Digital Commons Network^™

Nanopod Formation Through Gold Nanoparticle Templated And Catalyzed Cross-Linking Of Polymers Bearing Pendant Propargyl Ethers, Ke Zhang, Joshua I. Cutler, Jian Zhang, Dan Zheng, Evelyn Auyeung, Chad A. Mirkin

Department of Chemistry: Faculty Publications

A novel method for synthesizing polymer nanopods from a linear polymer bearing pendant propargyl ether groups, using gold nanoparticles as both the template and the catalyst for the crosslinking reaction, is reported. The transformations involved in the cross-linking process are unprecedented on the surface of a gold particle. A tentative cross-linking mechanism is proposed.

Includes Supporting Information.

Nanometer To Millimeter Scale Peptide-Porphyrin Materials, Daniil V. Zaytsev, Fei Xie, Madhumita Mukherjee, Alexey Bludin, Borries Demeler, Robert M. Breece, David L. Tierney, Michael Y. Ogawa

Chemistry Faculty Publications

AQ-Pal14 is a 30-residue polypeptide that was designed to form an alpha-helical coiled coil that contains a metal-binding 4-pyridylalanine residue on its solvent-exposed surface. However, characterization of this peptide shows that it exists as a three-stranded coiled coil, not a two-stranded one as predicted from its design. Reaction with cobalt(III) protoporphyrin IX (Co-PPIX) produces a six-coordinate Co-PPIX(AQ-Pal 14)(2) species that creates two coiled-coil oligomerization domains Coordinated to opposite laces of the porphyrin ring. It is found that this species undergoes a buffer-dependent Self-assembly process: nanometer-scale globular materials were formed when these components were reacted in unbuffered H(2)O, while millimeter-scale, rod-like …

Cox-2 Inhibitor Nimesulide Analogs Are Aromatase Suppressors In Breast Cancer Cells, Bin Su, Xiaohan Cai, Yanyan Hong, Shiuan Chen

Chemistry Faculty Publications

Cyclooxygenase-2 (COX-2) inhibitor nimesulide derivatives compounds A and B decreased aromatase activity in breast cancer cells via a novel mechanism different to aromatase inhibitors (AIs), and were defined as “aromatase suppressors”. Breast carcinoma cells (MCF-7aro and T47Daro) transfected with aromatase full gene were used to explore the mechanisms of the two compounds. They dose and time-dependently suppressed aromatase activity in MCF-7aro and T47Daro cells in the nanomole range. However, they neither directly inhibited aromatase, nor improved aromatase degradation even at much higher concentrations. They could also suppress androgen stimulated cell growth, but did not affect estrogen enhanced cell proliferation. These …

Solvent Effects On Emission Spectra Of Carminic Acid And Determination Of Its Ground And Excited State Dipole Moments, Sarika B. Jaggannagari

All Capstone Projects

Absorption and fluorescence emission spectra of Carminic acid were recorded in solvents with different solvent parameters like polarities, dielectric constant and refractive index. The solvents used in the experiment were water, DMSO, acetonitrile, methanol, propanol and butanol. The atomic radius of the molecule was found out using Hartree-Fock method in molecular modeling using Spartan software and it is applied to find out the dipole moments. The dipole moments of Carminic acid in the ground state and excited states have been determined and Solvatochromic shift method has been used to determine the excited state dipole moments. The linear progressions were made …

Synthesis And Characterization Of An Europium-Porphyrin Complex, Alejandro Blinder

All Capstone Projects

Photodynamic therapy (PDT) is a promising treatment that has continued to improve over the past thirty years when the first commercially approved photosensitizer (PS) was introduced. Although PDT has many successful applications, the terrifying number of new cancer cases reported each year makes scientists focus their efforts towards the development of new efficient PS for PDT. The biggest obstacle that prohibits PDT from becoming a more widely used therapy is the ineffective photosensitizers (PS) that are available on the market today. The purpose of this study was to evaluate the synthesized metal-porphyrin complex as a possible candidate as a PS. …

Ruthenium Complexes As Dna Photonucleases In Treatment Of Malignant Skin Carcinoma, Devi Kalyan Karumanchi

All Capstone Projects

A variety of Ruthenium complexes possessing terpyridine complexes as ligands in their coordination sphere have been investigated extensively as DNA photo nucleases in vitro. This work has led to the realization that compounds of Ruthenium bind to DNA purines and that the interactions are of an unprecedented bridging variety. Owing to the molar absorptivity of these complexes in the visible region, direct cleavage of duplex DNA by these complexes requires irradiation in the range of 400-500 nm.

Although the observation of DNA photo cleavage in vitro makes these systems good candidates for further investigation, it does not provide any information …

Purification And Analysis Of Folate-Dye Conjugate, Dilipkumar Sakhiya

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. Protein toxins, chemotherapeutic agents, radioimaging agents, magnetic resonance imaging (MRI) contrast agents liposomes with entrapped drugs, radiotherapeutic agents, …

Degree Of Labeling Of Folate-Bsa With Rhodamine Dye, Prathibha Yazala

All Capstone Projects

Folic acid is a very important vitamin. It is needed by cells for various physiological functions. It plays an important role in growth and multiplication of cells and therefore is needed very much by cancerous cells. One of the ways folate reaches the cells is the folate receptor mediated endocytosis. Therefore folate binding proteins are abundant on cancerous cells. Clinical trials proved that the folate receptor targeted drug delivery is very promising to increase the drug exposure to malignant cells and to reduce the toxicity to healthy cells. It was recently discovered that folate receptor is also over expressed on …

Dna-Nanoparticle Superlattices Formed From Anisotropic Building Blocks, Matthew R. Jones, Robert J. Macfarlane, Byeongdu Lee, Jian Zhang, Kaylie L. Young, Andrew J. Senesi, Chad A. Mirkin

Department of Chemistry: Faculty Publications

Directional bonding interactions in solid-state atomic lattices dictate the unique symmetries of atomic crystals, resulting in a diverse and complex assortment of three-dimensional structures that exhibit a wide variety of material properties. Methods to create analogous nanoparticle superlattices are beginning to be realized, but the concept of anisotropy is still largely underdeveloped in most particle assembly schemes. Some examples provide interesting methods to take advantage of anisotropic effects, but most are able to make only small clusters or lattices that are limited in crystallinity and especially in lattice parameter programmability. Anisotropic nanoparticles can be used to impart directional bonding interactions …

Synthesis And Structural Characterization Of The Peptide Epitope Of The Ovarian Cancer Biomarker Ca125 (Muc16), Rebecca J. Whelan, Zach T. Berman, Lee J. Moore, Kathleen E. Knudson

Faculty & Staff Scholarship

A highly conserved region of 21 amino acids flanked by cysteine residues, contained within a larger repeated domain, has been proposed to be the antibody-binding site in the ovarian cancer biomarker CA125 (MUC16). In this study solid-phase peptide synthesis with Fmoc protection chemistry was used to assemble a 21-mer peptide corresponding to the most frequently occurring antibody binding sequence in CA125. Potentially significant sequence variants were also synthesized. Peptide secondary structure was investigated using Fourier transform infrared spectroscopy, revealing the consensus sequence peptide to be largely unstructured at physiological pH whether the cysteine residues were reduced or were oxidized to …

Impact Of Interdisciplinary Undergraduate Research In Mathematics And Biology On The Development Of A New Course Integrating Five Stem Disciplines, Lester Caudill, April L. Hill, Kathy Hoke, Ovidiu Z. Lipan

Biology Faculty Publications

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a …

Jahn-Teller Coupling And Fragmentation After Core-Shell Excitation Ini Cf4 Investigated By Partial-Ion-Yield Spectroscopy, Renaud Guillemin, Wayne C. Stolte, Maria Novella Piancastelli, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We investigate fragmentation processes induced by core-level photoexcitation in CF4 at both the carbon and fluorine K edges by means of partial-ion-yield spectroscopy. The molecule CF₄ is a textbook example of systems in which Jahn-Teller coupling strongly manifests itself in the photoabsorption spectrum. Spectral features related to Jahn-Teller and quasi-Jahn-Teller splitting are observed, and important differences in the fragmentation pathways are revealed depending on the symmetries of the core-excited states. We interpret these experimental observations on the grounds of symmetry lowering from the Td to the C3v point group as well as preferential orientation with respect …

Detection Of Quercetin Using Polymer Coated Quartz Crystal Microbalance And The Modification Of Á-Zirconium Phosphate To Develop A Sorbent For Organic Pollutant Removal, Darlington Mlambo

Dissertations (1934 -)

Sorption processes involve physical and chemical interactions of sorbents with analytes. These may involve the physical and/or chemical processes in which a substance is accumulated at an interface between two phases, or the intermixing of a substance with the matrix of a second phase. The two processes are referred to as adsorption and absorption respectively. The sorption capacities of different classes of sorbents have many potential and demonstrated applications such as sensor development, water treatment, environmental remediation and chromatographic separations. The goal of this work is to explore the sorption capacity of polymers as well as nanodimensional layered materials for …

Impact Of Interdisciplinary Undergraduate Research In Mathematics And Biology On The Development Of A New Course Integrating Five Stem Disciplines, Lester Caudill, April L. Hill, Kathy Hoke, Ovidiu Z. Lipan

Department of Math & Statistics Faculty Publications

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a …

Structure Of The Cholera Toxin Secretion Channel In Its Closed State, Steve Reichow, Konstantin V. Korotkov, Wim Gj Hol, Tamir Gonen

Chemistry Faculty Publications and Presentations

The type II secretion system (T2SS) is a macromolecular complex spanning the inner and outer membranes of Gram-negative bacteria. Remarkably, the T2SS secretes folded proteins including multimeric assemblies like cholera toxin and heat-labile enterotoxin from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. The major outer membrane T2SS protein is the “secretin” GspD. Electron cryomicroscopy reconstruction of the V. cholerae secretin at 19 Å resolution reveals a dodecameric structure reminiscent of a barrel with a large channel at its center that appears to contain a closed periplasmic gate. The GspD periplasmic domain forms a vestibule with a conserved constriction, and binds …

Nmr-Based And Automated Docking Characterization Of Protein Structure, Dynamics, And Ligand Binding, Andrew Lawrence Olson

Dissertations (1934 -)

NMR-based methods used in conjunction with a technique called docking are used to characterize ligand binding to proteins. Standard NMR methods were used to study the backbone dynamics of substrate binding to phosphomevalonate kinase (PMK) and it was observed that ligand binding caused PMK to undergo large conformational changes. These changes were reflected by the appearance of many chemical shift changes upon binding of the natural substrates of PMK (both the binary and ternary complexes) in 1H-15N HSQC NMR titration experiments. The same process was used to characterize the effect ligand binding has on the many arginines in the active …

Hrc Enews — 2010 Fall, Megan K. Svarz

Publications (HRC)

This issue contains staff accomplishments and announcements, event listings, and a "new faces" listing for new staff, affiliates, and researchers.

4-Phenyl­Sulfon­Yl-2-(P-Tolyl­Sulfon­Yl)-1h,8h-Pyrrolo­[2,3-B]Indole, Jeanese C. Badenock, Jason A. Jordan, Erin T. Pelkey, Gordon W. Gribble, Jerry P. Jasinski

Dartmouth Scholarship

The title compound, C23H18N2O4S2, contains a pyrrolo group fused onto the plane of an indole ring with phenylsulfonyl and p-toluenesulfonyl groups bonded to the indole and pyrrolo rings. The angles between the mean planes of the pyrrolo- indole ring and the phenylsulfonyl and p-toluenesulfonyl rings are 73.7 (6) and 80.6 (0)􏰈, respectively. The dihedral angle between the mean planes of the two benzene rings is 78.7 (4)􏰈. In the crystal, both classical N—H􏰇 􏰇 􏰇O and non-classical C— H􏰇 􏰇 􏰇O intermolecular hydrogen-bonding interactions are observed, as well as weak 􏰁–􏰁 interactions [centroid–centroid distances = 3.6258 (8) and 3.9298 (8) …

Cooperative Interaction Of Transcription Termination Factors With The Rna Polymerase Ii C-Terminal Domain, Bradley M. Lunde, Steve Reichow, Minkyu Kim, Hyunsuk Suh, Thomas C. Leeper, Fan Yang, Hannes Mutschler, Stephen Buratowski, Anton Meinhart, Gabriele Varani

Chemistry Faculty Publications and Presentations

Phosphorylation of the C-terminal domain of RNA polymerase II controls the co-transcriptional assembly of RNA processing and transcription factors. Recruitment relies on conserved CTDinteracting domains that recognize different CTD phosphoisoforms during the transcription cycle, but the molecular basis for their specificity remains unclear. We show that the CTD-interacting domains of two transcription termination factors, Rtt103 and Pcf11, achieve high affinity and specificity both by specifically recognizing the phosphorylated CTD and by cooperatively binding to neighboring CTD repeats. Single amino acid mutations at the protein-protein interface abolish cooperativity and affect recruitment at the 3′-end processing site in vivo. We suggest that …

Characterization Of Metastasis-Associated Cell Surface Glycoproteins In Prostate Cancer, Lifang Yang

Theses and Dissertations in Biomedical Sciences

Prostate cancer (PCa) is a major health problem in males in the United States. Its lethality is mostly attributed to the primary tumor metastasizing to distant sites that are highly resistant to conventional therapies. Serum Prostate Specific Antigen (PSA) is the only protein biomarker used in clinic for prediction of prostate cancer recurrence following local therapies. Nonetheless, PSA lacks the ability to predict the behavior of an individual tumor in an individual patient. Therefore, development of reliable biomarkers for detection of metastatic potential in primary tumors, as well as discovery of new therapeutic targets, is in a great need for …

Orally Active Mmp-1 Sparing Α-Tetrahydropyranyl And Α-Piperidinyl Sulfone Matrix Metalloproteinase (Mmp) Inhibitors With Efficacy In Cancer, Arthritis, And Cardiovascular Disease, Daniel P. Becker, Thomas E. Barta, Louis J. Bedell, Terri L. Boehm

Chemistry: Faculty Publications and Other Works

α-Sulfone-α-piperidine and α-tetrahydropyranyl hydroxamates were explored that are potent inhibitors of MMP’s-2, -9, and -13 that spare MMP-1, with oral efficacy in inhibiting tumor growth in mice and left-ventricular hypertrophy in rats and in the bovine cartilage degradation ex vivo explant system. α-Piperidine 19v (SC-78080/SD-2590) was selected for development toward the initial indication of cancer, while α-piperidine and α-tetrahydropyranyl hydroxamates 19w (SC-77964) and 9i (SC-77774), respectively, were identified as backup compounds.

Unusually Conductive Carbon-Inherently Conducting Polymer (Icp) Composites: Synthesis And Characterization, Shawn Edward Bourdo

Theses and Dissertations

Two groups of materials that have recently come to the forefront of research initiatives are carbon allotropes, especially nanotubes, and conducting polymers-more specifically inherently conducting polymers. The terms conducting polymers and inherently conducting polymers sometimes are used interchangeably without fully acknowledging a major difference in these terms. Conducting polymers (CPs) and inherently conducting polymers (ICPs) are both polymeric materials that conduct electricity, but the difference lies in how each of these materials conducts electricity. For CPs of the past, an electrically conductive filler such as metal particles, carbon black, or graphite would be blended into a polymer (insulator) allowing for …

Design, Synthesis, And Characterization Of A Tetraamide Macrocyclic Ligand And Its Fe- Complex For Green Oxidation Chemistry, Shane Z. Sullivan

Theses and Dissertations

This work presents the spectroscopic characterization and catalytic investigation of a FeIII-complex of a tetraamidomacrocyclic ligand. Under catalytic conditions the complex is soluble in aqueous solutions and rapidly activates hydrogen peroxide under mild reaction conditions. Both the kinetics and extent of water-soluble dye and paper effluent H2O2-bleaching catalyzed was found to be comparable to known FeIII-TAML complexes. As an additional application, the complex showed potential for the synthesis of a variety of Noxides from their corresponding amines as demonstrated by its high turnover number and essentially stoichiometric yield in selected amines. Electrospray ionization-mass spectrometry of the complex reveals a peak …

Site-Specific Photocatalytic Splitting Of Methanol On Tio2(110), Chuanyao Zhou, Zefeng Ren, Shijing Tan, Zhibo Ma, Xinchun Mao, Dongxu Dai, Hongjun Fan, Xueming Yang, Jerry L. Larue, Russell Cooper, Alec M. Wodtke, Zhou Wang, Zhenyu Li, Bing Wang, Jinlong Yang, Jianguo Hou

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Clean hydrogen production is highly desirable for future energy needs, making the understanding of molecular-level phenomena underlying photocatalytic hydrogen production both fundamentally and practically important. Water splitting on pure TiO₂ is inefficient, however, adding sacrificial methanol could significantly enhance the photocatalyzed H₂ production. Therefore, understanding the photochemistry of methanol on TiO₂ at the molecular level could provide important insights to its photocatalytic activity. Here, we report the first clear evidence of photocatalyzed splitting of methanol on TiO₂ derived from time-dependent two-photon photoemission (TD-2PPE) results in combination with scanning tunneling microscopy (STM). STM tip induced molecular manipulation …

Axial Temperature Gradients In Gas Chromatography, Jesse Alberto Contreras

Theses and Dissertations

The easiest and most effective way to influence the separation process in gas chromatography (GC) is achieved by controlling the temperature of the chromatographic column. In conventional GC, the temperature along the length of the column is constant at any given time, T(t). In my research, I investigated the effects of temperature gradients on GC separations as a function of time and position, T(t,x), along the column. This separation mode is called thermal gradient GC (TGGC). The research reported in this dissertation highlights the fundamental principles of axial temperature gradients and the separation potential of the TGGC technique. These goals …

Determination Of Cyanide Exposure By Gas Chromatography–Mass Spectrometry Analysis Of Cyanide-Exposed Plasma Proteins, Stephanie L. Youso, Gary A. Rockwood, John A. Lee, Brian A. Logue

Chemistry and Biochemistry Faculty Publications

Exposure to cyanide can occur in a variety of ways, including exposure to smoke from cigarettes or fires, accidental exposure during industrial processes, and exposure from the use of cyanide as a poison or chemical warfare agent. Confirmation of cyanide exposure is difficult because, in vivo, cyanide quickly breaks down by a number of pathways, including the formation of both free and protein-bound thiocyanate. A simple method was developed to confirm cyanide exposure by extraction of protein-bound thiocyanate moieties from cyanide-exposed plasma proteins. Thiocyanate was successfully extracted and subsequently derivatized with pentafluorobenzyl bromide for GC–MS analysis. Thiocyanate levels as low …

Nano-Imprinted Thin Films Of Reactive, Azlactone-Containing Polymers: Combining Methods For The Topographic Patterning Of Cell Substrates With Opportunities For Facile Post-Fabrication Chemical Functionalization, Nathaniel J. Fredin, Ryan M. Flessner, Christopher M. Jewell, Shane L. Bechler, Maren E. Buck, David M. Lynn

Chemistry: Faculty Publications

Laser scanning confocal microscopy (LSCM) and atomic force microscopy (AFM) were used to characterize changes in nanoscale structure that occur when ultrathin polyelectrolyte multilayers (PEMs) are incubated in aqueous media. The PEMs investigated here were fabricated by the deposition of alternating layers of plasmid DNA and a hydrolytically degradable polyamine onto a precursor film composed of alternating layers of linear poly(ethylene imine) (LPEI) and sodium poly(styrene sulfonate) (SPS). Past studies of these materials in the context of gene delivery revealed transformations from a morphology that is smooth and uniform to one characterized by the formation of nanometer-scale particulate structures. We …

Nona-Arginine Facilitates Delivery Of Quantum Dots Into Cells Via Multiple Pathways, Yi Xu, Betty Revon Liu, Han Jung Lee, Katie Shannon, Jeffrey G. Winiarz, Tien-Chun Wang, Huey-Jenn Chiang, Yue-Wern Huang

Biological Sciences Faculty Research & Creative Works

Semiconductor quantum dots (QDs) have recently been used to deliver and monitor biomolecules, such as drugs and proteins. However, QDs alone have a low efficiency of transport across the plasma membrane. In order to increase the efficiency, we used synthetic nona-arginine (SR9), a cell-penetrating peptide, to facilitate uptake. We found that SR9 increased the cellular uptake of QDs in a noncovalent binding manner between QDs and SR9. Further, we investigated mechanisms of QD/SR9 cellular internalization. Low temperature and metabolic inhibitors markedly inhibited the uptake of QD/SR9, indicating that internalization is an energy-dependent process. Results from both the pathway inhibitors and …

Circular Dichroism Spectroscopy In The Undergraduate Curriculum, Adam R. Urbach

Chemistry Faculty Research

Circular dichroism spectropolarimetry (CD) is a method of optical spectroscopy that seems in most practical ways like UV−visible spectroscopy. The main difference between the two methods is that CD, instead of measuring the absorbance of light as a function of wavelength, measures the difference in absorbance of left versus right circularly polarized light as a function of wavelength. A CD spectrum is an observation of the structure of a chiral compound; it often serves as a “fingerprint” of the structure of biological molecules such as proteins and nucleic acids. For this reason, CD has been broadly applied in biochemistry and …

Creative Exercises In General Chemistry: A Student-Centered Assessment, Scott E. Lewis, Janet L. Shaw, Kathryn A. Freeman

Faculty Articles

Creative exercises (CEs) are a form of assessment in which students are given a prompt and asked to write down as many distinct, correct, and relevant facts about the prompt as they can. Students receive credit for each fact that they include that is related to the prompt and distinct from the other facts they list. With CEs, students have an opportunity to demonstrate their knowledge and the opportunity to select the information that they believe is related to the prompt. In addition, CEs encourage students to connect concepts because any relevant information presented can assist them in completing the …