Other Chemistry Commons^™

Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter

Masters Theses & Specialist Projects

Rapid docking of flexible biological macromolecules remains a significant open challenge in protein structure determination. While rigid docking is relatively simple with toolkits such as TagDock, a key obstacle to rapid flexible docking is the complexity and roughness of the free energy surface associated with protein conformational motion (often termed the many-minima problem), meaning conventional molecular dynamics methods do not effectively sample protein conformations near the interaction complex in accessible timescales. Methods such as metadynamics and replica exchange molecular dynamics exist to ameliorate this obstacle, yet these methods use nonphysical biases or random swaps to enhance sampling. In contrast, high …

Group 14 Metallocene Catalysts For Carbonyl Hydroboration And Cyanosilylation, Haley J. Robertson, Mallory N. Fujiwara, Allegra L. Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A series of six Group 14 metallocene compounds (M = Ge, Sn, Pb) were studied as catalysts for carbonyl hydroboration and cyanosilylation reactions at room temperature. Both bis(pentamethylcyclopentadienyl) and tetramethyldisiloxa[3]metallocenophane compounds were compared. The tin and lead metallocenophanes exhibited the highest reactivity in hydroboration and cyanosilylation reactions. Hammett analysis of aldehyde hydroboration provided a ρ value of 0.73, suggesting a buildup of negative charge during the turnover-limiting step, consistent with the transition state for hydride transfer to the carbonyl center. NMR studies of Lewis acidity indicate that the Ge, Sn, and Pb tetramethyldisiloxa[3]metallocenophane compounds are weak Lewis acids.

Enhanced Mechanical Strength Of Soybean Oil-Based Non-Isocyanate Polyurethane Adhesive For Wood Application By Introducing Nanofillers, Vatsal Chaudhari

Electronic Theses & Dissertations

Polyurethane (PU) is a versatile material that finds extensive use in various industries including bedding, construction, automotive, and packaging. Historically, this particular polymer relied significantly on petrochemical resources, a practice that was considered to have negative environmental impacts. The conventional method for preparing PU involves the use of isocyanate, which is a disadvantage due to its negative impact on the environment and human health. The resolution of this problem entails identifying an appropriate substitute for petroleum-derived products that minimize their impact on both the environment and human health. The researchers earlier utilized soybean oil, for the formulation of PUs in …

Exploring Soybean Oil-Based Polyol And Effect Of Non-Halogenated Flame Retardants In Rigid Polyurethane Foam, Sahithi Kondaveeti

Electronic Theses & Dissertations

To address the increasing demand for sustainable biomaterials due to the depletion of fossil fuel resources and growing environmental concerns, a new type of biodegradable and environmentally friendly rigid polyurethane foam (RPUF) has been synthesized. These foams are derived from chemically modified soybean oil-based polyol obtained from soybean oil by epoxidation followed by a ring-opening reaction. Polyurethane foam is generally used in construction, furniture, and automobile industries but is highly flammable and releases toxic gases and smoke during combustion. In this study, a highly efficient synergistic effect halogen-free flame-retardant (FR) melamine salt, 2-carboxyethyl(phenyl)phosphinic acid melamine salt (CMA) was synthesized from …

Dinitroxides In Rapid Scan Electron Paramagnetic Resonance Imaging, Lukas B. Woodcock

Electronic Theses and Dissertations

Local tissue physiology is an important parameter in understanding disease behavior. Rapid Scan (RS) electron paramagnetic resonance (EPR) offers a unique, non-invasive tool for investigation of these so-called microenvironments through EPR Imaging (EPRI). Research into advancement of EPRI falls into many categories. Not least among those are advances in instrumentation and methodology. Presented here are updates to a benchtop EPRI instrument operating at 1 GHz targeted at pre-clinical EPRI applications. Newly developed methods for reducing RS-EPR background through inversion of the magnetic field are also demonstrated. EPR applications are limited in native biological systems due to the miniscule concentration of …

Structural Integrity And Stability Of Dna In Ionic Liquid And Near-Infrared Indolizine Squaraine Dye, Ember Yeji Suh

Honors Theses

Luminol, the most common presumptive test for blood at a crime scene, has multiple issues, such as false positive results with chemical agents, no luminescence due to “active oxygen” cleaning agents on bloodstains, and inability to penetrate textile materials. A combination of indolizine squaraine dye and ionic liquid (IL), or Dye Enhanced Textile Emission for Crime Tracking (DETECT), have shown potential to address these issues. The purpose of this study was to assess the binding mechanism of CG (1:1) and SO₃SQ dye to HSA and how the mechanism can explain the W214 fluorescence quenching effect and to determine …

Nanoscale Imaging Of Electrocatalytic Nanomaterials By High-Resolution Scanning Electrochemical Microscopy, Xiang Wang

Dissertations, Theses, and Capstone Projects

Numerous insights of the structure–electrochemical activity relationship of nanocatalysts have been obtained by using macroscopic electrochemical measurements over the last several decades. However, signals measured by large electrodes are inevitably averaged out of many nanocatalysts, non-uniformed sizes, uneven morphologies, and multiple crystallographic facets. Over the last ten years, Scanning Electrochemical Microscopy (SECM) has advanced electrochemical measurements toward micro- to nanoscale level at a high spatial resolution. The advantages of using nanoelectrode in SECM include fast mass transfer of reactive species, dominated radial diffusion pattern, small double layer capacitance and small RC constant. In this thesis, high-resolution SECM is applied to …

The Effect Of Ionization Density In Applications Of Radiation Detection, Dosimetry, And Therapy, Daniel Mulrow

Arts & Sciences Electronic Theses and Dissertations

This dissertation covers a wide range of topics but is linked by the common theme of radiation interacting with materials and studying the result of those interactions. The introduction describes the fundamentals of how radiation interacts with material and how we are able to detect that radiation and the application of how we use those interactions in radiation oncology. The thesis starts with a chapter detailing the temperature dependence of the photophysics in two organic scintillators. This chapter is the foundation for a future study that will look the degree to which these scintillators can distinguish between gammas and neutrons …

Near-Ir Laser Ablation Of Simulated Radiologically Contaminated Oxides On Carbon Steel Feeder Pipes, Thao Viet Do

Electronic Thesis and Dissertation Repository

As nuclear power plants age and retire from service, many countries face significant challenges concerning the safe long-term storage and disposal of large volumes of low and intermediate level radioactive wastes (L&ILW). The volumes of metallic waste are of particular concern, as when metal corrodes it produces hydrogen that could lead to pressure build-up in interim storage and disposal. In Canada, a significant fraction of the metallic wastes for Canada Deuterium Uranium (CANDU) nuclear reactors are out-of-core reactor components, such as carbon steel (CS) feeder pipes. The radioactive contamination is expected to be largely confined to the surface oxide layers …

Expanding The Scope Of Clickable Azide-Functionalized Nanoclusters To Include Au144, Johanna A. De Jong

Electronic Thesis and Dissertation Repository

Thiolate-protected Au₁₄₄ nanoclusters (NCs) are an intriguing member of the gold NC family. Their geometric structure, distinct electrochemical features, and susceptibility to structural rearrangement under the duress of ligand exchange have been studied. However, there are currently no established protocols for surface modification or tuning of their ligand shells post synthesis. Here, the direct synthesis of three regioisomers of azide-modified Au₁₄₄ NCs with 60 azide moieties, i.e., Au₁₄₄(SC₂H₄C₆H₄-N₃)₆₀, is reported, in which the azide functionality is located at the ortho-, meta-, or …

Symmetry-Resolved Co Desorption And Oxidation Dynamics On O/Ru(0001) Probed At The C K-Edge By Ultrafast X-Ray Spectroscopy, Jerry Larue, Boyang Liu, Gabriel L. S. Rodrigues, Chang Liu, Jose Antonio Garrido Torres, Simon Schreck, Elias Diesen, Matthew Weston, Hirohito Ogasawara, Fivos Perakis, Martina Dell'angela, Flavio Capotondi, Devon Ball, Conner Carnahan, Gary Zeri, Luca Giannessi, Emanuele Pedersoli, Denys Naumenko, Peter Amann, Ivaylo Nikolov, Lorenzo Raimondi, Carlo Spezzani, Martin Beye, Johannes Voss, Hsin-Yi Wang, Filippo Cavalca, Jörgen Gladh, Sergey Koroidov, Frank Abild-Pedersen, Manuel Kolb, Piter S. Miedema, Roberto Costantini, Tony F. Heinz, Alan C. Luntz, Lars G. M. Pettersson, Anders Nilsson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report on carbon monoxide desorption and oxidation induced by 400 nm femtosecond laser excitation on the O/Ru(0001) surface probed by time-resolved x-ray absorption spectroscopy (TR-XAS) at the carbon K-edge. The experiments were performed under constant background pressures of CO (6 × 10⁻⁸ Torr) and O2 (3 × 10⁻⁸ Torr). Under these conditions, we detect two transient CO species with narrow 2π* peaks, suggesting little 2π* interaction with the surface. Based on polarization measurements, we find that these two species have opposing orientations: (1) CO favoring a more perpendicular orientation and (2) CO favoring a more parallel orientation …

Contact Angle & Electrochemical Measurements Of Metallic Atmospheric Corrosion On Copper And Carbon Steel, Jacob J.M. Bunting, Jiju M. Joseph, Heng-Yong Nie, Samantha M. Gateman

Undergraduate Student Research Internships Conference

Understanding atmospheric corrosion has been incredibly challenging due to the complex interplay between surface microstructures, environmental variables, and electrochemical processes. The methodology presented is being developed to apply to atmospheric corrosion models of metals and other advanced materials by observing the change in contact angle in situ as a function of corrosion parameters. Performed contact angle measurements on two industrially relevant metals (copper and carbon steel) over a 1 min to 30-day time span to track the change in wettability due to the formation of an air-formed oxide layer (aged) as a function of surface roughness.

Ketal-Azaborine Versus Ketal-Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Heteroaromatic Polycyclic Chromophores, Albert Campbell, Janiyah Riley, Samuel Moore, Albert Campbell

Symposium of Student Scholars

Flat-structured heteroaromatic polycyclic compounds with extended conjugated π-systems such as azaborines are in high demand in the material and imaging technology markets because of their unique features such as simultaneous tunability of fluorescence color and intensity. We have designed, synthesized, and investigated a series of novel conjugated thermally stable ketal-azaborine chromophores that contain a phenyl ring as a spacer between electronic moieties and the ketal-azaborine core as easily tunable high-luminescent organic materials. We investigated the impact of the phenyl spacer on the ketal-azaborine unit. We examined the structural effects on their photophysical properties by incorporating electron –donating and –withdrawing substituents …

Azaborine Versus Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Azaborine Chromophores, Kaia Ellis, Janiyah Riley, Lyric Gordon, Janiyah Riley

Symposium of Student Scholars

Azaborines are fascinating compounds because of their valuable and interesting optical properties making them suitable to be utilized in many optoelectronic devices. We have designed, synthesized, and investigated a series of novel conjugated thermally stable azaborine chromophores by incorporating a phenyl ring as a spacer linking the chromophore to different electronic moieties as easily tunable high-luminescent organic materials. We investigated the effect of the phenyl spacer on the azaborine unit. The substituent effects of different electronic moieties were investigated by the insertion of electron –withdrawing and –donating moieties to the phenyl spacer. We examined the role of the electron –donating …

Comparing And Contrasting Therapeutic Drugs Vs. Lifestyle Changes That Combattype-Ii Diabetes, Alexander Cline Helmuth

Chemistry & Biochemistry Student Projects

In this thesis, I will be presenting various preventive approaches to combat type-II diabetes. The focus of this paper will be comparing and contrasting therapeutic drug targets such as Metformin and Sulfonylureas that are prescribed for type-II diabetic patients versus taking preventative steps such as making lifestyle changes including weight management, physical activity, and having a balanced diet that prevents onset of type-II diabetes or helps patients manage type-II diabetes. From this paper, one will gain insight on how there are multiple approaches to combat type-II diabetes that are not in the form of the pill.

Microfluidic Paper Analytical Devices, Madison Page

Chemistry & Biochemistry Student Projects

Microfluidic paper analytical devices (µPADs) are small, paper-based matrices similar to Lab-on-a-Chip (LOC). They are capable of semi-quantitative analysis, with applications ranging from medical to environmental to food and beverage testing. Important to improving point-of-care devices (POCs), various techniques have been integrated into µPADs to customize analysis and fit different clinical situations.

The Application Of Biological Processes To Increase Energy Potential In Landfills, Ashlyn Eisenhart

Chemistry & Biochemistry Student Projects

There has been a dramatic increase in the amount of waste that we humans have created. This has been due to population growth, an increase in industrial manufacturing, along with urbanization and modernization.⁸ The number of tons of municipal solid waste entering landfills has increased from 82.5 million tons in 1960 to 146.1 million tons in 2018.¹⁷ However, thanks to recycling, composting, and energy recovery from combustion, the percentage of solid waste going to landfills has dramatically decreased, from around 93.6 to about 65.4 percent.¹⁷

Chemistry Of Toothpaste, Kayla Blanche Kirtley

Chemistry & Biochemistry Student Projects

The chemistry of toothpaste is explained, with a description of the chemical components and their mode of action in the role of toothpaste.

Inhibitors Of Alpha-Synuclein Aggregation, Jemil Ahmed

Electronic Theses and Dissertations

Alpha-Synuclein (αS) – a neuronal, disordered, presynaptic protein – aggregates into amyloid fibrils and accumulates in the substantia nigra pars compacta of Parkinson's Disease (PD) patients. The aggregation and accumulation of αS amyloid fibrils leads to death of dopaminergic neurons; a hallmark of PD. Although it’s not clear why αS aggregates, prior studies have found that intrastriatal injection of fibril alone is sufficient to cause PD pathology in mouse and non-human primates models. These observations implicate αS as a therapeutic target against PD.

Unfortunately, there are three caveats when attempting to target αS. First, αS is a neuronal protein expressed …

Self-Assembly Of Black Cumin Oil-Based Nanoemulsion On Various Surfactants: A Molecular Dynamics Study, Aulia Fikri Hidayat, Taufik Muhammad Fakih

Makara Journal of Science

Black cumin is commonly used as traditional medicine due to its wide range of pharmacological potential. Black cumin oil (BCO) was often prepared as nanoemulsion to improve its solubility, stability, and bioavailability. This study was conducted to investigate the molecular behavior as well as structural evolution of BCO-surfactant systems during self-assembly micellization using molecular dynamics (MD) simulations. Several BCO constituents and variations of surfactants were employed to model BCO-surfactant systems. 50 ns of MD simulations were performed to elucidate their evolution of structures and physicochemical properties during formation. Results showed that BCO-tween20 and BCO-lecithin were able to form spherical-shaped micelles …

Computational Analysis Of The Spin Trapping Properties Of Lipoic Acid And Dihydrolipoic Acid, Matthew Bonfield

Electronic Theses and Dissertations

While the spin trapping properties of thiols have been investigated through EPR analysis and kinetics studies, few groups have studied these properties using strictly computational methods. In particular, α-lipoic acid (ALA) and its reduced form, dihydrolipoic acid (DHLA), one of the strongest endogenously produced antioxidants, show potential for being effective, naturally occurring spin traps for the trapping of reactive oxygen species. This research covers electronic structure calculations of ALA, DHLA, and their corresponding hydroxyl radical spin adducts, performed at the cc-pVDZ/B3LYP/DFT level of theory. The effects on DHLA introduced by other radicals such as ·OOH, ·OCH₃, …

National Chemistry Week: From Irl To The Web, Ilayda Kelley, Daniela Mesa Sanchez

Purdue Journal of Service-Learning and International Engagement

National Chemistry Week, an outreach program initiated by the American Chemical Society (ACS), encourages scientists to bring their love of chemistry to their community. Celebrated nationwide, ACS invites businesses, schools, and individuals to organize and participate in community events to promote the value of chemistry in everyday life. The Purdue graduate student chapter of Iota Sigma Pi, a national honor society for women in chemistry, annually organizes one such celebration. On a normal year, this event is a large logistical undertaking in which 100+ volunteers go directly to over 70 local elementary school classrooms and perform a series of activities …

An Examination Of Factors Influencing Small Proton Chemical Shift Differences In Nitrogen-Substituted Monodeuterated Methyl Groups, Stuart J. Elliott, O. Maduka Ogba, Lynda J. Brown, Daniel J. O'Leary

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Monodeuterated methyl groups have previously been demonstrated to provide access to long-lived nuclear spin states. This is possible when the CH₂ D rotamers have sufficiently different populations and the local environment is chiral, which foments a non-negligible isotropic chemical shift difference between the two CH₂ D protons. In this article, the focus is on the N-CH₂ D group of N-CH₂ D-2-methylpiperidine and other suitable CH₂ D piperidine derivatives. We used a combined experimental and computational approach to investigate how rotameric symmetry breaking leads to a ¹H CH₂ D chemical shift …

From Small Molecules To Infinite Crystals: Probing Noncovalent Interactions Through Vibrational Spectroscopy, Sadisha Nanayakkara

Chemistry Theses and Dissertations

During my four years in the CATCO group supervised by Dr. Kraka, I have been exposed to various topics targeted to address a multitude of chemical problems, broadening our knowledge of modern chemistry research as we know it. In undertaking the age-old problem of understanding the nature of chemical bonding, I could modestly contribute with my work, using in-house tools based on vibrational spectroscopy.

First part of my dissertation is focused on inventing new methods and tools to efficiently investigate chemical bonding, followed by the study of some non-covalent interactions, imperative in catalysis and solid-state chemistry. This includes analysis of …

Crystal Structure Of 2-(2,6-Diisopropylphenyl)-N,Ndiethyl- 3,3-Dimethyl-2-Azaspiro[4.5]Decan-1- Amine: A Diethylamine Adduct Of A Cyclic(Alkyl)- (Amino)Carbene (Caac), Roxanne A. Naumann, Joseph W. Ziller, Allegra Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The structure of the title compound, C₂₇H₄₆N₂, at 93 K has monoclinic (P2₁/n) symmetry. The title compound was prepared by treatment of 2-(2,6-diiso­propyl­phenyl)-3,3-dimethyl-2-aza­spiro­[4.5]dec-1-en-2-ium hydrogen dichloride with two equivalents of lithium di­ethyl­amide. Characterization of the title compound by single-crystal X-ray diffraction and ¹H and ¹³C NMR spectroscopy is presented. Formation of the di­ethyl­amine adduct of the cyclic(alk­yl)(amino)­carbene (CAAC) was unexpected, as deprotonation using lithium diiso­propyl­amide results in free CAAC formation.

Purine Nucleosides Modified At C8 Or C2 Position With (Β-Halo)Vinylsulfone And Β-Ketosulfone Reactive Groups And Their Incorporation Into Dna: Synthesis Of The Organoarsenical Antibiotic Arsinothricin And Polyaromatic Hydrocarbons, Md Abu Hasan Howlader

FIU Electronic Theses and Dissertations

Modified nucleosides gained great attention as potential anticancer and antiviral therapeutics. In this dissertation, synthesis and reactivity of (β-iodovinyl)sulfone and β-ketosulfone groups incorporated into purine nucleosides at C8 or C2 positions and DNA incorporation of their 5' triphosphates have been developed. Moreover, synthesis of novel antibiotic arsinothricin (AST) as well as polycyclic aromatic hydrocarbons (PAHs) have been discussed. The 8-(1-iodo-2-tosylvinyl)-2'-deoxyadenosine and 8-(1-Iodo-2-tosylvinyl)adenosine were synthesized employing iodovinylsulfonation of 8-ethynyl precursors with TsNa/I₂/NaOAc. The 8-(β-iodovinyl)sulfonyl-2'-deoxyguanosine was prepared via radical mediated iodovinylsulfonation of 8-ethynyl-2'-deoxyguanosine with TsNHNH₂/KI/(BzO)₂. Conformationally different C2 substituted isomeric adenosine analogues were prepared by iodovinylsulfonation …

Ultrafast Adsorbate Excitation Probed With Subpicosecond-Resolution X-Ray Absorption Spectroscopy, Elias Diesen, Hsin-Yi Wang, Simon Schreck, Matthew Weston, Hirohito Ogasawara, Jerry Larue, Fivos Perakis, Martina Dell'angela, Flavio Capotondi, Luca Giannessi, Martin Beye, Filippo Cavalca, Boyang Liu, Jörgen Gladh, Sergey Koroidov, Piter S. Miedema, Roberto Costantini, Tony F. Heinz, Frank Abild-Pedersen, Johannes Voss, Alan C. Luntz, Anders Nilsson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We use a pump-probe scheme to measure the time evolution of the C K-edge x-ray absorption spectrum from CO/Ru(0001) after excitation by an ultrashort high-intensity optical laser pulse. Because of the short duration of the x-ray probe pulse and precise control of the pulse delay, the excitation-induced dynamics during the first picosecond after the pump can be resolved with unprecedented time resolution. By comparing with density functional theory spectrum calculations, we find high excitation of the internal stretch and frustrated rotation modes occurring within 200 fs of laser excitation, as well as thermalization of the system in the picosecond …

Assessing Competitive Reaction Rates In The Nitration Of 2-Methylbiphenyl, Biphenyl, And Toluene To Determine Steric Restriction In Resonance-Stabilized Planarization Of The Carbocation Intermediates, Victor A. Hanson, Tristan Wine, Kevin Bartlett, Joshua Padilla, Alessandro Rizzi

Honors Projects

Electrophilic aromatic substitution (EAS) reactions have long been a fundamental addition to sophomore-level organic chemistry classes, allowing students the opportunity to explore the electron donating and withdrawing effects of electrons contained in the substituents of the aromatic reactant. In this paper we present preliminary findings on the nitration of methylated biphenyls using kinetic and regioselective assessments to analyze steric influences on the planarization of 2-methylbiphenyl after EAS nitration. Our preliminary findings show that nitration favors the methylated phenyl ring of 2-methylbiphenyl, indicating that the steric influence of the methyl group restricts planarization of the carbocation intermediate. Furthermore, a competition nitration …

Computational Modeling Of Water And Proteins In Drug Discovery, Anthony Cruz Balberdy

Dissertations, Theses, and Capstone Projects

This thesis aims to improve how structural and thermodynamic properties of water on protein surfaces can be exploited to aid early stage drug discovery and lead optimization. We first discuss our development of SSTMap, a public domain software suite that maps out the properties of water on biomolecular surfaces. We then show the utility of these maps in describing differences in binding affinities between congeneric pairs of ligands. We then discuss our use of solvation maps in the prospective discovery of novel binders to cytochrome C peroxidase. Finally, we present our creation and validation of a homology model of Interleukin-24 …

A Theoretical Study Of Synchronous Proton Transfer In (Hf)N, (H2O) N, And (Hcl) N Where N = 3, 4, 5, Johnny Yang

Honors Theses

For (HF)_n, (H₂O)_n, and (HCl)_n (n = 3 − 5), we have rigorously characterized the structures for the minima and transition states for synchronous proton transfer (SPT) with the CCSD(T) method and aug-cc-pVTZ basis set. The electronic barrier heights (∆E^†) associated with these transition states have also been computed with the explicitly correlated CCSD(T)-F12 method and the aug-cc-pVQZ-F12 basis set (abbreviated aQZ-F12). (HCl)_n (n = 3 − 5) SPT transition states have not been previously identified to the best of our knowledge, and they have been found …