In this work, the development of parameters for a series of imidazolium-based ionic liquids molecules, now included in the AMOEBA force field, is discussed. The quality of obtained parameters is tested in a variety of calculations to reproduce structural, thermodynamic, and transport properties. First, it is proposed a novel method to parameterize in a faster, and more efficient way parameters for the AMOEBA force field that can be applied to any imidazolim-based cation. Second, AMOEBA-IL polarizable force field is applied to study the N-tert-butyloxycarbonylation of aniline reaction mechanism in water/[EMIM][BF4] solvent via QM/MM approach and compared with the reaction carried out in gas-phase and implicit solvent media. Third, AMOEBA-IL force field is applied in alchemical calculations. Free energies of solvation for selected solutes solvated in [EMIm][OTf] are calculated via BAR method implemented in TINKER considering the effect of polarization as well as the methodology to perform the sampling of the alchemical process. Finally, QM/MM calculations using AMOEBA to get more insights into the catalytic reaction mechanism of horseradish peroxidase enzyme, particularly the structures involved in the transition from Cp I to Cp II.

Monovalent coinage metal complexes have been of significant interest due to their rich photophysical properties. This dissertation focuses on the design, synthesis, and characterization of gold, silver, and copper phosphors. Chapter 2 investigates new physical and photophysical properties of a gold diphosphine dimer in the solid state. Thermally activated luminescence switching between two structural states is discussed. Chapter 3 includes the photochemistry of closed shell group 11 transition metals with dithiophosphonate and diphosphine ligands as heteroleptic, homoleptic and heterometallic systems. Chapter 4 reports the synthesis and characterization of a cyclic trinuclear gold imidazolate complex with high electron dentistry and π- base properties. The trinuclear gold (I) complexes reactivity with silver(I) and sodium cations is explored. The photochemistry of all complexes are screened for efficiency, emission profiles and lifetimes as potential materials to be used in OLEDs and other molecular devices.

The porous materials discussed in this dissertation are metal-organic frameworks (MOFs) and porous liquids. Due to their high surface areas, tunable structures, and controllable porosities, MOFs have been explored for a wide variety of drug delivery applications. In chapter 2, MOFs have been used as magnetothermal-triggered release carriers through spatially distributed iron oxide nanoparticles within MOF matrix as a magnetic heating mediator and surface-grafted thermal-responsive nanocap as an alternating magnetic field (AMF)-responsive gatekeepers, achieving monitoring of drug release via external AMF by a conformational change of nanocap. In chapter 3, MOF, as a non-toxic loading carrier, encapsulate naringin, a natural product to serve as a multifunctional bio-platform capable of treating Gram-positive bacteria and certain cancers by slowly and progressively releasing the encapsulated naringin as well as improving and modulating immune system functions through the synergies between naringin and MOF. In chapter 4, porous liquid with unique solvent-free fluidity properties as a drug delivery platform for the first time. The interaction between hollow silica nanoparticle and polymerized ionic liquid, followed by ionic grafting brush of poly (ethylene glycol) telomer, makes this designed porous liquid responsible for high drug-loading and pH-responsive drug-releasing abilities along with slow degradation behavior. In addition to their …

The recovery processes of critical metals from multiple sources have turned more and more attention due to the increasing demand and consumption of them in modern industry. Many metals are used as significant components in manufacturing of a variety of products and equipment, playing significant roles in the economic security and national security; those metals involve rare earth elements (REEs), precious metals which include gold, silver, and platinum group metals (PGMs), and other valuable metals such as lithium, uranium, nickel, et al. The traditional approach to obtaining the above metals is by hardrock mining of natural ores via chemical and physical processes. However, this method of mining and refining metals from minerals is usually energy-consuming, costly, and environmental-destructive. Thus, various approaches to extracting or recycling target metals from the seawater or the solution of secondary resources as an alternative to traditional hardrock mining have been developed, and thereinto, using functional porous adsorbents to selectively capture specific metal ions from the aqueous resources has attracted increasing attention due to its outstanding merits such as high efficiency, energy-saving process, low cost, and reduced environmental impacts

This dissertation demonstrates that it is possible to create a donor-acceptor system that can transform sunlight into electrons. By using site-directed synthesis, it was possible to create a novel trans-A2B2 porphyrin. In the pursuit of creating a supramolecular system, both the novel (TPA-BT)2ZnP and C60imidazole combined in solution such that the nitrogenous lone pair of C60 imidazole would coordinate axially to the zinc atom in the porphyrin. The conjugates' characterization utilized spectral, electrochemical, and computational techniques. Computational studies revealed in the optimized structure that the HOMO localized on the porphyrin and LUMO centered over the C60imidazole entity. Rehm-Weller calculations showed feasibility of singlet-electron transfer. Femtosecond transient absorption studies documented an efficient photoinduced charge separation in the conjugate. The subsequent work through steady-state and time-resolved transient absorption techniques that photoinduced electron transfer takes place between the synthesized phenylimidazole functionalized bisstyrylBODIPY (BDP(Im)2) and three selected zinc tetrapyrroles. This dyad consisted of BDP(Im)2 and either zinc tetratolylporphyrin (ZnP), zinc-tetra-t-butyl phthalocyanine (ZnPc), or zinc tetra-t-butyl naphthalocyanine (ZnNc) in a solution solvated by σ-dichlorobenzene (DCB). The three dyads (BDP(Im)2:ZnP, BDP(Im)2:ZnPc, and BDP(Im)2:ZnNc) were investigated by spectroscopic, computational, and electrochemical methods. The 1:1 complex of the dyads in optical absorption studies were approximately ~104 M-1 suggesting …

Molecular dynamics simulations and QM/MM calculations can provide insights into the structure and function of enzymes as well as changes due to mutations of the protein sequence.

Mechanical pressure offers unique control over the energy landscape of chemical reactions, opening up pathways that are inaccessible through conventional thermochemistry. We hypothesize that the reduced dimensionality defines the conformational space of the high-pressure reaction, giving rise to new selectivity that is unavailable in 3D systems. Here, we demonstrate this concept through the pressure-controlled topochemical polymerization of the diacetylene molecule deca‐3,5‐diyn‐1‐amine (DDA) incorporated in the two-dimensional (2D) perovskite [DDA]2PbBr4. Compression at 3 GPa drives the first topochemical polymerization through 1,2 addition, forming a polyene product at room temperature. The reaction is initiated by the mechanical bending of the linear DDA molecule, a mechanism fundamentally different from the 1,4-addition in 3D solids. Importantly, pressure hinders the second 1,2-addition by disfavoring the gauche conformation between the remaining acetylene groups, allowing for the selective formation of polyene versus polyacene products. We characterize the reaction mechanisms and products using spectroscopies (Raman, X-ray photoelectron, ultraviolet-visible), X-ray diffraction and density-functional theory simulations. These results highlight the important role of dimensionality in high-pressure chemistry, and offers a new paradigm for creating low-dimensional functional materials.

The Túngara frog (Engystomops pustulosus) from Central America creates a bio-foam that protects their young from dehydration, microbial degradation, and even predators during early development. The foam is composed of unique proteins known as Ranaspumin 1-6 (RSN 1-6). These RSN proteins have been synthetically synthesized and verified with Circular Dichroism (CD) to determine their critical micelle concentration, antimicrobial properties, and stability at varying temperatures and pH ranges. Throughout these characterizations, RSN 2 was determined to establish/produce antimicrobial properties, express stability at temperatures between 20 – 60oC, and express stability at a pH range of 5-8. Therefore, RSN 2 was isolated and utilized for medical and environmental applications. With the addition of RSN 2, the separation of aromatics was achieved in tar-sands with the assistance of a Tangential Flow Filtration (TFF) system. With only three passes through the TFF system, the RSN 2 solution isolated approximately 35% of the aliphatic region, and approximately 70% of the aromatic region. Finally, RSN 2 was implemented into an organ preservation solution for organ transplant surgery. By observing two different biomarkers, including Cardiolipin (CL) and alkali metals/alkaline earth metals for a change in concentration to verify organ viability. Resulting in the RSN 2 solution as …

This dissertation research work focuses on the investigation of novel donor-acceptor systems elucidating their photochemical properties, anion binding, and their potential application in the development of artificial photosynthetic systems. The explored systems are based on oxoporphyrinogen (OxPs), porphyrins, fullerene, and boron dipyrromethene (BODIPY) based donor-acceptor systems. The photochemical properties of novel molecular systems were elucidated using UV-vis spectroscopy, fluorescence spectroscopy, electrochemical methods, computational calculations, and ultrafast transient absorption spectroscopy. A novel BODIPY-oxoporphyrinogen dyad which is able to bind with fluoride anion promoting the excited state ultrafast electron and energy transfer events mimicking the primary events in natural photosynthesis was introduced. Further, self-assembly of supramolecular complexes based on oxoporphyrinogens, fullerene, and different zinc porphyrin dimers was explored. The formed self-assembled complexes have shown photoinduced electron transfer. A novel push-pull supramolecular construct based on the spiro-locked N-heterocycle-fused zinc porphyrin was studied. The excited state charge separation and stabilization of this push-pull system was enhanced by the complexation with fluoride anion. Also, the effect of BODIPY functionalization and linkers on the electron transfer properties of a series of carbazole–BODIPY and phenothiazine-BODIPY dyads were investigated. These findings are important to develop advanced and efficient BODIPY-based donor-acceptor systems for efficient light harvesting applications. The entire …

Computational techniques, mostly density functional theory (DFT), were applied to study metal-based catalytic processes for energy conversion reactions. In the first and second projects, the main focus was on activation of the light alkanes such as methane, which have thermodynamically strong and kinetically inert C–H bonds plus very low acidity/basicity. Two Mo-oxo complexes with the different redox non-innocent supporting ligands, diamide-diimine and ethylene-dithiolate, were modeled. These Mo-oxo complexes are modeled inspired by active species of a metalloenzyme, ethylbenzene dehydrogenase (EBDH). The results for the activation of the benzylic C–H bond of a series of substituted toluenes by modeled Mo-oxo complexes show there is a substantial protic character in the transition state which was further supported by the preference for [2+2] addition over HAA for most complexes. Hence, it was hypothesized that C–H activation by these EBDH mimics is controlled more by the pKa than by the bond dissociation free energy of the C–H bond being activated. The results suggest, therefore, promising pathways for designing more efficient and selective catalysts for hydrocarbon oxidation based on EBDH active site mimics. Also, it is found that the impact of supporting ligand and Brønsted/Lowry acid/base conjugate is significant on the free energy barrier of …

In this study, thiol and two disulfide compounds have been tested as new corrosion inhibitors for brass and aluminum alloys. Pyridine-2-thiol and 2,2'-dipyridyl disulfide were tested for brass alloys in 0.5 M H2SO4 solution and both inhibitors showed excellent corrosion protection against the aggressive corrosive ion attack. Both inhibitors adsorbed to brass surface forming a protective film via a chemisorption process. XPS studies showed formation of Cu-S bond which allows these molecules to chemisorb on to brass surfaces. Pyridine-2-thiol, 2,2'-dipyridyl disulfide and 4'4-diaminodiphenyl disulfide were tested as corrosion inhibitors for AA6061-T6 alloy in 1 M HCl solution and all inhibitors showed excellent corrosion protection over wide range of temperatures. To evaluate the corrosion inhibition efficiencies many different instruments and electrochemical techniques were used. Overall results from this study showed sulfur-based corrosion inhibitors can be used effectively to mitigate the corrosion process of brass and aluminum alloys in acidic solutions.

All oxide heterostructure Cr2O3/TiO2-x was deposited on Al2O3(0001) single crystal via MBE. The analysis of interfacial interactions involving two metal oxides resulting in magnetic properties gave insights for using such heterostructures as potential spintronic device materials. The corundum phase epitaxial growth of TiO2-x on Al2O3 was characterized using XPS, AES, EELS, and LEED. The data obtained gives evidence of presence of two-dimensional electron gas at titania surface due to oxygen vacancies formation after deposition. On titania, the deposition of chrome in UHV results in the formation of oxidized chromia overlayer by abstraction of oxygen from the TiO2-x underlayer further increasing the number of vacancies present. In industrial R&D project, dry etching of multiple optical device components was performed using a novel angled etch prototype tool. The first set of experiments involved plasma etching of SiC thin films optimized for target application. The best-known method (BKM) worked from 300mm full wafer to 200mm product. In second experimentation, a variety of gray-tone photoresist received from customers were etched using BKM. Customer received etch rate on each gray-tone material. The third experiments compared recipe R1 to test recipe R2 on the test vehicle VDC. R2 showed faster etch rate but lower process repeatability …

Cobalt oxynitride films formed by magnetron sputter deposition of a Co target in N2 or NH3 plasma or, alternatively, by NH3 plasma nitridation of a Co film deposited on Si(100), show a divergence of properties arising from (a) N and O interactions for N and O atoms bonded to each other or through a common metal center and (b) the oxophilicity of the metal center itself. Core and valence band X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and plane wave density functional theory (DFT) calculations have been used to probe chemical and electronic interactions of nitrogen-rich cobalt oxynitride CoO1-xNx (x > 0.7) films. DFT-based calculations supervised by the Cundari group show the zinc blende (ZB) structure is found to be energetically favored over the rocksalt (RS) structure for x > ~ 0.2, with an energy minimum observed in the ZB structure for x ~ 0.8 - 0.9. There is also agreement with experiment for core level binding energies obtained for DFT calculations based on the ZB structure and this forms the basis of a predictive model for understanding how N and O interactions impact the electronic and catalytic properties of these materials. Vanadium oxynitride films were deposited in a mixture …

The research presented in the dissertation deals with the synthesis, characterization, photophysical, electrochemical, and pump probe studies of porphyrin-fullerene based donor-acceptor conjugates. The first chapter provides insights into the introduction of the thesis, which explains the events that occur in natural photosynthesis and the mimicking process of an artificial photosynthesis based on natural photosynthesis, works done in covalently and non-covalently linked donor acceptor systems, and the penetration of the literature related to the long-lived charge-separated states donor-acceptor conjugates. The second chapter details the physical methods employed to monitor the various photochemical processes in the donor-acceptor moiety. The third chapter focusses on designing and synthesizing a platinum porphyrin-fullerene dyad used for long-lived charged-separated state. The formation of a high-energy, long-lived radical ion pair by electron transfer from the triplet excited state is orchestrated in the dyad. The porphyrin ring is modified with three triphenylamine which act as secondary electron donors. The spin state of the electrons leading to the formation of long-lived charge-separated state is demonstrated by time-resolved optical and EPR spectroscopy. The fourth chapter studies metal ligand axial coordination. Two porphyrins were self-assembled via metal-ligand axial coordination of phenyl imidazole functionalized fulleropyrrolidine. A 1:2 complex formation with ImC60 was observed …

Artificial photosynthesis is the process, which mimics the natural photosynthesis process in order to convert solar energy to chemical energy. This process can be separated into four parts, which are antenna system, reaction center, water oxidation center, and proton reduction center. If we only focus on the ‘antenna system and reaction center' modules, expanding the absorption band in antenna system and generating long-lived charge separated state in reaction center are two fantastic strategies to design the molecules in order to improve the efficiency of the artificial photosynthesis process. In the first work of this dissertation, mono-18-crown-6 and mono-ammonium binding strategy was used to connect BODIPY- C60 supramolecular based donor–acceptor conjugates. The meso- position of BODIPY was modified by benzo-18-crown-6, and the 3, 5 methyl positions were replaced by two styryl groups, which covered additional donor (triphenylamine or 10-methylphenothiazine). The acceptor is a fulleropyrrolidine derivative, which included an ethyl ammonium cation. The absorbance wavelengths of the donor covered 300-850 nm, which is the visible/near IR region (wide band capturing). The ultrafast charge separation and relatively slow charge recombination was found from femtosecond transient absorption study. Next, a ‘two point' bis-18-crown-6 and bis-ammonium binding strategy was utilized to link BODIPY- C60 supramolecular …

The presented dissertation encompasses three distinct investigations into novel complexes with diverse applications. Firstly, a Europium-based complex, K[Eu(hfa)4], exhibits remarkable potential for detecting dissolved CO2 in an ethylene glycol medium, offering a low limit of detection, rapid response times, and high signal-to-noise ratios. This complex demonstrates promise for quantifying CO2 concentrations and finds utility in sugar fermentation monitoring. Secondly, an innovative ratiometric optical sensor, Eu(tta)3([4,4'-(t-bu)2-2,2'-bpy)], showcases exceptional sensitivity and selectivity in detecting aluminum ions, making it suitable for environmental and biological applications. It exhibits reliable quantification in both methanol and aqueous samples, with remarkable accuracy validated by ICP-OES. Lastly, modifications to the Au3Pz3 complex synthesis enable the development of a silver ion sensor, paving the way for detecting silver ion leaching in real-life scenarios, such as silver nanoparticle-embedded bandages. The research extends to the synthesis of silver nanoparticles using various methods and foresees expanded in vitro and in vivo studies. These investigations collectively offer insights into the development of advanced sensing technologies with significant implications for a wide range of practical applications.

Addition reactions of ten neutral nucleophiles and seven anionic nucleophiles with the pentaosmium pentadecacarbonyl carbido cluster Os5C(CO)15 have been kinetically studied and several important reactivity trends have been established. The calculated activation parameters support an associative mechanism involving the attack of nucleophiles on the parent cluster in the rate-limiting step. Decarbonylation reactions of neutral arachno clusters Os5C(CO)15L have also been kinetically studied and different reactivity trends have been observed. Reactions of Os5C(CO)15 with both neutral and anionic nucleophiles produce corresponding arachno clusters in good yield. Neutral arachno clusters decarbonylate when heated to yield corresponding nido clusters. All studied anionic arachno clusters are resistant to decarbonylation, but most of them readily react with organic acids to form corresponding hydrido clusters. Reactions of anionic arachno clusters with methyl triflate yielded several new clusters. Exploration of metal-ligand bond lengths in the respective pairs of arachno and nido clusters yielded a valuable conclusion with regard to steric effects prevalent in these molecules. The mechanisms for polyhedral structural rearrangements between arachno and nido derivatives of the pentaosmium carbido cluster have been proposed. Thermolysis of cluster Ru3[Ph2PCH(Me)PPh2](CO)10 in the presence of diphenylacetylene yields alkyne-substituted clusters Ru3(PhCCPh)[Ph2PCH(Me)PPh2](CO)8 and Ru3(PhCCPh)[Ph2PCH(Me)PPh2](CO)7 as the major products. The backbone-modified diphosphine in …

Previous work was successful at delineating reaction pathways for the photoactivated synthesis of an amine, [CztBu(PyriPr)(NH2−PyriPr)], by double intramolecular C−H activation and functionalization via irradiating a metal(II) azido complex, [CztBu(PyriPr)2NiN3. The present work seeks to expand upon earlier research, and to substitute the metal with iron or cobalt, and to expand the study to photocatalyzed intermolecular C−H activation and functionalization of organic substrates. Density functional theory (DFT) – B3LYP/6-31+G(d') and APFD/Def2TZVP – and time-dependent density functional theory (TDDFT) were used to propose a detailed pathway comprised of intermediates of low, intermediate, or high spin multiplicity and photo-generated excited states for the reaction of the azido complex, [CztBu(PyriPr)2MN3] to form the amine complex [CztBu(PyriPr)M(NH2−PyriPr)], M = Co, Ni or Fe, and the intermediates along the reaction pathway. For applications on quantum computing, the photophysical properties of photoactive d8 nickel(II) complexes are modeled. Such systems take advantage of a two-level system pathway between ground to excited state electronic transitions and could be useful for the discovery of successful candidates for a room temperature qubit, the analogue of a classical computational bit. A modified organometallic model, inspired by a nitrogen vacancy selective intersystem crossing model in diamond, was developed to take advantage of …

Computational chemistry examination of the bond dissociation enthalpies of tungsten and main group elements. Includes quantification and calibration of theoretical methods to address the question of bond strengths including component σ and π molecular bonds.

Ultrafast charge and electron transfer, primary events in artificial photosynthesis, are key in solar energy harvesting. This dissertation provides insight into photo-induced charge and electron transfer in the donor and acceptor constructs built using a range of donor and acceptor entities, including transition metal dichalcogenides (TMDs, molybdenum disulfide (MoS2), and tungsten disulfide (WS2)), N-doped graphene, diketopyrrolopyrrol (DPP), boron-dipyrromethene (BODIPY), benzothiadiazole (BTD), free base and metal porphyrins, zinc phthalocyanine (ZnPc), phenothiazine (PTZ), triphenylamine (TPA), ferrocene (Fc), fullerene (C60), tetracyanobutadiene (TCBD), and dicyanoquinodimethane (DCNQ). The carefully built geometries and configurations of the donor and (D), acceptor (A), with a spacer in these constructs promote intramolecular charge transfer, and intervalence charge transfer to enhance charge and electron transfer efficiencies. Steady-state UV-visible absorption spectroscopy, fluorescence and phosphorescence spectroscopies, electrochemistry (cyclic voltammetry (CV) and differential pulse voltammetry (DPV)), spectroelectrochemistry (absorption spectroscopy under controlled potential electrolysis), transient absorption spectroscopy, and quantum mechanical calculations (density functional theory, DFT) are used to probe ground and the excited state events as well as excited state charge separation resulting in cation and anion species. The current findings are useful for the increased reliance on renewable energy resources, especially solar energy.

Synthesis of d10 complexes of monovalent coinage metals, copper(I) and gold(I), with dithiophosphinate/diphosphine ligands -- along with their targeted characterization and screening for inorganic or organic light emitting diodes (LEDs or OLEDs, respectively) -- represents the main scope of this dissertation's scientific contribution in inorganic and materials chemistry. Photophysical studies were undertaken to quantify the phosphorescence properties of the materials in the functional forms required for LEDs or OLEDs. Computational studies were done to gain insights into the assignment of the phosphorescent emission peaks observed. The gold(I) dinuclear complexes studied would be candidates of OLED/LED devices due to room temperature phosphorescence, visible absorption/excitation bands, and low single-digit lifetimes -- which would promote higher quantum yield at higher voltages in devices with concomitant lower roll-off efficiency. The copper(I) complexes were not suited to the OLED/LED applications but can be used for thermosensing materials. Crystallographic studies were carried to elucidate coefficients of thermal expansion of the crystal unit cell for additional usage in materials applications besides optoelectronic devices. This has uncovered yet another unplanned potential application for both copper(I) and gold(I) complexes herein, as both types have been found to surpass the literature's threshold for "colossal" thermal expansion coefficients. Two other investigations …