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Articles 1 - 30 of 112
Full-Text Articles in Chemistry
Analyzing The Free Energy Of Ions Sampling A Voltage Gated Sodium Ion Channel, Isabel Varghese
Analyzing The Free Energy Of Ions Sampling A Voltage Gated Sodium Ion Channel, Isabel Varghese
Honors Theses
Voltage gated sodium ion channels are implicated in cardiac diseases, seizures, etc., and they play a role in maintaining ionic homeostasis in cells. Computational studies use prokaryotic model because they are simpler but function similarly to human voltage gated sodium ion channels. This study uses molecular dynamics (MD) to study three specific questions regarding voltage gated sodium ion channels of Magnetococcus marinus. The first question in this study is how the free energy of sodium diffusion compares to that of calcium ion diffusion. We were not able to find any physically significant information due to poor sampling and a lack …
Artificial Reefs: A History, A Science, A Technology, Mairead D. Farrell
Artificial Reefs: A History, A Science, A Technology, Mairead D. Farrell
Honors Theses
Over the past 60 years, artificial reefs have expanded beyond the definition of a technology, and in turn have developed into a unique branch of marine science. To better emphasize this growth and separation, a brief history of artificial reef development and usage in chapter two shows some of the key shifts over time in this technology’s purpose and the materials used to achieve that goal. Likewise, to indicate the scientific development of artificial reefs as a branch of marine science, their usage for discovery and research is recorded in chapter three, along with the exponential increase in published scientific …
The Quantitative Assessment Of Pond Scum: An Examination Of The Biogeochemistry Of Phosphorus Cycling In The Belgrade Lakes, Abbey M. Sykes
The Quantitative Assessment Of Pond Scum: An Examination Of The Biogeochemistry Of Phosphorus Cycling In The Belgrade Lakes, Abbey M. Sykes
Honors Theses
The internal recycling phosphorus in freshwater lake bottom sediments represents a significant source of hypolimnetic phosphorus (P) release for many of Maine’s lakes. In summer months, Maine lakes often thermally stratify and the lake hypolimnion develops anoxia, leading to a reduction in redox potential at the sediment-water interface. These reducing conditions facilitate the reductive dissolution of ferric iron, and, since phosphorus is often present in freshwater lake sediments as solid FeOOH-PO4 complexes, results in release of soluble phosphorus into the water column. Our current study presents field and laboratory data from sediment fractionation extractions designed to quantify concentrations of …
Karena Mckinney: Mapping A Clearer Picture Of Air Pollution's Effects, Christina Nunez
Karena Mckinney: Mapping A Clearer Picture Of Air Pollution's Effects, Christina Nunez
Colby Magazine
"If we want to control air quality and address climate change, the solution won't involve fiddling with nature's emissions-it will be about cleaning up man-made ones." -Karena McKinney, associate professor of atmospheric chemistry
Generation And Reactions Of Cyclopropyl Vinylidene Carbenes, Nguyen Nhat Thu Le
Generation And Reactions Of Cyclopropyl Vinylidene Carbenes, Nguyen Nhat Thu Le
Honors Theses
This study aimed to generate cyclopropyl methyl vinylidene carbene and cyclopropyl phenyl vinylidene carbene via photochemical routes. The precursors to these two carbenes were synthesized from phenanthrene by a two-step procedure. However, these precursors could not be fully purified because the second step generated many side products with similar properties as the precursors. A crude sample of each precursor were photolyzed with UV light in the range of 315 to 400 nm. Vinylidene carbenes are known to rapidly rearrange into alkynes, so the formation of these cyclopropyl vinylidene carbenes was monitored through the formation of their rearrangement products, cyclopropyl methyl …
Detecting Cyanobacteria Toxins: The Human Health Impact Of An Environmental Problem, Lillian E. Naimie
Detecting Cyanobacteria Toxins: The Human Health Impact Of An Environmental Problem, Lillian E. Naimie
Honors Theses
Cyanobacteria blooms are a growing concern in the world, as they can form a dense and sometimes toxin scum on water bodies. This paper will outline and discuss the environmental conditions that produce cyanobacteria bloom with a focus on the toxins produced by blooms and specifically the detection of these toxins through two analytical methods. Of the various toxins cyanobacteria are capable of producing, this paper will focus on microcystins and BMAA, a family of hepatotoxins and a specific neurotoxin respectively. The two analytical methods discussed are liquid chromatography coupled mass spectrometry and ELISA kit techniques. The advantages and drawbacks …
Silicon And Tin Substituted Halocyclopropanes: Approaches To New Carbenes And Strained Cyclic Allenes, Noura Srour
Silicon And Tin Substituted Halocyclopropanes: Approaches To New Carbenes And Strained Cyclic Allenes, Noura Srour
Honors Theses
Chloro(trimethylsilyl)carbene and chloro(trimethylstannyl)carbene were generated through photolysis of cyclopropanated phenanthrene precursors which were synthesized in two steps. The photolysis reactions were done in the presence of cis and/or trans-beta-methylstyrene. Though product peaks corresponding to the carbene-alkene adducts were observed in the GCMS, the yields were too low for their isolation and complete characterization. Density functional theory (DFT) calculations were performed on the stereoisomers of the precursor to Chloro(trimethylsilyl)carbene and the carbene itself. Surprisingly, Chloro(trimethylsilyl)carbene’s triplet state was found to be more stable than the singlet at this level of theory.
In a related project, (1-bromo-1a,9b-dihydro-1H-cyclopropa[l]phenanthren-1-yl)trimethylstannane, was …
Presence And Potential Sources Of Pharmaceutical And Personal Care Product Chemicals In Messalonskee Lake, Alyssa T. Kullberg
Presence And Potential Sources Of Pharmaceutical And Personal Care Product Chemicals In Messalonskee Lake, Alyssa T. Kullberg
Honors Theses
Pharmaceuticals and personal care product chemicals (PPCPs) represent a large group of contaminants that are mostly not regulated in surface or drinking water and whose presence and environmental and health impacts are poorly understood. We investigated the presence and potential sources of 18 PPCPs in Messalonskee Lake. We collected samples four times over the summer of 2017 at 13 sites around the lake. Samples were tested for PPCPs using liquid chromatography-tandem mass spectrometry. We detected five out of the 18 PPCPs we tested for at the ng/L level: caffeine, 1,7-dimethylxanthine, acetaminophen, sulfachloropyridazine, and amphetamine. PPCPs showed a significant positive correlation …
Stable Bromine Isotope Signature Of Bromoform From Enzymatic And Abiotic Formation Pathways And Its Application In Identifying Sources Of Environmental Bromoform In The Damariscotta River, Chengyang Wang
Honors Theses
Bromoform is a major source of atmospheric bromine. Most bromoform is produced by marine organisms including macroalgae and phytoplankton, using the enzyme bromoperoxidase (BPO). Bromoform can also be a byproduct of industrial processes such as water disinfection. Identifying sources of environmental bromoform is still a challenge. A novel technique of using quadrupole mass spectrometry coupled to a gas chromatography (GCqMS) was developed and optimized for Br isotope analyses. The study shows that GCqMS in single ion monitoring (SIM) mode can measure 81Br with precision of around ±0.7‰ (60pmol bromoform injected). This study aims to investigate stable Br isotopes of bromoform …
Tying The Knot: Applications Of Topology To Chemistry, Tarini S. Hardikar
Tying The Knot: Applications Of Topology To Chemistry, Tarini S. Hardikar
Honors Theses
Chirality (or handedness) is the property that a structure is “different” from its mirror image. Topology can be used to provide a rigorous framework for the notion of chirality. This project examines various types of chirality and discusses tools to detect chirality in graphs and knots. Notable theorems that are discussed in this work include ones that identify chirality using properties of link polynomials (HOMFLY polynomials), rigid vertex graphs, and knot linking numbers. Various other issues of chirality are explored, and some specially unique structures are discussed. This paper is borne out of reading Dr. Erica Flapan’s book, When Topology …
A Novel Method For Determination Of Ammonium Isotope Ratios With Electrospray Ionization Mass Spectrometry, Rebecca J. Chmiel
A Novel Method For Determination Of Ammonium Isotope Ratios With Electrospray Ionization Mass Spectrometry, Rebecca J. Chmiel
Honors Theses
Nitrogen (15N) isotope tracer studies are an invaluable tool for understanding the rate of N transformations in the environment. A mechanistic understanding of N cycling is critical to management of excess N availability in freshwater and marine ecosystems. Conventional methods for measuring 15N:14N of dissolved inorganic nitrogen species are time consuming and require large sample volumes. Here, we present a technique for measuring 15N:14N in ammonium (NH4+) using electrospray ionization mass spectrometry (ESI-MS). NH4+ present in small volumes of sample (3 ml) is complexed with phenol via …
Photochemical Generation Of Carbenes And Ketenes From Phenanthrene-Based Precursors Part I: Dimethylalkylidene Part Ii: Diphenylketene, Tarini S. Hardikar, Tarini Hardikar
Photochemical Generation Of Carbenes And Ketenes From Phenanthrene-Based Precursors Part I: Dimethylalkylidene Part Ii: Diphenylketene, Tarini S. Hardikar, Tarini Hardikar
Honors Theses
Previous studies have shown that the photolysis of phenanthrene-based cyclopropyl precursors can generate carbenes. In this work, a novel phenanthrene precursor was synthesized and photolyzed to generate the dimethylalkylidene carbene, which was subsequently trapped by cyclohexene. The car- bene was not prone to an internal rearrangement as some other carbenes are, and instead favored the intermolecular addition reaction. The precursor also underwent a rearrangement via pericyclic processes. A theoretical analysis of the potential energy surface of the system is presented using coupled cluster and density functional methods. Preliminary analysis for the precursor via time-resolved laser flash photolysis (LFP) was performed. …
Part I: Photochemical Generation Of Cyclohexyne From A Hydrocarbon Precursor Part Ii: A Triptycenyl Flower, Daniel Maurer
Part I: Photochemical Generation Of Cyclohexyne From A Hydrocarbon Precursor Part Ii: A Triptycenyl Flower, Daniel Maurer
Honors Theses
Part I
Photolysis of phenanthrene-based methylenecyclopropane derivatives have previously been shown to generate alkylidenecarbenes, which readily rearrange to form alkynes. In this work, we show that photolysis of an analogous cyclic alkylidenecarbene precursor at ambi- ent temperature forms cyclohexyne via the putative cyclopentylidenecarbene, and can be trapped by dienes via a Diels-Alder reaction. Cyclohexyne and other strained cycloalkynes are of much interest to theoreticians and experimentalists alike. Results of coupled-cluster and DFT calculations on the potential energy surface of cyclopentylidenecarbene and the corresponding strained cyclohexyne are also presented. The photochemical generation of cy- clopentylidenecarbene, and thus cyclohexyne, from a hydrocarbon …
Phenanthrene...With A Twist!, Nicholas S. Kim
Phenanthrene...With A Twist!, Nicholas S. Kim
Honors Theses
The twisted and sterically hindered 4,5-dibromophenanthrene, was synthesized from 2,6-dibromoiodobenzene in a four-step pathway, or from 1,3-dibromobenzene in a three-step pathway. Then, 4,5-dibromophenanthrene was subjected to a Kumada coupling, leading to the synthesis of an even more twisted 4-bromo-5-tert-butylphenanthrene. Computational studies using density functional theory were performed to compare experimental and theoretical characteristics of these compounds, such as dihedral angles, optimized structures, and transition state energy barriers.
The purpose of these experiments is to fill gaps in chemical databases, synthesize more pronounced twists in normally planar phenanthrene molecules, and to ultimately synthesize 4,5-bis-tert-butylphenanthrene, which may have …
Experimental And Computational Study Of Methylphenylvinylidene And Its Rearrangements, Xi Yang
Experimental And Computational Study Of Methylphenylvinylidene And Its Rearrangements, Xi Yang
Honors Theses
In this study, the synthesis and properties were explored of the compound methylphenylvinylidene (MPV), a vinylidene carbene with methyl and phenyl groups as substituents. A phenanthrene-based precursor, 1-(1-phenylethylidene)-1a,9b-dihydro-1H-cyclopropa[l]phenanthrene, was synthesized in three steps and was subjected to photolysis in C6D6 at ambient temperature. During photolysis, the MPV carbene rearranged into 1-phenylpropyne via a 1,2-phenyl shift, instead of 1,2-methyl shift, confirmed by photolysis of 13C-labeled precursor. This experimental result is consistent with computational results using the CCSD(T)/cc-pVTZ//B3LYP/6-31+G* method. The calculations suggest that the 1,2-phenyl shift in singlet carbene requires 3.8 kcal/mol to overcome …
Experimental And Computational Investigation Of Selected Β-Hydroxy Carbenes, Joseph D. Deangelo
Experimental And Computational Investigation Of Selected Β-Hydroxy Carbenes, Joseph D. Deangelo
Honors Theses
The photolytic precursor to the sterically hindered β-bis(tert)-butanol carbene, 3-(1a,9b-dihydro-1H-cyclopropa[l]phenanthren-1-yl)-2,2,4,4-tetramethylpentan-3-ol was prepared in three steps from phenanthrene. Photolysis of the precursor generates the desired β-hydroxy carbene, an intermediate, which subsequently rearranges into two different observed products from an intramolecular C-H insertion and alkyl shift. Four intramolecular mechanisms were ultimately considered to account for the possible rearrangement pathways. Computational studies using density functional theory are also presented.
In addition, the photolytic precursors to two cyclic β-hydroxy carbenes, 1-(1a,9b-dihydro-1H-cyclopropa[l]phenanthren-1-yl)cyclopropan-1-ol and 1-(1a,9b-dihydro-1H-cyclopropa[l]phenanthren-1-yl)cyclobutan-1-ol, were also prepared through different synthetic routes from phenanthrene. …
Generation Of 2-Adamantylidenecarbene From A Phenanthrene-Based Precursor, Christine E. Wamsley
Generation Of 2-Adamantylidenecarbene From A Phenanthrene-Based Precursor, Christine E. Wamsley
Honors Theses
This thesis examines the generation of 2-adamantylidenecarbene from a phenanthrene-based precursor. A three-step synthetic procedure was used to generate the 2-adamantylidenecarbene precursor, which subsequently underwent photolysis to produce 2-adamantylidenecarbene. This product was trapped with cyclohexene. No evidence of a ring expansion to 4-homoadamantyne was observed. It was also noted that the target precursor underwent rearrangement during photolysis, leading to the formation of an isomer containing a seven-membered ring. This isomer did not photolyze. Additionally, computational studies were performed using Gaussian 09. Geometries were initially optimized and then, the single point energies of the singlet and triplet carbene states were calculated. …
Molecular Modeling Of Biological Carbon Fixation, William Lin, Andrew Kim, Scott Hansen
Molecular Modeling Of Biological Carbon Fixation, William Lin, Andrew Kim, Scott Hansen
CLAS: Colby Liberal Arts Symposium
Biological carbon fixation is primarily catalyzed by one enzyme: ribulose-1,5-bisphosphate carboxylase oxygenase. We use molecular modeling to explore and elucidate the origin of slow kinetics and poor specificity in this enzyme. We present primary results of correlated motion between the enzyme and the active site.
Influence Of The Sea Surface Microlayer On Ozone Deposition Velocity, Kathryn Moore
Influence Of The Sea Surface Microlayer On Ozone Deposition Velocity, Kathryn Moore
Honors Theses
The biogeochemical cycles of both iodine and ozone are strongly linked to human health and global climate and are tightly coupled through chemical processes occurring in the surface ocean and troposphere. The concentration and distribution of these compounds have the potential to drive the oxidizing capacity and suite of chemical reactions occurring in the marine boundary layer. However, modeling coupled ocean-atmosphere systems involving them is challenging because of a limited understanding of the magnitude and dominant mechanisms controlling the fluxes of both species, in addition to temporally and spatially heterogeneous distributions of ozone and iodine in the sea surface and …
Investigating The Interaction Of Zinc-Finger Peptides And Nicked Dna Using Phage Display, Rachel Maria Guerra
Investigating The Interaction Of Zinc-Finger Peptides And Nicked Dna Using Phage Display, Rachel Maria Guerra
Honors Theses
Recognition of structural features of DNA such as gaps, nicks and abasic sites is critical for many DNA-binding proteins, such as those involved in DNA damage repair. This study explores a novel strategy to model these protein-DNA interactions using phage display. Phage display has been commonly used to identity zinc fingers that bind to DNA sequences, but selection of peptides that binding to specific DNA structures has not been reported in the literature. A phage library of 109 variants was created based on one of three zinc finger domains of the DNA repair protein poly (ADP-ribose) polymerase I. The library, …
Analysis Of The Electron Withdrawing Capability Of Acetylene Groups For Promoting Nucleophilic Aromatic Substitution, Eric D. Braunstein
Analysis Of The Electron Withdrawing Capability Of Acetylene Groups For Promoting Nucleophilic Aromatic Substitution, Eric D. Braunstein
Honors Theses
It is well known that electron withdrawing groups, such as nitro or carbonyl groups, activate benzene rings for nucleophilic aromatic substitution. However, little research has been done to investigate the electron withdrawing capability of acetylene groups for substitution of aromatic halides. Experimental and computational investigations on the reactivity of halogenated phenylacetylenes with oxygen and other nucleophiles will be described.
Changes In Apoptotic Gene Expression Induced By Dna Cross-Linkers, Jordanne B. Dunn
Changes In Apoptotic Gene Expression Induced By Dna Cross-Linkers, Jordanne B. Dunn
Honors Theses
The Millard Research Laboratory is interested in the cytotoxic mechanisms of the bifunctional alkylators diepoxybutane (DEB), epichlorohydrin (ECH), and (1-chloroethenyl) oxirane (COX). Studies performed in the laboratory examine the dual nature of these DNA cross-linking compounds that can act as carcinogens or anti-cancer agents. The mechanisms through which these compounds induce cell death are explored in this study. Cells either undergo cell death due to necrosis or apoptosis. HL-60 cells were treated with varying concentrations of DEB, ECH, or COX. A caspase 3/7 assay was used to test for induction of apoptosis in the treated cells at varying incubation times. …
The Effects Of Exogenous Insulin And Exercise On Glucose And Lactate Metabolism In The Brown Anole, Anolis Sagrei, Kristen Marie Hitchcox
The Effects Of Exogenous Insulin And Exercise On Glucose And Lactate Metabolism In The Brown Anole, Anolis Sagrei, Kristen Marie Hitchcox
Honors Theses
Blood glucose homeostasis is tightly regulated in mammals. Insulin and exercise both stimulate glucose uptake into muscle cells via the GLUT4 transporter protein by independent pathways. Insulin triggers a tyrosine kinase pathway, but the mechanism stimulated by exercise is unknown. Discovering the mechanism may provide new therapeutic techniques for people with diabetes mellitus. While mammals have been studied extensively, research on a different model may elucidate aspects of this lesser known pathway. Reptiles rapidly deplete glycogen stores during bursts of activity and produce lactate as a byproduct of anaerobic metabolism. Lactate undergoes gluconeogenesis within muscle tissue, rather than liver tissue, …
Mechanisms Of Cytotoxicity Of Diepoxybutane, Epichlorohydrin And 1-(Chloroethenyl)Oxirane, Rebecca D. Kamins
Mechanisms Of Cytotoxicity Of Diepoxybutane, Epichlorohydrin And 1-(Chloroethenyl)Oxirane, Rebecca D. Kamins
Honors Theses
Diepoxybutane (DEB), epichlorohydrin (ECH), and 1-(chloroethenyl)oxirane (COX) are small molecules that can form DNA interstrand cross-links. All three of these compounds are, or are metabolites of, industrial chemicals linked to cancer. Additionally, DEB is a metabolite of treosulfan, an anti-cancer drug. We are trying to determine why some of these compounds cause cancer and some can also cure cancer. To do so, we are attempting to link cytotoxicity, cross-linking efficiency, and apoptotic potential of the three compounds to see if any correlations exist. The purpose of this project was to quantify apoptotic potential of DEB, ECH and COX. This was …
Effects Of Context Of Natural And Artifactual Objects On Categorization, Linsey Walker
Effects Of Context Of Natural And Artifactual Objects On Categorization, Linsey Walker
Honors Theses
Categorization of animals and vehicles in different contexts was investigated in three experiments using event related potentials (ERPs). The presence of a background and congruency of the background in relation to the object were both manipulated in order to determine the effects of context on visual processing. In Experiment 1, adults were presented with images of animals and vehicles in two conditions: situated in a congruent context (e.g. an animal in a field) and in the absence of a context (an animal in a white homogeneous background). In experiment 2, adults were presented with images of animals and vehicles in …
Foundations And Interpretations Of Quantum Mechanics, Cory Johnson
Foundations And Interpretations Of Quantum Mechanics, Cory Johnson
Honors Theses
The first famous thought experiment of Einstein gives rise to his theories of relativity, the bedrock of modern astrophysics and cosmology. His second famous thought experiment begins the investigation into the foundations of quantum mechanics. It leads to a paradox, inspiring various 'no-go' theorems proven by Bell, Kochen, and Specker. Physicists and philosophers worldwide become increasingly dissatisfied with the probabilistic complementarity interpretation (Born-Bohr) and eventually offer their own accounts of the theory. By the end of the 20th century two alternative approaches stand out as the best candidates: Both the hidden variables interpretation (de Broglie-Bohm) and the many worlds interpretation …
Temperature And Magnetic Field Dependence Of The Electronic Excitations In The Nickel Chain Compound Nino, Lucas Laviolet
Temperature And Magnetic Field Dependence Of The Electronic Excitations In The Nickel Chain Compound Nino, Lucas Laviolet
Honors Theses
Temperature and magnetic field dependent absorbance spectra were taken on the Ni2+ chain compound NINO (Ni(C?H??N?)?NO?(ClO?)) in the range from 8,500 to 25,000 cm-?. The identification of an effective C?v symmetry about the nickel ions is supported by assignment of the low temperature absorbance bands. The intensity of many bands is found to be temperature dependent, and in several bands, a shift to higher energy is observed at lower temperatures. A correlation is noted between the field dependence of the spin forbidden electronic transitions and the magnetic properties of NINO. Below a crossover magnetic field, Hc ? 10 T, the …
Reactions Of Atomic Carbon With Acid Chlorides, Daniel B. Herrick
Reactions Of Atomic Carbon With Acid Chlorides, Daniel B. Herrick
Honors Theses
This thesis is the first report of reactions of atomic carbon with acid chlorides. Carbon is known to react with phosgene to afford dichlorocarbene. We report a similar reaction with carbon and acid chlorides, generating alkylchlorocarbenes. We examine both the nature of the carbene products generated through deoxygenation and the general reactivity of carbon with the acid chlorides. We report two ways in which carbon reacts with acid chlorides. First, as expected from prior work with phosgene, carbon deoxygenates the carbonyl group yielding alkylchlorcarbenes, which rearrange as expected. Second, carbon abstracts the chlorine, and generates the acyl radical, which, in …
Using Azahetercyclic Electrophiles To Synthesize Novel Bicyclooxacalixarenes And Oxacalix[2]N-Hexylnaphthalimide[2]Naphthyridines, Doug Rooke
Honors Theses
Various bicyclooxacalixarenes, tricyclooxacalixarenes and oxacalix[2]N-hexylnapthalimide[2]naphthyridines are synthesized via SnAr condensation. This research has involved synthesis optimization. The oxacalix[2]N-hexylnaphthalimide[2]naphthyridines have exhibited host-guest binding in fluorescence experiments. These compounds have been characterized by NMR spectroscopy as well as single crystal X-ray diffraction.
Photochemical Generation And Intramolecular Chemistry Of Β-Alkoxycarbenes, Kimberly Graves
Photochemical Generation And Intramolecular Chemistry Of Β-Alkoxycarbenes, Kimberly Graves
Honors Theses
The photolytic phenanthrene-based precursors for both β-methoxycarbene and β-ethoxycarbene were synthesized with and without a deuterium label attached to the a carbon. The incorporation of this deuterium label allowed distinction between a 1, 2-H shift and a 1, 2-O shift pathway to the respective alkyl vinyl ether, without the influence of a primary kinetic isotope effect. Photolyses of these precursors gave rearrangement products of the expected β-alkoxycarbenes. In the case of β-methoxycarbene, no methyl vinyl ether was observed due to its volatility. However, the appearance of aldehyde peaks in the NMR spectra, from an apparent further rearrangement to acetaldehyde through …