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Microbial, mammalian and plant cells produce and contain secondary metabolites, which typically are soluble in water to prevent cell damage by crystallization. The formation of ion pairs, e.g. with carboxylic acids or mineral acids, is a natural blueprint to keep basic metabolites in solution. It was aimed at showing whether the mostly large carboxylates form soluble protic ionic liquids (PILs) with basic natural products resulting in enhanced aqueous solubility. Furthermore, their supramolecular pattern in aqueous solution was studied. Thereby, naturally occurring carboxylic acids were identified being appropriate counterions for natural basic compounds and facilitate the formation of PILs with their beneficial characteristics, like improved dissolution rate and enhanced apparent solubility. / Mikrobielle, Säugetier- und Pflanzenzellen produzieren und enthalten Sekundärmetaboliten, welche in Wasser gelöst vorliegen, um Zellschäden (z.B. durch Kristallisation) zu vermeiden. Die Bildung von Ionenpaaren, beispielsweise mit Carbonsäuren oder Mineralsäuren, ist eine natürliche Strategie, um basische Metaboliten in Lösung zu halten. Es sollte gezeigt werden, dass die vergleichsweise großen Carboxylate lösliche protische ionische Flüssigkeiten (PILs) mit basischen Naturstoffen bilden, was zu einer verbesserten Wasserlöslichkeit führt. Weiterhin wurde das supramolekulare Verhalten der PILs in wässriger Lösung untersucht. Dabei wurden natürlich vorkommende Carbonsäuren als geeignete Gegenionen für natürliche basische Verbindungen identifiziert. Die resultierenden PILs zeigten eine verbesserte Auflösungsrate und verbesserte scheinbare Löslichkeit.

Fire incidents are a major contributor to the number of deaths and property losses within the United States each year. Fire investigations determine the cause of the fire resulting in an assignment of responsibility. Current methods of fire debris analysis are reviewed including the preservation, extraction, detection and characterization of ignitable liquids from fire debris. Leak rates were calculated for the three most common types of fire debris evidence containers. The consequences of leaking containers on the recovery and characterization of ignitable liquids were demonstrated. The interactions of hydrocarbons with activated carbon during the extraction of ignitable liquids from the fire debris were studied. An estimation of available adsorption sites on the activated carbon surface area was calculated based on the number of moles of each hydrocarbon onto the activated carbon. Upon saturation of the surface area, hydrocarbons with weaker interactions with the activated carbon were displaced by more strongly interacting hydrocarbons thus resulting in distortion of the chromatographic profiles used in the interpretation of the GC/MS data. The incorporation of an additional sub-sampling step in the separation of ignitable liquids by passive headspace sampling reduces the concentration of ignitable liquid accessible for adsorption on the activated carbon thus avoiding saturation of the activated carbon. A statistical method of covariance mapping with a coincident measurement to compare GC/MS data sets of two ignitable liquids was able to distinguish ignitable liquids of different classes, sub-classes and states of evaporation. In addition, the method was able to distinguish 10 gasoline samples as having originated from different sources with a known statistical certainty. In a blind test, an unknown gasoline sample was correctly identified from the set of 10 gasoline samples without making a Type II error.

The fire debris analyst is often faced with the complex problem of identifying ignitable liquid residues in the presence of products produced from pyrolysis and incomplete combustion of common building and furnishing materials. The purpose of this research is to investigate a modified destructive distillation methodology provided by the Florida Bureau of Forensic Fire and Explosive Analysis to produce interfering product chromatographic patterns similar to those observed in fire debris case work. The volatile products generated during heating of substrate materials are extracted from the fire debris by passive headspace adsorption and subsequently analyzed by GC-MS. Low density polyethylene (LDPE) is utilized to optimize the modified destructive distillation method to produce the interfering products commonly seen in fire debris. The substrates examined in this research include flooring and construction materials along with a variety of materials commonly analyzed by fire debris analysts. These substrates are also burned in the presence of a variety of ignitable liquids. Comparisons of ignitable liquids, pyrolysis products, and products from pyrolysis in the presence of an ignitable liquid are performed by comparing the summed ion spectra from the GC-MS data. Pearson correlation was used to determine if substrates could be discriminated from one another. A pyrolysis products database and GC-MS database software based on comparison of summed ion spectra are shown to be useful tools for the evaluation of fire debris.

Thesis advisor: Udayan Mohanty / The conformational dynamics plays a significant role in a wide range of biological systems, from small RNA molecules to the large-scale ribonucleoprotein assemblies, in which ions are found critical and have notable structural and functional impacts. In the glass-forming liquids, the structural dynamics also calls for further investigations and deeper understandings. To this end, using four distinct chapters, this dissertation discusses the ion-related conformational dynamics in various scales of biomolecular systems, as well as the fluctuation effects in the glass-forming liquids. In chapter 1, we investigate the dynamics of ions and water molecules in the outer solvation sphere of a widely studied 58-nucleotide rRNA fragment. Molecular dynamics (MD) simulations with explicit solvent molecules and atomic details are performed for the RNA fragment in ionic solution. We determine all of the association sites and spatial distributions of residence times for Mg2+, K+, and water molecules in those sites. In accordance to the analysis of the dynamics of the RNA fragment, we provide insights into how the dynamics of ions and water molecules are intricately linked with the kinetics of the RNA fragment. In addition, the long-lived sites for Mg2+ ions identified from the simulation agree with the metal ion locations determined in the X-ray structure. The excess ion atmosphere around the RNA fragment is calculated and compared with the experimental measures. The results from this study indicate that the 58-mer rRNA fragment in ionic solution forms a complex polymer that is encased by a fluctuating network of ions and water. In chapter 2, the conformational dynamics of a large-scale ribonucleoprotein assembly, ribosome, is studied with molecular dynamics simulations with a newly developed model that accounts for electrostatic and ionic effects on the biomolecules. In this study, an all-atom structure based model is constructed with explicit representations of non-hydrogen atoms from biomolecules and diffuse ions. Implicit treatment is applied to the solvent molecules with the solvation effect associated with diffuse ions described by effective potentials. Parameters in this model are refined against explicit solvent simulations and experimental measures. This model with refined parameters is able to capture the excess Mg2+ ions for prototypical RNA systems and their dependence on the Mg2+ concentrations. Motivated by this, we apply the model to a bacterial ribosome and find that the position of the extended L1 stalk region can be controlled by the diffuse ions. This simulation also indicated ion-induced long-range interactions between L1 stalk and tRNA, which provides insights into the impact of ions on the functional rearrangements of ribosome. In chapter 3, we focus on the dynamics of the glass-forming liquids. In this study, we generalized the Adam-Gibbs model of relaxation in glass-forming liquids and take into account the fluctuations in the number of molecules inside the cooperative rearranging region. We obtain the expressions of configurational fractions at the glass-transition temperature with and without the fluctuation effect in Adam-Gibbs model, and determine the configurational fraction for several glass-forming liquids at glass-transition temperature in the absence of fluctuation effects. A connection between the β Kohlrausch-Williams-Watts parameters and the configurational fraction at the glass-transition temperature is also reported in this study. In chapter 4, we apply the model developed in chapter 2 to a ribosome structure to investigate the effects of diffuse ions on the aminoacyl-tRNA (aa-tRNA) accommodation process. The aa-tRNA accommodation is a critical step in the tRNA selection process which serves the purpose of protein synthesis in the ribosome. Experimental and computational efforts were made to reveal the mechanism and the energetic properties of the accommodation process, while the effects from diffuse ions on this process remain elusive. To this end, we design and perform MD simulations of ribosome structure with different treatment of electrostatics and diffuse ions in the system. Simulations with various ionic concentrations are also performed to study the concentration effects. The simulation trajectories indicate that diffuse ions can facilitate the aa-tRNA accommodation process and stabilize the accommodated configurations. In addition, we observe that Mg2+ ions play critical roles in stabilizing the accommodated configurations and a few millimolar change of Mg2+ concentration can alter the tendency of the tRNA configurational change during the accommodation process. This result shed light on the investigations of suitable ionic environment for the tRNA selection in the ribosome. It will be fruitful to extend this strategy into the investigations of other conformational rearrangements in the ribosome, such as tRNA translocation and subunit rotation, which will provide us with deeper understanding about the functional mechanism of the ribosome. / Thesis (PhD) — Boston College, 2021. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

<p> The separation of distilled water and coconut fatty acid (CNFA) was investigated in a 4 in. x 16 in. vertical gravity decanter to determine the most significant design variables. The design variables studied were tangential versus perpendicular feed flow, height/diameter ratio, the total feed flow rate, the temperature and the intertace position with respect to feed inlet. The criteria used were the calculated immiscible concentration of water in CNFA overflow (Cw) and that of CNFA in water underflow (Co), The test conditions were arranged according to a Central Composite Design based on Box Method of Experimentation. Two levels of inlet geometry and five levels of each of the other four variables were studied. The range of variables were 1. Inlet geometry Tangential and Perpendicular Feed Flow 2. Height/Diameter Ratio 3/1 to 4/1 3· Total Feed Flow rate 160 cc/min. to 320 cc/min. 4. Temperature 40° to 80°c. 5· Interrace Position 2" below feed inlet to 2" above feed inlet The Overall residence time in the decanter ranged from 7.5 to 12.5 minutes. The drop size distribution of the incoming dispersion was measured by taking photomicrographs for all the runs. </p> <p> It was found that the tangential feed flow was slightly better but not significantly better for the separation of two immiscible liquids. Statistical analysis revealed that 95% confidence level height/diameter ratio, flow rate and temperature, respectively, are the most important design variables for the separation of CNFA from water underflow. The dependence of Cw on height/diameter ratio of Co on the interface position was interpreted to mean that the theoretical, plug flow residence time within each phase is the most important design variable. Interaction between variables and second order constants were not found significant at 95% confidence level. Sedimentation rather than coalescence appeared to be the controlling factor in the present study. </p> / Thesis / Master of Engineering (MEngr)

Almost a century after its discovery, superconductivity (SC) is still the most challenging and fascinating topic in condensed matter physics. Organic superconductors show exotic phases and phase transitions with a change in temperature or pressure. In this dissertation, we studied the phases and phase-transitions in one-dimensional (1D) and two-dimensional (2D) organic materials. This dissertation itself is a group of three sub-projects. In project (i), we studied the properties of a novel state “paired electron crystal” (PEC) in the quarterfilled Hubbard model to understand the phases and properties of 2D organic materials. We also studied the effects of charge and spin frustration on the 2D strongly correlated quarterfilled band. Our conclusions are based on exact diagonalization (ED) studies that include electron-electron and adiabatic electron-phonon interactions. For moderate to strong frustration, the dominant phase is a novel spin-singlet PEC. We discuss the implications of the PEC concept for understanding several classes of quarterilled band materials that display unconventional superconductivity. In project (ii), we studied the thermodynamics of a zigzag ladder model, applicable to quasi-1D organic materials. Using the quantum Monte Carlo (QMC) method, we studied the thermodynamics of charge ordering in quarterilled quasi-1D organic charge transfer solids (CTS). Previous theoretical studies on these CTS have focused on ground state properties or purely 1D systems. In the zigzag ladder, no separate high-temperature ordering is expected; instead the ladder is metallic at high temperature, and as temperature decreases, a single transition to the PEC state with a spin-gap takes place. In project (iii), we studied superconducting pairing correlation and metal-insulator transitions in the halfilled Hubbard model. We employed the Hubbard model and used the path integral renormalization group (PIRG) method for this study. Antiferromagneticmediated SC was suggested for small to large frustration in anisotropic triangular lattices. Previous work on the halfilled Hubbard model using the ED method was successful in showing the absence of d-wave SC on a small anisotropic triangular lattice. We extended this study to larger lattices to investigate the existence of long-range order of superconducting pair-pair correlations. We also show the absence of d-wave SC in this model on larger lattices.

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