Chemistry Commons^™

Analysis Of Iasi Tropospheric O₃ Data Over The Arctic During Polarcat Campaigns In 2008, M. Pommier, C. Clerbaux, K. S. Law, G. Ancellet, P. Bernath, P.-F. Coheur, J. Hadji-Lazaro, D. Hurtmans, P. Nédélec, J.-D. Paris, F. Ravetta, T. B. Ryerson, H. Schlager, A. J. Weinheimer

Chemistry & Biochemistry Faculty Publications

Ozone data retrieved in the Arctic region from infrared radiance spectra recorded by the Infrared Atmospheric Sounding Interferometer (IASI) on board the MetOp-A European satellite are presented. They are compared with in situ and lidar observations obtained during a series of aircraft measurement campaigns as part of the International Polar Year POLARCAT activities in spring and summer 2008. Different air masses were sampled during the campaigns including clean air, polluted plumes originating from anthropogenic sources, forest fire plumes from the three northern continents, and stratospheric-influenced air masses. The comparison between IASI O₃ [0–8 km], [0–12 km] partial columns and …

Process-Evaluation Of Tropospheric Humidity Simulated By General Circulation Models Using Water Vapor Isotopic Observations: 2. Using Isotopic Diagnostics To Understand The Mid And Upper Tropospheric Moist Bias In The Tropics And Subtropics, Camille Risi, David Noone, John Worden, Christian Frankenberg, Gabriele Stiller, Michael Kiefer, Bernd Funke, Kaley Walker, Peter Bernath, Matthias Schneider, Sandrine Bony, Jeonghoon Lee, Derek Brown, Christophe Sturm

Chemistry & Biochemistry Faculty Publications

Evaluating the representation of processes controlling tropical and subtropical tropospheric relative humidity (RH) in atmospheric general circulation models (GCMs) is crucial to assess the credibility of predicted climate changes. GCMs have long exhibited a moist bias in the tropical and subtropical mid and upper troposphere, which could be due to the mis-representation of cloud processes or of the large-scale circulation, or to excessive diffusion during water vapor transport. The goal of this study is to use observations of the water vapor isotopic ratio to understand the cause of this bias. We compare the three-dimensional distribution of the water vapor isotopic …

Tunable Gold Nanostructures With Nanocapsules As Template Reaction Vessels, Balasubramanian Ramjee, Srujana Prayakarao, Sangbum Han, Wei Cao

Chemistry & Biochemistry Faculty Publications

Hollow, polymeric, thiol-ene resorcinarene nanocapsules can act as template reaction vessels for the synthesis of gold nanoshells or spherical aggregates of gold nanoparticles depending on the reaction conditions. The spherical nanoparticle aggregates were evaluated as catalysts in the biphasic reduction of 4-nitrophenol.

In Situ And Ex Situ Studies Of Molybdenum Thin Films Deposited By Rf And Dc Magnetron Sputtering As A Back Contact For Cigs Solar Cells, K. P. Aryal, H. Khatri, R. W. Collins, S. Marsillac

Electrical & Computer Engineering Faculty Publications

Molybdenum thin films were deposited by rf and dc magnetron sputtering and their properties analyzed with regards to their potential application as a back contact for CIGS solar cells. It is shown that both types of films tend to transition from tensile to compressive strain when the deposition pressure increases, while the conductivity and the grain size decreas. The nucleation of the films characterized by in situ and real time spectroscopic ellipsometry shows that both films follow a Volmer-Weber growth, with a higher surface roughness and lower deposition rate for the rf deposited films. The electronic relaxation time was then …

The Nature, Origin And Preservation Of Amide Organic Nitrogen In Organic Matter, Georgina Anne Mckee

Chemistry & Biochemistry Theses & Dissertations

Past studies have found much of nonliving sedimentary/aqueous nitrogen-containing organic matter (NCOM) is composed of amides, assumed to be peptides/proteins. Their lability calls into question their survival, and several hypotheses have been suggested to explain this. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and nuclear magnetic resonance (NMR) spectroscopy I investigated the molecular amide composition in sedimentary/aqueous systems while reassessing their preservation and formation routes.

Development of a suitable methodology is essential for successful NCOM study due to electrospray ionisation source requirements: sediment samples need to be rendered into solution. Based on NMR and FT-ICR-MS analysis, I determined …

Insights Into Chemical Structure Changes Of Kerogen From Bituminous Coal In Response To Dike Intrusions Investigated By Advanced Solid-State 13C Nmr, Yuan Li

Chemistry & Biochemistry Theses & Dissertations

Variations in the chemical structures of kerogens From highly volatile bituminous coal located near two igneous dike intrusions in the Illinois Basin were examined in detail by advanced solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy. Spectral-editing techniques were used to identify specific functional groups. Direct polarization was used to quantify different functional groups. ¹H-¹³C two- dimensional heteronuclear NMR was used to examine connectivities and proximities, and ¹H-¹³C long-range recoupled dipolar dephasing was used to estimate aromatic cluster sizes. With decreasing distance to dike contacts and increasing thermal maturity (vitrinite reflectance R₀ from …

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 89th Annual Meeting of the Virginia Academy of Science, May 25-27, 2011, University of Richmond, Richmond VA.

Bioinformatics, Thermodynamics And Kinetics Analysis Of An All Alpha Helical Protein With A Gree-Key Topology, Hai Li

Chemistry & Biochemistry Theses & Dissertations

Computational and experimental studies focusing on the role of conserved residues for folding and stability is an active and promising area of research. To further expand our understanding we present the results of a bioinformatics analysis of the death domain superfamily. The death domain superfamily fold consists of six α-helices arranged in a Greek-key topology, which is shared by the all β-sheet immunoglobulin and mixed α/β-plait superfamilies. Our sequence and structural studies have identified a group of conserved hydrophobic residues and corresponding long-range interactions, which we propose are important in the formation and stabilization of the hydrophobic core and native …

A Three Dimensional Green's Function Solution Technique For The Transport Of Heavy Ions In Laboratory And Space, Candice Rockell Gerstner

Mathematics & Statistics Theses & Dissertations

In the future, astronauts will be sent into space for longer durations of time compared to previous missions. The increased risk of exposure to ionizing radiation, such as Galactic Cosmic Rays and Solar Particle Events, is of great concern. Consequently, steps must be taken to ensure astronaut safety by providing adequate shielding. The shielding and exposure of space travelers is controlled by the transport properties of the radiation through the spacecraft, its onboard systems and the bodies of the individuals themselves. Meeting the challenge of future space programs will therefore require accurate and efficient methods for performing radiation transport calculations …

Computational Investigation Of The Bioactive Selenium Compounds Ebselen And Selenious Acid, Sonia Antony

Chemistry & Biochemistry Theses & Dissertations

Selenium, a toxic element, is required in trace quantities for the proper functioning of biological systems. The experimental mechanistic study of the reactions of ebselen and selenious acid is difficult due to complexity of the reaction mixtures and the presence of short-lived intermediates. Computational modeling of the reactivity of these species can give us an insight into their mechanisms, but the process is complicated by proton exchanges associated with the mechanistic steps. In gas phase modeling, this may be corrected to a certain level using the solvent assisted proton exchange (SAPE) method. SAPE is a modeling technique that mimics solvent …

Fourier Transform Mass Spectrometry For The Molecular Level Characterization Of Natural Organic Matter: Instrument Capabilities, Applications, And Limitations, Rachel L. Sleighter, Patrick G. Hatcher, Goran Nikolić (Ed.)

Chemistry & Biochemistry Faculty Publications

No abstract provided.

Characterization Of Heterogeneities And Domains In Aquatic And Sedimentary Organic Matter By 1 H Spin Diffusion: Potential For Elucidating The Formation Mechanisms, Jingdong Mao, Xiaoyan Cao

Chemistry & Biochemistry Faculty Publications

Although the information on domains and heterogeneities of natural organic matter (NOM) can provide insights into its formation mechanisms, the appropriate solid-state NMR technique for measuring them is still lacking. The traditional technique requires mobility differences in NOM whereas NOM components are primarily rigid. We introduced a new ¹H spin diffusion technique, ¹H-¹³C two-dimensional heteronuclear correlation (2D HETCOR) NMR with ¹H spin diffusion, for characterization of domains and heterogeneities in aquatic and sedimentary organic matter. It was achieved by collecting a series of 2D HETCOR spectra with a variable mixing time, t_m', and …

Localized Surface Plasmon Resonance Of Single Silver Nanoparticles Studied By Dark-Field Optical Microscopy And Spectroscopy, Wei Cao, Tao Huang, Xiao-Hong Nancy Xu, Hani E. Elsayed-Ali

Electrical & Computer Engineering Faculty Publications

Localized surface plasmon resonance (LSPR) of Ag nanoparticles (NPs) with different shapes and disk-shaped Ag NP pairs with varying interparticle distance is studied using dark-field optical microscopy and spectroscopy (DFOMS). Disk-, square-, and triangular-shaped Ag NPs were fabricated on indium tin oxide-coated glass substrates by electron beam lithography. The LSPR spectra collected from single Ag NPs within 5×5 arrays using DFOMS exhibited pronounced redshifts as the NP shape changed from disk to square and to triangular. The shape-dependent experimental LSPR spectra are in good agreement with simulations using the discrete dipole approximation model, although there are small deviations in the …

Fossil And Contemporary Aerosol Particulate Organic Carbon In The Eastern United States: Implications For Deposition And Inputs To Watersheds, Andrew S. Wozniak, James E. Bauer, Rebecca M. Dickhut

Chemistry & Biochemistry Faculty Publications

Atmospheric particulate matter samples were collected from mid-Atlantic and northeastern U. S. (Virginia and New York, respectively) sites to assess the fossil versus contemporary sources contributing to aerosol organic carbon (OC) and the implications for its deposition to watersheds. Mean particulate matter total OC (TOC) deposition rates (wet + dry deposition) were calculated to be 1.6 and 2.4 mg C m^-2 d^-1 for the Virginia and New York sites, respectively. Wet deposition of particulate TOC was determined to be the dominant depositional mode, accounting for >65% (Virginia) and >80% (New York) of total aerosol TOC deposition. Isotopic mass …

A Mini-Electrodialysis System For Desalting Small Volume Saline Samples For Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Hongmei Chen, Aron Stubbins, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

An affordable, commercially available mini-electrodialysis (mini-ED) system has been evaluated for the efficient desalting of small volume samples of seawater before analysis by electrospray Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). Mini-ED FT-ICR mass spectra were compared with spectra for samples that were treated by C₁₈ solid phase extraction, a commonly used method for rapid sample preparation for this type of analysis. In this comparison, it is clear that mini-ED provides more representative molecular information, compared with C₁₈ isolation, and recovers the overwhelming majority of peaks from salt-free samples, indicating that it adequately represents the …

Fourier Transform Emission Spectroscopy Of Yh And Yd: Observation Of New A¹Δ And B¹Π Electronic States, R. S. Ram, G. Li, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

The emission spectra of YH and YD molecules have been investigated in the 3600–12 000 cm⁻¹ region using a Fourier transform spectrometer. Molecules were formed in an yttrium hollow cathode lamp operated with a continuous flow of a mixture of Ne and Ar gases, and YH and YD were observed together in the same spectra. A group of bands observed near 1 μm have been identified as 0-0 and 1-1 bands of the A¹Δ-X¹Σ⁺ and B¹Π-X¹Σ⁺ transitions of YH and the 0-0 bands of the same two transitions …

Ace-Fts Measurements Of Trace Species In The Characterization Of Biomass Burning Plumes, K. A. Tereszchuk, G. González Abad, C. Clerbaux, D. Hurtmans, P.-F. Coheur, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

To further our understanding of the effects of biomass burning emissions on atmospheric composition, we report measurements of trace species in biomass burning plumes made by the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) instrument on the SCISAT-1 satellite. An extensive set of 15 molecules, C₂H₂, C₂H₆, CH₃OH, CH₄, CO, H₂CO, HCN, HCOOH, HNO₃, NO, NO₂, N₂O₅, O-3, OCS and SF₆ are used in our analysis. Even though most biomass burning smoke is typically confined to the …

Nonuniformity In Lattice Contraction Of Bismuth Nanoclusters Heated Near Its Melting Point, A. Esmail, M. Abdel-Fattah, Hani E. Elsayed-Ali

Electrical & Computer Engineering Faculty Publications

The structural properties of bismuth nanoclusters were investigated with transmission high-energy electron diffraction from room temperature up to 525 ± 6 K. The Bi nanoclusters were fabricated by thermal evaporation at room temperature on transmission electron microscope grids coated with an ultrathin carbon film, followed by thermal and femtosecond laser annealing. The annealed sample had an average cluster size of ∼14 nm along the minor axis and ∼16 nm along the major axis. The Debye temperature of the annealed nanoclusters was found to be 53 ± 6 K along the [012] direction and 86 ± 9 K along the [110] …

Precise Control Of Highly Ordered Arrays Of Nested Semiconductor/Metal Nanotubes, Diefeng Gu, Helmut Baumgart, Kandabara Tapily, Pragya Shrestha, Gon Namkoong, Xianyu Ao, Frank Müller

Electrical & Computer Engineering Faculty Publications

Lithographically defined microporous templates in conjunction with the atomic layer deposition (ALD) technique enable remarkable control of complex novel nested nanotube structures. So far three-dimensional control of physical process parameters has not been fully realized with high precision resolution, and requires optimization in order to achieve a wider range of potential applications. Furthermore, the combination of composite insulating oxide layers alternating with semiconducting layers and metals can provide various types of novel applications and eventually provide unique and advanced levels of multifunctional nanoscale devices. Semiconducting TiO₂ nanotubes have potential applications in photovoltaic devices. The combination of nanostructured semiconducting materials …

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 …

Oxygen Isotopes As A Tracer Of Dom Processes In River-Estuary Systems, Joy Ashley Matthews

OES Theses and Dissertations

In the biogeochemical study of dissolved organic matter (DOM) in natural waters, stable isotopes are used to provide insight into both the sources of DOM and the processes affecting its alteration. Through the research presented here, oxygen isotopes are incorporated into the study of DOM through the adaptation of a pyrolysis elemental analysis isotope ratio mass spectrometer method, and sample preparation using two-stage ultrafiltration.

The application of oxygen isotopes to the study of DOM is demonstrated in two studies. First, natural abundance of δ¹⁸O in DOM is explored in the Delaware estuary. Using a two end-member mixing model, …

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 88th Annual Meeting of the Virginia Academy of Science, May 20-21, 2010, James Madison University, Harrisonburg, VA.

Conformational Change And Topological Stability Of Proteins, Jeffrey Andrew Tibbitt

Chemistry & Biochemistry Theses & Dissertations

The conformation and topology of a protein changes when stabilizing forces are absent, but the mechanisms by which these changes occur remains elusive. This dissertation aims to broaden the understandings. On the conformational level, the M20 loop conformers of E. coli dihydrofolate reductase are interrogated to identify factors responsible for their stability as well as to determine how one conformer might change into another. Molecular dynamics is used to simulate the open, closed and occluded conformers (observed in X-ray crystal structures) under a series of different single ligand conditions. Analysis shows that all open conformers move to a similar new …

Molecular Characterization Of The Soluble Fraction Of Atmospheric Particulate Matter Obtained By Chemical Oxidation With Nitric Acid, Amanda Susan Priest

Chemistry & Biochemistry Theses & Dissertations

The availability of information regarding the composition of ambient atmospheric particulate matter and the transformations that these compounds may undergo upon atmospheric transit is surprisingly absent. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry is used in this study to rapidly evaluate the composition of the water-soluble organic fraction of standard and collected atmospheric particulate matter samples, and the changes that these mixtures undergo upon oxidation with nitric acid. The standard samples include representative particulate matter collected over the course of a year in Washington, D.C. and particulate matter from the exhaust of a diesel-powered engine. The collected sample …

Effluent Organic Nitrogen (Eon): Bioavailability And Photochemical And Salinity-Mediated Release, Deborah A. Bronk, Quinn N. Roberts, Marta P. Sanderson, Elizabeth A. Canuel, Patrick G. Hatcher, Rajaa Mesfioui, Katherine C. Filippino, Margaret R. Mulholland, Nancy G. Love

Chemistry & Biochemistry Faculty Publications

The goal of this study was to investigate three potential ways that the soluble organic nitrogen (N) fraction of wastewater treatment plant (WWTP) effluents, termed effluent organic N (EON), could contribute to coastal eutrophication - direct biological removal, photochemical release of labile compounds, and salinity-mediated release of ammonium (NH₄+). Effluents from two WWTPs were used in the experiments. For the bioassays, EON was added to water from four salinities (∼0 to 30) collected from the James River (VA) in August 2008, and then concentrations of N and phosphorus compounds were measured periodically over 48 h. Bioassay results, based …

Sequence And Structural Analysis Of The Chitinase Insertion Domain Reveals Two Conserved Motifs Involved In Chitin Binding, Hai Li, Lesley H. Greene

Chemistry & Biochemistry Faculty Publications

Background: Chitinases are prevalent in life and are found in species including archaea, bacteria, fungi, plants, and animals. They break down chitin, which is the second most abundant carbohydrate in nature after cellulose. Hence, they are important for maintaining a balance between carbon and nitrogen trapped as insoluble chitin in biomass. Chitinases are classified into two families, 18 and 19 glycoside hydrolases. In addition to a catalytic domain, which is a triosephosphate isomerase barrel, many family 18 chitinases contain another module, i.e., chitinase insertion domain. While numerous studies focus on the biological role of the catalytic domain in chitinase activity, …

Solvent Dependent Morphologies In Thiol-Ene Photopolymerization: A Facile Route To Synthesis Of Resorcinarene Nanocapsules, Zaharoula Marie Kalaitzis

Chemistry & Biochemistry Theses & Dissertations

Synthesis of morphologically distinct polymeric nanostructures is vital for their wide ranging applications from nanomedicine to material science. Among various polymeric nanostructures, nanocapsules in particular have attracted a lot of attention as nanoreactors and drug delivery vehicles in nanomedicine. Often, synthesis of nanocapsules is achieved by template-based approaches. A direct, template-free method for the fabrication of nanocapsules and a variety of other morphologically distinct polymeric architectures was developed. The photopolymerization of a resorcinarene thiol-ene surfactant in various solvents lead to the formation of nanocapsules, nanoparticles, fibers, distorted honeycomb-like lattices, and sheets. The progress of the polymerization reaction and the morphology …

Development Of Chemometric Models And Calibration Transfer For Rapid Diesel And Jet Fuel Analysis Using Near Infrared Spectroscopy, Christopher Matthew Larkin

Chemistry & Biochemistry Theses & Dissertations

Fuel quality assurance and analysis, as it pertains to the United States armed forces, is crucial for maintaining operability and upholding safety regulations with respect to fuel class. Currently a great amount of effort, money and manpower are dedicated to this task as fuel analysis takes place in off-site laboratories where quality assessment and property determination is performed manually by highly qualified lab technicians. This presents the military with a logistics problem with respect to refueling, transport, and fuel storage as the typical tum-around time is 1-2 weeks. In this thesis it has been demonstrated that near-infrared spectroscopy, in conjunction …

Theoretical Studies Of 2,3 -Sigmatropic Rearrangements Of Allylic Selenoxides And Selenimides, Craig A. Bayse, Sonia Antony

Chemistry & Biochemistry Faculty Publications

Density-functional theory is used to model the endo and exo transition states for [2,3]-sigmatropic rearrangement of allylic aryl-selenoxides and -selenimides. The endo transition state is generally preferred for selenoxides if there is no substitution at the 2 position of the allyl group. Based upon the relative energies of the endo and exo transition states, enantioselectivity of rearrangements is expected to be greatest for molecules with substitutions at the 1- or (E)-3- position of the allyl group. Ortho substitution of a nitro group on the ancillary selenoxide phenyl ring reduces the activation barriers, increases the difference between the endo and exo …

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 87th Annual Meeting of the Virginia Academy of Science, May 27-29, 2009, Virginia Commonwealth University, Richmond Virginia.