Chemistry Commons^™

Microchip Liquid Chromatography And Capillary Electrophoresis Separations In Multilayer Microdevices, Hernan Vicente Fuentes

Theses and Dissertations

In this dissertation, several microfabricated devices are introduced to develop new applications in the area of chemical analysis. Electrochemical micropumps, chip-based liquid chromatography systems and multilayer capillary electrophoresis microdevices with crossover channels were fabricated using various substrates such as poly(dimethylsiloxane) (PDMS), glass, and poly(methyl methacrylate) (PMMA). I have demonstrated pressure-driven pumping of liquids in microfabricated channels using electrochemical actuation. PDMS-based micropumps were integrated easily with channel-containing PMMA substrates. Flow rates on the order of ~10 µL/min were achieved using low voltages (10 V). The potential of electrolysis-based pumping in microchannels was further evaluated for pressure driven microchip liquid chromatography (LC). …

A Set Of Phosphatase-Inert “Molecular Rulers” To Probe For Bivalent Mannose 6-Phosphate Ligand-Receptor Interactions, Xiang Fei, Christopher M. Connelly, Richard G. Macdonald, David B. Berkowitz

David Berkowitz Publications

A set of bivalent mannose 6-phosphonate “molecular rulers” has been synthesized to examine ligand binding to the M6P/IGF2R. The set is estimated to span a P-P distance range of 16-26 Å (MMFF energy minimization on the hydrated phosphonates). Key synthetic transformations include sugar triflate displacement for phosphonate installation and Grubbs I cross-metathesis to achieve bivalency. Relative binding affinities were tested by radioligand displacement assays versus PMP-BSA (pentamannose phosphate-bovine serum albumin). These compounds exhibit slightly higher binding affinities for the receptor (IC₅₀’s = 3.7-5 &#;M) than the parent, monomeric mannose 6-phosphonate ligand and M6P itself (IC₅₀ = 11.5 …

Microfluidic Electro-Osmotic Flow Pumps, John Mason Edwards

Theses and Dissertations

The need for miniaturized, portable devices to separate and detect unknown compounds has greatly multiplied, leading to an increased interest in microfluidics. Total integration of the detector and pump are necessary to decrease the overall size of the microfluidic device. Using previously developed thin film technologies, an electroosmotic flow (EOF) pump was incorporated in a microfluidic liquid chromatography device. An EOF pump was chosen because of its simple design and small size. EOF pumps fabricated on silicon and glass substrates were evaluated. The experimental flow rates were 0.19-2.30 microliters/minute for 40-400 V. The theoretical pump efficiency was calculated along with …

Myricetin Inhibits Escherichia Coli Dnab Helicase But Not Primase, Mark A. Griep, Sheldon Blood, Marilynn A. Larson, Scott A. Koepsell, Steven H. Hinrichs

Mark A. Griep Publications

Primase and DnaB helicase play central roles during DNA replication initiation and elongation. Both enzymes are drug targets because they are essential, persistent among bacterial genomes, and have different sequences than their eukaryotic equivalents. Myricetin is a ubiquitous natural product in plants that is known to inhibit a variety of DNA polymerases, RNA polymerases, reverse transcriptases, and telomerases in addition being able to inhibit kinases and helicases. We have shown that myricetin inhibits Escherichia coli DnaB helicase according to a mechanism dominated by noncompetitive behavior with a K_i of 10.0 ± 0.5 μM. At physiological ATP concentration, myricetin inhibits …

Counter-Flow Ion Mobility Analysis: Design, Instrumentation, And Characterization, Nosa Agbonkonkon

Theses and Dissertations

The quest to achieve high resolution in ion mobility spectrometry (IMS) has continued to challenge scientist and engineers in the field of separation science. The low resolution presently attainable in IMS has continued to negatively impact its utility and acceptance. Until now, efforts to improve the resolution have mainly focused on better instrumentation and detection methods. However, since the resolution of IMS is diffusion limited, it makes sense to address this limitation in order to attain high resolution. This dissertation presents a new IMS technique, which utilizes a high electric field and opposing high gas flow velocity with the aim …

Microwave Spectra And Ab Initio Studies Of Ar-Propane And Ne-Propane Complexes: Structure And Dynamics, Karen I. Peterson, David Pullman, Wei Lin, Andrea J. Minei, Stewart E. Novick

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

Microwave spectra in the 7-26 MHz region have been measured for the van der Waals complexes, Ar-C H3 C H2 C H3, Ar- C13 H3 C H2 C H3, Ne20 -C H3 C H2 C H3, and Ne22 -C H3 C H2 C H3. Both a - and c -type transitions are observed for the Ar-propane complex. The c -type transitions are much stronger indicating that the small dipole moment of the propane (0.0848 D) is aligned perpendicular to the van der Waals bond axis. While the 42 transition lines observed for the primary argon complex are well fitted to …

Synthesis And Characterization Of Novel Chiral Conjugated Materials, Andrzej Rajca, Makoto Miyasaka

Andrzej Rajca Publications

Chirality is increasingly important in the design of organic π-conjugated materials. One of the aspects of the design involves optimization of achiral properties through the introduction of chirality. In this context, the inherent three-dimensional character of chirality and the control of intermolecular interactions associated with diastereomeric recognition provide a versatile handle for the optimization of supramolecular structures, film morphology and liquid crystalline order of π-conjugated polymers and oligomers in three dimensions. These inherently achiral properties have an impact on optoelectronic coupling, which may affect the fabrication of light-emitting diodes, field effect transistors, photodiodes, photovoltaic cells, fluorescent sensors and other devices. …

Supramolecular Chemistry: A Capstone Course, Adam R. Urbach, Christopher J. Pursell, John D. Spence

Chemistry Faculty Research

A fourth-year capstone course offers students an opportunity to integrate topics covered in the core disciplinary courses, to learn an advanced interdisciplinary topic, and to approach unfamiliar problems and literature. This article describes a fourth-year capstone course designed to incorporate components of faculty lectures, student seminars, and original, hands-on research projects in order to cover the topic of supramolecular chemistry in one semester with unusual depth. This approach should be applicable to other advanced topics in chemistry.

Reactivity Of Iso-Diiodomethane And Iso-Iodoform, Isomers Of Ch2i2 And Chi3, Toward The Double Bond Of A Variety Of Cycloalkenes, Alexander N. Tarnovsky, Irmin Pascher, Torbjorn Pascher

Chemistry Faculty Publications

The metastable CH2I-I and CHI2-I isomers formed by UV photolysis of CH2I2, and CHI3 transfer methylene and iodomethylene groups, respectively, to a variety of cycloalkenes, leading to their cyclopropanation. More than a 100-fold increase of the reaction rate with increasing solvent polarity suggests a dipolar transition state. The fastest second-order rates observed were in CH3CN. However, CH2Cl2 will be the more appropriate reaction medium because the isomer thermal stability is greater in CH2Cl2 than in the more polar CH3CN.

Assemblies Of Assemblies: Supramolecular Ordering Of Nanoscopic Ruthenium Polypyridyl Building Blocks, Kelly Lyle Wouters

Chemistry & Biochemistry Dissertations - Archive

Biological systems have long since perfected the development of nanoengineering. Cellular structure and machinery is based, to a significant extent, on the formation of nanometer to micron-sized assemblies of proteins. These architectures start with unique primary, secondary, tertiary, and quaternary structural complexity and can be constructed from a relatively simple set of building blocks. Using this strategy as inspiration, assemblies based on [Ru(phenanthroline)3]2+ building blocks have been synthesized forming polyruthenium species bridged by the tpphz (tetrapyrido[3,2-a:2’,3’-c:3’’,2’’-h:2’’’,3’’’-j]phenazine) and tatpp (9,11,20,22- tetraaza tetrapyrido[3,2-a:2’,3’-c:3’’,2’’-l:2’’’’,3’’’’-n]-pentacene) ligands. Importantly, these assemblies exhibit unique hierarchical structural components which arise directly from the chirality inherent in the octahedral …

Novel Phenomena In Encapsulating Hydrocarbon Gases, Anas W. Saleh

Chemistry & Biochemistry Theses - Archive

The use of hydrophobic forces for entrapment of gases in water will be discussed. Natural hydrocarbons, haloalkanes, and anesthetic gases are hydrophobic in nature. In the course of this investigation water-soluble molecular capsules that possess hydrophobic interiors were synthesized. The encapsulation of hydrocarbon gases in water and in solid state was achieved and monitored by NMR spectroscopy. Our findings may lead to novel, capsule-based materials for gas separation and purification. The work presented in this thesis is divided into two sections. The first section discusses the synthesis of two water soluble hemicarcerands and their use as hosts in encapsulating hydrocarbon …

⁵⁷Fe Mössbauer Spectral And Muon Spin Relaxation Study Of The Magnetodynamics Of Monodispersed Γ-Fe₂O₃ Nanoparticles, Leïla Rebbouh, Raphäel P. Hermann, Fernande Grandjean, Taeghwan Hyeon, Kwangjin An, Alex Amato, Gary J. Long

Chemistry Faculty Research & Creative Works

The Mössbauer spectra of monodispersed iron oxide nanoparticles with diameters of 4, 7, 9, and 11 nm have been measured between 4.2 and 315 K and fitted within the formalism for stochastic fluctuations of the hyperfine Hamiltonian. In this model, the hyperfine field is assumed to relax between the six ±x, ±y, and ±z directions in space with a distribution of relaxation rates that is temperature dependent. Muon spin relaxation measurements have been carried out on the 9 nm particles between 4.2 and 295 K. Both techniques reveal three regimes in the magnetic dynamics of these nanoparticles. In the low-temperature …

Ammonia Elimination From Protonated Nucleobases And Related Synthetic Substrates, Ming Qian, Shuo Yang, Hong Wu, Papiya S. Majumdar, Nathan D. Leigh, Rainer Glaser

Chemistry Faculty Research & Creative Works

The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH₃ elimination does present a major path for the fragmentations of the ions [1h + H]⁺, [2h + H]⁺, and …

Electrostatic Force Microscopy Studies Of Boron-Doped Diamond Films, Santosh Gupta, O. A. Williams, Eric W. Bohannan

Computer Science Faculty Research & Creative Works

Much has been learned from electrochemical properties of boron-doped diamond (BDD) thin films synthesized using microwave plasma-assisted chemical vapor deposition about the factors influencing electrochemical activity, but some characteristics are still not entirely understood, such as its electrical conductivity in relation with microscale structure. Therefore, to effectively utilize these materials, understanding both the microscopic structure and physical (electrical, in particular) properties becomes indispensable. in addition to topography using atomic force microscopy, electrostatic force microscopy (EFM) in phase mode measuring the long-range electrostatic force gradients, helps to map the electrical conductivity heterogeneity of boron-doped micro-/nanocrystalline diamond surfaces. the mapping of electrical …

Rheology Of Tin Fluorophosphate Glass/Polyamide 12 Hybrids In The Low Concentration Regime, Kevin Urman, Thomas Schweizer, Joshua U. Otaigbe

Faculty Publications

Phosphate glass (Pglass)/polymer hybrids are a unique material class that promises to help fulfill the growing need for new advanced materials. Rheological investigations into Pglass/polyamide 12 hybrids have shown a strong dependence on temperature and composition. Strong negative deviations from the log-additivity rule are also observed for these materials as well as a reduction in the activation energy for viscous flow. Hybrids containing < 2 vol. % Pglass are theologically simple fluids that display temperature independence in plots of storage modulus versus loss modulus. Hybrids containing >= 2 vol. % Pglass are rheologically complex and do not obey the time-temperature superposition principle. Through application of Han plots, we identified a structural change that occurs in hybrids containing >= 2 vol. % Pglass at …

Structure And Thermophysical Properties Of Single-Wall Si Nanotubes, Xinwei Wang, Zhen Huang, Tao Wang, Yuk Wai Tang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

In this work, molecular dynamics (MD) simulation based on the environment-dependent interatomic potential is carried out to explore the structure, atomic energy distribution, and thermophysical properties of single-wall Si nanotubes (SWSNTs). The unique structure of SWSNTs leads to a wider range energy distribution than crystal Si (c-Si), and results in a bond order in the range of 4.8~5. The thermal conductivity of SWSNTs is much smaller than that of bulk Si, and shows significantly slower change with their characteristic size than that of Si films. Out of the three types of SWSNTs studied in this work, pentagonal SWSNTs have the …

A Strategy To Protect And Sensitize Near-Infrared Luminescent Nd3+ And Yb3+: Organic Tropolonate Ligands For The Sensitization Of Ln3+-Doped Nayf4 Nanocrystals, Jian Zhang, Chad M. Shade, Demetra A. Chengelis, Stéphane Petoud

Department of Chemistry: Faculty Publications

A strategy to sensitize and protect near-infrared (NIR) emitting Nd³⁺ and Yb³⁺ is presented. Combining protection provided by the inorganic matrix of NaYF₄ nanocrystals and sensitization from tropolonate ligands capped on their surface, the lanthanide cation centered luminescence was observed through the ligand excitation. The extended lanthanide luminescence lifetimes indicate the success of this strategy.

An Overview Of The Genus Nardostachys, Asima Chatterjee, Utpal Dutta, Debasish Bandyopadhyay, Anupam Nayak, Bidyut Basak, Avijit Banerji, Julie Banerji

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

Nardostachys jatamansi, a medicinally important herb of Nepalese origin, has been used for centuries in the Ayurvedic and Unani systems of medicine. In combination with Marsilea minuta it is being used as an antistress and anticonvulsant drug and also finds use in the treatment of epilepsy. Recently, it has been reported that N. jatamansi, which plays an important role in protecting from cerebral ischemia and liver damage, is also used for the treatment of osteoporosis and hypercalcemia. The other member of the genus Nardostachys, N. chinensis, possesses antifungal and antimalarial properties. It is also used in the treatment of skin …

In-House Polymerase Chain Reaction For Affordable And Sustainable Chlamydia Trachomatis Detection In Trinidad And Tobago, Joanne Rampersad, Xiaohui Wang, Helen Gayadeen, Samuel Ramsewak, David Ammons

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

Objectives: To provide a preliminary assessment of in-house polymerase chain reaction (PCR) as an alternative to the more costly commercial test for detection of asymptomatic infection by Chlamydia trachomatis and to provide much needed demographic data on infection indicators within the Trinidad and Tobago public health care system.

Methods: An inexpensive in-house nested-PCR with an Internal Amplification Control was used to detect C. trachomatis and Neisseria gonorrhoeae in urine samples collected from 273 apparently healthy, pregnant women from March-September 2004 in Trinidad, West Indies. Demographic information on participants was collected and subjected to statistical analyses.

Results: C. trachomatis was detected …

Synthesis Of Cyclopropanes Via Organoiron Methodology: Preparation Of Rac-Dysibetaine Cpa, Tasneem A. Siddiquee, Julie Lukesh, Sergey Sergey Lindeman, William A. Donaldson

Chemistry Faculty Research and Publications

The cyclopropane containing betaine, rac-dysibetaine CPa, was prepared from (1-methoxycarbonylpentadienyl)-Fe(CO)₂PPh₃⁺ by nucleophilic addition of nitromethane anion followed by oxidatively induced reductive elimination.

Student Selected As Finalist For Chemistry Award, Heather Lindquist

News and Events (Discontinued Series)

No abstract provided.

Structure Of Arabidopsis Thaliana 5-Methylthioribose Kinase Reveals A More Occluded Active Site Than Its Bacterial Homolog, Shao Yang-Ku, Kenneth A. Cornell, P. Lynne Howell

Chemistry and Biochemistry Faculty Publications and Presentations

Background: Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target for the design of specific herbicides or antibiotics.

Results: The structure of Arabidopsis thaliana MTR kinase co-crystallized with ATPγS and MTR has been determined at 1.9 Å resolution. The structure is similar to B. subtilis MTR kinase and has the same protein kinase fold observed in other evolutionarily related …

1,3-Alternate Calix[4]Arene Nitronyl Nitroxide Tetraradical And Diradical: Synthesis, X-Ray Crystallography, Paramagnetic Nmr Spectroscopy, Epr Spectroscopy, And Magnetic Studies, Andrzej Rajca, Maren Pink, Sumit Mukherjee, Suchada Rajca, Kausik Das

Andrzej Rajca Publications

Calix[4]arenes constrained to 1,3-alternate conformation and functionalized at the upper rim with four and two nitronyl nitroxides have been synthesized, and characterized by X-ray crystallography, magnetic resonance (EPR and ¹H NMR) spectroscopy, and magnetic studies. Such calix[4]arene tetraradicals and diradicals provide scaffolds for throughbond and through-space intramolecular exchange couplings.

Includes Supplemental Data (27 pages).

Poly[(Nitrato-KO)Tris((Μ3-1h-1,2,4-Triazolato)Dizinc(Ii)]: A Three-Dimensional Coordination Polymer, Josephy M. Ellsworth, Mark D. Smith, Hans-Conrad Zur Loye

Faculty Publications

In the title compound, [Zn₂(C₂H₂N₃)₃(NO₃)], there are two unique Zn atoms, both with site symmetry m. One forms a ZnN₃O tetrahedron and the other a ZnN₆ octahedron. One and a half 1H-1,2,4-triazolate ligands, with the half-ligand located on a mirror plane, and a disordered nitrate anion complete the asymmetric unit of the structure. The polymeric connectivity is three-dimensional.

Structural Characterization Using The Multiple Scattering Effects In Grazing-Incidence Small-Angle X-Ray Scattering, Byeongdu Lee, Chieh-Tsung Lo, P. Thiyagarajan, Dong R. Lee, Zhongwei Niu, Qian Wang

Faculty Publications

The multiple scattering effects present in grazing-incidence small-angle X-ray scattering (GISAXS) data and interference between them are addressed theoretically as well as experimentally with measurement of a series of patterns at different incident angles, referred to as `incident-angle-resolved GISAXS' (IAR-GISAXS). X-ray reflectivity (XR), GISAXS and IAR-GISAXS of virus particles on Si-substrate supported-polystyrene films have been measured and all the data have been analyzed with appropriate formalisms. It was found that under certain conditions it is possible to extract the correct structural features of the materials from the GISAXS/IAR-GISAXS data using the kinematic SAXS formalisms, without the need to use the …

Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the π-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of …

Anti-Icing Coatings And Methods, Russell G. Alger

Michigan Tech Patents

A method of inhibiting or preventing bonding between snow or ice and a substrate. The method includes applying an adhesive to the substrate, broadcasting an aggregate onto the adhesive, the aggregate having the capacity to receive an anti-icing chemical into the aggregate, and applying the anti-icing chemical onto the aggregate so that at least a portion of the anti-icing chemical is received into at least a portion of the aggregate.

The Characterization Of Trna Modifying Enzymes S-Adenosylmethionine : Trna Ribosyltransferase-Isomerase (Quea) And A Novel Type I Gtp Cyclohydrolase, Shilah Amal Bonnett

Dissertations and Theses

Queuosine is a hypermodified nucleoside located in the wobble position of bacterial and eukaryotic tRNAs coding for Asp, Tyr, His and Asn. The biosynthesis involves the participation of S-adenosyl-methionine:tRNA ribosyltransferase-isomerase (QueA) and a GTP Cyclohydrolase-I. QueA catalyzes the transfer and isomerization of the ribosyl moiety from AdoMet to preQ1 modified tRNA. Substrate analogs of AdoMet were used to elucidate important substrate-enzyme interactions and to test key steps in the proposed chemical mechanism. Replacing AdoMet with SeAdoMet had little effect upon substrate binding but exhibited 30-fold reduction in kcat, consistent with deprotonation at C-5' as the first catalytic step. 7-deazaAdoMet failed …

Microcantilever Surface Modification For Chem-/Bio-Sensing, Hongwei Du

Doctoral Dissertations

One focus of the microcantilever (MCL) sensing area is to develop a novel surface modification approach to increase the microcantilever bending amplitudes and thus further improve sensitivities. In this dissertation, enzyme incorporated using the Layer by-Layer (LbL) process, LbL deposition of micro-, nano-hydrogel particles and electrophoretic deposition (EPD) of micro-, nano-hydrogel particles were applied to prepare a multilayer or thin hydrogel films on the surface of microcantilevers. Prior to applying to the microcantilevers, LbL and electrophoretic deposition techniques were also applied to gold coated silicon wafer surfaces to investigate the feasibility and deposition behavior using these techniques. The multilayers prepared …

Luminescent Charge-Transfer Platinum(Ii) Metallacycle, Fei Hua, Solen Kinayyigit, Aaron A. Rachford, Elena A. Shikhova, Sebastien Goeb, John R. Cable, Christopher J. Adams, Kristin Kirschbaum, A. Alan Pinkerton, Felix N. Castellano

Chemistry Faculty Publications

The photophysical and electrochemical properties of a platinum(II) diimine complex bearing the bidentate diacetylide ligand tolan-2,2'-diacetylide (tda), Pt(dbbpy)(tda) [dbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine] (1), are compared with two reference compounds, Pt(dbbpy)(C CPh)(2) (2) and Pt(dppp)tda [dppp = 1,3-bis(diphenylphosphino)propane] (3), respectively, The X-ray crystal structure of 1 is reported, which illustrates the nearly perfect square planarity exhibited by this metallacycle. Chromophore 2 possesses low-lying charge-transfer excited states analogous to 1, whereas structure 3 lacks such excited states but features a low-lying platinum-perturbed tda intraligand triplet manifold. In CH2Cl2, 1 exhibits a broad emission centered at 562 nm at ambient temperature, similar to 2, …