Chemistry & Chemical Biology Department Theses and Dissertations

Permanent URI for this collection

For more information about the Chemistry & Chemical Biology graduate programs visit:


Recent Submissions

Now showing 1 - 10 of 69
  • Item
    Electrochemical Tape-and-Paper-Based Sensor for the Quantification of Potassium
    (2023-08) Zhang, Tommy; Deiss, Frédérique; Webb, Ian
    Potassium levels in serum are used in the diagnosis of diseases involving cardiac arrhythmias, neuromuscular weakness, and chronic kidney diseases. These illnesses are becoming more prevalent, therefore, developing new potassium quantification methods would aid in advancing preventative care. Current methods of quantifying potassium mainly rely on the use of glass ion-selective electrodes which are costly, fragile, and requires frequent maintenance and recalibration. For faster and more accessible quantification of potassium, we are developing low cost, portable, and easy to fabricate electrochemical tape-and-paper-based devices. Our sensor bypasses the inconveniences of ion-selective electrodes and could ultimately serve as a point-of-care device to allow for regular monitoring or even home-use. Our sensing method relies on Prussian blue immobilized on the surface of electrodes as a potassium recognition element. Potassium ions intercalate into the Prussian blue lattice and subsequently changes the electrochemical characteristics of Prussian blue such as the redox peak potentials. These devices are highly robust, feature a limit of detection of 1.3 mM potassium and the response is linear to at least 100 mM, which contains the clinically relevant ranges required for diagnostics. Quantification was developed using cyclic voltammetry, demonstrated in Chapter 3. We observed changes in Prussian blue redox peak potentials at different concentrations of potassium and followed the expected Nernstian response. We investigated multiple methods of immobilizing Prussian blue onto the electrode surfaces to investigate stability and reproducibility in Chapter 4. Adsorption, in-situ synthesis, and carbon paste incorporation of Prussian blue was tested. Prussian blue-carbon paste devices had reproducibility issues and featured broad reduction peaks. In-situ synthesis of Prussian blue directly onto the surface of the electrodes also featured broad reduction peaks but the Prussian blue response was reproducible. The issue with in-situ synthesis was the stability of the Prussian blue layer, which was susceptible to degradation after repeated use of the device, which is required for evaluating the performance of the device. Although adsorption using Prussian blue in water had some reproducibility issues as well, this method led to the most stable Prussian blue layer, had distinct reduction peaks, and was simple to perform. Various solvents were used to dissolve Prussian blue in Chapter 5 to investigate methods of increasing device reproducibility when using adsorption. A few organic solvents were able to dissolve Prussian blue to form a stable solution with the goal of forming a more uniform Prussian blue layer and potentially improving consistency of the layer immobilization. While these alternative solvents were able to dissolve Prussian blue, they also damaged the graphite electrodes on the devices, which altered the electrochemical responses of the devices to the point where potassium quantification was no longer possible. Due to incompatibility between these alternative solvents and the devices, adsorption of Prussian blue in water continued to be used. Different modes of adsorption were explored and was optimized in Chapter 6. By altering the adsorption setup and allowing the Prussian blue particles to settle evenly onto a level electrode surface, device reproductivity increased substantially. To understand the applicability of the devices in real samples, interferent studies were performed in Chapter 7. Other cations such as Na+, Li+, Ca2+, Mg2+, and Ba2+ were not observed to enter the Prussian blue lattice in the cyclic voltammograms. Monovalent cations that share the same charge as K+ but have smaller ionic radius, Na+ and Li+, were able to decrease K+ sensitivity. Divalent cations that had a smaller ionic radius than K+ did not alter sensitivity. The exception was Ba2+, which also decreased K+ sensitivity. These results suggested that both ionic radius and charge of a species were important factors in impacting K+ intercalation into the Prussian blue lattice. Other interferents such as sulfates, phosphates, carbonates, urea, and lactic found in serum and sweat samples were tested. The presence of these interferents decreased the current intensity of the reduction peak of Prussian blue, which resulted in less definition in the peaks. For the future of this project, the effects of interferents found in serum and sweat must be investigated further. Additionally, reproducibility of the devices could be improved further if less harsh organic solvents are tested for adsorption, square wave voltammetry could be used for quantification to evaluate the viability of alternative voltametric techniques, and Prussian blue analogues could be implemented into the devices for quantification of other cations.
  • Item
    Design and Fabrication of Smart SERS Substrates for Forensic Science Applications
    (2023-08) Simas, Maria Vitoria; Sardar, Rajesh; Goodpaster, John; Manicke, Nicholas; Christoph, Naumann
    In the field of forensics and toxicology, it is crucial for analytical techniques to be practical, highly sensitive, and extremely accurate (specific and selective), especially when incorporating acquired data as evidence in a court case. To limit the breadth of this dissertation, the main forensic focuses are to assay (detection and quantification) drugs in patient biofluid specimens and to detect trace explosives. While currently there are a number of analytical tools such as LC/MS, GC/MS, ELISA immunoassays, and electrochemical and aptamer techniques utilized for these two applications, each one introduces its own unique drawback that hinders their accuracy, and therefore applicability, to be used in a legal environment. To overcome these disadvantages, surface enhanced Raman spectroscopy (SERS) has become increasingly popular in the forensic and toxicology field as it provides high sensitivity and specificity data while remaining flexible and efficient in critical situations such as an emergency department and/or an explosion site. In this dissertation, two different, novel SERS substrates are developed, each one designed to tackle a specific forensic application. While the fabrication method and materials of the substrates are significantly different from one another, both display ideal SERS properties due to their unique localized surface plasmon resonance (LSPR) properties at the nanoscale. LSPR is a phenomenon in which the free carriers (electrons or holes) on the surface of nanoparticles collectively oscillate upon light irradiation. In this current dissertation, we selectively focus on two different nanoparticle compositions where LSPR properties originate from the collective oscillation of free electrons. These oscillations of free carriers allow for an electromagnetic (EM) field enhancement of the incident laser which leads to an increase in the SERS enhancement. Particularly, the area in which the SERS signal is the most enhanced is the nanometer-sized gap between nanoparticles called “hot spots.” While primarily noble metal (e.g., Au and Ag) nanoparticles are heavily used for SERS substrate fabrication, this dissertation expands beyond that and focuses on both gold nanorods and oxygen deficient tungsten oxide (metal oxide semiconductor)-based SERS substrates. This dissertation is organized in three chapters, (1) Introduction, (2) Fabrication of a polymer microneedle-based, multimodal SERS and mass spectrometry substrate for the ultrasensitive detection of illicit drugs in human blood plasma, and (3) LSPR active WO3-x-based SERS substrate for the detection of explosives. In chapter 2, a multimodal substrate was strategically designed to serve as a SERS and electrospray ionization- mass spectrometry substrate by using a novel microneedle platform. The microneedles underwent a surface modification and gold nanorods were subsequently adsorbed onto the surface. Illicit drug analytes could then be drop-casted on the tip of the microneedles and left to dry for further SERS and mass spectrometry analysis. This novel platform detected two types of synthetic opioids, alprazolam and fentanyl, down to at least a picomolar limit of detection and successfully distinguished between the two when analyzing 10 patient blood plasma samples. Furthermore, the multimodal approach was confirmed through the detection of both drugs in patient plasma samples down to the ppb limit using mass spectrometry. Chapter 3 introduces an entirely new SERS substrate, which is fabricated using oxygen deficient tungsten oxide (WO3-x) nanoparticles for the detection of the target explosives, e.g., tetryl, TNT, and DNT. The oxygen deficiency in WO3-x nanoparticle lattice introduces free electrons in the conduction band that introduce LSPR properties into the nanoparticles giving rise to the EM field mechanism for SERS enhancement upon incident laser irradiation. Much like with noble metals, the oscillation of these free carriers at nanoparticle hot spots aid in the development of a functional and cheaper SERS substrate. The SERS enhancement factor (EF) of three different morphologies of WO3-x nanoparticles, i.e., nanorods, nanowires, and nanoplatelets are characterized and deemed comparable to noble metal nanoparticles. A Janowsky complex was formed using the explosive, tetryl, as the target analyte. Using our oxygen deficient WO3-x substrate, tetryl was successfully detected down to the nanomolar level. To our knowledge, this is the first time tetryl has been detected utilizing a non-noble metal-based SERS substrate. Taken together, this dissertation presents the unique aspect of nanotechnology for the development of (1) a multimodal MN-based ultrasensitive and (2) an inexpensive noble-metal comparable WO3-x-based SERS substrates, both of which that can be applied to forensic science research, specifically in forensic toxicology and explosive detection to better, and even save, the lives of individuals and improve their quality of life.
  • Item
    Machine Learning Facilitated Quantum Mechanic/Molecular Mechanic Free Energy Simulations
    (2023-08) Snyder, Ryan; Pu, Jingzhi; Naumann, Christoph; Webb, Ian; Deng, Yongming
    Bridging the accuracy of ab initio (AI) QM/MM with the efficiency of semi-empirical (SE) QM/MM methods has long been a goal in computational chemistry. This dissertation presents four ∆-Machine learning schemes aimed at achieving this objective. Firstly, the incorporation of negative force observations into the Gaussian process regression (GPR) model, resulting in GPR with derivative observations, demonstrates the remarkable capability to attain high-quality potential energy surfaces, accurate Cartesian force descriptions, and reliable free energy profiles using a training set of just 80 points. Secondly, the adaptation of the sparse streaming GPR algorithm showcases the potential of memory retention from previous phasespace, enabling energy-only models to converge using simple descriptors while faithfully reproducing high-quality potential energy surfaces and accurate free energy profiles. Thirdly, the utilization of GPR with atomic environmental vectors as input features proves effective in enhancing both potential energy surface and free energy description. Furthermore, incorporating derivative information on solute atoms further improves the accuracy of force predictions on molecular mechanical (MM) atoms, addressing discrepancies arising from QM/MM interaction energies between the target and base levels of theory. Finally, a comprehensive comparison of three distinct GPR schemes, namely GAP, GPR with an average kernel, and GPR with a system-specific sum kernel, is conducted to evaluate the impact of permutational invariance and atomistic learning on the model’s quality. Additionally, this dissertation introduces the adaptation of the GAP method to be compatible with the sparse variational Gaussian processes scheme and the streaming sparse GPR scheme, enhancing their efficiency and applicability. Through these four ∆-Machine learning schemes, this dissertation makes significant contributions to the field of computational chemistry, advancing the quest for accurate potential energy surfaces, reliable force descriptions, and informative free energy profiles in QM/MM simulations.
  • Item
    Phosphonium-Salt Mediated Activation of C-O Bonds: Applications and Mechanistic Studies
    (2023-05) Irving, Charles D.; Laulhé, Sébastien; Manicke, Nicholas; Minto, Robert; Deng, Yongming
    The C-O single bond is found in numerous functional motifs including carboxylic acids, alcohols, and ethers. These compounds represent ideal precursors towards C-X (X = C, H, or heteroatom) bond formation due to their inherent stability and abundance in nature. As such, synthetic chemists continue to develop new technologies for the transformation of these precursors into biologically useful targets such as amides and amines. However, due to the stability of the C-O single bond, accessing such targets remains a consistent challenge. The activation of the carboxylic acids towards peptide synthesis has been facilitated through various coupling agents, including organoboron and transition metal catalysts. However, coupling agents can generate stochiometric, difficult-to-remove, toxic waste by-products. Organoboron/transition metal catalyzed condensations offer a more atom economical approach but suffer from varying degrees of optical erosion and poor sustainability. Phosphonium-based deoxyaminative technologies provide access to amines from alcohols via a phosphorus oxygen double bond formation driving force, but possesses a narrow nucleophilic nitrogen source scope, and poor atom economy. Transition metal/enzyme catalyzed “hydrogen borrowings” represent atom economical deoxyaminative alternatives. Still, their respective use of costly metals, and multiple enzymatic cascade steps severely limit the sustainability and scope of such protocols. An ambient deoxyamidation of carboxylic acids and deoxyamination of alcohols was developed through the use of N-haloimides activated by triphenylphosphine. Such technologies were found to possess broad functional tolerance and formed C-N bonds via a coupling to free amines, and the direct installment of the imide motif. Mechanistic experiments suggest that such transformations take place via the in situ generation of two separate phosphonium reactive species.
  • Item
    QM/MM Applications and Corrections for Chemical Reactions
    (2023-05) Kim, Bryant; Pu, Jingzhi; Naumann, Christoph; Vilseck, Jonah; Webb, Ian
    In this thesis, we present novel computational methods and frameworks to address the challenges associated with the determination of free energy profiles for condensed-phase chemical reactions using combined quantum mechanical and molecular mechanical (QM/MM) approaches. We focus on overcoming issues related to force matching, molecular polarizability, and convergence of free energy profiles. First, we introduce a method called Reaction Path-Force Matching in Collective Variables (RP-FM-CV) that efficiently carries out ab initio QM/MM free energy simulations through mean force fitting. This method provides accurate and robust simulations of solution-phase chemical reactions by significantly reducing deviations on the collective variables forces, thereby bringing simulated free energy profiles closer to experimental and benchmark AI/MM results. Second, we explore the role of pairwise repulsive correcting potentials in generating converged free energy profiles for chemical reactions using QM/MM simulations. We develop a free energy correcting model that sheds light on the behavior of repulsive pairwise potentials with large force deviations in collective variables. Our findings contribute to a deeper understanding of force matching models, paving the way for more accurate predictions of free energy profiles in chemical reactions. Next, we address the underpolarization problem in semiempirical (SE) molecular orbital methods by introducing a hybrid framework called doubly polarized QM/MM (dp-QM/MM). This framework improves the response property of SE/MM methods through high-level molecular polarizability fitting using machine learning (ML)-derived corrective polarizabilities, referred to as chaperone polarizabilities. We demonstrate the effectiveness of the dp-QM/MM method in simulating the Menshutkin reaction in water, showing that ML chaperones significantly reduce the error in solute molecular polarizability, bringing simulated free energy profiles closer to experimental results. In summary, this thesis presents a series of novel methods and frameworks that improve the accuracy and reliability of free energy profile estimations in condensed-phase chemical reactions using QM/MM simulations. By addressing the challenges of force matching, molecular polarizability, and convergence, these advancements have the potential to impact various fields, including computational chemistry, materials science, and drug design.
  • Item
    Electroanalytical Paper-Based Sensors for In-Field Detection of Chlorate-Based Explosives and Quantification of Oxyanions
    (2023-05) Guimarães Vega, Carolina; Deiss, Frédérique; Manicke, Nicholas; Goodpaster, John; Long, Eric
    Improvised explosive devices (IEDs) are a global threat due to their destructive potential, the easy access to raw materials, and online instructions to manufacture them. These circumstances have led to an increase in the number of IEDs using potassium chlorate as an oxidizer. The standard methods to detect chlorate are mainly designed for laboratory-only testing. Thus, field instrumentation capable of detecting oxidizers from explosives fuel-oxidizers is critical for crime scene investigation and counterterrorism efforts (described in Chapter 1). We developed a paper-based sensor for the in-field detection of chlorate (described in Chapter 2). The sensor is low-cost, disposable, portable, and inexpensive to fabricate, and its flexibility features allow for surface sampling without sample destruction. The sensor has an electrodeposited molybdate sensing layer, as chlorate was reported to have a catalytic effect on the molybdate reduction. The chlorate detection relies on monitoring the change in redox activity of the molybdate sensing layer using different electroanalytical techniques. We effectively demonstrated the analytical performance of the sensor (Chapter 3), obtaining a limit of detection of 1.2 mM and a limit of quantification of 4.10 mM. We evaluated the selectivity of the sensor by testing other oxidizers, such as perchlorate and nitrate, which did not present any electrochemical activity with the molybdate sensing layer. Additionally, we performed an interferent study with sugar, commonly used as fuel in IEDs, and other common white household powders such as baking soda, flour, and corn starch and neither a false positive nor a false negative result was observed (Chapter 3). As bromate has been reported to have a stronger catalytic effect than chlorate on the redox activity of molybdate, the quantification of bromate was also explored, and a bromate sensor was developed using the findings of the chlorate sensor (Chapter 4). The reaction mechanism involved in the molybdate reduction was explored and discussed in Chapter 5. The capability of the sensor in detecting chlorate from combusted samples and post-blast samples was successfully demonstrated in Chapter 6, as well as the design of encased prototypes to allow for an in-field presumptive test, storage, and transport for in-laboratory confirmatory tests and compared the performance of the sensor to the available commercial tests.
  • Item
    Molecular dynamics simulations of spore photoproduct containing DNA systems
    (2023-05) Hege, Mellisa; Pu, Jingzhi; Blacklock, Brenda; Georgiadis, Millie; Deng, Yongming
    Bacterial endospores have been a topic of research interest over the last several decades given their high resistance to ultraviolet (UV) damage. Unlike vegetative bacterial cells, which form cyclobutane pyrimidine dimers (CPD) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs) as the major product upon UV irradiation, endospore bacteria form a spore photoproduct (5-(R-thyminyl)-5,6-dihydrothymine or SP) as the major product. Vegetative bacteria cells are subject to regular cell activities and processes such as division and deoxyribonucleic acid (DNA) replication, which are prone to damage from UV exposure. However, in endospores, which have a largely anhydrous inner environment, the DNA remains dormant when bound to spore-specific small acid-soluble proteins (SASP) and dipicolinic acid, making spores highly resistant to radiation, heat, desiccation, and chemical harm. During spore germination, SP lesions in DNA are repaired by a distinctive repair enzyme, spore photoproduct lyase (SPL). In this thesis, molecular dynamics (MD) simulations were carried out to (i) examine how the formation of the SP lesion in DNA affects the global and local structural properties of duplex DNA and (ii) study how this lesion is recognized and repaired in endospore. The first part of this work was focused on designing and developing a structurally and dynamically stable model for dinucleotide SP molecule (TpT), which was subsequently used as an SP patch incorporated into duplex DNA. Computationally, this requires modifications of the bond and nonbonded force field parameters. The stability of the patch and developed parameters was tested via solution-phase MD simulations for the SP lesion incorporated within the B-DNA dodecamer duplex (PDB 463B). The second part involved applying the new SP patch to simulate the crystallographic structure of the DNA oligomer containing SP lesions. Solution-phase MD simulations were performed for the SP-containing DNA oligomers (modeled based on PDB 4M94) and compared to the simulations of the native structure (PDB 4M95). Our analysis of the MD trajectories revealed a range of SP-induced structural and dynamical changes, including the weakened hydrogen bonds at the SP sites, increased DNA bending, and distinct conformational stability and distribution. In the third part of this thesis project, we carried out MD simulations of SP-containing DNA bound with SASPs to examine how the DNA interacts differently with SASP in the presence and absence of the SP lesion. The simulation results suggested decreased electrostatic and hydrogen bonding interactions between SASP and the damaged DNA at the SP site compared to the undamaged DNA-protein complex. In addition, decreased helicity percentage was observed in the SASPs that directly interact with the SP lesion. The last part of this this thesis work focused on the SP-dimer flipping mechanism, as the lesion is likely flipped out to its extrahelical state to be recognized and repaired by SPL. Using steered molecular dynamic (SMD) simulations and a pseudo-dihedral angle reaction coordinate, we obtained possible SP flipping pathways both in the presence and absence of SASP. Collectively, these simulation results lend new perspectives toward understanding the unique behavior of the SP lesion within the DNA duplex and the nucleoprotein complex. They also provide new insights into how the SP lesion is efficiently recognized and repaired during spore germination.
  • Item
    Combining Semiempirical QM Methods with Atom Dipole Interaction Model for Accurate and Efficient Polarizability Calculations
    (2022-12) Young, Ryan; Pu, Jingzhi; Long, Eric C.; Naumann, Christoph; Sardar, Rajesh
    Molecular polarizability plays a significant role in chemistry, biology, and medicine. Classical prediction of polarizability often relies on atomic-type specific polarizability optimized for training set molecules, which limits the calculations to systems of similar chemical environment. Although ab initio (AI) quantum mechanical (QM) methods are more transferable in predicting molecular polarizability, their high computational costs especially when used with large basis sets for obtaining quantitatively reliable results make them less practical. To obtain accurate QM polarizability in an efficient manner, we have developed a dual-level approach, where the polarizability (α) obtained from the efficient semiempirical QM (SE) method is corrected using a set of element-base atomic polarizabilities derived from the atomic dipole interaction model (ADIM) to reproduce the density functional theory (DFT) results. We have optimized the atomic polarizability correction parameters for CHON-containing systems using a small training set of molecules and tested the resulting SE-ADIM model on the neutral drug-like molecules in the QM7B database. SE-ADIM corrected AM1 showed substantial improvement with its relative percent error (RPE) compared to B3LYP reduced from 33.81% to 3.35%. To further test its robustness for larger molecules in broader chemical bonding situations, we applied this method to a collection of drug molecules from the e-Drug3D database. For the 1004 molecules tested, our SE-ADIM model, which only contains four empirical parameters, greatly reduces the RPE in AM1 polarizability relative to B3LYP from 26.8% to 2.9%. Error decomposition shows consistent improvements across molecules with diverse bond saturations, molecular sizes, and charge states. In addition, we have applied AlphaML, a promising machine learning (ML) technique for predicting molecular polarizability, to the e-Drug3D dataset to compare its performance with our SE-ADIM correction of AM1. We found SE-ADIM performs competitively with AlphaML bolstering our confidence in the value of our method. Errors distinct to AlphaML were also discovered. We found four molecules for which AlphaML predicts negative molecular polarizabilities, all of which were peroxides. In contrast, SE-ADIM has no such issue with these molecules or this chemical type. Finally, to improve performance of SE-ADIM when correcting AM1 molecular polarizability calculations for charged molecules, we introduce a charge dependent polarizability (CDP) enabled SE-ADIM. Training the CDP enabled SE-ADIM with a single additional parameter, B, we were able to reduce error in AM1 molecular polarizability calculations of charged molecules relative to B3LYP from 29.57% to 5.16%. By contrast, SE-ADIM without CDP corrected AM1 relative to B3LYP had an RPE of 8.56%. The most benefit of CDP was evident within negatively charged molecules where AM1 error relative to B3LYP fell from 32.20% to 3.77% while SE-ADIM without CDP enabled error for these same negative molecules was 10.06%.
  • Item
    Generation of Alkyl Radicals Via C-H Functionalization and Halogen Atom Transfer Processes
    (2022-12) Niu, Ben; Laulhé, Sébastien; Long, Eric; Minto, Robert E.; Pu, Jingzhi
    Alkyl radicals are powerful intermediates for the generation of carbon-carbon bonds, which play an indispensable role in the synthesis of natural products, pharmaceuticals, and pesticides. Traditionally, there are two main methods for the generation of alkyl radicals. The first is C-H bond functionalization via hydrogen-atom-transfer (HAT). HAT processes have been used as an effective approach for selectively activating C-H bonds via radical pathways. The other strategy to explore the generation of alkyl radicals is C-X bond functionalization via halogen-atom-transfer (XAT). Alkyl halides are one of the largest classes of building blocks in synthesis and they can be obtained from the corresponding alcohols. The most straightforward and effective way to form such alkyl radicals is the direct homolytic cleavage of C-X bonds. In past decades, photoredox catalysis has emerged as a powerful and greener tool for the synthesis of radicals under mild reaction conditions, which has brought tremendous attention. Although remarkable success has been made in this field, some methods still require costly transition metal catalysts or toxic reagents. Herein, we display a series of visible light-induced approaches under transition-metal free conditions or using earth-abundant metals. These novel photo-induced transformations and corresponding mechanistic work will be discussed in the following order: We will first present our work on metal-free visible-light-promoted C(sp3)-H functionalization of aliphatic cyclic ethers using trace O2. This reaction uses a trace amount of aerobic oxygen as the sole green oxidant under blue light at room temperature to achieve the synthesis of sulfone and phosphate derivatives in good to excellent yields using cyclic ethers and vinyl sulfones. Then, we report on a photo-induced C(sp3)-H chalcogenation of amide derivatives and ethers via a ligand-to-metal charge-transfer. This reaction converts secondary and tertiary amides, sulfonamides, and carbamates into the corresponding amido-N,S-acetal derivatives in good yields, using an earth abundant metal catalyst under mild conditions. Finally, we present a photoredox polyfluoroarylation of alkyl halides via halogen atom transfer. This method converts primary, secondary, and tertiary unactivated abundant alkyl halides into the corresponding polyfluoroaryl compounds in good yields and has good functional group compatibility.
  • Item
    Chemometric Analysis of Volatile Organic Compound Biomarkers of Disease and Development of Solid Phase Microextraction Fibers to Evaluate Gas Sensing Layers
    (2022-08) Woollam, Mark David; Agarwal, Mangilal; Deiss, Frédérique; Goodpaster, John; Naumann, Christoph
    Canines can detect different diseases simply by smelling different biological sample types, including urine, breath and sweat. This has led researchers to try and discovery unique volatile organic compound (VOC) biomarkers. The power of VOC biomarkers lies in the fact that one day they may be able to be utilized for noninvasive, rapid and accurate diagnostics at a point of care using miniaturized biosensors. However, the identity of the specific VOC biomarkers must be demonstrated before designing and fabricating sensing systems. Through an extensive series of experiments, VOCs in urine are profiled by solid phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) to identify biomarkers for breast cancer using murine models. The results from these experiments indicated that unique classes of urinary VOCs, primarily terpene/terpenoids and carbonyls, are potential biomarkers of breast cancer. Through implementing chemometric approaches, unique panels of VOCs were identified for breast cancer detection, identifying tumor location, determining the efficacy of dopaminergic antitumor treatments, and tracking cancer progression. Other diseases, including COVID-19 and hypoglycemia (low blood sugar) were also probed to identify volatile biomarkers present in breath samples. VOC biomarker identification is an important step toward developing portable gas sensors, but another hurdle that exists is that current sensors lack selectivity toward specific VOCs of interest. Furthermore, testing sensors for sensitivity and selectivity is an extensive process as VOCs must be tested individually because the sensors do not have modes of chromatographic separation or compound identification. Another set of experiments is presented to demonstrate that SPME fibers can be coated with materials, used to extract standard solutions of VOCs, and analyzed by GC-MS to determine the performance of various gas sensing layers. In the first of these experiments, polyetherimide (PEI) was coated onto a SPME fiber and compared to commercial polyacrylate (PAA) fibers. The second experiment tuned the extraction efficiency of polyvinylidene fluoride (PVDF) - carbon black (CB) composites and showed that they had higher sensitivity for urinary VOC extraction relative to a polydimethylsiloxane (PDMS) SPME fiber. These results demonstrate SPME GC-MS can rapidly characterize and tune the VOC adsorption capabilities of gas sensing layers.