Chemistry Commons^™

Water Diffusion In And Out Of The Β-Barrel Of Gfp And The Fast Maturing Fluorescent Protein, Turbogfp, Marc Zimmer, Binsen Li, Ramza Shahid, Paola Peshkepija

Chemistry Faculty Publications

The chromophore of fluorescent proteins is formed by an internal cyclization of the tripeptide 65SYG67 fragment and a subsequent oxidation. The oxidation is slow – the kinetics of this step is presumably improved in fast maturing GFPs. Water molecules can aid in the chromophore formation. We have used 50ns molecular dynamics simulations of the mature and immature forms of avGFP and TurboGFP to examine the diffusion of water molecules in-and-out of the protein β-barrel. Most crystal structures of GFPs have well-structured waters within hydrogen-bonding distance of Glu222 and Arg96. It has been proposed that they have an important role in …

Analysis Of The Penney-Ante Game Using Difference Equations: Development Of An Optimal And A Mixed-Strategies Protocol, Carl Barratt, Pauline Schwartz

Chemistry and Chemical Engineering Faculty Publications

Penney-Ante is a well known two-player (Player I and Player II) game based on an information paradox. We present a new approach, using difference-equations, to analyzing the outcome for each player. One strategy yields a winning outcome of 75% for Player II, the player playing second. The approach also permits investigation of non-optimal strategies, and demonstrates how mixing of such strategies can be used to tune the winning edge of either player. We generalize the analysis to accommodate the possibility of a biased coin.

Organic-Copper Sulfide Heterojunctions For Economical Solar Energy Harvesting Absorbers For Economically Efficient Photovoltaics, Adam Straith Brewer

Link Foundation Energy Fellowship Reports

As our population continues to grow, the author believes that efficiently harnessing clean, abundant solar energy would be a tremendous boon to society. To that end, the author has explored copper sulfide colloidal quantum dots (CQDs) as a potential route to efficient solar energy. However, because of their small size, we need to better understand what influences the surfaces of different quantum dot systems. The author' research has focused on studying the ligand shell on Cu2S quantum dots. He present the first explicit study on the effect of surface treatments on Cu2S colloidal quantum dots, specifically thiols, amine, pyridine and …

Using Mole Ratios Of Electrolytic Products Of Water For Analysis Of Household Vinegar: An Experiment For The Undergraduate Physical Chemistry Laboratory., Rajeev Dabke, Zewdu Gebeyehu

Faculty Bibliography

No abstract provided.

Identification Of New Inhibitors Of Human Low Molecular Weight Protein Tyrosine: Phosphatase Isoform B Via Virtual Screening, Christopher Seiler

Chemistry Student Work

The human low molecular weight protein tyrosine phosphatase (LMW-PTP) has been identified as a target for inhibition as its overexpression leads to metastatic transformation and invasivity in several human cancers such as breast, colon, bladder, and kidney. Extra precision docking with Glide on LMW-PTP isoform B was used to virtually screen 1356 compounds from the National Cancer Institute (NCI) diversity set II for new potential inhibitors. Twenty-one compounds identified as potential inhibitors by in silico screening methods were acquired from NCI. The compounds were kinetically analyzed on LMW-PTP isoform B to validate their selection as potential inhibitors. The best fit …

Toward A Regional Radiocarbon Model For The East Texas Woodland Period, Robert Z. Selden Jr., Timothy K. Perttula

CRHR: Archaeology

The East Texas Radiocarbon Database contributes to an analysis of tempo and place for Woodland era (ca. 500 B.C. - A.D. 800) archaeological sites within the region. The temporal and spatial distributions of calibrated radiocarbon (¹⁴C) ages (n=127) with a standard deviation (ΔT) of 61 from archaeological sites with Woodland components (n=51) are useful in exploring the development and geographical continuity of the peoples in East Texas, and lead to a refinement of our current chronological understanding of the period. While the analysis of the dates produces less than significant findings due to sample size, they are used …

Modeling Regional Radicarbon Trends: A Case Study From The East Texas Woodland Period, Robert Z. Selden Jr.

CRHR: Archaeology

The East Texas Radiocarbon Database contributes to an analysis of tempo and place for Woodland era (~500 BC–AD 800) archaeological sites within the region. The temporal and spatial distributions of calibrated ¹⁴C ages (n = 127) with a standard deviation (ΔT) of 61 from archaeological sites with Woodland components (n = 51) are useful in exploring the development and geographical continuity of the peoples in east Texas, and lead to a refinement of our current chronological understanding of the period. While analysis of summed probability distributions (SPDs) produces less than significant findings due to sample size, they are used …

The East Texas Caddo: Modeling Tempo And Place, Robert Z. Selden Jr., Timothy K. Perttula

CRHR: Archaeology

Analysis of the Caddo sample (n=889 dates) from the East Texas radiocarbon database is used to establish the tempo and place of Caddo era (ca. A.D. 800-1680) archaeological sites, site clusters, and communities across the region. The temporal and spatial distribution of radiocarbon ages from settlements, mound centers, and cemeteries across the region have utility in exploring the development and geographical continuity of the Caddo peoples; establishing the specific times when areas were abandoned or population sizes diminished; and defining times and areas illustrating an intensification in mound center construction and large cemeteries became a focus of community social practices.

From Cox-2 Inhibitor Nimesulide To Potent Anti-Cancer Agent: Synthesis, In Vitro, In Vivo And Pharmacokinetic Evaluation, Bo Zhong, Xiaohan Cai, Snigdha Chennamaneni, Xin Yi, Lili Liu, John J. Pink, Afshin Dowlati, Yan Xu, Aimin Zhou, Bin Su

Chemistry Faculty Publications

Cyclooxygenase-2 (COX-2) inhibitor nimesulide inhibits the proliferation of various types of cancer cells mainly via COX-2 independent mechanisms, which makes it a good lead compound for anti-cancer drug development. In the presented study, a series of new nimesulide analogs were synthesized based on the structure–function analysis generated previously. Some of them displayed very potent anti-cancer activity with IC50s around 100 nM–200 nM to inhibit SKBR-3 breast cancer cell growth. CSUOH0901 (NSC751382) from the compound library also inhibits the growth of the 60 cancer cell lines used at National Cancer Institute Developmental therapeutics Program (NCIDTP) with IC50s around 100 nM–500 nM. …

Characterization Of Pharmaceutical Materials By Thermal And Analytical Methods, Manik Pavan Kumar Maheswaram

ETD Archive

No abstract provided.

Large-Scale Synthesis Of High Moment Feco Nanoparticles Using Modified Polyol Synthesis, Mehdi Zamanpour, Yajie Chen, Bolin Hu, Kyler Carroll, Zachary J. Huba, E. E. Carpenter, Laura H. Lewis, Vincent G. Harris

Chemistry Publications

Binary alloys of Fe and Co have among the highest magnetizations of any transition metal alloy systems, but their affinity to form oxides act to reduce the magnetization of nanoparticles as their size is reduced below ∼30 nm. Here, we demonstrate the synthesis of single phase, size-controlled FeCo nanoparticles having magnetization greater than 200 emu/g via a non-aqueous method in which ethylene glycol served as solvent and reducing agent as well as surfactant. Experiments indicated pure-phase FeCo nanoparticles, having saturationmagnetization up to 221 emu/g for sizes of 20–30 nm, in single batch processes resulting in > 2 g/batch. Post-synthesis oxidation of …

Synthesis, Characterization And Computational Study Of [4]Octamethylferrocenophane, Benjamin Mark Wilson

Theses, Dissertations and Capstones

This thesis reports the synthesis of an organic molecule, 1,4-bis(2,3,4,5-tetramethylcyclopentadienyl)butane by two different methods, in about 75% and 85% crude yield. Deprotonation of this molecule followed by reaction with FeCl2 generated the tethered ferrocene, [4]octamethylferrocenophane. Although the yield was low in the first attempt (2%), this molecule has been characterized through NMR spectroscopy, X-ray crystallography, electronic spectroscopy, elemental analysis, and decomposition temperature. A computational study was performed to determine the energy gap between each minimum energy structure. It was found that the energy barrier was not high enough to prevent a rapid interconversion between the two structures of minimum energy …

Incorporation Of The Actin-Myosin Biomolecular Motor System Into A Microfluidic Device, Rebecca Marie Ragland

Theses, Dissertations and Capstones

Recently, the field of bionanotechnology has sought to develop a device containing a biomolecular motor nano-cargo transport system. Among many applications, a device of this sort could be used to sort, purify, or detect specific molecules. In this work, an attempt was made to incorporate the actin-myosin biomolecular motor system into a microfluidic device constructed out of polydimethylsiloxane (PDMS) and glass. Methods for cleaning and functionalizing the glass surface of the device were optimized. After performing actin-myosin motility assays in a variety of PDMS/glass devices, it was determined that the oxygen permeability of PDMS limited the quality of motility that …

Atmospheric Polycyclic Aromatic Hydrocarbon Profiles And Sources In Pine Needles And Particulate Matter In Dayton, Ohio, Usa, Timothy A. Tomashuk, Triet Minh Truong, Madhavi Mantha, Audrey E. Mcgowin Ph.D.

Chemistry Student Publications

Polycyclic aromatic hydrocarbons (PAHs) were measured in pine needles (passive sampling) and on high volume particulate matter (PM) filters (active sampling) over a period of eight to ten months at two separate sites in the Dayton, Ohio, USA metropolitan area: Moraine and Yellow Springs.

Total PAH concentrations for PM ranged from 77.4 μg/g to 837 μg/g (dry wt.) at both sites with high molecular weight PAHs being the predominant form that tended to be higher in concentration during the colder months. Total PAH concentrations for pine needles varied by tree species and location. With an average concentration of 4187 ng/g, …

Monitoring The Health Of Glen Helen Nature Preserve: Spring 2012 Sediment And Water, Audrey E. Mcgowin Ph.D., Triet Minh Truong, David Kammler Ph.D., Joe Solch

Chemistry Student Publications

This poster presents the results for environmental testing in Glen Helen by the Special Topics in Analytical Chemistry course at Wright State University under the direction of Professor Audrey McGowin in Spring 2012. Water quality data are presented for the Yellow Spring in Yellow Springs, Ohio for April and May of 2012. Other test sites range from locations along Yellow Springs Creek to the covered bridge near Little Miami River.

This poster was created by Triet M. Truong.

Detailed Comparison Of The Pnicogen Bond With Chalcogen, Halogen And Hydrogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The characteristics of the pnicogen bond are explored using a variety of quantum chemical techniques. In particular, this interaction is compared with its halogen and chalcogen bond cousins, as well as with the more common H-bond. In general, these bonds are all of comparable strength. More specifically, they are strengthened by the presence of an electronegative substituent on the electron-acceptor atom, and each gains strength as one moves down the appropriate column of the periodic table, for example, from N to P to As. These noncovalent bonds owe their stability to a mixture in nearly equal parts of electrostatic attraction …

Microwave, Infrared And Raman Spectra, R0 Structural Parameters, Ab Initio Calculations And Vibrational Assignment Of 1-Fluoro-1-Silacyclopentanea), James Durig, Savitha Panikar, Daniel Obenchain, Brandon Bills, Patrick Lohan, Rebecca Peebles, Sean Peebles, Peter Groner, Gamil Guirgis, Michael Johnston

Faculty Research and Creative Activity

The microwave spectrum (6500–18 500 MHz) of 1-fluoro-1-silacyclopentane, c-C4H8SiHF has been recorded and 87 transitions for the 28Si, 29Si, 30Si, and 13C isotopomers have been assigned for a single conformer. Infrared spectra (3050-350 cm−1) of the gas and solid and Raman spectrum (3100-40 cm−1) of the liquid have also been recorded. The vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twist form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers to be saddle points with nearly the same energies but much …

Accessibility And Selective Stabilization Of The Principal Spin States Of Iron By Pyridyl Versus Phenolic Ketimines: Modulation Of The 6A1 ↔ 2T2 Ground-State Transformation Of The [Fen4O2]+ Chromophore, Musa S. Shongwe, Usama A. Al-Zaabi, Faizah Al-Mjeni, Carla S. Eribal, Imaddin A. Al-Omari, Hussein H. Hamdeh, Dariusz Matoga, Harry Adams, Michael J. Morris, Arnold L. Rheingold, Eckhard Bill, David J. Sellmyer

David Sellmyer Publications

Several potentially tridentate pyridyl and phenolic Schiff bases (apRen and HhapRen, respectively) were derived from the condensation reactions of 2-acetylpyridine (ap) and 2′-hydroxyacetophenone (Hhap), respectively, with N-R-ethylenediamine (RNHCH₂CH₂NH₂, Ren; R = H, Me or Et) and com-plexed in situ with iron(II) or iron(III), as dictated by the nature of the ligand donor set, to generate the six-coordinate iron compounds [Fe^II(apRen)₂]X₂ (R = H, Me; X– = ClO4–, BPh4–, PF6–) and [Fe^III(hapRen)₂]X (R = Me, Et; X– = ClO_4–, BPh_4–). Single-crystal X-ray …

Size And Phase Control Of Cobalt-Carbide Nanoparticles Using Oh- And Cl- Anions In A Polyol Process, Zachary J. Huba, Everett E. Carpenter

Chemistry Publications

Exchange coupled cobalt–carbide nanocomposites and single-phase Co₂C nanoparticles were synthesized using the polyol process. Hydroxide and chloride anions were used to controlcarbide phase and particle shape. Synthesized Co _x C nanocomposites exhibited average diameters around 300 nm. Co _x C nanocomposites synthesized at 0.25 M [OH⁻] and [Cl⁻] formed clusters of capped nanorods, whereas synthesis at 0.37 M [OH⁻] and [Cl⁻] produced clusters of long blade-like particles. For single-phase Co₂C, an [OH⁻] and [Cl⁻] of 0.71 M was used and produced clusters of ellipsoidal …

Transmetallation Of A Lithium Porphyrin With Iron(Ii), Kidus Debesai

The Corinthian

Synthesis and characterization of the iron(III) derivative of the 2,3,7,8,12,13,17,18-octabromo-meso-tetrakis(N-methylpyridium-4-yl)porphyrin was accomplished via metal metathesis of the lithium porphyrin and iron(II) ion. Preliminary molecular orbital analysis of the iron(II) and iron(III) derivatives demonstrate that the iron(III) porphyrin exists at a lower energy state.

First Steps In Growth Of A Polypeptide Toward Β-Sheet Structure, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. …

Extrapolation To The Complete Basis Set Limit For Binding Energies Of Noncovalent Interactions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A means of extrapolating from double and triple-valence basis sets to a complete basis set is examined in the context of the pnicogen bonds in the BH2P⋯NH3 complexes, with B = CH3, H, NH2, CF3, OH, Cl, F, and NO2. Binding energies converge smoothly, and the trends for the various substituents B are unaffected by the basis set size, extrapolation, or level of inclusion of electron correlation, including MP2 and CCSD(T). The approach appears to be successful also for H-bonded systems, in particular the water dimer. In the event that full extrapolation within the context of CCSD(T) is not feasible, …

Plasma Spectroscopic Techniques Applied To Biological And Environmental Matrices, Morgan Steele Schmidt

Electronic Theses and Dissertations

The purpose of this research was to apply the use of direct ablation plasma spectroscopic techniques, including spark-induced breakdown spectroscopy (SIBS) and laser-induced breakdown spectroscopy (LIBS), to a variety of environmental matrices. These were applied to two different analytical problems. SIBS instrumentation was adapted in order to develop a fieldable monitor for the measurement of carbon in soil. SIBS spectra in the 200 nm to 400 nm region of several soils were collected, and the neutral carbon line (247.85 nm) was compared to total carbon concentration determined by standard dry combustion analysis. Additionally, Fe and Si were evaluated in a …

Sensitivity Of Noncovalent Bonds To Intermolecular Separation: Hydrogen, Halogen, Chalcogen, And Pnicogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

It is well known that noncovalent bonds are weakened when stretched from their equilibrium intermolecular separation. Quantum chemical calculations are used to examine and compare the sensitivity to stretches of hydrogen, halogen, chalcogen, and pnicogen bonds. NH3 was taken as the universal electron donor, paired with HOH and FH in H-bonds, as well as with FPH2, FSH, and FCl. Even though the binding energies span a wide range, stretching the intermolecular separation by 1 Å cuts this quantity by the same proportion, roughly in half, for each system. Taking the sum of van der Waals radii as an arbitrary cutoff, …

Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede

Faculty Publications, Chemistry

The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition …

Redox Proteomics In Selected Neurodegenerative Disorders: From Its Infancy To Future Applications, Allan Butterfield, Marzia Perluigi, Tanea Reed, Tasneem Muharib, Christopher P. Hughes, Rena A.S. Robinson, Rukhsana Sultana

Chemistry Faculty and Staff Scholarship

Several studies demonstrated that oxidative damage is a characteristic feature of many neurodegenerative diseases. The accumulation of oxidatively modified proteins may disrupt cellular functions by affecting protein expression, protein turnover, cell signaling, and induction of apoptosis and necrosis, suggesting that protein oxidation could have both physiological and pathological significance. For nearly two decades, our laboratory focused particular attention on studying oxidative damage of proteins and how their chemical modifications induced by reactive oxygen species/reactive nitrogen species correlate with pathology, biochemical alterations, and clinical presentations of Alzheimer's disease. This comprehensive article outlines basic knowledge of oxidative modification of proteins and lipids, …

Dynamic Light Scattering And Microelectrophoresis: Main Prospects And Limitations, Vuk Uskoković

Pharmacy Faculty Articles and Research

Microelectrophoresis based on the dynamic light scattering (DLS) effect has been a major tool for assessing and controlling the conditions for stability of colloidal systems. However, both the DLS methods for characterization of the hydrodynamic size of dispersed submicron particles and the theory behind the electrokinetic phenomena are associated with fundamental and practical approximations that limit their sensitivity and information output. Some of these fundamental limitations, including the spherical approximation of DLS measurements and an inability of microelectrophoretic analyses of colloidal systems to detect discrete charges and differ between differently charged particle surfaces due to rotational diffusion and particle orientation …

Indole Based Antioxidants For The Treatment Of Ischemia Reperfusion Injury, Andrew Chapp

Dissertations, Master's Theses and Master's Reports - Open

With the number of ischemia reperfusion (I/R) injuries on the rise, and a lack of pharmacological intervention aimed at reducing free radical damage associated with I/R, we have developed 30 indole phenolic antioxidants that were synthesized by click chemistry to couple our indole with a phenolic or anisole derivative. The total antioxidant activity of the analogues was tested in vitro using the ferric thiocyanate lipid emulsion method. Compounds containing hydroxyl or methoxy aromatics at the 3 or 4 position on the aromatic coupled to the indole exhibited increased antioxidant scavenging. 4-methoxyindole derivatives (8a-e) exhibited increased scavenging (p < 0.05) compared to the known antioxidant butylated hydroxyanisole (BHA).

Preferred Configurations Of Peptide-Peptide Interactions, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The natural and fundamental proclivities of interaction between a pair of peptide units are examined using high-level ab initio calculations. The NH···O H-bonded structure is found to be the most stable configuration of the N-methylacetamide (NMA) model dimer, but only slightly more so than a stacked arrangement. The H-bonded geometry is destabilized by only a small amount if the NH group is lifted out of the plane of the proton-accepting amide. This out-of-plane motion is facilitated by a stabilizing charge transfer from the CO π bond to the NH σ* antibonding orbital. The parallel and antiparallel stacked dimers are nearly …

Electrochemical Studies Of Nanoscale Composite Materials As Electrodes In Direct Alcohol Fuel Cells, Jordan Anderson

Electronic Theses and Dissertations

Polymer electrolyte membrane fuel cells (PEMFCs) have recently acquired much attention as alternatives to combustion engines for power conversion. The primary interest in fuel cell technology is the possibility of 60% power conversion efficiency as compared to the 30% maximum theoretical efficiency limited to combustion engines and turbines. Although originally conceived to work with hydrogen as a fuel, difficulties relating to hydrogen storage have prompted much effort in using other fuels. Small organic molecules such as alcohols and formic acid have shown promise as alternatives to hydrogen in PEMFCs due to their higher stability at ambient conditions. The drawbacks for …