Chemistry Commons^™

A Near-Global Atmospheric Distribution Of N2o Isotopologues, Peter F. Bernath, Mahdi Yousefi, Eric Buzan, Chris D. Boone

Chemistry & Biochemistry Faculty Publications

The distributions of the four most abundant isotopologues and isotopomers (N₂O, ¹⁵NNO, N¹⁵NO, and NN¹⁸O of nitrous oxide have been measured in the Earth's stratosphere by infrared remote sensing with the Atmospheric Chemistry Experiment (ACE) Fourier transform spectrometer. These satellite observations have provided a near-global picture of N₂O isotopic fractionation. The relative abundances of the heavier species increase with altitude and with latitude in the stratosphere as the air becomes older. The heavy isotopologues are enriched by 20-30% in the upper stratosphere and even more over the poles. These observations are …

Selenium Distribution And Cycling In The Eastern Equatorial Pacific Ocean, Zoe Wambaugh

OES Theses and Dissertations

Oxygen minimum zones in oceanic waters have become increasingly important to the marine environment and society. Low oxygen waters affect not only the distribution and abundance of marine organisms, but also impact the solubility and transport of trace elements that are of biological importance, with the chemical speciation and solubility depending on the actual redox poise of the waters. One redox sensitive trace element of interest is selenium, which can be both toxic and essential for organisms, depending on its chemical speciation. In 2013, the US GEOTRACES program completed the GP16 transect from Peru to Tahiti, going through the oxygen …

Synthesis, Characterization And Application Of Sugar-Based Low Molecular Weight Gelators, Ifeanyi Simeon Okafor

Chemistry & Biochemistry Theses & Dissertations

Low molecular weight gelators (LMWGs) are an interesting class of compound that have gained considerable attention especially because of their potential applications for soft biomaterials. Carbohydrate based low molecular weight hydrogelators and organogelators are able to selfassemble and form ordered supramolecular structures, which are useful for exploring biomedical applications. The resulting gelators are responsive to external stimuli because of the weak noncovalent intermolecular forces and interaction that influences self-assembly. Stimuli-responsive supramolecular organogels with interesting properties in response to external environmental stimuli have gained considerable attention due to their applications in biomaterials, sensors and for drug delivery.

One of the major …

High Resolution Spectra Of Carbon Monoxide, Propane And Ammonia For Atmospheric Remote Sensing, Christopher Andrew Beale

OES Theses and Dissertations

Spectroscopy is a critical tool for analyzing atmospheric data. Identification of atmospheric parameters such as temperature, pressure and the existence and concentrations of constituent gases via remote sensing techniques are only possible with spectroscopic data. These form the basis of model atmospheres which may be compared to observations to determine such parameters. To this end, this dissertation explores the spectroscopy of three molecules: ammonia, propane and carbon monoxide.

Infrared spectra have been recorded for ammonia in the region 2400-9000 cm^-1. These spectra were recorded at elevated temperatures (from 293-973 K) using a Fourier Transform Spectrometer (FTS). Comparison between …

Observations Of Greenhouse Gas Isotopologues With Ace-Fts And Waccm, Eric Michael Buzan

Chemistry & Biochemistry Theses & Dissertations

Increases in greenhouse gas concentrations in the atmosphere are the major driver of climate change. Quantifying the sources and sinks of these gases is a major focus of research. Measuring isotopologues, or molecules that differ in isotopic composition, is one useful way of constraining the budget of a molecule as they are highly sensitive to different sources and sinks. However, measurements above the surface have been restricted to a few locations and have only reached the lower stratosphere. Satellite-based remote sensing can achieve nearly global measurement coverage, but so far no satellites have measured isotopologues.

Presented here are measurements of …

Characterization Of 3-Ester And 3-Carbamate Derivatives Of N-Acetyl-D-Glucosamine And Their Use In Controlled Drug Delivery, Consuelo Garcia

Chemistry & Biochemistry Theses & Dissertations

Low molecular weight gelators (LMWGs) are a class of compounds which reversibly form a network that traps solvents to form gels. Gelation by LMWGs is driven solely by non-covalent interactions such as hydrogen bonding, π - π stacking, and hydrophobic interactions. LMWGs can be designed such that the gel-sol and sol-gel transitions happen as a response to a specific stimulus. These stimulus responsive gels or “smart” gels can be used in a wide variety of applications including tissue regeneration, biosensing, and controlled drug delivery.

Among the different types of compounds that are LMWGs, carbohydrate based systems are especially interesting. Carbohydrates …

Lignin Contribution To The Global Carbon Pool: Investigating The Abiotic Modification Of Lignin By Reactive Oxygen Species, Derek Charles Waggoner

Chemistry & Biochemistry Theses & Dissertations

Evidence suggests that reactive oxygen species (ROS), largely generated through photochemical processes, are important in transforming the chemical composition of the large pool of terrestrially-derived dissolved organic matter (DOM) exported from land to water annually. However, due to the challenges inherent in isolating the effects of individual ROS on DOM composition, the role of ROS in the photochemical alteration of DOM remains poorly characterized. The main focus of the studies within this dissertation aim to more thoroughly characterize the alterations to lignin, used as an analog for terrestrial DOM, resulting from reactions with ROS.

To investigate the possibility that the …

Depletion Of Ozone And Reservoir Species Of Chlorine And Nitrogen Oxide In The Lower Antarctic Polar Vortex Measured From Aircraft, T. Jurkat, C. Voigt, S. Kaufmann, J.-U. Grooß, H. Ziereis, A. Dörnbrack, P. Hoor, H. Bozem, A. Engel, H. Bönisch, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

Novel airborne in situ measurements of inorganic chlorine, nitrogen oxide species, and ozone were performed inside the lower Antarctic polar vortex and at its edge in September 2012. We focus on one flight during the Transport and Composition of the LMS/Earth System Model Validation (TACTS/ESMVal) campaign with the German research aircraft HALO (High-Altitude LOng range research aircraft), reaching latitudes of 65°S and potential temperatures up to 405 K. Using the early winter correlations of reactive trace gases with N₂O from the Atmospheric Chemistry Experiment-Fourier Transform Spectrometer (ACE-FTS), we find high depletion of chlorine reservoir gases up to ∼40% …

The Role Of Sulfur Dioxide In Stratospheric Aerosol Formation Evaluated By Using In Situ Measurements In The Tropical Lower Stratosphere, A. W. Rollins, T. D. Thornberry, L. A. Watts, P. Yu, K. H. Rosenlof, M. Mills, E. Baumann, F. R. Giorgetta, T. V. Bui, M. Höpfner, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

Stratospheric aerosols (SAs) are a variable component of the Earth's albedo that may be intentionally enhanced in the future to offset greenhouse gases (geoengineering). The role of tropospheric-sourced sulfur dioxide (SO₂) in maintaining background SAs has been debated for decades without in situ measurements of SO₂ at the tropical tropopause to inform this issue. Here we clarify the role of SO₂ in maintaining SAs by using new in situ SO₂ measurements to evaluate climate models and satellite retrievals. We then use the observed tropical tropopause SO₂ mixing ratios to estimate the global flux of …

Fourier Transform Spectroscopy Of The A3Π–X3Σ− Transition Of Oh+, James N. Hodges, Peter F. Bernath

Chemistry & Biochemistry Faculty Publications

The OH⁺ ion is of critical importance to the chemistry in the interstellar medium and is a prerequisite for the generation of more complex chemical species. Submillimeter and ultraviolet observations rely on high quality laboratory spectra. Recent measurements of the fundamental vibrational band and previously unanalyzed Fourier transform spectra of the near-ultraviolet A³Π-X 3Σ^- electronic spectrum, acquired at the National Solar Observatory at Kitt Peak in 1989, provide an excellent opportunity to perform a global fit of the available data. These new optical data are approximately four times more precise as compared to the previous values. …

Alicyclic And Aromatic Carboxylic Acids In Soil Organic Matter: An Investigation Of Potential Origin And Association With Plutonium Using Advanced Analytical Techniques, Nicole Didonato

Chemistry & Biochemistry Theses & Dissertations

Carboxylic acids are a defining component of soil organic matter, responsible for many of the physical and chemical properties, including metal-organic matter interactions, which govern its role as an important constituent of soils. However, there is a shortage of detailed molecular level information regarding orientation and structural arrangement of carboxylic acids within soil organic matter. This dissertation utilizes electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) as well as solid-state and multi-dimensional nuclear magnetic resonance (NMR) to investigate the molecular formula composition within several organic matter sources and the primary structures that feature carboxylic acids. Soil organic matter …

A Statistical Analytical Model For Hydrophilic Electropore Characterization: A Comparison Study, P. Marracino, M. Liberti, P.T. Vernier, F. Apollonio

Bioelectrics Publications

Molecular dynamics (MD) simulations have proved to be a useful tool for unveiling many aspects of pore formation in lipid membranes under the influence of external electric fields. In order to compare the size-related properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed for characterizing pore geometry and its evolution over time. In the present paper three different methodologies for evaluating electropore geometrical behavior will be compared: (i) the first allows analysis of the dimensions of the pore through an algorithm that uses a Monte Carlo simulated annealing …

Phytoplankton Plastid Proteomics: Cracking Open Diatoms To Understand Plastid Biochemistry Under Iron Limitation, Skyler J. Nunn, Phoebe Dreux Chappell, Kristofer Gomes, Anasthasia Bonderenko, Bethany D. Jenkins, Brook L. Nunn

OES Faculty Publications

Diatoms, such as Thalassiosira pseudonana, are important oceanic primary producers, as they sequester carbon dioxide (CO₂) out of the atmosphere, die, and precipitate to the ocean floor. In many areas of the world’s oceans, phytoplankton, such as diatoms, are limited in growth by the availability of iron (Fe). Fe is an essential nutrient for phytoplankton, as it is central in the electron transport chain component of photosynthesis. Through this study, we examined if Fe-limitation makes a significant difference in the proteins expressed within the chloroplast, the power source for diatoms. Here, we utilized a new plastid isolation technique specific …

Enhancement Of The Physicochemical Properties Of Pt(Dien)(Nucleobase) (2+) For Hivncp7 Targeting, S. D. Tsotsoros, P. B. Lutz, A. G. Daniel, E. J. Peterson, R. E. F. De Paiva, E. Rivera, Y. Qu, C. A. Bayse, N. P. Farrell

Chemistry & Biochemistry Faculty Publications

Physicochemical properties of coordination compounds can be exploited for molecular recognition of biomolecules. The inherent π-π stacking properties of [Pt(chelate)(N-donor)]²⁺([PtN₄]) complexes were modulated by systematic variation of the chelate (diethylenetriamine and substituted derivatives) and N-donor (nucleobase or nucleoside) in the formally substitution-inert PtN₄ coordination sphere. Approaches to target the HIV nucleocapsid protein HIVNCp7 are summarized building on (i) assessment of stacking interactions with simple tryptophan or tryptophan derivatives to (ii) the tryptophan-containing C-terminal zinc finger and (iii) to the full two-zinc finger peptide and its interactions with RNA and DNA. The xanthosine nucleoside was identified …

Improving Cavity Enhanced Spectroscopy Of Molecular Ions In The Mid-Infrared With Up-Conversion Detection And Brewster-Plate Spoilers, Charles R. Markus, Adam J. Perry, James N. Hodges, Benjamin J. Mccall

Chemistry & Biochemistry Faculty Publications

The performance of sensitive spectroscopic methods in the mid-IR is often limited by fringing due to parasitic etalons and the background noise in mid-infrared detectors. In particular, the technique Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy (NICE-OHVMS), which is capable of determining the frequencies of strong rovibrational transitions of molecular ions with sub-MHz uncertainty, needs improved sensitivity in order to probe weaker transitions. In this work, we have implemented up-conversion detection with NICE-OHVMS in the 3.2 - 3.9 μm region to enable the use of faster and more sensitive detectors which cover visible wavelengths. The higher bandwidth enabled …

New And Improved Infra-Red Absorption Cross Sections And Ace-Fts Retrievals Of Carbon Tetrachloride (Ccl4), Jeremy J. Harrison, Christopher D. Boone, Peter F. Bernath

Chemistry & Biochemistry Faculty Publications

Carbon tetrachloride (CCl₄) is one of the species regulated by the Montreal Protocol on account of its ability to deplete stratospheric ozone. As such, the inconsistency between observations of its abundance and estimated sources and sinks is an important problem requiring urgent attention (Carpenter et al., 2014) [5]. Satellite remote-sensing has a role to play, particularly limb sounders which can provide vertical profiles into the stratosphere and therefore validate stratospheric loss rates in atmospheric models. This work is in two parts. The first describes new and improved high-resolution infra-red absorption cross sections of carbon tetrachloride/dry synthetic air over …

The Hitran2016 Molecular Spectroscopic Database, I. E. Gordon, L. S. Rothman, C. Hill, R. V. Kochanov, Y. Tan, P. F. Bernath, M. Birk, V. Boudon, A. Campargue, K. V. Chance

Chemistry & Biochemistry Faculty Publications

This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional …

Synthesis And Characterization Of Amide Linked Triazolyl Glycolipids As Molecular Hydrogelators And Organogelators, Guijun Wang, Anji Chen, Hari P. R. Mangunuru, Jayasudhan Reddy Yerabolu

Chemistry & Biochemistry Faculty Publications

Carbohydrate based small molecular gelators are important classes of compounds which can form useful soft materials with many practical applications. Although many different types of effective gelators have been reported, the rational design of a molecular hydrogelator is still challenging. In this research, we combined the structural features of two classes of monosaccharide based molecular gelators and obtained a new class of glycolipids that can function as molecular gelators. These new compounds were synthesized by introducing a triazole functional group to a protected 2-glucosamine through Cu(i) catalyzed azide/alkyne cycloaddition reaction (CuAAC). A series of eighteen new glycolipids containing 4,6-O …

Introducing Global Peat-Specific Temperature And Ph Calibrations Based On Brgdgt Bacterial Lipids, B.D.A. Naafs, G. N. Imglis, Y. Zheng, M. J. Amesbury, H. Biester, R. Bindler, J. Blewett, M. A. Burrows, D. Del Castillo Torres, F. M. Chambers, P. G. Hatcher

Chemistry & Biochemistry Faculty Publications

Glycerol dialkyl glycerol tetraethers (GDGTs) are membrane-spanning lipids from Bacteria and Archaea that are ubiquitous in a range of natural archives and especially abundant in peat. Previous work demonstrated that the distribution of bacterial branched GDGTs (brGDGTs) in mineral soils is correlated to environmental factors such as mean annual air temperature (MAAT) and soil pH. However, the influence of these parameters on brGDGT distributions in peat is largely unknown. Here we investigate the distribution of brGDGTs in 470 samples from 96 peatlands around the world with a broad mean annual air temperature (−8 to 27 °C) and pH (3–8) range …

Version 1.3 Aim Sofie Measured Methane (Ch4): Validation And Seasonal Climatology, P. P. Rong, J. M. Russell Iii, B. T. Marshall, D. E. Siskind, M. E. Hervig, L. L. Gordley, P. F. Bernath, K. A. Walker

Chemistry & Biochemistry Faculty Publications

The V1.3 methane (CH₄) measured by the Aeronomy of Ice in the Mesosphere (AIM) Solar Occultation for Ice Experiment (SOFIE) instrument is validated in the vertical range of ~25–70 km. The random error for SOFIE CH₄ is ~0.1–1% up to ~50 km and degrades to ~9% at ∼ 70 km. The systematic error remains at ~4% throughout the stratosphere and lower mesosphere. Comparisons with CH₄ data taken by the SCISAT Atmospheric Chemistry Experiment-Fourier Transform Spectrometer (ACE-FTS) and the Envisat Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) show an agreement within ~15% in the altitude range ~30–60 …

Preface-Jes Focus Issue On Electrolysis For Increased Renewable Energy Penetration, B. Pivovar, M. Carmo, K. Ayers, X. Zhang, J. O'Brien

Mechanical & Aerospace Engineering Faculty Publications

(First paragraph) Today represents a particularly exciting time, as our planet’s energy system is undergoing major changes due to dramatically decreasing renewable energy prices and increasing societal concerns over greenhouse gas emissions, criteria pollutants (arsenic, mercury, NOx, particulate matter), and climate change. These factors are pushing society toward deep decarbonization of our energy system, perhaps the most challenging issue facing the planet today. Unfortunately, wind and solar energy, while both promising generation sources, come with intermittency challenges and have limitations in their abilities to impact industrial and transportation sector demands where fossil fuel energy carriers based on chemical bonds have …

Bioenergetics: Experimental Demonstration Of Excess Protons And Related Features, Haitham A. Saeed

Chemistry & Biochemistry Theses & Dissertations

Over the last 50 years, ever since the Nobel-prize work of Peter Mitchell’s Chemiosmotic theory, the question whether bioenergetics energy transduction occurs through localized or delocalized protons has been a controversial issue among scientists. Recently, a proton-electrostatics localization hypothesis was formulated which may provide a new and clear understanding of localized and delocalized proton-coupling energy transduction in many biological systems. The aim of this dissertation was to test this new hypothesis.

To demonstrate the fundamental behavior of localized protons in a pure water-membrane-water system in relation to the newly derived pmf equation, excess protons and excess hydroxyl anions were generated …

Discoloration Of A Green Pigment In Tintoretto’S Allegorical Figure Of Spring And Analysis Of The Chemical Properties And Stability Of Copper Resinate, Sarah Wells Conner Horn

Chemistry & Biochemistry Theses & Dissertations

The focus of this thesis is the discoloration of a common historical green pigment, copper resinate. In this research the discoloration was investigated in Jacopo Tintoretto’s painting, Allegorical Figure of Spring, painted c. 1555. This painting is believed to have been painted with copper resinate which has discolored to brown over the centuries. The state of repair of the painting was determined using visual analysis under visible and UV light and the use of copper green pigments was confirmed using energy-dispersive X-ray fluorescence, including copper resinate based upon supplementary historical evidence. Substantial evidence was found from visual inspection and …

Possible Sources And Impacts Of Biochar Water Extractable Organic Compounds On Aquatic Microorganisms, Cameron Russell Smith

Chemistry & Biochemistry Theses & Dissertations

Smokeless biomass pyrolysis with application of biochar as a soil amendment could be a significant approach for carbon sequestration to possibly control climate change for energy and environmental sustainability. If biochar were to be utilized as a soil amendment and a carbon sequestration agent at Gt C scales, the release of potentially toxic compounds into soils and associated hydrological systems, through soil rainwater runoff and leaching, might have negative consequences, in both agro-ecosystems and aquatic environmental systems. Therefore, the main focus of this dissertation was to study the sources and chemical composition of biochar water extractable (soluble) organic compounds and …

Experimental Energy Levels And Partition Function Of The 12c2 Molecule, Tibor Furtenbacher, István Szabó, Attila G. Császár, Peter F. Bernath, Sergei N. Yurchenko, Jonathan Tennyson

Chemistry & Biochemistry Faculty Publications

The carbon dimer, the ¹²C₂ molecule, is ubiquitous in astronomical environments. Experimental-quality rovibronic energy levels are reported for ¹²C₂, based on rovibronic transitions measured for and among its singlet, triplet, and quintet electronic states, reported in 42 publications. The determination utilizes the Measured Active Rotational-Vibrational Energy Levels (MARVEL) technique. The 23,343 transitions measured experimentally and validated within this study determine 5699 rovibronic energy levels, 1325, 4309, and 65 levels for the singlet, triplet, and quintet states investigated, respectively. The MARVEL analysis provides rovibronic energies for six singlet, six triplet, and two quintet electronic states. For …

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 94th Annual Virginia Academy of Science Meeting, May 18-20, 2016, at University of Mary Washington, Fredericksburg, VA.

Low-Temperature Artificial Maturation Studies Of Type Ii And Type Iii Kerogens: Implications For Biogenic Gas Production, Albert Willy Nguena Kamga

Chemistry & Biochemistry Theses & Dissertations

Ancient organic matter (OM) in shales and coals, known mainly as Type II and Type III OM are known to produce both biogenic, thermogenic gas and oil. In this dissertation, mild artificial maturation, via closed system pyrolysis, is employed to determine the thermal reactivity of Type II and Type III OM beyond diagenesis. We select three Type II kerogens: i) Type II kerogen isolated from recent cores (3.3 Ma, Ro = 0.28) recovered from an upwelling basin in Namibia, Africa referred to as ODP Sediment, ii) Type II-S isolated from sediments (150 Ma, Ro = 0.38) recovered from an outcrop …

The Marine Cyanate Cycle, Brittany Widner

OES Theses and Dissertations

Cyanate (OCN-) is a reduced nitrogen compound with the potential to serve as a nitrogen and carbon source for marine microbes. Evidence from genomes and culture studies indicated that several marine cyanobacterial groups, including representatives of the globally important genera Synechococcus and Prochlorococcus, might be capable of cyanate assimilation. However, prior to this study, the distribution, bioavailability, and production pathways of cyanate were unknown in natural systems due to the absence of a sensitive cyanate assay; and the ability of organisms to assimilate cyanate on relevant timescales was unknown because we lacked a suitable tracer for measuring uptake. I developed …

Synthesis And Mechanistic Investigations Of Transition Metal Complexes And Ligands For Chemotherapeutic Applications, Jimmie Lee Bullock Jr.

Chemistry & Biochemistry Theses & Dissertations

Transition metal complexes have played a critical role in antitumor therapy with many complexes incorporating platinum, ruthenium, and lanthanum having been investigated in preclinical and clinical trials. The best known transition metal therapeutic is cisplatin, which is utilized in nearly 50% of all cancer therapies, despite its significant toxic side effects. The toxic side effects of current FDA approved platinum-based chemotherapeutics are often overlooked due to the “special status” granted to these drugs due to their ability to fight, what is often considered an incurable disease with life expectancies often measured in months. Oncology drug development has therefore now focused …

Synthesis, Morphological Control, Dispersion Stabilization And In Situ Self-Assembly Of Noble Metal Nanostructures Using Multidentate Resorcinarene Surfactants, Sangbum Han

Chemistry & Biochemistry Theses & Dissertations

In this dissertation, a detailed investigation on the influence of various macrocyclic resorcinarene surfactants in determining the morphology, stabilization and self-assembly of mono- and bi- metallic nanoparticles was undertaken. Chapter 2 describes the influence of resorcinarene surfactants functionalized with amine- and thiol- headgroups in determining the morphology of monometallic Pt nanoparticles synthesized via the Brust-Schiffrin reaction. We found that while resorcinarene benzylthiol can lead to the formation of highly branched Pt nanostructures, resorcinarene amine can lead to the formation of anisotropic crystalline Pt nanoparticles. Further, we have evaluated the influence of resorcinarene ligands in determining the catalytic activity of these …