Chemistry Commons^™

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. …

‘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.

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 .

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 …

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.

Crystallographic,Vibrational Modes And Optical Properties Data Of Α-Dipabcrystal, Ahmad Alsaad, Chris M. Marin, Nabil Alaqtash, Hsien-Wen Chao, Tsun-Hsu Chang, Chin Li Cheung, A. Ahmad, I. A. Qattan, Renat F. Sabirianov

Department of Chemistry: Faculty Publications

The Crystallographic data of the α-DIPAB sample was measured using powder X-ray diffraction (PXRD). The crystal structure was also optimized using density functional based method. The calculations were performed both including vander Waals (vdW) interactions and excluding them to quantify the effects of vdW interaction on the crystal formation. The vibrational modes of DIPAB crystal corresponding to the Bromine deficient samples are calculated and presented. These show the origin of drastic change in dielectric response in Br deficient samples as compared to the ideal stoichiometric DIPAB crystal (Alsaad et al. 2018) [4]. Optical properties of an ideal α-DIPAB were calculated …

Elastic Properties Of 2d Ti3c2tx Mxene Monolayers And Bilayers, Alexey Lipatov, Haidong Lu, Mohamed H. Alhabeb, Babak Anasori, Alexei Gruverman, Yury Gogotsi, Alexander Sinitskii

Department of Chemistry: Faculty Publications

Two-dimensional (2D) transition metal carbides and nitrides, known as MXenes, are a large class of materials that are finding numerous applications ranging from energy storage and electromagnetic interference shielding to water purification and antibacterial coatings. Yet, despite the fact thatmore than 20 different MXenes have been synthesized, the mechanical properties of a MXene monolayer have not been experimentally studied. We measured the elastic properties of monolayers and bilayers of the most important MXene material to date, Ti₃C₂T_x (T_x stands for surface termination).We developed amethod for preparingwell-strainedmembranes of Ti₃C₂T_x monolayers …

Application Of Group I Metal Adduction To The Separation Of Steroids By Traveling Wave Ion Mobility Spectrometry, Alana L. Rister, Tiana L. Martin, Eric D. Dodds

Department of Chemistry: Faculty Publications

Steroids represent an interesting class of small biomolecules due to their use as biomarkers and their status as scheduled drugs. Although the analysis of steroids is complicated by the potential for many isomers, ion mobility spectrometry (IMS) has previously shown promise for the rapid separation of steroid isomers. This work is aimed at the further development of IMS separation for the analysis of steroids. Here, traveling wave ion mobility spectrometry (TWIMS) was applied to the study of group I metal adducted steroids and their corresponding multimers for five sets of isomers. Each set of isomers had a minimum of one …

Magnetic Assembly Of Soft Robots With Hard Components, Sen Wai Kwok, Stephen A. Morin, Bobak Mosadegh, Ju-Hee So, Robert F. Shepherd, George M. Whitesides

Department of Chemistry: Faculty Publications

Reconfigurable soft robotic actuators with hard components are described. Magnetic attraction is used to couple flexible molded bodies capable of actuation upon pressurization with other flexible molded bodies and/or with hard components (e.g., frames and connectors) to form a seal for fluidic communication and cooperative actuation. Pneumatic decoupling chambers built into the hard components to decouple the hard components from the magnetically-coupled soft molded bodies are described. The use of magnetic self- alignment coupling and pneumatic de-coupling allows for the remote assembly and disassembly of complex structures involving hard and soft components. The magnetic coupling allows for rapid, reversible reconfiguration …

Flexible Thin Robotic Actuators, Aaron D. Mazzeo, Stephen A. Morin, Robert F. Shepherd, George M. Whitesides, William B. Kalb

Department of Chemistry: Faculty Publications

Some embodiments of the disclosed subject matter includes a laminated robotic actuator. The laminated robotic actuator includes a strain-limiting layer comprising a flexible, non extensible material in the form of a sheet or thin film, a flexible inflatable layer in the form of a thin film or sheet in facing relationship with the strain-limiting layer, wherein the inflatable layer is selectively adhered to the strain-limiting layer, and wherein a portion of an un-adhered region between the strain-limiting layer and the inflatable layer defines a pressurizable channel, and at least one fluid inlet in fluid communication with the pressurizable channel. The …

Toward The Detection Of The Triatomic Negative Ion Spn−: Spectroscopy And Potential Energy Surfaces, Tarek Trabelsi, Majdi Hochlaf, Joseph S. Francisco

Department of Chemistry: Faculty Publications

High level theoretical calculations using coupled-cluster theory were performed to provide an accurate description of the electronic structure, spectroscopic properties, and stability of the triatomic negative ion comprising S, N, and P. The adiabatic electron affinities (AEAs) and vertical detachment energies

(VDEs) of PNS, SPN, PSN, and cyc-PSN were calculated. The predicted AEA and VDE of the linear SPN isomer are large: 2.24 and 3.04 eV, respectively. The potential energy surfaces (PESs) of the lowest-lying electronic states of the SPN isomer along the PN and SP bond lengths and bond angle were mapped. A set of spectroscopic parameters for …

Characterization Of Solution-Phase Drug-Protein Interactions By Ultrafast Affinity Extraction, Sandya Beeram, Xiwei Zheng, Kyungah Suh, David S. Hage

Department of Chemistry: Faculty Publications

A number of tools based on high-performance affinity separations have been developed for studying drug-protein interactions. An example of one recent approach is ultrafast affinity extraction. This method has been employed to examine the free (or non-bound) fractions of drugs and other solutes in simple or complex samples that contain soluble binding agents. These free fractions have also been used to determine the binding constants and rate constants for the interactions of drugs with these soluble agents. This report describes the general principles of ultrafast affinity extraction and the experimental conditions under which it can be used to characterize such …

Systems And Methods For Actuating Soft Robotic Actuators, Robert F. Shepherd, Adam Stokes, Stephen A. Morin, Ludovico Cademartiri, Jacob Freake, Rui Nunes, Xin Chen, George M. Whitesides

Department of Chemistry: Faculty Publications

Systems and methods for providing a soft robot is provided. In one system , a robotic device includes a flexible body having a fluid chamber, where a portion of the flexible body includes an elastically extensible material and a portion of the flexible body is strain limiting relative to the elastically extensible material. The robotic device can further include a pressurizing inlet in fluid communication with the fluid chamber, and a pressurizing device in fluid communication with the pressurizing inlet, the pressurizing device including a reaction chamber configured to accommodate a gas producing chemical reaction for providing pressurized gas to …

Tin Nanoparticles Encapsulated Carbon Nanoboxes As High-Performance Anode For Lithium-Ion Batteries, Ziming Yang, Hong-Hui Wu, Zhiming Zheng, Yong Cheng, Pei Li, Qiaobao Zhang, Ming-Sheng Wang

Department of Chemistry: Faculty Publications

One of the crucial challenges for applying Sn as an anode of lithium-ion batteries (LIBs) is the dramatic volume change during lithiation/delithiation process, which causes a rapid capacity fading and then deteriorated battery performance. To address this issue, herein, we report the design and fabrication of Sn encapsulated carbon nanoboxes (denoted as Sn@C) with yolk@shell architectures. In this design, the carbon shell can facilitate the good transport kinetics whereas the hollow space between Sn and carbon shell can accommodate the volume variation during repeated charge/discharge process. Accordingly, this composite electrode exhibits a high reversible capacity of 675 mAh g^{−1 …}

Anatomy Of Stem Teaching In American Universities: A Snapshot From A Large-Scale Observation Study, Marilyne Stains, Jordan Harshman, Megan K. Barker, Stephanie V. Chasteen, Renee Cole, Sue Ellen Dechenne-Peters, M. Kevin Eagan Jr., Joan M. Esson, Jennifer K. Knight, Frank A. Laski, Marc Levis-Fitzgerald, Christopher J. Lee, Stanley M. Lo, Lisa M. Mcdonnell, Timothy A. Mckay, Nicole Michelotti, Michael S. Palmer, Kathryn M. Plank, Tamara M. Rodela, Erin R. Sanders, Natalie G. Schimpf, Patricia M. Schulte, Michelle Smith, Mackenzie Stetzer, Jackie Stewart, Blaire Van Valkenburgh, Erin Vinson, Laura K. Weir, Paul J. Wendel, Lindsay B. Wheeler, Anna M. Young

Department of Chemistry: Faculty Publications

National and local initiatives focused on the transformation of STEM teaching in higher education have multiplied over the last decade. These initiatives often focus on measuring change in instructional practices, but it is difficult to monitor such change without a national picture of STEM educational practices, especially as characterized by common observational instruments. We characterized a snapshot of this landscape by conducting the first large scale observation-based study. We found that lecturing was prominent throughout the undergraduate STEM curriculum, even in classrooms with infrastructure designed to support active learning, indicating that further work is required to reform STEM education. Additionally, …

Reductive Cleavage Of Organic Peroxides By Iron Salts And Thiols, Anderw Olson, Abigail J. Jameson, Shiva K. Kyasa, Boone W. Evans, Patrick H. Dussault

Department of Chemistry: Faculty Publications

Despite the low bond strength of the oxygen− oxygen bond, organic peroxides are often surprisingly resistant to cleavage by nucleophiles and reductants. As a result, achieving decomposition under mild conditions can be challenging. Herein, we explore the reactivity of a selection of peroxides toward thiolates, phenyl selenide, Fe(II) salts, and iron thiolates. Peroxides activated by conjugation, strain, or stereoelectronics are rapidly cleaved at room temperature by thiolate anions, phenylselenide, or Fe(II) salts. Under the same conditions, unhindered dialkyl peroxides are only marginally reactive; hindered peroxides, including triacetone triperoxide and diacetone diperoxide (DADP), are inert. In contrast, all but the most …

The Secant Rate Of Corrosion: Correlating Observations Of The Uss Arizona Submerged In Pearl Harbor, Donald L. Johnson, Robert J. Deangelis, Dana J. Medlin, Jon E. Johnson, James D. Carr, David L. Conlin

Department of Chemistry: Faculty Publications

Contrary to previous linear projections of steel corrosion in seawater, analysis of an inert marker embedded in USS Arizona concretion since the 7 December 1941 attack on Pearl Harbor reveals evidence that the effective corrosion rate decreases with time. The secant rate of corrosion, or SRC correlation, derived from this discovery could have a significant impact on failure analysis investigations for concreted shipwrecks or underwater structures. The correlation yields a lower rate of metal thinning than predicted. Development of the correlation is described.

Study Of The Oxidation Kinetics Of Nitrite Ions By Potassium Ferrate(Vi), J. Carr, I. Goncharova, D. Golovko, C. Mclaughlin, I. Golovko, J. Erickson

Department of Chemistry: Faculty Publications

Вивчено кiнетику окиснення нiтрит до нiтрат йонiв калiй фератом(VI) в широкому дiапазонi рН, вiд нейтрального до лужного сере- довища. Проведено двi серiї кiнетичних експе- риментiв, заснованих на рiзних технологiях одержання калiй ферату(VI). В першiй серiї експериментiв кристалiчний калiй ферат(VI) отримували хiмiчним синтезом. В дiапазонi рН 6.5–11 твердий K₂FeO₄ додавали до роз- чинiв нiтрит йонiв при вiдомiй концентрацiї та рН. Експерименти проводили пiд контролем рН та йонної сили. Кiнетичнi дослiдження коливалися вiд мiлiсекунд до декiлькох хви- лин. В другiй серiї експериментiв розчини K₂FeO₄ було отримано електрохiмiчним син- тезом. Лужнi розчини калiй ферату(VI) в 8.0 М …

Iterative Non-Proteinogenic Residue Incorporation Yields Α/Β-Peptides With A Helix-Loop-Helix Tertiary Structure And High Affinity For Vegf, James W. Checco, Samuel H. Gellman

Department of Chemistry: Faculty Publications

Inhibition of specific protein-protein interactions is attractive for a range of therapeutic applications, but the large and irregularly shaped contact surfaces involved in many such interactions make it challenging to design synthetic antagonists. Here, we describe the development of backbone-modified peptides containing both α- and β-amino acid residues (“α/β-peptides”) that target the receptor-binding surface of vascular endothelial growth factor (VEGF). Our approach is based on the Z-domain, which adopts a three-helix bundle tertiary structure. We show how a two-helix “mini-Z-domain” can be modified to contain β and other non-proteinogenic residues while retaining the target-binding epitope using iterative non-natural residue incorporation. …

Fluorogenic Protein Labeling Using A Genetically Encoded Unstrained Alkene, Xin Shang, X. Song, C. Faller, R. Lai, H. Li, R. Cerny, Wei Niu, Jiantao Guo

Department of Chemistry: Faculty Publications

We developed a new fluorogenic bioorthogonal reaction that is based on the inverse electron-demand Diels–Alder reaction between styrene (an unstrained alkene) and a simple tetrazine. The reaction forms a new fluorophore with no literature precedent. We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a styrene-containing amino acid into proteins in response to amber nonsense codon. Fluorogenic labeling of purified proteins and intact proteins in live cells were demonstrated. The fluorogenicity of the styrene–tetrazine reaction can be potentially applied to the study of protein folding and function under physiological conditions with low background fluorescence interference.