Chemistry Commons^™

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

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In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Understanding The Interaction Of Environmental Contaminants With Polystyrene Nanoparticles And Dna Using Nuclear Magnetic Resonance Spectroscopy And Density Functional Theory, Saduni Arachchi

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The objective of the thesis is to study the effect of environmental pollutants on polystyrene nanoparticles and biomolecules. This is done in two different techniques, particularly NMR and density functional theory. In this thesis, we use a combination of 1H NMR, Saturation-Transfer Difference (STD) NMR and relaxation experiments to study the interactions, kinetics and dynamics of antibiotics with polystyrene nanoparticles. (PS NPs) Density functional theory (DFT) is used to study the binding of commonly used non-oxidative hair dyes to biomolecules (DNA and amino acids) and PS particles.

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

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The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

Electron-Transfer Mediated Photo-Switching In Nanoparticles, Liaoran Cao

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Previous publications from our lab demonstrated viable approaches to design a photo-switching nanoparticle with arguably superior brightness and photostability resulting in an improved resolution in localization-based microscopy, as compared to other photo-switching dyes or particles. As a follow-up, this dissertation is focused on two major tasks: first, developing nanoparticles with better photo-switching properties for super-resolution imaging; second, trying to achieve a better physical picture of the mechanisms involved in photo-switching, including polaron dynamics, charge transfer, and energy transfer. A new class of photo-switchable nanoparticles was developed by blending conjugated polymer semiconductor with fullerene-based electron acceptors, and further blending with polystyrene …

Designing Noncentrosymmetric Multifunctional Materials, Ebube Oyeka

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Noncentrosymmetric (NCS) materials with crystal lattices lacking spatial inversion symmetry display a wide range of exciting functionalities. This dissertation covers two classes of functional NCS materials: magnetic skyrmion-host compounds and multifunctional materials. Magnetic skyrmion and multifunctional materials combining optical and magnetic responses are providing avenues for developing and optimizing the performance of electronic devices that can have uses in memory storage, laser technology, medicine, sensors, etc. The formation of skyrmions is driven by asymmetric Dzyaloshinskii–Moriya (DM) interaction facilitated by broken spatial inversion symmetry and large spin-orbit coupling (SOC), while multiple functionalities arise when spin carriers and optical chromophores are optimally …

Understanding Dynamics Of Polymers Under Confinement: A Molecular Dynamics And Neutron Scattering Study, Supun Samindra Kamkanam Mohottalalage

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The current study probes the structure, dynamics, and rheological behavior of associating polymers including ionomers in melts and solutions as well as conjugated polymers confined into nanoparticles, using molecular dynamics (MD) simulations and neutron scattering techniques. The study focuses on two families of associative polymers, ion containing macromolecules and conjugated polymers.

Polymers that consist of ionizable groups along their backbone found uses in a broad range of applications. Examples include light weight energy storage and generation systems, and biomedical applications, where the polymers act as ion exchange membranes, and actuators. The ionic groups tend to form clusters that are in …

Automated Parallel Optimization Of Simulation Parameters Using Modified Nelder-Mead Simplex Algorithm, Erina Mills

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Computational simulations used in many fields have parameters that define models that are used to evaluate simulated properties. When developing these models, the goal is to choose the parameters that best replicate a set of desired properties. Mathematical optimization methods can be used to optimize the simulation parameters by defining a function that uses simulation parameters as input and outputs a value describing how well a set of experimental properties are reproduced.

Because simulated properties are often calculated using stochastic sampling methods, this optimization involves an objective function that is noisy and expensive to evaluate. Also, optimization of the simulation …

Bombardment Simulations And Intercalation Studies Of Carbon Materials, Charles Lowe

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Molecular bombardment experiments have led to the possibility of altering materials with properties not normally associated with those materials. Molecular bombardment leads to defect formation in the material, potentially creating a pore, depending on the material and bombarding molecule. Carbon allotropes, specifically graphite and graphene, make excellent candidates for molecular bombardment experimentation. Depending on the bombarding molecule and the kinetic energy associated with that molecule, the defects induced will be sufficient to create a pore in the graphene. The AIREBO potential is used to simulate a graphene bilayer being bombarded with a single Ar atom, or a fullerene molecule, to …

Neutron Study Of Structure And Dynamics Of Rigid Polymers, Naresh Osti

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The structure and the dynamics in two different classes of rigid polymers; ionomers and rigid luminescent polymers, have been investigated predominantly by neutron techniques. Rigidity of the backbones of both polymers affects their properties. For ionomers, it affects transport pathways, therefore, their applications for energy and separation membranes. In luminescent polymers, it determines the conformations of the chains and their electro-optical response. One group of the polymers consists of rigid hydrophobic para-phenylene backbone decorated with pendant phenyl side chains functionalized with sulfonic acid (SPP). The other family of polymers consists of poly para-phenyleneethynylene (PPE) backbone that becomes conjugated upon conformational …

Neutron Study Of Structured Polymers At Interfaces, Thusitha Etampawala

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This work focuses on interfacial structure and dynamics of structured polymers in thin films and in solutions using neutron techniques accompanied by atomic force microscopy. We probed polymers with a common theme that were highly segregated either because of presence of ionic groups or topological constraints. In these polymers the interfacial regions often define their function in different applications such as clean energy, printing adhesions and drug delivery systems. Thin film studies include systems of polystyrene/sulfonated polystyrene, a rigid sulfonated polyphenylene and polystyrene three-arm stars/linear polystyrene. The first two systems include ionic components and the last exhibits topological constraints. Polystyrene …

Environmental Implications And Applications Of Nanomaterials, Priyanka Bhattacharya

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Recent advances in material science and nanotechnology have given rise to a myriad of developments, while in the meantime call for research into the impacts of nanomaterials on the environment and human health. Although considerable progress has been made in the past decade concerning the behavior of nanomaterials in biological systems, such understanding is critically lacking with respect to the fate of nanomaterials in ecosystems.
Accordingly, this dissertation addresses the interactions between nanomaterials and algae--the major constituent of the aquatic food chain (Part I, Chapter two), and exploits the physicochemistry of nanoscaled synthetic dendritic polymers for environmental applications, especially for …

A Theoretical Investigation Examining Dna Conformational Changes And Their Effects On Glycosylase Function, Allyn Brice

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Glycosylase enzymes initiate the process of base excision repair (BER) in order to prevent the irreversible modification of the genome. In the BER process a damaged DNA base is recognized, removed from the DNA sequence, and then the remaining abasic site is repaired. Glycosylase enzymes are responsible for the base recognition mechanism and catalysis of the base excision. One of the most studied glycosylase superfamilies is uracil DNA glycosylase (UDG). The UDG superfamily has demonstrated specificity for excising uracil, which is the deamination product of cytosine, from DNA sequences of prokaryotes and eukaryotes. Mismatch-specific uracil DNA glycosylase (MUG) is a …

Synthesis And Development Of Novel Fullerene-Based Structures For Photovoltaics, Electronic Applications And Mri Contrast Agents, Manuel Chaur

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Metallic nitride endohedral metallofullerenes (EMFs) are one of the most interesting types of metallofullerenes due to their high yields and interesting electronic properties. The synthesis of these compounds allows the encapsulation of different metals inside fullerenes making it possible to combine the properties of the metal with those of the fullerene. Their interesting electrochemical and optical features make them potential candidates for several applications such as molecular electronics, biomedical imaging, non-linear optical devices, and magnetic resonance imaging (MRI) agents. This thesis reports the synthesis of novel metallic nitride EMFs based on Gd, Nd, Pr, Ce and La. These families of …

Fluorescent Conjugated Polymer Dots For Single Molecule Imaging And Sensing Applications, Changfeng Wu

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While single molecule imaging and sensing hold the promise of providing unprecedented detail about cellular processes, many advanced applications are limited by the lack of appropriate fluorescence probes. In many cases, currently available fluorescent labels are not sufficiently bright and photostable to overcome the background associated with various autofluorescence and scattering processes. This dissertation describes research efforts focused on the development of a novel class of fluorescent nanoparticles called conjugated polymers dots (CPdots) for single molecule fluorescence detection. The CPdots contain highly fluorescent π-conjugated polymers that have been refined over the last decades as the active material in polymer light-emitting …

Hybrid Bond-Order Potential For Silicon, Suleiman Oloriegbe

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ABSTRACT
A new hybrid bond-order potential for silicon is developed. The functional form of the potential is derived from hybrid of expressions from empirical bond-order formalism and first principles approximations. The total energy is expressed as the sum of attractive, repulsive and promotion energies. By introducing a screening function derived from approximations to first principles expressions, the potential is made long-ranged by allowing covalent interactions beyond the first nearest neighbor shell of atoms in agreement with quantum mechanical descriptions of the bonding in silicon. Environment-dependent promotion energy is introduced that accurately accounts for energetic interactions due to changes in hybridization …

Strategies For Expanding The Halogen Bonding Periodic Table And Desigining Complementary Halogen/Hydrogen Bonding Synthons, Hadi Arman

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Halogen bonding is the donation of electron density from an electron donor, such as N, O, S, Se atoms, to an electron acceptor such as a dihalogen or organohalogen. This interaction plays an important role in biological systems, such as the thyroid gland and is useful in many other fields such as drug design, crystal engineering, synthetic chemistry, material science and bioinorganic chemistry. However, currently there is a lack of information for this interaction in systems involving organoiodines with sulfur and selenium electron donors.
A variety of sulfur and selenium Lewis base donors were investigated with various organoiodines. The main …

Structure And Transport Characteristics Of Highly Rigid Ionomers, Lilin He

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The structure and transport characteristics in a novel family of ionomers consisting of a hydrophobic polyphenylene backbone substituted by sulfonic acid functionalized phenyl side chains (sPPs) have been investigated. These polymers have potential applications in electrochemistry as well as separation both as membranes and thin films. The bulk structure as a function of hydration has been explored by X-ray and neutron scattering. Interfacial structure was studied by AFM and neutron reflectometry. The characteristics of water in the bulk were studied by NMR and FTIR and that in thin films by neutron reflectometry.

The sPPs exhibit characteristic structure due to their …

Synthesis, Electronic Structure, And Reactivity Of Endohedral Metallofullerenes And Other Endohedral Carbon Nanostructures, Bevan Elliott

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The discovery in 1985 of fullerenes combined with the development of STM beginning in 1981 is credited as the starting point of the current nanoscience revolution. Endohedral fullerenes, discovered shortly after, have drastically different electronic properties when compared with the empty fullerenes. This dissertation has as its central focus the synthesis and electronic properties of endohedral metallofullerenes and other endohedral nanostructures.
The opening two chapters give a brief background of the discovery of fullerenes. A comprehensive literature list is given for the various families of trimetallic nitride endohedral fullerenes as well as other large endohedral metallic cluster fullerenes. Finally, a …

Structure And Dynamics Of Poly (Para-Phenyleneethynylene)S In Solutions And Thin Films, Yunfei Jiang

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This research focuses on the structure and dynamics of a family of rigid polymers, poly(para-phenyleneethynylene)s (PPEs) in solutions and thin films using small angle neutron scattering, neutron spin echo, nuclear magnetic resonance, X-ray scattering, atomic force microscopy and fluorescence spectroscopy. The effects of the solvent and the side chain on the molecular conformation and the association of PPEs have been investigated.
In dilute solutions, the phase diagram of dinonyl PPE in toluene and cyclohexane exhibits three distinct phases. At higher temperatures, PPEs form molecular solutions with extended conformations in toluene and worm-like chains in cyclohexane. With decreasing temperatures, PPEs associate …

Mixed Quantum-Classical Molecular Dynamics Study Of A Hydrated Electron And An Investigation Of Temperature Control Algorithms, Janet Aremu-Cole

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The use of classical and quantum mechanics has been employed in this dissertation to study temperature control algorithms and a hydrated electron. A comparison of the effects of four commonly used temperature control algorithms on the energetics and dynamics of liquid water has been executed, in efforts to better understand the non-equipartitioning effects caused by some thermostats. The Berendsen, Andersen, Langevin, and velocity rescaling temperature control algorithms were applied to both dimer and bulk water systems, using the TIP4P water model. The two deterministic thermostats, Berendsen and velocity rescaling, display the 'flying ice cube effect' that had been noticed earlier …

Adaptive Treatment Of Van Der Waals Interactions In Empirical Bond-Order Potentials With Application To Junction Formation In Carbon Nanotubes, Aibing Liu

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Molecular dynamics (MD) simulation of reactive condensed-phase hydrocarbon systems is a challenging research area. The AIREBO potential is particularly useful in this area because it can simulate bond breaking and bond forming during chemical reactions. It also includes non-bonded interactions for systems with significant intermolecular interactions.

The first part of this dissertation describes a method to adaptively incorporate van der Waals interaction of carbon atoms into the AIREBO force field. In bond-order potentials, the covalent bonding interactions adapt to the local chemical environment, allowing bonded interactions to change in response to local chemical changes.
Non-bonded interactions should adjust to their …

Path Integral Formulation Of Langeinv Dynamics With Applications To Rare-Event Systems, Bradley Dickson

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In the last decade great efforts have been made to efficiently study the behaviors of rare-event systems. The methods and theories developed in pursuit of this goal are far from unified and are instead applied on a case-by-case basis where one makes a best educated guess as to which approach may afford the greatest chance of studying the rare-event system in question. The work contained here is directed at further development of one of these sets of methods and theories. Specifically, a new theory of dynamics in the Langevin path space is developed with emphasis on generating and sampling Langevin …

The Interaction Between Hydrogen And Various Carbon Allotropes Calculated Using Bond-Order Potentials, Michael Knippenberg

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Carbon-based materials are an exciting component of materials science. The understanding of interactions at the atomic level provide useful information for creating materials with specific properties. This dissertation examines three hydrocarbon systems: amorphous carbon (with and without hydrogenation), hydrogen adsorption in carbon nanotubes, and reconstructions of the diamond surface.
A melting/quenching procedure is used to produce amorphous carbon films at 2.0, 2.6, and 3.0 g/cm³. The sp³ fraction at each density is calculated and found to be qualitatively similar to experimental data at low densities. The inclusion of hydrogen in the amorphous film causes the sp^{3 …}