Organic Chemistry Commons^™

Techniques, Skills, And Synthesis For “Cooking” In The Organic Laboratory, Emily C. Sylvester, Tim Evans

Open Education Materials

Lab manual for CHEM 211L, Organic Chemistry I Laboratory. Provides background and procedures for laboratory experiments, including fundamental techniques and several organic syntheses.

Creative Commons attribution.

Arylation Of Nitrogen, Oxygen And Carbon Nucleophiles By Aryl(Tmp)Iodonium Salts, Joseph Jordan Hatton

Dissertations and Theses

Substituted aromatic rings are present in industry in a plethora of organic molecules such as pharmaceuticals, agrochemicals, materials and beyond. Therefore, methods for broadly installing aryl rings into other compounds to create substituted aromatic rings are valuable to many organic chemists. Historically these transformations are achieved through methods such as nucleophilic aromatic substitution and metal catalyzed cross-coupling. Nucleophilic aromatic substitution is a user-friendly method in this space but is limited by reliance on specific electronics. Metal catalyzed cross-coupling reduced the dependence on electronics in this space, but metals are generally unattractive reagents due to high costs, toxicity and challenges with …

Increased Backbone Rigidity Of Artificial Transcription Factors, Jasmine Glover, Emma Otey, Joanna K. Kwao, Nicholas Truex

Senior Theses

Programming DNA-binding proteins is an effective strategy for developing therapeutics that regulate gene expression. These proteins can directly bind to DNA to activate or repress transcription of specific genes. Zinc finger proteins are a class of DNA-binding proteins commonly found in eukaryotic organisms. Their DNA-binding function is derived from unique amino acid sequences within each domain that recognizes specific nucleotides, allowing each finger to selectively recognize three DNA base pairs. Adjoining of multiple domains in tandem allows recognition of a specific DNA sequence. Artificial transcription factors can be made of multiple zinc finger domains arranged in tandem and engineered to …

Discovery Of The Multi-Ion Bridge Intermediate: A Computational Exploration Of The Mechanism For Azomethine Ylide Formation From N-Oxides, Martin J. Neal

Electronic Theses and Dissertations

Density functional theory (DFT) provides a method for calculating the ground-state energies of complex molecular systems through evaluating the electron density instead of the full wave function. When results match either experimental outcomes, calculations with DFT offer a computationally efficient method to help explain chemical phenomena. The transformation of tertiary amine N-oxides to azomethine ylides, a simple route to the precursor for 1,3-dipolar cycloadditions that result in the pyrrolidine scaffolds found in natural products, has received only minimal attention due to concerns that its mechanism includes a highly electrophilic intermediate. Utilizing DFT to model the mechanism of the conversion …

The Potential Importance Of Microenvironment On Polymer Bound Chemical Reagents, Nathan Joseph Halsteter

Theses and Dissertations

In this thesis will provide a brief history of polymer bound reagents, their uses, and advancements. The importance of polymer microenvironments will be explored using a model kinetic resolution reaction utilizing polymer bound reagents to observe how changes in a polymer’s microenvironment effects the yield and selectivity of a reaction. It was found that there are copious factors that affect polymer bound reagents, and no direct conclusion could be drawn from the study.

Lighting Up The Cell: Developing A Luminescent Lanthanide Probe For Detecting Rnas, Jonathan Savell

Honors Projects

An anion detecting luminescent probe, Tb:DO2A-Cs124, was repurposed for use in RNA imaging. Potential RNA aptamers were identified for the molecule using Capture-SELEX and MinION sequencing. Fluorimetry data revealed these aptamers did not allow for the probe to luminesce in the presence of target RNAs due to adenosine monophosphate’s ability to quench the emission signal.

Complementary Design Of Optical And Photochemical Systems, Joshua Plank

Chemistry Theses and Dissertations

The ability to manipulate chemical systems has been prized through history as the bridge between the macroscopic and microscopic worlds. As an example, the camera obscura has arguably existed since the earliest days of humanity; however, it was the discovery of early silver halide chemistry that lead to the ability to fix these images into the earliest photographs. In modern photolithography employed in electronics manufacturing, the primary resolution limits arise not from the chemistry of the molecules involved, but from the limits of the systems used to project light. Thus, as much as photochemistry advances, optical imaging and projection techniques …

The Importance Of Atomic Charges For Predicting Site-Selective Ir-, Ru-, And Rh-Catalyzed C-H Borylations, Shannon M. Stephens, Kyle M. Lambert

Chemistry & Biochemistry Faculty Publications

A supervised machine learning model has been developed that allows for the prediction of site selectivity in late-stage C-H borylations. Model development was accomplished using literature data for the site-selective (≥95%) C-H borylation of 189 unique arene, heteroarene, and aliphatic substrates that feature a total of 971 possible sp² or sp³ C-H borylation sites. The reported experimental data was supplemented with additional chemoinformatic descriptors, computed atomic charges at the C-H borylation sites, and data from parameterization of catalytically active tris-boryl complexes resulting from the combination of seven different Ir-, Ru-, and Rh-based precatalysts with eight different ligands. Of the over …

Knowledge Management Of Historical Data: Ontology Development For Chemical Reactions, Quynh D. Tran, Alexander Harding Bradley, Balashanmuga Priyan Rajamohan, Jonathan E. Gordon, Van D. Tran, Kiefer Lin, Erika I. Barcelos, Laura S. Bruckman, Roger H. French

Researchers, Instructors, & Staff Scholarship

Knowledge management of the literature and historical data is critical to accelerated drug and materials discovery. Currently, literature knowledge is scattered in journal articles in various formats: diagrams, texts, plots, etc. Historical data from past experiments are saved in a number of local computers under confusing folder structures with ambiguous file names. To manage and organize historical data and knowledge, our group (SDLE) at CWRU follows FAIR (Findable, Accessible, Interoperable, Reusable) principles, which outline the best practices for data stewardship and data provenance, and ontology, a formal representation of terms and concepts and their relationships, as a tool to improve …

I. Degradable Polymers And Networks Based On Furan-Maleimide Diels-Alder Reactions Of Silyl Ether Derivatives And Maleimides, And Ii. The Michael Addition Of Amines To 1,3,5-Triacryloylhexahydro-1,3,5-Triazine (Tat) As A Synthetic Route To Novel Chelating Agents, Reyad Alkhazalah

Chemistry Theses and Dissertations

Degradable Polymers and Networks Based on Furan-Maleimide Diels-Alder Reactions of Silyl Ether Derivatives and Maleimides. I.

I. Part 1. Two groups of silyl ether monomers, A and B, were synthesized, each containing four different monomers. The monomers of group A were obtained by reacting furfuryl alcohol with four dichlorosilanes with varying siloxane spacers. The monomers of group B were obtained by reacting n-(2-hydroxyethyl)maleimide (HEMI-1c) with the same four dichlorosilanes. Each monomer from group A was individually reacted with each monomer from group B via a Diels-Alder reaction to produce a series of sixteen degradable linear polymers with a variety …

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

Design And Synthesis Of Dinucleating Phthalazine-Based Ligands Toward Bimetallic Ruthenium Catalysts For Water Oxidation, Alex Bromley

Honors Theses

Two synthetic pathways were developed to construct dinucleating ligands towards the synthesis of bimetallic ruthenium-based water oxidation catalysts. The motivation for this work stems from earlier observations of related ligands that are susceptible to oxidative decomposition. The design pursued here incorporates a phthalazine core into the dinucleating ligand, which, we hypothesize, will prevent the previously established cleavage of a pyridazine unit at the same position. The ligand precursors involved in the multi-step syntheses are characterized by Nuclear Magnetic Resonance (NMR) spectroscopy. Synthetic protocols were refined to ensure reproducibility. In addition, our hypothesis for which of the two target ligands will …

Microscale Chemical Manipulation And Imaging Using Photoactive Molecules And Light, Uroob Haris

Chemistry Theses and Dissertations

Chemical manipulation with light has been an active and growing area of research with important implications in materials science, biotechnology, and environmental science. From early investigations of light sensitive materials for photography in the 19^th century, to printing billions of transistors on a semiconductor chip in present day, scientists have gained a deep understanding of photochemistry and the processes that allow us to harness light for everyday applications. In this work, we explore microscale fabrication and molecular imaging using light and photoactive molecules as foundational tools. We develop a visible-light mediated technique for high resolution microscale chemical lithography comprising …

Paek- And Pes-Like Perarylated Phosphonium Ionenes: Synthesis, Thermal Properties, And Conductivity, Samantha Sims

Murray State Theses and Dissertations

Ionic liquids (ILs) are useful for many applications due to the tunability of their characteristic properties making these salts ideal for many applications. To further increase possible areas of application for these materials, some ILs can be incorporated into polymer structures to form poly ionic liquids (PILs) or ionenes. The specific ions used within the material will determine the thermal, mechanical, and chemical stability properties exhibited by the polymer. Adjustments can be made to the ion structures during the synthetic process to influence these observed properties.

Fuel cells, batteries, solar cells, and capacitors, all require materials that can withstand high …

Reduced Metal Nanocatalysts For Selective Electrochemical Hydrogenation Of Biomass-Derived 5-(Hydroxymethyl)Furfural To 2, 5-Bis(Hydroxymethyl)Furan In Ambient Conditions, Baleeswaraiah Muchharla, Moumita Dikshit, Ujjwal Pokharel, Ravindranath Garimella, Adetayo Adedeji, Kapil Kumar, Wei Cao, Hani Elsayed-Ali, Kishor Kumar Sadasivuni, Naif Abdullah Al-Dhabi, Sandeep Kumar, Bijandra Kumar

Chemistry & Biochemistry Faculty Publications

Selective electrochemical hydrogenation (ECH) of biomass-derived unsaturated organic molecules has enormous potential for sustainable chemical production. However, an efficient catalyst is essential to perform an ECH reaction consisting of superior product selectivity and a higher conversion rate. Here, we examined the ECH performance of reduced metal nanostructures i.e., reduced Ag (rAg) and reduced copper (rCu) prepared via electrochemical or thermal oxidation and electrochemical reduction process, respectively. Surface morphological analysis suggests formation of nanocoral and entangled nanowire structure formation for rAg and rCu catalysts. rCu exhibits slight enhancement in ECH reaction performance in comparison to the pristine Cu. However, the rAg …

The Chemistry And Catalytic Activity Of Dehydrogenative Silylation And Hydroboration Of Complexes Bearing Semirigid Ligands With Group 14 Elements, Niroshani S. Abeynayake

Theses and Dissertations

Incorporation of silicon in the ligand backbone would yield electron-rich metal complexes upon coordination to transition metal complexes. The coordination chemistry of semirigid benzyl phosphines bearing a single or multiple phosphorus atoms and varying number of Si−H moieties has gained interest in recent years. This dissertation focuses on synthesizing silyl and germyl transition metal complexes of groups 9 and 10. Chapter II presents the synthesis of a family of four coordinated 14-electron rhodium complexes. The newly synthesized complexes were characterized in solution by multinuclear NMR spectroscopy and in the solid-state by single-crystal X-ray diffraction. These d⁶ complexes possess sawhorse …

Prediction And Confirmation Of A Switch-Like Region Within The N-Terminal Domain Of Hsirt1, Angelina T. Huynh, Thi-Tina N. Nguyen, Carina A. Villegas, Saira Montemorso, Benjamin Strauss, Richard A. Pearson, Jason G. Graham, Jonathan Oribello, Rohit Suresh, Brooke Lustig, Ningkun Wang

Faculty Research, Scholarly, and Creative Activity

Many proteins display conformational changes resulting from allosteric regulation. Often only a few residues are crucial in conveying these structural and functional allosteric changes. These regions that undergo a significant change in structure upon receiving an input signal, such as molecular recognition, are defined as switch- like regions. Identifying these key residues within switch-like regions can help elucidate the mechanism of allosteric regulation and provide guidance for synthetic regulation. In this study, we combine a novel computational workflow with biochemical methods to identify a switch-like region in the N-terminal domain of human SIRT1 (hSIRT1), a lysine deacetylase that plays important …

Fast Photochemical Oxidation And Footprinting Of Proteins Via Trifluoromethyl Radical Chemistry, Elaine Morrow

Honors Theses

Fast photochemical oxidation of proteins (FPOP) is a useful tool in proteomics because of the ability for modifications to occur on the scale of microseconds which reduces the modifications to tertiary and quaternary structure allowing for more accurate labeling of the protein. Labels for FPOP are generated from various radicals in our experiments which include hydroxyl radicals and trifluoromethyl radicals. Hydroxyl radicals are easily generated by using an excimer laser (KrF laser, 248 nm) or a UV flash lamp (as a part of the Fox™ System) by the photolysis of hydrogen peroxide. Trifluoromethyl radicals, however, need hydroxyl radicals to be …

Synthesis Of Phosphonate-Based Diimide Ligands, Kenya V. Medina

Honors Program Theses and Research Projects

There has been a resurged interest in the synthesis of metal-organic frameworks because of their potential applications in energy production and drug delivery. Although diimides are insoluble in aqueous solutions, the addition of phosphonic acid allows the complex to be water soluble, which greatly increases their application. Therefore, the creation of a hybrid metal-organic complex by the addition of phosphonic groups to diimide ligands can result in a polar porous compound. In this project the ligand design included the use of dianhydrides including pyromellitic dianhydride, naphthalenetetracarboxylic dianhydride, perylenetetracarboxylic dianhydride, and biphenyl-tetracarboxylic acid dianhydride. These dianhydride precursors were refluxed under argon …

Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig

Faculty Research, Scholarly, and Creative Activity

Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.

Identification Of Chemical Structures And Substructures Via Deep Q-Learning And Supervised Learning Of Ftir Spectra, Joshua D. Ellis

Graduate Theses/Dissertations

Fourier-transform infrared (FTIR) spectra of organic compounds can be used to compare and identify compounds. A mid-FTIR spectrum gives absorbance values of a compound over the 400-4000 cm^-1 range. Spectral matching is the process of comparing the spectral signature of two or more compounds and returning a value for the similarity of the compounds based on how closely their spectra match. This process is commonly used to identify an unknown compound by searching for its spectrum’s closes match in a database of known spectra. A major limitation of this process is that it can only be used to identify …

Emergent Photophysics In Diketopyrrolopyrrole Superstructures, Andrew Levine

Dissertations, Theses, and Capstone Projects

Organic semiconductors have received substantial attention as active components in optoelectronic devices because of their processability and customizable electronic properties. Tailoring the organic active layer in these devices to exhibit desirable optoelectronic properties requires understanding the complex and often subtle structure-property relationships governing their photophysical response to light. Both structural organization and frontier molecular orbitals (FMO) play pivotal roles in energy relaxation processes, and complex interplay between organization and orbital energies are difficult to anticipate based upon the molecular structure of the components alone, especially in systems comprised of multiple components. In pursuit of design rules, there is a need …

Cu-Promoted C-H Bond Hydroxylation Inspired By Cu-Dependent Metalloenzymes, Rachel Trammell

Chemistry Theses and Dissertations

From 2003 to 2015, Schӧnecker and Baran proposed a dinuclear Cu/O₂ species in their mechanistic proposal for the hydroxylation of sp³ C-H bonds within their systems (proposed based on yields). Inspired from the site selectivity of this methodology and poor analysis of the mechanism, the first project was inspired to re-examine the sp³ C-H bond hydroxylation by Schrӧnecker and Baran and perform an intensive investigation into understanding how Cu/O₂ interact which led us to propose a new mechanism based on the evidence collected (i.e., LCu^II-hydroperoxide species that undergoes homolytic O-O bond cleavage). From there …

Applications Of Sodium Azide In The Synthesis Of Tetrazines And Hydrolysis Reactions, My Le

Honors Theses

The inverse electron demand Diels−Alder cycloadditions of heterocyclic azadienes have provided a robust methodology for synthesizing highly substituted and functionalized heterocycles. It is widely used in organic synthesis and the pharmaceutical industry in the divergent construction of screening libraries and bioorthogonal conjugation. Each heterocyclic azadiene was found to possess a unique reactivity toward different classes of dienophiles, display predictable modes of cycloaddition, and exhibit substantial substituent electronic effects impacting their intrinsic reactivity and cycloaddition regioselectivity. Synthesis of 1,2,4,5-tetrazine has been reported in the literature since the late 19th century, showing scientists' tremendous interest in its application.

Herein we attempt to …

Synthesis Of A Dd-Π-Aa Organic Dye For Dye-Sensitized Solar Cells, Hope Lovell

Honors Theses

This project investigates the synthesis of a DD-π-AA (dual donor/dual acceptor) organic dye as a potential sensitizer for dye-sensitized solar cells (DSCs). The design of this dye was based off previous research that found dual donor/dual acceptor dyes exhibited promising results when used in a DSC. The donor groups, acceptor groups, and π-bridge were chosen for their stability, ability to absorb in the near-infrared (NIR) region, and intramolecular charge transfer (ICT) abilities.

While many components of the dye were synthesized, the final stages of the synthetic scheme were not completed due to the loss of time from COVID-19. Had the …

Synthesis Of A Zinc Dipyrrin Complex For Photocatalytic Reduction Of Co2, Sylvia Meredith

Undergraduate Honors Theses

Zinc dipyrrin complexes have the potential to act as cheap, effective photosensitizers. Synthesizing and studying different types could lead to more efficient solar energy harvesting processes, especially the production of solar fuel. Here, two attempts to synthesize 1,3,7,9-tetraphenyl-5-mesityldipyrromethene are reported and discussed. According to ¹H NMR, the first synthesis attempt was not successful. The second synthesis attempt was not purified effectively, so ¹H NMR produced inconclusive results. Further purification strategies or alternate synthesis methods are required.

Indolizine Donor-Based Dyes For Applications In Fluorescence Biological Imaging, William Meador

Honors Theses

NIR emissive fluorophores are intensely researched due to their potential to replace modern imaging procedures. Many molecular strategies have been employed in the literature to optimize fluorophores for deeper NIR absorption and emission, biocompatibility, and higher fluorescence quantum yields. Amongst the fluorophores studied to date, proaromatic indolizine donors are attractive alternatives to traditional alkyl amine and indoline based donors due to their 1) lower energy absorption and emission facilitated by proaromaticity, 2) large Stokes shifts due to increased dihedral angles about the π-system, 3) ease of functionalization and capacity for bioconjugation at the phenyl ring, and 4) potential for further …

Visualization Without Vision – How Blind And Visually Impaired Students And Researchers Engage With Molecular Structures, Croix J. Laconsay, Henry B. Wedler, Dean J. Tantillo

Journal of Science Education for Students with Disabilities

This article examines the tools and techniques currently available that enable blind and visually impaired (BVI) individuals to visualize three-dimensional objects used in learning chemistry concepts. How BVI individuals engage with and visualize molecular structure is discussed and recent tactile (or haptic) and auditory methods for visualization of various chemistry concepts are summarized. Remaining challenges for chemistry education researchers are described with the aim of highlighting the potential value of educational research in further enabling BVI students to pursue careers in science, technology, engineering, and mathematics (STEM) fields.

I. Non-Degradable Polysiloxane Networks For Controlled Release Applications, And Ii. Additive Free, Degradable Silyl-Ether Furyl-Maleimide Networks, Caleb M. Bunton

Chemistry Theses and Dissertations

I. Two different series of non–degradable polysiloxane networks were prepared for the encapsulation and controlled release of a small molecule agent. For the first series, hydrosilylation was utilized to prepare networks of varying crosslink densities, as determined from swelling studies, from vinyl terminated and silylhydride functional poly(dimethyl)siloxanes. For the second series, the thiol-ene reaction was utilized to prepare networks of varying crosslink densities, as determined from swelling studies, from vinyl terminated and mercaptopropyl functional poly(dimethyl)siloxanes. Nile red dye was used as an encapsulated agent and dye release from each series of networks was measured using UV–vis spectroscopy to determine controllability …

Green Chemistry: The Oxidation Of Benzaldehyde Using Atmospheric Oxygen And N-Heterocyclic Carbenes As Catalysts, Alex Brody, John Morgan

Student Research Poster Presentations 2020

Oxidation is a vital process in organic and biochemical reactions. In particular, the oxidation of aromatic aldehydes to carboxylic acids and esters is a vital process used in many different environments. Benzaldehyde is one common subject of this type of reaction, used in the synthesis of benzoic acid and benzoate derivatives. Unfortunately, the industrial synthesis of these compounds uses harmful heavy metal oxidants such as Chromium(VI) and Manganese(VII), which are very harmful to the environment. We proposed to eliminate these pollutants by using atmospheric oxygen and an organic catalyst in a solvent free reaction. This reaction would then be microwaved …