Chemistry & Biochemistry Theses and Dissertations

Permanent URI for this collectionhttp://hdl.handle.net/1903/2752

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Start date: 2022End date: 2022

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    Next-generation Mass Spectrometry With Multi-omics For Discoveries In Cell And Neurodevelopmental Biology
    (2022) Li, Jie; Nemes, Peter; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Understanding tissue formation advances our understanding of the causes of disease and the obtained knowledge can be potentially applied to develop personalized interventions. However, to explore the underlying mechanisms that govern tissue formation, there is a high and unmet need to develop new technologies to characterize different types of biomolecules from early-stage embryonic precursor cells and their descendent cells during development. This dissertation discusses new technological advancements to facilitate multi-omic (proteomic and metabolomic) analysis to explore cell-to-cell differences and uncover mechanisms underlying tissue formation. The work presented herein illustrates the development of in vivo microsampling and single-cell mass spectrometry (MS) to uncover cell heterogeneity among embryonic cells. Additionally, this dissertation work studies the biological role of metabolites in cell fate determination by exploring the mechanisms underlying metabolite-induced cell fate change. Moreover, this work introduces a novel technique called MagCar developed to track and isolate tissue-specific cells at later stages, which enables studying temporal molecular changes to gain new information about tissue formation.
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    A Breath of Fresh Air: Study of Reactive Porous Metal Oxides for Chemical Warfare Agent and Simulant Defeat
    (2022) Leonard, Matthew; Rodriguez, Efrain E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Organophosphorus molecules are a wide class of compounds that are used commerciallyas fire retardants, plasticizers, and pesticides. Organophosphorus pesticides were developed to replace environmentally persistent pesticides, such as dichlorodiphenyltrichloroethane, more commonly known as DDT. However, organophosphorus pesticides have been proven to be carcinogenic and to affect neurodevelopment negatively. A sub-class of organophosphorus molecules are highly toxic acetylcholinesterase (AChE) inhibitors, known as nerve agents. Although the Geneva convention banned the use of chemical warfare agents (CWA), the nerve agent sarin has been used as recently as 2013 on Syrian civilians. In 2018, a Novichok nerve agent was used in the attempted assassination of a former Russian spy and his daughter. Current CWA respiratory protection employs bituminous coal (BPL), carbon which is impregnated with a mixture known as ASZM-TEDA. BPL carbon impregnated with ASZM-TEDA has a wide range of reactivity, but has not changed significantly since its inception. The next-generation filtration material will need to have a large surface area to maximize reactive sites and be robust to withstand degradation. Mesoporous and nanoparticle metal oxides are highly active materials that show promise in nerve agent defeat. Within this dissertation, the goal is to develop and study reactive metal oxides to understand the factors that are important for the decomposition of CWAs and CWA simulants. In Chapter 1, I introduce the history of CWAs, the downfalls of current filtration technology, and the candidates for the next generation filter. In Chapter 2, the methods and characterization techniques used within this work are presented and discussed. In Chapter 3, to determine the effects of cation selection on methyl paraoxon decomposition, Ce4+ was isovalently doped into anatase type TiO2. Through UV/Vis spectroscopy, the degradation of methyl paraoxon was tracked and fit to pseudo-first-order kinetics, then normalized to the synthesized material’s surface area. The rate constant, normalized to the material’s surface area (kSA), reveals CeO2 is 3 to 4.6 times larger than that of TiO2 and the Ce-doped titanias. The Ce-doped titanias showed little to no change in methyl paraoxon decomposition compared to TiO2. The lack of change within the Ce-dopant titania revealed that crystal structure is a larger driving factor for methyl paraoxon decomposition than the cation identity (i.e. Ce4+ and Ti4+). Chapter 4 presents a study on the gas surface interaction between sarin and dry CuO nanoparticles (NP) through infrared (IR) spectroscopy. Sarin adsorbs to CuO through the P=O bond, and proceeds to decompose on the surface. Distinct red shifts in the delta(P-CH3) and rho(P-CH3) modes indicate the cleavage of the P-F bond, producing isopropyl methyl phosphonic acid (IMPA). Concurrently, a mode attributed to (O-P-O) begins to grow in, demonstrating that sarin forms a bridging species on the surface. Sarin continues to degrade on the dry CuO surface once the sarin feed is removed. Upon heating above 423 K, all modes associated with IMPA simultaneously decrease, indicating that IMPA desorbs from the surface. These observations were further corroborated through computational methods. Finally, in Chapter 5, I seek to enhance the reactivity of CuO by placing the cation Cu2+ within a Jahn-Teller active geometry. Mesoporous NiO and Cu-doped NiO were synthesized and exposed to diisopropyl fluorophosphate (DFP) in different environments and studied through diffuse reflectance IR Fourier transform spectroscopy (DRIFTS). Ordered mesoporous Cu-doped NiO was successfully synthesized through a hard templating method. Through X-ray diffraction (XRD), Cu2+ was incorporated into the NiO rock-salt lattice without phase separation for < 20%. The mesoporous metal oxides (MMO) maintained high surface areas (67.89-94.38 m2/g), with a main pore size of ~2.4 nm. Shifts in the Raman spectra indicate the dopant, Cu2+, reduces nickel vacancies resulting in a decrease in Ni3+ defect states. Upon DFP exposure, NiO was highly oxidative producing CO, CO2, carbonyls, and carbonates due to the active oxygen species formed by the Ni2+ vacancies. The mesoporous Cu-doped NiO samples were less reactive to DFP oxidation, due to the Cu2+ occupying the nickel vacancies, resulting in a reduction of active oxygen species.
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    Foundational Theoretical Issues of Quantum Heat Engines and Hot Entanglement
    (2022) Arisoy, Onat; Hu, Bei-Lok; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    We study open quantum systems in the contexts of quantum heat engines, refrigerators and quantum entanglement in systems in contact with high temperature reservoirs. Emphasizing the underlying theoretical foundations rather than practical aspects such as enhancement in efficiency of engines and refrigerators or in entanglement measures for a particular set of system and bath parameters, this work focuses on some important aspects of open quantum systems and quantum thermodynamics and provide in-depth analysis of them using relatively simple yet robust models in non- equilibrium statistical mechanics. These examples include a refrigerator for quantum many-body systems in the Markovian regime, a single harmonic oscillator quantum Otto cycle with its generalization to squeezed thermal baths and the entanglement dynamics of two coupled harmonic oscillators each having its own separate thermal baths in the non-Markovian regime. The investigation of these setups in a unified context in this dissertation also brings up the discussion on the validity of Markovian approximation for open quantum systems and the qualitative differences in Markovian versus non-Markovian open system dynamics, which is addressed on multiple occasions throughout the cases we study. Our analysis of quantum Otto cycle with squeezed thermal reservoirs show that the efficiency of the cycle does not change due to the squeezing in the bath in contrast to previous works studying the same cycle restricted by Markovian assumptions. In our investigation of the effects of time-dependent coupling in a system of two harmonic oscillators with two separate baths in both Markovian and non-Markovian regimes, we find that the driving-induced instability of the solutions of the Langevin equations of the oscillator system is necessary to sustain entanglement at late times with hot reservoirs which mayrender hot entanglement untenable. The effects of Markovianity/non-Markovianity, non-thermal reservoirs, contact with multiple reservoirs and time-dependent system Hamiltonians in quantum thermodynamics are addressed in this thesis.
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    Correlating Chemical Activity and Structure in Mesoporous Metal Oxides for Nerve Agent Decomposition
    (2022) Li, Tianyu; Rodriguez,, Efrain E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    GB (sarin), a chemical ware fare agent (CWA), due to its extreme fatal toxicity and its involvement in a few terrorist and battle attacks, has become an increasing concern for the national public and military safety. Developing filter materials that can strongly adsorb and effectively decompose GB thus attracts growing research interest. The great diversity of metaloxides and their abundant surface chemistry suggest an opportunity to realize their potential as filter materials. This dissertation outlines our effort to gain a fundamental understanding of the interaction between GB (also its simulant DMMP) and metal oxides. We aim to determine the structural factors that influence the performance of metal oxides on adsorbing and decomposing GB and to ultimately predict the behavior of a given metal oxide. We used two mesoporous metal oxides (TiO2 and CeO2) as two model systems and performed systematic studies on their interaction with GB and its simulant DMMP. We utilized multiple techniques to fully characterize the crystal and surface characters of the mesoporous metal oxides. The interactions between GB/DMMP and metal oxides were explored by different spectroscopic techniques (majorly infrared techniques). Combining the experimental observations and DFT calculations on two different metal oxides, we propose several governing parameters of the metal oxides to impact their reactivity for decomposing GB. We also derive a simplified and qualitative model to predict the reaction behavior and activity of metal oxides when interacting with GB.
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    Solution-Processed Clean SWCNTs and Their Use as Templates for One-Dimensional van der Waals Heterostructures
    (2022) Zhang, Chiyu; Wang, YuHuang; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Single-walled carbon nanotubes (SWCNTs) have shown exceptional electrical, optical, mechanical, and thermal properties. Solution processing is a critical first step to harness these nanomaterials for applications in electronics, biomedicine, and energy technologies. However, dispersion of SWCNTs in solutions requires assistance by surfactants or polymers, which cannot be cleanly removed easily and become unwanted contaminants, resulting in degraded performance of SWCNTs.In this dissertation, I developed strategies to attain clean, solution-processed SWCNTs and further demonstrated their applications as templates for the synthesis of van der Waals heterostructures. We investigated the role of surfactants in dispersing SWCNTs and found that the highest efficiency in dispersing SWCNTs occurs at the critical micelle concentration of surfactants, which is well below the typically required surfactant concentrations. Furthermore, we synthesized a thermally removable surfactant, ammonium deoxycholate (ADC) which can be removed cleanly at a relatively low temperature without damaging the SWCNT structure. Compared to a commonly used surfactant, sodium deoxycholate (DOC), ADC features the same anion, but contains an ammonium (NH4+) cation in place of the metal ion (Na+). ADC exhibits the same high dispersion efficiency for SWCNTs as DOC, but the peak thermal decomposition temperature of ADC is nearly 70 oC lower than that of DOC. A two-step annealing process can remove this new nanotube surfactant while keeping the SWCNTs intact, even with a small diameter of just 0.76 nm. This work also reveals the chemical origin of residues from thermal annealing of surfactant-processed carbon nanomaterials. The clean SWCNTs enable the synthesis of van der Waals heterostructure consisting of pure chiral single-wall carbon nanotubes nested in boron nitride (SWCNT@BN). Transmission electron microscopy and electron energy-loss spectroscopic mapping confirm the successful synthesis of SWCNT@BN from the solution-purified nanotubes. The photoluminescence peak of (7,5)-SWCNT@BN heterostructure is found to redshift by 10 nm relative to that of (7,5)-SWCNT and the Raman G peak of (7,5)-SWCNTs downshift by 10 cm-1 after BN coating.
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    Defect Engineering of Supported Metal Catalysts for Selective Hydrogenation
    (2022) Zhang, Yuan; Liu, Dongxia; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Supported metal catalysts have been used extensively in industry. To construct supported metal catalysts with low cost and high catalytic performance, high dispersion of metal on the support material is greatly favored in recent years. With the downsizing of metal active phase, new challenges in catalyst synthesis and characterization have emerged. The highly dispersed metal active phase is prone to aggregate to decrease surface free energy, which requires innovative synthesis strategy to stabilize the metal species on support. High metal dispersion also created more interfacial sites and bonds between metal and support, therefore the metal-support interaction has more significant effects on the catalytic properties of high dispersion catalysts. Defect engineering has attracted much attention due to its ability to help stabilizing metal species and tune the metal-support interaction.This dissertation focuses on utilizing defect engineering to develop catalysts with high activity and selectivity in hydrogenation reaction. Harsh pH condition was applied in wetness impregnation process to generate cavity sites on TiO2 support surface, which resulted in stronger metal-support interaction between Pt and TiO2. The catalyst synthesized under harsh condition showed higher hydrogenation activity towards -NO2 group. Laser engraving was used as another defect engineering technique to create defects on TiO2 support. The laser engraved support showed distinct electronic and redox properties, which enhanced the electronic metal-support interaction of Pt and TiO2 support. The Pt/TiO2-LE catalyst showed superior activity and selectivity in the hydrogenation of 3-nitrostyrene and furfural alcohol. In addition, an effective method to probe the metal dispersion of Pt by styrene hydrogenation reaction kinetics was developed. This method has the potential to be applied to other catalysts systems and could be used to study the metal-support interaction in catalysts.
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    Tuning Crystallographic and Magnetic Symmetry in Lithium Transition Metal Phosphates and Thiophosphates
    (2022) Diethrich, Timothy; Rodriguez, Efrain E.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Ferroic ordering needs no introduction; ferromagnetic, ferroelectric, and ferroelastic materials have had a significant impact on the materials science community for many years. While these three main types of ferroic ordering are well known, there is a fourth and final, lesser known ferroic ordering known as ferrotoroidicity. A ferrotoroidic material undergoes a spontaneous, physical alignment of toroidal moments under a critical temperature. This study is focused on broadening our current understanding of ferrotoroidics by studying two families of materials: LiMPO4, and Li2MP2S6, where M = Fe, Mn, and Co. While these two materials initially appear to be similar in some regards, many differences can be observed as a deeper dive is taken into their crystallography and magnetic structures. For a toroidal moment to exist, a specific orientation of magnetic moments is required, because of this, only certain magnetic point groups are allowed. For example, LiFePO4 has an “allowed” magnetic point group of m’mm, while it’s delithiated counterpart FePO4 has a “forbidden” magnetic point group of 222. This work has found that by using a new selective oxidation technique, lithium concentration can be controlled in the Li1−xFexMn1−xPO4 solid solution series. Neutron powder diffraction and representational analysis were used to find the magnetic point groups of each member of this series. In the end, each structure was solved and the largest transition temperature to date was reported for a potential ferrotoroidic material. The magnetic exchange interactions can be used to describe the magnetic phase changes that occuracross the Li1−xFexMn1−xPO4 series. The second group of materials in this study is the lithium transition metal thiophosphates of the formula Li2MP2S6, where M = Fe, Co. The structure of Li2FeP2S6 has been previously studied but no magnetic properties of this material have been reported. In addition, neither the structural nor magnetic properties have been reported for the cobalt analog. Single crystalXRD was used to confirm the previously reported crystal structure of Li2FeP2S6 and to find the novel crystal structure of Li2CoP2S6; both crystallize in a trigonal P31m space group. While isostructural in some regard, there are some crucial differences between these materials. The site occupancies are different, resulting in non-trivial charge balances and a unique thiophosphate distortion. Originally, these materials were chosen because their nuclear structure was predicted to host long-range antiferromagnetic order and potentially ferrotoroidic order. Contrary to expectations, magnetic susceptibility and field dependent measurements demonstrated paramagnetic behavior for both the iron and the cobalt sample down to 2 K. This result was further confirmed by a lack of magnetic reflections in the time-of-flight neutron powder diffraction data. While the phosphates and the thiophosphates demonstrated very different structural andmagnetic results, they both remain relevant materials for not only ferrotoroidics, but also magnetoelectrics, spintronics, quantum materials, and much more.
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    Non Traditional Solvent Effect On Protein Behavior
    (2022) Lee, Pei-Yin; Matysiak, Silvina; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Protein preservation has been a long lasting research topic due to its importance in many bio-pharmaceutical applications. A ”cold chain” is a commonplace solution to protein preservation, which stores biochemical products at a refrigerated temperature. A big advantage of cold chain is that the storing process is straightforward, without many further processes before the use of stored bio-products. However, it can also experience malfunction of the cooling system and results in economic lost and health care crisis. Ionic liquids (ILs), as a type of non traditional solvents, consist only of ions and are reported to be a potential candidate to replace the use of cold chain. The advantages of ILs include low flammability, high conductivity and less toxicity compared to some organic solvents. The most interesting feature of ILs is their extremely large number of cation-anion combinations, that can be tailored for specific use according to different needs. This thesis aims to investigate specific mechanism behind how ILs modulate protein behavior, specifically, how ILs affect protein stability, activity, and aggregation. We approach the research questions through the lens of molecular dynamics (MD) simulations and complement with experimental findings. In the first part of the thesis we first investigate the effects of two imidazolium based ILs (1-ethyl-3-methylimidazolium ethylsulfate, [EMIM]+[EtSO4]− and 1-ethyl-3-methylimidazolium diethylphosphate, [EMIM]+[Et2PO4]−) on lysozyme stability and activity. We collaborate with an experiment group at the University of Massachusetts (Bermudez lab) to complement our simulation results. Both ILs are found to destabilize lysozyme stability. In addition, both the cation and anions lower the stability of lysozyme, but in a different fashion. [EMIM]+ interacts with an Arg-Trp-Arg bridge that is critical in lysozyme stability through π–π and cation–π interactions, leading to a local induced destabilization. On the other hand, both anions interact with the whole protein surface through short-range electrostatic interactions, with [Et2PO4]− having a stronger effect than [EtSO4]−. Lysozyme activity is also reduced by the presence of the two ILs, but can be recovered after rehydration. It is found that the protein-ligand complex is less stable in the presence of ILs. In addition, a dense cloud of [EMIM]+ is found in the vicinity of the lysozyme active site residues, possibly leading to a competition with the sugar ligand. A fast leaving of these [EMIM]+ is observed after rehydration, which explains the reappearance of the active site and the recover of lysozyme activity. Although classical all-atom MD simulations can provide us with a great deal of microscopic information, they are often limited by the temporal-spatial scale of the simulated systems. For example, systems with high viscosity solvents or systems involving large number of atoms will be difficult to reach convergence for all-atom MD. In this case, coarse grained (CG) MD can come into play to achieve the desired time- and length- scales. The faster sampling obtained from CG MD is achieved by reducing the degree of freedom of the system and by removing local energetic barriers. In CG MD, similar atoms are grouped to functional groups and thus the free energy landscape is smoothen. We develop a novel CG MD named ”Protein Model with Polarizability and Transferability (ProMPT)”. The novelty of this model is the inclusion of the charged dummies that can result in change of dipoles. These dipoles can reflect the change of environments and thus allow the model to respond to different environmental stimulus. We validate ProMPT with several benchmark proteins: Trp-cage, Trpzip4, villin, ww-domain, and β-α-β. ProMPT is able to simulate folding-unfolding and secondary structure transformation with minimal constraints, which is not feasible with previous CG models. In addition, ProMPT can also reproduce the experimental results for the dimerization of glycophorin A (GpA) with different point mutations. Here we demonstrate the ability of the model to capture the change of conformational space caused by point mutation. In the last part of this thesis, we combine ProMPT and an in-house CG IL model to study the effects of [TEA]+[Ms]− on amyloid beta 16-22 (Aβ16−22) aggregation. Aβ16−22 is the hydrophobic core region and is the smallest fragment of Aβ that can fibrilize. Aβ has been extensively linked to the pathogenesis of the Alzheimer’s disease. [TEA]+[Ms]− is reported to suppress the formation of β-sheets and induce helices at high concentration. From our results, both β-sheet content and the aggregate size decrease with the increase of IL concentration, which are in agreement with experiments. Aggregates can form in both water and IL, but with different morphologies. In water, a nice hydrophobic core involving Phe-Phe interactions can form as well as intact β-sheet contacts. In addition, a cross β-sandwich structure is also observed, as seen from previous literature. However, the same hydrophobic core can not persist in the presence of IL. Aggregate structures in IL are not stable over time due to the [TEA]+-Phe interaction. Helicity is also computed for Aβ16−22 in water and in IL at different concentrations and a positive correlation is found. The increase in helicity at high [TEA]+[Ms]− concentration can be explained by the reduction of the inter-peptide contacts, which then increases the opportunity for the peptides to form helical structures. Single peptide studies also reveal that [TEA]+[Ms]− increases the helicity, possibly through cation-induced dipole enhancement. In this thesis, a series of detailed investigations on the effects of ILs on protein behavior is performed. Specific interactions between IL functional groups and protein local/global structures are examined. The mechanisms we studied here will help constructing a holistic view for the design of IL-protein pair applications. The construction of the new CG protein/IL model provides another tool for the scientific community to study secondary structure transformation, folding- unfolding, and other biochemical processes that are sensitive to the environment with CG MD.
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    DESIGN AND SYNTHESIS OF POLYOLEFIN MATERIALS FOR NANOSTRUCTURED SELF-ASSEMBLY: BUILDING BLOCKS, COPOLYMERS, AND POLYMER CONJUGATES
    (2022) Wentz, Charlotte Maria; Sita, Lawrence R; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Polyolefin based materials are essential to today’s society in both simplistic commodity plastics to complex nanostructured materials and optoelectronic devices. In order to better understand these materials and make new impactful innovations, there is a barrier of fabrication, scalability, versatility, and programmability. The answer to the world’s plastic waste problem lies not in removing our use of polymers but relies in better understanding their properties, utilizing them as building blocks in advanced materials, and creating a long-lasting advanced material. Towards the goal of overcoming limitations in fabrication and scalability the work herein presents on utilizing a toolbox of living polymerization techniques such as living chain transfer polymerization (LCCTP) where new functionalities, stereochemical microstructures, optical properties, and physical properties of the polyolefin can be designed and systematically controlled. The polyolefins made through these techniques are scalable and versatile with end-group functionalization creating a seemingly endless choice of polymer building blocks and polymer materials. In line with creating new technologies that are programable the polyolefin building blocks made herein are utilized in multiple conjugates to create and understand methods and mechanisms of solid-state nanostructured self-assembly and access rare nonclassical phases that are highly desirable for their properties and uses in a plethora of applications. The conjugates investigated involve either a sugar-based head group covalently bond to a polymer tail to access rare and misunderstood Frank Kasper phase order-order transitions, or a perylene chromophore core covalently bond on both sides of the core in a linear fashion to polymer domains to create highly florescent or optically active materials that are useful in organic technologies such as solar cells, light emitting diodes, or nanotechnology. These perylene based conjugates can self-assemble into unique columnar phases and single gyroid phase. These results with conjugates provide methods for reliable and programmable access to rich phase behavior through the design of the polyolefin domains.
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    UNDERSTANDING AND TAILORING THE REACTIVE CHARACTERISTICS OF NANOENERGETIC COMPOSITES VIA STRUCTURAL AND CHEMICAL MODIFICATIONS
    (2022) XU, FEIYU; Zachariah, Michael R; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Nanoenergetic composites are nanostructured fuel and oxidizer mixtures that store a large amount of chemical energy and release it, typically in the form of heat, upon ignition. They are promising candidates for energy intensive applications such as propellants and pyrotechnics, due to their high energy density. The overall reaction kinetics of the heterogenous nanoenergetic system is controlled by mass transfer. The use of nanoparticles is to reduce diffusion length and thus increase energy release rate. The objective of the proposed research is to understand how intrinsic properties of fuel and oxidizer affect the reaction of nanoenergetic composites, and to develop novel, multifunctional nanoenergetic materials with tunable ignition threshold and energy release rate. Experiments were conducted utilizing primarily a time resolved Temperature-Jump time-of-flight mass spectrometer (T-Jump TOFMS) to analyze gas phase reaction intermediatespecies and products at a high heating rate (~105 K/s), along with a combustion cell for reactivity evaluation. New fuels including hydrogenated amorphous silicon, and oxidizers including oxygen deficient Co3O4-x and ferroelectric Bi2WO6 were investigated. The role of surface chemistry in the energetic characteristics of silicon nanoparticles was investigated, leading to the uncovering of a new reaction mechanism. Modulating the initiation temperature of aluminothermic reaction via defect engineered metal oxide was demonstrated. A study of piezoelectric oxidizers reveals the superior reactivity of a complex metal oxide. Moreover, tuning the energy release rate of I2O5 based biocidal nanoenergetic composites via a ternary system was studied. These results indicate that by modifying the chemistry or structure of fuels and oxidizers, the combustion characteristics of nanoenergetic composites can be tailored.