Digital Commons Network^™

Validation Of The Global Distribution Of Co2 Volume Mixing Ratio In The Mesosphere And Lower Thermosphere From Saber, L. Rezac, Y. Jian, J. Yue, J. M. Russell Iii, A. Kutepov, R. Garcia, K. Walker, P. Bernath

Chemistry & Biochemistry Faculty Publications

The Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument on board the Thermosphere Ionosphere Mesosphere Energetics and Dynamics satellite has been measuring the limb radiance in 10 broadband infrared channels over the altitude range from ~ 400 km to the Earth's surface since 2002. The kinetic temperatures and CO₂ volume mixing ratios (VMRs) in the mesosphere and lower thermosphere have been simultaneously retrieved using SABER limb radiances at 15 and 4.3 μm under nonlocal thermodynamic equilibrium (non-LTE) conditions. This paper presents results of a validation study of the SABER CO₂ VMRs obtained with a two-channel, self-consistent …

Energy-Efficient Computational Chemistry: Comparison Of X86 And Arm Systems, Kristopher Keipert, Gaurav Mitra, Vaibhav Sunriyal, Sarom S. Leang, Masha Sosonkina, Alistair P. Rendell, Mark S. Gordon

Computational Modeling & Simulation Engineering Faculty Publications

The computational efficiency and energy-to-solution of several applications using the GAMESS quantum chemistry suite of codes is evaluated for 32-bit and 64-bit ARM-based computers, and compared to an x86 machine. The x86 system completes all benchmark computations more quickly than either ARM system and is the best choice to minimize time to solution. The ARM64 and ARM32 computational performances are similar to each other for Hartree-Fock and density functional theory energy calculations. However, for memory-intensive second-order perturbation theory energy and gradient computations the lower ARM32 read/write memory bandwidth results in computation times as much as 86% longer than on the …

Source-Specific Molecular Signatures For Light-Absorbing Organic Aerosols, Amanda Susan Willoughby

Chemistry & Biochemistry Theses & Dissertations

Organic aerosols (OA) are universally regarded as an important component of the atmosphere based on quantitative significance as well as the far-reaching impact they have on global climate forcing and human health. Despite the acknowledged importance, OA amounts and impacts remain the largest uncertainties regarding radiative forcing estimates. Incomplete chemical characterization of aerosol organic matter (OM) and a lack of concrete source apportionment is a major source of this uncertainty. The primary focus of this study is to provide much needed molecular details regarding ambient OA from key emission sources, and establish links between molecular and optical properties.

Complete chemical …

Synthesis, Characterisation, Electrochemical, And Spectroscopic Studies Of Cobaloximes: Unique Clues Of Cobalt(I) Species In Various Solvents, Michael John Celestine

Chemistry & Biochemistry Theses & Dissertations

With the dwindling amount of fossil fuels in the world’s reserve is said to run out in the future. The use of alternative fuels such as hydrogen can be produced from renewable sources. One source is the use of first row transition metal complexes that can harness the power of the sun to reduce protons to hydrogen. In this thesis we investigated a well-known hydrogen evolution catalyst in a quest to understand the behavior of different oxidation states that occur during the catalytic cycle.

In an attempt to synthesize a binuclear ruthenium(II) complex, [{Ru(phen)2}2{µmes(1,4-phO-Izphen)3}](PF6)4, as a possible photosensitizer for the …

Computational Investigation Of Pernicious Compounds: Arsenic And High Energy Density Materials And Their Relevant Mechanisms, Lenora Kathleen Harper

Chemistry & Biochemistry Theses & Dissertations

The underlying mechanisms of chemical warfare agents (CWAs) and high energy density materials (HEDMs) are poorly understood, yet important to the development of chemical applications in military science and technology. The reactivity of arsenite and arsenic-based CWA lewisite with biological thiols plays an important role in toxicity of these elements. Toxic effects of arsenite are eliminated when arsenite and selenite are co-administered, due to their antagonistic relationship. The arsenic-based CWA lewisite is detoxified by the dithiol-containing British anti-lewisite (BAL). The reduction of arsenous acid by thiol, the formation of an As-Se species, and the detoxification of lewisite with BAL have …

Artificial Maturation Studies Of Polymethylenic Plant Biopolymers: Investigating The Chemical Alterations From Plant Material To Coal, Blaine Elizabeth Hartman

Chemistry & Biochemistry Theses & Dissertations

The thermal maturation and alternation of vascular plant material into coals and as expelled petroleum-like compounds is the main focus of this dissertation. Utilizing artificial maturation studies, like hydrothermal liquefaction, yields useful information regarding how plant material is preserved in coals and the potential certain plant biopolymers possess to generate liquid fuels is acquired. The studies within this dissertation focus on utilizing the aliphatic biopolymers, cutin, cutan, and suberan, found in the epidermis of certain plants. These biopolymers contain minimal amounts of heteroatoms and are comprised of long polymethylenic chains, which are desirable characteristics in generating bio-oils. Additionally, understanding the …

Study Of Photochemical Formation Of Hydroxyl Radical In Natural Waters, Luni Sun

Chemistry & Biochemistry Theses & Dissertations

This dissertation mainly focuses on the sources of the hydroxyl radical (•OH) from photochemical reactions in natural waters, in particular from reactions involving dissolved organic matter (DOM). Firstly, an accurate method for estimating •OH formation rate during long-term irradiation was developed. It was observed that previous methods for measuring •OH formation rates in the natural waters, which were based upon sequentially determined cumulative concentrations of probe photoproducts, significantly underestimated actual •OH formation rates. It was found that the underestimation was mainly due to the degradation of the probe photoproducts and that only ‘instantaneous’ formation rates were appropriate for accurately estimating …

Simulation Of Energetic Particle Precipitation Effects During The 2003-2004 Arctic Winter, C. E. Randall, V. L. Harvey, L. A. Holt, D. R. Marsh, D. Kinnison, B. Funke, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

Energetic particle precipitation (EPP) during the 2003-2004 Arctic winter led to the production and subsequent transport of reactive odd nitrogen (NO_x=NO+NO₂) from the mesosphere and lower thermosphere (MLT) into the stratosphere. This caused NO_x enhancements in the polar upper stratosphere in April 2004 that were unprecedented in the satellite record. Simulations of the 2003-2004 Arctic winter with the Whole Atmosphere Community Climate Model using Specified Dynamics (SD-WACCM) are compared to satellite measurements to assess our understanding of the observed NO_x enhancements. The comparisons show that SD-WACCM clearly displays the descent of NO_x produced …

Growth In Stratospheric Chlorine From Short-Lived Chemicals Not Controlled By The Montreal Protocol, R. Hossaoni, M. P. Chipperfield, A. Saiz-Lopez, J. J. Harrison, R. Von Glasow, R. Sommariva, E. Atlas, M. Navarro, S. A. Montzka, W. Feng, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

We have developed a chemical mechanism describing the tropospheric degradation of chlorine containing very short-lived substances (VSLS). The scheme was included in a global atmospheric model and used to quantify the stratospheric injection of chlorine from anthropogenic VSLS (Cl_y^VSLS) between 2005 and 2013. By constraining the model with surface measurements of chloroform (CHCl₃), dichloromethane (CH₂Cl₂), tetrachloroethene (C₂Cl₄), trichloroethene (C₂HCl₃), and 1,2-dichloroethane (CH₂ClCH₂Cl), we infer a 2013 Cl_y^VSLS mixing ratio of 123 parts per trillion (ppt). Stratospheric injection …

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 93rd Annual Meeting of the Virginia Academy of Science, May 21-23, 2015, James Madison University, Richmond, Virginia

Blue Carbon In Freshwater / Brackish Marshes On The Barrier Islands Of Virginia Aboveground Net Primary Productivity And Carbon Pools, Emily Caitlin Adams

Biological Sciences Theses & Dissertations

"Blue carbon" is a relatively new concept describing carbon distributed tidally and sequestered via net production within coastal ecosystems, including seagrass beds, mangrove forests, and salt-water marshes. These systems sequester carbon at least 10 times faster than terrestrial systems. Fresh to brackish wetlands that receive irregular tidal influence due to overwash and storm events have not been typically studied as blue carbon systems. My objective was to quantify carbon pools within four interdunal fresh to brackish marshes on Hog Island, Virginia to determine their blue carbon potential. Marshes 1 and 2 were farthest from the ocean, below and above a …

In Vivo Near Ir Fluorescent Imaging Of Hollow Polymeric Nanocapsules, Venkata Suresh Patthipati

Biological Sciences Theses & Dissertations

Medical Imaging has been an integral component in medical diagnosis and therapeutics. It is frequently used in conjunction with other treatment modalities and has been used for developing applications that range from cancer management to clinical practice. Nanotechnology and its applications are foreseen to have a profound impact on life sciences. Nanomaterial based imaging has a significant potential in addressing medical challenges such as tumor localization, targeted delivery of drugs and real time diagnosis and management of circulation pathology. In particular, polymer based nanoparticles are increasingly being developed as they can be customized according to the diagnostic and/or therapeutic requirements. …

Exploring The Effect Of Climate Change On Biological Systems, Nardos Sori

Chemistry & Biochemistry Theses & Dissertations

The present and potential future effect of global warming on the ecosystem has brought climate change to the forefront of scientific inquiry and discussion. For our investigation, we selected two organisms, one from cyanobacteria and one from a cereal plant to determine how climate change may impact these biological systems. The study involved understanding the physiological and adaptive responses at both the genetic and protein function levels to counteract environmental stresses. An increase in atmospheric carbon dioxide is a key factor in global climate change and can lead to alterations in ocean chemistry. Cyanobacteria are important, ancient and ubiquitous organisms …

Investigation Of The Potential For Algaenan To Produce Hydrocarbon Based Fuels From Algae By Hydrous Pyrolysis, Wassim Adel Obeid

Chemistry & Biochemistry Theses & Dissertations

The use of algae as a feedstock for hydrous pyrolysis has a high potential for producing biofuels. The non-food nature of algae in addition to the various advantages associated with the hydrous pyrolysis process makes this combination for the production of biofuels of high interest. However, current results from algae processing have alluded to some challenges: byproducts arising from the thermal transformation of carbohydrates and proteins, which become incorporated in the oil fraction, result in high oxygen and nitrogen contents of the oil. Accordingly, this produces an oil of low quality for refineries. This dissertation investigates use of a pretreatment …

Blue Carbon In Coastal Freshwater/Brackish Marshes On The Barrier Islands Of Virginia: Belowground Carbon Dynamics, Nathan M. Sedghi

Biological Sciences Theses & Dissertations

Some coastal ecosystems sequester substantially more carbon (blue carbon) than land locked systems due to high net primary production and deposition associated with oceanic influences. Most blue carbon research has focused on mangroves, seagrass beds, and salt marshes. Studies on blue carbon potential of coastal freshwater marshes are less common. Barrier islands frequently flood, with seawater reaching interior ecosystems. I examined brackish/freshwater marshes on Virginia barrier islands for possible roles as blue carbon systems. I studied four interior marshes on Hog Island, which varied in proximity to a direct overwash path and protection by a trail berm that divides northern …

Simultaneous Analysis Of The Ballik-Ramsay And Phillips Systems Of C2 And Observation Of Forbidden Transitions Between Singlet And Triplet States, Wang Chen, Kentarou Kawaguchi, Peter F. Bernath, Jian Tang

Chemistry & Biochemistry Faculty Publications

6229 lines of the Ballik-Ramsay system (b₃Σ_g^--a₃Π_u) and the Phillips system (A¹Π_u-X¹Σ_g⁺) of C₂ up to v = 8 and J = 76, which were taken from the literature or assigned in the present work, were analyzed simultaneously by least-squares fitting with 82 Dunham-like molecular parameters and spin-orbit interaction constants between the b₃Σ_g^- and X¹Σ_g⁺ states with a standard deviation of 0.0037 cm^-1 for the whole data set. As a …

Experimental Demonstration Of Localized Excess Protons At A Water-Membrane Interface, Haitham A. Saeed, James W. Lee

Chemistry & Biochemistry Faculty Publications

The widespread Mitchellian proton motive force equation has recently been revised with the proton-electrostatics localization hypothesis, which, for the first time, successfully elucidates the 30-year longstanding energetic conundrum of ATP synthesis in alkalophilic bacteria. 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 by utilizing an "open-circuit" water-electrolysis system and their distributions were tested using a proton-sensing aluminum membrane. The proton-sensing film placed at the membrane-water interface displayed dramatic localized proton activity while that placed into the bulk water phase …

Note: Improved Line Strengths Of Rovibrational And Rotational Transitions Within The X3Σ⁻ Ground State Of Nh, James S.A. Brooke, Peter F. Bernath, Colin M. Western

Chemistry & Biochemistry Faculty Publications

Recently, a line list including positions and transition strengths was published for the NH X³Σ⁻ rovibrational and rotational transitions. The calculation of the transition strengths requires a conversion of transition matrix elements from Hund’s case (b) to (a). The method of this conversion has recently been improved during other work on the OH X²Π rovibrational transitions, by removing an approximation that was present previously. The adjusted method has been applied to the NH line list, resulting in more accurate transition strengths. An updated line list is presented that contains all possible transitions with v′ and …

Proton-Electrostatic Localization: Explaining The Bioenergetic Conundrum In Alkalophilic Bacteria, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The decades-longstanding energetic conundrum of alkalophilic bacteria as to how they are able to synthesize ATP has now, for the first time, been clearly solved using the proton-electrostatics localization hypothesis. This is a major breakthrough advance in understanding proton-coupling bioenergetics over the Nobel-prize work of Peter Mitchell’s chemiosmotic theory. The widespread textbook Mitchellian proton motive force (pmf) equation has now been significantly revised. Use of the newly derived equation results in an overall pmf value (215~233 mV) that is more than 4 times larger than that (44.3 mV) calculated from the Mitchellian equation for the alkalophilic bacteria growing at pH …

Peptide Inhibitor Of Complement C1 (Pic1) Rapidly Inhibits Complement Activation After Intravascular Injection In Rats, Julia A. Sharp, Pamela S. Hair, Haree K. Pallera, Parvathi S. Kumar, Clifford T. Mauriello, Julius O. Nyalwidhe, Cody A. Phelps, Dalnam Park, Nicole M. Thielens, Stephen M. Pascal, Waldon Chen, Diane M. Duffy, Frank A. Lattanzio, Kenji M. Cunnion, Neel K. Krishna

Chemistry & Biochemistry Faculty Publications

The complement system has been increasingly recognized to play a pivotal role in a variety of inflammatory and autoimmune diseases. Consequently, therapeutic modulators of the classical, lectin and alternative pathways of the complement system are currently in preclinical and clinical development. Our laboratory has identified a peptide that specifically inhibits the classical and lectin pathways of complement and is referred to as Peptide Inhibitor of Complement C1 (PIC1). In this study, we determined that the lead PIC1 variant demonstrates a salt-dependent binding to C1q, the initiator molecule of the classical pathway. Additionally, this peptide bound to the lectin pathway initiator …

Characterization And Photodegradation Of Dissolved Organic Matter (Dom) From A Tropical Lake And Its Dominant Primary Producer, The Cyanobacteria Microcystis Aeruginosa, Thais B. Bittar, Aron Stubbins, Armando A. H. Vieira, Kenneth Mopper

Chemistry & Biochemistry Faculty Publications

This study investigates optical and high-resolution molecular signatures and photochemical degradation of DOM from the Barra Bonita Reservoir (BB-DOM), a tropical eutrophic lake, as well as from its dominant phytoplankton species, the cyanobacteria Microcystis aeruginosa (Microcystis-DOM). Consistent with a predominantly autotrophic source, BB-DOM and Microcystis-DOM exhibited high protein-like fluorescence and contained a large number of aliphatics. Microcystis-DOM was enriched in peptide-like formulae, while BB-DOM had higher chromophoric and fluorescent DOM(CDOM and FDOM) and was enriched in moderately unsaturated formulae, indicating additions of terrigenous DOM and/or in situ processing of autochthonous material in the lake. Consistent with …

Interesting Properties Of P-, D-, And F-Block Elements When Coordinated With Dipicolinic Acid And Its Derivatives As Ligands: Their Use As Inorganic Pharmaceuticals, Michael J. Celestine, Jimmie L. Bullock, Shivani Boodram, Varma H. Rambaran, Alvin A. Holder

Chemistry & Biochemistry Faculty Publications

This is a review of the literature concerning the interesting properties of p-, d-, and f-block elements when coordinated with 2,6-pyridinedicarboxylic acid (dipicolinic acid, H₂dipic) and its derivatives as ligands, with a focus on their use as inorganic pharmaceuticals. Some of the complexes reported were used as insulin-like, bioimaging contrasting agents, antimicrobial agents, and anticancer agents.

Characterization Of Terrestrial Dissolved Organic Matter Fractionated By Ph And Polarity And Their Biological Effects On Plant Growth, Rachel L. Sleighter, Paolo Caricasole, Kristen M. Richards, Terry Hanson, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Background: Humic substances are ubiquitous in the environment, complex mixtures, and known to be beneficial to plant growth. To better understand and identify components responsible for plant growth stimulation, a terrestrial aquatic DOM sample was fractionated according to pH and polarity, obtaining acid-soluble and acid-insoluble portions, as well as acid-soluble hydrophobic and hydrophilic fractions using C18. The various fractions were characterized then evaluated for their biological effects on plant growth using bioassays with corn at two carbon rates.

Results: Approximately 43% and 57% of the carbon, and 31% and 69% of the iron, was found in the acid-insoluble and acid-soluble …

Effect Of Methoxy Substituents On The Activation Barriers Of The Glutathione Peroxidase-Like Mechanism Of An Aromatic Cyclic Seleninate, Craig A. Bayse, Ashley L. Shoaf

Chemistry & Biochemistry Faculty Publications

Density functional theory (DFT) models including explicit water molecules have been used to model the redox scavenging mechanism of aromatic cyclic seleninates. Experimental studies have shown that methoxy substitutions affect the rate of scavenging of reactive oxygen species differently depending upon the position. Activities are enhanced in the para position, unaffected in the meta, and decreased in the ortho. DFT calculations show that the activation barrier for the oxidation of the selenenyl sulfide, a proposed key intermediate, is higher for the ortho methoxy derivative than for other positions, consistent with the low experimental conversion rate.

Interpretation Of Complexometric Titration Data: An Intercomparison Of Methods For Estimating Models Of Trace Metal Complexation By Natural Organic Ligands, I. Pižeta, S. G. Sander, R. J. M. Hudson, D. Omanović, O. Baars, K. A. Barbeau, K. N. Buck, R. M. Bundy, G. Carrasco, P. L. Croot

OES Faculty Publications

With the common goal of more accurately and consistently quantifying ambient concentrations of free metal ions and natural organic ligands in aquatic ecosystems, researchers from 15 laboratories that routinely analyze trace metal speciation participated in an intercomparison of statistical methods used to model their most common type of experimental dataset, the complexometric titration. All were asked to apply statistical techniques that they were familiar with to model synthetic titration data that are typical of those obtained by applying state-of-the-art electrochemical methods – anodic stripping voltammetry (ASV) and competitive ligand equilibration-adsorptive cathodic stripping voltammetry (CLE-ACSV) – to the analysis of natural …

Use Of Esi-Fticr-Ms To Characterize Dissolved Organic Matter In Headwater Streams Draining Forest-Dominated And Pasture-Dominated Watersheds, Yuehan Lu, Xiaping Li, Rajaa Mesfioui, James E. Bauer, R. M. Chambers, Elizabeth A. Canuel, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) has proven to be a powerful technique revealing complexity and diversity of natural DOM molecules, but its application to DOM analysis in grazing-impacted agricultural systems remains scarce. In the present study, we presented a case study of using ESI-FTICR-MS in analyzing DOM from four headwater streams draining forest-or pasture-dominated watersheds in Virginia, USA. In all samples, most formulas were CHO compounds (71.8-87.9%), with other molecular series (CHOS, CHON, CHONS, and CHOP (N, S)) accounting for only minor fractions. All samples were dominated by molecules falling in the lignin-like region (H/C …

Retrieval And Validation Of Carbon Dioxide, Methane, And Water Vapor For The Canary Islands Ir-Laser Occultation Experiment, V. Proschek, G. Kirchengast, S. Schweitzer, J.S. A. Brooke, P. F. Bernath, C. B. Thomas, J. G. Wang, K. A. Tereszchuk, G. González Abad, R. J. Hargreaves, C. A. Beale, J. J. Harrison, P. A. Martin, V. L. Kasyutich, C. Gerbig, O. Kolle, A. Loescher

Chemistry & Biochemistry Faculty Publications

The first ground-based experiment to prove the concept of a novel space-based observation technique for microwave and infrared-laser occultation between low-Earthorbit satellites was performed in the Canary Islands between La Palma and Tenerife. For two nights from 21 to 22 July 2011 the experiment delivered the infrared-laser differential transmission principle for the measurement of greenhouse gases (GHGs) in the free atmosphere. Such global and long-term stable measurements of GHGs, accompanied also by measurements of thermodynamic parameters and line-of-sight wind in a self-calibrating way, have become very important for climate change monitoring. The experiment delivered promising initial data for demonstrating the …

Relative Drifts And Biases Between Six Ozone Limb Satellite Measurements From The Last Decade, N. Rahpoe, M. Weber, A. V. Rozanov, K. Weigel, H. Bovensmann, J. P. Burrows, A. Laeng, G. Stiller, T. Von Clarmann, E. Kyrölä, V. F. Sofieva, J. Tamminen, K. Walker, D. Degenstein, A. E. Bourassa, R. Hargreaves, P. Bernath, J. Urban, D. P. Murtagh

Chemistry & Biochemistry Faculty Publications

As part of European Space Agency's (ESA) climate change initiative, high vertical resolution ozone profiles from three instruments all aboard ESA's Envisat (GOMOS, MIPAS, SCIAMACHY) and ESA's third party missions (OSIRIS, SMR, ACE-FTS) are to be combined in order to create an essential climate variable data record for the last decade. A prerequisite before combining data is the examination of differences and drifts between the data sets. In this paper, we present a detailed analysis of ozone profile differences based on pairwise collocated measurements, including the evolution of the differences with time. Such a diagnosis is helpful to identify strengths …

Mass Loss And Chemical Structures Of Wheat And Maize Straws In Response To Ultravoilet-B Radiation And Soil Contact, Guixiang Zhou, Jiabao Zhang, Jingdong Mao, Congzhi Zhang, Lin Chen, Xiuli Xin, Bingzi Zhao

Chemistry & Biochemistry Faculty Publications

The role of photodegradation, an abiotic process, has been largely overlooked during straw decomposition in mesic ecosystems. We investigated the mass loss and chemical structures of straw decomposition in response to elevated UV-B radiation with or without soil contact over a 12-month litterbag experiment. Wheat and maize straw samples with and without soil contact were exposed to three radiation levels: a no-sunlight control, ambient solar UV-B, and artificially elevated UV-B radiation. A block control with soil contact was not included. Compared with the no-sunlight control, UV-B radiation increased the mass loss by 14-19% and the ambient radiation by 9-16% for …

Global Ozone Chemistry And Related Trace Gas Data Records For The Stratosphere (Gozcards): Methodology And Sample Results With A Focus On Hcl, H20, And 03, L. Froidevaux, J. Anderson, H. J. Wang, R. A. Fuller, M. J. Schwartz, M. L. Santee, N. J. Livesey, H. C. Pumphrey, P. F. Bernath, J. M. Russell Iii, M. P. Mccormick

Chemistry & Biochemistry Faculty Publications

We describe the publicly available data from the Global OZone Chemistry And Related trace gas Data records for the Stratosphere (GOZCARDS) project and provide some results, with a focus on hydrogen chloride (HCl), water vapor (H₂O), and ozone (O₃). This data set is a global long-term stratospheric Earth system data record, consisting of monthly zonal mean time series starting as early as 1979. The data records are based on high-quality measurements from several NASA satellite instruments and the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) on SCISAT. We examine consistency aspects between the various data sets. …