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Templated Synthesis Of Glycoluril Hexamer And Monofunctionalized Cucurbit[6]Uril Derivatives, Derick Lucas, Tsuyoshi Minami, Greg Iannuzzi, Liping Cao, James B. Wittenberg, Pavel Anzenbacher Jr., Lyle Isaacs

Chemistry Faculty Publications

We report that the p-xylylenediammonium ion (11) acts as a template in the cucurbit[n]uril forming reaction that biases the reaction toward the production of methylene bridged glycoluril hexamer (6C) and bis-nor-seco-CB [10]. Hexamer 6C is readily available on the gram scale by a one step synthetic procedure that avoids chromatography. Hexamer 6C undergoes macrocylization. with (substituted) phthalaldehydes 12,14,.15, and 18-in 9 M H2SO4 or concd HCl at room temperature to deliver monofunctionalized CB[6] derivatives 13,16,17, and 19 that are poised for further functionalization reactions: The kinetics of the macrocyclization reaction between hexamer and formaldehyde or phthalaldehyde depends on the presence …

Synthesis And Antiproliferative Activity Of Some Steroidal Lactams, Yanmin Huang, Jianguo Cui, Sijing Chen, Chunfang Gan, Aimin Zhou

Chemistry Faculty Publications

Using cholesterol as starting material, a series of 6-substituted-3-aza-A-homo-3-oxycholestanes and 6-substituted-4-aza-A-homo-3-oxycholestanes were synthesized by the oxidation, reduction, oximation, Beckman rearrangement and condensation reaction. These synthesized compounds displayed a distinct cytotoxicity against MGC 7901, HeLa and SMMC 7404 cancer cells. Our results revealed that the structures of functional groups at position-6 on the steroidal ring are crucial for the IC50 value of antiproliferative activities of these compounds and the cytotoxic activity against MGC 7901 and SMMC 7404 cells was not significantly different between 4-N-lactams and 3-N-lactams when its 6-substituted group was a carbonyl or a hydroximino, but all 3-N-lactams showed a …

The Evolution Of Function In Strictosidine Synthase-Like Proteins, Michael A. Hicks, Alan E. Barber, Lesley Ann Giddings, Jenna Caldwell, Sarah E. O'Connor, Patricia C. Babbitt

Chemistry: Faculty Publications

The exponential growth of sequence data provides abundant information for the discovery of new enzyme reactions. Correctly annotating the functions of highly diverse proteins can be difficult, however, hindering use of this information. Global analysis of large superfamilies of related proteins is a powerful strategy for understanding the evolution of reactions by identifying catalytic commonalities and differences in reaction and substrate specificity, even when only a few members have been biochemically or structurally characterized. A comparison of >2500 sequences sharing the six-bladed β-propeller fold establishes sequence, structural, and functional links among the three subgroups of the functionally diverse N6P superfamily: …

Analysis Of Binding Site Hot Spots On The Surface Of Ras Gtpase, Greg Buhrman, Casey O'Connor, Brandon Zerbe, Bradley M. Kearney, Raeanne Napoleon, Elizaveta A. Kovrigina, Sandor Vajda, Dima Kozakov, Evgenii L. Kovrigin, Carla Mattos

Chemistry Faculty Research and Publications

We have recently discovered an allosteric switch in Ras, bringing an additional level of complexity to this GTPase whose mutants are involved in nearly 30% of cancers. Upon activation of the allosteric switch, there is a shift in helix 3/loop 7 associated with a disorder to order transition in the active site. Here, we use a combination of multiple solvent crystal structures and computational solvent mapping (FTMap) to determine binding site hot spots in the “off” and “on” allosteric states of the GTP-bound form of H-Ras. Thirteen sites are revealed, expanding possible target sites for ligand binding well beyond the …

Reactivity Of Acyclic (Pentadienyl)Iron(1+) Cations: Synthetic Studies Directed Toward The Frondosins, Do W. Lee, Rajesh K. Pandey, Sergey V. Lindeman, William A. Donaldson

Chemistry Faculty Research and Publications

A short, 4-step route to the scaffold of frondosin A and B is reported. The [1-methoxycarbonyl-5-(2′,5′-dimethoxyphenyl)pentadienyl]Fe(CO)₃⁺ cation was prepared in two steps from (methyl 6-oxo-2,4-hexadienoate)Fe(CO)₃. Reaction of this cation with isopropenyl Grignard or cyclohexenyllithium reagents affords (2-alkenyl-5-aryl-1-methoxycarbonyl-3-pentene-1,5-diyl)Fe(CO)₃ along with other addition products. Oxidative decomplexation of these (pentenediyl)iron complexes, utilizing CuCl₂, affords 6-aryl-3-methoxycarbonyl-1,4-cycloheptadienes via the presumed intermediacy of a cis-divinylcyclopropane.

Removal Of 2,4-Dichlorophenoxyacetic Acid By Calcined Zn–Al–Zr Layered Double Hydroxide, Allen Chaparadza, Jeanne Hossenlopp

Chemistry Faculty Research and Publications

The adsorption equilibrium, kinetics, and thermodynamics of removal of 2,4-dichlorophenoxy-acetic acid (2,4-D) from aqueous solutions by a calcined Zn–Al layered double hydroxide incorporated with Zr⁴⁺ were studied with respect to time, temperature, pH, and initial 2,4-D concentration. Zr⁴⁺ incorporation into the LDH was used to enhance 2,4-D uptake by creating higher positive charges and surface/layer modification of the adsorbent. The LDH was capable of removing up to 98% of 2,4-D from 5 to 400 ppm aqueous at adsorbent dosages of 500 and 5000 mg L⁻¹. The adsorption was described by a Langmuir-type isotherm. The percentage 2,4-D …

Nanomolar Binding Of Peptides Containing Noncanonical Amino Acids By A Synthetic Receptor, Leigh A. Logsdon, Christopher L. Schardon, Vijayakumar Ramalingam, Sharon K. Kwee, Adam R. Urbach

Chemistry Faculty Research

This paper describes the molecular recognition of phenylalanine derivatives and their peptides by the synthetic receptor cucurbit[7]uril (Q7). The 4-tert-butyl and 4-aminomethyl derivatives of phenylalanine (tBuPhe and AMPhe) were identified from a screen to have 20–30-fold higher affinity than phenylalanine for Q7. Placement of these residues at the N-terminus of model tripeptides (X-Gly-Gly), resulted in no change in affinity for tBuPhe-Gly-Gly, but a remarkable 500-fold increase in affinity for AMPhe-Gly-Gly, which bound to Q7 with an equilibrium dissociation constant (K_d) value of 0.95 nM in neutral phosphate buffer. Structure–activity studies revealed that three functional groups …

Fabrication Of Size-Tunable Metallic Nanoparticles Using Plasmid Dna As A Biomolecular Reactor, Jacopo Samson, Irene Piscopo, Alex Yampolski, Patrick Nahirney, Andrea Parpas, Amit Aggarwal, Raihan Saleh, Charles Michael Drain

Publications and Research

Plasmid DNA can be used as a template to yield gold, palladium, silver, and chromium nanoparticles of different sizes based on variations in incubation time at 70 °C with gold phosphine complexes, with the acetates of silver or palladium, or chromium acetylacetonate. The employment of mild synthetic conditions, minimal procedural steps, and aqueous solvents makes this method environmentally greener and ensures general feasibility. The use of plasmids exploits the capabilities of the biotechnology industry as a source of nanoreactor materials.

Open Data, Open Source, And Open Standards In Chemistry: The Blue Obelisk Five Years On, Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, Peter Murray-Rust

College of Science and Engineering Faculty Research and Scholarship

Background: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions: We show that the Blue …

Preparation And Characterization Of A Composite Of Gold Nanoparticles And Single-Walled Carbon Nanotubes And Its Potential For Heterogeneous Catalysis, Anne Shanahan, James Sullivan, Mary Mcnamara, Hugh Byrne

Articles

A single-walled carbon nanotube-supported gold nanoparticle composite was prepared and characterized by X-ray diffraction, scanning transmission electron microscopy/scanning electron microscopy/transmission electron microscopy, energy-dispersive X-ray analysis, atomic absorption spectroscopy, nitrogen adsorption, Raman spectroscopy, and ultraviolet-visible spectroscopy. The Au particles were found to be crystalline, with a well-defined and narrow particle-size distribution, centered around 7 nm. The activity and selectivity of the composite for solventless aerobic oxidation of a secondary alcohol were examined, and a conversion efficiency of 95% was obtained.

Total Synthesis Of 4'-Ester Resveratrol Analogs And 8.9-Amido Geldanamycin Analog And Toward The Total Synthesis Of (-)-Englerin A, Yong Wang

Theses and Dissertations

Total Synthesis of 4'-ester Resveratrol Analogs and 8, 9-amido Geldanamycin Analog and toward the Total Synthesis of (-)-Englerin A Yong Wang Department of Chemistry and Biochemistry, BYU Doctor of Philosophy The phytoalexin resveratrol and its 4'-ester analogs have been prepared with a decarbonylative Heck reaction. The deprotecting step has been modified and improved to increase yield and avoid chromatography. A set of resveratrol analogs and resveratrol have been tested with melanoma and pancreatic cell assays. The 8, 9-amido Geldanamycin analog has been synthesized with a convergent route, involving 28 simplified steps in its longest linear sequence. Synthetic methodologies, such as …

Substrate Binding Modulates The Activity Of Mycobacterium Smegmatis G, A Flavin-Dependent Monooxygenase Involved In The Biosynthesis Of Hydroxamate-Containing Siderophores, Reeder Robinson, Pablo Sobrado

Chemistry Faculty Research & Creative Works

Mycobacterium smegmatis G (MbsG) is a flavin-dependent monooxygenase that catalyzes the NAD(P)H- and oxygen-dependent hydroxylation of the terminal amino group on the side chain of l-lysine in the biosynthetic pathway of the siderophore mycobactin. Mycobactins are essential for mycobacterium growth under iron-limiting conditions encountered during infection in mammals. Thus, enzymes involved in the biosynthesis of mycobactin represent potential drug targets. MbsG was expressed in Escherichia coli and purified using metal affinity and ionic exchange chromatographies. Recombinant MbsG represents the first member of this class of enzymes isolated in the active form, with a tightly bound FAD cofactor. The k cat …

Polycyclic Aromatic Compounds As Anticancer Agents: Evaluation Of Synthesis And In Vitro Cytotoxicity, Debasish Bandyopadhyay, Jose C. Granados, John D. Short, Bimal K. Banik

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Polycyclic aromatic hydrocarbons (PAHs) are considered to be significant environmental carcinogens. Additionally, various planar ring systems are capable of intercalating with DNA, leading to a number of drugs that possess chemotherapeutic activity. In this study, three new polyaromatic compounds with a side chain were synthesized, and spectroscopic as well as elemental analyses were performed. The addition of the long chains to either chrysene or pyrene caused a red-shift in the spectral emission when compared to the corresponding polycyclic aromatic hydrocarbons itself. Furthermore, the cytotoxicity of the three novel polyaromatic compounds was evaluated in vitro in a panel of cultured mammalian …

Chemistry & Biochemistry Newsletter, Department Of Chemistry & Biochemistry, South Dakota State University

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 International Year of Chemistry Recognizes SDSU program

Page 3 Student Research Focuses on Soil Health

Page 4 Medial Laboratory Science Receives Accreditation; Pat Tille is Honored by ASCLS and Alpha Mu Tau

Page 5 Mass Spec Open House; Foundation Donors; Grad Student Chosen NSF Scholar

Page 6 Researcher Featured on SDSU’s Web site; Recent Grants

Page 7 New Graduate Students

Page 8 New Faculty; Alumni Updates

An Lcms Based Assay For Detection And Quantification Of Bacterial Cell Wall Intermediates, Chandra Sekhar Arigapudi

All Capstone Projects

The main objective of my project is to determine the bacterial cell wall intermediates in E.coli and develop an LCMS method that Phosphomycin is a PEP analogue that irreversibly inhibits UDP-GluNAc-enolpyruvate transferase (MurA enzyme), which prevents the formation of N-acetyl muramic acid, which is an essential element in the Peptidoglycan cell wall. Antibacterial agents have a tremendous impact on human health. Most of the antibacterial agents, including beta lactams target the bacterial cell wall biosynthesis.The pathway for Escherichia coli is shown in page 19. Among the most widely used antibiotics, beta lactams inhibit the penicillin binding protein (PBPs)which block the …

Evaluation And In Vitro Studies Of Folate Peg Biotin And Other Peg Agents, Vikram Reddy Kasarala

All Capstone Projects

Folate is an essential component for cell growth and cell division, playing a major role in DNA synthesis. It is common sense that the rapidly dividing cells synthesize more DNA, including cancer cells. Also, it was reported that cancer cells over express Folate receptors and this was the basis for our probe for cancer cells. We used long PEG biotin in conjugation with Folate. Previous studies in our group showed that the PEG could be used in the sensor to detect and capture cancer cells. The present study was aimed at evaluating the effect of Long PEG containing Folate based …

Evaluation And In Vitro Studies Of Folate Peg Biotin And Other Peg Agents, Christopher E. Zmudka

All Capstone Projects

Folate receptor alpha is a membrane-bound protein displaying high affinity for folic acid. This receptor is believed to serve as a receptor-mediated transport system of folic acid into cancer and cells associated with inflammation. Interesting, most normal cells in the body have little if no high affinity folate receptor alpha. Based on these attributes, folate based drug delivery, imaging systems, and diagnostic systems are in several stages of development worldwide.

Numerous methods have been explored in the literature in an attempt to detect low levels of free folate receptor and/or rare circulating cancer cells. In an attempt to further exploit …

Nanoparticles For Mercury Abatement, Sunil Krishna Thanikanti

All Capstone Projects

Mercury is considered to be a global contaminant. It does not break down in the environment and can build up in living organisms. Mercury can be carried long distances on wind currents, staying in the atmosphere for long periods of time, when in its vapor form. High mercury exposure results in permanent nervous system and kidney damage. Mercury exists in three different chemical forms: elemental, inorganic, and organic. The routes of exposure can be inhalation, ingestion, or skin contact. Vapor from liquid elemental mercury and methyl mercury are more easily absorbed than inorganic mercury salts and can, therefore, cause more …

Wound Healing And The Role Of Biomarkers And Biofilms, Mujtaba Khan

All Capstone Projects

An injury to the skin alters the integrity of underlying tissues and microcirculation and thus certainly culminates in a wound. Wound healing is a highly complex, dynamic, interactive and well regulated physiological process involving blood cells, extracellular matrix, parenchyma cells and soluble mediators. It starts with alteration in integrity of tissues and ends with the formation of scar. The process of wound healing is distinguished into Haemostasis, Inflammation, Proliferation and Remodeling. Various cells like platelets, neutrophils, macrophages, lymphocytes, angiocytes, keratinocytes, fibroblasts and factors like platelet derived growth factor, transforming growth factor, platelet derived epidermal growth factors, fibroblasts growth factor, albumin, …

Layer-By-Layer Fabrication Of Covalently Crosslinked And Reactive Polymer Multilayers Using Azlactone-Functionalized Copolymers: A Platform For The Design Of Functional Biointerfaces, Maren E. Buck, David M. Lynn

Chemistry: Faculty Publications

We report a method for modulating the physicochemical properties of surfaces that is based on the reactive layer-by-layer fabrication of covalently crosslinked thin films using azlactone-functionalized copolymers. We demonstrate that copolymers containing different molar ratios of methyl methacrylate (MMA) and 2-vinyl-4,4-dimethylazlactone (VDMA) can be alternately deposited with poly(ethyleneimine) to assemble covalently crosslinked thin films. Characterization using ellipsometry demonstrates that, in general, film growth and thickness decrease as the content of reactive, azlactone functionality in the copolymer used to assemble the film decreases. Reflective infrared spectroscopy experiments demonstrate that films fabricated from MMA:VDMA copolymers contain residual azlactone functionality and that these …

Analytical Evaluation Of Imaging Agents, Vineela Chowdary Talluri

All Capstone Projects

The folate receptor has achieved great importance for use in targeted drug delivery and in vitro and in vivo diagnostic assays. The folate receptor (FR) is over expressed on several cancer cell types and activated macrophages, but exists in relatively low abundance on the surface of non-cancerous tissue and non inflammatory cells. This unique attribute is the hallmark of folate – targeted methodologies allowing the diagnostic agent and/or drug to be ferried to the specific disease sites while preventing “off target” effects in normal tissues. Although several folate-based dyes have been reported, simple and detailed synthetic and purification methods for …

Capture And Analysis Of Cells Using Magnetic Beads, Alexandro Dominguez

All Capstone Projects

Magnetic separation of cells and bacterium is a fascinating field of study. There are tremendous capabilities in separation, selectivity, and sensitivity. Magnetic separation reduces complex techniques, time consuming preparation, and complicated multistep methods of separation.The separation of cells, bacterium, and macromolecules can be extremely challenging. Fortunately, magnetically tagged cells, bacterium and macromolecules can be easily separated without great expertise. Antibody magnetic micro beads are specific to a cell, bacterium, or macromolecules. Separating a mixture can lead to a better, more accurate analysis of samples that can be crucial in the medical field, therapeutic drug delivery systems, and in some circumstances …

A Modified Stokes-Einstein Equation For A Beta Aggregation, Srisairam Achuthan, Bong Jae Chung, Preetam Ghosh, Vijayaraghavan Rangachari, Ashwin Vaidya

Faculty Publications

Background: In all amyloid diseases, protein aggregates have been implicated fully or partly, in the etiology of the disease. Due to their significance in human pathologies, there have been unprecedented efforts towards physiochemical understanding of aggregation and amyloid formation over the last two decades. An important relation from which hydrodynamic radii of the aggregate is routinely measured is the classic Stokes-Einstein equation. Here, we report a modification in the classical Stokes-Einstein equation using a mixture theory approach, in order to accommodate the changes in viscosity of the solvent due to the changes in solute size and shape, to implement a …

Fluorescence Probes For Cellular Thiol And Disulfide Detection: Sythesis And Biophysical Characterization, Timothy Jonhera

Dissertations (1934 -)

The total concentration of cellular thiols is about 30 mM, and use of current fluorescent chemical probes to quantitate these thiols inside cells is impractical. We recently reported fluorescent dithio probes (donor-S-S-acceptor, DSSA) with unusually low reduction potential (- 0.6 V) that can detect changes in intracellular thiols and cross membranes of bacterial and mammalian cells, but they could not quantify thiol redox state. Here we report a new variant of the DSSA series, which has hydroxy coumarin (Ex: 320 nm, Em: 460 nm) as donor and fluorescein (Ex: 485 nm, Em: 520 nm) as acceptor. The probe was characterized …

Nmr And Computational Studies Of Nad(P)(H) Cofactor Binding, Junghwa Kim

Master's Theses (2009 -)

Tuberculosis (TB) is one of the most dangerous diseases in a sense of spread method. According W.H.O., one third of world population has this disease and annual one of these infected people spreads 10 -15 people unintentionally. To protect human from this bacterial, the unique feature of mycrobacterial [sic] TB was studied previously. The unique cell wall, peptidoglycan, has high content of DAP (diaminopimelic acid). The disruption of synthesis DAP results in cell death due to instability of cell wall. One way to inhibiting synthesis of DAP is to modify cofactor which acts with dehydrogenase. To do that the study …

A Truly Green Synthesis Of A-Aminonitriles Via Strecker Reaction, Debasish Bandyopadhyay, Juliana M. Velazquez, Bimal K. Banik

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Background: The classical Strecker reaction is one of the simplest and most economical methods for the synthesis of racemic a-aminonitriles (precursor of a-amino acids) and pharmacologically useful compounds.

Results: Indium powder in water is shown to act as a very efficient catalyst for one-pot, three-component synthesis of a-aminonitriles from diverse amines, aldehydes and TMSCN. This general rapid method is applicable to a wide range of amines and aldehydes and produces products in excellent yield.

Conclusions: The present one-pot, three-component environmentally benign procedure for the synthesis of aaminonitriles will find application in the synthesis of complex biologically active molecules.

Exploring The Roles Of Nucleobase Desolvation And Shape Complementarity During The Misreplication Of O6-Methylguanine, Delia Chavarria, Andrea Ramos Serrano, Ichiro Hirao, Anthony J. Berdis

Chemistry Faculty Publications

O6-methylguanine is a miscoding DNA lesion arising from the alkylation of guanine. This report uses the bacteriophage T4 DNA polymerase as a model to probe the roles hydrogen-bonding interactions, shape/size, and nucleobase desolvation during the replication of this miscoding lesion. This was accomplished by using transient kinetic techniques to monitor the kinetic parameters for incorporating and extending natural and non-natural nucleotides. In general, the efficiency of nucleotide incorporation does not depend on the hydrogen-bonding potential of the incoming nucleotide. Instead, nucleobase hydrophobicity and shape complementarity appear to be the preeminent factors controlling nucleotide incorporation. In addition, shape complementarity plays a …

Rna Oxidation Adducts 8-Ohg And 8-Oha Change With Aβ42 Levels In Late-Stage Alzheimer's Disease, Adam M. Weidner, Melissa A. Bradley, Tina L. Beckett, Dana M. Niedowicz, Amy L.S. Dowling, Sergey V. Matveev, Harry Levine, Mark A. Lovell, M. Paul Murphy

Sanders-Brown Center on Aging Faculty Publications

While research supports amyloid-β (Aβ) as the etiologic agent of Alzheimer's disease (AD), the mechanism of action remains unclear. Evidence indicates that adducts of RNA caused by oxidation also represent an early phenomenon in AD. It is currently unknown what type of influence these two observations have on each other, if any. We quantified five RNA adducts by gas chromatography/mass spectroscopy across five brain regions from AD cases and age-matched controls. We then used a reductive directed analysis to compare the RNA adducts to common indices of AD neuropathology and various pools of Aβ. Using data from four disease-affected brain …

The Regulation Of Skeletal Muscle Protein Turnover During The Progression Of Cancer Cachexia In The ApcMin/+ Mouse, James P. White, John W. Baynes, Stephen L. Welle, Matthew C. Kostek, Lydia E. Matesic, Shuichi Sato, James A. Carson

Faculty Publications

Muscle wasting that occurs with cancer cachexia is caused by an imbalance in the rates of muscle protein synthesis and degradation. The Apc(Min/+) mouse is a model of colorectal cancer that develops cachexia that is dependent on circulating IL-6. However, the IL-6 regulation of muscle protein turnover during the initiation and progression of cachexia in the Apc(Min/+) mouse is not known. Cachexia progression was studied in Apc(Min/+) mice that were either weight stable (WS) or had initial (≤5%), intermediate (6-19%), or extreme (≥20%) body weight loss. The initiation of cachexia reduced %MPS 19% and a further ∼50% with additional weight …

Cucurbit[8]Uril Rotaxanes, Vijayakumar Ramalingam, Adam R. Urbach

Chemistry Faculty Research

The synthesis of [2]rotaxanes, each comprising a viologen core threaded through a cucurbit[8]uril (Q8, Figure 1) macrocycle and stoppered by tetraphenylmethane groups, and their binding to second guests as inclusion complexes in organic and aqueous media are described. Stoppering was observed to have little effect on binding. Chemical modification of the threaded guest was used to control solubility and binding characteristics, thus demonstrating a novel approach to making artificial receptors with readily modifiable properties.