Biochemistry, Biophysics, and Structural Biology Commons^™

Sharing The Salt Bowl: Counterion Identity Drives N-Alkyl Resorcinarene Affinity For Pyrophosphate In Water, Kwaku Twum, Seyed Iraj Sadraei, Jordan Feder, S. Maryamdokht Taimoory, Kari Rissanen, John F. Trant, Ngong Kodiah Beyeh

Chemistry and Biochemistry Publications

N-Alkyl ammonium resorcinarene chloride receptors, NARX4, have been shown to act as high-sensitivity detectors of pyrophosphate (PPi), a biomarker of disease, in aqueous media through the chloride-to-PPi exchange [NAR(Cl)4 to NARPPi]. The nature of the anion of the macrocyclic NARX4 (X = Cl−, Br−, triflate OTf−) receptor greatly influences the PPi-affinity in aqueous media. The binding affinity for [NAR (Cl)4] is 3.61 × 105 M−1, while the NAR (Br)4 and NAR (OTf)4 show stronger binding of 5.30 × 105 M−1, and 6.10 × 105 M−1, respectively. The effects of upper rim ammonium cation, –N+H2R substituents (R = 3-hydroxypropyl, cyclohexyl, …

Reaction Of Alkynyl- And Alkenyltrifluoroborates With Propargyldicobalt Cations: Alkynylation, Alkenylation, And Cyclopropanation Product Pathways, Brent St Onge, S. Maryamdokht Taimoory, Jeffrey Battersby, John F. Trant, James R. Green

Chemistry and Biochemistry Publications

The Lewis acid-mediated Nicholas reactions of propargyl acetate–Co2(CO)6 complexes with a series of potassium alkynyltrifluoroborates and potassium alkenyltrifluoroborates are described. Alkynyltrifluoroborates directly alkynylate the intermediate propargyldicobalt cations. In contrast, alkenyltrifluoroborates proceed through one of the three modes of dominant reactivity: C-2-substituted alkenyltrifluorobrates directly alkenylate, predominantly with the retention of stereochemistry. C-1-substituted alkenyltrifluoroborates alkenylate at C-2. Potassium vinyltrifluoroborate incorporates a cyclopropane at the site propargyl to alkynedicobalt. Computational analysis of these systems explains the differential modes of reactivity of alkenyltrifluoroborates and outlines the probable mechanisms for the formation of each product.

Protocol For Fabricating Electroless Nickel Immersion Gold Strain Sensors On Nitrile Butadiene Rubber Gloves For Wearable Electronics, Sara S. Mechael, Yunyun Wu, Yiting Chen, Tricia Breen Carmichael

Chemistry and Biochemistry Publications

This protocol describes the fabrication of patterned conductive gold films on nitrile butadiene rubber (NBR) gloves for wearable strain sensors using electroless nickel immersion gold (ENIG) plating, a solution-based metallization technique. The resulting NBR/ENIG films are strain sensitive; resistance measurements of a patterned sensing array can be used to map human hand motions. This protocol also describes challenges related to the ENIG process and troubleshooting steps to achieve conformal gold films for strain sensing over a large working range. For complete details on the use and execution of this protocol, please refer to Mechael et al. (2021).

Synergistic Broad-Spectrum Antibacterial Activity Of Hypoxis Hemerocallidea-Derived Silver Nanoparticles And Streptomycin Against Respiratory Pathobionts, Oluwole S. Aremu, T. Qwebani-Ogunleye, Lebogang Katata-Seru, Zimbili Mkhize, John F. Trant

Chemistry and Biochemistry Publications

Respiratory tract infections arise due to the introduction of microbes into the airway, disrupting the normal, healthy, complex interdependent microbiome. The selective disruption of this community can be either beneficial or dangerous. Nanoparticles are a potential tool for modifying this population. Coated silver nanoparticles (AgNPs) were synthesized using ethanolic extracts of Hypoxis hemerocallidea (EEHH), a Southern African plant used extensively in traditional medicine and the source of many bioactive secondary metabolites. The room temperature reaction between silver nitrate and EEHH forms largely spherical AgNPs with an average diameter of 6–20 nm. These nanoparticles show similar levels of antibacterial activity as …

New Isolate From Salvinia Molesta With Antioxidant And Urease Inhibitory Activity, Nadra Naheed, Saima Maher, Farooq Saleem, Ajmal Khan, Abdul Wadood, Saima Rasheed, M. Iqbal Choudhary, Matheus Froeyen, Iskandar Abdullah, Muhammad Usman Mirza, John F. Trant, Sarfraz Ahmad

Chemistry and Biochemistry Publications

Urease plays a significant role in the pathogenesis of urolithiasis pyelonephritis, urinary catheter encrustation, hepatic coma, hepatic encephalopathy, and peptic acid duodenal ulcers. Salvinia molesta was explored to identify new bioactive compounds with particular emphasis on urease inhibitors. The aqueous methanol extract was fractionated using solvents of increasing polarity. A series of column chromatography and later HPLC were performed on butanol extract. The structures of the resulting pure compounds were resolved using NMR (1D and 2D), infrared, and mass spectroscopy. The novel isolate was evaluated for antioxidant activity (using DPPH, superoxide anion radical scavenging, oxidative burst, and Fe+2 chelation assays), …

From Fat To Bilayers: Understanding Where And How Vitamin E Works, Jeffrey Atkinson, Drew Marquardt, Mitchell Dipasquale, Thad Harroun

Chemistry and Biochemistry Publications

Vitamin E was one of the last fat-soluble vitamins to be discovered. We provide here an historical review of the discovery and the increasingly more detailed understanding of the role of α-tocopherol both as an antioxidant and as a structural component of phospholipid bilayer membranes. Despite the detailed descriptions now available of the orientation, location, and dynamics of α-tocopherol in lipid bilayers, there are still gaps in our knowledge of the effect of α-tocopherol and its potential receptors than control gene transcription.

Efficient And Reproducible Synthesis Of An Fmoc-Protected Tn Antigen, Sabrina M. Piazza, Michael R. Reynolds, Jonathan Chiaramonte, Peihan Xu, Fabiola A. Chapa-Villarreal, John F. Trant

Chemistry and Biochemistry Publications

This concise total synthesis of the Thomsen-Nouveau (Tn) glycoconjugate was accomplished using a palladium-catalyzed coupling between the glycosyl donor and Fmoc-protected serine acceptor. This is, to the best of our knowledge, the shortest synthesis reported from galactose for preparing this essential building block for large-scale solid phase peptide synthesis.

A Calorimetric, Volumetric And Combined Sans And Saxs Study Of Hybrid Siloxane Phosphocholine Bilayers, Mark B. Frampton, Doruntina Yakoub, John Katsaras, Paul M. Zelisko, Drew Marquardt

Chemistry and Biochemistry Publications

Siloxanes are molecules used extensively in commercial, industrial, and biomedical applications. The inclusion of short siloxane chains into phospholipids results in interesting physical properties, including the ability to form low polydispersity unilamellar vesicles. As such, hybrid siloxane phosphocholines (SiPCs) have been examined as a potential platform for the delivery of therapeutic agents. Using small angle X-ray and neutron scattering, vibrating tube densitometry, and differential scanning calorimetry, we studied four hybrid SiPCs bilayers. Lipid volume measurements for the different SiPCs compared well with those previously determined for polyunsaturated PCs. Furthermore, the different SiPC's membrane thicknesses increased monotonically with temperature and, for …

Accident Experiences And Reporting Practices In Canadian Chemistry And Biochemistry Labs: A Pilot Investigation, Dana Ménard, John F. Trant

Chemistry and Biochemistry Publications

Accidents in chemistry and biochemistry laboratories are a regular occurrence and have been associated with injuries, property damage, and deaths. However, despite a high prevalence rate of accident involvement reported in previous investigations of academic lab personnel (approximately 30%), little is known about the context in which academic lab accidents occur. Previous findings also suggest a high degree of accident underreporting (25–40%), but again, little is known about this phenomenon. Pilot data was gathered from a convenience sample of 104 students and postdoctoral fellows in chemistry-related fields through an online survey. Results showed a high level of accident involvement (56.7%); …

Fabrication Of An Autonomously Self-Healing Flexible Thin-Film Capacitor By Slot-Die Coating, Susanna Vu, Gnanesh Nagesh, Nastaran Yousefi, John F. Trant, David S.K. Ting, M. Jalal Ahamed, Simon Rondeau-Gagné

Chemistry and Biochemistry Publications

Flexible pressure sensors with self-healing abilities for wearable electronics are being developed, but generally either lack autonomous self-healing properties or require sophisticated material processing methods. To address this challenge, we developed flexible, low-cost and autonomously self-healing capacitive sensors using a crosslinked poly(dimethylsiloxane) through metal-ligand interactions processed into thin films via slot-die coating. These films have excellent self-healing properties, approximately 1.34 × 105 μm3 per hour at room temperature and 2.87 × 105 μm3 per hour at body temperature (37 °C). Similarly, no significant change in capacitance under bending strain was observed on these flexible thin-films when assembled on poly(ethyleneterephthalate) (PET) …

Synthesis, Characterization And Stress-Testing Of A Robust Quillaja Saponin Stabilized Oil-In-Water Phytocannabinoid Nanoemulsion, Abhinandan Banerjee, Justin Binder, Rayan Salama, John F. Trant

Chemistry and Biochemistry Publications

Background

This study describes the design, optimization, and stress-testing of a novel phytocannabinoid nanoemulsion generated using high-pressure homogenization.QNaturale®" role="presentation">QNaturale®, a plant-derived commercial emulsifier containing quillaja saponin, was used to stabilize the lipid phase droplets in water. Stress-testing was performed on this nanoemulsion in order to evaluate its chemical and colloidal stability under the influence of different environmental factors, encompassing both physical and chemical stressors.

Methods

Extensive optimization studies were conducted to arrive at an ideal nanoemulsion formulation. A coarse emulsion containing 16.6 wt% CBD-enriched cannabis distillate and 83.4 wt% carrier (soybean) oil dispersed in 10 wt%QNaturale®" role="presentation">QNaturale®

(1.5 …

Catechin And Other Catechol-Containing Secondary Metabolites: Bacterial Biotransformation And Regulation Of Carbohydrate Metabolism, Sara Knezevic, Asma Ghafoor, Samaneh Mehri, Ali Barazi, Maksymilian Dziura, John F. Trant, Christopher A. Dieni

Chemistry and Biochemistry Publications

Background: Catechol, 1,2-dihydroxybenzene, prepared through bacterial biotransformation from higher order polyphenols, has been proposed to regulate carbohydrate metabolism, especially in the context of type 2 diabetes. This review aims to contextualize this finding. It describes the bacterial biosynthesis of catechol both from glucose, and as a degradation product of higher order natural products through bacterial transformation. The review then considers the mechanism of action of glycemic-regulating catechol-containing materials and the complications arising from balancing their inherent activity with that of catechol, their common degradation product. It then enumerates potential dietary sources of catechin from common foods. Methods: Articles were found …

Simulated Breathing: Application Of Molecular Dynamics Simulations To Pulmonary Lung Surfactant, Maksymilian Dziura, Basel Mansour, Mitchell Dipasquale, P. Charukeshi Chandrasekera, James W. Gauld, Drew Marquardt

Chemistry and Biochemistry Publications

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to …

Ready-To-Wear Strain Sensing Gloves For Human Motion Sensing, Sara S. Mechael, Yunyun Wu, Yiting Chen, Tricia Breen Carmichael

Chemistry and Biochemistry Publications

Integrating soft sensors with wearable platforms is critical for sensor-based human augmentation, yet the fabrication of wearable sensors integrated into ready-to-wear platforms remains underdeveloped. Disposable gloves are an ideal substrate for wearable sensors that map hand-specific gestures. Here, we use solution-based metallization to prepare resistive sensing arrays directly on off-the-shelf nitrile butadiene rubber (NBR) gloves. The NBR glove acts as the wearable platform while its surface roughness enhances the sensitivity of the overlying sensing array. The NBR sensors have a sheet resistance of 3.1 ± 0.6 Ω/sq and a large linear working range (two linear regions ≤70%). When stretched, the …

Fragment-Based In Silico Design Of Sars-Cov-2 Main Protease Inhibitors, Sarfraz Ahmad, Muhammad Usman Mirza, Lee Yean Kee, Mamoona Nazir, Noorsaadah Abd Rahman, John F. Trant, Iskandar Abdullah

Chemistry and Biochemistry Publications

3CLpro is essential for SARS-CoV-2 replication and infection; its inhibition using small molecules is a potential therapeutic strategy. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. All small molecules co-crystallized with SARS-CoV-2 3CLpro with structures deposited in the Protein Data Bank were used as inputs. Fragments sitting in the binding pocket (87) were grouped into eight geographical types. They were interactively coupled using various synthetically reasonable linkers to generate larger molecules with divalent binding modes taking advantage of two different fragments' interactions. In total, 1,251 compounds were proposed, and …

The 2021 Flexible And Printed Electronics Roadmap, Yvan Bonnassieux, Christoph J. Brabec, Yong Cao, Tricia Breen Carmichael, Michael L. Chabinyc, Kwang Ting Cheng, Gyoujin Cho, Anjung Chung, Corie L. Cobb, Andreas Distler, Hans Joachim Egelhaaf, Gerd Grau, Xiaojun Guo, Ghazaleh Haghiashtiani, Tsung Ching Huang, Muhammad M. Hussain, Benjamin Iniguez, Taik Min Lee, Ling Li, Yuguang Ma, Dongge Ma, Michael C. Mcalpine, Tse Nga Ng, Ronald Österbacka

Chemistry and Biochemistry Publications

This roadmap includes the perspectives and visions of leading researchers in the key areas of flexible and printable electronics. The covered topics are broadly organized by the device technologies (sections 1–9), fabrication techniques (sections 10–12), and design and modeling approaches (sections 13 and 14) essential to the future development of new applications leveraging flexible electronics (FE). The interdisciplinary nature of this field involves everything from fundamental scientific discoveries to engineering challenges; from design and synthesis of new materials via novel device design to modelling and digital manufacturing of integrated systems. As such, this roadmap aims to serve as a resource …

Conducting Materials As Building Blocks For Electronic Textiles, Anja Lund, Yunyun Wu, Benji Fenech-Salerno, Felice Torrisi, Tricia Breen Carmichael, Christian Müller

Chemistry and Biochemistry Publications

Abstract: To realize the full gamut of functions that are envisaged for electronic textiles (e-textiles) a range of semiconducting, conducting and electrochemically active materials are needed. This article will discuss how metals, conducting polymers, carbon nanotubes, and two-dimensional (2D) materials, including graphene and MXenes, can be used in concert to create e-textile materials, from fibers and yarns to patterned fabrics. Many of the most promising architectures utilize several classes of materials (e.g., elastic fibers composed of a conducting material and a stretchable polymer, or textile devices constructed with conducting polymers or 2D materials and metal electrodes). While an increasing number …

A Concise Synthesis Of A Methyl Ester 2-Resorcinarene: A Chair-Conformation Macrocycle, Michael R. Reynolds, Fraser S. Pick, John J. Hayward, John F. Trant

Chemistry and Biochemistry Publications

Anions are important hydrogen bond acceptors in a range of biological, chemical, environ-mental and medical molecular recognition processes. These interactions have been exploited for the design and synthesis of ditopic resorcinarenes as the hydrogen bond strength can be tuned through the modification of the substituent at the 2-position. However, many potentially useful compounds, especially those incorporating electron-withdrawing functionalities, have not been prepared due to the challenge of their synthesis: their incorporation slows resorcinarene formation that is accessed by electrophilic aromatic substitution. As part of our broader campaign to employ resorcinarenes as selective recognition elements, we need access to these specialized …

A Dft Study Of The Adsorption Of Deep Eutectic Solvents Onto Graphene And Defective Graphene Nanoflakes, Mehdi Shakourian-Fard, S. Maryamdokht Taimoory, Hamid Reza Ghenaatian, Ganesh Kamath, John F. Trant

Chemistry and Biochemistry Publications

The interaction of four deep choline chloride-derived eutectic solvents (DESs) with both graphene nanoflakes (GNF) and its defective double-vacancy and Stone–Wales forms (DV-GNF and SW-GNF), was evaluated using density functional theory (DFT). The presence of defects increases the adsorption energy of DESs, following the order DES∩DV-GNF > DES∩SW-GNF > DES∩GNF. Non-covalent interaction and energy decomposition analyses show that the interactions are noncovalent and dominated by dispersive forces. Furthermore, we find that the presence of aromatic moieties in the DESs increases the van der Waals interactions with the surfaces. These interactions decrease the HOMO-LUMO (Eg) energy gap of the surfaces and thus increase …

Carbon Dots For Specific “Off-On” Sensing Of Co2+ And Edta For In Vivo Bioimaging, Xiangping Wen, Guangming Wen, Wenyan Li, Zhonghua Zhao, Xine Duan, Wenjun Yan, John F. Trant, Yingqi Li

Chemistry and Biochemistry Publications

Fluorescent carbon dots (CDs) were hydrothermally synthesized from a mixture of frozen tofu, ethylenediamine and phosphoric acid in an efficient 64% yield. The resulting CDs exhibit good water solubility, low cytotoxicity, high stability, and excellent biocompatibility. The CDs selectively and sensitively detect Co2+ through fluorescent quenching with a detection limit of 58 nM. Fluorescence can be restored through the introduction of EDTA, and this phenomenon can be used to quantify EDTA in solution with a detection limit of 98 nM. As both analytes are detected by the same CD platform, this is an “off-on” fluorescence sensor for Co2+ and EDTA. …

The Biosynthesis Of The Cannabinoids, M. Nazir Tahir, Fred Shahbazi, Simon Rondeau-Gagne, John F. Trant

Chemistry and Biochemistry Publications

Cannabis has been integral to Eurasian civilization for millennia, but a century of prohibition has limited investigation. With spreading legalization, science is pivoting to study the pharmacopeia of the cannabinoids, and a thorough understanding of their biosynthesis is required to engineer strains with specific cannabinoid profiles. This review surveys the biosynthesis and biochemistry of cannabinoids. The pathways and the enzymes’ mechanisms of action are discussed as is the non-enzymatic decarboxylation of the cannabinoic acids. There are still many gaps in our knowledge about the biosynthesis of the cannabinoids, especially for the minor components, and this review highlights the tools and …

Not-So-Innocent Anions Determine The Mechanism Of Cationic Alkylators, S. Maryamdokht Taimoory, Vincenzo Alessandro Cataldo, Andreas Schäfer, John F. Trant, Ryan Guterman

Chemistry and Biochemistry Publications

Alkylating reagents based on thioimidazolium ionic liquids were synthesized and the influence of the anion on the alkylation reaction mechanism explored in detail using both experimental and computational methods. Thioimidazolium cations transfer alkyl substituents to nucleophiles, however the reaction rate was highly dependent on anion identity, demonstrating that the anion is not innocent in the mechanism. Detailed analysis of the computationally-derived potential energy surfaces associated with possible mechanisms indicated that this dependence arises from a combination of anion induced electronic, steric and coordinating effects, with highly nucleophilic anions catalyzing a 2-step process while highly non-nucleophilic, delocalized anions favor a 1-step …

Time-Resolved Sans Reveals Pore-Forming Peptides Cause Rapid Lipid Reorganization, Michael H.L. Nguyen, Mitchell Dipasquale, Brett W. Rickeard, Caesar G. Yip, Kaity N. Greco, Elizabeth G. Kelley, Drew Marquardt

Chemistry and Biochemistry Publications

Cells depend on proper lipid transport and their precise distribution for vital cellular function. Disruption of such lipid organization can be initiated by external agents to cause cell death. Here, we investigate two antimicrobial pore-forming peptides, alamethicin and melittin, and their influence on lipid intervesicular exchange and transverse lipid diffusion (i.e. flip-flop) in model lipid vesicles. Small angle neutron scattering (SANS) and a strategic contrast matching scheme show the mixing of two isotopically distinct dimyristoylphosphocholine (DMPC) vesicle populations is promoted upon the addition of high (1/40) and low (1/150, 1/1000) peptide-to-lipid (P/L) molar ratios. Parsing out the individual exchange and …

A Prototype Compact Accelerator-Based Neutron Source (Cans) For Canada, Robert Laxdal, Dalini D. Maharaj, Mina Abbaslou, Zin Tun, Daniel Banks, Alexander Gottberg, Marco Marchetto, Eduardo Rodriguez, Zahra Yamani, Helmut Fritzsche, Ronald Rogge, Ming Pan, Oliver Kester, Drew Marquardt

Chemistry and Biochemistry Publications

Canada's access to neutron beams for neutron scattering was significantly curtailed in 2018 with the closure of the National Research Universal (NRU) reactor in Chalk River, Ontario, Canada. New sources are needed for the long-term; otherwise, access will only become harder as the global supply shrinks. Compact Accelerator-based Neutron Sources (CANS) offer the possibility of an intense source of neutrons with a capital cost significantly lower than spallation sources. In this paper, we propose a CANS for Canada. The proposal is staged with the first stage offering a medium neutron flux, linear accelerator-based approach for neutron scattering that is also …