Chemistry Commons^™

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

Department of Chemistry: 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 …

Detailed Characterization Of The Solution Kinetics And Thermodynamics Of Biotin, Biocytin And Haba Binding To Avidin And Streptavidin, Roberto F. Delgadillo, Timothy C. Mueser, Kathia Zaleta-Rivera, Katie A. Carnes, Jose Gonzalez-Valdez, Lawrence J. Parkhurst

Department of Chemistry: Faculty Publications

The high affinity (K_D ~ 10⁻¹⁵ M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (10⁹ M^-1s^-1) but recent single molecule and surface binding studies indicate that they are slower than expected (10⁵ to 10⁷ M^-1s^-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic …

Diisopropylammonium Bromide Based Two-Dimensional Ferroelectric Monolayer Molecular Crystal With Large In-Plane Spontaneous Polarization, Liang Ma, Yinglu Jia, Stephen Ducharme, Jinlan Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

In light of their easy processing, light weight and mechanical flexibility, ferroelectric molecular crystal with large spontaneous polarization (P_s) is highly desired for many advanced applications. Herein, we report the first theoretical study of two-dimensional (2D) ferroelectric molecular crystals via ab initio calculations. Specifically, we show that diisopropylammonium bromide (DIPAB) based 2D ferroelectric monolayer molecular crystal with large in-plane P_s of ∼1.5 × 10⁻⁶ μC cm⁻¹ can be achieved by slicing the bulk DIPAB along a specific plane while keeping the space group unchanged. The important roles of hydrogen bonds are …

The Inductive Effect In Organic Chemistry, Charles A. Kingsbury

Department of Chemistry: 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.

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

Department of Chemistry: 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 …

In Situ Monitoring Of Linear Rgd-Peptide Bioconjugation With Nanoscale Polymer Brushes, Evmorfia Psarra, Ulla Konig, Martin Muller, Eva Bittrich, Klaus-Jochen Eichhorn, Petra B. Welzel, Manfred Stamm, Petra Uhlmann

Department of Chemistry: Faculty Publications

Bioinspired materials mimicking the native extracellular matrix environment are promising for biotechnological applications. Particularly, modular biosurface engineering based on the functionalization of stimuli-responsive polymer brushes with peptide sequences can be used for the development of smart surfaces with biomimetic cues. The key aspect of this study is the in situ monitoring and analytical verification of the biofunctionalization process on the basis of three complementary analytical techniques. In situ spectroscopic ellipsometry was used to quantify the amount of chemisorbed GRGDS at both the homopolymer poly(acrylic acid) (PAA) brush and the binary poly(N-isopropylacrylamide) (PNIPAAm)− PAA brushes, which was finally confirmed …

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

Department of Chemistry: 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 …

Molecular Insights Into Organic Particulate Formation, Manoj Kumar, Emily Burrell, Jason C. Hansen, Joseph S. Francisco

Department of Chemistry: Faculty Publications

Carboxylic acids have been detected in particles collected in various regions of the world. Here, we use experiments and Born–Oppenheimer molecular dynamics simulations to better understand the mechanism of particle formation from gas phase mixtures of formic acid (HCOOH), (CH₃)₃N, and water vapor. A flow reaction cell coupled to two scanning mobility particle sizers has been used to measure particle size, absolute number of particles and kinetics of particle formation. Experimental results show that the addition of (CH₃)₃N to a mixture of HCOOH and water vapor results in a dramatic increase in …

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

Department of Chemistry: 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 …

Development Of A Microcolumn One-Site Immunometric Assay For A Protein Biomarker: Analysis Of Alpha1-Acid Glycoprotein In Serum, Chenhua Zhang, Shae Lott, William Clarke, David S. Hage

Department of Chemistry: Faculty Publications

A one-site immunometric assay based on affinity microcolumns was developed for the analysis of alpha₁-acid glycoprotein (AGP) as a model protein biomarker. In this assay, a sample containing AGP was incubated with an excess amount of a labeled binding agent, such as fluorescein-labeled anti-AGP antibodies or F_ab fragments. The excess binding agent was removed by passing this mixture through a microcolumn that contained an immobilized form of AGP, while the signal was measured for the binding agent-AGP complex in the non-retained fraction. Theoretical and practical factors were both considered in selecting the concentration of labeled binding agent, …

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

Department of Chemistry: 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

Department of Chemistry: 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

Department of Chemistry: 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. …

Glycoform Analysis Of Alpha1-Acid Glycoprotein By Capillary Electrophoresis Using Electrophoretic Injection, Chenhua Zhang, William Clarke, David S. Hage

David Hage Publications

Human alpha₁-acid glycoprotein (AGP) is an acute phase glycoprotein that has a heterogeneous glycosylation pattern. This pattern can change in certain diseases, which has resulted in interest in using AGP glycoforms as potential biomarkers for these diseases. This report describes a method that uses capillary electrophoresis to characterize and analyze AGP glycoforms both in purified samples of AGP and in human serum. This method uses static and dynamic coatings of poly (ethylene oxide) that are applied to a silica capillary for separation of AGP glycoforms in the reversed-polarity mode of CE and in the presence of negligible electroosmotic …

Synthesis, Characterization, And Catalytic Activity Of Copper Palladium Oxide Solid Solutions., Gregory L. Christensen

Department of Chemistry: Dissertations, Theses, and Student Research

Cu_xPd_1-xO forms a homogeneous solid solution over the wide range of 0 ≤ x ≤ 0.725 in which compositional variation can be correlated with structural and chemical environmental changes. After a small lag at low Cu²⁺ concentrations, where the lattice cell parameters are pinned to that of the pure PdO structure, Cu_xPd_1-xO lattice parameters follow Vegard’s law in which the cell volume decreases linearly with x, indicating a homogenous solution in which Cu²⁺ randomly replaces the larger Pd²⁺ cation. The crystal structure also undergoes an increase in the c/a …

Global Minimum Search And Carbon Monoxide Binding Studies Of Novel Gold Nanoclusters, Navneet S. Khetrapal

Department of Chemistry: Dissertations, Theses, and Student Research

In bulk form, gold is a well-known noble metal. However, gold nanoparticles exhibit remarkable catalytic behavior towards various types of chemical reactions. These catalytic properties are highly dependent upon the size and shape and therefore knowledge of the geometries of these nanoparticles is of prime importance. The main goal of this dissertation is, therefore, going to be towards the elucidation of the structures of novel gold clusters using a combined experimental and theoretical approach and subsequent modeling to explore the binding of simple substrates like carbon monoxide with gold clusters. The theoretical method used to study the structural evolution of …

Mass Spectrometry And Nuclear Magnetic Resonance In The Chemometric Analysis Of Cellular Metabolism, Eli Riekeberg

Department of Chemistry: Dissertations, Theses, and Student Research

The development and awareness of Machine Learning and “big data” has led to a growing interest in applying these methods to bioanalytical research. Methods such as Mass Spectrometry (MS), and Nuclear Magnetic Resonance (NMR) can now obtain tens of thousands to millions of data points from a single sample, due to fundamental instrumental advances and ever-increasing resolution. Simple pairwise comparisons on datasets of this magnitude can obfuscate more complex underlying trends, and does a disservice to the richness of information contained within. This necessitates the need for multivariate approaches that can more fully take advantage of the complexity of these …

‘Cassette’-Ises (In Situ Enzymatic Screening) Identifies Complementary Chiral Scaffolds For Hydrolytic Kinetic Resolution Across A Range Of Epoxides, Sangeeta Dey, Douglas R. Powell, Chunhua Hu, David B. Berkowitz

Department of Chemistry: Faculty Publications

‘Cassette’-ISES (In Situ Enzymatic Screening) Identifies Complementary Chiral Scaffolds for Hydrolytic Kinetic Resolution Across a Range of Epoxides

A new ‘Cassette’-In Situ Enzymatic Screen (ISES) for combinatorial catalysis is introduced. This allows the experimentalist to obtain an information-rich readout, in real time, providing an estimate of the sense and magnitude of enantioselectivity across more than one substrate. In its first iteration, the screen identified Co^III-salen catalysts with β-pinene- and α-naphthylalanine-derived chiral scaffolds with broad, yet complementary, substrate specificities.

Guanidinium Compounds, Stephen Dimagno, Bao Hu

Department of Chemistry: Faculty Publications

The present application provides , inter alia , chemical com pounds useful as synthesis intermediates , said compounds comprising one or more guanidinium moieties and a hyper valent iodine atom . Methods for making these compounds are also provided.

Pre- And Post-Research Group Selection: Evolving Roles For Chemistry Librarians, Sarah Jeong, Kiyomi D. Deards

University of Nebraska-Lincoln Libraries: Presentations

Librarian consultations with research groups, flipped classroom exercises, active learning, and Just-In-Time instruction sessions are increasing at public and private doctoral granting universities at a time when many library staffs are shrinking. As the needs and points of contact with graduate students evolve it will be critical for the depth of knowledge and resources of chemistry librarians to be understood and shared both in-person and on-demand online. This presentation will outline the strategies used to meet the evolving needs of chemistry graduate students as they move from pre-research group selection into established research groups.

Radioiodinated Compounds, Stephen Dimagno, Bao Hu

Department of Chemistry: Faculty Publications

This disclosure relates to reagents and methods useful in the synthesis of aryl iodines ,for example , in the preparation of iodine labeled radiotracers . The reagents and methods provided herein may be used to access a broad range of compounds , including aromatic compounds , heteroaromatic compounds , amino acids , nucleotides , and synthetic com pounds .

Alkene Ozonolysis In The Academic Lab, Patrick Dussault

Organic Peroxides: Safety Issues

The following information is offered as a guide based upon our experience with application of ozone for organic oxidations and hydroperoxide synthesis. Please send suggestions, requests, or corrections to [email protected].

Introduction and leading references

Overview of ozonolysis: Mechanism, Substrate reactivity, Typical reaction conditions, Reaction monitoring, Reaction work-ups

Safety Issues

Acknowledgements:

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The following provides a brief introduction to the application of ozonolysis within academic labs. Ozonolysis remains among the most frequently used of methods for oxidative cleavage of alkenes. While best known as a means by which to introduce aldehydes and ketones, ozonolysis can also be used to generate other …

Safe Use Of Hydrogen Peroxide In The Organic Lab, Patrick Dussault

Organic Peroxides: Safety Issues

The article describes good practices for use of hydrogen peroxide (H₂O₂) in an organic lab setting. Major headings include:

Leading references; Toxicity; Physical properties; Chemical properties; Stability and incompatibilities; Confinement/pressure; and, References to accidents involving H₂O₂.

Working With Organic Peroxides In The Academic Lab, Patrick Dussault

Organic Peroxides: Safety Issues

ABSTRACT: The following is a brief introduction to peroxide safety from the viewpoint of a synthetic chemist. Major topics include: classes of organic peroxides; peroxide reactivity; hazard identification and minimization; reaction monitoring; and, hazards associated with auto-oxidation of peroxidizable solvents.

KEYWORDS: peroxide, hydroperoxide, hydroperoxyacetal, ozonide, perester, dihydroperoxide, monoperoxyacetal, active oxygen, peroxide strips, TLC indicator, self-accelerating decomposition, radical, exothermicity, transition metals.

CONTENTS: 1. Literature resources 2. Major classes of peroxides 3. Basis for peroxide reactivity 4. Determining reactivity and minimizing hazards a. Steps to take before an experiment b. Minimizing hazard during reactions c. Monitoring reactions d. Working with isolated peroxides …

Ultrafast Affinity Extraction And High-Performance Affinity Chromatography Applications For Measuring Free Drug Fractions: Interactions Of Sulfonylurea Drugs With Normal And Glycated Human Serum Albumin, Bao Yang

Department of Chemistry: Dissertations, Theses, and Student Research

Ultrafast affinity extraction was used with microcolumns containing human serum albumin (HSA) to measure the free fractions of several sulfonylurea drugs in the presence of solution-phase HSA and for the analysis of these drugs at therapeutic levels or determining their binding strengths with this protein. This approach was first used with normal HSA and the drugs glibenclamide, glipizide and glimepiride. This work used both one- and two-dimensional affinity systems based on HSA microcolumns. The first microcolumn was used to extract the free drug fractions in injected drug/protein mixtures. As the retained drug eluted from the first microcolumn, it was passed …

A High Throughput Approach For The Generation Of Orthogonally Interacting Protein Pairs, Justin Lawrie, Xi Song, Wei Niu, Jiantao Guo

Department of Chemistry: Faculty Publications

In contrast to the nearly error-free self-assembly of protein architectures in nature, artificial assembly of protein complexes with pre-defined structure and function in vitro is still challenging. To mimic nature’s strategy to construct pre-defined three-dimensional protein architectures, highly specific proteinprotein interacting pairs are needed. Here we report an effort to create an orthogonally interacting protein pair from its parental pair using a bacteria-based in vivo directed evolution strategy. This high throughput approach features a combination of a negative and a positive selection. The newly developed negative selection from this work was used to remove any protein mutants that retain effective …

Spermidine-Regulated Biosynthesis Of Heat-Stable Antifungal Factor (Hsaf) In Lysobacter Enzymogenes Oh11, Yuan Chen, Fengquan Liu, Liangcheng Du

Liangcheng Du Publications

Heat-Stable Antifungal Factor (HSAF) and its analogs are antifungal natural products produced by the biocontrol agent Lysobacter enzymogenes. The production of HSAF is greatly influenced by environmental stimuli and nutrients, but the underlying molecular mechanism is mostly unclear. Here, we found that HSAF production in L. enzymogenes OH11 is strictly controlled by spermidine, which is the most prevalent triamine in bacteria. When added into OH11 cultures, spermidine regulated the production of HSAF and analogs in a concentration-dependent manner. To verify the role of spermidine, we deleted LeSDC and LeADC genes, encoding S-adenosylmethionine decarboxylase and arginine decarboxylase, respectively, that are the …

Structural Evolution Of Gold-Doped Bismuth Clusters AubiN– (N = 4−8), Seema Pande, Tian Jian, Navneet S. Khetrapal, Lai-Sheng Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

The structures of gold-doped bismuth clusters, AuBi_n⁻ (n = 4−8), are investigated through a joint photoelectron spectroscopy and density functional theory (DFT) study. Well-resolved photoelectron spectra are obtained at several photon energies. Global minimum searches coupled with DFT calculations yield low-lying structures, whose relative energies are further evaluated by single-point energy calculations at the CCSD(T) level of theory. Vertical detachment energies are calculated with the inclusion of spin−orbit effects to compare with the experimental data. Three-dimensional structures are found to be dominant in this size range, while a planar low-lying isomer is observed only for AuBi_{4 …}

Flexible Robotic Actuators, Stephen A. Morin, Robert F. Shepherd, Adam Stokes, Filip Ilievski, Ramses V. Martinez, Jamie L. Branch, Carina R. Fish, Lihua Jin, Rui M. D. Nunes, Zhigang Suo, George M. Whitesides

Department of Chemistry: Faculty Publications

Systems and methods for providing flexible robotic actuators are disclosed. Some embodiments of the disclosed subject matter include a soft robot capable of providing a radial deflection motions; a soft tentacle actuator capable of providing a variety of motions and providing transportation means for various types of materials; and a hybrid robotic system that retains desirable characteristics of both soft robots and hard robots. Some embodiments of the disclosed subject matter also include methods for operating the dis closed robotic systems.

Chemists Atwitter, Raychelle Burks, Stephani Page, Kiyomi D. Deards, Joan Barnes

University of Nebraska-Lincoln Libraries: Faculty Publications

Twitter can be used to promote chemists, their work, and their events to other scientists and the general public. From checklists to timelines; how to use Twitter successfully as an individual or institution is discussed. This chapter includes: examples of how the authors have used Twitter, how to find and use common subject tags, tags most used when Tweeting about chemistry and science, and a discussion about measuring success. Knowing when and how to Tweet will help chemists communicate successfully with their peers and the general public in 280 characters or less.