Chemistry Commons^™

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 …

Synthesis And Analytical Evaluation Of Folate Conjugates For Use In Cancer Cell Detection, Sneha Reddy Kuthuru

All Capstone Projects

Recent clinical studies have shown the importance of folate receptor in drug delivery system as they increase the potency and reduce toxicity of many cancer therapies. The folate receptor alpha ( FR-a) binds with high affinity for folic acid and serves for receptor mediated transport of folate into cells. Folate is necessary for DNA metabolism and thus it is speculated that rapidly dividing cancer cells have an increased requirement for folic acid. It is known that FR-a levels are elevated in specific malignant diseases (solid tumors, leukemia) and thus the FR receptor serves as useful targeting moiety for the diagnosis …

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.

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 …

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 …

Photodissociation Of Ozone In The Hartley Band: Product State And Angular Distributions, George C. Mcbane, Luan T. Nguyen, Reinhard Schinke

Peer Reviewed Articles

Product state properties from the photodissociation of ozone in the ultraviolet Hartley band are investigated by trajectory surface-hopping calculations. The diabatic B and R state potential energy and coupling surfaces of Schinke and McBane [J. Chem. Phys. 132, 044305 (2010)] are employed. The properties computed include rotational and vibrational distributions in both the singlet and triplet channels, the total internal energy distribution in the triplet channel, and the photodissociation anisotropy parameter β" role="presentation" style="display: inline; line-height: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px …

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 …

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 …

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 …

Extensive Aerosol Optical Properties And Aerosol Mass Related Measurements During Tramp/Texaqs 2006 – Implications For Pm Compliance And Planning, Monica Elizabeth Wright, Dean B. Atkinson, Luke Ziemba, Robert Griffin, Naruki Hiranuma, Sarah D. Brooks, James Flynn, Ryan Perna, Bernhard Rappenglück, Winston Luke, Paul Kelley

Chemistry Faculty Publications and Presentations

Extensive aerosol optical properties, particle size distributions, and Aerodyne quadrupole aerosol mass spectrometer measurements collected during TRAMP/TexAQS 2006 were examined in light of collocated meteorological and chemical measurements. Much of the evident variability in the observed aerosol-related air quality is due to changing synoptic meteorological situations that direct emissions from various sources to the TRAMP site near the center of the Houston-Galveston-Brazoria (HGB) metropolitan area. In this study, five distinct long-term periods have been identified. During each of these periods, observed aerosol properties have implications that are of interest to environmental quality management agencies. During three of the periods, long …

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) …

Determination Of Threshold Exposure And Intensity For Recording Holograms In Thick Green-Sensitive Acrylamide-Based Photopolymer, Mohammad Sultan Mahmud, Izabela Naydenova, Tzwetanka Bebeva, Raghavendra Jallapuram, Suzanne Martin, Vincent Toal

Articles

For optical data storage applications, it is essential to determine the lowest intensity (also known as threshold intensity) below or at which no data page or grating can be recorded in the photosensitive material, as this in turn determines the data capacity of the material. Here, experiments were carried out to determine the threshold intensity below which the formation of a simple hologram—a holographic diffraction grating in a green-sensitized acrylamide-based photopolymer—is not possible. Two main parameters of the recording layers—dye concentration and thickness—were varied to study the influence of the density of the generated free radicals on the holographic properties …

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 …

Facile Pyrolytic Synthesis Of Silicon Nanowires, Joo C. Chan, Hoang Tran, James W. Pattison, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

One-dimensional nanostructures such as silicon nanowires (SiNW) are attractive candidates for low power density electronic and optoelectronic devices including sensors. A new simple method for SiNW bulk synthesis[1, 2] is demonstrated in this work, which is inexpensive and uses low toxicity materials, thereby offering a safe, energy efficient and green approach. The method uses low flammability liquid phenylsilanes, offering a safer avenue for SiNW growth compared with using silane gas. A novel, duo-chamber glass vessel is used to create a low-pressure environment where SiNWs are grown through vapor-liquid-solid mechanism using gold nanoparticles as a catalyst. The catalyst decomposes silicon precursor …

Fragmentation Of Chloroperoxides: Hypochlorite-Mediated Dehydration Of Hydroperoxyacetals To Esters, Thomas J. Fisher, Patrick Dussault

Patrick Dussault Publications

Hypochlorites efficiently dehydrate hydroperoxyacetals to furnish the corresponding esters. The reaction, which can be accomplished with stoichometric Ca(OCl)₂ or with catalytic amounts of t-BuOCl, appears to involve formation and heterolytic fragmentation of secondary chloroperoxides, species not previously described in solution chemistry.

Includes Supporting Information (52 pp).

Synthesis And Analysis Of N-Acetyltyrosine-N-Ethyl Amide From N-Acetyl Yyrosine Ethyl Ester, Ravinder Reddy Akkuluri

All Capstone Projects

Amino acids gets oxidized when they are interacted with oxygen and light. And it is always difficult for the researchers to find and isolate a particular amino acid from a protein, unless they completely know how it behaves when interacted with light. For this we are synthesizing amide form of the amino acid which mimics the structure of a protein, and we induce light and find out the exact behavior of the particular amino acid. Here, the aim is to know the tyrosine interaction with light, so we synthesize amide form of tyrosine which is N-Acetyl tyrosine ethyl amide from …

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. …

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 …

Labeling Of Fluorescein Dye On Folate Binding Protein, Sravanth Reddy Lakshmareddygari

All Capstone Projects

Discovery and development of folic acid based receptor targeting started in late 1991 and early 1992 when researchers came to know that folate receptors (FR) are over expressed on malignant tissues. The malignant tissues over express special folate receptors to capture more folate from the blood stream as folate is required for cell division. The researchers found that folate can be used as an optimal targeting ligand that would bind selectively to pathologic cells, displaying no affinity for healthy cells. Then they focused on attaching a drug molecule to the folate ligand that can be delivered directly to the cells …

Labeling Of Folic Acid On Bovine Serum Albumin, Hari Krishna Kosuri

All Capstone Projects

Recent Clinical research focused mainly on the therapeutic safety which mainly involves the avoidance of toxicities. To prevent the toxicities, site targeted drugs are improved which exhibit their therapeutic action on the specific target or the diseased target without disturbing the healthy cells. Folic acid, a natural Vitamin (Vit B9) has shown promising results in site specificity mainly in the cancer cells where they are abundantly present.

Folic acid is of great importance because of the promising results of several clinical trials which demonstrate that Folic acid increases the potency and simultaneously reducing the toxicity of the cancer therapies. Various …

Total Protein Determination Using Micro Plate Assay, Julie Ruffatti

All Capstone Projects

One of the largest challenges that food manufactures are facing today is the management of food allergens. Allergenic protein in trace amounts, part per million concentrations, will trigger a reaction in some individuals. Food manufacturers need to prevent allergen cross-contamination by performing adequate sanitation after production of an allergenic containing food. Allergen detection kits are used to determine if sufficient protein was removed from the equipment surfaces during sanitation. One kit on the market is the 3M™ Clean- Trace™ Surface Protein (Allergen) swab tests. The test qualitatively detects the presence of protein based on the biuret reaction and will yield …

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 …

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 …

Pltl Impacts A Career – From Peer Leader To The Professoriate, Jason Gillmore

Faculty Publications

No abstract provided.

A Low-Temperature Phase Of Bis(Tetrabutylammonium) Octa-L3-Chloridohexachlorido- Octahedro-Hexatungstate, Dean H. Johnston, Chris M. Brown, Andrew S. Yu, Judith C. Gallucci

Chemistry Faculty Scholarship

The article discusses the low-temperature phase of bis(tetrabutylammonium) octa-µ3-chlorido-hexachlorido-octahedro-hexa-tungstate, which undergoes a reversible phase transition at 268 K. The unit cells of the room- and low-temperature polymorphs of this compound are found to be closely related. The hydrocarbon chain of one of the tetrabutylammonium cations is found to be disordered at both 150 and 200 K.

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.