Chemistry Commons^™

Synthesis Of 2-Arylpyridines By The Suzuki–Miyaura Cross-Coupling Of Pyfluor With Hetero (Aryl) Boronic Acids And Esters, Juan Rueda-Espinosa, Dewni Ramanayake, Nicholas Ball, Jennifer A. Love

Pomona Faculty Publications and Research

The Suzuki–Miyaura cross-coupling of pyridine-2-sulfonyl fluoride (PyFluor) with hetero(aryl) boronic acids and pinacol boronic esters is reported. The reactions can be performed using Pd(dppf)Cl2 as the catalyst, at temperatures between 65 and 100 °C and in the presence of water and oxygen. This transformation generates 2-arylpyridines in modest to good yields (5%–89%).

Computational Investigation Of The Ionization Potential Of Lead Sulfide Quantum Dots, Jessica Beyer

Scripps Senior Theses

The purpose of this work was to determine the impact of quantum dot size on ionization potential and to determine how the presence of carbonyl-based ligands affect the ionization potential of lead sulfide quantum dot systems. Ionization potential (IP) is defined as the energy required to remove an electron from an atom, molecule, or material. IP helps scientists determine how reactive the material of interest is, which is crucial information when manufacturing nanomaterials. Accurate quantum chemical calculations of ionization potential are challenging due to the computational cost associated with the numerical solution of the Dyson equation. In this work, the …

Calcium Bistriflimide-Mediated Sulfur (Vi)–Fluoride Exchange (Sufex): Mechanistic Insights Toward Instigating Catalysis, Nicholas Ball, Brian Han, Samuel R. Khasnavis, Matthew Nwerem, Michael Bertagna, O Maduka Ogba

Pomona Faculty Publications and Research

We report a mechanistic investigation of calcium bistriflimide-mediated sulfur(VI)–fluoride exchange (SuFEx) between sulfonyl fluorides and amines. We determine the likely pre-activation resting state─a calcium bistriflimide complex with ligated amines─thus allowing for corroborated calculation of the SuFEx activation barrier at ∼21 kcal/mol, compared to 21.5 ± 0.14 kcal/mol derived via kinetics experiments. Transition state analysis revealed: (1) a two-point calcium-substrate contact that activates the sulfur(VI) center and stabilizes the leaving fluoride and (2) a 1,4-diazabicyclo[2.2.2]octane additive that provides Brønsted-base activation of the nucleophilic amine. Stable Ca–F complexes upon sulfonamide formation are likely contributors to inhibited catalytic turnover, and a proof-of-principle redesign …

Sulfondiimidamides Unlocked As New S(Vi) Hubs For Synthesis And Drug Discovery, Nicholas Ball

Pomona Faculty Publications and Research

Despite their promise as drug targets, access to nitrogen-rich S(VI) compounds has been a significant synthetic challenge. In this issue of Chem, Zhang and Willis explore a new class of S(VI) compounds-sulfondiimidamides-providing robust strategies toward their synthesis, derivation, and promise as new sulfonamide bioisosteres.

Here, There, And Everywhere: Probing Ubiquitin-Cavitand Binding Via 15n-1h Hsqc, Julia Didziulis

Scripps Senior Theses

Ubiquitination and other post-translational modifications play a major role in the proliferation of many neurodegenerative diseases, developmental disorders, and cancers, and as such are subjects of recently increased biochemical interest. Expanding upon such research, this study confirmed a robust method of ubiquitin expression and purification, then used 15N-1H HSQC to analyze ubiquitin samples containing varying concentrations of a deep cavitand with affinity for lysine and arginine side chains. In the pure ubiquitin spectrum, arginine side chain chemical shifts were detected in the nitrogen 80-85 ppm range and lysine side chain signals were undetected. However, upon introduction of the cavitand, collection …

Using Powder Diffraction To Give Insight Into Structures Of Ir2(Diisocyanomenthane)4x2 [Dimen] (X = Cl; Pf6; Bph4), Mairead Brownell

Scripps Senior Theses

Ir2(dimen)42+ (dimen = 1,8-diisocyanomenthane) has been studied extensively as model compound to better understand catalysis of photochemical reactions. Although Ir2(dimen)42+ has been used primarily to observe the photophysical changes of metal-metal transitions, it gives great insight into the transitions that allow other d8-d8 metal complexes to undergo photochemical processes and generate hydrogen gas. The large visible range by which Ir2(dimen)42+ (1) can be electronically excited in solution is indicative of its two solution phase ground states, which interestingly have been hypothesized to resemble two unique packing structures observed in the powder state. In this study, the powder diffraction patterns of …

Spatial Geochemical Changes In Central And East Texas Soils Over Time Resulting From Human Decomposition, Isabela Marisol Overturf

CMC Senior Theses

Human decomposition is studied to aid forensic investigations and better understand the impact of cemeteries on urban resources like soil and groundwater. The purpose of this study was to identify changes in soil geochemistry at and around a human grave to search for lateral nutrient movement and possibly identify new patterns in elemental concentrations that could be used in estimating post-mortem intervals (PMIs). At the Forensic Anthropology Research Facility (FARF) at Texas State San Marcos, soil samples were collected from a shallow grave over the course of 54 days to conduct analysis for organic matter content, texture, pH, and bulk …

The Emerging Applications Of Sulfur (Vi) Fluorides In Catalysis, Nicholas Ball, Cayo Lee, Jonathan E. Elisabeth, Nathan C. Friede, Glenn M. Sammis

Pomona Faculty Publications and Research

The past decade has witnessed remarkable growth of catalytic transformations in organic sulfur(VI) fluoride chemistry. This Perspective concentrates exclusively on foundational examples that utilize catalytic strategies to synthesize and react S(VI) fluorides. Key mechanistic studies that aim to provide insight toward future catalytic systems are emphasized.

Using Augmented Reality As A Tool For Distance Learning Of Vsepr Theory, Isabelle Lopez

Scripps Senior Theses

Distance learning poses challenges in most academic settings, especially at the undergraduate laboratory level. Improving this mode of learning diminishes the impact of current events on young scientists’ development of foundational laboratory concepts. Our work explores the use of augmented reality (AR) in a laboratory setting. We developed a completely virtual valence shell electron pair repulsion (VSEPR) theory lab activity consistent with the goals of Keck Science Department’s Introduction to Chemistry course’s in-person VSEPR lab activity. We were able to maintain a hands-on learning experience for students while using a tool many students already own: an iPhone as an alternative …

Influence Of Iceberg-Discharge Events On The Climate And Circulation Of The Central North Atlantic Ocean During The Last Glaciation, Ava Mcilvaine

Scripps Senior Theses

The repeated occurrence of episodic iceberg-discharge events and abrupt climate change in the North Atlantic Ocean is well-documented for the late Quaternary period. However, much of the evidence for these periods known as Heinrich Events comes from the subpolar region, where deposition can be dominated by ice-rafted debris (IRD) and overwhelm other oceanographic and climatic indicators. Thus, the following analysis of coarse sediment from Integrated Ocean Drilling Program (IODP) Core Site U1313 (41°0.0'N, 32°57.42'W) evaluated ocean cooling related to ice-rafting, water mass migration, and climate change over the approximate last 100,000 years. Site U1313 is located near the North Atlantic …

Using Nmr Spectroscopy And Computational Chemistry To Confirm The Structure Of Novel Antibiotic Nocamycin O, Stephanie Lewis

CMC Senior Theses

In recent years, many medically promising antibiotics have been discovered in nature, especially in insect-microbe symbioses. One of the better-studied examples of this kind of defensive relationship is that of fungus-growing ants and the antibiotic-producing Actinobacteria. These bacteria produce several defensive chemicals with myriad uses, including one antibiotic that inhibits the growth of several bacterial strains, including other Actinobacteria. This antibiotic (known as nocamycin O) is a promising candidate for medicinal use due to its similarities to bacterial RNA polymerase inhibitors tirandamycin and streptolydigin, which inhibit several human pathogens. The determination of the structure of nocamycin O will be an …

Sufex Activation With Ca(Ntf2)2: A Unified Strategy To Access Sulfamides, Sulfamates, And Sulfonamides From S(Vi) Fluorides, Nicholas Ball, Subham Mahapatra, Cristian P. Woroch, Todd W. Butler, Sabrina N. Carneiro, Sabrina C. Kwan, Samuel R. Khasnavis, Junha Gu, Jason K. Dutra, Beth C. Vetelino, Justin Bellenger, Christopher W. Am Ende

Pomona Faculty Publications and Research

A method to activate sulfamoyl fluorides, fluorosulfates, and sulfonyl fluorides with calcium triflimide and DABCO for SuFEx with amines is described. The reaction was applied to a diverse set of sulfamides, sulfamates, and sulfonamides at room temperature under mild conditions. Additionally, we highlight this transformation to parallel medicinal chemistry to generate a broad array of nitrogen-based S(VI) compounds.

Gravity-Drawing Flexible Silicone Filaments As Fiber Optics And Model Foldamers, Katherine Snell

CMC Senior Theses

Here, we present a method of gravity-drawing polydimethylsiloxane (PDMS) silicone fibers with application as fiber optics and as model foldamers. Beginning as a viscous liquid, PDMS is cured using heat until its measured viscosity reaches 4000 mPa•s. The semi-cured elastomer is then extruded through a tube furnace to produce thin (diameters on the order of hundred micrometers) filaments with scalable lengths. PDMS is biocompatible, gas-permeable, flexible, and hydrophobic. Additionally, the PDMS surface hydrophobicity can be modified via UV exposure, O2 plasma, and corona discharge. We demonstrate the patternibility (i.e patterns of hydrophobicity) of PDMS fibers, adding complexity to potential foldamer …

Antifungal Defense Molecules From Bacterial Symbionts Of North American Trachymyrmex Ants, Georgia Scherer

CMC Senior Theses

Defensive symbioses, in which microbes provide molecular defenses for an animal host, hold great potential as untapped sources of therapeutically useful antibiotics. Fungus-growing ants use antifungal defenses from bacterial symbionts to suppress pathogenic fungi in their nests. Preliminary chemical investigations of symbiotic bacteria from this large family of ants have uncovered novel antifungal molecules with therapeutic potential, such as dentigerumycin and selvamicin.

In this study, the bacterial symbionts of North American Trachymyrmex fungus-growing ants are investigated for antifungal molecules. Plate-based bioassays using ecologically-relevant fungal pathogens confirmed that these bacteria have antifungal activity. In order to purify and identify the antifungal …

Synthesis And Reactivity Of A New Platinum(Ii) Complex, Maria Lew

Scripps Senior Theses

Alkanes are some of the most abundant organic molecules, yet currently there are no efficient ways of directly converting them to more functional molecules. One viable method of direct functionalization is C–H bond activation by transition metal catalysts. The focus of this research has been the synthesis of a new Pt(II) pincer complex to be used in mechanistic investigations of C–H activation, as well as the beginnings of those investigations. The complex [NN^ON]PtMe was successfully synthesized. Reactions with various acids indicated that [NN^ON]PtMe is capable of reductively eliminating methane after addition of two equivalents of acid. …

Sulfonamide Synthesis Via Calcium Triflimide Activation Of Sulfonyl Fluorides, Nicholas Ball, Paramita Mukherjee, Cristian P. Woroch, Leah Cleary, Mark Rusznak, Ryan W. Franzese, Matthew R. Reese, Joseph W. Tucker, John M. Humphrey, Sarah M. Etuk, Sabrina C. Kwan, Christopher W. Am Ende

Pomona Faculty Publications and Research

A method using calcium triflimide [Ca(NTf₂)₂] as a Lewis acid to activate sulfonyl fluorides toward nucleophilic addition with amines is described. The reaction converts a wide array of sterically and electronically diverse sulfonyl fluorides and amines into the corresponding sulfonamides in good yield.

Synthesis And Characterization Of A Novel Platinum Ligand Complex ((Κ-N,C,N- 2,6-Bis(Diethylaminomethyl)Phenyl)(4- Tert-Butylphenyl) Platinum(Ii)), Carly Roleder

CMC Senior Theses

A novel platinum ligand complex (NCN)PtAr, ((κ-N,C,N- 2,6-bis (diethylaminomethyl)phenyl)(4- tert-butylphenyl) platinum(II)), was synthesized. A reaction of 1-Bromo-4-tert-butylbenzene Grignard with (NCN)PtCl, (where NCN = 2,6-bis(diethylaminomethyl)phenyl) yielded the (NCN)PtAr (where Ar = 4-tert­-butylphenyl). The product was then characterized with NMR spectra through ¹H NMR, ¹³C NMR, COSY, HSQC, and HMBC to verify it structure.

Pd-Catalyzed Conversion Of Aryl Iodides To Sulfonyl Fluorides Using So2 Surrogate Dabso And Selectfluor, Nicholas Ball, Ariana L. Tribby, Ismerai Rodríguez, Shamira Shariffudin

Pomona Faculty Publications and Research

A one-pot Pd-catalyzed conversion of aryl iodide to aryl sulfonyl fluorides using DABSO and Selectfluor has been developed generating aryl sulfonyl fluorides in good to excellent yields. The reaction results in the generation of electronically and sterically diverse sulfonyl fluorides. Additionally, sulfonyl fluorides can be converted to aryl sulfonamides and sulfonic esters using Cs₂CO₃ under mild conditions.

Phage Display To Identify Functional Resistance Mutations To Rigosertib, Nedim Filipovic

CMC Senior Theses

In vitro protein selection has had major impacts in the field of protein engineering. Traditional screens assay individual proteins for specific function. Selection, however, analyzes a pool of mutants and yields the best variants. Phage display, a successful selection technique, also provides a reliable link between variant phenotype and genotype. It can also be coupled with high throughput sequencing to map protein mutations; potentially highlighting vital mutations in variants. We propose to apply this technique to cancer therapy. RAF, a serine/threonine kinase, is critical for cell regulation in mammals. RAF can be activated by oncogenic RAS, found in over 30% …

Quantifying Carbonyl Sulfide And Other Sulfur-Containing Compounds Over The Santa Barbara Channel, Julia Black

Scripps Senior Theses

Carbonyl sulfide (OCS) is emitted to the atmosphere through the outgassing of ocean surface waters. OCS is also the primary source of sulfur-containing compounds in the stratosphere and contributes to the formation of the stratospheric sulfate layer, an essential controller of the radiative balance of the atmosphere. During the 2016 Student Airborne Research Program (SARP), 15 whole air samples were collected on the NASA DC-8 aircraft over the Santa Barbara Channel. Five additional surface samples were taken at various locations along the Santa Barbara Channel. The samples were analyzed using gas chromatography in the Rowland-Blake lab at UC Irvine, and …

Small Molecule Inhibitor Design For Anaplastic Lymphoma Kinase Inhibition, Theodore D. Hansel, David J. Grabovsky

Interface Compendium of Student Work

The Anaplastic Lymphoma Kinase (ALK) gene has been linked to tumorigenesis in a number of human cancers, including anaplastic large cell lymphoma (ALCL) and neuroblastoma. While ALK mutations in ALCL and many other cancers occur as a result of gene fusions with wild type kinase domains, those in neuroblastoma stem from single nucleotide polymorphisms (SNPs) in the kinase domain. These lead to autophosphorylation and constitutive signaling by ALK for cell growth and division, ultimately causing cancer. Crizotinib, an ATP-competitive ALK inhibitor, has proven to be an effective inhibitor of both ALKWT and ALKMutant kinase domains, and is in the middle …

Direct, Biomimetic Synthesis Of (+)-Artemone Via A Stereoselective, Organocatalytic Cyclization, Eric D. Nacsa, Brian C. Fielder, Shannon P. Wetzler, Veerasak Srisuknimit, Jonathan P. Litz, Mary J. Van Vleet, Kim Quach, David A. Vosburg

All HMC Faculty Publications and Research

We present a four-step synthesis of (+)-artemone from (–)- linalool, featuring iminium organocatalysis of a doubly diastereoselective conjugate addition reaction. The strategy follows a proposed biosynthetic pathway, rapidly generates stereochemical complexity, uses no protecting groups, and minimizes redox manipulations.

Comparing Bulk Aerosol Profiles In The Mixed Layer In Coastal Los Angeles And The Inland Empire, Taia Sean Wu

Scripps Senior Theses

Characteristic westerly sea breeze carries air over the Los Angeles Basin in Southern California to the Inland Empire approximately 50 miles inland, directly impacting air quality in both of these two highly polluted regions. As particles play a critical role in air quality and human health, this study compares the bulk aerosol profiles of the Los Angeles pollution "source" and Inland Empire "receptor" regions during the 2013 and 2014 NASA Student Airborne Research Program (SARP) campaigns onboard the NASA DC-8 airborne laboratory. The source and receptor regions were characterized by a series of missed approaches at the Los Angeles International …

Exploration Of Materials Used In 3-Dimensional Printing For The Dental Industry, Holly Chang Hayden

Scripps Senior Theses

A limiting factor in the digitization of dental devices is the availability of materials suitable for use in both dentistry and the new digital technologies. As a rapidly growing industry, three-dimensional printing (3DP) has the potential to disrupt traditional manufacturing and prototyping methods. A review of both restorative materials and the current 3DP materials has lead to a focus on fiber- reinforced composites in the exploration for a new 3DP material. In addition, another area worth exploring and investing in would be 3D bioprinting as it opens up the possibility of regenerative dentistry.

Big Horned, Juniper Harrower

The STEAM Journal

Tinta y tinto (Spanish for black ink and red wine)
Through a process of oxidation, reduction, and light manipulation, Juniper stains and colors paper with red wine and a rich black pigment made of the wild harvested mushroom Coprinopsis atramentaria.

Wetlands And Greenhouse Gas Fluxes: Causes And Effects Of Climate Change – A Meta-Analysis, Robert E. Ventura

Pomona Senior Theses

Climate change is one of the largest problems facing this generation. Anthropogenically caused increases of greenhouse gas emissions is a significant culprit to this problem. Although the obvious problems such as cars, industry, and urbanism garnish a significant amount of the criticism, natural sources such as wetlands are also beginning to contribute to this issue. This is becoming increasingly significant as wetlands shift from being sinks of greenhouse gases to becoming sources as various anthropogenic impacts, including global warming itself, begin to affect the health of the wetlands. The aim of this project is to look at four common types …

A Volumetric Study Of Aqueous Butanol Solutions, Priyanka P. Chary

Scripps Senior Theses

Alcohol molecules consist of two distinct regions: a polar, hydrophilic alcohol group, and an aliphatic hydrocarbon chain. These regions interact with solvent water molecules in different ways. While the alcohol group acts as a solvent structure breaker by hydrogen bonding with nearby water molecules, the hydrophobic carbon chain acts instead as a solvent structure maker and causes the surrounding water molecules to align themselves in a Clathrate structure. The presence of these two contrasting solute-solvent interactions affects the properties of the solution, among them the molar volume. The partial molar volume of the alcohol is analyzed with respect to three …

Analysis Of Biodiesel Quality Using Reversed Phase High-Performance Liquid Chromatography, Kellyann M. Murphy

Pomona Senior Theses

The alternative fuel biodiesel is produced from the transesterification of vegetable oils or animal fat to fatty acid methyl esters. Pomona has a reactor on campus that can be used to run this reaction and produce biodiesel. The use of biodiesel has been found to lower air pollutant and greenhouse gas emissions, but can be potentially harmful to the engines if it contains impurities. This paper proposes a method using high-performance liquid chromatography to test the quality of biodiesel. This method utilizes instrumentation and materials that are available in Pomona College's Chemistry Department, requires very little sample preparation, and is …

Biologically-Derived Dye-Sensitized Solar Cells: A Cleaner Alternative For Solar Energy, Erika S. Falsgraf

Pomona Senior Theses

This project employs the biological compounds hemin, melanin, and retinoic acid as photoactive dyes in dye-sensitized solar cells (DSSCs). These dyes are environmentally and economically superior to the standard ruthenium-based dyes currently used in DSSCs because they are nontoxic and widely available. Characterization by linear sweep voltammetry yielded averaged maximum overall conversion efficiency values of 0.059% for retinoic acid, 0.023% for melanin, and 0.015% for hemin. Absorption spectra of hemin and retinoic acid suggest that they would complement each other well when used in tandem in one cell because hemin has a secondary maximum absorption peak at 613nm and retinoic …

Arsenic Contamination In Groundwater In Vietnam: An Overview And Analysis Of The Historical, Cultural, Economic, And Political Parameters In The Success Of Various Mitigation Options, Thuy M. Ly

Pomona Senior Theses

Although arsenic is naturally present in the environment, 99% of human exposure to arsenic is through ingestion. Throughout history, arsenic is known as “the king of poisons”; it is mutagenic, carcinogenic, and teratogenic. Even in smaller concentrations, it accumulates in the body and takes decades before any physical symptoms of arsenic poisoning shows. According to the World Health Organization (WHO), the safe concentration of arsenic in drinking water is 10 µg/L. However, this limit is often times ignored until it is decades too late and people begin showing symptoms of having been poisoned.

This is the current situation for Vietnam, …