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.

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 …

Transition metal oxynitrides are of growing interest for their use as electrocatalyst for nitrogen reduction reaction. The metals in the oxynitride used for catalytic process are stabilized in intermediate state for effective activation of nitrogen. Therefore, studying the interaction of metal oxynitrides films to ambient exposure is necessary. Here, sputter deposited vanadium oxynitride is compared to cobalt oxynitride using insitu Auger electron spectroscopy (AES), ex situ X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and scanning electron microscopy (SEM). After deposition in Ar/N2 environment, in situ AES spectra indicate that film is vanadium oxynitride despite oxygen is not the reactive gas. In contrast, in situ AES indicate film is pure cobalt nitride at the same base pressure and deposition condition (as vanadium). For ambient exposure, in situ AES indicate the incorporation of oxygen in the cobalt nitride film to form cobalt oxynitride. Ex situ XPS indicate both films get more oxidized but uniformly distributed as there is only slight difference in grazing and normal emission XPS. XRD and SEM also indicate how homogeneously distributed both films are. These finding confirms how important it is that transition metal centers are kept in intermediate oxidation state for the activation of nitrogen bond.

Design and development of novel one-step reactions that produce nitrogen-containing scaffolds is an invaluable area of chemistry due to the abundance of these moieties in natural products and biologically active molecules. Discovering novel methods using uncommon substrates and rare earth metals to access these significant scaffolds present a challenge. Over the course of my doctoral studies, I have designed, developed and optimized novel reactions by using rarely known substrates and rare earth metals that have afforded important nitrogen-containing scaffolds. The products obtained allow access to otherwise long-to-synthesize molecules and expeditious construction of biologically active molecules.

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

As countries pledge their commitment to a net-zero future, much of the previously forgotten climate change research were revitalized by efforts from both governmental and private sectors. In particular, the utilization of lignocellulosic materials saw a special spotlight in research interest for its abundance and its carbon removal capability during photosynthesis. The initial effort in mimicking enzymatic active sites of β-glucosidase will be explored. The crystalline covalent organic frameworks (COFs) allowed for the introduction of a variety of noncovalent interactions, which enhanced the adsorption and the catalytic activity against cellobiose and its glycosidic bonds. The physical processes associated with this reaction, such as the kinetics, equilibrium, and activation energies, will be closely examined and compared with existing standard materials and comparable advanced catalysts. In addition, several variants of COFs were synthesized to explore the effect of various noncovalent interactions with cellobiose. A radical-bearing COF was synthesized and characterized. The stability of this radical was examined by electron paramagnetic resonance spectroscopy (EPR) and its oxidative capability tested with model lignin and alcoholic compounds. The reaction products are monitored and identified using gas chromatography-mass spectroscopy (GC-MS). An oxidative coupling of phenol was explored, and its initial results are presented in chapter 5.

Seventeen new dithiophenyl- and napthodithiophenyl- fused porphyrins were synthesized; from these an additional 7 porphyrin oligomers were also synthesized. Additionally freebase 2,7-dimethoxytriphenylene fused porphyrin was also synthesized from a freebase precursor. Aromatic indices NICS and AICD were used to evaluate these new molecules.

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 …

Many previous studies have demonstrated that gold compounds possess successful results in catalysis and in medicinal chemistry. The central aim of this dissertation is the design and synthesis of novel gold (I) acyclic diamino carbene complexes as a chemotherapeutic agent for triple-negative breast cancer (TNBC) and for catalysis. In this study, a series of chiral neutral and cationic gold (I) acyclic diamino carbene (ADC) complexes and neutral gold (I) bis- ADC complexes have been synthesized. As the chiral neutral gold (I) ADCs, four diastereomers of S binaphthyl L proline tertiary butyl ester gold (I) chloride, S binaphthyl D proline tertiary butyl ester gold (I) chloride, R binaphthyl L proline tertiary butyl ester gold (I) chloride, and R binaphthyl D proline tertiary butyl ester gold (I) chloride have been synthesized and characterized. Different chiral gold (I) ADC complexes with bulky chiral binaphthyl group and with different amine groups of morpholine, chiral proline methyl ester, and benzyl ester have been synthesized and characterized. After that four diastereomers of the nitrile adduct of cationic binaphthyl proline tertiary butyl ester nitrile and four diastereomers of the isonitrile versions of it have been synthesized and characterized. A series of gold (I) cationic bis ADC complexes …

This study addressed five key applications of paper spray mass spectrometry (PS-MS): (i) comparative analysis of the microporous substrate with the cellulose-based substrate in drug detection; (ii) detection of more than 190 fentanyl analogs with their fragmentation pattern can be implemented in the future reference for quicker, accurate and sensitive determination; (iii) exploring sweat in a fingerprint to be considered an alternate method to recognize non-invasive markers of metabolites, lipids, narcotics, and explosive residues that can be used in forensic testing applications; (iv) extending and improving better, cost-effective and quick real-time monitoring of the diseased stage using biofluid samples to obtain vastly different lipid information in viral infection such as COVID-19; and (v) mass spectral detection in chemical warfare agent (CWA) stimulant gas exposure with microporous structure absorbency capabilities in air quality monitoring. This novel synthetic material is known as Teslin® (PPG Industries), consisting of a microporous polyolefin single-layered silica matrix, can be used for precise, sensitive, selective, and rapid sample analysis with PS-MS. The Teslin® substrate provided longer activation time for samples and an active signal with a higher concentration of ion formation and mobility compared to cellulose-based papers. Direct analysis of multiple samples showed that, besides being more …

This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).

The direct epitaxial growth of multilayer BN by atomic layer deposition is of critical significance forfo two-dimensional device applications. X-ray photoelectron spectroscopy (XPS) and low energy electron diffraction (LEED) demonstrate layer-by-layer BN epitaxy on two different substrates. One substrate was a monolayer of RuO2(110) formed on a Ru(0001) substrate, the other was an atomically clean Ni(111) single crystal. Growth was accomplished atomic layer deposition (ALD) cycles of BCl3/NH3 at 600 K substrate temperature and subsequent annealing in ultrahigh vacuum (UHV). This yielded stoichiometric BN layers, and an average BN film thickness linearly proportional to the number of BCl3/NH3 cycles. The BN(0001)/RuO2(110) interface had negligible charge transfer or band bending as indicated by XPS and LEED data indicate a 30° rotation between the coincident BN and oxide lattices. The atomic layer epitaxy of BN on an oxide surface suggests new routes to the direct growth and integration of graphene and BN with industrially important substrates, including Si(100). XPS and LEED indicated epitaxial deposition of h-BN(0001) on the Ni(111) single crystal by ALD, and subsequent epitaxially aligned graphene was deposited by chemical vapor deposition (CVD) of ethylene at 1000 K. Direct multilayer, in situ growth of h-BN on magnetic substrates such as …

Donor-acceptor systems have unique properties that make them ideal candidates for solar energy harvesting through mimicry of natural photosynthesis. This dissertation is focused on unraveling those unique properties in various types of donor-acceptor systems. The systems investigated are categorized as closely linked, push-pull, supramolecular, and multi-unit. As part of the study, photosynthetic analogues based on BF2-chelated dipyrromethene (BODIPY), porphyrin, phthalocyanine, truxene, ferrocene, quinone, phenothiazine (PTZ), perylenediimide (PDI), fullerene (C60), dicyanoquinodimethane (DCNQ), tetracyanobutadiene (TCBD), and triphenylamine (TPA) are investigated. The effects of proximity between donor-acceptor entities, their geometrical orientation relative to each other, push-pull character of substituents, and competitive energy and electron transfer are examined. In all systems, primary events of photosynthesis are observed, that is absorption and energy transfer and/or electron transfer is witnessed. Ultrafast transient absorption spectroscopy is utilized to characterize the photo-induced events, while other methods such as steady-state luminescence, cyclic voltammetry, differential pulse voltammetry, chronoamperometry, and computational calculations are used to aid in the characterization of the donor-acceptor systems, in particular their applicability as solar energy harvesters.

The deposition of boron oxide (B₂O₃) films on silicon substrates is of significant interest in microelectronics for ultrashallow doping applications. However, thickness control and conformality of such films has been an issue in high aspect ratio 3D structures which have long replaced traditional planar transistor architectures. B₂O₃ films are also unstable in atmosphere, requiring a suitable capping barrier for passivation. The growth of continuous, stoichiometric B₂O₃ and boron nitride (BN) films has been demonstrated in this dissertation using Atomic Layer Deposition (ALD) and enhanced ALD methods for doping and capping applications. Low temperature ALD of B₂O₃ was achieved using BCl₃/H₂O precursors at 300 K. In situ x-ray photoelectron spectroscopy (XPS) was used to assess the purity and stoichiometry of deposited films with a high reported growth rate of ~2.5 Å/cycle. Free-radical assisted ALD of B₂O₃ was also demonstrated using non-corrosive trimethyl borate (TMB) precursor, in conjunction with mixed O₂/O-radical effluent, at 300 K. The influence of O₂/O flux on TMB-saturated Si surface was investigated using in situ XPS, residual gas analysis mass spectrometer (RGA-MS) and ab initio molecular dynamics simulations (AIMD). Both low and high flux regimes were studied in order to understand the trade-off between ligand removal and B₂O₃ …

This dissertation details the use of computational methods to understand the effect that cancer-related mutations have on proteins that complex with nucleic acids. Firstly, we perform molecular dynamics (MD) simulations of various mutations in DNA polymerase κ (pol κ). Through an experimental collaboration, we classify the mutations as more or less active than the wild type complex, depending upon the incoming nucleotide triphosphate. From these classifications we use quantum mechanics/molecular mechanics (QM/MM) to explore the reaction mechanism. Preliminary analysis points to a novel method for nucleotide addition in pol κ. Secondly, we study the ten-eleven translocation 2 (TET2) enzyme in various contexts. We find that the identities of both the substrate and complementary strands (or lack thereof) are crucial for maintaining the complex structure. Separately, we find that point mutations within the protein can affect structural features throughout the complex, only at distal sites, or only within the active site. The mutation's position within the complex alone is not indicative of its impact. Thirdly, we share a new method that combines direct coupling analysis and MD to predict potential rescue mutations using poly(ADP-ribose) polymerase 1 as a model enzyme. Fourthly, we perform MD simulations of mutations in the protection of …

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.

Mother nature has laid out a beautiful blueprint to capture sunlight and convert to usable form of energy. Inspired by nature, donor-acceptor systems are predominantly studied for their light harvesting applications. This dissertation explores new donor-acceptor systems by studying their photochemical properties useful in building artificial photosynthetic systems. The systems studied are divided into phthalocyanine-porphyrin-fullerene-based, perylenediimide-based, and aluminum porphyrin-based donor-acceptor systems. Further effect of solvents in determining the energy or electron transfer was studied in chapter 6. Such complex photosynthetic analogues are designed and characterized using UV-vis, fluorescence spectroscopy, differential pulse voltammetry and cyclic voltammetry. Using ultrafast transient absorption spectroscopy, the excited state properties are explored. The information obtained from the current study is critical in getting one step closer to building affordable and sustainable solar energy harvesting devices which could easily unravel the current energy demands.

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.

Benzannulation to porphyrin 2,3 positions has previously been accomplished using various methodologies in the past century, yet there remain limited methodologies to both annulate to the porphyrin periphery and add functional moieties that can then be derivatized for diverse applications. This dissertation describes the development of synthetic routes and characterization of a variety of linearly-annulated, functionalized, β,β'-π-extended porphyrins. There are five chapters in this dissertation, the first of which introduces synthesis and properties of porphyrins and π-extended porphyrins. Chapter 2 describes synthesis of pentacenequinone-fused and pentacene-fused poprhyrins with distinct and new optical absorbance properties. In chapter 3, synthesis and characterization of benzimidazole-fused porphyrins displaying external metal binding capability is described. The synthetic method developed in chapter 3 is extended in chapter 4 to synthesis of bisbenzimidazole-fused porphyrin dimers that show split Soret character, likely due to excitonic coupling between porphyrins of the dimer. Chapter 5 summarizes this dissertation and describes future directions that this dissertation provides foundation for.

The dissertation covers three major topics: metal-assisted aromaticity, synthetic approaches to tailor donor-acceptor supramolecular stacks, and photoluminescence properties of cyclic trinuclear complexes (CTCs) of d10 metals. First, multiple theoretical approaches are adapted to discuss in detail the origin of aromaticity of CTCs, putting forward a metal-assisted aromaticity model. Next are the discoveries of donor-acceptor stacked CTC–CTC' complexes from both experimental and computational perspectives, reporting multiple novel crystallography-determined structures and revealing their pertinent intermolecular ground-state charge transfer. The spontaneous binding behavior is also determined by UV-vis and NMR titrations and rationalized as the cooperation of multiple supramolecular interactions, including metallophilicity, electrostatic attraction, and dispersion. The last part includes systematic investigations of photoluminescence properties of halogen-metal-bonded CTCs and sandwich-like cation–π-bonded heptanuclear clusters based on CTCs. The cooperative effects of metal-centered conformation, the heavy-atom and relativistic effects from both the halogen and metal atoms play complementary roles in the phosphorescence process to promote the inter-system crossing and radiative transitions.

Opioid abuse and in particular fentanyl, a synthetic opioid, has been of concern in the last decade. Fentanyl is an illicit drug of concern to due to its prevalence and potency. Research to date has focused on supporting law enforcement by developing methods suitable for chemical profiling and identifying fentanyl from various matrices. However, methods geared towards analysis of fentanyl isomeric analogues are rare. Analysis of isomers is challenging due to similar mass spectral fragmentation patterns and exhibiting co-elution using common gas chromatographic columns. Developing methods to use in forensic labs utilizing already available equipment will advance current capabilities in the detection of fentanyl compounds. Thus, investigation into alternative stationary phases and development of special gas-liquid chromatographic (GLC) based methods for isomeric fentanyl analogues has been done. Several studies were done to investigate the use of ionic liquid chromatographic phases in analyzing fentanyl analogues. The first study focused on investigating the thermal stability of ionic liquids to identify those suitable to withstand the high oven temperatures that was needed to elute fentanyl analogues in gas chromatography. Total synchronous fluorescence spectroscopy and differential scanning calorimetry were demonstrated to be sensitive enough to detect the decomposition products of ionic liquids. In the …

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.

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.

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 …