a lack of druggability is one of the major causes of failure in the development of a new compound. The concept of druggability can be used to describe proteins with the capability to bind drug-like compounds. A general consensus suggests that around 10% of the human genome codes for molecular targets that can be considered as druggable. Over the years, the protein druggability was studied with a particular interest to capture structural descriptors in order to develop computational methodologies for druggability assessment. Different computational methods have been published to detect and evaluate potential binding sites at protein surfaces. The majority of methods currently available are designed to assess druggability of a static structure. However it is well known that sometimes a few local rearrangements around the binding site can profoundly influence the affinity of a small molecule to its target. The use of techniques such as molecular dynamics (MD) or Metadynamics could be an interesting way to simulate those variations. The goal of this thesis was to design a new computational approach, called JEDI, for druggability assessment using a combination of empirical descriptors that can be collected ‘on-the-fly’ during MD simulations. JEDI is a grid-based approach able to perform the druggability assessment of a binding site in only a few seconds making it one of the fastest methodologies in the field. Agreement between computed and experimental druggability estimates is comparable to literature alternatives. In addition, the estimator is less sensitive than existing methodologies to small structural rearrangements and gives consistent druggability predictions for similar structures of the same protein. Since the JEDI function is continuous and differentiable, the druggability potential can be used as collective variable to rapidly detect cryptic druggable binding sites in proteins with a variety of MD free energy methods.

Knowledge about the structure, conformation and dynamics of carbohydrates is important in our understanding of the way carbohydrates function in biological systems, for example in intermolecular signaling and recognition. This thesis is a summary of five papers studying these properties in carbohydrate-containing molecules with NMR spectroscopy and molecular dynamics simulations. In paper I, the ring-conformations of the six-membered rings of two carbaiduronic analogs were investigated. These carbasugars could potentially be used as hydrolytically stable mimics of iduronic acid in drugs. The study showed that the equilibrium is entirely shifted towards the 4C1 conformation. Paper II is an investigation of the conformational flexibility and dynamics of two (1→6)-linked disaccharides related to an oligosaccharide epitope expressed on malignant tumor cells. In paper III, the conformational space of the glycosidic linkage of an alfa-(1→2) linked mannose disaccharide present in N- and O-linked glycoproteins, was studied. A maximum entropy analysis using different priors as background information was used and four new Karplus equations for 3JC,C and 3JC,H coupling constants, related to the glycosidic linkage, were presented. Paper IV describes a structural elucidation of the exopolysaccharide (EPS) produced by Streptococcus thermophilus ST1, a major dairy starter used in yoghurt and cheese production. The EPS contains a hexasaccharide repeating unit of d-galactose and d-glucose residues, which is a new EPS structure of the S. thermophilus species. In paper V, the dynamics of three generations of glycodendrimers were investigated by NMR diffusion and 13C NMR relaxation studies. Three different correlations times were identified, one global correlation time describing the rotation of the dendrimer as a whole, one local correlation time describing the reorientation of the C-H vectors, and one correlation time describing the pulsation of a dendrimer branch.

It is well known that folded proteins in water are destabilized by the addition of urea. When a protein loses its ability to perform its biological activity due to a change in its structure, it is said to denaturate. The mechanism by which urea denatures proteins has been thoroughly studied in the past but no proposed mechanism has yet been widely accepted. The topic of this thesis is the study of the mechanism of urea-induced protein denaturation, by means of Molecular Dynamics (MD) computer simulations and Nuclear Magnetic Resonance (NMR) spectroscopy. Paper I takes a thermodynamic approach to the analysis of protein – urea solution MD simulations. It is shown that the protein – solvent interaction energies decrease significantly upon the addition of urea. This is the result of a decrease in the Lennard-Jones energies, which is the MD simulation equivalent to van der Waals interactions. This effect will favor the unfolded protein state due to its higher number of protein - solvent contacts. In Paper II, we show that a combination of NMR spin relaxation experiments and MD simulations can successfully be used to study urea in the protein solvation shell. The urea molecule was found to be dynamic, which indicates that no specific binding sites exist. In contrast to the thermodynamic approach in Paper I, in Paper III we utilize MD simulations to analyze the affect of urea on the kinetics of local processes in proteins. Urea is found to passively unfold proteins by decreasing the refolding rate of local parts of the protein that have unfolded by thermal fluctuations. Based upon the results of Paper I – III and previous studies in the field, I propose a mechanism in which urea denatures proteins mainly by an enthalpic driving force due to attractive van der Waals interactions. Urea interacts favorably with all the different parts of the protein. The greater solvent accessibility of the unfolded protein is ultimately the factor that causes unfolded protein structures to be favored in concentrated urea solutions.

Hydrogen sensor technology is a crucial component for safety and many other practical concerns in the hydrogen economy. To achieve a desired sensor performance, proper choice of sensing material is critical, because it directly affects the main features of a sensor, such as response time, sensitivity, and selectivity. Palladium is well-known for its ability to sorb a large amount of hydrogen. Most hydrogen sensors use Pd-based sensing materials. Since hydrogen sensing is based on surface and interfacial interactions between the sensing material and hydrogen molecules, nanomaterials, a group of low dimensional systems with large surface to volume ratio, have become the focus of extensive studies in the potential application of hydrogen sensors. Pd nanowires and Pd-coated carbon nanotubes have been successfully used in hydrogen sensors and excellent results have been achieved. Motivated by this fact, in this dissertation, we perform theoretical modeling to achieve a complete and rigorous description of molecular interactions, which leads to the understanding of molecular behavior and sensing mechanisms.To demonstrate the properties of Pd-based sensing materials, two separate modeling techniques, but with the same underlying aim, are presented in this dissertation. Molecular dynamic simulations are applied for the thermodynamic, structural and dynamic properties of Pd nanomaterials. Ab initio calculations are utilized for the study of sensing mechanism of Pd functionalized single wall carbon nanotubes. The studies reported in this dissertation show the applications of computational simulations in the area of hydrogen sensors. It is expected that this work will lead to better understanding and design of molecular sensor devices.

Polymers that undergo dramatic changes in structural conformations in response to numerous stimuli such as temperature, pH, electric and magnetic fields, light inten- sity, biological molecules, and solvent polarity, are known as stimuli-responsive or ”smart” polymers. There is a broad range of very promising applications of these materials in catalysis, environmental remediation, sensors or actuator systems, and as delivery systems of therapeutic agents. Researchers have been trying to mimic smart polymers based on properties of polymers found in nature such as proteins, carbohydrates and nucleic acids. Novel bio-compatible polymers with a variety of chemical functional groups, diverse topologies, and cross-linking patterns with the ability to self-assemble in vivo are being engineered. Experimental and theoretical studies indicate that the thermodynamic properties relating to the hydrophobic effects play a pivotal role in determining the self-assembly process in smart polymers. At the same time, computational approaches based on simulation and modeling provide an understanding of this phenomenon on the micro- scopic level. Building empirical models based on statistical mechanics methods and simulation data helps to design polymeric materials with desirable traits. My research is mainly focused on investigating physicochemical characteristics of stimuli-responsive polymers under different conditions. I used atomistic molecular dynamics simulations to investigate these effects on polymer conformation. Given the size and complexity of our polymeric systems, we employed Graphical Process- ing Units (GPU) and enhanced sampling techniques such as REDS2 to increase the sampling time. These methods allow for the study of polymeric structural dynamics in solvents of varying polarity and in human skin epidermis. Our constant pH simulation of poly(methacrylic acid) revealed that the overall response is made up of local and global structural changes. The local structural re- sponse depends on the tacticity of the polymer, which leads to distinct cooperative effects for polymers with varying stereochemistry. Such simulations help to under- stand the principal driving forces behind the mechanism of self-assembly processes.

This dissertation focuses on the fundamental understanding of liquid dynamics confined in polymer membranes. Such knowledge guides the development of better polymer membranes for practical applications and contributes to the general understanding of confined liquid dynamics in various nanoporous materials. First, we investigate the membrane transport by experimental measurements on a PFSA membrane and computer modeling of the confined liquid molecules. We probe the nano-scale environment in the ionomer membrane by determining the activation energy of diffusion. We notice two structural features of the PFSA membrane that dominate membrane transport. At relatively high hydrations, the nano-scale phase-separation creates bulk-like water in the ionomer membrane and prompts fast transport of mobile species. At relatively low hydrations, the nanoconfinement of the polymer matrix leads to the ordering of confined water and prompts a high energy barrier for transport. We then delve deeper into the confinement effect by molecular modeling of various nanoconfining geometries, including carbon nanotubes, parallel graphene sheets, and parallel rigid rods. We notice retarded water dynamics under hydrophobic confinement regardless of the geometry. We further investigate the confined water by determining the residence time of water around water, which evaluates the timescale of associations between water molecules. We learn that a decreasing confinement size prompts longer associations among water molecules. Further, we propose that the prolonged associations are responsible for the retarded water dynamics under hydrophobic confinement. Next, we turn our attention to the effect of interactions between mobile species (mostly water molecules) and a confining surface. In ionomer membranes, interactions between mobile species and the ionic groups dominate the water-surface interactions. We start by looking at water-ion interactions in bulk solutions. Using solutions at varying concentrations, we notice a temperature-concentration superposition behavior from diffusion coefficients of water molecules and ions in the solutions in both experimental and computational results. Observation of this superposition behavior in bulk solutions is unprecedented. The temperature-concentration superposition parallels the well-known time-temperature superposition. We are able to extract the offset of reciprocal temperature, which fits well to a Williams-Landel-Ferry type equation. The temperature-concentration superposition points to the new perspective that the effect of ions on water dynamics can be similar to the effect of lowering temperature. We further investigate the effect of ions by modeling ions/charges onto confining geometries. Remarkably, we reveal that the presence of ions can break the ordered water structure induced by confinement. The hydrophobic confinement prompts the ordering of water molecules, which leads to slower diffusion and higher activation energy. The presence of ions/charges on the confining surface has multiple effects on the dynamics of confined water. First, the ions associate strongly with neighboring water molecules while breaking the hydrogen-bonding network between water molecules. Second, the disruption of the hydrogen-bonding network leads to decreased activation energy of diffusion and enhanced water mobility. At relatively high ion density, the water-ion interactions overcome the structure-breaking effect and lead to retarded water diffusion. Overall, the studies presented in this dissertation augment our understanding of water transport in nanostructures by revealing the rich behavior of liquid-water dynamics under both hydrophobic and ionic confinement. / Doctor of Philosophy / Polymer separations membranes contribute to important applications such as fuel cells and water desalination. Optimizing the separation ability of polymer membranes improves their practical performance. The transport property of a polymer membrane depends on its nanoscale and microscale structures. This dissertation focuses on the nanoscale structure-transport relations in ionic polymer membranes. We utilize nuclear magnetic resonance techniques and molecular dynamics simulations to probe the transport properties. We investigate the effects of membrane nanostructure and water-ion interactions on the dynamics of confined water. Such knowledge not only guides the development of high-performance membranes but also contributes to the fundamental understanding of liquid dynamics in nanoporous materials.

Macromolecular transitions such as conformational changes and protein-protein association underlie many biological processes. Conformational changes in the N-terminal domain of the transmembrane protein DsbD (nDsbD) were studied by NMR and molecular dynamics (MD) simulations. nDsbD supplies reductant to biosynthetic pathways in the oxidising periplasm of Gram-negative bacteria after receiving reductant from the C-terminal domain of DsbD (cDsbD). Reductant transfer in the DsbD pathway happens via protein-protein association and subsequent thiol-disulphide exchange reactions. The cap loop shields the active-site cysteines in nDsbD from non-cognate oxidation, but needs to open when nDsbD bind its interaction partners. The loop was rigid in MD simulations of reduced nDsbD. More complicated dynamics were observed for oxidised nDsbD, as the disulphide bond introduces frustration which led to loop opening in some trajectories. The simulations of oxidised and reduced nDsbD agreed well with previous NMR spin-relaxation and residual dipolar coupling measurements as well as chemical shift-based torsion angle predictions. NMR relaxation dispersion experiments revealed that the cap loop of oxidised nDsbD exchanges between a major and a minor conformation. The differences in their conformational dynamics may explain why oxidised nDsbD binds its physiological partner cDsbD much tighter than reduced nDsbD. The redox-state dependent interaction between cDsbD and nDsbD is thought to enhance turnover. NMR relaxation dispersion experiments gave insight into the kinetics of the redox-state dependent interaction. MD simulations identified dynamic encounter complexes in the association of nDsbD with cDsbD. The mechanism of the conformational changes in the transport cycle of LacY were also investigated. LacY switches between periplasmic open and cytoplasmic open conformations to transport sugars across the cell membrane. Two mechanisms have been proposed for the conformational change, a rocker-switch mechanism based on rigid body motions and an “airlock” like mechanism in which the transporter would switch conformation via a fully occluded structure. In MD simulations using the novel dynamics importance sampling approach such a fully occluded structure was found. The simulations argued against a strict “rocker-switch” mechanism.