Chemistry Commons^™

The Synthesis And Evaluation Of Thioxothiazolidin-4-One Compounds As Pim Kinase Inhibitors, Kelly Malzewski

Master's Theses (2009 -)

The Proviral integration site for Moloney Murine Leukemia virus (PIM) kinases belongs to the family of serine/threonine kinases consisting of three isoforms; PIM1, PIM2, PIM3. PIM kinase is involved in multiple cellular processes through the phosphorylation of several proteins within the JAK/STAT pathway, leading to cell proliferation, apoptosis inhibition, cell migration, transcription, and energy metabolism. However, disruption or overexpression of PIM within the cycle can have negative, tumorigenesis effects with increased fatality rates. Currently, there are no FDA approved PIM kinase inhibitors available for specific cancer target therapies, despite the growing need and high demand research interests. It is widely …

Organic Photocatalysts For Desulfurization Of Fuels, A K M Maksudul Hasan

Master's Theses (2009 -)

Desulfurization of fuels is a critical process for reducing sulfur contents in petroleum-based fuels to mitigate environmental pollution and meet the regulatory standards. Among various pollutants, Sulfur is the deadliest as inhaling leads to coughing, shortness of breath, sinus problem as well as the death of brain cells. Petroleum has a number of organosulfur derivatives, for example in crude oil (0.1 to 6wt% sulfur), which should be removed before using in combustion engines and other applications. High sulfur containing petroleum products used in engines and power plants would lead to the formation of sulfurdioxide (SO2) which would contribute to the …

Neural Network Ensemble For Computing Cross Sections Of Rotational Transitions In H2O + H2O Collisions, Bikramaditya Mandal, Dmitri Babikov, Phillip C. Stancil, Robert C. Forrey, Roman V. Krems, Naduvalath Balakrishnan

Chemistry Faculty Research and Publications

Water (H₂O) is one of the most abundant molecules in the universe and is found in a wide variety of astrophysical environments. Rotational transitions in H₂O + H₂O collisions are important for modeling environments rich in water molecules but they are computationally intractable using quantum mechanical methods. Here, we present a machine learning (ML) tool using an ensemble of neural networks (NNs) to predict cross sections to construct a database of rate coefficients for rotationally inelastic transitions in collisions of complex molecules such as water. The proposed methodology utilizes data computed with a mixed …

Linking Core Concepts And Competencies In General Chemistry Via Gowin’S Theory Of Learning And Vee Heuristic, Vijay Vyas, Scott A. Reid

Chemistry Faculty Research and Publications

The content in introductory science courses has often been criticized as “miles wide and inches deep”. In general chemistry, several revisions have focused on framing around a set of core or anchoring concepts, and we recently adapted the anchoring concepts content map (ACCM) of the American Chemical Society (ACS) to develop an anchoring concept-based curriculum for our general chemistry courses. In this article, we describe efforts to connect this curriculum with laboratory learning using Gowin’s theory of learning and the associated knowledge Vee heuristic. Within this framework, the laboratories themselves become events connecting the conceptual and methodological domains, …

On The Chlorobenzene-Ammonia Cluster Reaction: Entrance Channel Dynamics, 2cr2pi Spectroscopy, And Ion Imaging Of The Reaction Dynamics, Ronald Mutete, Damian Kokkin, Natan Fessahaye, Thomas R. Howell, Richard A. Loomis, Scott A. Reid

Chemistry Faculty Research and Publications

Prior studies of halobenzene–ammonia complexes have shown that the nature of the cationic intermediate (i.e., Wheland-type vs ion-radical) may play a key role in determining the reaction products. To probe this link, we report here the reaction dynamics of the chlorobenzene-ammonia 1:1 complex (PhCl···NH₃) using product ion imaging following two-color resonant two-photon ionization. A threshold value of 8.863 ± 0.008 eV was determined for the appearance of protonated aniline, which accompanies Cl atom loss and is the dominant product channel at energies near threshold. Scanning down to energies close to threshold, we find no evidence for a roaming …

Flash Communication: Visible-Light-Driven, Cobalt-Mediated Selective C–H Arylation Of 2,2′-Bipyridine, Xi Chen, Eric R. Allen, Mckenzie L. Stack, Zachary M. Garozzo, Dian Wang

Chemistry Faculty Research and Publications

Herein, we report a visible-light-driven, cobalt-mediated, highly selective C–H arylation method to afford aryl-2,2′-bipyridine, a widely used class of ancillary ligands in transition metal catalysis. This arylation reaction exhibits good-to-excellent C6 selectivity for a variety of aryl groups, allowing for isolation of the 6-isomer in its pure form. Mechanistic studies provided evidence for the generation of an aryl radical by the joint action of [Co(bpy)₃] species and visible light, enabling arylation under mild conditions. Compared to previous work, this method employs cost-effective reagents and provides one-step, direct access from 2,2′-bipyridine to a broad range of electronically varied 6-aryl-2,2′-bipyridine …

Magnetospectroscopic Studies Of A Series Of Fe(Ii) Scorpionate Complexes: Assessing The Relationship Between Halide Identity And Zero-Field Splitting, Daniel J. Santa Lucia, Laxmi Devkota, Sergey Lindeman, Andrew Ozarowski, J. Krzystek, Mykhaylo Ozerov, Samuel M. Greer, Daniel C. Cummins, Klaus H. Theopold, Mihail Atanasov, Joshua Telser, Adam T. Fiedler

Chemistry Faculty Research and Publications

Ferrous ions in four-coordinate environments are common in protein structures, synthetic catalysts, and molecular magnets. The 3d⁶ configuration of high-spin Fe(II) imparts an S = 2 ground state, whose analysis using conventional spectroscopic methods is often hindered by substantial zero-field splitting (ZFS). Herein, we provide detailed electronic-structure descriptions for [Fe^IIX(Tp^tBu,Me)] (1-X; X = F, Cl, Br, I), where (Tp^tBu,Me)− is hydrotris(3-tert-butyl-5-methyl-pyrazol-1-yl)borate. The three pyrazolyl N-donors of the “scorpionate” ligand facially coordinate to Fe(II), giving idealized C_3v symmetry with the halide occupying the axial position. Although originally reported …

Direct Photopatterning Of Quantum Dots Via Thiol-Yne Click Chemistry, Nicholas Langer, Ofer Kedem

Chemistry Faculty Research and Publications

Functional nanomaterials are revolutionizing electronic devices such as displays and photovoltaics, yet existing semiconductor manufacturing methods struggle to adapt to the unique properties of nanoparticles. In particular, quantum dots (QDs) display density-dependent properties such as tunable energy transfer, yet current preferred methods of producing QD patterns lack control over the density of QDs deposited in specific locations on a surface. Here, we present a photochemical method to generate QD patterns directly from solution onto a functionalized surface, which enables density control. The overall dose of light used in the pattern (visible or UV) determines the surface density of deposited QDs …

Mixed Quantum/Classical Theory Approach To Rotationally Inelastic Molecular Collisions Implemented On A Quantum Computer, Jonathan Andrade-Plascencia, Tamila Kuanysheva, Dulat Bostan, Brian K. Kendrick, Dmitri Babikov

Chemistry Faculty Research and Publications

All elements of a quantum algorithm for calculations of rotationally inelastic molecule + atom scattering within the framework of a mixed quantum/classical theory are outlined. In this approach, the rotational motion of the molecule is described quantum mechanically using the time-dependent Schrödinger equation, while the scattering process of two collision partners is treated classically. The matrix of potential coupling is precomputed on a classical processor, whereas the quantum hardware is used to propagate the system of coupled equations for the rotational state-to-state transitions. All quantum circuits needed for practical implementation of the algorithm are presented. First, the quantum codes written …

Quantum Simulation Of Molecular Dynamics Processes─A Benchmark Study Using A Classical Simulator And Present-Day Quantum Hardware, Tamila Kuanysheva, Brian K. Kendrick, Lukasz Cincio, Dmitri Babikov

Chemistry Faculty Research and Publications

We explore how the fundamental problems in quantum molecular dynamics can be modeled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes propagation of a free wave packet, vibration of a harmonic oscillator, and tunneling through a barrier. Each of these problems starts with the initial wave packet setup. Although Qiskit provides a general method for initializing wave functions, in most cases it generates deep quantum circuits. While these circuits perform well on noiseless simulators, they suffer from excessive noise on quantum hardware. To overcome this …

Exploring Rotational Energy Transfer Of Intermolecular Collisions In Complex Systems: A Mqct Approach, Carolin Anna Joy

Dissertations (1934 -)

The accurate modeling of molecular spectra in astrophysical environments requires detailed understanding of collisional energy transfer processes, which remains a significant challenge due to the computational complexity of quantum mechanical calculations for larger molecules, heavier projectiles, and higher collision energies. This dissertation addresses this challenge through the development and application of Mixed Quantum/Classical Theory (MQCT), a hybrid approach that combines quantum mechanical treatment of internal molecular motion with classical description of translational degrees of freedom. The methodology was first validated through detailed study of rotational energy transfer in the ND3 + D2 system, demonstrating excellent agreement with full quantum results …

Quantum Effects In Collisional Energy Transfer Simulated Using Mixed Quantum/Classical Theory, Dulat Bostan

Dissertations (1934 -)

Mixed quantum/classical theory (MQCT) was used to study collisional energy transfer between the rotational states of molecules with the focus on reproducing quantum effects related to this process. Namely, rotational energy transfer in the N₂ + O system was studied to replicate quantum interference effects observed as oscillations of scattering cross section as a function of collision energy. Both MQCT code and the full-quantum code MOLSCAT were used for calculations, and results were in excellent agreement with the experiment and the full-quantum infinite-order sudden method from literature. The CO + CO system was used as a case study for …

Synthetic And Mechanistic Investigations Of Ruthenium Catalyzed Coupling Reactions Via C−C And C−N Bond Activation, Aldiyar Shakenov

Dissertations (1934 -)

Transition-metal catalyzed C-N and C-C bond activation reactions are synthetically valuable reactions for selective and atom-economical synthesis of complex organic molecules. Catalytic reactions that involve activation of unreactive bonds are important for the stereoselective synthesis of molecular scaffolds from readily available substrates derived from bio-mass feedstock. Despite these advances, designing a broadly applicable catalytic method faces challenges of selectivity and harsh reaction conditions. A five coordinate Ru-H complex was found to be an effective catalyst for promoting the multicomponent deaminative coupling reaction of anilines, aldehydes and tertiary amines to selectively afford 2,3-disubstituted quinoline products. The scope of the reaction was …

Experimental And Computational Investigation Of Ethylene Oxide Hydrate And Its Mixed Hydrates With Propane And Isobutane, Adebayo Paul Adeleye

Master's Theses (2009 -)

Gas hydrates represent an important class of crystalline solids, where water molecules form cage-like frameworks that encapsulate gas molecules. They have garnered significant attention for their unique properties and diverse applications in energy and environmental science. This study investigates the formation and vibrational properties of the ethylene oxide (EO) hydrate (structure I, sI) and EO-seeded hydrates of propane and isobutane (structure II, sII) using matrix isolation Fourier-transform infrared (FTIR) spectroscopy, supported by Density Functional Theory (DFT) calculations at the B3LYP/6-311++G(d,p) level of theory. Under low-temperature and low-pressure conditions, EO hydrate was formed by co-depositing a premix of EO and argon …

Visible-Light-Driven Catalytic Dehalogenation Of Trichloroacetic Acid And Α-Halocarbonyl Compounds: Multiple Roles Of Copper, Abigail J. Thillman, Erin C. Kill, Alexander N. Erickson, Dian Wang

Chemistry Faculty Research and Publications

Herein, we report the reaction development and mechanistic studies of visible-light-driven Cu-catalyzed dechlorination of trichloroacetic acid for the highly selective formation of monochloroacetic acid. Visible-light-driven transition metal catalysis via an inner-sphere pathway features the dual roles of transition metal species in photoexcitation and substrate activation steps, and a detailed mechanistic understanding of their roles is crucial for the further development of light-driven catalysis. This catalytic method, which features environmentally desired ascorbic acid as the hydrogen atom source and water/ethanol as the solvent, can be further applied to the dehalogenation of a variety of halocarboxylic acids and amides. Spectroscopic, X-ray crystallographic, …

Scope And Mechanism Of The Ruthenium-Catalyzed Sp3 C–H Coupling Reaction Of 2-Alkylindoles With Enones For The Synthesis Of Carbazole Derivatives, Krishna Prasad Gnyawali, Mina Son, Donghun Hwang, Nuwan Asanka Pannilawithana, Mu-Hyun Baik, Chase S. Yi

Chemistry Faculty Research and Publications

The catalytic system consisting of a cationic Ru–H complex 1 and 3,4,5,6-tetrachloro-1,2-benzoquinone (L1) was found to be highly effective for the dehydrative sp³ C–H coupling reaction of 2-alkyl substituted indoles with enones to form 2,4-disubstituted carbazole products. The analogous coupling reaction of 2-alkylindoles with linear enones bearing the cyclic olefinic group afforded tetracyclic carbazole products. A normal deuterium kinetic isotope effect was measured from the coupling reaction of 1,2-dimethylindole versus 1-methyl-2-(methyl-d₃)indole with (E)-3-penten-2-one (k_H/k_D = 2.5). The Hammett plot was constructed from the reaction of para-substituted …

Rate Coefficients For Rotational State-To-State Transitions In H2O + H2 Collisions As Predicted By Mixed Quantum–Classical Theory, Carolin Joy, Dulat Bostan, Bikramaditya Mandal, Dmitri Babikov

Chemistry Faculty Research and Publications

Aims. A new dataset of collisional rate coefficients for transitions between the rotational states of H₂O collided with H₂ background gas is developed. The goal is to expand over the other existing datasets in terms of the rotational states of water (200 states are included here) and the rotational states of hydrogen (10 states). All four symmetries of ortho- and para-water combined with ortho- and para-hydrogen are considered.

Methods. The mixed quantum–classical theory of inelastic scattering implemented in the code MQCT was employed. A detailed comparison with previous datasets was conducted to ensure that this …

The Novel Estrogen Receptor Beta Agonist Egx358 And Apoe Genotype Influence Memory, Vasomotor, And Anxiety Outcomes In An Alzheimer’S Mouse Model, M. R. Schwabe, A. W. Fleischer, R. K. Kuehn, S. Chaudhury, J. M. York, D. S. Sem, William A. Donaldson, M. J. Ladu, K. M. Frick

Chemistry Faculty Research and Publications

Introduction: Alzheimer’s disease (AD) prevalence and severity are associated with increased age, female sex, and apolipoprotein E4 (APOE4) genotype. Although estrogen therapy (ET) effectively reduces symptoms of menopause including hot flashes and anxiety, and can reduce dementia risk, it is associated with increased risks of breast and uterine cancer due to estrogen receptor alpha (ERα)-mediated increases in cancer cell proliferation. Because ERβ activation reduces this cell proliferation, selective targeting of ERβ may provide a safer method of improving memory and reducing hot flashes in menopausal women, including those with AD. APOE genotype influences the response to ET, although it is …

Stability Of The S-N Bond In S-Nitrosothiols: Computational And Experimental Approach, Rustam Sabitov

Dissertations (1934 -)

S-Nitrosothiols (RSNOs) are chemical compounds capable to transport nitric oxide (NO) and show promise in the treatment of cardiovascular diseases. RSNOs occur naturally in-vivo, and others have been synthesized in-vitro as potential drug candidates for NO transport and release. However, RSNOs are inherently unstable due to their weak S–N bond (D0(S-N)=25–30 kcal/mol), so developing a deeper understanding of the factors influencing the RSNOs stability is crucial. In Chapter 2, we investigated the substituent effect on the -SNO group properties. Substituting R– in RSNOs with more electro-donating character can stabilize the –SNO group according to the Natural Resonance Theory (NRT). But …

Rotational State-To-State Transition Rate Coefficients For H2O + H2O Collisions At Nonequilibrium Conditions, Bikramaditya Mandal, Michal Zoltowski, Martin Cordiner, François Lique, Dmitri Babikov

Chemistry Faculty Research and Publications

Aims. The goal is to develop a database of rate coefficients for rotational state-to-state transitions in H₂O + H₂O collisions that is suitable for the modeling of energy transfer in nonequilibrium conditions, in which the distribution of rotational states of H₂O deviates from local thermodynamic equilibrium.

Methods. A two-temperature model was employed that assumed that although there is no equilibrium between all possible degrees of freedom in the system, the translational and rotational degrees of freedom can be expected to achieve their own equilibria independently, and that they can be approximately characterized by Boltzmann …

Precision Deuteration And Hydrofunctionalization Of Aryl Alkynes And Alkenes, Samantha E. Sloane

Dissertations (1934 -)

The similar nature of the hydrogen atom to its isotope, deuterium, allows for the simple exchange of hydrogen atoms for deuterium atoms in drug molecules to alter the absorption, distribution, metabolism, and excretion properties. Installing the deuterium functionality into a specific site in the molecule is essential. Selective hydrofunctionalization reactions of alkynes and alkenes using the highly reactive catalytic Cu–H species have been well developed, and synthetic organic chemistry methods to selectively incorporate one or two deuterium atoms into the benzylic site of organic compounds, a key metabolic position, are elusive. A Cu–H catalytic approach offers selectivity and reactivity to …

Synthetic And Mechanistic Studies Of Ruthenium Catalyzed C–N And C–H Bond Activation Reactions, Krishna Prasad Gnyawali

Dissertations (1934 -)

Transition metal catalyzed C–H and C–N functionalization methods have emerged as an innovative tool for designing efficient synthesis of fine chemicals by using readily available starting materials without the formation of wasteful byproducts. One of the paramount challenges in C–H functionalization research field has been to promote regio- and stereoselective C–H bond activation on saturated hydrocarbon substrates. While much progress has been achieved on promoting selective sp2 C–H activation reactions on unsaturated hydrocarbon substrates in the past decades, catalytic sp3 C–H bond and functionalization methods on saturates hydrocarbon substrates remain as the frontier topic of C–H functionalization research. The well-defined …

Pressure Dependence Of The Rate Coefficient Of Ozone Using Master Equation Simulations Of Recombination Kinetics, Adil Yermek

Master's Theses (2009 -)

The ozone layer in Earth’s atmosphere is distinctive and crucial for the evolution of life. Investigating the process of ozone formation aids in comprehending the evolution of our planet’s atmosphere. The reaction that forms ozone is O + O2 → O3. One can describe ozone forming reaction approximately using Lindeman mechanism, which is very handy. However, its limitation arises from assuming a steady-state approximation, which neglects transient dynamics and complexities that could impact reaction kinetics under non-equilibrium conditions. For this reason, Master Equation simulations can be seen as an enhancement or extension of the Lindemann mechanism, providing a thorough understanding …

Visible-Light-Driven Reactions From A Six-Coordinate Nickel(Ii) Complex, Lakmini Lochana Edirisinghe Arachchilage

Master's Theses (2009 -)

Transition metal complexes capable of absorbing visible light can be excited upon light irradiation and facilitate chemical bond formation and cleavage. In this approach, a transition metal-substrate complex is formed in the ground state, followed by photoinduced substrate activation via an inner-sphere mechanism. Unlike well-established photoredox catalysis that does not involve substrate binding, the ground-state interaction here is important for substrate activation. Among the 3d transition metals, nickel is considered a cost-effective alternative to Ru- and Ir-based photocatalysts due to its ability to accommodate different oxidation states. However, the application of Ni photocatalysis in synthesis had remained largely underexplored. In …

Preferential Crystallization Of (±)-Pinenyllithium·Tmeda, Alexander N. Erickson, Curtis Haltiwanger, Masoumeh Rahim, Charles M. Garner

Chemistry Faculty Research and Publications

(±)-Pinenyllithium·TMEDA or (tetra­methyl­ethylenedi­amine-κ²N,N′)(η³-6,6-di­methyl-2-methylenebi­cyclo­[3.1.1]hept­yl)lithium, [Li(C₁₀H₁₅)(C₆H₁₆N₂)], is readily pre­pared from β-pinene, butyl­lithium and TMEDA, and the racemic material pre­fer­entially crystallizes even from 96:4 (92% ee) mixtures of (−)- and (+)-β-pinene, respectively. The structure is monomeric, with the geminal-dimethyl bridge of the bicyclic structure shielding one face of the allyl system, restricting the lithium to the opposite face and preventing the Li–all­yl–Li aggregation observed with some other allyl­lithium systems. The symmetry of the allyl system, bond lengths, bond angles and out-of-plane deviations …

Efforts Toward Difunctionalization Of (Hetero)Arenes Enabled By Visible Light, Eric Allen

Master's Theses (2009 -)

Functionalized arenes and heteroarenes are ubiquitous motifs in natural products, pharmaceuticals, and functional materials. As such, methods to place multiple functionalities on (hetero)arenes in one synthetic step create molecular complexity quickly and are highly valued. The vast majority of current strategies are metal-mediated, although others such as utilizing aryne intermediates and cycloadditions have also been reported. The premier challenge in this research area is the difficulty in controlling regioselectivity. Strategies of controlling regioselectivity have included tuning the electronic nature of the substrate, the use of directing groups (DGs), steric influences, ligand control, and photochemically initiated methods. Certain strategies tend to …

Probing Charge Transport Mechanisms In 2d Semiconductive Metal Organic Framewoks, James Nyakuchena

Dissertations (1934 -)

Metal organic frameworks (MOFs) are a class of highly porous crystalline materials constructed from metal nodes connected by multitopic organic ligands. Due to their unique properties such as large surface area, tunable pore structure, and structural diversity, they have demonstrated potential in a wide array of applications including gas storage and separation, sensing, catalysis, and drug delivery. However, there are only a handful of MOFs reported that have electrical conductivity, which prevents their applications in photoelectronic and photocatalytic applications. This is because hard metals and redox inactive ligands with terminal hard linking bases such as carboxylates are often used in …

Elucidating The Effect Of Surface Modifications On Nanomaterial Function, Nicholas Langer

Dissertations (1934 -)

Nanoparticles (NPs) are an exciting class of materials with unique properties that inspire their use in sensing, catalysis, optoelectronic devices, and more. NPs are frequently coated in organic molecules, termed ligands, to increase their stability, but ligands also influence NP catalytic activity and their interactions with neighboring molecules. To fully realize the potential of nanomaterials as key components in novel complex systems, a more nuanced understanding of the relationships between NPs, ligands, and their surrounding microenvironment is critical. After a brief review of the NP field in Chapter 1, Chapter 2 begins the investigation of structure-function relationships with a cross-class …

Magnetic Properties And Biological Relevance Of Scorpionate-Based Transition Metal Complexes, Laxmi Devkota

Dissertations (1934 -)

There are two major components to this research dissertation. The first component describes the synthesis and characterization of high-spin, first-row transition metal complexes supported by facially-coordinating “scorpionate” ligands. These studies have sought to uncover fundamental relationships between molecular structure and magnetic properties, with the ultimate aim of assisting in the design of single molecule magnets (SMMs). To this end, comprehensive series of four and five-coordinated M(II)-X complexes (M = Co, Fe, and Cu; and X = F, Cl, Br, and I) were prepared using hydrotris(pyrazol-1-yl)borate ligands (TpR,R’; where R and R’ indicate substituents at the 3- and 5-position of the …

Basecol2023 Scientific Content, Dmitri Babikov

Chemistry Faculty Research and Publications

Context. The global context of making numerous data produced by researchers available requires collecting and organising the data, assigning meaningful metadata, and presenting the data in a meaningful and homogeneous way. The BASECOL database, which collects inelastic rate coefficients for application to the interstellar medium and to circumstellar and cometary atmospheres, meets those requirements.

Aims. We aim to present the scientific content of the BASECOL2023 edition.

Methods. While the previous versions relied on finding rate coefficients in the literature, the current version is populated with published results sent by the producers of data. The paper presents the …