Browsing by Author "Sum, Amadeu K."
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- Application of COSMO-SAC to Solid Solubility in Pure and Mixed Solvent Mixtures for Organic Pharmacological CompoundsMullins, Paul Eric (Virginia Tech, 2007-01-24)In this work, we present two open literature databases, the VT-2005 Sigma Profile Database and the VT-2006 Solute Sigma Profile Database, that contain sigma profiles for 1,645 unique compounds. A sigma profile is a molecular-specific distribution of the surface-charge density, which enables the application of solvation-thermodynamic models to predict vapor-liquid and solid-liquid equilibria, and other properties. The VT-2005 Sigma Profile Database generally focuses on solvents and small molecules, while the VT-2006 Solute Sigma Profile Database primarily consists of larger, pharmaceutical-related solutes. We design both of these databases for use with the conductor-like screening model−segment activity coefficient (COSMO-SAC), a liquid-phase activity-coefficient model. The databases contain the necessary information to perform binary and multicomponent VLE and SLE predictions. We offer detailed tutorials and procedures for use with our programs so the reader may also use their own research on our research group website (www.design.che.vt.edu). We validate the VT-2005 Sigma Profile Database by pure component vapor pressure predictions and validate the VT-2006 Solute Sigma Profile Database by solid solubility predictions in pure solvents compared with literature data from multiple sources. Using both databases, we also explore the application of COSMO-SAC to solubility predictions in mixed solvents. This work also studies the effects of conformational isomerism on VLE and SLE property prediction. Finally, we compare COSMO-SAC solubility predictions to solubility predictions by the Non-Random Two-Liquid, Segment Activity Coefficient (NRTL-SAC) model. We find UNIFAC is a more accurate method for predicting VLE behavior than the COSMO-SAC model for many of the systems studied, and that COSMO-SAC predicts solute mole fraction in pure solvents with an average root-mean-squared error (log10(xsol)) of 0.74, excluding outliers, which is greater than the RMS error value of 0.43 using the NRTL-SAC model.
- Experimental Study of the PVTX Properties of the System H₂O-CH₄Lin, Fang (Virginia Tech, 2005-09-23)The system H₂O-CH₄ is found in a variety of geological environments in the earth’s crust, from sedimentary basins to low grade metamorphic terrains. Knowledge of the PressureVolume-Temperature-Composition (PVTX) properties of the H₂O-CH₄ system is necessary to understand the role that these fluids play in different geological environments. In this study the properties of the H₂O-CH₄ fluid system at elevated temperatures and pressures has been investigated experimentally to determine the PVTX properties of H₂O-CH₄ fluids in the P-T range equivalent to late diagenetic to low grade metamorphic environments, and XCH₄≤4mol%. A study has also been conducted to determine methane hydrate stability over the temperature range of -40~20°C. Synthetic fluid inclusions were employed in both studies as miniature autoclaves. Experimental data for the PVTX properties of H₂O-CH₄ fluids under late diagenetic to low grade metamorphic conditions was used to calculate the slopes of isoTh lines (the line connecting the P-T conditions of the inclusions at formation and at homogenization) at different PTX conditions. An empirical equation to describe the slope of iso-Th line as a function of homogenization temperature and fluid composition was developed. The equation is applicable to natural H₂O-CH₄ fluid inclusions up to 500°C and 3 kilobars, for fluid compositions ≤4 mol% CH₄. The Raman peak position of CH₄ gas is a function of the pressure and temperature. This relationship was used to determine the pressure along the methane hydrate stability curve in the H₂O-CH₄ system. The combined synthetic fluid inclusion, microthermometry and Raman spectroscopy method is a novel experimental approach to determine the P-T stability conditions of methane hydrates. The method is fast compared to conventional methods, and has the potential to be applied to study other gas hydrate systems.
- Molecular Dynamics Simulations for the Study of Biophysical Processes on Biological MembranesLeekumjorn, Sukit (Virginia Tech, 2008-09-19)Phospholipid bilayers constitute the primary structural element of biological membranes, and as such, they play a central role in biochemical and biophysical processes at the cellular level, including cell protection, intercellular interactions, trans-membrane transport, cell morphology, and protein function, to name a few. The properties of phospholipid bilayers are thus of great interest from both experimental and theoretical standpoints. Although experiments have provided much of the macroscopic functions and properties of biological membranes, insight into specific mechanisms at the molecular level are seldom accessible by conventional methods. To obtain a better understanding of biochemical and biophysical processes at the molecular level involving phospholipid bilayers, we apply molecular simulation methods to investigate the complexity of the membrane matrix using atomistic models. Here, we discuss three specific biological processes that are associated with biological membranes: 1) membrane stabilization, 2) membrane phase behavior, and 3) fatty acid-induced toxicity in cell membranes. For membrane stabilization, molecular dynamics studies were performed for mixed phospholipid bilayers containing two of the most prevalent phospholipids (phosphatidylcholine and phosphatidylethanolamime) in biological membranes. We presented structural and dynamics properties of these systems, as well as the effect of stabilizing agents, such as trehalose, on their properties. Furthermore, we performed a comprehensive analysis of the phase transition of lipid bilayers and investigated the interactions of stabilizing agents (glucose or trehalose) with lipid bilayers under dehydrated conditions to understand the mechanisms for preservation of cellular systems. For membrane phase behavior, a comprehensive study of the structural properties of saturated and monounsaturated lipid bilayers near the main phase transition were investigated using molecular dynamics simulations. In this study, we demonstrated that atomistic simulations are capable of capturing the phase transformation process of lipid bilayers, providing a valuable set of molecular and structural information at and near its transition state. Lastly, the third study investigated the mechanism for fatty acid-induced toxicity by integrating in vitro and in silico experiments to reveal the biophysical interactions of saturated fatty acid (palmitate) with the cellular membranes and the role of trehalose and unsaturated fatty acids (oleate and linoleate) in preventing changes to the membrane structure. Knowledge gained from this study is essential in the prevention and treatment of obesity-associated cirrhosis diseases.
- A Molecular Dynamics Study on the Interaction of Tea Catechins and Theaflavins with Biological MembranesSirk, Timothy Wayne (Virginia Tech, 2009-04-03)Molecular dynamics simulations were performed to study the interactions of bioactive catechins and theaflavins commonly found in tea with lipid bilayers, as a model for cell membranes. Previously, multiple experimental studies rationalized the anticarcinogenic, antibacterial, and other beneficial effects of these compounds in terms of physicochemical molecular interactions with cell membranes. To contribute toward understanding the molecular role of tea polyphenols on the structure of cell membranes, simulation results are presented for seven catechins and three theaflavins in lipid bilayer systems which are both pure (POPC) and representative of HepG2 cancer cells (POPC and POPE). Our simulations show that the catechins and theaflavins evaluated have a strong affinity for the lipid bilayer \textit{via} hydrogen bonding to the bilayer surface, with many of the catechins able to penetrate beneath the surface. Epigallocatechin-gallate (EGCG) and Theaflavin-3,3'-digallate showed the strongest interaction with the lipid bilayers based on the number of hydrogen bonds formed with lipid headgroups. The simulations also provide insight into the functional characteristics of the tea compounds that distinguish them as effective compounds to potentially alter the lipid bilayer properties. The results on the hydrogen-bonding effects may contribute to a better understanding of proposed multiple molecular mechanisms of the action of catechins and theaflavins in microorganisms, cancer cells, and tissues.
- Molecular Study of Capsaicin in Aqueous and Hydrophobic EnvironmentsLambert, Joseph Walter (Virginia Tech, 2006-06-08)Anyone who has eaten spicy foods has experienced the adverse effects of capsaicin, the pungent chemical found in hot chili that causes a burning sensation. The specific action of capsaicin occurs by the activation of receptors in sensory neurons. This thesis investigates the interaction of capsaicin with model cell membranes representing the structure of neurons. In particular, we are interested in the changes induced by capsaicin to the structure and dynamics of membranes. Molecular dynamics simulations are used to study the molecular interactions. The first part of this study evaluates different molecular representations for capsaicin in an 1-octanol/water system. This inhomogeneous system is commonly used to determine the partition of compounds between hydrophilic and hydrophobic environments, as that found in biological membranes. The results of these simulations validate the OPLS united-atom force field as a reasonable molecular representation of capsaicin, as it describes the behavior of capsaicin both quantitatively and qualitatively in 1-octanol/water mixtures. In the second part, simulations are performed for capsaicin and model cell membranes consisting of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylethanolamine, two of the most commonly found lipids. Simulations investigated capsaicin in the aqueous and lipid phases. The results provide insight into the changes to the bilayers caused by capsaicin. Bilayers containing dipalmitoylphosphatidylethanolamine showed lower permeabilities to capsaicin than those composed of pure dipalmitoylphosphatidylcholine. Temperature is found to be an important factor in the permeability of capsaicin in the bilayer. Capsaicin in the bilayer concentrated in a region beneath the lipid/water interface, in which favorable hydrophilic and lipophilic interactions occur. The structure of the bilayer is not significantly changed at the concentrations of capsaicin considered. One important result from the simulations indicates that the interfacial density decreases with increasing capsaicin concentration in the bilayer, supporting the experimental observations of increased permeability in bilayers exposed to capsaicin.
- Quantitative Studies of Intracellular Trafficking of Two Classes of Resident Golgi Apparatus ProteinsStarr, Tregei Nicole (Virginia Tech, 2006-04-24)The research presented in this dissertation consists of two primary parts. The initial focus centered on understanding the distribution of Golgi resident glycosyltransferases between the ER and Golgi at steady-state. Retrograde trafficking of these Golgi proteins has been demonstrated experimentally mandating the existence of a dynamic equilibrium between the Golgi apparatus and ER. Our published studies also included the development of a quantitative method for analysis of data collected using fluorescent microscopy. The second part of this dissertation presents results pertaining to the quantification of a unique Golgi resident protein that cycles in the late endosome bypass pathway. Using the published method of analysis and techniques developed during the initial project, the anterograde and retrograde transport kinetics of this Golgi protein were determined and used to develop a compartmental model for pH sensitive trafficking in the bypass pathway. The spatial Golgi distribution of the protein during retrograde transport to the Golgi following endosomal exit was also investigated. This research lies at the interface of experimental cell biology and quantitative computational analysis. These experiments combined more traditional experimental biological approaches with more recent computational approaches to understanding cellular mechanisms. Additionally, development of a quantitative method of analysis validated the use of fluorescent microscopy as a quantitative tool for studying intracellular proteins.
- Reactivity and Structure of Supported Nickel Phosphides (Ni₂P) in Deep Hydrodesulfurization CatalysisLee, Yong-Kul (Virginia Tech, 2004-12-16)This dissertation describes preparation and characterization of Ni₂P catalysts and their application in deep hydrodesulfurization (HDS) of a model sulfur compound, 4,6-dimethyldibenzothiophene (4,6-DMDBT), one of the most refractory S-compounds. This topic is of great importance in addressing recently enacted environmental regulations limiting the sulfur content in fuels. The work carried out includes synthesis of Ni₂P on different siliceous supports, SiO₂, MCM-41, and ultra-stable Y zeolite (USY). It also includes determining the characteristics of the supported Ni₂P catalysts with a wide range of techniques: X-ray powder diffraction (XRD), transmission electron microscopy (TEM), Fourier transform infrared (FTIR) and X-ray absorption fine structure (XAFS) spectroscopy. The use of these techniques allowed better understanding of the nature of the active sites as well as the effect of supports. Activity tests were conducted in the HDS of 4,6-DMDBT and the HDN of quinoline. The performance of the catalysts will be compared to that of a conventional sulfide hydrotreating catalyst, Ni-Mo-S/Al₂O₃. Investigation of the reaction mechanism in the hydrodenitrogenation (HDN) of 2-methylpiperidine together with in situ FT-IR measurements were conducted to understand how catalyst properties affect activity and selectivity.
- Study of Nanoparticle/Polymer Composites: I) Microstructures and Nonlinear Optical Solutions Based on Single-Walled Carbon Nanotubes and Polymers and II) Optical Properties of Quantum Dot/Polymer CompositesWoelfle, Caroline (Virginia Tech, 2006-03-31)The overall research theme of this dissertation was the study of nanoparticle/polymer composites. Two types of nanoparticles were utilized: Single-Walled Carbon Nanotubes and quantum dots. Chapter 1 of this thesis comprises an extensive literature review on Carbon Nanotubes, which presents theoretical aspects relevant to the structure and properties of CNTs, methods of purifying and solubilizing CNTs in aqueous and organic solvents and selected applications. This literature review is followed by the study and comparison of the optical limiting performances of different Single-Walled Carbon Nanotubes/conjugated polymer dispersions (Chapter 2). The results obtained are discussed in terms of dispersion of the SWNTs in the polymer solutions and resulting SWNT bundle diameters. Chapter 3 presents the spontaneous assembly of dendrimer patterns induced by SWNTs. Finally, chapter 4 presents a new method for fabricating quantum dot/polymer composites, which uses the extraction of positively charged quantum dot into a hydrophobic liquid. The resulting solution is used as a compatible polymerization medium for poly(methylmethacrylate ) networks enabling the formation of transparent and fluorescent composites.