Physical Chemistry Commons^™

From Flasks To Applications: Design And Optimization Of Giant Quantum Dots Using Traditional And Automated Synthetic Methods, Christina J. Hanson

Nanoscience and Microsystems ETDs

Semiconducting nanocrystals, also known as quantum dots (QDs), that emit light with near-unity quantum yield and are extremely photostable are attractive options as down-conversion and direct electricity-to-light materials for a variety of applications including solid-state lighting, display technologies, bio-imaging and optical tracking. Standard QDs with a core/thin shell structure display fluorescence intermittency (blinking) and photobleaching when exposed to prolonged room temperature excitation for single dot measurements, as well as significant reabsorption and energy transfer when densely packed into polymers or at high solution concentrations.

We have developed thick shell “giant” QDs (gQDs), ultra-stable photon sources both at the ensemble and …

Synthesis, Characterization, And Spectroscopy Of Donor-Acceptor Charge Transfer Complexes, Dominic Kofi Kersi

Chemistry and Chemical Biology ETDs

A series of square-planar metal (diimine)(dichalcogenolene) chromophoric complexes have been synthesized, characterized and studied spectroscopically. Studies conducted on diimineplatinum(II) dichalcogenolene complexes (LPtL’) using time resolved spectroscopic techniques such as transient absorption and emission, reveal a charge-separated excited state of the type dichalcogenolene → diimine charge-transfer (LL’CT) [(dichalcogenolene^•+)Pt(diimine^•-) with an open shell donor-acceptor biradical character. This makes the low-energy ligand-to-ligand charge-transfer (LL’CT), or the mixed-metal ligand-to-ligand charge-transfer (MMLL’CT), transitions of diimineplatinum(II) dichalcogenolene complexes particularly interesting to us in facilitating our knowledge of biradical charge-separated states. Long-live excited state lifetimes were observed for these complexes upon visible photoexcitation …

Novel Design Strategies For Platinum-Containing Conjugated Polymers And Small Molecules For Organic Solar Cells, Wenhan He

Chemistry and Chemical Biology ETDs

Current state-of-the-art organic solar cells (OSCs) adopt the strategy of using conjugated polymers or small molecules as donors and fullerene derivatives as acceptors in their active layers. Regarding to the donors of interest, the conjugated polymers and small molecules coupled with heavy metals have been less explored compared to their counterparts. Among various transition metal complexes applied, Pt(II) complexes are unique because of their intrinsic square planar geometries and ability to serve as building blocks for conjugated systems. Furthermore, the heavy metal Pt facilitates the formation of triplet excitons with longer life times through spin-orbital coupling which are of benefit …

Universal Disorder In Organic Semiconductors Due To Fluctuations In Space Charge, Tzucheng Wu

Physics & Astronomy ETDs

This thesis concerns the study of charge transport in organic semiconductors. These materials are widely used as thin-film photoconductors in copiers and laser printers, and for their electroluminescent properties in organic light-emitting diodes. Much contemporary research is directed towards improving the efficiency of organic photovoltaic devices, which is limited to a large extent by the spatial and energetic disorder that hinders the charge mobility. One contribution to energetic disorder arises from the strong Coulomb interactions between injected charges with one another, but to date this has been largely ignored. We present a mean-field model for the effect of mutual interactions …

Development Of Organocatalytic Reactions For The Assembly Of Complex Molecules, Chenguang Yu

Chemistry and Chemical Biology ETDs

Development of efficient organocatalytic reactions for the facile assembly of synthetically and medicinally useful molecules is an important task in modern organic synthesis. Towards this end, my Ph. D. study focuses on the development of novel organocatalytic reactions for the construction of structurally diverse molecular architectures. A chiral bifunctional amine thiourea as promoter has been developed as an efficient solution to a long standing challenging issue in atropo-enantioselective transesterification of the Bringmann lactones. This organocatalytic approach delivers the first highly enantioselective, high yielding dynamic kinetic resolution process for the preparation of axially chiral biaryl compounds with a broad substrate scope …

Molecular Structure And Exciton Dynamics In Organic Conjugated Polymers, Alan K. Thomas

Chemistry and Chemical Biology ETDs

Intermolecular electronic interactions, dipole coupling and orbital overlap, caused by π-π stacking in organic conjugated polymers lead to unique structures and properties that can be harnessed for optoelectronic applications. These interactions define structure-function relationships in amorphous and aggregated forms of polymers in the solid state and determine their efficiencies and functionality in electronic devices, from transistors to solar cells. Organic polymer electronic device performance depends critically upon electronic coupling between monomer units --mediated by conformation and packing characteristics -- that dictates electronic properties like conductivity and capacitance as well as electronic processes, such as charge carrier generation and transport. This …

Development Of Oligo(P-Phenylene Ehynylene)(Ope) Applications Against Chemical And Biological Threats, Suhyun Yoon

Chemistry and Chemical Biology ETDs

Four new applications of oligo-phenylene ethynylene (OPE) and poly-PE (PPE) compounds for detection and destruction of biological and chemical threats have been investigated. Mixed surfaces composed of PPEs and a thermoswitchable polymer were created, and were shown to be able to capture, kill, and reversibly release pathogenic bacteria. In order to develop fluorescent sensors for CW agents, the spectral changes of OPEs with surfactants and malathion (a simulant for nerve agents) were measured. Formation of OPE-dimers in the presence of surfactants can cause fluorescence enhancement (turn-on) or quenching (turn-off). Among six positive and negative OPEs, only OPEs with ethyl ester …

Design, Synthesis And Evaluation Of Bivalent Inhibitors Of Trehalose-6-Phosphate Phosphatase, Chunliang Liu

Chemistry and Chemical Biology ETDs

The D-glucose disaccharide α, α-D-trehalose is synthesized by a variety of bacteria, fungi, plants and invertebrates to support cell survival by functioning as a fuel, a metabolic regulator or a protectant against environmental stress. Five different trehalose biosynthetic pathways are known to exist, one of which, the OtsA/OtsB pathway is common among pathogenic bacteria and fungi and is also found in parasitic nematodes. Previously reported otsA and otsB gene knockout (or knockdown) experiments have shown that both pathway enzymes are essential for M. tuberculosis cell growth and host colonization. RNAi gene silencing carried out in the nematode model system Caenohabditis …

Mining Public Databases For Discovery Of Structure And Function Within The Hotdog-Fold Thioesterase And Had Phosphatase Enzyme Families, Sarah Toews Keating

Chemistry and Chemical Biology ETDs

For my doctoral work, I have developed strategies to mine public databases for data that can be used to infer structural and functional information for the hotdog-fold and HADSF superfamilies. For the hotdog-fold superfamily, I used curated and automatically applied annotations of structure, taxonomic lineage, function, and subfamily membership from the UniProtKB, gene context and taxonomic information from the NCBI, and the results of several in-depth explorations of subfamily/function and structural class membership. Based on the distribution of the aforementioned annotations mapped onto a sequence similarity network (SSN), I applied structural assignments to sequences and/or specific function/subfamily assignments to ~143,000 …

Case Studies Of The Hot Dog-Fold And Acyl-Adenylate-Forming Superfamilies: Characterizing The Importance Of Functional Divergence In Cellular Metabolism, Lucas R. Zimney

Chemistry and Chemical Biology ETDs

Some of the biggest contributors to cellular respiration (and cellular metabolism in general) are acyl-CoA derivatives, a subclass of biological thioesters. Known to function in a variety of pathways, the regulation of their formation and breakdown are critical, carried about by acyl-CoA synthetases and thioesterases, respectively. The work reported within this dissertation will focus on functional divergence within two enzyme superfamilies -- the hot dog-fold and acyl-adenylate-forming superfamilies — and can be broken down into two main parts. Part one will look at tracking the functional divergence within the hot dog-fold superfamily thioesterases. A highly evolved thioesterase, flK, has been …

The Electronic Structure Of The Pyranopterin Dithiolene Cofactor And Radical Reporters Of Excited State Interactions, Benjamin William Stein

Chemistry and Chemical Biology ETDs

Crystal structures of multiple molybdenum enzymes clearly demonstrate interesting structural distortions involving the pyranopterin dithiolene. These distortions can be correlated with pyranopterin oxidation state through the use of DFT geometry optimized structures of the possible oxidation states, and these are correlated with enzyme family. The potential role of the pyranopterin dithiolene in electron transfer in the varied enzyme familes has been explored through the use of non-equilibrium Green's function (NEGF) electron transport calculations. These calculations demonstrate clear differences in electron transport behavior as a function of pyranopterin oxidation state. The Jahn-Teller effect can strongly impact the geometric and electronic structures …

Electrochemical Investigation Of Homogenous Species At An Electrode Interface, Christopher Alan Larsen Iii

Chemistry and Chemical Biology ETDs

CO₂ reduction is a pressing problem worldwide, and one obstacle in the electrochemical conversion of CO₂ to more useful C₁ products such as methanol and formic acid is the kinetic barrier known as overpotential. The overpotential of rearranging the nuclei in CO₂ to accommodate electron transfer can be lowered by pre-bending the CO₂ molecule in an adduct-mediated complex. The work presented in Part I utilizes a combination of hard and soft donors on pincer-like ligands to effect the bending of CO₂ prior to electrochemical reduction. A large majority of the work consists of using …

Theory, Multiscale Simulations, And Experiments On Mesoscale Multifunctional Systems, Lance Edward Edens

Chemistry and Chemical Biology ETDs

Computational simulations use theoretical models to reproduce, as accurately as possible, the observed real-world behavior of complex structures. Guided by experimental observations, many multiscale/coarse-grained simulations seek to explore increasingly complicated systems. Here, a multiscale/coarse-grained simulation program (called TM2) is developed with applications to 1) properties and mechanisms of DNA and DNA polymerases, and 2) adhesion between whole bacterial cells and patterned surfaces. Results from the bacterial adhesion application form a part of a larger collaborative effort aimed at creating multifunctional, controllable surfaces to capture and kill pathogenic bacteria. The application of TM2 is first demonstrated by a coarse-grained model for …

Spectroscopic And Computational Studies Of Molybdenum Enzymes And Models, Chao Dong

Chemistry and Chemical Biology ETDs

In this dissertation spectroscopic methods such as electronic absorption (EAS), resonance Raman (rRaman), electron paramagnetic resonance (EPR), and MCD spectroscopies have been used in combination with DFT calculations for the interpretation of experimental results. These methods have been used to investigate the molybdenum coordination environment in enzymes and model complexes. Xanthine oxidase (XO), one of the canonical molybdenum enzyme families, hydroxylizes heterocyclic substrates by inserting an oxygen atom from molybdenum-activated water into a substrate C-H bond. This generates reducing equivalents that pass through two iron sulfur clusters and then to FAD, where oxidation of the FAD takes place. In this …

Study Of Novel Synthetic Methodologies For Indolyl Derivatives And Beta-Fluoroenals, Xiaobei Chen

Chemistry and Chemical Biology ETDs

One of the central goals in modern organic synthesis is to develop efficient synthetic strategies for the preparation and study of complex molecules possessing interesting structural, biological, and physical properties. Toward this end, my Ph. D. work focuses on the development of novel synthetic methodologies for the facile construction of synthetically and biologically significant molecular architectures. The tert-prenylated indoles and indolines are widely present in a large collection of natural products and biologically active compounds. Although significant efforts have been made on the development of efficient methods to prepare these intriguing molecular architectures, few methods have been explored to introduce …

Development Of Novel Efficient Organocatalytic Reactions For The Construction Of Complex Molecular Architectures, Aiguo Song

Chemistry and Chemical Biology ETDs

Facile construction of synthetically and medicinally significant optically active molecular architectures from simple and readily available materials via catalytic enantioselective cascade processes is the cental goal in organic synthesis. Toward this end, my Ph.D. work focuses on the development of novel organocatalytic asymmetric cascade reactions and their application in the synthesis of versatile molecular structures. A novel amine catalyzed decarboxylative enantioselective Diels—Alder reaction between aldehydes and readily available coumarin-3-carboxylic acids as dienophiles via dienamine catalysis has been realized. Notably, the decarboxylation facilitates the release of the catalyst in the Diels—Alder reaction adducts and achieves high reaction efficiency in terms of …

Criteria For Evolution Of Successful Proteins: Fold Fitness And Domain Dynamics Explored, Tyrel Bryan

Chemistry and Chemical Biology ETDs

The Haloacid Dehalogenase Superfamily (HADSF) is a ubiquitous family of enzyme with more than 32,000 members. A variety of reactions are catalyzed by HAD members, but a majority of HAD members are phosphatases. Dephosphorlyation of organophosphate metabolites are carried out in the conserved Rossmann-like core domain. The Rossman-like core domain houses the conserved active site residues necessary for catalysis and also supports domain inserts associated with substrate binding. This dissertation will focus primarily on investigating fold fitness and domain dynamics of HAD proteins more specifically three C2 capped proteins. The first part will focus on whether or not the prevailing …

Development Of Novel Small Molecules For Imaging And Drug Release, Yanting Cao

Chemistry and Chemical Biology ETDs

Small organic molecules, including small molecule based fluorescent probes, small molecule based drugs or prodrugs, and smart multifunctional fluorescent drug delivery systems play important roles in biological research, drug discovery, and clinical practices. Despite the significant progress made in these fields, the development of novel and diverse small molecules is needed to meet various demands for research and clinical applications. My Ph.D study focuses on the development of novel functional molecules for recognition, imaging and drug release. In the first part, a turn-on fluorescent probe is developed for the detection of intracellular adenosine-5'-triphosphate (ATP) levels based on multiplexing recognitions. Considering …

Spectroscopic Studies Of Conjugated Polymer Nanostructures And Polymer/Acceptor Blends, Jian Gao

Chemistry and Chemical Biology ETDs

This dissertation presents the results of investigations into organic semiconducting systems at the nano- to mesoscales through spectroscopic and electrical imaging techniques. Particular emphasis was put on capturing the role of conformation and morphology on electronic properties and processes. The combination of experimental methods and data analysis techniques used in this work reveals useful insights into the correlations between polymer structures and their photovoltaic device performance, and provide clues to developing better performing organic solar cells. The main approach of this work is using prototypical conjugated polymer systems, either ensemble or in their nanostructures, to study the solar cell active …

Stable Solar Cells Through Controlled Block Copolymer Self-Assembly And Cooperative Hydrogen Bonding Interactions, Fei Li

Chemistry and Chemical Biology ETDs

Current state-of-the-art polymer solar cells adopt the bulk-heterojunction (BHJ) morphologies where the electron donors (i.e. conjugated polymer) and electron acceptors (i.e. fullerenes) as active layers are mixed in an intimate way. The phase separation that modulates the exciton diffusion and charge transport in the current BHJ morphology is an uncontrolled process and thus results in random domain sizes of the polymer/fullerene blend. In addition, the polymer and fullerenes in the blend are intrinsically two immiscible materials and they tend to undergo macrophase separation eventually, which leads to deteriorated device performance. One way to address the abovementioned issues is to attach …

Theoretical Studies Of Transition Metal Catalysis, Ryan S. Johnson

Chemistry and Chemical Biology ETDs

Transition metal catalysis, being critical to nearly all aspects of the modern industrial world, is the focus of a series of theoretical studies which seek to elucidate the fundamental and electronic origins of enhanced chemical activity and selectivity. The application of density functional theory on extended single metal and alloyed surfaces, supported single metal atoms, and gas phase cationic species illuminate various aspects of transition metal catalysis in a wide range of enviornments. Adsorption, reactivity, and other mechanistic details developed here suggest possible mechanisms used to aid interpretation of experimental results and guide developement of future catalysts.

Simulations Of Chemical Catalysis, Gregory K. Smith

Chemistry and Chemical Biology ETDs

This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows.

Project 1 — Bacterial Enzyme SpvC

The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a β-elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC …

Synthesis, Characterization, And Electrochemical Evaluation Of Novel, Highly Active Catalysts For The Oxygen Reduction Reaction In Alkaline Media, Danae Jacquelyne Davis

Chemistry and Chemical Biology ETDs

Efficient electrocatalysts for the oxygen reduction reaction (ORR) are needed for fuel cells and next generation metal-air batteries, as the overall efficiency of these systems is currently limited by cathode kinetics. While Pt and Pt-based alloys demonstrate excellent electrocatalytic activities, their prohibitive cost and rarity ultimately prevents their widespread utilization. Catalyst materials that are highly active, stable, and cost effective are needed. Manganese oxide (α-MnO₂) catalysts doped with varying amounts of Cu or Ni were synthesized, characterized, and evaluated for their performance as catalysts for the oxygen reduction reaction in alkaline electrolyte. Cu-α-MnO₂ nanowire catalysts consistently attained …

Spectroscopic Studies Of Conformation And Packing In Polythiophenes, Edwards T. Niles

Chemistry and Chemical Biology ETDs

This thesis employs variants of spectroscopic techniques to evaluate intermolecular interactions between P3HT chains in solution and in the solid state. Emphasis was put on understanding not only how intermolecular interactions within P3HT chains affect electronic properties, but also to assess changes due to the addition of weak and strong electron acceptors. To this end, optical and magnetic spectroscopies were focused on to correlate observed changes in electronic properties to physical changes in the polymer structure. To assess changes in intermolecular interactions, self-assembly was used to form P3HT nanofibers and were studied using resonance Raman, and transient absorption, and temperature- …

Determining The Function Of Hotdog-Fold Thioesterases, Yajun Wu

Chemistry and Chemical Biology ETDs

The enzymes that hydrolyze thioesters to the free acids and free thiols are called thioesterases. Based on the different folding strategy, most thioesterases are classified into two superfamiles: the hotdog-fold enzyme superfamily or alpha/beta-fold hydrolase enzyme superfamily. Hotdog-fold thioesterases share high degree similarity in structure which resembles a hotdog'. YigI is one of the last two uncharacterized hotdog-fold thioesterases from E.coli. To study the function of YigI, substrate specificity profile was determined by thioesterase activity assay. YigI possesses a preference for long chain acyl-CoA over shorter chain acyl-CoA. The highest activity was found in catalysis of myristoyl-CoA. By alignment with …

Development Of Novel Reaction-Based Fluorescent Probes, Weimin Xuan

Chemistry and Chemical Biology ETDs

Fluorescent probes have been proved to be very valuable tools in chemical and biological applications, and extensive exploration has been made. Recently, reaction-based fluorescent probes became a new design trend and displayed great potential with remarkable implementation to the conventional design method. However, this field is still underdeveloped, and a lot of problems remain to be solved. As part of our groups research interest, my Ph.D. study centered on the development of new reaction-based fluorescent probes. Firstly, our previous research on Hg²⁺ was continued. In this work, we developed a novel ratiometric fluorescent probe for Hg²⁺ with impressive …

Antimicrobial Activity And Mechanistic Study For The Poly(Phenylene Ethynylene) (Ppe)-Based Cationic Conjugated Polyelectrolytes And Oligo-Phenylene Ethynylenes, Ying Wang

Chemistry and Chemical Biology ETDs

My dissertation work focuses on recent progress made in elucidating the intermolecular interactions between a novel class of synthetic phenylene ethynylene (PPE)-based conjugated polyelectrolyte polymers (CPEs) and oligomers (OPEs) and multiscale cellular targets that give rise to their remarkable broad spectrum biocidal activity. We studied the interactions and self-assembly behaviors of the CPEs and OPEs with a set of vital biomolecules, including lipids, proteins and nucleic acids, that reveal the potential pathways by which the synthetic biocidal agents could exert toxicity. Then, we explored the antimicrobial effects and mechanisms of the CPEs and OPEs on multiple clinically relevant pathogens, with …

Spectroscopic And Computational Electronic Structure Studies Of Donor-Acceptor Systems, Diana Habel-Rodriguez

Chemistry and Chemical Biology ETDs

Three molecular systems have been studied, which exhibit strong intramolecular electronic communication between constituent moieties. Experimental results for electronic absorption, resonance Raman, electron paramagnetic resonance (EPR), and magnetic circular dichroism (MCD) spectroscopies are presented. Density functional theory (DFT) electronic structure calculations were employed to augment the interpretation of experimental results. Using a valence bond configuration interaction (VBCI) model we show that the ground state properties of the molecules are influenced by excited state configurations. Donor ( = semiquinone)-bridge-acceptor ( = nitronylnitroxide) biradicals show strong ferromagnetic donor-acceptor coupling, and contributions to the ferromagnetic coupling from spin delocalization and spin polarization mechanisms …

Catalytic Mechanism And Function Evolvement Studies Of Phosphatases Within Haloacid Dehalogenase Superfamily (Hadsf), Li Zheng

Chemistry and Chemical Biology ETDs

The haloacid dehalogenase superfamily (HADSF) is one of the largest known enzyme superfamilies, having more than 32,000 nonredundant members. Enzymes in this superfamily catalyze a number of different chemical reactions including dehalogenation, phosphoryl transfer, and hydrolysis of phosphate esters and phosphates. The vast majority of HADSF members are phosphatases, which contain a highly conserved core domain that is constructed to catalyze hydrolysis reactions of phosphorylated sugars or nucleotides by using an active site Asp nucleophile and a Mg²⁺ cofactor. Most phosphatases possess a cap domain, which in association with the core domain assists active site desolvation and binds the …

Structure To Function: Case Studies Of Hotdog-Fold Superfamily Thioesterases From Escherichia Coli, John A. Latham

Chemistry and Chemical Biology ETDs

My doctoral research primarily focuses on the Escherichia coli hotdog-fold thioesterases ydiI and ybgC. The ydiI gene is colocalized in the operon ydiHIJ. A substrate screen provided evidence that YdiI prefers aryl-CoA substrates and discriminated against the analogous aryl-ACP, unlike the paralog YbdB which works on 2,4-DHB-EntB in the enterobactin synthesis pathway. A bioinformatic approach showed that in some bacteria, ydiI is colocalized with genes from the menaquinone pathway. YdiI was shown to catalyze the hydrolysis of DHNA-CoA with physiological relevance (k_cat/K_M ~ 10⁵). Furthermore, the E. coli YdiI- strain was shown to …