Chemistry Commons^™

Pt (Iv) Complexes As Prodrugs For Cisplatin, Yi Shi, Shu-An Liu, Deborah J. Kerwood, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

The antitumor effects of platinum(IV) complexes, considered prodrugs for cisplatin, are believed to be due to biological reduction of Pt(IV) to Pt(II), with the reduction products binding to DNA and other cellular targets. In this work we used pBR322 DNA to capture the products of reduction of oxoplatin, c,t,c-[PtCl ₂(OH) ₂(NH ₃) ₂], 3, and a carboxylate-modified analog, c,t,c-[PtCl ₂(OH)(O ₂CCH ₂CH ₂CO ₂H)(NH ₃) ₂], 4, by ascorbic acid (AsA) or glutathione (GSH). Since carbonate plays a significant role in the speciation of platinum complexes in solution, we …

Manipulating Protein Conformations By Single-Molecule Afm-Fret Nanoscopy, Yufan He, Maolin Lu, Jin Cao, H. Peter Lu

Chemistry Faculty Publications

Combining atomic force microscopy and fluorescence resonance energy transfer spectroscopy (AFM-FRET), we have developed a single-molecule AFM-FRET nanoscopy approach capable of effectively pinpointing and mechanically manipulating a targeted dye-labeled single protein in a large sampling area and simultaneously monitoring the conformational changes of the targeted protein by recording single-molecule FRET time trajectories. We have further demonstrated an application of using this nanoscopy on manipulation of single-molecule protein conformation and simultaneous single-molecule FRET measurement of a Cy3-Cy5-labeled kinase enzyme, HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase). By analyzing time-resolved FRET trajectories and correlated AFM force pulling curves of the targeted single-molecule enzyme, we are able …

Toward A Stable Α-Cycloalkyl Amino Acid With A Photoswitchable Cationic Side Chain, Riccardo Rossi Paccani, Donato Donati, Stefania Fusi, Loredana Latterini, Grazia Farina, Vinicio Zanirato, Massimo Olivucci

Chemistry Faculty Publications

The N-alkylated indanylidenepyrroline (NAIP) Schiff base 3 is an unnatural a-amino acid precursor potentially useful for the preparation of semisynthetic peptides and proteins incorporating charged side chains whose structure can be modulated via Z/E photoisomerization. Here we report that the heteroallylic protons of 3 led to partial loss of ethanol accompanied by formation of the novel heterocyclic system 4 during attempted deprotection. We also show that the same protons catalyze the thermal isomerization of 3, making the light-driven conformational control concept ineffective for times longer than a few hours. These problems are not present in the previously unreported compound 5 …

Function Assignment Within The Haloacid Dehalogenase Superfamily, Hua Huang

Chemistry and Chemical Biology ETDs

The HaloacidDehalogenase Enzyme Superfamily (HADSF) is a ubiquitous family of enzymes. Presently, more than 45,000 deposited gene sequences encode proteins of the HADSF, and only a fraction of these have defined structure and/or function. The work described in this thesis focuses on function determination in several members of the HADSF. An integrated bioinformatic-protein structure-enzyme mechanism approach was used to differentiate and track D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GHMB) and histidinol phosphatephosphatase (HisB)orthologues; 2-keto-3-deoxynononic acid 9-phosphatephosphatase (KDN9PP) and 2-keto-3-deoxy-D-manno-octulosonic acid 8-phosphatephosphatase (KDO8PP)orthologues; inorganic pyrophosphatase and β-phosphoglucomutase(β-PGM) orthologues. In addition, a structure-function/bioinformatic analysis was carried-out on the bifunctional 1,3-diposphoglycerate acyltransferase/Cys-S-glyceryl-3-phosphate phosphatase (FKBH). Each study began …

Evolution Of Structure And Function Among Hotdog-Fold Thioesterases And Had Family Phosphatases, Wang Min

Chemistry and Chemical Biology ETDs

My doctoral research began with the function assignment to two domains of fusion protein BT4699, from Bacteriodes thetaiotaomicron, BF1314 from Bacteriodes fragilis and PG1653 from Porphyromonas gingivalis. BT4699, however, is insoluble, so its orthologue BF1314 and PG1653 were prepared and studied. The fusion proteins consist of a domain that belong to a large family of phosphatases known as Haloacid Dehalogenase (HAD) superfamily, and a domain belong to the hotdog-fold thioesterase superfamily. The genes encoding the fusion proteins located at an operon that encoding enzymes involved in the menaquinone biosynthetic pathway. So we assumed that the thioesterase domain is connected to …

Synthesis, Characterisation, And Preliminary In Vitro Studies Of Vanadium(Iv) Complexes With A Schiff Base And Thiosemicarbazones As Mixed Ligands, Nerissa A. Lewis, Fange Liu, Luke Seymour, Anthony Magnusen, Travis R. Erves, Jessa Faye Arca, Floyd A. Beckford, Ramaiyer Venkatraman, Antonio González-Sarrías, Frank R. Fronczek, Don G. Vanderveer, Navindra P. Seeram, Aimin Liu, William L. Jarrett, Alvin A. Holder

Faculty Publications

[VO(sal‐L‐tryp)(H₂O)] (1, sal‐L‐tryp = N‐salicylidene‐L‐tryptophanate) was used as a precursor to produce the new complexes [VO(sal‐L‐tryp)(MeATSC)]·1.5C₂H₅OH [2, MeATSC = 9‐Anthraldehyde‐N(4)‐methylthiosemicarbazone], [VO(sal‐L‐tryp)(N‐ethhymethohcarbthio)]·H₂O [3, N‐ethhymethohcarbthio = (E)‐N‐ethyl‐2‐(4‐hydroxy‐3‐methoxybenzylidene)hydrazinecarbothioamide] and [VO(sal‐L‐tryp)(acetylethTSC)]·C₂H₅OH {4, acetylethTSC = (E)‐N‐ethyl‐2‐[1‐(thiazol‐2‐yl)ethylidene]hydrazinecarbothioamide} by reaction with the respective thiosemicarbazone. The chemical and structural properties of these ligands and complexes were characterised by elemental analysis, ESI‐MS, FTIR, UV/Vis, ESR and ¹H and …

Preparation And Rapid Analysis Of Antibacterial Silver, Copper And Zinc Doped Sol–Gel Surfaces, Brendan Duffy, Swarna Jaiswal, Patrick Mchale

Articles

The colonisation of clinical and industrial surfaces with microorganisms, including antibiotic-resistant strains, has promoted increased research into the development of effective antibacterial and antifouling coatings. This study describes the preparation of metal nitrate (Ag, Cu, Zn) doped methyltriethoxysilane (MTEOS) coatings and the rapid assessment of their antibacterial activity using polyproylene microtitre plates. Microtitre plate wells were coated with different volumes of liquid sol–gel and cured under various conditions. Curing parameters were analysed by thermogravimetric analysis (TGA) and visual examination. The optimum curing conditions were determined to be 50–70C using a volume of 200ul. The coated wells were challenged with Gram-positive …

Dalton, David R.: Foundations Of Organic Chemistry: Unity And Diversity Of Structures, Pathways & Reactions (Book Review), Jeffrey H. Glans

Chemistry & Physics Faculty Publications

Book review by Jeffrey Glans.

Dalton, David R. Foundations of Organic Chemistry: Unity and Diversity of Structures, Pathways & Reactions. Hoboken, NJ: Wiley, 2011.

ISBN 9780470479087

Comprehensive Survey And Geometric Classification Of Base Triples In Rna Structures, Neocles B. Leontis, Amal S. Abu Almakarem, Anton I. Petrov, Jesse Stombaugh, Craig L. Zirbel

Chemistry Faculty Publications

Base triples are recurrent clusters of three RNA nucleobases interacting edge-to-edge by hydrogen bonding. We find that the central base in almost all triples forms base pairs with the other two bases of the triple, providing a natural way to geometrically classify base triples. Given 12 geometric base pair families defined by the Leontis-Westhof nomenclature, combinatoric enumeration predicts 108 potential geometric base triple families. We searched representative atomic-resolution RNA 3D structures and found instances of 68 of the 108 predicted base triple families. Model building suggests that some of the remaining 40 families may be unlikely to form for steric …

Properties Of Cu(In,Ga) Se2 Thin Films And Solar Cells Deposited By Hybrid Process, S. Marsillac, H. Khatri, K. Aryal, R. W. Collins

Electrical & Computer Engineering Faculty Publications

Cu(In,Ga)Se-2 solar cells were fabricated using a hybrid cosputtering/evaporation process, and efficiencies as high as 12.4% were achieved. The films were characterized by energy-dispersive X-ray spectroscopy, glancing incidence X-ray diffraction, scanning electron microscopy, auger electron spectroscopy, and transmittance and reflectance spectroscopy, and their properties were compared to the ones of films deposited by coevaporation. Even though the films were relatively similar, the ones deposited by the hybrid process tend to have smaller grains with a slightly preferred orientation along the (112) axis and a rougher surface. Both types of films have uniform composition through the depth. Characterization of these films …

Depositional Ice Nucleation Onto Hydrated Nacl Particles: A New Mechanism For Ice Formation In The Troposphere, M. E. Wise, K. J. Baustian, T. Koop, M. A. Freedman, E. J. Jensen, M. A. Tolbert

CUP Faculty Research

Sea-salt aerosol (SSA) particles are ubiquitous in the marine boundary layer and over coastal areas. Therefore SSA have ability to directly and indirectly affect the Earth's radiation balance. The influence SSA have on climate is related to their water uptake and ice nucleation characteristics. In this study, optical microscopy coupled with Raman spectroscopy was used to detect the formation of a crystalline NaCl hydrate that could form under atmospheric conditions. NaCl_(s) particles (~1 to 10 μm in diameter) deliquesced at 75.7 ± 2.5% RH which agrees well with values previously established in the literature. NaCl_(aq) particles effloresced to …

The Mechanical Properties Of Epoxy Composites Filled With Rubbery Copolymer Grafted Sio2, Jianing Gao, Junting Li, Brian C. Benicewicz, Su Zhao, Henrik Hillborg, Linda S. Schadler

Faculty Publications

This study demonstrated a method for toughening a highly crosslinked anhydride cured DGEBA epoxy using rubbery block copolymer grafted SiO2 nanoparticles. The particles were synthesized by a sequential reversible addition-fragmentation chain transfer (RAFT) polymerization. The inner rubbery block poly(n-hexyl methacrylate) (PHMA) had a glass transition temperature below room temperature. The outer block poly(glycidyl methacrylate) (PGMA) was matrix compatible. A rubbery interlayer thickness of 100% and 200% of the particle core radius was achieved by grafting a 20 kg/mol and a 40 kg/mol PHMA at a graft density of 0.7 chains/nm² from the SiO₂ surface. The 20 kg/mol rubbery …

Optimization Of Magnetic Powdered Activated Carbon For Aqueous Hg(Ii) Removal And Magnetic Recovery, Emily K. Faulconer, Natalia Hoogesteijn Von Reitzenstein, David W. Mazyck

Physical Sciences - Daytona Beach

Activated carbon is known to adsorb aqueous Hg(II). MPAC (magnetic powdered activated carbon) has the potential to remove aqueous Hg to less than 0.2 mg/L while being magnetically recoverable. Magnetic recapture allows simple sorbent separation from the waste stream while an isolated waste potentially allows for mercury recycling. MPAC Hg-removal performance is verified by mercury mass balance, calculated by quantifying adsorbed, volatilized, and residual aqueous mercury. The batch reactor contained a sealed mercury-carbon contact chamber with mixing and constant N₂(g) headspace flow to an oxidizingtrap. Mercury adsorption was performed using spiked ultrapure water (100 mg/L Hg). Mercury concentrations …

Superarmed Glycosyl Donors In Chemical Glycosylation, Hemali Deepthika Premathilake

Dissertations

Only recently has the tremendous biological significance and therapeutic potential of carbohydrates and conjugates thereof (glycoproteins, glycolipids, proteoglycans, etc.) begun to emerge. As the appreciation for the biological roles of carbohydrates a growing demand for efficient and scalable methods towards the synthesis of these challenging molecules has become even more imperative. This has led to the development of a variety of expeditious strategies for oligosaccharide assembly. Amongst these strategies, the so-called armed-disarmed strategy introduced by Fraser-Reid is of particular attractiveness as it allows for chemoselective oligosaccharide synthesis. Recently, the conformational changes as well as the strategic placement of common protecting …

One-Pot Synthesis In Polyamines For Preparation Of Water-Soluble Magnetite Nanoparticles With Amine Surface Reactivity, Haiou Qu, Hui Ma, Aurélien Riviere, Weilie Zhou, Charles J. O'Connor

Chemistry Faculty Publications

Magnetite nanoparticles with hydrophilic surface coating are prepared in polyamine solvents. The resulting products are highly stable in polar solvent. The surface amine groups are available for secondary reactions.

Existence Of A Minimizer For The Quasi-Relativistic Kohn-Sham Model, Carlos Argáez García, Michael Melgaard

Articles

We study the standard and extended Kohn-Sham models for quasi-relativistic N-electron Coulomb systems; that is, systems where the kinetic energy of the electrons is given by the quasi-relativistic operator (see article) . For spin-unpolarized systems in the local density approximation, we prove existence of a ground state (or minimizer) provided that the total charge Z of K nuclei is greater than N-1 and that Z is smaller than a critical charge (see article).

Horizontally-Aligned Carbon Nanotubes Arrays And Their Interactions With Liquid Crystal Molecules: Physical Characteristics And Display Applications, Frederick Roussel, Jean-Francois Brun, Alexandre Allart, Limin Huang, Stephen O'Brien

Publications and Research

We report on the physical characteristics of horizonthally-grown Single-Walled Carbon Nanotubes (h-al-SWNT) arrays and their potential use as transparent and conducting alignment layer for liquid crystals display devices. Microscopy (SEM and AFM), spectroscopic (Raman) and electrical investigations demonstrate the strong anisotropy of h-al-SWNT arrays. Optical measurements show that h-al-SWNTs are efficient alignment layers for Liquid Crystal (LC) molecules allowing the fabrication of optical wave plates. Interactions between h-al-SWNT arrays and LC molecules are also investigated evidencing the weak azimuthal anchoring energy at the interface, which, in turn, leads to LC devices with a high pretilt angle. The electro-optical reponses of …

Identification And Quantification Of Protein Carbonylation By Mass Spectrometry, Qingyuan Liu

Theses and Dissertations

Accumulated evidence indicates oxidative stress plays important roles in disease and aging. Under oxidative stress, lipid peroxidation (LPO) leads to reactive carbonyl species (RCS) that can modify a wide range of biomolecules including protein, DNA and carbohydrate. In this dissertation, we investigate the modification of two model proteins, human serum albumin (HSA) and aconitase (ACO), by the LPO-relevant a, b-unsaturated aldehydes, acrolein (ACR) and 4-hydroxy-2-nonenal (HNE). The investigation is focused on the characterization and quantification ACR and HNE addition to the model proteins. A correlation between HNE modification and ACO activity is also determined. These results provide insights into the …

Fully Enclosed Microfluidic Paper-Based Analytical Devices, Kevin M. Schilling, Anna L. Lepore, Jason A. Kurian, Andres W. Martinez

Chemistry and Biochemistry

This article introduces fully enclosed microfluidic paper-based analytical devices (microPADs) fabricated by printing toner on the top and bottom of the devices using a laser printer. Enclosing paper-based microfluidic channels protects the channels from contamination, contains and protects reagents stored on the device, contains fluids within the channels so that microPADs can be handled and operated more easily, and reduces evaporation of solutions from the channels. These benefits extend the capabilities of microPADs for applications as low-cost point-of-care diagnostic devices.

Scope And Mechanistic Study Of The Coupling Reaction Of Α,Β-Unsaturated Carbonyl Compounds With Alkenes: Uncovering Electronic Effects On Alkene Insertion Vs Oxidative Coupling Pathways, Ki Hyeok Kwon, Do W. Lee, Chae S. Yi

Chemistry Faculty Research and Publications

The cationic ruthenium-hydride complex [(C₆H₆)(PCy₃)(CO)RuH]⁺BF₄^– (1) was found to be a highly effective catalyst for the intermolecular conjugate addition of simple alkenes to α,β-unsaturated carbonyl compounds to give (Z)-selective tetrasubstituted olefin products. The analogous coupling reaction of cinnamides with electron-deficient olefins led to the oxidative coupling of two olefinic C–H bonds in forming (E)-selective diene products. The intramolecular version of the coupling reaction efficiently produced indene and bicyclic fulvene derivatives. The empirical rate law for the coupling reaction of ethyl cinnamate with propene was …

Basis Set Dependence Of Higher-Order Correlation Effects In Π-Type Interactions, Emily J. Carrell, Cara M. Thorne, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

The basis set dependence of higher-order correlation effects on -type interaction energies was examined by scanning the potential energy surfaces of five dimer systems. The dimers of acetylene (H-CC-H), diacetylene (H-CC-CC-H), cyanogen (NC-CN), diphosphorous (PP), and 1,4-diphosphabutadiyne (PC-CP) were studied in three different configurations: cross, parallel-displaced, and t-shaped. More than 800 potential energy curves (PECs) were generated by computing the interaction energies for all 15 dimer configurations over a range of intermolecular distances with the MP2, coupled-cluster single double (CCSD), and coupled-cluster single double triple (CCSD(T)) methods in conjunction with 21 basis sets ranging from a small 6-31G*(0.25) split-valence basis …

Applications Of Electronic Structure Theory To Problems In Strong-Field Chemistry, Inorganic Chemistry, And Nanomaterial Systems, Jason Anthony Sonk

Wayne State University Dissertations

This dissertation covers research performed on applications of electronic structure theory to various fields of chemistry and is divided into eight chapters. Chapters 2 through 4 describe a series of related works which explore applications of excited state electronic structure methods to problems in strong field chemistry. Chapters 5, 6, and 7 discuss the application of electronic structure theory methods to solving problems in inorganic chemistry. Finally, Chapter 8 looks at an application of electronic structure theory to nanomaterials.

Chapter 2 covers the modeling of electron dynamics of butadiene interacting with a short, intense laser pulse in the absence of …

Metal Complexes Of Non-Heme Ligands: Biological Applications, Jai Prakash

Wayne State University Dissertations

Oxidative inactivation of proteins (carbonic anhydrase–I, trypsin, chymotrypsin and 20S proteasome) by non–heme iron complexes, and glutathionylation of non–heme cobalt complexes mimicking the N5 coordination environment like that of biologically important cofactor cobalamin or B₁₂ (Cbl) are reported. Different non–heme ligand sets or inhibitors were used to inactivate different proteins. Carbonic anhydrase–I (CA–I) and 20S proteasome were inactivated by iron complexes in the presence of O₂ and a reductant (DTT), consistent with a pathway involving the reductive activation of O₂, whereas serine proteases trypsin and chymotrypsin were inactivated by ferryls (single turnover), and by an iron …

"Fine-Tuning" Of Ribosomal Structure And Functions By Pseudouridylation And Rna-Protein Interactions, Jun Jiang

Wayne State University Dissertations

ABSTRACT

"Fine-tuning" of ribosomal structure and functions by pseudouridylation and RNA-protein interactions

by

JUN JIANG

AUGUST 2012

Advisor: Prof. John SantaLucia Jr.

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Ribosomal structure and functions appear to be "fine-tuned" by pseudouridylation and RNA-protein interactions. Pseudouridylation may promote base stacking interactions by mediating the base stacking between residues on both sides. In the RNA duplex region, this enhanced stacking interaction contributes to stabilization of duplex folding. In the loop region, enhanced stacking in one structural motif may destabilize the conformation of adjacent structural residues. This hypothesis is supported by both UV-melting experiments, where …

Stable Coexpression Of Vitamin C Enhancing Genes For Improved Production Of A Recombinant Therapeutic Protein, Hil-12, In Arabidopsis Thaliana, Jessica Patricia Yactayo-Chang

Student Theses and Dissertations

Human interleukin-12 (hIL-12) has been studied as a potential therapeutic factor in the immune response against viral disease and cancer. Plants are a promising platform for the production of complex mammalian proteins, as they can produce large amounts of functional polypeptides free of animal pathogens, and protein production can be increased to agricultural scale in a relatively short period of time. The presence of vitamin C (ascorbic acid, AsA) has been reported to have a positive effect on recombinant protein recovery. In a previous study we have demonstrated the favorable impact of the exogenous addition of AsA on the accumulation …

State-Resolved Slice Imaging Of Photochemical Dynamics, Herath Mudiyans Nuradhika Herath

Wayne State University Dissertations

This dissertation focuses on the understanding the unimolecular photochemistry and dynamics

utilizing state-resolved slice imaging approach combined with the quantum-state selective

spectroscopy technique called resonance enhanced multi photon ionization (REMPI)

method. This powerful technique allows selecting the initial quantum states of the reactants

and determining the nal quantum states, energy, the orientation and alignments of

the products. In the investigations of photodissociation dynamics of acetone at 230 nm,

a bimodal distribution for the resulting CO photoproduct is identied. This observation

indicated the presence of unimolecular dissociation mechanism analogues to the roaming

dynamics reported in formaldehyde photodissociation. Moreover, another type of …

Unusual Activities Of The Thioesterase Domain For The Biosynthesis Of The Polycyclic Tetramate Macrolactam Hsaf In Lysobacter Enzymogenes C3, Lili Lou, Haotong Chen, Ronald Cerny, Yaoyao Li, Yuemao Shen, Liangcheng Du

Ronald Cerny Publications

HSAF is an antifungal natural product with a new mode of action. A rare bacterial iterative PKSNRPS assembles the HSAF skeleton. The biochemical characterization of the NRPS revealed that the thioesterase (TE) domain possesses the activities of both a protease and a peptide ligase. Active site mutagenesis, circular dichroism spectra and homology modeling of the TE structure suggested that the TE may possess uncommon features that may lead to the unusual activities. The iterative PKS-NRPS is found in all polycyclic tetramate macrolactam gene clusters, and the unusual activities of the TE may be common to this type of hybrid PKS-NRPS.

Magnetic Properties Of Co2c And Co3c Nanoparticles And Their Assemblies, Kyler J. Carroll, Zachary J. Huba, Steven R. Spurgeon, Meichun Qian, Shiv N. Khanna, Daniel M. Hudgins, Mitra L. Taheri, Everett E. Carpenter

Chemistry Publications

Nano-composite material consisting of Co₂C and Co₃C nanoparticles has recently been shown to exhibit unusually large coercivities and energy products. Experimental studies that can delineate the properties of individual phases have been undertaken and provide information on how the coercivities and the energy product change with the size and composition of the nanoparticles. The studies indicate that while both phases are magnetic, the Co₃C has higher magnetization and coercivity compared to Co₂C. Through first principles electronic structure studies using a GGA+U functional, we provide insight on the role of C intercalation on …

Controlled Synthesis Of Superparamagnetic Iron-Oxide Nanoparticles By Phase Transformation, Mark A. Laurenzi, Everett E. Carpenter

Chemistry Publications

A synthesis procedure for generating a uniform distribution of iron-oxide nanoparticles from an amorphous precursor is reported. The investigation suggests no evidence of the formation of unwanted surface oxide layers, internal stress, and multiple phases. This is likely because the physical properties of the diffusion fields surrounding the nanoparticles are self-limiting by Fe(II) depletion. Inside the diffusion field surrounding the nucleation site, decreasing Fe(II) concentration results in a decrease in the diffusion rate that continues to decrease until self-limiting kinetic arrest occurs. The initial Fe(II) concentration is established by reducing a system abundant in Fe(III) by means of exposure to …

Wettability Of Pristine And Alkyl-Functionalized Graphane, Davide Vanzo, Dusan Bratko, Alenka Luzar

Chemistry Publications

Graphane is a hydrogenated form of graphene with high bandgap and planar structure insensitive to a broad range of chemical substitutions. We describe an atomistic simulation approach to predict wetting properties of this new material. We determine the contact angle to be 73°. The lower hydrophobicity compared to graphene is explained by the increased planar density of carbon atoms while we demonstrate that the presence of partial charges on carbonand hydrogen atoms plays only a minor role. We further examine the effects of graphane functionalization by alkyl groups of increasing chain lengths. The gradual increase in contact angle with chain …