Other Chemistry Commons^™

Nmr Metabolomics Protocols For Drug Discovery, Fatema Bhinderwala, Robert Powers

Chemistry Department: Faculty Publications

Drug discovery is an extremely difficult and challenging endeavor with a very high failure rate. The task of identifying a drug that is safe, selective and effective is a daunting proposition because disease biology is complex and highly variable across patients. Metabolomics enables the discovery of disease biomarkers, which provides insights into the molecular and metabolic basis of disease and may be used to assess treatment prognosis and outcome. In this regard, metabolomics has evolved to become an important component of the drug discovery process to resolve efficacy and toxicity issues, and as a tool for precision medicine. A detailed …

Reversible Mechanical Deformations Of Soft Microchannel Networks For Sensing In Soft Robotic Systems, Abhiteja Konda, Donghee Lee, Taesun You, Xiaoyan Wang, Sangjin Ryu, Stephen Morin

Chemistry Department: Faculty Publications

Microfluidics has enabled numerous applications in, for example, analytical chemistry, medical diagnostics, microelectronics, and soft robotics. In most of these applications, the geometries of the microchannels are of fixed dimensions that (ideally) remain invariant during operation. In soft robotics, however, the geometries of the microchannels contained in soft actuation systems are inherently dynamic, and the specific dimensions are expected to change during operation, and, by extension, the fluid transport properties of the system are variable. If this characteristic is not properly considered, or if methods are not developed to control it, the progress of soft robotic devices with distributed fluid …

Design Of Single-Molecule Multiferroics For Efficient Ultrahigh-Density Nonvolatile Memories, Qing Yang, Tingting Zhong, Zhengyuan Tu, Lin Zhu, Menghao Wu, Xiao Cheng Zeng

Chemistry Department: Faculty Publications

It is known that an isolated single-molecule magnet tends to become super- paramagnetic even at an ultralow temperature of a few Kelvin due to the low spin switching barrier. Herein, single-molecule ferroelectrics/multiferroics is proposed, as the ultimate size limit of memory, such that every molecule can store 1 bit data. The primary strategy is to identify polar molecules that possess bistable states, moderate switching barriers, and polarizations fixed along the vertical direction for high-density perpendicular recording. First- principles computation shows that several selected magnetic metal porphyrin molecules possess buckled structures with switchable vertical polarizations that are robust at ambient conditions. …

Growth Of Carbon Dioxide Whiskers, Avinash Kumar Both, Chin Li Cheung

Chemistry Department: Faculty Publications

We report the growth of carbon dioxide (CO₂) whiskers at low temperatures (–70 °C to –65 °C) and moderate pressure (4.4 to 1.0 bar). Their axial growth was assessed by optical video analysis. The identities of these whiskers were confirmed as CO₂ solids by Raman spectroscopy. A vapor– solid growth mechanism was proposed based on the influence of the relative humidity on the growth.

Magnetic Exploration Of The Crescent Formation, Washington: The Search For A Hidden Fault Near Dusk Point, Samuel G. Furmanski

Summer Research

The mafic rocks of the Olympic Peninsula, Washington, are part of an accreted terrane known as Siletzia which experienced transpressional stresses as far as 50 Ma ago in the early Eocene. The Peninsula has an accretion-thrust marine sedimentary interior and a mafic volcanic periphery juxtaposed along the Hurricane Ridge fault; a terrane-scale thrust fault. The mafic Crescent Formation (CF) can be subdivided into two units: The Lower Crescent member (LC) and the Upper Crescent member (UC) as defined by Tabor and Cady (1978). The LC consists of submarine basalt flows that have composition similar to mid-oceanic ridges with zircon fission-track …

Urease Is An Essential Component Of The Acid Response Network Of Staphylococcus Aureus And Is Required For A Persistent Murine Kidney Infection, Chunyi Zhou, Fatema Bhinderwala, Mckenzie K. Lehman, Vinai C. Thomas, Sujata S. Chaudhari, Kelsey J. Yamada, Kirk W. Foster, Robert Powers, Tammy Kielian, Paul D. Fey

Chemistry Department: Faculty Publications

Staphylococcus aureus causes acute and chronic infections resulting in significant morbidity. Urease, an enzyme that generates NH₃ and CO₂ from urea, is key to pH homeostasis in bacterial pathogens under acidic stress and nitrogen limitation. However, the function of urease in S. aureus niche colonization and nitrogen metabolism has not been extensively studied. We discovered that urease is essential for pH homeostasis and viability in urea-rich environments under weak acid stress. The regulation of urease transcription by CcpA, Agr, and CodY was identified in this study, implying a complex network that controls urease expression in response to changes …

Electrocaloric Effect In Ferroelectric Ceramics With Point Defects, Ming Wu, Qingshan Zhu, Jianting Li, Dongsheng Song, Honghui Wu, Mengyao Guo, Jinghui Gao, Yang Bai, Yujun Feng, Stephen J. Pennycoock, Xiaojie Lou

Chemistry Department: Faculty Publications

The electrocaloric effect has drawn much attention due to its potential application in cooling devices. A negative electrocaloric effect is predicted to be induced in defect-doped ferroelectrics by computational results [A. Grunebohm and T. Nishimatsu, Phys. Rev. B 93, 134101 (2016) and Ma et al., Phys. Rev. B 94, 094113 (2016)], but it need to be confirmed by experimental results. In this work, we prepared a 1mol. % Mn-doped Pb(Zr_0.2,Ti_0.8)O₃ ceramics (Pb((Zr_0.2,Ti_0.8)_0.99,Mn_0.01)O₃), and the electrocaloric effect of the defect-containing ferroelectric ceramics has …

Molecular Memory With Downstream Logic Processing Exemplified By Switchable And Self-Indicating Guest Capture And Release, Brian Daly, Thomas S. Moody, Allen J.M. Huxely, Chaoyi Yao, Benjamin Schazmann, Andre Alves-Areias, John F. Malone, H.Q. Nimal Gunaratne, Peter Nockemann, A. Prasanna De Silva

Articles

Molecular-logic based computation (MLBC) has grown by accumulating many examples of combinational logic gates and a few sequential variants. In spite of many inspirations being available in biology, there are virtually no examples of MLBC in chemistry where sequential and combinational operations are integrated. Here we report a simple alcohol-ketone redox interconversion which switches a macrocycle between a large or small cavity, with erect aromatic walls which create a deep hydrophobic space or with collapsed walls respectively. Small aromatic guests can be captured or released in an all or none manner upon chemical command. During capture, the fluorescence of the …

Highly Selective Fluorimetric Turn-Off Detection Of Copper (Ii) By Two Different Mechanisms In Calix[4]Arene-Based Chemosensors And Chemodosimeters, Justine O'Sullivan, John Colleran, Brendan Twamley, Frances Heaney

Articles

Isoxazolo‐pyrene tethered calix[4]arenes selectively detect copper(II) ions without interference from related perchlorate ions. The fluorescence emission of the probes, synthesised by nitrile oxide alkyne cycloaddition, and characterised by spectroscopic and crystallographic data, is rapidly reduced by Cu(II) ions. Detection limits are in the micromolar or sub‐micromolar range (0.3–3.6 μM) based on a 1 : 1 sensor:analyte interaction. Voltammetric behaviour and 1H NMR data provide new insights into the sensing mechanism which is dependent on the calixarene substitution pattern. When the calixarene lower rim is fully substituted, Cu(II) detection occurs through a traditional chelation mechanism. In contrast, for calixarenes 1,3‐disubstituted on …

First Generation Amperometric Biosensing Of Galactose With Xerogel-Carbon Nanotube Layer-By-Layer Assemblies, Najwa Labban, Mulugeta B. Wayu, Ciara M. Steele, Tess S. Munoz, Julie A. Pollock, William S. Case, Michael C. Leopold

Chemistry Faculty Publications

A first-generation amperometric galactose biosensor has been systematically developed utilizing layer-by-layer (LbL) construction of xerogels, polymers, and carbon nanotubes toward a greater fundamental understanding of sensor design with these materials and the potential development of a more efficient galactosemia diagnostic tool for clinical application. The effect of several parameters (xerogel silane precursor, buffer pH, enzyme concentration, drying time and the inclusion of a polyurethane (PU) outer layer) on galactose sensitivity were investigated with the critical nature of xerogel selection being demonstrated. Xerogels formed from silanes with medium, aliphatic side chains were shown to exhibit significant enhancements in sensitivity with the …

Role Of Water On The Rotational Dynamics Of The Organic Methylammonium Cation: A First Principles Analysis, Ross D. Hoehn, Joseph S. Francisco, Sabre Kais, Ali Kachmar

Chemistry Department: Faculty Publications

Understanding the degradation mechanisms of lead-halide perovskites (CH₃NH₃PbI₃) under exposure to liquid/aerosol water is an essential problem within the photovoltaic community. Herein we investigate both the static and the dynamic properties of the methylammonuim cation (MA) as it coordinates with invading water molecules (MA.(H₂O)_n, n = 1, 2, 3, 4) using both stationary state quantum mechanics and first principle molecular dynamics simulations. Various solvation structures of MA were characterized by their stabilization energies, dipoles, and Maximally-Localized Wannier Function (MLWF) centers. Calculation – and analysis – of vibrational shifts in the …

The Inductive Effect In Organic Chemistry, Charles A. Kingsbury

Chemistry Department: Faculty Publications

The subtle difference between the successive polarization model and the flow of electrons through sigma bonds is explored, as well as the alternating charge model of Pople and the pervasive field model. The present paper is concerned with the ability of alkyl groups to serve as sigma inductive electron donors.

Catalytic Mechanism Of Amyloid-Β Peptide Degradation By Insulin Degrading Enzyme: Insights From Qm/Mm Mp2 Calculation, Rui Lai, Wei-Jen Tang, Hui Li

Chemistry Department: Faculty Publications

Insulin degrading enzyme (IDE), a metalloprotease that degrades amyloid-β (Aβ) peptides and insulin, is associated with Alzheimer’s disease and diabetes. The mechanism of IDE catalyzed degrading of Aβ peptides, which is of fundamental importance in the design of therapeutic methods for Alzheimer’s disease, has not been fully understood. In this work, combined quantum mechanics and molecular mechanics (QM/MM) style Møller-Plesset second order perturbation theory (MP2) geometry optimization calculations are performed to investigate the catalytic mechanism of the Aβ40 Phe19-Phe20 peptide bond cleavage by human IDE. The analyses using QM/MM MP2 optimization suggest that a …

In-Situ-Investigation Of Enzyme Immobilization On Polymer Brushes, Meike Koenig, Ulla König, Klaus-Jochen Eichhorn, Martin Muller, Manfred Stamm, Petra Uhlmann

Chemistry Department: Faculty Publications

Herein, we report on the use of a combined setup of quartz-crystal microbalance, with dissipation monitoring and spectroscopic ellipsometry, to comprehensively investigate the covalent immobilization of an enzyme to a polymer layer. All steps of the covalent reaction of the model enzyme glucose oxidase with the poly(acrylic acid) brush by carbodiimide chemistry, were monitored in-situ. Data were analyzed using optical and viscoelastic modeling. A nearly complete collapse of the polymer chains was found upon activation of the carboxylic acid groups with N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide and N-Hydroxysuccinimide. The reaction with the amine groups of the enzyme occurs simultaneously with re-hydration of the …

Insights Into Gemcitabine Resistance And The Potential For Therapeutic Monitoring, Teklab Gebregiworgis, Fatema Bhinderwala, Vinee Purohit, Nina V. Chaika, Pankaj K. Singh, Robert Powers

Chemistry Department: Faculty Publications

Introduction—Gemcitabine is an important component of pancreatic cancer clinical management. Unfortunately, acquired gemcitabine resistance is widespread and there are limitations to predicting and monitoring therapeutic outcomes.

Objective—To investigate the potential of metabolomics to differentiate pancreatic cancer cells that develops resistance or respond to gemcitabine treatment.

Results—We applied 1D ¹H and 2D ¹H-¹³C HSQC NMR methods to profile the metabolic signature of pancreatic cancer cells. ¹³C₆-glucose labeling identified thirty key metabolites uniquely altered between wild-type and gemcitabine-resistant cells upon gemcitabine treatment. Gemcitabine resistance was observed to reprogram glucose metabolism and to enhance the pyrimidine …

Electro- And Photocatalytic Carbon Dioxide Reduction And Thermal Isomerization Of Highly Strained Tricyclocompounds, Weiwei Yang

Electronic Theses and Dissertations

Anthracene-bridged dinuclear rhenium complexes are reported for electrocatalytic and photocatalytic carbon dioxide (CO2) reduction to carbon monoxide (CO). Related by hindered rotation of each rhenium active site to either side of the anthracene bridge cis and trans conformers have been isolated and characterized. Electrochemical studies reveal distinct mechanisms whereby the cis conformer operates via cooperative bimetallic CO2 activation and conversion and the trans conformer reduces CO2 through well-established single-site and bimolecular pathways analogous to Re(bpy)(CO)3Cl. Higher turnover frequencies are observed for the cis conformer (35.3 s−1) relative to the trans conformer (22.9 s−1) with both outperforming Re(bpy)(CO)3Cl (11.1 s−1). Photocatalytic …

Probing Atypical Noncovalent Interactions Using Electronic Structure Theory, Katelyn Mae Dreux

Electronic Theses and Dissertations

Some of the most important topics in modern chemistry involve noncovalent interactions in a variety of ways, from pharmacological processes to materials design. Due to the comparatively weak nature of these interactions, they can be difficult to investigate experimentally. Beyond what might be considered the ‘typical’ noncovalent interactions such as hydrogen bonding or London dispersion, there are less well known noncovalent interactions such as coordinate covalent, dihydrogen, and nonconventional hydrogen bonding, which have been the focus of much of this research. Through the use of electronic structure theory, fundamental information about the structure, energetics, and molecular properties of noncovalently bound …

Characterization Of Hydrogen Bonding, Halogen Bonding And Argyrophilic Interactions Using Computational Modeling, Sarah Nicole Arradondo

Electronic Theses and Dissertations

Non-covalent interactions govern multiple important chemical processes throughout nature from those within the human body to the complex environment of the atmosphere. Quantum mechanical electronic structure modeling of these relatively weak interactions can provide molecular level insight that can further our understanding of specific macroscopic properties. In the present work different non-covalent interactions are computationally evaluated within four systems. A small prototypical hydrogen bonded system and the various structural motifs that promoted proton transfer within concentrated acid and water clusters are characterized with sophisticated wavefunction based methods and large robust basis sets in order to accurately predict the structures energies …

Indole Reverses Intrinsic Antibiotic Resistance By Activating A Novel Dual-Function Importer, Yan Wang, Tian Tian, Jingjing Zhang, Xin Jin, Huan Yue, Xiao-Hua Zhang, Liangcheng Du, Fan Bai

Chemistry Department: Faculty Publications

Bacterial antibiotic resistance modulation by small signaling molecules is an emerging mechanism that has been increasingly reported in recent years. Several studies indicate that indole, an interkingdom signaling molecule, increases bacterial antibiotic resistance. However, the mechanism through which indole reduces antibiotic resistance is largely unknown. In this study, we demonstrated a novel mechanism for indole-mediated reversal of intrinsic antibiotic resistance in Lysobacter. This reversal was facilitated by a novel BtuD-associated dual-function importer that can transfer both vitamin B₁₂ and antibiotics. Indole stimulated btuD overexpression and promoted efficient absorption of extracellular vitamin B₁₂; meanwhile, the weak selectivity …

Structural Basis Of 7sk Rna 5′ Γ-Phosphate Methylation And Retention By Mepce, Yuan Yang, Catherine D. Eichhorn, Yaqiang Wang, Duilio Cascio, Juli Feigon

Chemistry Department: Faculty Publications

Among RNA 5′-cap structures, γ-phosphate monomethylation is unique to a small subset of noncoding RNAs, 7SK and U6 in humans. 7SK is capped by methylphosphate capping enzyme (MePCE), which has a second non-enzymatic role as a core component of the 7SK RNP that is an essential regulator of RNA transcription. We report 2.0 and 2.1 Å X-ray crystal structures of human MePCE methyltransferase domain bound to S-adenosylhomocysteine (SAH) and uncapped or capped 7SK substrates, respectively. 7SK recognition is achieved by protein contacts to a 5′ hairpin-single-stranded RNA region, explaining MePCE specificity for 7SK and U6. The structures reveal SAH and …

Spheroid-3d And Monolayer-2d Intestinal Electrochemical Biosensor For Toxicity/Viability Testing: Applications In Drug Screening, Food Safety, And Environmental Pollutant Analysis, Evangelia Flampouri, Shahzad Imar, Kieran O'Connell, Baljit Singh

Articles

The rise of three-dimensional cell culture systems that provide in vivo-like environments for pharmaco-toxicological models has prompted the need for simple and robust viability assays suitable for complex cell architectural structures. This study addresses that challenge with the development of an in vitro enzyme based electrochemical sensor for viability/cytotoxicity assessment of two-dimensional (2D) monolayer and three-dimensional (3D) spheroid culture formats. The biosensor measures the cell viability/toxicity via electrochemical monitoring of the enzymatic activity of nonspecific esterases of viable cells, through the hydrolysis of 1-naphthyl acetate to 1-naphthol. The proposed sensor demonstrated strong correlation (r = 0.979) with viable …

Photoluminescent Zirconium Complexes For Visible Light Photoredox Catalysis, Yu Zhang

Graduate Theses, Dissertations, and Problem Reports

Early transition metals like zirconium are attractive candidates for the design of luminescent molecules based on earth-abundant elements. Here, a series of zirconium complexes carrying two pyrrolyl-based ligands have been synthesized and characterized. These complexes are photoluminescent upon excitation with visible light and exhibit remarkably long emission lifetimes of hundreds of μs in solution at room temperature. Computational studies using time-dependent density functional theory (TD-DFT) were conducted to identify the nature of the luminescent excited states as mixed intra-ligand/ligand-to-metal charge-transfer (ILCT/LMCT) states. The electrochemistry studies revealed multiple reversible redox events for each zirconium complex. Furthermore, the excited state of the …

Chemical Kinetics Using A Smartphone Spectrometer, Mary Greggila

Williams Honors College, Honors Research Projects

In a time where many high school science classes are lacking in quality laboratory education, there is a need for accessible chemical equipment that enhance teaching fundamental concepts of chemistry with ease and at a low cost. The DualSpec handheld smartphone spectrometer aims to be a quality open-source spectroscopic instrument that can easily be made and used at home by people of any scientific level. This research sought to show that the DualSpec could be used to teach higher level spectroscopic concepts such as those used in chemical kinetics. The DualSpec was compared to a commercial spectrometer using the commonly …

Characterization Of Ambient Aerosols And Their Evolution Under Various Atmospheric Conditions In The Northeast U.S, Jie Zhang

Legacy Theses & Dissertations (2009 - 2024)

The University at Albany Atmospheric Sciences Research Center (ASRC) mobile laboratory, which includes a High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS), a Scanning Mobility Particle Sizer (SMPS), and several gas sensors, etc., has been used to characterize atmospheric aerosols and air quality at different locations in the Northeastern US (including urban, forest, and mountain areas) and the aerosol evolutions under a variety of atmospheric conditions (including extreme weather, fog, and cloud, etc.). In this dissertation, I present the findings of the several field measurements using the ASRC mobile lab, focusing on the influences of extreme events (including high O3, heatwave, …

Near-Infrared Fluorescent Probes For Sensitive Determination Of Lysosomal & Mitochondrial Ph In Live Cells, Wafa Mazi

Dissertations, Master's Theses and Master's Reports

Varied intracellular pH levels are critical for various physiological processes such as enzymatic activity, cell proliferation and apoptosis, ion transport, and muscle contraction. Cellular compartments, like lysosomes, must retain an acidic environment (pH ~ 4.5) to activate hydrolytic enzymes necessary for the breakdown of large biomolecules. Another cellular organelle, the mitochondria, provides the cell with energy and must retain an alkalis environment (pH ~ 8.0) for proper function. Substantial lysosomal and mitochondrial pH deviation is associated with cellular dysfunction and disease. Therefore, the precise detection of lysosomal and mitochondrial pH is essential to provide a better understanding of cellular physiological …

Characterization Of The Microbial Phosphonate-Activating Pntc Enzymes, Kyle Rice

Theses and Dissertations (Comprehensive)

New strategies are urgently needed to combat infectious diseases in an era of rising antibiotic resistance. Furthermore, an emerging appreciation for the human microbiome’s role in maintaining health motivates discovery of species-specific antibiotics that minimally disrupt our native bacterial communities. Small molecule modifications to bacterial cell surfaces represent a potentially rich source of new targets for next generation antibiotics, as these molecules mediate virulence and evasion of the host immune response. Phosphocholine (PCho) is a rare cell surface modification that contributes to virulence, and modifications with phosphonates like 2-aminoethylphosphonate (AEP) are even more unusual and therefore provide opportunities for species- …

Identification Of Burnt Smokeless Gunpowders Through Physical Characteristics, Cameron Taylor Hartwig

Graduate Theses, Dissertations, and Problem Reports

Firearms are one of the most commonly used weapons by violent criminals throughout the United States. In crimes involving the discharge of a firearm, residues from the combustion products are deposited on the shooter and in the firing direction. Some of the residues left behind are unburnt and partially burnt particles of the propellant. The most common propellant used in modern firearms is smokeless powder. The identification of particles as smokeless powder and the determination of the brand of the powder are two ways a forensic examiner may be able to utilize smokeless powder evidence. The determination of the brand …