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School of Chemistry and Biochemistry

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College of Sciences

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https://finding-aids.library.gatech.edu/agents/corporate_entities/153

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Now showing 1 - 10 of 1898

Ionic Liquids: Understanding Behavior at Electrochemical Interfaces

(Georgia Institute of Technology, 2024-02-08) Parmar, Shehan ; McDaniel, Jesse

Ionic liquids (ILs) are room-temperature molten salts composed of cation/anion pairs. Over the past several decades, the discovery of new ILs has led to exciting battery electrolyte alternatives that improve energy storage capacity and safety. Understanding compatible ILs for battery applications requires a fundamental understanding of the electrochemical interface—the layer of ILs that accumulate and uniquely order near the charged electrode surface. In this work, we examine how a novel, quaternary ammonium-based IL, methyltrioctylammonium bis(trifluoromethylsulfonyl)imide or [N1888][TFSI], rearranges near a gold electrode surface. We showcase the power of statistical mechanics and advanced computational chemistry methods in interpreting macroscopic implications at the application level via microscopic studies. We compare our simulations with experimental results to improve our current understanding of electrical double layers (EDL) for [N1888][TFSI].
Optically Modulated Fluorescence-Informed Photoacoustic Imaging

(Georgia Institute of Technology, 2023-12-10) Islam, Md Shariful

Advanced imaging technology is crucial for detecting early anomalies in deep tissue. While current medical imaging techniques show great potential, there is still a persistent need for improvements in sensitivity, resolution, penetration depth, and cost-effectiveness. Photoacoustic imaging combines optical excitation with acoustic detection to enhance tissue penetration depth and functional imaging capabilities. However, despite these advantages, photoacoustic imaging still suffers from poor signal-to-noise ratio and interference from endogenous chromophores in the background. Dual-laser background suppression techniques have the potential to enhance imaging sensitivity, especially in high-background noise situations. Synchronously amplified fluorescence image recovery (SAFIRe) reduces background interference in fluorescence imaging by manipulating ground-state and intermediate-state populations of contrast agents through pump and probe excitations. The main focus of this thesis is to combine the benefits of SAFIRe with photoacoustic imaging using the same pump-probe technique. Photoacoustic imaging provides signals from deep tissue, and SAFIRe removes the background from that signal. To achieve this objective, optically modulatable contrast agents and their nanoparticles, such as Rose Bengal (RB) and Eosin Y (EY), were used to produce synchronously amplified photoacoustic image recovery (SAPhIRe) signals from tissue-mimicking phantoms and dead rat muscles. This thesis explores the possible uses of SAPhIRe in temporal unmixing, a technique that allows for the separate detection of multiple contrast agents with the same absorption window simultaneously by using their unique triplet-state lifetimes. The study demonstrated the unmixing of RB and EY signals using both fluorescence and photoacoustic techniques. This was achieved by adjusting the pump-probe delay to distinguish their distinct triplet-state lifetimes. The fitting coefficients of triplet-state lifetimes were used to reconstruct images within tissue-mimicking phantoms. Prior to photoacoustic imaging, fluorescence was used for modulation screening. In addition, this work investigates the photophysical properties of three near-infrared (NIR) thiacarbocyanine dyes. Various optical modulation techniques, such as single and dual laser modulation, were conducted to explore their modulation depth, optical properties, and dark-state lifetimes. The results revealed that 3,3'-Diethylthiatricarbocyanine iodide (DTTCI) and 3,3'-Diethylthiacarbocyanine (DTCI) iodide have long dark states and are optically modulatable. Among the two, DTTCI appears to be an ideal candidate for SAPhIRe as it absorbs around 760 nm.
Synthesis and analysis of low-valent NHC supported nickel complexes

(Georgia Institute of Technology, 2023-12-10) Dodd, Neil Alexander

This thesis focuses on the synthesis of N-heterocyclice carbene (NHC) supported nickel complexes and their reactivity in bond-breaking and bond forming reactions. The body of this work discusses isolation of (NHC)Nickel(I) alkoxides and their subsequent chemical transformations into different (NHC)Nickel complexes. First, we demonstrate that (IDipp)Ni(I) hexamethyldisilazide (IDipp = 1,3-bis(2,6- diisopropylphenyl)-imidazole-2-ylidene) cleanly deprotonates neopentyl and methyl alcohols to form the corresponding (IDipp)Ni(I) alkoxides. Both alkoxides form dimeric solid-state structures. Abstraction of one alkoxide fragment forms the corresponding alkoxy-bridged dinickel cation species with an inner sphere bridging triflate. Abstraction of both neopentoxide fragments result in formation of (IDipp)Ni(OTf)(Et2O), a synthetic equivalent of (IDipp)Ni(I)+. Next, we show that the reaction of [(IDipp)Ni)]2(μ-ONp)(μ-OTf) with pentamethyldisiloxane results in isolation of {[(IDipp)Ni]2(μ-H)}[OTf]. Deprotonation of this hydride complex results in formation of [(IDipp)Ni]2, further supporting the interpretation of {[(IDipp)Ni]2(μ-H)}+ as proton bridging two (IDipp)Ni(0) fragments. The reactivity of {[(IDipp)Ni]2(μ-H)}[OTf] with alkyl nitriles was further studied by 1H NMR. [(IDipp)Ni(CN)2]4, a product of the reaction between {[(IDipp)Ni]2(μ-H)}+ with alkyl nitriles, can be synthesized by the reaction of [(IDipp)Ni(Cl)]2(μ-Cl)2 with trimethylsilyl cyanide. Subsequently, we show that the mixed valent complex, {[(IDipp)Ni]2}+ [OTf]− can be synthesized by combining synthetic equivalents of (IDipp)Ni(0) and (IDipp)Ni(I)+. Computational studies of this complex classify it as Robin-Day Class II. Cyclic voltammetry shows that the [Ni2]2+/+ and [Ni2]+/0 couples are reversible. The reactions of {[(IDipp)Ni]2}+ [OTf]− with CO and NO form mononuclear products and the reaction of {[(IDipp)Ni]2}+ [OTf]− with aryl bromide leads to predominant C-arylation of IDipp. Lastly, we show our pursuit of the first reported (NHC)Ni(I) fluoride. The reaction of [(IDipp)Ni)]2(μ-ONp)(μ-OTf) with benzoyl fluoride resulted in isolation of crystals of {[(IDipp)Ni]2(μ-F)(μ-C7H8)}[OTf] suitable for study by X-ray diffraction. Despite varying synthetic attempts, bulk isolation of {[(IDipp)Ni]2(μ-F)(μ-C7H8)}[OTf] was ultimately unsuccessful. Next, we show that {[(IDipp)Ni]2(μ-PPh2)}[OTf] can be isolated from the reaction of [(IDipp)Ni)]2(μ-OMe)(μ-OTf) with (trimethylsilyl)diphenylphosphine. We also show that (IDipp)Ni(C6H6) reacts with acyl fluorides to form the corresponding [(IDipp)Ni(R)(μ-F)]2 complexes. Lastly, we show that sodium naphthalenide can reduce [(IDipp)Ni(μ-Cl)]2 to form a synthetic equivalent of (IDipp)Ni(0).
Seed-Mediate Synthesis of Gold Nanocrystals: The Effects of Lattice Mismatch on Growth Patterns

(Georgia Institute of Technology, 2023-12-08) Pawlik, Veronica Dana

Nanomaterials have long fascinated both the casual observer and scientific mind alike. The utility of Au nanocrystals in particular has inspired applications ranging from plasmonics to catalysis. Over time, the ability to finely tune both shape and size has greatly improved their merits for these applications. To further expand and enhance the properties of Au nanocrystals, bimetallic compositions were introduced. Of the various atomic arrangements possible for bimetallic nanocrystals, the core-shell structure is most commonly utilized. This morphology is typically synthesized through a seed-mediated process. Growing one metal on another can introduce challenges. In this dissertation, I explore the effects that increasing lattice mismatch has on the seed-mediated growth of noble-metal nanocrystals. First, the case of no lattice mismatch was investigated during the growth of Au on Au spherical seeds to generate AuRD fully enclosed by {110} facets. The lack of lattice mismatch led to layer-by-layer growth. The kinetics of the synthesis could easily be tuned to favor either deposition or diffusion to achieve concave RD, trisoctahedra, or octahedra. These AuRD were then utilized in another seed-mediated growth to improve the thermal stability of the AuRD. Specifically, 1 ML of Pt was added and this ultrathin layer of Pt was able to improve the thermal stability of the high energy {110} facets from degrading at 100 °C to persisting at 450 °C. Computational studies revealed that the thermal stability of the Au-supported Pt skin was even greater than that expected for pure Pt. This effect was attributed to the strain induced by the formation of a 3.8% lattice-mismatched Pt overlayer on Au. Finally, single-crystal Rh@Au truncated octahedra were synthesized at a lattice mismatch of 7.2%. The large mismatch led to an island growth mode, which, could be tuned through the use of gentle kinetic knobs. The addition of NaOH indirectly increased the reduction rate to help modulate the number of Au islands formed on the Rh seeds. Conversely, the addition of KBr slowed down the reduction, allowing the Au adatoms to diffuse across the Rh seed. This work provides insight into the effects of lattice mismatch on the growth mode of nanocrystals, moving one step closer to the rational synthesis of novel nanomaterials with desired characteristics.
Interlaboratory Comparison of a Complex Targeted Assay: Improving Consistency and Reliability in Metabolomics Analyses

(Georgia Institute of Technology, 2023-12-07) Phillips, Emily R.

Ideal isotope-labeled internal standards for analysis via targeted metabolomics approaches are presented for negative and positive ion modes for both hydrophilic interaction liquid chromatography (HILIC) and reverse phase liquid chromatography (RPLC) chromatography coupled to mass spectrometry. These best performing analytes (BPA) were deduced after experimentation from a collaborative research project involving six top metabolomics research laboratories in the country. These results are detailed in this work, supported by observed behaviors of included chemical classes and chromatographic behaviors, and align with the group hypothesis and expectations
Redox non-innocent bis(phenoxide) pincer ligand cobalt complexes for selective radical C–H (trifluoro)alkylation through photoinduced cobalt–R(f) bond weakening

(Georgia Institute of Technology, 2023-11-10) Kuehner, Chris S.

Photoredox catalysis has become an important tool for bond-breaking and -making methods via efficient conversion of light into chemical energy. However, many methods utilize later row transition metals which have adverse economic, biologic, and environmental impacts, thus motivating efforts to explore cheaper more sustainable catalysts such as earth abundant metals. The use of 3d metals for bimolecular single electron transfer has been challenged by their ultra-short-lived excited states. My PhD thesis research harnesses LMCT to promote ligand lability in a Co chromophore for bond-making processes as an alternative strategy to utilize first row metals for photoredox catalysis. Chemical oxidation of a previously reported (OCO)Co complex that contains a redox-active [OCO] pincer ligand affords a Co–CF3 complex two oxidation states above Co(II), computational and structural data is consistent with formulation as [(OCO•–)CoIII(CF3)(THF)OTf]. This complex is thermodynamically stable but upon exposure to blue (440 nm) light induces Co–CF3 bond homolysis and release of •CF3 which is trapped by radical acceptors such as TEMPO•, (hetero)arenes, or the [OCO•] ligand. The radical trapping by the ligand backbone is a competitive pathway which is overcame by utilizing catalytic conditions. Alternatively, II can be synthesized by treating (OCO)CoII(THF) with Umemoto’s dibenzothiophenium trifluoromethylating reagent completes a photoredox catalytic cycle for C–H (hetero)arene trifluoromethylation utilizing visible light. The rearomatization of the cyclohexadienyl radical by the Co containing byproduct negates the need or a sacrificial or substrate derived oxidant, thus increasing the overall atom-economy of the catalytic trifluoromethylation and the (OCO)Co core can act as both the chromophore and the redox-center. Efforts to expand this observed VLIH reactivity of the Co–CF3 core to alkylation focused on radical decarboxylation of carboxylates via Co–O VLIH. A class of four new Co(III)–carboxylate complexes supported by the redox active [OCO] ligand were synthesized. Computational data suggests that these (OCO)CoIIIO2CR (1) complexes retain the photophysical properties for low-energy Co–O bond homolysis. Exposure of 1 to red (660 nm) light results in alkylation of radical acceptors such as TEMPO• or (hetero)arenes. Co–O bond homolysis occurs in either coordinating or non-coordinating solvents, but the use of coordinating solvents suppresses formation of the photoinert dimer [(OCO)Co]2O2CR. However, the monomer dimer equilibrium is highly sensitive to the presence of coordinating solvents such that full conversion of the dimer back to the monomeric species is observed using as little as 1.75 equivalents of a coordinating solvent. The sum of this thesis demonstrates the utility of the (OCO)Co core as a chromophore for stoichiometric and catalytic trifluoro(alkylation) of (hetero)arenes. In terms of organic product yields and distributions, these reactions are not advantageous to the current state-of-the art methods, but our catalytic approach is a distinct strategy to activate inherently strong M–R(f) bonds for applications in photocatalysis.
Reactive Molecular Dynamics in Ionic Media

(Georgia Institute of Technology, 2023-08-03) Stoppelman, John Paul

Chemical reactions are among the most fundamental phenomena within the field of chemistry. In many contexts, reactions are conducted or occur in condensed phase environments. Environmental effects can cause a host of complicated changes to a given chemical process, such as altering thermodynamic equilibrium, reaction rates or the associated mechanism. Solvents can thus be used to tune a given reaction. In particular, ionic media can cause substantial changes to a reaction due to the long-range Coulombic interactions between the reacting complex and solvent molecules, which, energetically, can be quite large in magnitude. Further study of reactions within ionic solvents would allow for modulating these interactions for selected applications. Theoretical approaches, such as quantum chemistry, represent one tract of methods that can be applied for this purpose. However, while quantum chemical techniques can effectively investigate many gas phase reactions, condensed phase reactions are much more challenging to investigate. The many degrees of freedom associated with the bulk solvent makes first principles modeling infeasible due to unfavorable scaling with respect to system size. Force fields derived from ab initio methods specifically designed for simulating reactions can significantly enhance insight into solvent modulation of chemical reactions. A sufficiently accurate force field can be used to perform molecular dynamics at quantum chemistry-level accuracy within an external environment at a fraction of the cost. However, such reactive force fields have been challenging to parameterize and use, as typical physics-based expressions used in force fields are better suited for asymptotic interactions than describing short-ranged effects associated with chemical bond-breaking/formation. Recent machine learning approaches have proved effective at learning a wide range of physical interactions, however, and can potentially be combined with standard force fields in order to build an extensive framework for modeling chemical reactions. This thesis details our development of a reactive force field framework that combines these two methodologies. We describe our procedure for building reactive force fields and apply it and similar methods to study reactions and other phenomenon within condensed phases. The systems we examine include N-heterocyclic carbene formation in [EMIM+][OAc-], proton transport in ionic liquid/water mixtures, density scaling within molecular liquids and negative thermal expansion in the materials ScF3 and CaZrF6. Through comparison with experimental and first principles predicted properties throughout this work, we demonstrate the utility of physics-based and machine learning models for understanding complex processes within challenging chemical environments.
Biochemical and Biophysical Characterization of Archaeal Intramembrane Aspartyl Proteases – Decoding Substrate Specificity, Kinetic Properties, and Solution Structure

(Georgia Institute of Technology, 2023-08-02) Wu, Yuqi

Intramembrane proteolysis is a conserved biochemical process, where the cleavage products are involved in diverse critical signaling events including cell differentiation, development, immune response and surveillance, and cholesterol metabolism. Conversely, IP dysfunction is often associated with human diseases. However, a complicated ternary complex composed of intramembrane protease (IP), transmembrane substrate, and lipid environment is always present and remains a major challenge in the study of IPs. Intramembrane aspartyl proteases, or IAPs, are least understood despite an increasing number of solved structures in recent years. In this work, we aim to understand IAP substrate specificity, kinetic properties, and solution structure through various biochemical and biophysical techniques and how lipid environment plays a role.
Prebiotic assembly and replication of nucleic acids

(Georgia Institute of Technology, 2023-07-30) Clifton, Bryce E.

One of the most researched hypotheses for the origins of life, known as the “RNA world”, relies on replication of ribonucleic acid (RNA) before the advent of protein enzymes and deoxyribonucleic acid (DNA). Essentially, the hypothesis relies on what some researchers believe is a parsimonious claim that RNA was the central molecule of heredity and metabolic catalysis from which life evolved. To test this hypothesis, many critical steps in the formation of a replicating RNA have been attempted under purportedly plausible prebiotic conditions in the laboratory. For example, polymerization of monomer units of RNA directed by base pairing interactions with an RNA template strand has been achieved in the absence of enzymes through a process called template-directed synthesis. Despite such popularity and over half a century of laboratory experiments, there remain many problems in elucidating a pathway from formation of mononucleotides from small organic molecules to template-directed synthesis and replication of nucleic acids. This dissertation is primarily dedicated to resolving one of the outstanding problems of nucleic acid replication: The Strand Inhibition Problem. The interactions that allow assembly of mono- or oligonucleotides as substrates for a template-directed synthesis reaction are the same interactions that prevent further copying as the resulting product strand is bound to the template with greater affinity than that of shorter substrates. Effectively, the product strand inhibits further substrate assembly and synthesis, thus forming the problem of strand inhibition. The individual strands of the product-template duplex must be separated to allow substrate annealing to the free original template and product strands for further copying reactions. Attempts to separate the product-template and then anneal substrates, typically by heating and cooling, only result in reassociation of the product and template strands, establishing open ended template-directed replication as a problem of thermodynamics. In this dissertation, I will elaborate on the relevance of nucleic acid replication at the origins of life and the remaining challenges in replication of nucleic acids in Chapter 1. Then, I will discuss various kinetic solutions to overcoming strand inhibition to achieve nucleic acid replication in Chapter 2, using low-water solvents coupled to heating and cooling cycles, and in Chapter 3, using wet-dry cycles as a robust and efficient prebiotic method. In Chapter 4, I will explore nonenzymatic ligation of substrates once assembled on templates that is required to demonstrate a nucleic acid replication cycle in the absence of enzymes. In Chapter 5, I will present other interesting observations related to these chapters along with possible future directions that can be explored to demonstrate nucleic acid replication. Finally, in Chapter 6, we will draw our conclusions.
Kinetically-Controlled Synthesis Of Mono-, Bi-, And Multi-Metallic Nanocrystals

(Georgia Institute of Technology, 2023-07-24) Wang, Chenxiao

Crucial in a myriad of applications ranging from catalysis to biomedicine, noble-metal nanocrystals exhibit physicochemical properties strongly governed by their size, morphology, and composition. The strong correlations offer opportunities to optimize their figures of merit, thereby augmenting their overall effectiveness. As research advances from simple mono-metallic nanocrystals to multi-metallic and hybrid nanostructures with diverse architectures and atomic distributions, the escalating complexity presents synthetic chemists with ever-increasing challenges. In this dissertation, I develop two general strategies, namely template-mediated growth and dropwise injection of precursor, aiming to control the structural characteristics of mono-, bi-, and multi-metallic nanocrystals, while exploring their potential applications in catalysis and biomedicine. First, amorphous Se nanospheres were employed as templates to mediate the nucleation and growth of Au nanoparticles through a galvanic replacement reaction. By leveraging the reducing power of Se and the pH-sensitive reaction kinetics, precise control over the size and number of Au particles on each Se sphere was achieved, resulting in hybrid nanoparticles with diverse morphologies. The presence of Au patches on these hybrid nanoparticles provides an experimental handle to optimize the ligand distribution, significantly augmenting cellular uptake and cytotoxicity for the Se nanospheres. Shifting focus to a bi-metallic system, I employed Pd cubic nanocrystals as templates to direct the surface deposition of Rh in a layer-by-layer manner. With rigorous regulation of the reaction kinetics, I successfully synthesized Pd@Rh nanocrystals featuring smooth, well-defined {100} facets and large sizes. The strong Rh−Rh binding within the shell imparted exceptional thermal stability to the core–shell nanocubes. Afterwards, chemical wet etching was employed to fabricate Rh nanocages with well-defined {100} surface and ultrathin walls from the core–shell nanocubes. Building upon these insights, I extended the two strategies to control the composition of complex alloys. By utilizing well-defined and highly stable Rh cubic nanocrystals as templates, together with a tight control over the reduction kinetics through dropwise injection of the precursor mixture, cubic-shaped nanocrystals featuring a nearly equimolar RuRhPdPt alloy surface were obtained. These alloy nanocubes demonstrated superior thermal stability in terms of both shape and composition, along with enhanced catalytic performance toward ethanol oxidation.