Chemistry Commons^™

Titanium Trisulfide Monolayer: Theoretical Prediction Of A New Direct-Gap Semiconductor With High And Anisotropic Carrier Mobility, Jun Dai, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

A new two-dimensional (2D) layered material, namely, titanium trisulfide (TiS₃) monolayer, is predicted to possess novel electronic properties. Ab initio calculations show that the perfect TiS₃ monolayer is a direct-gap semiconductor with a bandgap of 1.02 eV, close to that of bulk silicon, and with high carrier mobility. More remarkably, the in-plane electron mobility of the 2D TiS₃ is highly anisotropic, amounting to about 10,000 cm² V⁻¹ s⁻¹ in the b direction, which is higher than that of the MoS₂ monolayer, whereas the hole mobility is about two orders of magnitude lower. …

A Multilaboratory Comparison Of Calibration Accuracy And The Performance Of External References In Analytical Ultracentrifugation, Huaying Zhao, Rodolfo Ghirlando, Carlos Alfonso, Fumio Arisaka, Ilan Attali, David L. Bain, Et Al. ..., Donald F. Becker, Peter Schuck

Department of Biochemistry: Faculty Publications

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy …

Analysis Of Free Solute Fractions And Solute-Protein Interactions Using Ultrafast Affinity Extraction And Affinity Microcolumns, Xiwei Zheng

Department of Chemistry: Dissertations, Theses, and Student Research

This dissertation describes the use of a high-performance affinity chromatography method based on ultrafast affinity extraction and microcolumns to study biological interactions.

In the first project, a new method was created and based on ultrafast affinity extraction to determine both the dissociation rate constants (k_d) and association equilibrium constants (K_a) for drug-protein interactions in solution. Various conditions to optimize the use of ultrafast affinity extraction for equilibrium and kinetic studies were considered.

The objective of the next portion of this dissertation was to develop a chromatographic approach to measure free drug fractions in more …

Chromatographic Analysis Of Drug-Protein Interactions During Diabetes And Characterization Of Human Serum Albumin Through Multidimensional Mass Spectrometry, Ryan E. Matsuda

Department of Chemistry: Dissertations, Theses, and Student Research

Diabetes is a metabolic disease that can lead to the non-enzymatic glycation of serum proteins such as human serum albumin (HSA). Previous studies have indicated that glycation can affect the structure and function of these proteins. This dissertation describes the development of tools and techniques based on high performance affinity chromatography (HPAC) and multidimensional mass spectrometry to analyze the effects of glycation on the function and structure of HSA.

A major portion of this research involved the utilization of HPAC to examine the effect of glycation on the binding of three second-generation sulfonylurea drugs and one third-generation sulfonylurea drug. These …

Investigations Into The Molecular Mechanisms Of Bacterial Pathogen–Host Interactions: Construction Of A Dual Plasmid System For Incorporation Of Unnatural Amino Acids Into Pseudomonas Syringae Pv. Tomato Dc3000, Scotty D. Raber

Department of Chemistry: Dissertations, Theses, and Student Research

A dual plasmid system for the incorporation of unnatural amino acids into plant pathogen, Pseudomonas syringae pv. tomato DC3000, has been designed. This invention is expected to allow (a) mutations of proteins synthesized by the bacterium, P. syringae pv. tomato DC3000, that can capture molecular targets, especially for such modified proteins secreted by the phytopathogen into the host plant cells of A. thaliana and S. lycopersicum, (b) expression of biological probes in the bacterial species to monitor changes in redox, nutritional, and other small molecule states over pre-, post- and in situ disease stages, and secretion of such biological …

Molecular Mechanism For The Biosynthesis Of Antifungal Hsaf And Antibacterial Wap-8294a2, Haotong Chen

Department of Chemistry: Dissertations, Theses, and Student Research

Bioactive natural products are a major source of anti-infectives. Many ubiquitous inhabitants of soil and water, such as the Gram-negative, prolific producers of natural products, Lysobacter, remain largely unexplored. This PhD thesis reports our studies of the biosynthetic mechanism for a novel antifungal natural product HSAF and a potent anti-MRSA natural product WAP-8294A2.

In the first chapter, we give a short review of the biosynthesis of polyketides, focusing on those which exhibit new biosynthetic features. In subsequent chapters, we present original research on the biosynthetic mechanisms of dihydromaltophilin, a heat stable antifungal factor (HSAF). HSAF is the main antifungal …

Unraveling Structures Of Protection Ligands On Gold Nanoparticle Au68(Sh)32, Wen Wu Xu, Yi Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

New low-energy atomic structures of the thiolate-protected gold nanoparticle Au₆₈(SH)₃₂ are uncovered, where the atomic positions of the Au atoms are taken from the recent single-particle transmission electron microscopy measurement by Kornberg and co-workers, whereas the pattern of thiolate ligands on the gold core is attained on the basis of the generic formulation (or rule) of the “divide and protect” concept. Four distinct low-energy isomers, Iso1 to Iso4, whose structures all satisfy the generic formulation, are predicted. Density-functional theory optimization indicates that the four isomers are all lower in energy by 3 to 4 eV than the …

Toward The Measurement Of Biodistribution Of 18F-Labeled Industrial Chemicals With Positron Emission Tomography (Pet), Katelyenn S. Mccauley

Department of Chemistry: Dissertations, Theses, and Student Research

Plasticizers are added to polymeric materials to increase flexibility and durability, thus they constitute a common, and widely used class of industrial chemicals. Plasticizers have been suspected of a number of adverse health effects including the interference with the endocrine system.¹ These substances have the tendency to migrate to the surfaces of materials, where they can be absorbed, ingested, or inhaled. ⁵ The iniquitousness of plasticizers and the daily contact with polymeric materials has given rise to concern about the toxicity and health effects of these substances. Many long-term and excessive-dose studies have been conducted on many of these …

The 8-Silyloxyquinoline Scaffold As A Versatile Platform For The Sensitive Detection Of Aqueous Fluoride, Xinqi Zhou

Department of Chemistry: Dissertations, Theses, and Student Research

As one of the most essential elements in nature, fluoride has been well known and extensively studied since the 16^th century. Since then the two-edged nature of fluoride in biological systems has been well described. Specifically, moderate fluoride exposure can aid in tooth and bone development, while fluoride overexposure results in the depilating disease known as fluorosis. Because of the side effects upon overexposure of fluoride, there is a need to develop fast and straight forward methods to sensitively and selectively detect and quantify fluoride concentration in drinking water. With this goal in mind and by taking advantage of …

Bio-Crosslinking Of Starch Films With Oxidized Sucrose, Hazal Canisag

Department of Textiles, Merchandising and Fashion Design: Dissertations, Theses, and Student Research

In this work, corn starch films were crosslinked with a novel bio-based agent; oxidized sucrose and their strength and stability were improved. Although starch is an inexpensive, biodegradable and abundant source, industrial applications of starch films are limited due to their poor mechanical properties. Crosslinking is one of the most common methods to enhance the mechanical properties of starch films. However, most of the available crosslinkers, such as gluteraldehyde, phosphorus oxychloride, sodium trimetaphosphate, and epichlorohydrin, are either toxic, expensive or with low crosslinking efficiencies. Oxidized sucrose, which is derived by periodate cleavage, has aldehyde groups in the structure and this …

New Methods For Synthesis Of Organic Peroxides And Application Of Peroxide Electrophiles To Synthesis Of Functionalized Ethers, Shiva Kumar Kyasa

Department of Chemistry: Dissertations, Theses, and Student Research

New Method for Synthesis of Alkyl Hydroperoxides: There are a number of methods reported for synthesis of alkyl hydroperoxides, but most of them suffer either from poor yields or the formation of unwanted side products. I will be discussing new methodology for efficient synthesis of pure samples of 1° and 2° alkyl hydroperoxides via alkylation of readily available cyclododecanone 1,1-dihydroperoxide followed by hydrolysis of the resulting bis peroxyacetals.

Peroxide Electrophiles for Synthesis of Functionalized Ethers: Peroxides are underexplored functional groups as precursors for C-O bond formation and ether synthesis. The reactivity of dialkyl peroxides towards organometallics such as alkyl lithium …

Toward An Expanded Role For Collision-Induced Dissociation In Glycoproteomic Analysis, Venkata Kolli

Department of Chemistry: Dissertations, Theses, and Student Research

This thesis begins with an overview of the state-of-the-art in tandem mass spectrometry (MS/MS) analysis of glycopeptides. In this introduction, the primary focus is on utilization of different ion dissociation techniques for MS/MS to obtain structural information of N-glycopeptides. This includes a discussion of the importance of complementary MS/MS methods to attain complete structural characterization of N-glycopeptides. Emerging methods involving the use of a single ion dissociation technique for complete glycopeptide connectivity analysis were also presented. Next, the application of collision-induced dissociation (CID) to provide both amino acid sequence and monosaccharide connectivity for model N-glycopeptides was discussed in detail. Implementation …

Energetics, Structure, And Rovibrational Spectroscopic Properties Of The Sulfurous Anions Sno− And Osn−, Ryan C. Fortenberry, Joseph S. Francisco

Department of Chemistry: Faculty Publications

The SNO⁻ and OSN⁻ anions are shown in this work to be very stable negatively charged species in line with other recent work [T. Trabelsi et al., J. Chem. Phys. 143, 164301 (2015)]. Utilizing established quartic force field techniques, the structural and rovibrational data for these anions are produced. The SNO⁻ anion is less linear and has weaker bonds than the corresponding neutral radical giving much smaller rotational constants.OSN⁻ is largely unchanged in these regards with inclusion of the additional electron.The S–N bond is actually stronger,and the rotational constants of OSN⁻ versus OSN are …

The Importance Of Context: An Exploration Of Factors Influencing The Adoption Of Student-Centered Teaching Among Chemistry, Biology, And Physics Faculty, Travis J. Lund, Marilyne Stains

Department of Chemistry: Faculty Publications

Background: Research at the secondary and postsecondary levels has clearly demonstrated the critical role that individual and contextual characteristics play in instructors’ decision to adopt educational innovations. Although recent research has shed light on factors influencing the teaching practices of science, technology, engineering, and mathematics (STEM) faculty, it is still not well understood how unique departmental environments impact faculty adoption of evidence-based instructional practices (EBIPs) within the context of a single institution. In this study, we sought to characterize the communication channels utilized by STEM faculty, as well as the contextual and individual factors that influence the teaching practices …

Hfq Regulates Antibacterial Antibiotic Biosynthesis And Extracellular Lytic-Enzyme Production In Lysobacter Enzymogenes Oh11, Gaoge Xu, Yuxin Zhao, Liangcheng Du, Guoliang Qian, Fengquan Liu

Department of Chemistry: Faculty Publications

Lysobacter enzymogenes is an important biocontrol agent with the ability to produce a variety of lytic enzymes and novel antibiotics. Little is known about their regulatory mechanisms. Understanding these will be helpful for improving biocontrol of crop diseases and potential medical application. In the present study, we generated an hfq (encoding a putative ribonucleic acid chaperone) deletion mutant, and then utilized a new genomic marker-free method to construct an hfq-complemented strain. We showed for the first time that Hfq played a pleiotropic role in regulating the antibacterial antibiotic bio- synthesis and extracellular lytic enzyme activity in L. enzymogenes. Mutation of …

Long-Lifetime Reverse Saturable Absorption In A Bipyridyl Platinum(Ii) Complex Bearing Naphthalimidylethynyl-Substituted Fluorenylacetylide Ligands, Timothy M. Pritchett, Michael J. Ferry, Andrew G. Mott, William Shensky Iii, Joy E. Haley, Rui Hui, Wenfang Sun

United States Air Force: Publications

By fitting femtosecond transient difference absorption time series at multiple wavelengths, the singlet excited-state lifetime of a particular platinum(II) 2,2’-bipyridyl complex bearing naphthalimidylethynyl- substituted fluorenyl-acetylide ligands was determined to be 83.5 ± 39 ps in toluene solution. A triplet quantum yield of 0.06 was measured using relative actinometry. Excited-state absorption cross sections of 5.6 X 10^-17 cm² (singlet) and 7.8 X 10^-16 cm² (triplet) at 532 nm were obtained by using a five-level dynamic model to fit open-aperture Z scans at picosecond and nanosecond pulse widths and a variety of pulse energies. Most significantly, …

Unraveling The Mechanism Of Selective Ion Transport In Hydrophobic Subnanometer Channels, Hui Li, Joseph S. Francisco, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Recently reported synthetic organic nanopore (SONP) can mimic a key feature of natural ion channels, i.e., selective ion transport. However, the physical mechanism underlying the K⁺/Na⁺ selectivity for the SONPs is dramatically different from that of natural ion channels. To achieve a better understanding of the selective ion transport in hydrophobic subnanometer channels in general and SONPs in particular, we perform a series of ab initio molecular dynamics simulations to investigate the diffusivity of aqua Na⁺ and K⁺ ions in two prototype hydrophobic nanochannels: (i) an SONP with radius of 3.2 Å, and (ii) single-walled …

Medium-Sized Au40(Sr)24 And Au52(Sr)32 Nanoclusters With Distinct Gold-Kernel Structures And Spectroscopic Features, Wen Wu Xu, Yadong Li, Yi Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We have analyzed the structures of two medium-sized thiolateprotected gold nanoparticles (RS-AuNPs) Au₄₀(SR)₂₄ and Au₅₂(SR)₃₂ and identified the distinct structural features in their Au kernels [Sci. Adv., 2015, 1, e1500425]. We find that both Au kernels of the Au₄₀(SR)₂₄ and Au₅₂(SR)₃₂ nanoclusters can be classified as interpenetrating cuboctahedra. Simulated X-ray diffraction patterns of the RS-AuNPs with the cuboctahedral kernel are collected and then compared with the X-ray diffraction patterns of the RS-AuNPs of two other prevailing Au-kernels identified from previous experiments, namely the Ino-decahedral kernel and icosahedral kernel. …

Extremely Strong Tubular Stacking Of Aromatic Oligoamide Macrocycles, Mark A. Kline, Xiaoxi Wei, Ian J. Horner, Rui Liu, Shuang Chen, Si Chen, Ka Yi Yung, Kazuhiro Yamato, Zhonghou Cai, Frank V. Bright, Xiao Cheng Zeng, Bing Gong

Xiao Cheng Zeng Publications

As the third-generation rigid macrocycles evolved from progenitor 1, cyclic aromatic oligoamides 3, with a backbone of reduced constraint, exhibit extremely strong stacking with an astoundingly high affinity (estimated lower limit of K_dimer > 10¹³ M^–1 in CHCl₃), which leads to dispersed tubular stacks that undergo further assembly in solution. Computational study reveals a very large binding energy (–49.77 kcal mol^–1) and indicates highly cooperative local dipole interactions that account for the observed strength and directionality for the stacking of 3. In the solid-state, X-ray diffraction (XRD) confirms that the aggregation of 3 results …

Titanium Dioxide Nanoparticles Trigger Loss Of Function And Perturbation Of Mitochondrial Dynamics In Primary Hepatocytes, Vaishaali Natarajan, Christina L. Wilson, Stephen L. Hayward, Srivatsan Kidambi

Department of Chemical and Biomolecular Engineering: Faculty Publications

Titanium dioxide (TiO₂) nanoparticles are one of the most highly manufactured and employed nanomaterials in the world with applications in copious industrial and consumer products. The liver is a major accumulation site for many nanoparticles, including TiO₂, directly through intentional exposure or indirectly through unintentional ingestion via water, food or animals and increased environmental contamination. Growing concerns over the current usage of TiO₂ coupled with the lack of mechanistic understanding of its potential health risk is the motivation for this study. Here we determined the toxic effect of three different TiO₂ nanoparticles (commercially available …

B27−: Appearance Of The Smallest Planar Boron Cluster Containing A Hexagonal Vacancy, Wei-Li Li, Rhitankar Pal, Zachary A. Piazza, Xiao Cheng Zeng, Lai-Sheng Wang

Xiao Cheng Zeng Publications

Photoelectron spectroscopy and ab initio calculations have been carried out to probe the structures and chemical bonding of the B₂₇⁻ cluster. Comparison between the experimental spectrum and the theoretical results reveals a two-dimensional (2D) global minimum with a triangular lattice containing a tetragonal defect (I) and two low-lying 2D isomers (II and III), each with a hexagonal vacancy. All three 2D isomers have 16 peripheral boron atoms and 11 inner boron atoms. Isomer I is shown to be mainly responsible for the observed photoelectron spectrum with isomers II and III as minor contributors. Chemical bonding analyses of these …

Electronic Structures And Electronic Spectra Of All-Boron Fullerene B40, Rongxing He, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

This study is motivated by the recent discovery of the first all-boron fullerene analogue, a B₄₀ cluster with D_2d point-group symmetry, dubbed borospherene (Nat. Chem., 2014, 6, 727). Insight into the electronic structures and spectral properties of B₄₀ is timely and important to understand the borospherene and the transition from open-ended plate or ribbon-like structures to a hollow-cage structure at B₄₀. Optimized geometries of borospherene B₄₀ for both the ground state and the first excited state allow us to compute spectral properties including UV-vis absorption, infrared (IR) and Raman spectra. Highly resolved absorption and …

Room-Temperature Distance Measurements Of Immobilized Spin-Labeled Protein By Deer/Peldor, Virginia Meyer, Michael A. Swanson, Laura J. Clouston, Przemysław J. Boratyński, Richard A. Stein, Hassane S. Mchaourab, Andrzej Rajca, Sandra S. Eaton, Gareth R. Eaton

Andrzej Rajca Publications

Nitroxide spin labels are used for double electron-electron

resonance (DEER) measurements of distances between sites in

biomolecules. Rotation of gem-dimethyls in commonly used

nitroxides causes spin echo dephasing times (T_m) to be too

short to perform DEER measurements at temperatures between

∼80 and 295 K, even in immobilized samples. A spirocyclohexyl

spin label has been prepared that has longer T_m between 80

and 295 K in immobilized samples than conventional labels. Two

of the spirocyclohexyl labels were attached to sites on T4 lysozyme introduced by site-directed spin labeling. Interspin

distances up to ∼4 nm were …

Exploiting Enzymatic Dynamic Reductive Kinetic Resolution (Dyrkr) In Stereocontrolled Synthesis, Gregory A. Applegate, David B. Berkowitz

David Berkowitz Publications

Over the past two decades, the domains of both frontline synthetic organic chemistry and process chemistry have seen an increase in crosstalk between asymmetric organic/organometallic approaches and enzymatic approaches to stereocontrolled synthesis. This review highlights the particularly auspicious role for dehydrogenase enzymes in this endeavor, with a focus on dynamic reductive kinetic resolutions (DYRKR) to “deracemize” building blocks, often setting two stereocenters in so doing. The scope and limitations of such dehydrogenase-mediated processes are overviewed, as are future possibilities for the evolution of enzymatic DYRKR.

Research-Based Implementation Of Peer Instruction: A Literature Review, Trisha Vickrey, Kaitlyn Rosploch, Reihaneh Rahmanian, Matthew Pilarz, Marilyne Stains

Department of Chemistry: Faculty Publications

Current instructional reforms in undergraduate science, technology, engineering, and mathematics (STEM) courses have focused on enhancing adoption of evidence-based instructional practices among STEM faculty members. These practices have been empirically demonstrated to enhance student learning and attitudes. However, research indicates that instructors often adapt rather than adopt practices, unknowingly compromising their effectiveness. Thus, there is a need to raise awareness of the research-based implementation of these practices, develop fidelity of implementation protocols to understand adaptations being made, and ultimately characterize the true impact of reform efforts based on these practices. Peer instruction (PI) is an example of an evidence-based instructional …

New Insight Into The Helium-Induced Damage In Max Phase Ti3Alc2 By First-Principles Studies, Yiguo Xu, Xiaojing Bai, Xianhu Zha, Qing Huang, Jian He, Kan Luo, Yuhong Zhou, Timothy C. Germann, Joseph S. Francisco, Shiyu Du

Department of Chemistry: Faculty Publications

In the present work, the behavior of He in the MAX phase Ti3AlC2 material is investigated using first-principle methods. It is found that, according to the predicted formation energies, a single He atom favors residing near the Al plane in Ti3AlC2. The results also show that Al vacancies are better able to trap He atoms than either Ti or C vacancies. The formation energies for the secondary vacancy defects near an Al vacancy or a C vacancy are strongly influenced by He impurity content. According to the present results, the existence of trapped He atoms in primary Al vacancy can …

Communication: Spectroscopic Consequences Of Proton Delocalization In Ochco+, Ryan C. Fortenberry, Qi Yu, John S. Mancini, Joel M. Bowman, Timothy J. Lee, T. Daniel Crawford, William F. Klemperer, Joseph S. Francisco

Department of Chemistry: Faculty Publications

Even though quartic force fields (QFFs) and highly accurate coupled cluster computations describe the OCHCO⁺ cation at equilibrium as a complex between carbon monoxide and the formyl cation, two notable and typical interstellar and atmospheric molecules, the prediction from the present study is that the equilibrium C_∞v structure is less relevant to observables than the saddle-point D_∞h structure. This is the conclusion from diffusion Monte Carlo and vibrational self-consistent field/virtual state configuration interaction calculations utilizing a semi-global potential energy surface. These calculations demonstrate that the proton “rattle” motion (ν₆) has centrosymmetric delocalization of the …

Structural And Optical Properties Of Cobalt Slanted Nanopillars Conformally Coated With Few-Layer Graphene, Peter M. Wilson, Alexey Lipatov, Daniel Schmidt, Eva Schubert, Mathias Schubert, Alexander Sinitskii, Tino Hofmann

Department of Chemistry: Faculty Publications

Optical characterization of anisotropic multicomponent nanostructures is generally not a trivial task, since the relation between a material’s structural properties and its permittivity tensor is nonlinear. In this regard, an array of slanted cobalt nanopillars that are conformally coated with few-layer graphene is a particularly challenging object for optical characterization, as it has a complex anisotropic geometry and comprises several materials with different topologies and filling fractions. Normally, a detailed characterization of such complex nanostructures would require a combination of several microscopic and spectroscopic techniques. In this letter, we demonstrate that the important structural parameters of these graphene-coated sculptured thin …

Few-Layer Titanium Trisulfide (Tis3) Field-Effect Transistors, Alexey Lipatov, Peter M. Wilson, Mikhail Shekhirev, Jacob D. Teeter, Ross Netusil, Alexander Sinitskii

Department of Chemistry: Faculty Publications

Titanium trisulfide (TiS₃) is a promising layered semiconductor material. Several-mm-long TiS₃ whiskers can be conveniently grown by the direct reaction of titanium and sulfur. In this study, we exfoliated these whiskers using the adhesive tape approach and fabricated few-layer TiS₃ field-effect transistors (FETs). The TiS₃ FETs showed an n-type electronic transport with roomtemperature field-effect mobilities of 18-24 cm²V^-1s^-1 and ON/OFF ratios up to 300. We demonstrate that TiS₃ is compatible with the conventional atomic layer deposition (ALD) procedure for Al₂O₃. ALD of alumina on TiS3 …

Biotechnological Production Of 1,2,4-Butanetriol: An Efficient Process To Synthesize Energetic Material Precursor From Renewable Biomass, Yujin Cao, Wei Niu, Jiantao Guo, Mo Xian, Huizhou Liu

Department of Chemistry: Faculty Publications

1,2,4-Butanetriol (BT) is a valuable chemical with extensive applications in many different fields. The traditional chemical routes to synthesize BT suffer from many drawbacks, e.g., harsh reaction conditions, multiple steps and poor selectivity, limiting its industrial production. In this study, an engineered Escherichia coli strain was constructed to produce BT from xylose, which is a major component of the lignocellulosic biomass. Through the coexpression of a xylose dehydrogenase (CCxylB) and a xylonolactonase (xylC) from Caulobacter crescentus, native E. coli xylonate dehydratase (yjhG), a 2-keto acid decarboxylase from Pseudomonas putida (mdlC) and …