Physical Sciences and Mathematics Commons^™

Self-Assembling Biomolecular Catalysts For Hydrogen Production, Dustin Patterson

Dustin Patterson

Spectroscopic And Functional Characterization Of The Nitric Oxide Adducts Of The Fe(Iii) And Fe(Ii) States Of The Co-Sensing Transcription Factor, Cooa, From Carboxydothermus Hydrogenoformans, Robert Clark, Edra Jani, Arathi Francis, Elise Laroche, Isabel Malone

Robert Clark

CooA is a carbon monoxide (CO) sensing transcription factor that is found in several bacteria and regulates CO metabolism. CO binding to CooA’s heme groups initiates a conformation change that activates protein DNA binding. This study investigates the reaction of Fe(III) Carboxydothermus hydrogenoformansCooA (Ch CooA) with nitric oxide (NO). Previously, Clark and coworkers reported Fe(II) Ch CooA bound NO to form a 6-coordinate (6-C) Fe(II)-NO adduct that was active for DNA binding in vivo and in vitro. This is in contrast to the best studied CooA homolog from R. rubrum (Rr) that was exquisitely specific for CO and formed an …

Mechanism Of Redox- And Co-Sensing By The Heme Protein, Cooa: Cryoradiolysis Studies, Robert Clark, Deanna Kalafut

Robert Clark

Gas-sensing heme proteins participate in a variety of signal-transduction mechanisms across a broad range of biological systems. This class of proteins functions by undergoing an allosteric conformational change in response to the binding of a small gas molecule to a heme group. CooA, which is a redox- and CO-sensing transcription factor that is found in several bacteria, regulates gene expression that enables growth on CO as a sole energy source. In the current study, we have employed the technique of gamma-irradiation / cryoreduction spectroscopy (cryoradiolysis) to investigate facile changes that occur to the heme coordination structure of CooA during activation. …

Silica-Bound Copper(Ii) Triazacyclononane As A Phosphate Esterase: Effect Of Linker Length And Surface Hydrophobicity, Brett Bodsgard, Robert Clark, Anthony Ehrbar, Judith Burstyn

Robert Clark

A series of silica-bound Cu(II) triazacyclononane materials was prepared to study the effect of linker length and surface hydrophobicity on the hydrolysis of phosphate esters. The general synthetic approach for these heterogeneous reagents was rhodium-catalyzed hydrosilation between an alkenyl-modified triazacyclononane and hydride-modified silica followed by metallation with a Cu(II) salt. Elemental analysis confirmed that organic functionalization of the silica gel was successful and provided an estimate of the surface concentration of triazacyclononane. EPR spectra were consistent with square pyramidal Cu(II), indicating that Cu(II) ions were bound to the immobilized macrocycles. The hydrolytic efficacies of these heterogeneous reagents were tested with …

Isomer Distribution Of Succinylcyclohexenyl, Acetylcyclohexenyl And Acetylcyclopentenyl Enamines, A. Cook, Sarah Folk

A. Gilbert Cook

The isomeric distributions of some cyclohexenyl enamines substituted by succinyl or acetyl groups at either the 2- or 6-positions are reported as are the isomeric distributions of similarly substituted cyclopentenyl enamines. Correlation between the C-13 NMR chemical shifts in these enamines and isomer distribution is shown. Density functional molecular modeling is used to demonstrate resonance and electrostatic effects on isomeric distributions.

Impact Of Heme Reconstitution On The Spectroscopic Properties And Dna Binding Activity Of The H82a Variant Of The Carbon Monoxide-Sensing Heme Transcription Factor, Cooa, Rachel Troester, Robert Clark

Robert Clark

CooA is a gas-sensing heme protein that regulates the expression of genes responsible for growth by carbon monoxide (CO) in several bacteria. CO binding to the CooA heme groups results in an allosteric conformation change that initiates the protein’s DNA binding function. All known CooA homologs have a conserved histidine residue that i) acts as the proximal heme ligand and ii) istrans to CO. Together with the results from mutagenesis studies, this observation suggests the presence of a proximal histidine ligand is required for CooA’s DNA-binding activity. However, since mutants lacking this His have been observed to lose heme …

Gas-Binding Studies Of The Carbon Monoxide Sensor, Cooa, Joshua Wagoner, Lindsey Dillingham, Robert Clark

Robert Clark

CooA is a carbon monoxide-sensing (CO-sensing) heme protein transcription factor that regulates gene activation in several bacteria and is a convenient model for studying analogous proteins in the human body. The goal of this study is to understand the specificity and mechanism of gas binding of CooA. To accomplish this, wild type CooA and selected protein variants were purified and then reacted with different diatomic gas molecules. The resulting species were characterized by UV-Visible and fluorescence spectroscopy.

Mutagenesis Studies To Investigate Ligand Binding To The Carbon Monoxide-Sensing Heme Protein, Cooa, From Carboxydothermus Hydrogenoformans, Laura Wagoner, Josh Wagoner, Thomas Goyne, Robert Clark

Robert Clark

The work reported here is part of a larger effort to determine how amino acid residues that compose the heme pockets of gas-sensing heme proteins impact the proteins’ regulation mechanisms and gas specificity. In the present study, we have employed site-directed mutagenesis to prepare protein variants of the carbon monoxide (CO)-sensing heme protein, CooA, from Carboxydothermus hydrogenoformans. These mutants have been designed in an attempt to rationally alter CooA’s effector specificity. We have prepared, isolated, and purified several protein variants to date, including C80T CooA. The C80T substitution is expected to increase the steric bulk on the proximal face of …

Alcohol Reduction Of Enamines, A. Cook

A. Gilbert Cook

Primary or secondary alcohols will reduce enamines to their corresponding saturated amines when heated in a microwave apparatus at a temperature of 160 degrees C for a period of one hour.

Impact Of Nitric Oxide (No) Treatment On The Spectroscopic Properties And Dna Binding Activity Of The Carbon Monoxide-Sensing Heme Transcription Factor, Cooa, Edra Jani, Robert Clark

Robert Clark

CooA is a carbon monoxide (CO)-sensing heme transcription factor that regulates CO metabolism in several bacteria including Carboxydothermus hydrogenoformans (Ch). The goal of this research was to investigate the spectroscopic properties and DNA binding activity of Fe(III) Ch CooA that was reacted with NO. Based on electronic absorbance spectra, addition of NO to Fe(III) CooA resulted in the formation of a 6-coordinate (6-C) Fe(III)-NO intermediate species, which slowly converted to a 5-coordinate (5-C) Fe(II)-NO complex. A fluorescence anisotropy assay revealed appreciable DNA binding activity by the 6-C Fe(III)-NO form and lesser activity by the 5-C adduct. DNA binding by 5-C …

A Knoevenagel Initiated Annulation Reaction Using Room Temperature Or Microwave Conditions, A. Cook

A. Gilbert Cook

An experiment is presented that has the student execute a Knoevenagel initiated annulation reaction. The reaction can be carried out either through use of a microwave reactor or by allowing the mixture to stand at room temperature for two days. The student is then challenged to identify the reaction product through a guided prelab exercise of the synthesis of the Hagemann ester, and then through GC–MS, NMR, and IR spectra of the product. The stereochemistry of the product is determined through the NMR spectrum and the Karplus curve. The student is required to write a mechanism for the reaction.

Spectroscopic Study Of Host-Guest Inclusion Complexes, Jenessa Lucas, Jennifer Holt

Jennifer Holt

A host-guest complex is formed by a host molecule encapsulating a guest molecule within it. The host materials in this study are basket-shaped structures, known as cyclodextrins, which can easily incorporate a variety of guests, such as drug molecules. These inclusion complexes made with cyclodextrins and drugs can be developed to have different release rates within the body. The cyclodextrin can be used to protect the drug until it reaches its destination within the body. This study focuses on Brooker’s merocyanine (BM) as the guest molecule, since it has a similar structure to stilbene-related drugs. UV/Vis and fluorometer spectroscopic studies …

What Students Think And How They Really Perform In Chemistry, Ross Hudson

Dr Ross Hudson

This research was part of a larger study into student performance in senior chemistry with regard to question type and content. This paper examines student perceptions about question type and context and compares these perceptions to actual performance. How students perceive different types of questions and how it influences their self-belief and motivation were the focus of this study. Student responses to different styles or types of questions have been well researched over time. In this study Year 11 chemistry students were quizzed about their preferences to Multiple-Choice questions and Open Response question types and how the presence of each …

Diosphenol-Based Approach To The A-Ring Functionalization Of Advanced Taxol Precursors., John Hofferberth

John E Hofferberth

Several different approaches to the A-ring functionalization of an advanced, highly functionalized diosphenol precursor to Taxol are described. The first phase of the undertaking consists of an assessment of those reagents conducive to reaction at the enolic oxygen (silylation, methylation, allylation, and acylation). Transformations involving an alternative attack at the enol carbon center (bromination, selenation) have also been defined. Sodium borohydride reduction operates from the beta-face of C-14 as long as the C-1 hydroxyl is not protected so as to offer steric exclusion. Complications associated with various aspects of these methodological undertakings are addressed. The most advanced oxygenation achievements were …

A Divergent Approach To The Diastereoselective Synthesis Of Several Ant-Associated Iridoids, John Hofferberth

John E Hofferberth

The ant-associated iridoids nepetalactol, actinidine, dolichodial, isoiridomyrmecin, and dihydronepetalactone were prepared from citronellal using a divergent approach. Key features include a three-step synthesis of the individual antipodes of actinidine by a novel tandem cycloaddition/pyridine formation and a facile diastereoselective synthesis of both enantiomers of dolichodial.

Lactide Cyclopolymerization Kinetics, X-Ray Structure, And Solution Dynamics Of (Tbu-Salamee)Al And A Cautionary Tale Of Polymetalate Formation, Yutan Getzler

Yutan D.Y.L. Getzler

The complex (tBu-SalAmEE)Al (tBu-SalAmEEH3 = N,N-bis(3,5-di-tert-butyl-2-hydroxybenzyl)-2-(2-aminoethoxy)ethanol, 1) catalyzes the ring-expansion polymerization of lactide to form cyclic poly(lactide) (cPLA). The X-ray structure of 1 was determined, its polymerization kinetics were examined and its interactions with Lewis bases were observed. The data from these experiments are consistent with a coordination–insertion mechanism whose rate-determining step is catalyst rearrangement by loss of a hemilabile, datively bound, bridging ligand ether. cPLA was examined by thermogravimetric analysis and found more stable than its linear counterpart. In the course of these studies, we unexpectedly observed the formation of polymetalate (AlMe(tBu-SalAmEE)AlMe2)2 (6), which was characterized (X-ray, EA, and …

Catalytic Carbonylation Of Β-Lactones To Succinic Anhydrides, Yutan Getzler

Yutan D.Y.L. Getzler

A well-defined, highly active and selective catalyst for the synthesis of succinic anhydrides from CO and β-lactones is reported. At 200 psi of CO, the catalyst [(N,N‘-bis(3,5-di-tert-butylsalicylidene)phenylenediamino)Al(THF)2][Co(CO)4] carbonylates β-propiolactones to succinic anhydrides in high yield. (R)-β-Butyrolactone is carbonylated to (S)-methylsuccinic anhydride with clean inversion of stereochemistry, while cis-2,3-dimethyl-β-propiolactone yields exclusively trans-2,3-dimethylsuccinic anhydride. These data are consistent with a mechanism involving nucleophilic attack by [Co(CO)4]- on the β carbon of the lactone, followed by CO insertion and anhydride formation.

Lactide Cyclopolymerization By An Alumatrane-Inspired Catalyst, Yutan Getzler

Yutan D.Y.L. Getzler

Control of molecular structure is an enduring motivation for chemists. From total synthesis(1) to self-assembly(2) to crystal growth,(3) the pursuit continues unabated. Polymer synthesis, in particular, has seen a revolution in control. It is now possible to precisely predetermine chain length, extent of cross-linking, comonomer incorporation, block length, stereochemistry and topology.(4) There has even been success in sequence control,(5) previously achieved only in biological systems. The difficulties inherent in the synthesis of pure macrocycle(6) have limited their availability, despite their compelling predicted properties. A variety of strategies have been employed but only two avoid …

The Mechanism Of Epoxide Carbonylation By [Lewis Acid]+[Co(Co)4]- Catalysts, Yutan Getzler

Yutan D.Y.L. Getzler

A detailed mechanistic investigation of epoxide carbonylation by the catalyst [(salph)Al(THF)2]+ [Co(CO)4]- (1, salph = N,N‘-o-phenylenebis(3,5-di-tert-butylsalicylideneimine), THF = tetrahydrofuran) is reported. When the carbonylation of 1,2-epoxybutane (EB) to β-valerolactone is performed in 1,2-dimethoxyethane solution, the reaction rate is independent of the epoxide concentration and the carbon monoxide pressure but first order in 1. The rate of lactone formation varies considerably in different solvents and depends primarily on the coordinating ability of the solvent. In mixtures of THF andcis/trans-2,5-dimethyltetrahydrofuran, the reaction is first order in THF. From spectroscopic and kinetic data, the catalyst resting state was assigned to be the neutral …

Synthesis Of An Epoxide Carbonylation Catalyst: Exploration Of Contemporary Chemistry For Advanced Undergraduates, Yutan Getzler

Yutan D.Y.L. Getzler

This lab presents an opportunity for advanced students of organic or inorganic chemistry to prepare a compound that belongs to a recently introduced class of catalyst that are active for the carbonylation of epoxides and related substrates to β-lactones and related products. Epoxides are inexpensive and readily available while β-lactones are not and have broad utility in both small molecule and polymer synthesis. Consequently, these catalysts, and related systems, have been the subject of intense investigation recently. The ability to work with a contemporary system was a major source of excitement and satisfaction to undergraduates at Cornell University who performed …

Synthesis And Flammability Testing Of Epoxy Functionalized Phosphorous-Based Flame Retardants, Vladimir Benin, Xuemei Cui, Alexander Morgan, Karl Seiwert

Vladimir Benin

Several potential new phosphorus-containing flame retardant molecules were evaluated for heat release reduction potential by incorporation of the molecules into a polyurethane, generated from methylene diphenyl diisocyanate and 1,3-propane diol. The heat release reduction potential of these substances was evaluated using the pyrolysis combustion flow calorimeter (PCFC). The polyurethanes were prepared in the presence of the potential flame retardants via solvent mixing and copolymerization methods to qualitatively evaluate their potential reactivity into the polyurethane prior to heat release testing. The functionality of the flame retardants was epoxide based that would potentially react with the diol during polyurethane synthesis. Flammability testing …

Synthesis, Structural Studies And Desilylation Reactions Of Some N-2-(Trimethylsilyl)Ethyl-N-Nitrosocarbamates, Arpitha Thakkalapally, Vladimir Benin

Vladimir Benin

The present report describes the preparation and characterization of several N-2-(trimethylsilyl)ethyl-N-nitrosocarbamates, designed as precursors to thermally unstable secondary N-nitrosocarbamate anions via fluoride-assisted cleavage. X-ray structural studies demonstrate that the core N-nitrosocarbamate moiety has a nearly planar geometry, with an s-E orientation at the N–N bond. DFT calculations (B3LYP/6-31+G(d)) reproduce accurately the structural features of the title compounds and detailed conformational analysis at the same level of theory addresses the long-standing issue of preferred geometries for three classes of related structures: N-nitrosocarbamates, N-nitrosoureas and N-nitrosoamides. Desilylation studies demonstrate that both the …

Nanomolar Binding Of Peptides Containing Noncanonical Amino Acids By A Synthetic Receptor, Leigh Logsdon, Christopher Schardon, Vijayakumar Ramalingam, Sharon Kwee, Adam Urbach

Adam R Urbach

This paper describes the molecular recognition of phenylalanine derivatives and their peptides by the synthetic receptor cucurbit[7]uril (Q7). The 4-tert-butyl and 4-aminomethyl derivatives of phenylalanine (tBuPhe and AMPhe) were identified from a screen to have 20–30-fold higher affinity than phenylalanine for Q7. Placement of these residues at the N-terminus of model tripeptides (X-Gly-Gly), resulted in no change in affinity for tBuPhe-Gly-Gly, but a remarkable 500-fold increase in affinity for AMPhe-Gly-Gly, which bound to Q7 with an equilibrium dissociation constant (Kd) value of 0.95 nM in neutral phosphate buffer. Structure–activity studies revealed that three functional groups work in a positively cooperative …

Charge-Mediated Recognition Of N-Terminal Tryptophan In Aqueous Solution By A Synthetic Host, Meghan Bush, Nicole Bouley, Adam Urbach

Adam R Urbach

The molecular recognition of peptides and proteins in aqueous solution by designed molecules remains an elusive goal with broad implications for basic biochemical research and for sensors and separations technologies. This paper describes the recognition of N-terminal tryptophan in aqueous solution by the synthetic host cucurbit[8]uril (Q8). Q8 is known to form 1:1:1 heteroternary complexes with methyl viologen (MV) and a second aromatic guest. Here, the complexes of Q8·MV with (i) the four natural aromatic α-amino acids, (ii) four singly charged tryptophan derivatives, and (iii) four tryptophan-containing tripeptides were characterized by isothermal titration calorimetry, mass spectrometry, and UV−visible, fluorescence, and …

Molecular Recognition Of Insulin By A Synthetic Receptor, Jordan Chinai, Alexander Taylor, Lisa Ryno, Nicholas Hargreaves, Christopher Morris, P Hart, Adam Urbach

Adam R Urbach

The discovery of molecules that bind tightly and selectively to desired proteins continues to drive innovation at the interface of chemistry and biology. This paper describes the binding of human insulin by the synthetic receptor cucurbit[7]uril (Q7) in vitro. Isothermal titration calorimetry and fluorescence spectroscopy experiments show that Q7 binds to insulin with an equilibrium association constant of 1.5 × 106 M−1 and with 50−100-fold selectivity versus proteins that are much larger but lack an N-terminal aromatic residue, and with >1000-fold selectivity versus an insulin variant lacking the N-terminal phenylalanine (Phe) residue. The crystal structure of the Q7·insulin complex shows …

A Cucurbit[8]Uril Sponge, Vijayakumar Ramalingam, Sharon Kwee, Lisa Ryno, Adam Urbach

Adam R Urbach

This paper describes a convenient approach to quantitative removal of the synthetic host cucurbit[8]uril (Q8) from aqueous mixtures using a sepharose resin coated in memantine groups to selectively sequester Q8 in the presence of competing hosts and guests. The “Q8 sponge” can separate Q8 from Q6 and reverse the Q8-mediated dimerization of peptides.

Multivalent Recognition Of Peptides By Modular Self-Assembled Receptors, Joseph Reczek, Aimee Kennedy, Brian Halbert, Adam Urbach

Adam R Urbach

Developing nontraditional approaches to the synthesis and characterization of multivalent compounds is critical to our efforts to study and interface with biological systems and to build new noncovalent materials. This paper demonstrates a biomimetic approach to the construction of discrete, modular, multivalent receptors via molecular self-assembly in aqueous solution. Scaffolds presenting 1−3 viologen groups recruit a respective 1−3 copies of the synthetic host, cucurbit[8]uril, in a noncooperative manner and with a consistent equilibrium association constant (Ka) value of 2 × 106 M−1 per binding site. The assembled mono-, di-, and trivalent receptors bind to their cognate target peptides containing 1−3 …

Solid-Phase Synthesis Of Peptide−Viologen Conjugates, Joseph Reczek, Elisa Rebolini, Adam Urbach

Adam R Urbach

This paper presents a robust method for the conjugation of viologens to peptides using an amide coupling strategy that is compatible with standard Fmoc solid-phase peptide synthesis. Methodology is presented for monitoring the milligram scale process quantitatively by UV spectroscopy. This chemistry enables the synthesis of a broad range of asymmetric viologens in high yield at room temperature and is compatible with a wide range of functional groups, including amine, guanidinyl, thiol, carboxylic acid, phenol, and indole.

Sequence-Specific Inhibition Of A Nonspecific Protease, Leigh Logsdon, Adam Urbach

Adam R Urbach

A nonspecific exopeptidase, aminopeptidase N (APN), is inhibited sequence-specifically by a synthetic host, cucurbit[7]uril (Q7), which binds with high affinity and specificity to N-terminal phenylalanine (Phe) and 4-(aminomethyl)phenylalanine (AMPhe) and prevents their removal from the peptide. Liquid chromatography experiments demonstrated that in the presence of excess Q7, APN quantitatively converts the pentapeptides Thr-Gly-Ala-X-Met into the dipeptides X-Met (X = Phe, AMPhe). The resulting Q7-bound products are completely stable to proteolytic digestion for at least 24 h. Structure–activity studies revealed a direct correlation between the extent of protection of an N-terminal amino acid and its affinity for Q7. Therefore, Q7 provides …

Effects Of Sequence Context On The Binding Of Tryptophan-Containing Peptides By The Cucurbit[8]Uril-Methyl Viologen Complex, Omar Ali, Eric Olson, Adam Urbach

Adam R Urbach

This paper describes a novel assay for measuring the relative extent of peptide binding in a large parallel format and the use of this assay to explore the effects of sequence context on the binding of tryptophan (Trp)-containing peptides by the synthetic receptor comprising the noncovalent complex between cucurbit[8]uril and methyl viologen (i.e. Q8√MV). The extent of quenching of Trp fluorescence upon binding to Q8√MV was used to measure the relative extent of binding and thus the relative affinities of 104 Trp-containing peptides, in parallel, using a fluorescence plate reader. This study resulted in the remarkable observation that the identity …