2024-03-29T06:00:07Z
http://surface.syr.edu/do/oai/
oai:surface.syr.edu:che_etd-1001
2010-09-01T16:57:31Z
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publication:che
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publication:coscde
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Chemical gradients and bioactive hydrogels for mechanistic studies of protein binding and cell adhesion
Burton, Erik Alvan
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Yan-Yeung Luk
Dacheng Ren
Chemical gradients
Hydrogels
Protein binding
Cell adhesion
Chemistry
The interactions among cells, biological molecules and surfaces have long been the subject of much study. These ubiquitous interactions are critically important for such processes as growth and development, but can also be problematic, as in biofouling caused by bacterial biofilm growth. A fundamental understanding of these interactions is important in engineering systems to control them or exploit them for a variety of purposes. The bulk of this work consists of a study of the mechanisms and the control of cell adhesion on surfaces, and the development of systems to detect specific biological molecules in water.
The first two chapters herein describe two different methods of producing chemical gradients of alkanethiol self-assembled monolayers on gold films, and using these chemical gradients for the study of cell adhesion. One of these methods depends on gradient nanometer-scale topography in the gold film. The other involves modifying a gold surface with two components, such that the ratio of the components changed in a gradient fashion along the length of the surface. Cells cultured on these gradients had a significant difference in cell growth from one end of the gradient to the other. This work revealed mechanistic differences between mammalian and bacterial cell adhesion on surfaces.
The third and fourth chapters contain details of efforts to produce a system to quickly and reliably detect the presence of specific antigens in water. These systems involve hydrogels modified with antigen-antibody pairs to respond to the target antigen. In one method, the hydrogels have an integrated diffraction grating, such that exposure to the target antigen will be reflected as a change in the diffraction of a beam of light projected through the gel. The other method uses fluorescently tagged antibodies to signal detection.
The fifth chapter involves an investigation into the molecular organization of liquid crystal phases of disodium cromoglycate (DSCG), and presents a new hypothesis for the arrangement of molecules in DSCG solutions. Cholesteric phase was produced in polymer dispersions of DSCG by doping with chiral molecules, and these dispersions were used as templates for porous hydrogels with unique pore structure.
https://surface.syr.edu/che_etd/10
oai:surface.syr.edu:che_etd-1002
2010-09-01T17:07:13Z
publication:etd
publication:che
publication:cas
publication:coscde
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publication:dche
From small molecules to large proteins: Delivery through B family vitamin uptake pathways
Vortherms, Anthony R.
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Robert Doyle
Vitamin uptake
Vitamin B12
Folic acid
Methatrexate
Azidodeoxythymidine
Chemistry
Delivery of therapeutic molecules using the B family vitamin uptake pathways is presented. First a study examining targeting the folate receptor to deliver AZT was successfully conducted in vitro. Conjugation of AZT to folic acid resulted in a drug that showed an increase in cytotoxicity of ∼20-fold compared to free AZT, when tested in the A2780/AD drug resistant ovarian cell line. This compound was taken to pilot in vivo studies. Conjugates of the folic acid analogue methotrexate with nucleoside analogues AZT, IUdR and ddC were subsequently studied. The strategy was to conjugate two drugs that would work synergistically together. The individual conjugates did not show any synergism, but a cocktail of the AZT and IUdR conjugates showed a synergistic relationship with a lower IC 50 over 24 hours compared to cocktails of the free drugs.
In an attempt to create an oral vaccine, conjugates of tetanus toxoid and B12 were explored. It was hypothesized that the B 12 uptake pathway could protect the toxoid in the digestive tract and facilitate crossing of the enterocyte. The pilot B 12 -tetanus toxoid conjugates were synthesized and characterized. Different ratios of B 12 /tetanus toxoid were synthesized. The conjugates were fluorescently tagged and intestinal uptake was modeled using BeWo placental carcinoma cells, followed by confocal microscopy.
https://surface.syr.edu/che_etd/9
oai:surface.syr.edu:che_etd-1010
2010-09-01T17:32:04Z
publication:etd
publication:che
publication:cas
publication:coscde
publication:che_etd
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A study on the formation of solid state nanoscale materials using polyhedral borane compounds
Romero, Jennifer V.
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James T. Spencer
Titanium boride
Thin films
Aerosol pyrolysis
Carborane dicarboxylic acid
Boron-dopped carbon nanotubes
Carborane metal organic frameworks
Metal borides
Chemistry
The formation of boron containing materials using a variety of methods was explored. The pyrolysis of a metal boride precursor solution can be accomplished using a one-source method by combining TiCl 4 , B 10 H 14 and CH 3 CN in one reaction vessel and pyrolyzing it at temperatures above 900 °C. Amorphous dark blue colored films were obtained after the pyrolysis reactions. Well-defined spherical shaped grains or particles were observed by SEM. The amorphous films generated contained titanium, however, the determination of the boron content of the films was inconclusive. This one pot method making metal boride thin films has the advantage of being able to dictate the stoichiometry of the reactants.
Another part of this work represents the first report of both the use of metal boride materials and the use of a titanium-based compound for the formation of nanotubes. This method provides a facile method for generating well-formed boron-containing carbon nanotubes in a "one-pot" process through an efficient aerosol process.
The formation of metal boride corrosion resistant layers was also explored. It was shown that metallic substrates can be effectively boronized using paste mixtures containing boron carbide and borax. The formation of a Fe 4 B 2 iron boride phase was achieved, however, this iron boride phase does not give enough corrosion protection. The formation of a corrosion resistant metal boride coating with strong adhesion was accomplished by boronization of a thermal sprayed nickel layer on the surface of steel.
Surfactants were explored as possible nanoreactors in which metal boride nanoparticles could be formed to use as nanotube growth catalyst via room temperature reaction. Different surfactants were used, but none of them successfully generated very well dispersed metal boride nanoparticles. Nanoparticles with varying shapes and sizes were generated which were highly amorphous.
The carboxylic acid derivative of closo -C 2 B 10 cages was explored as a ligand in the hydrothermal preparation of coordination polymers with zinc salts. It was found that the stability of the cage is apparently insufficient under these conditions and cage degradation was observed. Consequently, a preliminary investigation of the preparation of dipyridyl derivatives of both the closo -C 2 B 10 and the closo -B 12 cages was performed.
https://surface.syr.edu/che_etd/1
oai:surface.syr.edu:che_etd-1007
2010-09-01T17:19:01Z
publication:etd
publication:che
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Studies toward the synthesis of forskolin and phomactin A using the dihydropyrone Diels-Alder reaction
Wang, Bo
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Nancy I. Totah
Eleanor M. Maine
Forskolin
Phomactin A
Dihydropyrone
Diels-Alder reaction
Oxadecalin
Chemistry
1-Oxadecalin containing natural products have interesting biological activities and have generated a wide variety of interest among synthetic organic chemists. Cycloaddition reactions especially [4+2] cycloadditions, are the most common and important reactions to construct the 1-oxadecalin moiety. The dihydropyrone Diels-Alder reaction, initially developed in our laboratory, features expedient access to the oxadecalone unit and tolerance of diverse functionality.
Forskolin is a labdane diterpene isolated from the Indian herb Coleus Forskkolii and is used mainly for increasing the cyclic adenosine monophosphate level in cells. A model study showed that a Lewis acid-mediated dihydropyrone Diels-Alder reaction could provide the tricyclic core of a forskolin model compound. It was found later that the cycloaddition reaction proceeds through an exo transition state. Further investigation focused on introduction of the C7 hydroxy group, the C7,C8 double bond, and removal of an extra carbon at the C9 position. The C7 hydroxy group was successfully incorporated into the core using the Rubottom oxidation. The C7,C8 double bond could not be generated under the reaction conditions explored. The C9 extra carbon could not be removed when the A/B ring is trans fused. In contrast, the C9 extra carbon was successfully excised when the A/B ring is cis fused.
Phomactin A, isolated from marine fungus phoma sp. (SANK 11486), was a second target for synthesis. Again the dihydropyrone Diels-Alder chemistry was used to build the 1-oxadecalone moiety of phomactin A. A newly designed dihydropyrone was synthesized and underwent Diels-Alder reaction to generate the 1-oxadecalone core structure. In this way the reaction sequence was shortened and the yield improved. A simplified side chain was introduced to the core structure and cyclized to give a model compound. This work also demonstrated that the cis-fused 1-oxadecalin core was essential to generate the macrocycle. Progress was also made toward the side chain bearing a trisubstituted olefin.
https://surface.syr.edu/che_etd/4
oai:surface.syr.edu:che_etd-1008
2010-09-01T17:21:12Z
publication:etd
publication:che
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Synthetic studies on maoecrystal V and studies on the rhodium catalyzed 1,2-addition of alkynes to activated ketones and aldehydes
Carberry, Patrick
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
John D. Chisholm
Maoecrystal
Rhodium
Alkynes
Ketones
Aldehydes
Chemistry
The first section of this document discusses attempts at synthesizing a model system of the natural product maoecrystal V. Maoecrystal V was isolated from the leaves of a Chinese medicinal herb, Isodon eriocalyx, and displays selective growth inhibitory activity toward HeLa cells. The first generation synthetic plan involved the synthesis of an advanced intermediate through an intramolecular hetero Diels-Alder (IHDA) reaction between an aldehyde dienophile and a highly substituted cyclopentadiene. Several conditions were explored to facilitate the [4+2] cycloaddition, but none resulted in product formation.
The problem with this approach was unclear. The inability to induce a [4+2] cycloaddition may have been due to the dithiane present in the molecule, the strain caused by the bicyclic core, or the poor reactivity of the cyclopentadiene. Two model systems incorporating the IHDA reactions were studied to address these questions. In the first model system a pyran ring system could be formed under thermal and Lewis acid conditions; the dithiane was ruled out as the problematic issue. A second, more complex, model system was then synthesized to study the reactivity of the cyclopentadiene functionality in the IHDA reaction. All attempts to induce the IHDA reaction were unsuccessful and this appeared to be an insurmountable problem; a new synthetic strategy was required.
A second generation synthetic approach was initiated which will employ an intramolecular Aldol reaction as the key step. An advanced tricyclic intermediate and fully substituted dithiane have been successfully synthesized en route to complete the synthesis of the desired target molecule. This synthetic sequence would then be incorporated towards the total synthesis of maoecrystal V.
The second section of the dissertation discusses the activation of an alkyne to induce its nucleophilic addition to activated ketones and aldehydes with the use of Rh(acac)(CO) 2 in the presence of a phosphine ligand. Attempts were made to induce enantioselectivity with the use of chiral phosphine ligands. α-Chiral substituents were also explored to probe diastereoselectivity. As a prelude to the synthesis of chiral rhodium complexes, several rhodium complexes with substituted acac ligands were synthesized and tested. The reactions were found to be first order with respect to the alkyne, with bulky electron donating groups on the acac increasing the rate of reaction.
https://surface.syr.edu/che_etd/3
oai:surface.syr.edu:che_etd-1011
2010-09-14T17:11:48Z
publication:etd
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Development of time-gated protein detection assays with luminescent nucleotide sensors
Homsher, Michelle F.
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Bruce S. Hudson
Luminescent
Nucleotide sensors
Protein binding
Terbium
Aptassensors
Biochemistry
Chemistry
Physical Sciences and Mathematics
Time-gated detection allows for the exclusion of autofluorescent background signals, improving detection sensitivity. In order to develop a time-gated protein switch the luminescent terbium ion was used with the terbium chelation complex (cs124-DTPA). To observe changes in switch structure, the terbium ion was combined with a nitroxide quencher TEMPO. The terbium/nitroxide pair was first investigated in solution then applied to various unimolecular nucleic acid constructs, each increasing in complexity. Nucleic acid binding sequences, or aptamers, were used for switch development because of their ease of design and generation as well as their avoidance of incubation and wash steps to result in a rapid binding assay. The resulting structures are the initial uses of terbium and TEMPO as a sensor pair to achieve time-gated aptasensors. The aptasensors produced here all displayed rapid responses to the binding targets which were observed with time-gated measurements. However, the aptasensors also exhibited lower than expected contrast ratios. It is proposed that the lower than expected contrast ratios are a result of the unexpected coordination of the TEMPO nitroxide with the terbium ion. Methods to improve the contrast ratios are suggested. Despite the low contrast ratios, novel time-gated switches were developed for the intended binding target, the HIV protein NCp7 which could be used to develop a drug screen. These switches performed as well as the less complicated hairpin and thrombin binding aptamer (TBA) constructs, demonstrating the success of the nucleic acid switch concept. In addition, the methodology presented here can easily be utilized to produce new terbium/TEMPO based switches upon discovery of new nucleic acid binding sequences.
https://surface.syr.edu/che_etd/13
oai:surface.syr.edu:che_etd-1013
2010-09-16T17:01:42Z
publication:etd
publication:che
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Investigating the pharmacodynamic and magnetic properties of pyrophosphate-bridged coordination complexes
Ikotun, Oluwatayo (Tayo) F.
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Robert Doyle
Pharmacodynamic
Pyrophosphate
Oxidative stress
Adriamycin
Chemistry
Inorganic Chemistry
Physical Sciences and Mathematics
The multidentate nature of pyrophosphate makes it an attractive ligand for complexation of metal cations. The participation of pyrophosphate in a variety of biological pathways and its metal catalyzed hydrolysis has driven our investigation into its coordination chemistry.
We have successfully synthesized a library of binuclear pyrophosphate bridge coordination complexes. The problem of pyrophosphate hydrolysis to phosphate in the presence of divalent metal ions was overcome by incorporating capping ligands such as 1,10-phenanthroline and 2,2'-bipyridine prior to the addition of the pyrophosphate. The magnetic properties of these complexes was investigated and magneto-structural analysis was conducted.
The biological abundance of pyrophosphate and the success of metal based drugs such as cisplatin, prompted our investigation of the cytotoxic properties of M(II) pyrophosphate dimeric complexes (where M(II) is Co II , Cu II , and Ni II ) in adriamycin resistant human ovarian cancer cells. Thess compounds were found to exhibit toxicity in the nanomolar to picomolar range. We conducted in vitro stability studies and the mechanism of cytoxicity was elucidated by performing DNA mobility and binding assays, enzyme inhibition assays, and in vitro oxidative stress studies.
https://surface.syr.edu/che_etd/21
oai:surface.syr.edu:che_etd-1015
2010-09-16T17:29:19Z
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Molybdophosphonate clusters as building blocks in the oxomolybdate-organodiphosphonate/M(II)-organoamine system: Structural influences of secondary metal, organoamine, and diphosphonate tether length (M=copper, nickel, cobalt)
Armatas, Nathan Gabriel
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon Zubieta
Gustav Engbretson
Molybdophosphonate
Building blocks
Organoamine
Diphosphonate
Hydrothermal
Chemistry
Inorganic Chemistry
Physical Sciences and Mathematics
This research focused on the development of organic-inorganic hybrid materials, with a particular focus on the factors that affected the formation of, and structural variation in the resulting solid materials. Using a bottom-up approach, two major components were formed and studied: the oxomolybdate-diphosphonate anionic building block and the M(II)/organoimine cationic charge compensating unit. Hydrothermal synthesis was used to produce various products in an attempt to better understand which factors influence their formation. Of particular importance were stoichiometry, pH, acidic component, temperature, and time. A typical reaction included four components: molybdenum as the primary metal within the cluster, an organodiphosphonic acid to produce the desired anionic cluster, a secondary metal (Co, Ni, Cu) provided charge compensation, and an organoimine completed the cationic unit and also increased dimensionality. This study observed how these four components could be modified to alter the final product; the major goal being to understand how these alterations influenced structure.
The reactions of MoO 3 , cobalt(II) acetate or cobalt(II) acetylacetonate, tetra-2-pyridylpyrazine (tpyprz), and organodiphosphonic acids H 2 O 3 P(CH 2 ) n PO 3 H 2 ( n = 1-5 and 9) of varying tether lengths yielded compounds of the general type {Co 2 (tpyprz)(H 2 O) m } 4+ /Mo x O y {O 3 P(CH 2 ) n PO 3 } z . The recurring theme of the structural chemistry was the incorporation of {Mo 5 O 15 (O 3 PR) 2 } 4- clusters as molecular building blocks observed in the structures of nine phases found within the study. The structural consequences of variations in reaction conditions were most apparent in the series with propylene diphosphonate, where four unique structures were observed, including two distinct three-dimensional architectures for compounds whose formulations differed only in the number of water molecules of crystallization. The structural chemistry of these compounds were quite distinct from that of the {Ni 2 (tpyprz)(H 2 O) m } 4+ /Mo x O y {O 3 P(CH 2 )nPO 3 } z family, as well as that of the copper-based family. The structural diversity of this general class of materials reflected the coordination preferences of the M(II) sites, the extent of aqua ligation to the M(II) sites, the participation of both phosphate oxygen atoms and molybdate oxo-groups in linking to the M(II) sites, and the variability in the number of attachment sites at the molybdophosphonate clusters. Since the charge densities at the peripheral oxygen atoms of the clusters were quite uniform, the attachment of {M 2 (tpyprz)} 4+ subunits to the molybdophosphonates appeared to be largely determined by steric, coulombic, and packing factors, as shown by extensive density functional theory calculations.
The second study covered they synthesis and physical characterization of eight different copper(II) bipyrimidine compounds. Altering the linking organonitrogen ligand had a profound effect on the resulting structure. Bipyrimidine produced two two-dimensional layers and six three-dimensional networks. Further analysis of these materials is being performed, but early results showed that bipyrimidine tightened up the network structures providing little pore volume, but closer metal-metal interactions provided some interesting magnetic communication between metal sites.
The focus of the previous projects was to develop hybrid materials using the [Mo 5 O 15 (PO 3 ) 2 ] 4- cluster as the building block. Providing the system a organophosphonate produced this result the majority of the time, with a few exceptions due to sterics or anomalous effects. In the final study the pnictide was altered to arsenic; due to its expanded atomic radii it expanded to produce a larger molybdenum unit, the cluster added an additional MoO 3 polyhedra to become {Mo 6 O 18 (O 4 As) 2 } 4- . Although it was only slightly larger, the products showed a significant change in the coordination. It should also be noted that the new cluster was symmetrical so some of the bending that was observed for the pentamolybdate cluster would be avoided.
https://surface.syr.edu/che_etd/19
oai:surface.syr.edu:che_etd-1016
2010-09-16T17:39:20Z
publication:etd
publication:che
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publication:che_etd
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Olefin metathesis for metal incorporation and ligand exchange reactions for the preparation of new ruthenium compounds and materials
Schuehler Sherwood, Danielle E.
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
M.B. Sponsler
Metathesis
Ligand exchange
Ruthenium
Polyacetylene
Polymers
Chemistry
Physical Sciences and Mathematics
Two different strategies have been employed for the synthesis of ruthenium compounds and materials: Olefin Metathesis for Metal Incorporation (OMMI) and ligand exchange. OMMI was used to attach Ru to polyenes large and small, including PA, to give an orgamometallic polymer and compounds of the form L 2 Cl 2 Ru=CH(CH=CH) n CH=RuL 2 Cl 2 ( n = 0, 1).
Metal containing polymers have been prepared by treating polyacetylene (PA) with the olefin metathesis catalyst (H 2 IMes)RuCl 2 (=CHPh)(3-bromopyridine) 2 (G2B) to form "metal-incorporated polyacetylene" (MIPA). Many properties of the MIPAs mimicked those of the untreated polyacetylene, including iodine-doped conductivity. The resulting MIPA materials have been shown to be metathesis active. This process uses a new method for the preparation of the polymer through the polymerization of acetylene with G2B. The application of this method to graphite, rather than polyacetylene, has shown small amounts of incorporation of the ruthenium into the material. The ruthenium incorporated in the graphite no longer remains active towards methathesis.
The synthesis of complexes with n = 0 or 1 has been studied using the combination of two previously known strategies for metathesis reactions, namely OMMI and Relay Ring-Closing Metathesis (RRCM). Relay OMMI has been used in a proof-of-principle experiment to prepare a known conjugated diruthenium bisalkylidene complex, [(Cy 3 P) 2 Cl 2 Ru] 2 (μ-CHCH=CHCH). This method was applied towards the preparation of compounds previously inaccessible by direct OMMI on the CH 2 -terminated polyene. Spectroscopic evidence is suggestive that [(Cy 3 P) 2 Cl 2 Ru](μ-CH=CH) was formed in small quantities in the reaction. The steric strain in the molecule presumably makes it highly reactive.
The synthesis of several other ruthenium compounds using ligand exchange reactions began primarily with (PCy 3 ) 2 RuCl 2 (=CHPh) ( G1 ). One class of compounds used bridging bis(imidazolium) ligands. Benzobis(imidazolium) salts have been synthesized with many different substituents and numerous attempts have been made to attach these ligands to Ru to form metathesis active, diruthenium complexes. In all but one case, this has resulted in the recovery of starting materials. Reactions between tetrakis(tolyl) benzobis(imidazolium) chloride and G1 have resulted in the isolation of a new ruthenium compound. This new compound has been shown to be methathesis active.
Through the addition of measured amounts of carbon monoxide to (H 2 IMes)(PR 3 )RuCl 2 (=CHPh) (R = Me or Bu), saturated 18-electron complexes have been isolated. Excess CO resulted in the insertion of the benzylidene moiety into the N-heterocyclic carbene ligand, H 2 IMes.
Ligand exchange reactions have also been used for a class of compounds being developed that are aurophilic versions of Grubbs first-generation catalyst (G1) through the ligand substitution of G1 with bipyridine and a triazolium ligand. These compounds are intended to be used for single molecule conductivity studies. The progress towards aurophilic compounds is reported.
https://surface.syr.edu/che_etd/18
oai:surface.syr.edu:che_etd-1014
2010-09-16T17:24:01Z
publication:etd
publication:che
publication:cas
publication:coscde
publication:che_etd
publication:dche
2-methylenetetrahydropyrans in the carbonyl-ene reaction: Studies toward the synthesis of spirastrellolide A
Lam, Troy
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Nancy I. Totah
Carbonyl-ene reaction
Spirastrellolide
Methylenetetrahydropyrans
Zinc chloride
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
Catalyzed by ZnCl 2 , 2-methylenetetrahydropyran has been shown to readily undergo carbonyl-ene reactions with a variety of activated and unactivated aldehydes and ketones. In efforts to broaden the scope of the enol ether component of the reaction, substituted 2-methylenetetrahydropyrans were studied. Use of elelctron-rich exocyclic enol ethers provides higher yields in shorter reaction times. This new carbon-carbon bond forming reaction allows rapid access to tetrahydropyranyl ketides.
Isolated from the marine sponge Spirastrella coccinea , spirastrellolide A (SPA) is an example of a biologically active natural product that contains the tetrahydropyranyl ketide motif. Therefore, studies toward the synthesis of this natural product have been made employing carbonyl-ene reactions of 2-methylenetetrahydropyrans. In particular, the synthesis of [4.5]- and [5.5]-spiroketal model systems of SPA has been achieved through intramolecular cyclization of carbonyl-ene adducts. Cross-coupling of a [4.5]-spiroketal model system to the C40-C47 side chain has also been demonstrated. The synthesis of the C40-C47 fragment featured Wittig olefination to generate the Z -double bond.
In addition, progress has been made toward the synthesis of the C26-C47 segment of spirastrellolide A. Approach towards the DEF-spiroketal system exploited the exocyclic enol ether carbonyl-ene reaction in a bidirectional manner.
https://surface.syr.edu/che_etd/20
oai:surface.syr.edu:che_etd-1020
2010-09-16T19:07:30Z
publication:etd
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Terahertz spectroscopy and molecular modeling of molecules connected by a network of non-covalent interactions
Motley, Tanieka L.
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Timothy M. Korter
Terahertz
Molecular modeling
Hydrogen-bonding
Electrostatic interactions
Cluster formation
Chemistry
Physical Chemistry
Physical Sciences and Mathematics
Experimental terahertz (THz) spectroscopy and molecular modeling were used to investigate the network of non-covalent interactions that serve to connect molecules in the solution-phase and solid-state. The intermolecular forces found in the molecules studied included hydrogen-bonding, electrostatic interactions, π-π stacking, and long-range dispersion forces. These types of non-covalent forces define cluster formation in solution and the packing arrangement of a crystalline solid. Molecular modeling was utilized to predict the structure and vibrations of the samples and guide the analysis of the experimental data. For solution-phase experiments, isolated-molecule calculations were carried out using density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2) methods. Solid-state DFT using periodic boundary conditions was used to interpret crystalline solids. These periodic calculations include the relevant molecular environment found in solids which isolated-molecule calculations can not provide. In all cases, several density functionals were tested to determine how well they reproduce the experimental observation of structure and THz motions.
https://surface.syr.edu/che_etd/14
oai:surface.syr.edu:che_etd-1017
2010-09-16T18:50:59Z
publication:etd
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Structural direction of hybrid organic-inorganic materials: Synthesis of vanadium oxyfluoride, copper vanadate, and copper molybdate solid state materials through solvuthermal and solution methods
DeBurgomaster, Paul
2009-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon A. Zubieta
Metal oxides
Vanadium oxyfluoride
Copper vanadate
Molybdates
Chemistry
Inorganic Chemistry
Physical Sciences and Mathematics
Polymer Chemistry
The vast structural complexity of inorganic oxides with structure directing organocations, nitrogen containing ligands and organophosphonate ligands was explored. The hydrothermal reaction conditions utilized herein include the variables of temperature, pH, fill volume and stoichiometry. The systems studied included: (1) the complex materials rendered from reactions of organoamine cations on the structure of vanadium oxides, oxyfluorides and fluorides. As with other systems, the influence of the mineralizer HF was not limited to pH as fluorine incorporation was not uncommon. In specific cases this coincided with reduction of vanadium sites. (2) The copper-organonitrogen ligand/vanadium oxide/aromatic phosphonate system has been studied. The rigid aromatic di- and triphosphonate tethers have provided a series of materials which are structurally distinct from the previously investigated aliphatic series. The inclusion of copper-coordinated nitrogen bi- and tri- dentate ligands also provided structural diversity. Product composition was highly influenced by the HF/V ratio. A similar study was conducted with the ligand 1,4-carboxy-phenylphosphonic acid. (3) The preparation of a series of bimetallic organic-inorganic hybrid materials of the M(II)/V x O y /organonitrogen ligand class was further evidence of the utility of thermodynamically driven hydrothermal synthesis. (4) While decomposition of the spherical Keplerate molybdenum clusters is encountered under hydrothermal conditions, this highly soluble form of molybdate was investigated for the development of hybrid organic-inorganic room temperature solution synthesis.
https://surface.syr.edu/che_etd/17
oai:surface.syr.edu:che_etd-1021
2010-09-17T17:59:32Z
publication:etd
publication:che
publication:cas
publication:coscde
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A FRET based bistable oligonucleotide switch, AlloSwitch, designed for specific recognition of HIV-1 NCp7 and use in High Throughput Screening
DeCiantis, Christopher Loreto
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Molecular beacons
High-throughput screening
HIV
Aptamers
Detector
Oligonucleotide switch
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Biophysics
Chemistry
Life Sciences
Physical Sciences and Mathematics
A unimolecular oligonucletide switch referred to here as an Alloswitch, alternately as an OrthoSwitch, binds selectively to mature HIV-1 nucleocapsid protein, NCp7. This switch is covalently labeled with a fluorescent probe and a quencher molecule to allow Fluorescence Resonance Energy Transfer (FRET). The switch has two thermodynamically stable conformations, H and O, which are distinguishable by the fluorescence reporter. Transformation between the two conformations is kinetically labile under physiological and lab conditions allowing for rapid monitoring of the switch's current conformation. Results show that that the O form has a 170-fold greater affinity for NC than does the H form. It is also demonstrated that a known competitor, HIV-1 psi regions Stem Loop 2 (SL2), is able to displace the AlloSwitch from the NC binding site resulting in a change in fluorescence reported by the switch. The AlloSwitch has also proven to be amenable to a High Throughput Screening (HTS) Assay for screening small molecule competitors for NC which may prove to be possible drug leads. The HTS has advantages of being in a 96 well plate format (suitable for 384 well plate format) requiring simple mix-and-read steps which can be easily automated, and does not require any long equilibration periods or wash steps. This makes the HTS desirable for screening libraries of hundreds of thousands or even millions of compounds. This Alloswitch demonstrated that these types of molecules can be rationally designed and thermodynamically tuned to desired specifications by researchers; some guidelines for this process are included in this thesis. AlloSwitches can also be of importance for their use as diagnostic indicators for the presence of the target molecule, such as biological toxins or organisms.
https://surface.syr.edu/che_etd/24
oai:surface.syr.edu:che_etd-1023
2010-09-17T18:48:03Z
publication:etd
publication:che
publication:cas
publication:coscde
publication:che_etd
publication:dche
Carboplatin: Exploring mechanism of action and improved drug delivery (1) Role of carbonate in the mechanism of action of carboplatin; (2) Cytotoxicity of mesoporous silica nanomaterials
Di Pasqua, Anthony J.
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James C. Dabrowiak
Carboplatin
Platinum anticancer drugs
Carbonate
Cytotoxicity
Mechanism of action
Mesoporous silica
Chemistry
Inorganic Chemistry
Physical Sciences and Mathematics
(1) The second generation Pt 2+ anticancer drug carboplatin, cis -[Pt(NH 3 ) 2 (CBDCA- O,O' )], where CBDCA is cyclobutane-1,1-dicarboxylate, is here shown to react with carbonate, which is present in blood, interstitial fluid, cytosol, and culture medium, to produce platinum-carbonato and -hydroxo complexes, using 1D 13 C and 1 H NMR spectroscopy, 2D [ 1 H, 15 N] HSQC NMR spectroscopy and 15 N-labeled carboplatin, an UV-visible spectroscopy. Observed rate constants for the reaction of carboplatin in various media show that CO 3 2- is an important nucleophile for the ring opening of carboplatin, and that this reaction is important in the nucleophile-rich RPMI culture medium. In the presence of Jurkat cells, carboplatin is modified not only by substances present in culture medium, such as carbonate, but also by substances released by the c themselves. Using 13 C NMR, resonances have been detected that, by comparison to previously reported carbonato complexes, are due to carbonato species produced when carboplatin is allowed to react in carbonate buffer. This corroborates [ 1 H, 15 N] HSQC NMR, which shows the formation of carbonato and hydroxo complex cis -[Pt(NH 3 ) 2 (CO 3 )(OH)] - . The products formed in this reaction are taken up by cells a interact with critical cellular components. Aging carboplatin in carbonate buffer produces species that are more toxic toward human neuroblastoma, renal proximal tubule, and Namalwa-luc Burkitt's lymphoma cells, than is intact carboplatin. When exposed to carboplatin or carboplatin aged in carbonate, normal Jurkat cells take up/bind approximately the same amount of Pt, while cisplatin-resistant Jurkat cells take up/bind less Pt when exposed to the latter. Collectively, the studies presented here show that carbonate may play an important role in the mechanism of action of carboplatin in vivo.
(2) Mesoporous silica MCM-41 is here shown to adsorb carboplatin, using UV-visible spectroscopy, and [ 1 H, 15 N] HSQC NMR spectroscopy and 15 N-labeled carboplatin. The toxicity of MCM-41, two of its functionalized analogs, and spherical silica nanoparticles, toward human neuroblastoma cells was also investigated. Cytotoxicity, reported in terms of the number of particles required to inhibit normal cell growth by 50%, appears related to the adsorptive surface area of the particle; however, factors such as size and shape also appear to be important. Collectively, these studies explore the suitability of mesoporous silica nanomaterials as vehicles for drug delivery.
https://surface.syr.edu/che_etd/22
oai:surface.syr.edu:che_etd-1024
2010-09-20T17:00:42Z
publication:etd
publication:che
publication:cas
publication:coscde
publication:che_etd
publication:dche
Heavy alkaline earth metal amides: Synthetic and structural investigations
Gillett-Kunnath, Miriam M.
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Alkaline earth metals
Nontoxic reagents
Primary and secondary amines
Redox transmetallation/ligand exchange
Organoamides
Coordination chemistry
Chemistry
Inorganic Chemistry
Physical Sciences and Mathematics
During the last decade, heavy alkaline earth organometallic chemistry has emerged from obscurity to becoming a vibrant area of research, owing to a number of synthetic pathways that provide reliable access to these highly reactive target compounds. Nevertheless, synthetic methodologies are all associated with various disadvantages. Thus, the development of improved synthetic routes will have a significant impact on the further development of alkaline earth metal chemistry.
Further, analysis of recent work emphasizes difficulties associated with the predictions of the coordination chemistry of these large metals, thus preventing the urgently needed structure/function correlation. As such, the study of ligand and donor effects on the coordination chemistry of these metals provides an avenue for further advancement of alkaline earth organometallics. Part I of this thesis analyzes, in detail, parameters responsible for the coordination chemistry of alkaline earth metal amides, ultimately providing the tools for the development of novel materials for chemical vapor deposition to allow the preparation of advanced precursor materials.
Part II evaluates a novel synthetic methodology that provides facile, reliable, inexpensive access to alkaline earth metal amides circumventing many of the known synthetic difficulties associated with the well-established procedures. Importantly, this synthetic methodology represents an environmentally conscious synthetic route, that is amenable towards other ligand systems (i.e. N(R)(SiMe 3 ) (R = SiMe 3 ; 2,4,6-Me 3 C 6 H 2 ; 2,6- i Pr 2 C 6 H 3 ) thus providing unprecedented access to organo alkaline earth metal derivatives.
The final part of this work reports on preliminary studies geared to preparing non silylated amides in an attempt to address the commonly observed problem of N-Si bond cleavage in the silylated complexes. This work will ultimately provide attractive precursors for synthetic and solid-state applications.
https://surface.syr.edu/che_etd/31
oai:surface.syr.edu:che_etd-1025
2010-09-20T17:29:18Z
publication:etd
publication:che
publication:cas
publication:coscde
publication:che_etd
publication:dche
Improving access to biologically and pharmaceutically relevant molecules by understanding mechanisms of biosynthesis and improving chemical synthesis
Houghton, Stephen Richard
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laulimalides
Sialic acid
Tenofovir
Escherichia coli BL21(PL3)
Drug development
Polyketides
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
The development of innovative strategies to produce complex bioactive molecules in quantities necessary for drug development, diagnostics, or research tools is a challenging endeavor. The process must be efficient, commercially feasible, and environmentally sustainable to be considered viable for development. Biotechnology offers promise as an efficient mechanism of drug manufacturing. By utilizing a diverse portfolio of chemical and biological tools (biosynthesis, fermentation, genetic engineering, and chemical synthesis) access to pharmaceutically and biologically significant molecules becomes a reality. Exploring the biosynthesis of natural products such as laulimalide, offers an alternative methodology to chemical synthesis for application as an anticancer agent. Fermentation-based strategies to produce sialic acid have been realized and the in vitro enzymatic pathway presented here provides insight to improve its yield. Genetic engineering of bacterial protein expression strains such as E. coli BL21(DE3) can provide improved metabolism capable of increased utilization of carbon sources or incorporation of inexpensive isotopically labeled substrates into proteins. Synthesis of drugs in a manufacturing setting such as tenofovir require efficient, cost-effective, and robust synthetic methodologies to have an impact on the cost of the drug in the marketplace. These strategies represent a new set of interdisciplinary drug development tools capable of providing more efficacious and affordable drugs to the public.
https://surface.syr.edu/che_etd/30
oai:surface.syr.edu:che_etd-1026
2010-09-20T17:38:49Z
publication:etd
publication:che
publication:cas
publication:coscde
publication:che_etd
publication:dche
Inelastic neutron scattering and quantum mechanical calculations of polymorphic organic crystals
Rivera, Sharon
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Neutron scattering
Organic crystals
Polymorphic crystals
Glycine
Chemistry
Physical Chemistry
Physical Sciences and Mathematics
This research focuses on obtaining vibrational spectra from organic systems using inelastic neutron scattering (INS) and its reproducibility when comparing experimental data to quantum mechanical calculations via single molecule and solid state density functional theory (DFT). This information allows the investigation of hydrogen bonding polymorph thermodynamics. Other techniques, such as X-ray diffraction and terahertz (THz) spectroscopy are employed in order to further investigate phenomena of interest.
In particular, there are four different organic systems investigated in this research. The first two are aromatic hydrocarbons, triphenylene and azulene, where interest is focused on the bonding structure of the molecule upon packing. As well as, two systems that represent increasing interest in hydrogen bonded polymorphic interactions, a complex between 4-methylpyridine and pentachlorophenol (4-MPPCP) and three polymorphs of glycine.
The research regarding triphenylene provides information into a highly symmetric molecule (D 3h ) that reduces its symmetry upon packing into a lower symmetry lattice site in its monoclinic crystal structure (C 1 ). INS and solid state DMol 3 vibrational spectra support the lack of symmetry in the molecule in the crystal. It is found that a single triphenylene molecule in its crystal structure has asymmetric bond length deviations from D 3h and that these deviations are not induced by crystal packing forces which therefore means these deviations are not real. It is possible that the unequal bonds in D 3h symmetry only appear unequal because of the zero point thermal motion. It is also found that the bond lengths differ in a random way to support DMol 3 calculations providing a more accurate description of the bond lengths than X-ray diffraction when the X-ray diffraction crystal structure is provided as a starting point. Further studies using other Mills-Nixon type molecules are needed to confirm a trend in DFT bond length description. The same type of investigation is needed on different types of molecules (ie: non Mills-Nixon) to see if DFT also provides better bond lengths when the diffraction structure is used as a starting point.
Azulene continues to elude definitive single molecule and crystal structure determination. INS, THz spectroscopy and DFT calculations are performed in this research to obtain the crystal structure. Previous research concludes there are two molecules per unit cell which is represented by room temperature X-ray diffraction as if there were two azulene molecules superimposed on each site. This suggests a thermodynamically favorable 180° in plane rotation at room temperature, an even distribution of parallel and antiparallel configurations or predominantly parallel azulenes in small domains with the domain direction being random in orientation. This work continues to be a work in progress, however THz spectroscopy in combination with INS and DMol3 suggests the parallel configuration is lower in energy than the antiparallel configuration.
Two of the three polymorphs of glycine, α and γ, are extensively investigated in this research by INS and solid state DFT, DMol 3 . The third polymorph of glycine, β, has been difficult to prepare and converts to the α form when cooled; it is investigated by DMol 3 methods only. The INS data reveals differences in the anharmonic -NH 3 region of the polymorphs that are related to thermodynamics. This research has uncovered increasing isotopomeric polymorphism upon deuteration of the amino group and induced stress. γ-Glycine-ND 3 is stable under stress, while α-glycine-ND 3 converts to γ-glycine-ND 3 upon grinding and cooling. The thermodynamics of the system is also investigated. Previous research suggested α-glycine to be more stable than γ-glycine. However, it has recently been determined that γ-glycine is lower in energy than α-glycine. Calculations reported in the literature support α-glycine having a lower lattice energy than γ-glycine; therefore, this research attempts to explain why the difference occurs, how to keep track of it when performing future studies, and how to obtain the proper answer for this particular system. In short, when calculating the energies of different polymorphic forms, the zero point energy (ZPE) of the polymorphs must be taken into account. The ZPE difference calculated for γ-α glycine is 162.5 cm -1 or 1.94 kJ/mol. While this may seem alarmingly large, a proper method to calculate the difference in energies of the polymorphs is necessary, such as molecular mechanics. The ZPE difference for α-glcine-ND 3 and γ-glycine ND 3 is 135.7 cm -1 . Additional ZPE differences are reported in Chapter 5. The contribution of vibrational energy to the ZPE should not be ignored when considering polymorph stability.
4-MPPCP is known to exhibit isotopomeric polymorphism upon deuteration of the hydrogen bond between the molecules. (Abstract shortened by UMI.)
https://surface.syr.edu/che_etd/29
oai:surface.syr.edu:che_etd-1027
2010-09-20T17:44:15Z
publication:etd
publication:che
publication:cas
publication:coscde
publication:che_etd
publication:dche
I. Water-driven chemoselective reactions of squarate derivatives with amino acids and peptides: Mechanism and applications. II. Biocompatible hydrogels: Transferring bioinert chemistry from surfaces to 3-dimensional materials
Sejwal, Preeti
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Yan-Yeung Luk
Surface immobilization
Water-driven
N-terminal cysteine
Chemoselective
Squarate derivatives
Bioinert
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
Chemoselective organic reactions in entirely aqueous environment are useful for interfacing chemistry with life sciences, including immobilization of peptides and mammalian cells on surfaces, and running designed reaction in living systems. This dissertation describes a fundamentally new class of highly chemoselective reaction employing rationally designed squarate derivatives - molecules with abiotic structures - and N-terminal cysteine residue of peptides (or proteins) in an entirely aqueous solution at neutral pH. The mechanistic study of this chemoselective ligation revealed that the reaction not only proceeds in water, but also promoted by the hydrogen bonding of water. By fine tuning the reactivity of squarate derivative and controlling the pH of the solution, a methodology had been established for immobilizing peptides and mammalian cells using only the N-terminus cysteine for conjugation to surface bound squarates. This highly resolved control of selectivity enables the immobilization and biological studies of peptides and protein containing internal cysteines. Few other potential application of this reaction were also presented including a new class of labeling reagent for peptides, proteins and mammalian cells that have long-term stability in water and has potential for the development of a biotin probe that can survive the complex biological environment. Mimics of the ligand for mediating mammalian cell adhesion, Agr-Gly-Asp (RGD) tripeptide, were also constructed based on a squarate core structure. The synthesis of this new class of non-peptidic molecules is highly efficient - consisting of 1-5 steps. Inhibition assays suggest that this class of molecules block the specific binding site on integrin membrane protein for the natural ligand RGD. Cell adhesion assays were conducted on bioinert self-assembled monolayers (SAMs) of alkanethiols on gold film to reduce the high signal-to-noise ratio usually associated with traditional fibronectin based assay. Exploring the transfer of the bioinert anti-biofouling surface chemistry of the mannitol-terminated self-assembled monolayer into three-dimensional materials, a novel hydrogel composed of mannitol-derivatized acrylamide monomers was synthesized. This polymeric material prevents mammalian cell adhesion more effectively than other hydrogel materials based on monomers such as glycerol and acrylamide. This result validates the hypothesis that assembly of molecules known as Kosmotropes, which render the folding structure of proteins, also exhibit bioinertness.
https://surface.syr.edu/che_etd/28
oai:surface.syr.edu:psc_etd-1007
2010-09-20T18:13:42Z
publication:etd
publication:che
publication:maxwell
publication:coscde
publication:cas
publication:dpsc
publication:dche
publication:psc_etd
No need to argue: Why does concurrence continue within foreign policy groups despite receiving negative feedback?
Van Assche, Tobias
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Margaret G. Hermann
Concurrence
Foreign policy groups
Negative feedback
Commitment
International Relations
Political Science
Social and Behavioral Sciences
This study examines why groups that initially rallied around a policy--in what Janis (1972) describes as groupthink--continue to unanimously support the original course of action despite receiving negative feedback further into the case. This behavior is puzzling as one would rationally assume that evidence that a chosen strategy is not working would lead to renewed debate on whether to continue the same approach or to alter the course of action. This study proposes that foreign policy groups continue this behavior for two different and mutually exclusive reasons, depending on whether they are initially confronted with a perceived threat or an opportunity. Escalation of commitment (side-bet pressures, social pressures, and self-justification) is responsible for the continuation of concurrence in cases of perceived threat, while the high initial expectancies and corresponding policies cause lack of discussion in cases of perceived opportunity.
This study uses a case study approach to examine four sequential foreign policy cases, two examples of opportunity and two of threat. The cases of perceived opportunity are the crossing of the 38 th parallel in Korea and the decision to go to war in Iraq. The cases of perceived threat are the British appeasement of Hitler and the escalation of the war in Vietnam. Each case is divided into occasions for decision--or moments in which the policy makers are forced to or choose to address the problem. Then a structured focused comparison is used, in which the same set of questions are asked with a limited number of possible responses at each occasion for decision.
This study finds that in all four cases the group remained concurrent, until the policy makers were faced with a 'shock', which significantly changed the nature of the crisis (such as the Chinese offensive in the Korean war), or consistent negative feedback. The cases also provided evidence that high initial expectancies caused groups to continue to be concurrent following a perceived opportunity, and that escalation of commitment variables were responsible for the group's concurrence and commitment to the original course following a perceived threat. This study found that these two categories were mutually exclusive.
https://surface.syr.edu/psc_etd/7
oai:surface.syr.edu:che_etd-1028
2010-09-20T17:57:31Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Manipulation of the ligand sphere of ruthenium metathesis catalysts for the synthesis of organometallic molecular wires
Bolton, Sarah L.
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Michael Sponsler
Olefin metathesis
Molecular wires
Ruthenium
Metathesis catalysts
Chemistry
Inorganic Chemistry
Organic Chemistry
Physical Sciences and Mathematics
The Grubbs first- and second-generation catalysts were used as the building blocks toward organometallic molecular wires. Two main strategies were employed to modify the catalysts: olefin metathesis and ancillary ligand exchange.
Two equivalents of the first-generation catalyst were reacted with 1,3,5,7-octatetraene to give the new diruthenium compound [(PCy 3 ) 2 Cl 2 Ru] 2 (μ-CHCH=CHCH=CHCH). This stoichiometric reaction was named olefin metathesis for metal incorporation (OMMI) describing the metathesis replacement of the terminal CH 2 groups with a metal center. Structural characterization of the complex was done using NMR spectroscopy and NMR simulation. The electronic characterization using UV-vis and CV/DPV indicated that the new complex does exhibit intermetal communication.
Several attempts were made to produce aurophilic catalysts as precursors for molecules to be studied using an STM break junction method. This study utilized both ancillary ligand exchange (using pyrizine, dimethylaminopyridine, bipyridine, and mercaptopyridine) and OMMI (using vinylpyridine and vinylimidazole) to alter the ligand sphere around ruthenium. The catalysts with the new pyridinyl ligands were not suitable for the synthesis of diruthenium complexes using OMMI as their metathesis activity was too low.
The metathesis activity of the 3-bromopyridine analog of the first-generation catalyst was studied and found to be almost identical to the Grubbs first-generation catalyst in initiation but inferior when it came to stability during a reaction. While the usefulness of this complex as a metathesis catalyst is limited, it was found to be useful for ancillary ligand exchange. Ligand exchange using PBu 3 was also successfully done using the first-generation complexes to give a mixture of two new metathesis inactive complexes in situ. The new complexes could not be isolated but were characterized using 1 H and 31 P NMR.
Phosphine exchange using PMe 3 and PBu 3 was performed to the synthesize second-generation complexes (H 2 IMes)RuCl 2 (=CHPh)(PMe 3 ) and (H 2 IMes)RuCl 2 (=CHPh)(PBu 3 ) with reduced metathesis activity. The rates of OMMI with ethyl vinyl ether using phosphine-exchanged products were over two orders of magnitude less than that of Grubbs second generation catalyst. The PMe 3 complex was also shown to undergo an unprecedented associative phosphine exchange mechanism. The reaction of PBu 3 with the PMe 3 complex was faster than metathesis, depended on the concentration of incoming phosphine, gave second order kinetic plots, and through Eyring analysis showed a negative entropy of activation.
The PMe 3 complex, (H 2 IMes)RuCl 2 (=CHPh)(PMe 3 ), possessed an open coordination site that was more available than in other phosphine containing Grubbs-type catalysts. Carbon monoxide (CO) was stoichiometrically added to give a new saturated complex where a CO ligand filled the open coordination site. Excess CO led to a product that had two CO ligands and the benzylidene inserted into a mesityl group on the imidazolylidine. Phosphine exchange was also performed on diruthenium complexes in an attempt to make the bimetallic complexes more stable. Two stable diruthenium complexes were prepared but purification was not completely successful. The synthesis of the new diruthenium complexes along with the work on aurophilic complexes has paved the way for future work toward diruthenium organometallic molecular wires.
https://surface.syr.edu/che_etd/27
oai:surface.syr.edu:che_etd-1029
2010-09-20T18:03:34Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Mid-infrared and near-infrared vibrational circular dichroism: New methodologies for biological and pharmaceutical applications
Ma, Shengli
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Vibrational circular dichroism
Near-infrared spectroscopy
Infrared spectroscopy
Analytical Chemistry
Chemistry
Physical Sciences and Mathematics
New methodologies have been developed at the cutting-edge of Fourier transform vibrational circular dichroism (FT-VCD) spectroscopy aimed at various pharmaceutical and biological applications. VCD spectra of a series of proteins with different secondary structures were obtained with a modified ChiralIR (BioTools, Jupiter, FL) FT-VCD spectrometer in the near-infrared (near-IR) region from 6000 to 4000 cm -1 and the mid-infrared (mid-IR) region from 2000 to 800 cm -1 . High quality mid-IR-VCD spectra were obtained to support accurate quantitative analysis based on VCD data. The NIR-VCD spectra of proteins show distinct spectral features for different protein structural motifs, indicating a new valuable method to study protein structures.
For the first time, VCD spectroscopy is applied to study the structures and associated formation dynamics of insulin and lysozyme proteins fibrils. Mid-IR VCD spectra show remarkable sensitivity to these protein fibrils which are β-rich structural fibrils developed under the conditions of heating native protein solutions at low pH, indicating that VCD is a powerful tool to study such complex systems. In addition, VCD shows successful results on monitoring the protein structural changes during fibrillation. The potential for new insight into the mechanism and dynamics of the fibril formation process is elucidated.
Two-dimensional correlation VCD spectroscopy (2D-COS VCD) is developed to enhance the applications of VCD. The pD-dependence of the VCD and IR spectra of Lalanine in D 2 O solution in the mid-IR CH-bending and CH-stretching regions, and near-IR region are presented. Analysis of the 2D correlation plots provide further insight into the relative sensitivities of structural changes that take place in L-alanine as a function of pD. Near-IR band assignments are facilitated by hetero-spectral-region 2D-COS spectra that correlate the combination band region to that of the underling fundamental modes. Furthermore, 2D COS VCD was applied to investigate structures of insulin fibrils during the formation process. New insight into the functional groups associated with the fibrillation process is thereby obtained.
Enhanced VCD and magnetic VCD (MVCD) in transition metal complexes are presented. Similar to previous VCD results, resonance-enhanced MVCD spectra are observed for a series of complexes with open-shell transition metals at coordination sites, further confirming that the resonance enhancement comes from low-lying excited electronic states (LLESs). Moreover, regular MVCD are obtained from several complexes without LLESs, suggesting a promising research method for structural determination of a wide range of molecules.
The structure of amylose tris-(dimethylphenylcarbamate) (ADMPC) and its conformational changes with respect to polar solvents were investigated by VCD for the first time. By providing rich information on a number of different functional groups, VCD was shown to be a powerful and innovative molecular-level probe to study the structures of this type of chiral polymer. In addition, the conformations of side chains and the backbone of ADMPC were monitored using VCD in the solid film state in the presence of different concentrations of alcohols. VCD results revealed new insight into the behavior of ADMPC in the presence of these polar solvents when in combination with nonpolar solvents such as hexane.
https://surface.syr.edu/che_etd/26
oai:surface.syr.edu:che_etd-1030
2010-09-20T18:11:42Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
NMR analysis of structural features of the HIV-1 nucleocapsid protein in response to mutation and interaction with RNA and drug candidates
Yang, Lingchun
2008-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
HIV-1
Nucleocapsid protein
Zinc fingers
HSQC
NMR
NCp7 mutation
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Chemistry
Life Sciences
Physical Sciences and Mathematics
The Human Immunodeficiency Virus (HIV), responsible for the Acquired Immunodeficiency Syndrome (AIDS), is a member of the retroviral family. The nucleocapsid (NC) domain of the Gag precursor is critical for the recognition and packaging of the viral genome and appears to be important for viral particle formation. NC has both specific and non-specific modes of interaction with genomic RNA. When the divalent Mg 2+ replaces univalent Na + in buffer it can suppress the non-specific electrostatic interaction to a great extent and does not affect the nature of the complex when the specific binding is most important. Mutants N5A (similar binding affinity as wild type) and F6A (lower binding affinity) were examined by 1 H- 15 N HSQC spectra and Trp titration results, as were the variants of RNA, SL3 GUG and SL1iA. Based on previous research in our group (DeCiantis, 2007), 21 compounds from the NCI Diversity set were found to interfere with NCp7 binding to the HIV-RNA packaging signal. According to the HSQC spectra of a series of ligands bound to NC, we find that 20 of the top 21 hits denature the protein in the presence of a 4 to 16-fold excess of drug. The analyses show that D9 (NSC 107684) binds NCp7 and gradually changes the structure of NCp7 with increasing ratio, and finally denatures the protein. The comparison of HSQC spectra between free NCp7 and NCp7 bound with D17 (NSC 305819) or D19 (NSC 13950) proves that D17 and D19 first react with the second zinc finger, then the first zinc finger, and finally denature the protein. The rest of 20 compounds also can denature NCp7 when the ratio is above 4:1. These results suggest that these compounds may be useful lead compounds for drugs which can interact with zinc fingers and change the structure of NCp7.
https://surface.syr.edu/che_etd/25
oai:surface.syr.edu:che_etd-1031
2010-09-21T13:19:29Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Basic and applied studies of blue & green proteorhodopsin
Xi, Bangwei
2006-08-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Robert R. Birge
Proteorhodopsin
Photoactive
Long-term storage
Biochemistry
Low temperature UV-Vis evaluation of proteorhodopsin. Low temperature UV-Vis spectroscopy has been used to characterize the photocycle intermediates of wild type green and blue proteorhodopsins. Our data shows that in wild type green proteorhodopsin, the K, M, and N states can be trapped at low temperatures, either alone or mixed with other intermediates. The L and O state, however, cannot be identified from our data. In wild type blue proteorhodopsin, M appears at extremely low temperatures and is always mixed together with either K or N. Absorption spectra of photoproducts were calculated using Fitspectra, an in-house software package developed by Robert R. Birge developed by Robert R. Birge, et al , for manipulating spectral data.
Evaluation of proteorhodopsin as a holographic material. Photodiffractive properties including diffraction efficiency, rise time, etc . of proteorhodopsin (wild type green and blue proteorhodopsin, E108Q green and blue proteorodopsin) based films in the volume holographic regime were measured. Lifetimes of the intermediates involved in the holographic recording process were calculated using the decay portion of the holographic growth curve.
Characterization of an extremely long-lived photo-generated state in proteorhodopsin. A long-lived intermediate was found in wild type proteorhodopsin upon continuous illumination. The absorption spectrum of this long-lived intermediate is blue shifted and is close to that of the M state. The lifetime of this long-lived intermediate is about two hundred hours. This long-lived intermediate can be almost totally driven back to the protein resting state with blue light illumination. These collective features make it a potential candidate for long-term data storage applications.
https://surface.syr.edu/che_etd/34
oai:surface.syr.edu:che_etd-1033
2010-09-21T19:02:19Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Application of the [2,3] Wittig rearrangement to synthetic studies toward the total synthesis of (+)-discodermolide
Liang, Guohua
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James Kallmerten
Wittig rearrangement
Discodermolide
Hydroboration
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
The application of the [2,3] Wittig rearrangement to the total synthesis of (+)-discodermolide is the subject of this dissertation. (+)-Discodermolide is a unique polyketide that was isolated in 1990 and was found to have impressive anti-tumor activities. (+)-Discodermolide is under Phase I clinical trials as a potential antitumor drug.
Background information and stereochemical consequences of the [2,3] Wittig rearrangement are discussed. Examples of the application of the [2,3] Wittig rearrangement to the total synthesis of natural products are described, as are previous total syntheses of (+)-discodermolide also presented.
Considerable effort has been focused on the construction of fragments A (C1-C8), B (C9-C13), and C (C15-C21) of (+)-discodermolide. The syntheses of each fragment begins with a common intermediate prepared from Z-2-buten-1,4-diol. A [2,3] Wittig rearrangement of the common intermediate, followed by hydroboration, installs the C4, C5, and C7 stereocenters in fragment A. Fragment B is synthesized in a single step. Fragment C is prepared by applying a [2,3] Wittig rearrangement followed by hydroboration. The alkylation of a tertiary allylic alcohol with tributyltin methylene iodide is improved. The selective deprotection of a di-TBS ether is realized. Possible routes for completion of the total synthesis of (+)-discodermolide are proposed.
https://surface.syr.edu/che_etd/32
oai:surface.syr.edu:che_etd-1032
2010-09-21T18:40:17Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Analysis of cytotoxicity of anticancer drugs
Tao, Zhimin
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Cytotoxicity
Anticancer drugs
Apoptosis
Cellular respiration
Doxorubicin
Chemistry
Life Sciences
Pharmacology
Pharmacology, Toxicology and Environmental Health
Physical Sciences and Mathematics
Apoptosis, induced in cancer cells by anticancer agents such as doxorubicin, dactinomycin, and the platinum drugs, is characterized by impaired respiration, decreased ATP, and activated caspases. Respiration rates of Jurkat or HL-60 cells treated with drugs are measured using a Pd (II) phosphor to monitor [O 2 ]. Cellular ATP is determined using the luciferin-luciferase bioluminescence system, and intracellular caspase activation measured by allowing caspases to cleave Ac-DEVD-AFC to the fluorescent AFC, which is detected on HPLC. A decline in the rate of respiration was evident in Jurkat and HL-60 cells exposed to doxorubicin. The decline was abrupt, occurring after about 2 h of incubation. The inhibition was concentration-dependent and was completely blocked by the pan-caspase inhibitor benzyloxycarbonyl-Val-Ala-DL-Asp-fluoromethylketone. Respiration in resistant HL-60/MX2 cells, characterized by an altered topoisomerase II activity, was not inhibited by doxorubicin. A decline in cellular ATP was measured in Jurkat cells after 2 to 4 h of incubation with 20 μM doxorubicin, paralleling the decline in respiration rate. In the presence of dactinomycin, k decreased gradually with time. The decrease was more pronounced at higher concentrations of the drug. Cellular ATP remained constant for 5 hr in untreated cells, but decreased gradually in the presence of 20 μM dactinomycin (to one tenth the value at 5 hr for untreated cells). The drug-induced inhibition of respiration and decrease in ATP level were both blocked by the pancaspase inhibitor zVAD-fmk. Caspase activity was first noted after about 2 h of incubation with doxorubicin or dactinomycin, the production of AFC being linear with time afterwards. Caspase activation by doxorubicin was delayed in HL-60/MX2 cells, reflecting the critical role of topoisomerase-II in doxorubicin cytotoxicity. For both drugs, caspase activity increased rapidly between ∼2 and ∼6 hours, went through a maximum, and decreased after ∼8 hours ("caspase storm"). Cisplatin treatment induced noticeable caspase activity only after ∼14 h of incubation, and the fluorescent intensity of AFC became linear with time at ∼16 h. Exposure of the cells to all of the drugs studied led to impaired cellular respiration and decreased cellular ATP, concomitant with caspase activation. Thus, the mitochondria are rapidly targeted by active caspases. Comparing the ways in which respiration, ATP level, and caspase activity vary with time points up differences between the mechanisms of actions of doxorubicin, dactinomycin, and the platinum drugs. These results should also be useful in choosing the most effective drug for a particular clinical application.
https://surface.syr.edu/che_etd/33
oai:surface.syr.edu:che_etd-1035
2010-09-23T18:30:30Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Placing heavy alkaline earth metals on the map: Synthetic access, structure evaluation and reactivity studies of heavy alkaline earth organometallics
Guino-o, Marites A.
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Alkaline earth organometallics
Alkaline eath metal acetylides
Alkaline earth metals
Di- and triphenylmethanides
Alkaline earth metal tetraphenylborates
Alkaline earth metal aryloxide
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
The recent surge in the interest in heavy alkaline earth metal organometallics can be attributed to its increasing list of applications in synthetic organic, organometallic and materials chemistry. Progress in this chemistry has been thwarted by the high reactivity of the target compounds; as such further growth in this area of chemistry depends on the development of synthetic methods and detailed structure function analysis. To bridge this gap, this thesis examines synthetic methodologies and strives to increase the number of well characterized alkaline earth organometallic compounds to provide the basis for further development.
A significant portion of this work illustrates structural principles of the organometallic compounds of heavy group 2 metals and their tendency to display unexpected bent X ligand - M - X ligand geometries as demonstrated by the alkaline earth acetylides. Other aspects illuminated here pertain to the three ion association modes of the target compounds, specifically heavy alkaline earth di- and triphenylmethanides in solution and the solid state, which for the closely related organolithium compounds have been shown to affect the reactivity of the compounds.
Synthetic investigations associated with the structural examination strengthen the viability of toluene elimination and transmetallation pathways towards the entry to these species.
Accordingly, the results presented here extend the understanding of the structural models for heavy group 2 organometallic compounds while providing synthetic tools for the further development of this rapidly developing area of organometallic chemistry.
https://surface.syr.edu/che_etd/38
oai:surface.syr.edu:che_etd-1036
2010-09-23T18:37:16Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Progress in molecular heterobimetallic alkaline earth metal chemistry: New synthetic strategies, structural features and properties
Zuniga, Maria Felisa A.
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Alkaline earth metals
Organomettalic complexes
Aryloxides
Secondary interactions
Heterobimetallic
Group 2
Chemistry
Inorganic Chemistry
Physical Sciences and Mathematics
Heterobimetallic compounds continue to be vital in synthetic and materials chemistry. In comparison their homometallic components, heterobimetallic compounds display unique chemical properties. Investigations on mixed metal compounds involving the alkaline earth metals are extensive for magnesium but the coordination chemistry and potential applications of corresponding heavy Group 2 (Ca, Sr, and Ba) metals have yet to be explored. Previous attempts to prepare such compounds only led to the isolation of homometallic species. The preparation of these species remains a challenge due to limited available synthetic strategies, and suitable ligand and solvent systems.
This work describes the synthesis and characterization of a family of molecular heterobimetallic alkaline earth metal complexes. The combinations of alkaline earth metals with alkali metals, rare earth metals and combination of metals within Group 2 are explored. A series of novel mixed metal lithium/magnesium complexes bearing different aryloxo ligands, in addition to a selection of donors have been prepared and analyzed to demonstrate their intricate role in the structural chemistry of the target compounds.
In addition, a new class of heterobimetallic compounds involving heavy Group 2 and Group 1 metals using 2,6-diphenylphenol (HOdpp) as the ligand is presented. These compounds, of the type [M n {Ae(Odpp) 2+n }] (M = Li, Na, K or Cs; Ae = Ca, Sr or Ba), are the first representatives of alkali/heavy alkaline earth metal species of low nuclearity. All compounds display extensive metal-p-interactions, believed to be a key factor in stabilizing these highly reactive species. Prepared as donor-free as well as heteroleptic complexes, these compounds provide critical insights into solvation versus intramolecular interactions.
Investigations on heterobimetallic compounds were also extended to mixed metal Ae/Ae' (Ae = Ba, Ae' = Sr or Mg) and Ae/Ln (Ae = Ba, Ln = Eu, Sm, Yb). The structural features displayed by these complexes further illuminate the similarities and differences in the chemistry of alkaline earth and rare earth metals.
The target compounds were prepared using a powerful synthetic methodology, solid state direct metalation. We present this approach as a highly promising entry into heavy alkaline earth metal derivatives.
https://surface.syr.edu/che_etd/37
oai:surface.syr.edu:che_etd-1034
2010-09-23T18:10:24Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Nitro- and oxazoline-derivatized antennas: Structural and photophysical characterization of their lanthanide complexes
Viswanathan, Subha
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Ana de Bettencourt-Dias
Antennas
Lanthanide
Oxazoline
Nitrobenzoates
Chemistry
Physical Sciences and Mathematics
Polymer Chemistry
Trivalent lanthanide ions are being increasingly used for the development of various kinds of luminescent materials, with Eu(III) and Tb(III) being the most popular. Eu(III) compounds show intense red luminescence with characteristic emission in the 615-625 nm region, while the Tb(III) compounds show intense green luminescence with characteristic emission in the 540-550 nm region. Because of the large size of lanthanide ions and of the numerous possible non-radiative de-excitation pathways available in their complexes, the design of efficient ligands for sensitization of Ln(III) emission is very challenging.
One of the main objectives of our research is the development of Eu(III) and Tb(III)-based luminescent complexes that are covalently linked to a polymer backbone for use in polymer light-emitting diodes. Towards this aim, we are interested in the design of new ligands that can efficiently sensitize lanthanide ions. At the same time, we are also keen on investigating the electronic and structural effects encountered in the lanthanide complexes when a polymerizable moiety is introduced in the ligand.
Two classes of ligands have been developed and are discussed extensively in this work: nitro-derivatized and oxazoline-derivatized compounds, with thiophene being chosen as the polymerizable moiety. The nitro-derivatized ligands further fall into two categories of widely different compounds, benzoic acid and 2,2'-bipyridine. The rationale behind the choice of these ligands along with extensive characterization in solid-state and in solution of their lanthanide complexes are presented in this work. In addition, through this work a new class of highly efficient sensitizers, based on the oxazoline compounds, has been revealed.
https://surface.syr.edu/che_etd/39
oai:surface.syr.edu:che_etd-1037
2010-09-23T18:56:54Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Rhenium and technetium radiopharmaceuticals: Design and development for applicatons in nuclear medicine
James, Shelly
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Rhenium
Technetium
Radiopharmaceuticals
Nuclear medicine
Biotin
PSMA
Chemistry
Medicinal-Pharmaceutical Chemistry
Organic Chemistry
Physical Sciences and Mathematics
This study focuses on the design, development, and synthesis of technetium and rhenium radiopharmaceutical agents for imaging and therapy applications in nuclear medicine. In conjunction with a bioactive molecule, the use of rhenium and technetium can be powerful tools in targeting disease, since 99m Tc presents ideal nuclear decay properties. The pendant approach was implemented in the design of the radiopharmaceuticals. The three major components of this strategy, the biologically active molecule, a tridentate chelator, and a radiometal core, were explored.
Studies of the interaction of the coupling of the technetium tridentate chelator with a bioactive molecule with receptor specific interactions constitutes a significant segment of this work. After a careful investigation of the coordination preferences of the metal cores towards the different donor ligand systems, a series of single amino acid chelates (SAAC) and their complexes with biologically active molecules such as biotin and PSMA analogues were designed, synthesized, and their biological activity evaluated.
Chapters 2 and 3 focus on biotin as a potentially valuable pretargeting agent in conjunction with avidin, and the biological properties this biotin-avidin system maintains. Chapter 4 elaborates on the flexibility and utility of the biotin-avidin system and further expands the applicability into the arena of luminescence. Chapter 5 demonstrates the utility of a series of cationic and urea based N-acetylaspartyl glutamate (NAAG) analogues as potentially useful reagents in the battle against prostate cancer, and the seemingly discrete area of neuroimaging. The improved synthesis of a critical starting material is elaborated on in Chapter 6 which also presents thorough characterization of the newly synthesized [Re(H 2 O) 3 (CO) 3 ]Br starting material.
https://surface.syr.edu/che_etd/36
oai:surface.syr.edu:che_etd-1038
2010-09-23T19:03:50Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Rhodium-catalyzed addition of terminal alkynes to vinyl ketones and studies toward the synthesis of peyssonenynes A and B
Lerum, Ronald Vivas
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Rhodium-catalyzed
Synthesis
1
4-addition
Enynes
Dimerization
DNMT-1
Peyssonenynes
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
The 1,4-addition of terminal alkynes to conjugated ketones is a problematic reaction because typical copper-mediated additions perform poorly. To address this limitation, a rhodium catalyzed reaction was developed. After some optimization, the best reaction conditions involved the use of catalytic Rh(acac)(CO) 2 and catalytic P-( o -C 6 H 4 OCH 3 ) 3 in refluxing benzene.
Formation of γ,δ-alkynyl ketones is a synthetically useful reaction, as they can be transformed into other key structures and are present in many natural products. In contrast to other methods, the rhodium catalyzed 1,4-addition of alkynes to enones does not require anhydrous conditions, strong Lewis acids and/or a stoichiometric amount of activating agent. The reaction is also compatible with a variety of functional groups including unprotected alcohols, halides and esters.
These studies also resulted in the discovery of a rhodium-catalyzed three component coupling reaction leading to a conjugated enyne 1,4-addition adduct under similar conditions. By altering the phosphine ligand to P-( o -C 6 H 5 CH 3 ) 3 , we can dramatically increase the yield of this dimer-addition product while suppressing the 1,4- addition reaction manifold. Using 2D-NMR studies we established the connectivity and the geometry of the enyne 1,4-addition product. Other studies included optimization of this reaction and determination of the scope with respect to alkyne and enone.
Additionally, studies toward the total synthesis of peyssonenynes A & B were performed. Harvested and extracted in minute quantities from a red marine alga, Peyssonnelia caulifera , these natural products strongly inhibit the activity of DNA methyltransferases. Due to the minute quantities isolated and facile decomposition of these natural products, their structural assignment remains incomplete. An efficient synthesis of peyssonenynes A & B will provide material for biological testing and complete structural assignment.
Several approaches toward the synthesis of peyssonenynes A & B are discussed. The four pathways differ by featuring different key reactions such as: (1) a rhodium-catalyzed 1,4 addition of a terminal enediyne to acrolein, (2) the Sonogashira reaction, (3) a linear Cadiot-Chodkiewicz approach and (4) a convergent Cadiot-Chodkiewicz approach.
https://surface.syr.edu/che_etd/35
oai:surface.syr.edu:che_etd-1041
2010-09-24T17:48:07Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Terahertz spectroscopy of the intermolecular and intramolecular vibrations of molecules in solution
Fedor, Anna M.
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Terahertz
Intermolecular
Intramolecular
Hydrogen-bonding
Low-frequency
Solution-phase
Chemistry
Physical Chemistry
Physical Sciences and Mathematics
Studies combining experimental terahertz (THz) spectroscopy, density functional theory (DFT), and ab initio methods have been used to predict the intermolecular and intramolecular vibrations of several molecular species in solution. There are a range of molecular interactions that are of interest in these molecules including strong and weak hydrogen bonding, cation-anion pair interactions, and extended conjugation. These types of interactions are typically described as global interactions that usually involve the simultaneous movement of all atoms in a molecule, which can be directly investigated using THz radiation. Experimental data from all molecules presented is supported by calculations predicting their structures and vibrational motions. Most molecular interactions studied in solution can be accurately described using DFT, however ab initio methods, in particular, MP2 calculations, have been useful in describing weak interactions, including weak hydrogen bonding. This research has led to a greater understanding of the types of theoretical methods necessary in the prediction of low-frequency vibrational spectra and the improvements that have been made, both experimentally and theoretically, will be highlighted in the following chapters.
https://surface.syr.edu/che_etd/40
oai:surface.syr.edu:che_etd-1039
2010-09-24T17:37:10Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Structural diversity of the oxovanadium organodiphosphonate and the M(I,II)/1,2,4-triazolate systems: A platform for the design of multifunctional hybrid organic-inorganic materials
Ouellette, Wayne
2007-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Oxovanadium organodiphosphonate
Triazolate
Metal-organic framework
Microporosity
Photoluminescence
Magnetism
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
This research work encompasses the detailed investigation of the design and synthesis of hybrid organic-inorganic materials involving the oxovanadium diphosphonate system and the M(I, II)/1,2,4-triazolate system in order to expand our understanding of the principles which render the chemistry of hybrid organic-inorganic materials more controllable and predictable. In addition, this research investigates the development of properties in these classes of compounds. Furthermore, the hydrothermal reaction conditions, such as stoichiometry, temperature, pH and fill volume influence the product identity.
In an attempt to elaborate the structural systematics of these materials, we have investigated the oxovanadium organodiphosphonate system, focusing on a number of variables, specifically: variations in tether length of α, ω-alkyldiphosphonates, the introduction of organic or metal complex cations, and the incorporation of fluoride anions into the V-P-O substructure.
In order to explore the structural consequences of diverse anions on materials of the M(I/II)/triazole/anion system for M = Cu(I), Cu(II), Zn(II), and Cd(II) numerous novel phases were prepared and their properties studied. We have described the exploitation of hydrothermal synthesis in the preparation of these metal-triazolates with complex framework structures, photoluminescent properties, microporosity, and unusual magnetic properties.
https://surface.syr.edu/che_etd/42
oai:surface.syr.edu:che_etd-1042
2010-09-27T13:22:46Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Influence of organic building blocks on the structures of bimetallic organic/inorganic hybrid frameworks
Yucesan, Gundog
2006-05-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon Zubieta
Bimetallic
Organic/inorganic hybrid
Chemistry
The search for new inorganic materials reflects an urgent need to address today's industrial necessity for materials that can store hydrogen in high quantities at ambient temperatures that act as catalysts and that allow more data storage in hard discs. So far the synthesis of important inorganic materials has been done according to the traditional methods; the same mix and wait strategy will be applied for their synthesis in the following decades until synthesis of inorganic materials by design is achieved. But this goal has proven to be elusive. To address this problem, I focused on [{Cu(II)/L} n 2n+ /V x O y z- /(O 3 PRPO 3 ) i 4i- ], system and synthesized numerous compounds by introducing different organic structural units and changing reaction conditions to produce a library of this class of compounds for future mechanistic studies. Initially, I surveyed the effect of temperature on the structures of this system. In addition to this, I introduced different organoimine {L) and organophosphonate {H 2 O 3 PRPO 3 H 2 ) building blocks to observe their influence on the final structures of the system. As it is expected, bridging organoimine ligands like tetrapyridylporphyrine and 4,4'-bipyridine produced mainly three dimensional structures. On the other hand chelating ligands like terpyridine and 2,2'-bipyridine produced one or two dimensional structures. The same trend was observed upon the introduction of different organophosphonate units to the system. Mono and sterically hindered phosphonic acids produced mainly one dimensional compounds, whereas bridging diphosphonic acids produced structures in higher dimensions. The reactions were conducted under hydrothermal conditions. The products of the reactions were characterized by single crystal and powder x-ray spectroscopy and thermogravimetric analysis along with magnetic studies of selected compounds
https://surface.syr.edu/che_etd/44
oai:surface.syr.edu:che_etd-1043
2010-09-27T14:33:20Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Liquid crystalline holography: The effect of various additives on photopolymerization
Tucker, Lucas J.
2006-11-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Michael B. Sponsler
Liquid-crystalline
Holography
Additives
Photopolymerization
Chemistry
A switchable holographic material based on a free-radical photopolymerizable nematic diacrylate was improved by addition of the trithiocarbonate, EtO 2 CCH 2 SC(S)SCH 2 CO 2 Et, at levels near 0.1% by mass. Diffraction efficiencies as high as 34%, the thin-grating theoretical maximum, were achieved at large (10-14 μm) grating spacings. Improved diffraction efficiency was seen over a range of grating spacings (0.35-10 μm) demonstrating increased resolution. The exposure window for grating formation was increased by an order of magnitude, resulting in much improved reproducibility and grating uniformity.
The concentration of the two liquid crystal components of the trithiocarbonate-containing switchable material were varied from 9:1 to 1:9 in order to investigate effects on recording mechanism and efficiency. This study showed that a mixture with 80% difunctional liquid crystal monomer gave the best results and that recording depends on immobilization but not phase separation.
The mechanism of action of the trithiocarbonate was investigated through electrically switchable holographic grating results, along with results from initiator bleaching experiments, concentration studies, addition and in-situ generation of trithiocarbonate-trapped radicals, EPR studies, cyclic voltammetry measurements, and determination of diffraction grating refractive index profiles. This additive was shown to simultaneously promote the rate and inhibit the photopolymerization process, but not through the traditional RAFT (reversible addition fragmentation chain transfer) mechanism often seen with trithiocarbonates.
Various other additives were applied to the holographic systems and grating formation was studied. A tertiary amine coinitiator was added to the system leading to overexposure even in the low light of dark room conditions. A phenol inhibitor required longer exposures and reduced diffraction efficiency. An iodium salt accelerator showed the best results when added with the trithiocarbonate, giving higher diffraction efficiencies. For example, a 3-μm grating spacing improved from 25% with trithiocarbonate alone to 34% with added accelerator.
https://surface.syr.edu/che_etd/43
oai:surface.syr.edu:che_etd-1044
2010-09-28T15:18:37Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Proteorhodopsin: A study on its photocycle and its place in the evolution of the bacteriorhodopsin superfamily
Krebs, Richard A.
2006-05-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Mark Braiman
Proteorhodopsin
Photocycle
Bacteriorhodopsin
Membrane protein
Analytical Chemistry
Biochemistry
Proteorhodopsin (pR) is a light-activated proton pump homologous to bacteriorhodopsin and recently discovered in oceanic [gamma]-proteobacteria. One perplexing difference between these two proteins is the absence in pR of homologues of bacteriorhodopsin residues Glu-194 and Glu-204. These two residues, along with Arg-82, have been implicated in light-activated fast H + release to the extracellular medium in bR. A purification protocol was developed and flash-photolysis experiments were performed to show that fast H + release does occur in proteorhodopsin, at least under elevated pH conditions that resemble somewhat those of [gamma]-proteobactefa's native open ocean environment.
Further studies of proteorhodopsin's structure utilizing Resonance Raman indicate that there are 2 subpopulations of pR in a light-adapted state. These populations most likely arise from different post-translational modifications of the heterologously-expressed protein. The identities of these modifications were not investigated.
Finally, the evolutionary history of proteorhodopsin, bacteriorhodopsin and their homologues was investigated utilizing protein sequence comparison techniques. Two alternative hypotheses of the origin of the archaeal rhodopsins and their homologues are discussed. First, the extant rhodopsins may have evolved from a H + pump protein in a last universal common ancestor (LUCA). Second, these light-activated H + pumps may have emerged after LUCA.
https://surface.syr.edu/che_etd/46
oai:surface.syr.edu:che_etd-1045
2010-09-28T18:08:39Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Advances in the design of heavy alkaline earth metal complexes as precursors for chemical vapor deposition
O'Brien, Anna Yosick
2005-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Karin Ruhlandt-Senge
Alkaline earth metal
Chemical vapor deposition
Oxygen templating
Pyrazolates
Ketoiminates-beta
Electronic thin films
Chemistry
Materials Chemistry
Physical Sciences and Mathematics
The heavy alkaline earth metals, calcium, strontium, and barium, are components in thin films with electronic properties such as high-capacitance, superconductance and electroluminescence. The formation of these thin films by chemical vapor deposition (CVD) methods requires precursors that are volatile, but the high reactivity of the heavy alkaline earth metal precursors has made this challenging. Historically, heavy alkaline earth metal β-diketonates have been utilized as precursors, but their tendency towards aggregation and hydrolysis affords high molecular weight compounds with low volatility. The lack of a suitable heavy alkaline earth metal precursor is a major limiting factor in the production of these electronic thin films by CVD. As a result, improved precursor materials have been pursued, yet a number of drawbacks, including limited synthetic methodologies, lack of availability, and incorporation of undesired elements into the films, have prevented their widespread use in industry.
This thesis work focuses on the development of novel alkaline earth metal precursors based on pyrazolate and β-ketoiminate ligand systems, which are thermally robust, readily available, and devoid of undesired elements such as silicon and fluorine. One of the key factors in precursor design is control of the coordination environment of the metal, to prevent aggregation and hydrolysis, and to keep the volatility high. However, the coordination chemistry of the heavy alkaline earth metals is only in its infancy, which is a major roadblock in the design of future precursors. Concurrently with the development of new precursors, this thesis work uncovers new insights into their coordination chemistry, most significantly, the effects of agostic interactions on the thermal stability of the compounds. Secondary interactions, such as agostics and π-bonding, appear to play a large role in the coordination chemistry of these metals, with implications in the design of future precursors. Additional findings in this work reveal the reproducible formation of an alkaline earth metal-hydroxide framework with triply bridging pyrazolate ligands in novel binding modes. Furthermore, the effect of synthetic methodologies on a β-ketoiminate ligand system is presented, specifically, the use of direct metallation by ammonia activation.
https://surface.syr.edu/che_etd/45
oai:surface.syr.edu:che_etd-1046
2010-09-29T14:37:45Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Synthesis of highly functionalized natural products from carbohydrates: Application of the [2,3] Wittig rearrangement and advancement toward nonlinear optical materials
Perreira, Melissa
2004-04-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James Kallmerten
Carbohydrates
Wittig rearrangement
Natural products
Nonlinear optical
Organic Chemistry
A library of [alpha]-alkoxy allylstannyl ether substrates was synthesized to examine the stereochemical outcome of the unstabilized [alpha]-alkoxy allylstannyl ether [2,3] Wittig rearrangement. Well-defined stereoselectivities transpired for the generation of di- and tri-substituted olefins via the [2,3] Wittig rearrangement. Lithiation of [alpha]-alkoxy allylstannyl ethers and subsequent rearrangement produced a mixture of E and Z olefins and the reliability of the unstabilized [2,3] Wittig rearrangement was determined.
Upon completion of the unstabilized [2,3] Wittig methodology study, our next project consisted of utilizing carbohydrates, as chiral templates, toward the asymmetric synthesis of natural products. Our ultimate goal was to use this approach to install a Z disubstituted alkene in the target molecule.
The partial synthesis of (-)-discodermolide and dictyostatin, a potent immunosuppressive agent against lymphoma and breast carcinoma cells and a cytotoxic agent towards 60 different human cancer cell lines respectively, began with a common carbohydrate precursor methyl-[alpha]-D-glucopyranoside.
The preparation of a novel nonlinear optical substrate via molecular engineering of organic materials features a highly conjugated five-membered ring linker fragment. It was postulated that the molecular rigidity of this molecule thereby conformationally locks it into a planar structure thus increasing the [pi]-stacking abilities and NLO properties.
https://surface.syr.edu/che_etd/47
oai:surface.syr.edu:che_etd-1047
2010-09-30T17:04:48Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Design, synthesis and characterization of rhenium complexes for the development of diagnostic and therapeutic agents in nuclear medicine
Wei, Lihui
2005-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon A. Zubieta
Rhenium
Diagnostic
Therapeutic
Nuclear medicine
Technetium
Radiopharmaceuticals
Chemistry
Medicine and Health Sciences
Pharmacy and Pharmaceutical Sciences
Physical Sciences and Mathematics
We have explored the coordination chemistry of rhenium in the attempt to develop radiopharmaceuticals as diagnostics and therapeutics in nuclear medicine. Since rhenium and technetium are Group VII congeners, the periodic similarity has allowed for the study of the non-radioactive metal rhenium instead of technetium, which exists only as radioactive isotopes.
We investigated the three components of the conjugate (pendant) design: (1) arylpiperazine and nucleosides as biologically active molecules (BAMs); (2) single amino acid chelates (SAAC) as bifunctional chelates (BFCAs) for conjugation of small peptides; (3) {Re I (CO) 3 } + , {Re III Cl 3 } and {Re V O} 3+ as metal cores.
First, we successfully developed a family of BFCAs constructed from pyridine, imidazole, aliphatic amine and carboxylate derivatived single amino acid to provide a tridentate donor set for coordination to the {M I (CO) 3 } + (M = Tc, Re) core and a linker for attachement to small peptides. We also examined the coordination chemistry of the same SAAC ligands with the {Re III Cl 3 } core. Second, we combined the tridentate chelating moiety with arylpiperazine derivatives with potential applications as brain imaging agents. Third, we coupled the SAAC ligands with nucleoside analogues to provide potential inhibitors for nucleoside kinases. Finally, we demonstrated the unusual and complex redox reactivity of the {Re V O} 3+ core with the "simple" ligand N-methyl diaminobenzene, an observation which raises serious caveats in the design of radiopharmaceuticals.
https://surface.syr.edu/che_etd/52
oai:surface.syr.edu:che_etd-1048
2010-09-30T17:26:19Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Enhanced VCD in transition metal complexes and metalloproteins
He, Yanan
2005-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laurence A. Nafie
Teresa B. Freedman
Transition metal
Metalloproteins
Vibrational circular dichroism
Chemistry
Physical Sciences and Mathematics
Enhanced vibrational circular dichroism (VCD) in transition metal complexes and metalloproteins bound with small ligands, VCD studies of conformational transitions in metal-bound polynucleic acids, and applications of VCD to absolute configuration and solution conformation determination are presented in this thesis. The metal complexes studied include metal-(-)-sparteine (metal = Co(II), Ni(II) and Zn(II)) complexes, and metal complexes with chiral Schiff base ligands (metal = Co(II), AI(III), Cr(III), Mn(III), Ni(II), and Zn(II)). Metal complexes with low-lying d-d transitions exhibit 10- to 100-fold enhanced VCD intensities in both the CH-stretching region and the mid-IR (800-2000 cm -1 ) region compared to the complexes without low-lying electronic states. The small-ligand-bound metalloproteins studied include cytochrome c and carboxymethylated cytochrome c bound with azide, cyanide, imidazole and pyrindine, Co(II)-substituted carbonic anhydrase bound with cyanate, and Co(II)-substituted insulin bound with azide. For cytochrome c and carboxymethylated cytochrome c bound with small ligands, anisotropy ratios on the order of 10 -3 were observed for the ligand-stretching modes, and enhanced VCD intensities were also observed in the 1600-1000 cm -1 region compared to the reduced (Fe(II)) proteins. Both the cyanate-bound Co(II)-carbonic anhydrase and the azide-bound Co(II)-insulin exhibit enhanced VCD anisotropy ratios for the ligand stretching modes, and are the first observations of VCD enhancement in non-heme metalloproteins. These studies provide more solid evidence for the argument based on vibronic coupling theory, that low-lying electronic states of the metal center in these complexes and the metal center in the active sites of the metalloproteins are the origins of the large enhanced VCD anisotropy ratio.
The conformational transitions between double, triple and single stranded forms of polynucleic acids poly(rA)·poly(rU), poly(dA)·poly(dT) and their metal bound derivatives as a function of temperature were studied using VCD. The double stranded structure of the nucleic acids were stabilized when bound with Mg 2+ or Ni 2+ , but were destabilized when bound with Cd 2+ .
The absolute configurations and solution conformations of seven selected molecules with pharmaceutical and biological interest were studied by combining VCD measurement with VCD calculation at the DFT level using Gaussian 98/03.
https://surface.syr.edu/che_etd/51
oai:surface.syr.edu:che_etd-1050
2010-09-30T19:45:29Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Studies toward the total synthesis of epothilone A
St. Denis, Francine Joy
2005-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James Kallmerten
Epothilone A
Natural products
Wittig rearrangement-[2
3]
Chemistry
Medicinal-Pharmaceutical Chemistry
Organic Chemistry
Physical Sciences and Mathematics
The goal of this work was the total synthesis of the promising antitumor candidate epothilone A. Recent work in our laboratories has focused on the use of stereocontrolled sigmatropic reactions for the construction of complex, polyketide-derived natural products. Particularly useful for the elaboration of polypropionate systems is the [2,3] Wittig rearrangement of tertiary allylic ethers, which generates stereodefined trisubstituted olefins.
Our approach to the epothilones, focused on the development of the C1-C12 subunit of the parent macrolide using the stabilized [2,3] Wittig rearrangement, was unique in that the C-3 hydroxyl stereochemistry was to be installed not through a stereoselective reduction of a carbonyl group, but via the [2,3] Wittig rearrangement. The [2,3] Wittig rearrangement of our epothilone A tertiary allylic ether intermediate produced trans olefin selectivity with low stereoselectivity observed at C-3.
The introduction of stereochemistry at C-6 was to be accomplished by stereoselective hydroboration of the trisubstituted trans olefin generated by [2,3] Wittig rearrangement; chemistry developed in this regard will find direct application to the synthesis of other biologically significant polyketide systems. However, attempts to investigate the stereoselective hydroboration of the stabilized [2,3] Wittig rearrangement product were unsuccessful.
https://surface.syr.edu/che_etd/49
oai:surface.syr.edu:che_etd-1049
2010-09-30T19:35:58Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Ruthenium incorporation into molecules and materials: New catalysts and strategies to prepare stable ruthenium-capped olefins
Williams, Joseph Ephraim
2005-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Michael B. Sponsler
Triflates
Ruthenium
Olefins
Chemistry
Physical Sciences and Mathematics
Strategies such as olefin metathesis were investigated to make stable mixed-valence compounds and materials incorporating metal atoms in polyolefin chains, which are potential precursors in molecular electronics.
New olefin metathesis catalysts, having the general molecular formula (H 2 IMes)Ru(=CHR)(Cl) 2 (3-bromopyridine) 2 and (H 2 IMes)Ru(=CHR)(Cl) 2 (PCy 3 ), where R = Me, Et, and Pr, were prepared. Their kinetic reactivity towards olefins was studied. The PCy 3 catalysts initiated faster (6-14 times) than the Grubbs catalyst where R = Ph. The 3-bromopyridine catalysts were similar in reactivity to the Grubbs catalyst, where R = Ph.
Polyacetylene was prepared in powder and film forms from acetylene using ruthenium olefin metathesis. A new material, metathesis-doped polyacetylene (MDPA), with ruthenium incorporation in the polyacetylene, which was soluble in common organic solvents, was prepared. The 3-bromopyridine catalyst where R = Ph effected the polymerization of 1-hexyne and propargyl alcohol.
Two new ring-constrained polyenes, 1,5-dimethylene-1,2,3,4,5,6,7,8-octahydronapthalene and 1,5-dimethylene-decahydronapthalene, and two polyynes, 1,4-pentadiyne and 3,3,6,6-tetramethyl-1,4,7-octatriyne, were investigated as precursors for ring-constrained diruthenium complexes through sequential ene-yne, ring-closing, and stoichiometric olefin metathesis reactions. All compounds failed to give the desired complexes under a variety of conditions.
A new class of ruthenium alkylidene complexes of trimethylphosphine (H 2 IMes)Ru(=CHR)(Cl) 2 (PMe 3 ), where R = Ph and Et, were prepared. They were metathesis-unreactive at room temperature. Thus, a method of stopping the metathesis reactivity was found by the simple addition of PMe 3 . A new ruthenium alkylidene, namely (PCy 3 )Ru(=CHC 6 H 5 )(Cl) 2 (3-bromopyridine) 2 , was prepared. A new set of Fischer carbenes was prepared, including a tris(trimethylphosphine) complex with molecular formula (PMe 3 ) 3 Ru(=CHOCH 2 CH 3 )(Cl) 2 .
Two dienyl ditriflates, 2,3,4,6,7,8-hexahydronapthalene-1,5-ditriflate and 3,4,4a,7,8,8a-hexahydronapthalene-1,5-ditriflate, were prepared, the former in higher yield and greater reproducibility than done before. Their reactivity and potential application as ring-constrained precursors to prepare diruthenium complexes were investigated.
https://surface.syr.edu/che_etd/50
oai:surface.syr.edu:che_etd-1051
2010-09-30T19:54:51Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Technetium and rhenium radiopharmaceutical agents in nuclear medicine: Design and synthesis
Lazarova, Neva
2005-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon A. Zubieta
Technetium
Rhenium
Radiopharmaceutical
Nuclear medicine
Chemistry
Physical Sciences and Mathematics
This study focuses on the design, development, and synthesis of technetium and rhenium radiopharmaceutical agents for imaging and therapy in nuclear medicine. Due to the inherent chemical similarities between technetium and rhenium, the non-radioactive rhenium was used as a surrogate for the technetium metal, which exists only as radioactive isotopes.
Studies of the interaction of the metal ions Tc(I, III, V) and Re(I, III, V) with aromatic and aliphatic amines, carboxyl groups, thiols, and thioethers constitutes a significant segment of this work. After a careful investigation of the coordination preferences of the metal cores towards the different donor ligand systems, a series of single amino acid chelates (SAAC) and their complexes were designed and synthesized.
The conjugate (pendant) approach was implemented in the design of the radiopharmaceuticals. The three major components of this strategy, the biologically active molecule (BAM), the bifunctional chelator (BFCA), and the radiometal core, were explored. Chapters 2 and 3 focus on the single amino acid chelates, as the BFCA, for conjugation to a small peptide, acting as the BAM. Chapter 4 discusses the importance of thiols and thioethers in the development of technetium and rhenium metal complexes with charges ranging from +1 to -1. Chapter 5 demonstrates the utility of a series of cationic and ether-based agents as myocardial perfusion agents. Chapter 6 concentrates on the synthesis of brain imaging agents for the DAT, 5-HTT, and NET. Chapter 7 presents the improved and very convenient synthesis and thorough characterization of the [Re(H 2 O) 3 (CO) 3 ]Br starting material.
https://surface.syr.edu/che_etd/48
oai:surface.syr.edu:che_etd-1052
2010-10-01T13:17:08Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Theoretical and experimental studies on intermetal communication in dinuclear complexes of ruthenium with conjugated bridging ligands
Seetharaman, Sripriya K.
2006-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Michael Sponsler
Dinuclear
Ruthenium
Conjugated bridging
Ligands
Chemistry
Ruthenium hydride addition to alkynes to give to alkenyl complexes, [RuH(CO)Cl(PR 3 ) 2 (CH=CHR)] was used to prepare conjugated diruthenium complexes. Addition of RuH(CO)Cl(PR 3 ) n = 2, 3 to 1,3-butadiyne and 1,4-diethenylbenzene gave the complexes [Ru(CO)Cl(PR 3 ) 2 ] 2 (µ-CH=CH-X-CH=CH) where R = P(iPr) 3 or PPh 3 and X = nothing or C 6 H 4 . These symmetrical, dinuclear metal complexes undergo one-electron oxidation to give rise to mixed-valence radical cations and then dications. These compounds were analyzed by various techniques such as Near-IR, UV-Visible, and EPR spectroscopies, cyclic voltammetry and theoretical methods.
Compounds with P(iPr) 3 as the phosphine ligand behave as completely delocalized class III mixed-valence compounds, as confirmed by spectroscopy, where the electron is spread throughout the molecule. The coupling parameter H ab , however, decreases from 0.87 eV (X = nothing) to 0.5 eV (X = C 6 H 4 ) when the length of the bridge is increased. For the PPh 3 compounds, conclusive results could not be obtained. The results for the compound with the longer bridge were affected by coordination of excess PPh 3 at low temperatures. This compound did not give good spectra when excess phosphine was removed.
In order to evaluate spectroscopic results for [Ru(CO)Cl(PPh 3 ) 2 ] 2 (µ-CH=CH-C 6 H 4 -CH=CH), the coordination behavior of PPh 3 at low temperatures had to be understood. To study this coordination behavior, an analogous monoruthenium complex [Ru(CO)Cl(PPh 3 ) 2 ](CH=CHC 6 H 5 ) was studied. Variable temperature 31 P and 1 H NMR were performed at seven different temperatures in the presence of PPh 3 and showed that the PPh 3 bound species at low temperature was highly favored. From the NMR data, thermodynamic and kinetic data were determined for the coordination process. The [Delta]H and [Delta]S values for the process of coordination were found to be -17.6 kcal/mol and -58.2 e.u and the [Delta]H [double dagger] and [Delta]S [double dagger] values for decoordination were 20.5 kcal/mol and 38.9 e.u.
A theoretical study was also undertaken on simplified but similar molecules in neutral, cationic and dicationic states. The DFT calculated vibrational frequencies showed good agreement with the experimental ones and the calculated electronic spectra showed reasonable correlation with experimental spectra. DFT computations were also consistent with strongly delocalized structures.
Synthesis of a jumper cable molecule was attempted. The bridging ligand, a tetra substituted benzdiimidazole molecule, was synthesized. This molecule was synthesized from relatively inexpensive starting materials in six steps and in two steps from a known compound. The intermediate products were easy to isolate and required minimal or no purification. The introduction of substituents was done only in the second to last step, making the synthesis a general one. The attachment of the bridging ligand to the ruthenium metal was unsuccessful so far.
https://surface.syr.edu/che_etd/56
oai:surface.syr.edu:che_etd-1053
2010-10-01T13:51:00Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Thermal isomerizations through [1,5]-hydrogen shifts in mono-deuterium-labeled cis,cis-1,3-cyclononadienes
Raghavan, Anuradha S.
2006-12-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
John E. Baldwin
Thermal isomerizations
Hydrogen shifts
Deuterium labeling
Cyclononadienes
Organic Chemistry
Thermal [1,5] hydrogen shifts in conjugated cycloalkadienes have been recognized isomerization reactions since the early 1960s. Recent studies of isomerizations exhibited by deuterium-labeled 1,3-cyclohexadienes, 1,3-cycloheptadienes and 1,3-cyclooctadienes have provided activation parameters for these [1,5] sigmatropic rearrangements.
Activation energies for such reactions determined through experimental studies or theoretical calculations may be strongly conditioned by geometrical constraints in transition structures and by ground state conformational effects. Theory-based and experimental activation energies for the three cyclic dienes that have been investigated are in qualitative agreement, but the calculated values are higher than the observed energy barriers, by some 1.8 to 6.2 kcal/mol---a disquieting disagreement. Towards understanding these discrepancies, a specific mono-deuterium-labeled cis,cis -1,3-cyclononadiene has been synthesized and the thermal isomerizations equilibrating it with its four isomers were followed to secure log A and E a values for the hydrogen shifts involved. The kinetic experiments providing rate constants from 240°C to 287°C led to activation parameters: E a = 37.1 kcal/mol and log A = 11.6. The activation energy is in remarkable agreement with theoretically determined values. Whether variations in transition structure geometries might correlate with reactant specific tunneling effects on reaction rates and activation parameters for cis,cis -1,3-cycloalkadienes remains to be clarified.
https://surface.syr.edu/che_etd/55
oai:surface.syr.edu:che_etd-1054
2010-10-01T18:17:46Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Affinity of the HIV-1 nucleocapsid protein for structural motifs in the genomic RNA packaging domain
Paoletti, Andrew
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Philip N. Borer
HIV-1
Nucleocapsid
RNA packaging
Aptamers
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Chemistry
Life Sciences
Physical Sciences and Mathematics
The HIV-1 nucleocapsid protein (NCp7) plays several vital roles in the lifecycle of HIV and thus presents a valuable new target for drug discovery. A fluorescence based binding assay for NCp7 was developed that allows the measurement of NCp7 affinity for specific regions of the HIV-1 genome and can be adapted to develop a competition assay for NCp7. Utilizing this assay, the affinity of NCp7 for four apical stem loops and two internal stem bulges within the HIV-1 packaging region have been determined. Also, a total of three NCp7 proteins were found to bind a 154mer encompassing the majority of the HIV-1 packaging region. Within the HIV-1 packaging region, one stem loop (SL3), is responsible for approximately 90% of packaging efficiency. In order to better understand the determinants of SL3 affinity for NCp7, we modified the sequence and size of SL3. From this study, it was determined that the guanine bases at positions 318 and 320 are primarily responsible for affinity to NCp7. Also, a stem of four base pairs is necessary to maintain strong affinity for NCp7. Finally, aptamers for NCp7 developed by other groups were tested for affinity to NCp7 utilizing our assay. These longer aptamers were found to bind multiple NCp7 proteins and to contain smaller stem loops with the tight binding GUG sequence in the apical loop as determined by the Mfold program. Binding assays performed with these smaller stem loops seem to indicate these are the regions of the aptamers responsible for NCp7 affinity.
https://surface.syr.edu/che_etd/54
oai:surface.syr.edu:che_etd-1055
2010-10-01T18:31:38Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Aromatic thiol based redox buffers: Increasing the folding rates of disulfide containing proteins
Gough, Jonathan David
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Watson J. Lees
Aromatic thiol
Redox buffers
Disulfide
Protein folding
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Biophysics
Chemistry
Life Sciences
Organic Chemistry
Physical Sciences and Mathematics
Disulfide-containing proteins are regularly produced for pharmaceutical, industrial, and academic purposes. The yield-limiting and most expensive step in the production of active protein is the formation of the correct disulfide bonds. Current technology uses aliphatic thiols as redox buffers for folding disulfide-containing proteins. Aliphatic thiols limit the conditions (pH) at which the proteins can be folded. A group of aqueous soluble aromatic thiols were tested for their ability to improve the folding rate constant of a disulfide-containing protein, ribonuclease A (RNase A). The folding of RNase A was measured at pH 6.0, 7.0 and 7.7 using various concentrations of each of the thiols. The aromatic thiols increased the folding rate of RNase A by a factor of 4-20 times that measured for glutathione (GSH), the naturally occurring aliphatic thiol commonly used for folding disulfide-containing proteins. It was observed that optimal protein folding conditions correlated to an equal concentration of protonated thiol ([SH]), rather than total thiol. The data for the para -substituted aromatic thiols were fit to the model: log k app = -4.31 (±0.03) + 0.592 (±0.004) pH - 0.227 (±0.005) p K a + log (1-e -0.98 (±0.02) [SH] ). The equation gave good regression statistics (r 2 = 0.914, s = 0.10). Thirteen data points were used as a validation set (r 2 validation = 0.94 and S validation = 0.083). Additionally, the equation was used to predict the measured values of the apparent rate constant for RNase A folding in the presence of five aqueous soluble ortho - and meta -substituted aromatic thiols (N = 124, r2 = 0.80, s = 0.0046). Protein disulfide isomerase (PDI) is a catalyst typically added to redox buffers for folding inclusion bodies of disulfide-containing proteins. The para -substituted aromatic thiols were tested for their ability to increase the activity of PDI, activity increased up to three times. Aromatic thiols are expected to be excellent candidates for increasing the yield of active protein from inclusion bodies of disulfide-containing proteins.
https://surface.syr.edu/che_etd/53
oai:surface.syr.edu:che_etd-1056
2010-10-01T18:56:37Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Computational quantum chemistry in initial designs and final analyses
Allis, Damian Gregory
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James T. Spencer
Bruce S. Hudson
Quantum chemistry
Computational chemistry
Molecular crystals
Carboranes
Chemistry
Physical Sciences and Mathematics
The broad utility of computational quantum chemical studies of molecular properties and their interactions is examined in a number of research projects covering molecular property prediction, chemical structure analyses, and the vibrational spectroscopy of molecular crystals. The broader scopes of the research serve to explore (1) the utility of theoretical studies for providing a greater understanding of molecules and their interactions, (2) the importance of considering the molecular environment in computational studies for understanding the properties of single molecules as they are currently considered experimentally, and (3) the importance of the selection of appropriate levels of theory for addressing specific questions raised from experimental results given the ever-present need to balance chemical accuracy and computational resources. Five research projects are presented in this work, including (1) the study of molecular crystals by periodic density functional theory and inelastic neutron scattering spectroscopy, (2) the electronic coupling behavior of the phenyl- and tropyl-substituted closo -boranes and closo -carboranes, (3) the design of a new class of borane- and carborane-based nonlinear optical materials through purely theoretical means as an example of the rational design of any class of molecules through a coupling of theory and structure-property relationships, (4) a computational study of the isomer energies of the eight known octamolybdates clusters and rationalizations for their rearrangement pathways as identified in their crystal forms, and (5) a computational study of binding interactions and structural features among the alkali organometallic complexes.
https://surface.syr.edu/che_etd/64
oai:surface.syr.edu:che_etd-1057
2010-10-01T19:12:51Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Enantiomeric excess determination and reaction monitoring of chiral molecules using near-infrared and mid-infrared vibrational circular dichroism
Guo, Changning
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laurence A. Nafie
Teresa B. Freedman
Enantiomeric excess
Chiral
Near-infrared
Vibrational circular dichroism
Analytical Chemistry
Chemistry
Physical Sciences and Mathematics
Fourier transform vibrational circular dichroism (FT-VCD) spectrometers equipped with various types of light sources and detectors and modified to dual polarization modulation (DPM) were set up in our laboratory on the basis of commercial instruments--the Chiral IR from BioTools, Inc. VCD spectra of nine terpenes and derivatives were recorded with the DPM-FT-VCD spectrometers in Near-infrared (NIR) regions from 10000 to 4000 cm -1 and Mid-infrared (MIR) region from 4000 to 800 cm -1 . The NIR-VCD spectra were the first measured by FT-VCD instruments, with unsurpassed quality in spectral precision, signal-to-noise ratio, spectral resolution and simplicity of instrumentation.
The first use of FT-VCD in conjunction with partial least squares (PLS) chemometric analysis to follow changes in the percent enantiomeric excess (%EE) of chiral sample molecules with time using a flow-cell sampling apparatus is reported. The flow-cell sampling simulates the progress of the chemical reaction from a chiral reactant to a chiral product where the %EE of both molecules can change with time. For the molecules studied, α-pinene, camphor and borneol, %EE changes were successfully followed by MIR- and NIR-VCD spectroscopy, and predicted by PLS models with decent accuracy. These findings demonstrate the potential for VCD to be used for real-time monitoring of the composition and %EE of chemical reactions involving the synthesis of chiral molecules.
NIR-VCD spectroscopy and the PLS method have been applied to follow real reactions involving chiral molecules. The epimerization reactions of (S)-(+)-2,2-Dimethyl-1,3-dioxolane-4-methanol (S-DDM) in different solvents were successfully monitored by following the NIR-VCD spectral changes of the O-H combination bands of S-DDM in the spectral range of 5050 to 4700 cm -1 . An interesting solvent effect of the DDM epimerization reaction was discovered. A preliminary NIR-VCD investigation of an SN2 substitution reaction, preparation of 2-chlorobutane, is also reported.
To obtain high signal-to-noise ratio and better quantitative analysis accuracy, the optimal instrument settings and data collection parameters for VCD measurements, such as measurement time, resolution, aperture size, optical filters and preamplifier feedback resistor were explored.The best spectral resolutions for VCD measurements have been recommended.
https://surface.syr.edu/che_etd/63
oai:surface.syr.edu:che_etd-1058
2010-10-01T19:31:51Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
From polymerization initiators to precursors for solid-state materials: Syntheses and structures of a series of molecular alkali and alkaline earth metal derivatives
Teng, Weijie
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Karin Ruhlandt-Senge
Organometallics
Magnesium amide
Thiolates
Polymerization
Alkaline earth metal
Chemistry
Physical Sciences and Mathematics
The syntheses and characterizations of a series of molecular alkali and alkaline earth organometallics are presented.
We here report the syntheses and structures of a family of novel heteroleptic magnesium amide/thiolates by ligand redistribution chemistry involving the reaction of equimolar amounts of magnesium amide and thiolates. Utilization of thiolates with different degree of steric bulk results in either monomeric or dimeric species. We then attempted to convert the target molecules into the heteroleptic magnesium thiolate/selenolate materials that in conjunction with the analogous zinc derivatives would comprise the potential precursor for the preparation of blue-green lasers and diodes.
We also studied the hydrolysis of magnesium alkoxides and aryloxides to obtain insight into the formation of brucite, Mg(OH)2, through controlled hydrolysis of molecular alkoxide and aryloxide precursors. By applying appropriate donors, we aimed to stabilize partially hydrolyzed cluster species. The resulting cluster motif has also important applications in the biochemistry field.
Heavy alkali and alkaline earth organometallics, especially the σ-bonded compounds involving heavy group 14 ligands have important applications in synthetic and polymerization chemistry. Since little is known about the exact nature of heavy alkali and alkaline earth metal tris(trimethylsilyl)silanides and -germanides, we developed synthetic routes toward the target compounds, followed by detailed characterizations. Depending on the donor added, either contact molecules or separated ions are obtained in the solid state, whereas in solution, separated ions are observed. A family of heavy alkali metal germanium hydrides was isolated while preparing the germanides. These compounds display the rare GeH 3 - anion and are believed to be the product of ether cleavage chemistry, thus demonstrating the high reactivity of the germanides.
Compounds reported here were typically characterized using single crystal X-ray diffraction, 1 H, 13 C, 29 Si, IR spectroscopy and melting point analysis.
https://surface.syr.edu/che_etd/62
oai:surface.syr.edu:che_etd-1059
2010-10-01T20:00:49Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Near-infrared vibrational circular dichroism of polypeptides and small pharmaceutical molecules
Zhao, Taiping
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laurence A. Nafie
Teresa B. Freedman
Polypeptides
Pharmaceutical molecules
Small molecules
Norephedrine
Pseudoephedrine
Analytical Chemistry
Chemistry
Medicinal-Pharmaceutical Chemistry
Physical Sciences and Mathematics
The near-infrared vibrational circular dichroism (VCD) spectra of three small pharmaceutical molecules, (1S, 2R)-norephedrine, (1S, 2S)-pseudoephedrine and (1S, 2R)-methylephedrine, and three polypeptides, poly-γ-benzyl-L-glutamate, poly-β-benzyl L-aspartate and poly-L-lysine have been measured and compared to the VCD spectra in the fundamental region 3800-900 cm -1 . The near-infrared VCD bands of the three ephedra molecules found in the spectral region of 8000-3800 cm -1 have been assigned to the OH, NH and CH combinations and overtones. Six near-infrared VCD bands of polypeptides have been identified in the spectral region of 5200-3800 cm -1 . Four of the six bands have been assigned to the combinations and overtone of amide group modes, and have been named as: Amide A+11, Amide 3xII, Amide A+IV and Amide A+V. VCD is a tool for identifying the absolute configuration and solution conformations of chiral molecules. The near-infrared VCD spectra of three ephedra molecules have provided new information on near-infrared VCD involving amino and hydroxyl overtone and combination bands. The near-infrared VCD spectra of polypeptides have provided initial information for characterizing the secondary structure of polypeptides, including α-helix and extended helix forms. All spectra were obtained with a rapid-scan near-infrared Fourier transform VCD spectrometer, newly built in our laboratory. The assignments of spectral bands were made by comparing the spectral data with the data from the literature and the data from the isotope substitution experiment carried out in this research.
https://surface.syr.edu/che_etd/61
oai:surface.syr.edu:che_etd-1060
2010-10-01T20:02:12Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Nitrogen-based alkaline earth metal compounds: Syntheses, structures and applications
Vargas Gregory, Wilda
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Karin Ruhlandt-Senge
Organometallics
Amides
Nitrogen-based
Alkaline earth metal
Chemistry
Physical Sciences and Mathematics
Novel alkaline earth metal aryl substituted silylamides were prepared using alkane (Mg) or salt elimination reactions (Mg, Ca, Sr, and Ba). The salt elimination regime involved the treatment of the alkaline earth metal iodides with two equivalents of the respective potassium amide KNR(SiMe 3 ) (R = 2,6- i -Pr 2 C 6 H 3 and 2,4,6-Me 3 C 6 H 2 ). The organomagnesium source for the alkane elimination was ( n Bu/ s Bu) 2 Mg. Efforts to obtain the beryllium analog resulted in the isolation of a bimetallic lithium-beryllium amido enolate.
The alkane elimination route was also extended to the preparation of primary magnesium amides in the absence of donor solvent. A donor-free heteroleptic magnesium dimer was obtained by reacting dibutylmagnesium with one equivalent of the primary amine H2NMes* (Mes* = 2,4,6- t Bu 3 C 6 H 2 ).
The synthesis and characterization of novel alkaline earth metal pyrrolates as potential precursors for group 2 containing solid state materials are described. Calcium target molecules were synthesized using two different synthetic schemes: transamination and metallation, involving either the treatment of calcium bis (bis(trimethylsilyl)amide) with two equivalents of 2-dimethylaminomethylpyrrole (2-DMAMP) or the reaction of elemental calcium with two equivalents of 2-DMAMP. Magnesium pyrrolates were synthesized using alkane elimination reactions, involving the treatment of Bu2Mg with two equivalents of 2-DMAMP. The metallation regime was employed to prepare strontium and barium 2-DMAMP derivatives. The 2-DMAMP capacity for σ and π bonding is reflected in the solid state structure of the strontium dimer [Sr(2-DMAMP) 2 THF] 2 .
https://surface.syr.edu/che_etd/60
oai:surface.syr.edu:che_etd-1062
2010-10-01T20:36:42Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Role of conserved arginine in solar energy conversion: Infrared spectroscopy of bacteriorhodopsin, proteorhodopsin, and model compounds
Xiao, Yaowu
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Mark S. Braiman
Conserved arginine
Solar energy
Bacteriorhodopsin
Proteorhodopsin
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Biophysics
Chemistry
Life Sciences
Physical Sciences and Mathematics
Time-resolved Fourier transform infrared (FT-IR) difference spectroscopy has been used to investigate the photocycles of two membrane proteins, bacteriorhodopsin and proteorhodopsin, that serve as light-driven H + pumps. In the initial studies presented, two programs important for time-resolved FT-IR experiments are described. The first program divides automatically a 9-hour time-resolved FT-IR measurement into any specified sub-measurements; while the second global multi-exponential fit program can extract intermediate spectra and their time constants from time-resolved FT-IR spectra. Further studies have concentrated on understanding the molecular mechanisms of active H + transport in these systems. A characteristic positive band at 1556 cm -1 in the bR[arrow right]M difference spectra, which shows isotopic downshift and pH dependence, is assigned to arg-82 in M; making it likely that arg-82 itself functions as the fast H + -release group in bacteriorhodopsin. Time-resolved FT-IR spectra of proteorhodopsin under conditions that allow so-called fast H + -release suggest that the released H + cannot originate from the Schiff base or asp-97. Since pR lacks homologs of residues glu-194/-204 of bacteriorhodopsin, the highly conserved arg-94 (analog of arg-82 in bacteriorhodopsin) is the strongest candidate for the fast H + -release group in proteorhodopsin. In the last chapter, the vibrational spectra of arg-82 side chain in the M state of bR (arg-94 for pR) is modeled by a deprotonated alkylguanidine group in a nonpolar solvent; and the deprotonated arg-82 at physiological pH is modeled as being stabilized by an indirect H-bond with tyr-83 (tyr-95 for pR).
https://surface.syr.edu/che_etd/58
oai:surface.syr.edu:che_etd-1061
2010-10-01T20:10:16Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Organic charge transfer complexes and an open-shell organic radical studied by inelastic neutron scattering spectroscopy and DFT methods
Ciezak, Jennifer A.
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Bruce S. Hudson
Charge transfer
Open-shell
Organic radical
Inelastic neutron scattering spectroscopy
Chemistry
Physical Sciences and Mathematics
The existence of intermolecular forces stronger than predicted by van der Waals forces is widely known and studied. Charge transfer (CT) molecules are complexes in which an electron is transferred from a donor component to an acceptor component upon complex formation. These complexes range from 'weak' to 'strong' in terms of the extent of their charge transfer, which results in a coulomb attraction and a covalent interaction between the two components. Little vibrational and theoretical work has been performed on CT complexes. These systems are a challenge to theoretical descriptions because of their open-shell character and interactions that occur in their crystalline states.
The practical use of density functional theory (DFT) depends on a good approximation to the unknown exchange correlation contribution to the total electronic energy. Reproduction of an inelastic neutron scattering (INS) vibrational spectrum provides an excellent method for testing the validity of a particular technique to reproduce both the vibrational dynamics and molecular structure. Two different types of computational methods were used in this work. One employs a conventional atom-centered basis using an isolated complex model with the B3LYP functional. The other method is based on the use of plane-wave basis set with periodic functions to simulate a molecular solid. In this method, we used the popular solid state functional, LDA, and the newly developed generalized gradient approximated functional, HCTH/120.
It is observed in this work that the isolated complex model applied to weak charge transfer complexes provides an adequate description of their molecular geometry and vibrational spectra, but that the periodic solid does not. The reverse is observed in the case of strong charge transfer complexes. This work explores the idea that the reason for the observed differences in the ability of the isolated complex and periodic solid in treating the limiting types of charge transfer is due to the nature of the functionals used.
Density functional theory was also test in the challenging case of an open-shell organic radical. It was found that an unSurface provides description only. Full text is available to ProQuest subscribers. Ask your Librarian for assistance. calculation in conjunction with a scaling factor could reproduce the INS spectrum.
https://surface.syr.edu/che_etd/59
oai:surface.syr.edu:che_etd-1063
2010-10-01T20:53:28Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Solid state chemistry: Structural influences of the binucleating transition metal/tetra-2-pyridylpyrazine complex on the molybdophosphonate and molybdoarsonate class of materials
Burkholder, Eric M.
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon Zubieta
Binucleating
Molybdophosphonate
Molybdoarsonate
Pyridylpyrazine-tetra-2
Chemistry
Physical Sciences and Mathematics
Rational design synthesis in inorganic-organic hybrid materials has proven elusive. While the hydrothermal method provides a route that affords single crystalline products that are easily characterized, the multitude of reaction variables as well as the inability to view the reaction at maximum temperature, offers little insight into the mechanistic understanding of product formation. Considering the immensity of the oxide domain, it is important to focus on a few related reaction systems, in this case the molybdenum phosphonates and the molybdenum arsonates. By utilizing subtle changes in starting materials I was able to synthesis numerous compounds with similar building blocks. The best examples of recurring building blocks are seen in chapters two and three with the Mo 5 O 15 (O 3 PR) 2 and Mo 6 O 18 (O 3 AsR) 2 clusters, respectively.
All compounds were synthesis hydrothermally and characterized by single-crystal x-ray diffraction. The structures discussed herein range from the rather simplistic one-dimensional chain [{Cu 2 (tpypyz)(H 2 O)} 2 (Mo 3 O 8 ) 2 (O 3 PCH 2 PO 3 ) 3 ] 16.9H 2 O to the much more complex three-dimensional [{Ni 2 (tpyprz)(H 2 O) 2 }(Mo 3 O 8 ) 2 (O 3 PCH 2 PO 3 ) 2 ]. Individually, each structure merely represents a novel compound, together they start to reveal knowledge about the structural preferences and coordination tendencies that are critical if one expects to someday gain mechanistic control over this domain.
https://surface.syr.edu/che_etd/57
oai:surface.syr.edu:che_etd-1064
2010-10-05T18:01:52Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Structure and excitation energy in retinals and retinal proteins
Ren, Lei
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Robert R. Birge
Retinals
Retinylidene proteins
Bacteriorhodopsin
Excitation energy
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
Retinylidene proteins, also know as retinal proteins, are membrane-bound protein pigments that bind retinal through a Schiff base linkage. Retinal proteins are photochemically reactive proteins. Though all proteins in this class have the same light absorbing moiety, a retinal chromophore attached via a protonated Schiff base linkage, their absorption maxima cover a wide range. Sensory rhodopsin II (SRII) is unique among archaeal-type rhodopsins in that it has a λ max = 500 nm, about 70 nm blue-shifted from bacteriorhodopsin (BR). The MOZYME ground state optimizations and MNDO-PSDCI (partial single-double configuration interaction) excited state calculations reveal that the relocation of Arg72 in SRII (Arg 82 in BR) is associated with spectral difference between SRII and BR. The dispersive effect of protein residues with regard to spectral tuning was also quantitatively obtained.
High-performance liquid chromatography (HPLC) method was developed to separate and collect geometric isomers of retinal, 3-dehydro retinal and 13-desmethyl retinal. The excitation energy results, using density functional theory (DFT) optimization and MNDO-PSDCI calculations, successfully predict the absorption bands of each isomer and are in good agreement with experimental data. The results also show that modifications on the polyene chain have significant impacts on the conformational energies of the chromophore.
In the study of photochemistry of 13-desmethyl BR analog, a long-lived P-like state with λ max = 525 nm and 9- cis chromophore conformation was discovered. This P-like state is obtained via either direct conversion from the all- trans resting state or sequential conversion from a 13-cis conformation. Theoretical studies and circular dichroism (CD) reveal that rotational freedom of the 13-desmethyl chromophore is associated with the formation and stability of this P-like state.
https://surface.syr.edu/che_etd/66
oai:surface.syr.edu:che_etd-1065
2010-10-05T18:19:02Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Syntheses and structural survey of novel alkaline earth and rare earth metal complexes
Hitzbleck, Julia
2004-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Karin Ruhlandt-Senge
Alkaline earth
Earth metal
Pyrazolate
Ytterbium
Europium
Chemistry
Physical Sciences and Mathematics
The work delineated here represents a variety of novel synthetic schemes towards alkaline earth metal complexes based on direct synthesis from the metals; namely redox transmetallation, redox transmetallation/ligand exchange, and direct metallation at elevated temperatures. The feasibility of metal based, direct synthesis for Group 2 complexes is strengthened with the results obtained in this work, and shows outstanding synthetic utility in addition to the more widely employed alkane elimination reaction from dibutylmagnesium as well as direct metallation by ammonia activated metals. This work proves the latter scheme not only useful for the heavy Group 2 elements, but also for the rare earth metals ytterbium and europium, a synthetic pathway rarely considered towards divalent lanthanide complexes.
Part one of this work investigates the reactivity of the two groups of metals on the basis of feasibility of synthetic schemes towards pyrazolate complexes (3,5-di- tert -butylpyrazolate, 3,5-di- iso -propylpyrazolate, 3-methyl-5-phenylpyrazolate, 3,5-diphenylpyrazolate). Similarities are dominant, as expected from the high electropositive character of both groups, but differences are seen in the slightly increased reactivity of the alkaline earth metals and the potential formation of trivalent species for the rare earth metals. The resulting complexes from this survey nicely demonstrate structural similarities based on closely related charge/size ratios and highly ionic bonding in the pyrazolate compounds, often showing isostructural behavior for metals of comparable size (Ca 2+ /Yb 2+ ; Sr 2+ /Eu 2+ /Sm 2+ ).
The second part of the thesis explores the proposed intermediate in the redox transmetallation/ligand exchange pathway M(C 6 F 5 ) 2 (M = Ca, Sr, Ba), and the formation of cationic complexes as solvent separated ion pairs of type [M(thf) n ][BPh 4 ] 2 (M = Ca, Sr) and also [Ba(BPh 4 )(thf) 4 ][BPh 4 ]. The metal-based reaction schemes established in the first part of this study are also applied towards the formation of alkaline earth 3,5-di- tert -butylphenolates, revealing the preferential formation of cluster species with less bulky ligand systems.
In summary, the results presented in this work greatly extend the synthetic schemes available towards alkaline earth metal complexes and further the understanding of structural preferences and similarities between alkaline earth and rare earth metal compounds.
https://surface.syr.edu/che_etd/65
oai:surface.syr.edu:che_etd-1067
2010-10-06T13:09:55Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Design, synthesis, and characterization of photochromic organic compounds: Advances toward optical memory
Wolak, Mason Atom
2002-08-23T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Watson J. Lees
Photochromic
Optical memory
Fulgides
Indolylfulgides
Organic Chemistry
The design, synthesis, and characterization of over 20 indolylfulgides and indolylfulgide derivatives are detailed herein. Each compound has been fully evaluated for such properties as optical absorption spectra, photostationary states, quantum yields, and photochemical and thermal stability. The parent trifluoromethyl isopropylidene indolylfulgide can undergo nearly 3000 repeated cycles of coloration and bleaching in solution before 20% loss of absorbance. The methoxy-substituted cyclohexylidene indolylfulgide degrades at only 0.006% per cycle, the strongest photochemical fatigue resistance of any fulgide reported to date.
Other significant findings include the identification of the thermal decomposition pathway for the Z-form of fluorinated indolylfulgides and the production of hydrolytically stable indolylfulgimides. The UV-vis spectral characteristics of the indolylfulgimides can be predictively tuned by incorporating phenyl groups substituted with electron-withdrawing groups of varying strength.
Using the information gathered in the thermal decomposition study, a new class of photochromic organic compounds (aryletheneanhydrides) has been prepared from fluorinated cycloalkylidene indolylfulgides. These compounds maintain outstanding thermal stability with both forms showing little to no loss of absorbance after 3 weeks at 80°C. Furthermore, the methoxy-substituted indolylcyclohexenylanhydride displayed outstanding photochemical stability; no discernable loss of absorbance was observed after 600 photochemical cycles. Finally, the studies have helped to advance the basic understanding of structure activity relationships for photochromic fulgides.
https://surface.syr.edu/che_etd/69
oai:surface.syr.edu:che_etd-1066
2010-10-06T12:42:42Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Database and algorithmic applications in nucleic acid sequence, structure and NMR frequencies, and an efficient chemical depiction
Lin, Yong
2002-08-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Philip N. Borer
Nucleic acid
Sequence analysis
Molecular structure
Chemical shifts
Chemistry
A total of 1760 Human Immunodeficiency Virus type 1 (HIV-1) sequences from GeneBank covering the 5 ' -leader region (388 nucleotides long) have been analyzed. Variation at each position is obtained by parsing the output of the sequence alignment program, BLAST. Comparative sequence analysis has been performed and a total of 2218 covariances and highly favorable variances generated. Potential secondary structures for this region have been discussed. Results from this research should be helpful for studies of viral packaging and other interactions with the 5 ' -leader.
The three-dimensional conformation of a 24-nucleotide variant of the RNA binding sequence for the coat protein of bacteriophage R17 has been analyzed using NMR, molecular dynamics, and energy minimization. The unpaired A8-residue is stacked in the stem, and the entire region from G7-C15 in the upper stem and loop appears to be flexible. Several of these residues have a large fraction of S-puckered ribose rings. There is considerable variation in the low-energy loop conformations that satisfy the distance constraints at this preliminary level of refinement. The Shine-Dalgarno ribosome binding site is exposed and only two apparently weak base pairs would have to break for the 16S ribosomal RNA to bind and the ribosome to initiate translation of the replicase gene.
The distribution of 1 H nuclear magnetic resonance chemical shifts of nucleic acids in double stranded regions has been analyzed from a database consisting of 1395 non-exchangeable proton chemical shifts. A three-term expression to describe proton chemical shift has been proposed using a nearest neighbor approach. Values for those three terms have been determined for both sugar and base (H6 or H8) protons for each residue using singular value decomposition. The general agreement between the observed and calculated chemical shifts indicates that the expression accounts for the main effects on nucleic acid chemical shifts. By using this three-term expression, the chemical shifts of nucleic acids can be predicted for double-stranded sequences within 0.1 ppm.
An algorithm has been developed to depict two-dimensional organic structures ranging from simple chain and ring systems to fused, bridged, and caged ring systems. The algorithm combines algorithmic and template strategies to deal with complicated situations, such as structures with mixtures of chains, fused rings, and caged ring systems. The algorithm is implemented in C language on both UNIX and Microsoft Windows platforms.
https://surface.syr.edu/che_etd/70
oai:surface.syr.edu:che_etd-1068
2010-10-06T15:21:17Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Experimental and theoretical measurements of vibrational circular dichroism and instrumental development of Raman optical activity
Dunmire, David Allen
2002-09-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laurence A. Nafie
Theresa B. Freedman
Vibrational circular dichroism
Raman optical activity
Ketoconazole
Itraconazole
Miconazole
Organic Chemistry
Vibrational optical activity (VOA) spectroscopies are employed to probe molecular structure. Vibrational circular dichroism (VCD) measurements in conjunction with computational modeling are used to determine absolute configurations of three different fungicides. The reported configuration of (+)-ketoconazole is confirmed to be (2 R ,4 S ) and the absolute configuration of (+)-itraconazole assigned to be (2 R ,4 S ) and (+)-miconazole to be ( S ). In addition, VCD measurements and computational modeling provide insight into the mechanism of VCD intensity enhancement for ligand-bound metalloproteins containing open shell metals. VCD measurements identify heme modes being enhanced for azide- and cyanide-bound metmyoglobins with open-shell iron(III) centers. DFT calculations of six heme models using the LanL2DZ and Wachters+f basis sets demonstrate the importance of the chiral environment of the heme in addition to an open shell iron(III) species in the generation of larger anisotropy ratios of ligand stretches and VCD intensity enhanced vibrations below 1500 cm -1 .
The advanced spectroscopies used to obtain spectral data display performance levels of current instrumentation. Data obtained in VCD measurements of the proteins myoglobin, albumin, lysozyme and concanavalin A, show a new level of spectral quality in FT-VCD measurements. The VCD spectra obtained display a high signal-to-noise ratio and can be used to identify protein structure at a quantitative level. Raman optical activity (ROA) measurements demonstrate the limitations of current instrumentation in the acquisition of spectra of the proteins albumin and lysozyme. Spectra obtained demonstrate the problem of fluorescence in current DCP I ROA measurements.
https://surface.syr.edu/che_etd/68
oai:surface.syr.edu:che_etd-1069
2010-10-07T19:03:43Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
A study of the role of polyhedral borane compounds in solid state materials, nanotechnology and main group cluster substitution chemistry
Caruso, John David, III
2003-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James T. Spencer
Carborane
Borane
Nanotechnology
Cluster substitution
Polyhedral
Chemistry
Physical Sciences and Mathematics
The work described here consists of the synthesis and characterization of new materials utilizing polyhedral borane cluster compound as starting materials, including solid state titanium diborides, molecular nanosystems, and polyhedral boron cage substitution compounds.
The first chapter of this work describes attempts to prepare titanium diboride through the use of aerosol techniques. The reaction involved titanium(IV) chloride and decaborane in organic solvents at elevated temperatures and atmospheric pressure, producing the first known spherical particles containing both titanium and boron in the final material. Scanning electron microscopy (SEM), energy dispersive X-ray (EDAX) and powder X-ray diffraction data are reported here for these experiments.
The synthesis and complete characterization of new molecular nanosystems are reported in the second chapter of this work. In particular, the failed attempts at coupling ortho -carborane cages at the 9- or the 12-positons of the cage framework are presented. Progress on the molecular building block compound was made by switching from the 1,1 ' -bis( ortho -carborane) system to the modified system of 2,3-benzo-4,5- ortho -carborane-1-one. This modification gives all of the desired structural properties of the original molecular building block, with a much simpler synthesis to achieve the overall target molecule. The synthesis of 2,3-benzo-4,5- ortho -carborane-1-one ( 2.2 ) from 2-phenyl-1,2-dicarba- closo -dodecaborane-1-carboxylic acid by an intramolecular Friedel-Crafts reaction is reported. Complete spectroscopic analysis and a single crystal X-ray study is reported for these compounds.
The third chapter of this work focuses on the synthesis and characterization of methyltriphenylphosphonium 5-iodo-7,8-dicarba- nido -undecaborate ( 3.1 ), with a focus on the bridging proton in a C-H-C position on the open face of the 5-iodo-7,8-dicarba- nido -undecaborate anion. The complete spectroscopic characterization and the X-ray crystal structure of compound 3.1 are reported here.
https://surface.syr.edu/che_etd/67
oai:surface.syr.edu:che_etd-1070
2010-10-11T13:29:11Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Ligand influences on the structures of organically-templated mixed-metal molybdenum and vanadium oxides prepared via hydrothermal synthesis
Rarig, Randy S., Jr.
2002-12-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon A. Zubieta
Ligand
Organically-templated
Mixed-metal
Vanadium oxides
Molybdenum oxides
Chemistry
The use of a structure directing organic ligand on mixed metal molybdenum and vanadium oxides has led to a series of new and interesting materials with varying properties. By directing the formation of the mixed metal oxide sub-structure with the size, shape, and flexibility of the organic ligand new organic/inorganic hybrid materials exhibiting an unusual structural diversity may be synthesized with a variety of new and interesting properties. By utilizing chelating bidentate, chelating tridentate, bis-chelating tridentate, tethering, and tridentate ligands a variety of novel organic/inorganic mixed metal molybdenum and vanadium oxide materials showing the influence of the organic ligand on the inorganic oxide sub-structure have been synthetically created and characterized. Hydrothermal synthesis is a simple synthetic pathway that leads to the formation of single crystal products allowing for characterization via single crystal x-ray diffraction. The use of the hydrothermal medium overcomes the differential solubility problems associated with many organic and inorganic starting materials. The following research endeavor contains a variety of examples of the family M ' /Mo/O/Ligand and M ' /V/O/Ligand utilizing the various ligand formations stated above. This poses as merely a start at the seemingly endless chemistry available in the realm of hydrothermal synthesis.
https://surface.syr.edu/che_etd/75
oai:surface.syr.edu:che_etd-1071
2010-10-11T17:50:13Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Not just Grignards: New developments in the organometallic chemistry of the heavy alkali and alkaline earth metals
Alexander, Jacob S.
2003-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Karin Ruhlandt-Senge
Grignard reagents
Organometallic
Earth metals
Potassium
Rubidium
Cesium
Chemistry
Physical Sciences and Mathematics
Despite considerable efforts being given to organometallic complexes of lithium and magnesium (Grignard reagents), the amount of information available for the heavier alkali congeners potassium, rubidium and cesium and the alkaline earth metals calcium, strontium and barium are much more poorly understood. Even as the heavy organoalkali organometallics have become a standard in synthesis as a result of "superbase" chemistry, understanding of bonding and solid-state structure and behavior of these compounds remains murky.
Similarly, the chemistry of the alkaline earth metals, particularly σ-bonded organometallic species, remains poorly developed, and structural information on such compounds was nonexistent until very recently. Especially considering the surprising tendency for heavy alkaline earth metal compounds to display unexpected geometries that defy standard VSEPR models, it is critical to create as large a library as possible for these compounds to assist in further investigations.
In this work, an array of contact and charge separated heavy alkali and alkaline earth organometallics are presented. In addition, two powerful new synthetic routes--hydrocarbon elimination and desilylation--are made available as new entries into these compounds. Synthetic aspects and structural details are discussed and theoretical studies are conducted in an attempt to elucidate some of the interesting questions encountered in this field.
https://surface.syr.edu/che_etd/74
oai:surface.syr.edu:che_etd-1073
2010-10-11T19:05:36Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Studies directed towards syntheses of multivalent carbohydrates suitable for binding to E. coli Shiga-like toxin
Kim-Beca, Jennifer Ji Young
2003-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Watson J. Lees
Shiga toxins
Trisaccharides
Cyclodextrin
Carbohydrates
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
In order to investigate multivalent binding enhancement between carbohydrate molecules and Shiga-like toxins, two different synthetic approaches were performed: (1) synthesis of polymerizable C-1 modified P k trisaccharide and (2) synthesis of trisaccharide-branched α-cyclodextrin.
A polymerizable C-1 modified P k trisaccharide derivative 88 was synthesized through ten steps from lactose with 3.5% overall yield. The synthetic route included three coupling reactions: α-glycosidic coupling of lactose unit 18 and galactose unit 20 , β-glycosidic coupling of trisaccharide trichloroacetimidate 28 and methyl ester linker 72 , and amide bond formation between the carboxylic end of trisaccharide 90 and the amine linker 89 . As a continuation of the research, the compound 88 will be copolymerized with acrylamide in varying ratios to form linear polymers to be subjected for assay.
Trisaccharide-branched α-cyclodextrin 111 was synthesized by coupling trisaccharide 90 to α-cyclodextrin via a spacer arm. Incorporation of a spacer arm to α-cyclodextrin included perbromination of the primary hydroxyl groups on α-cyclodextrin followed by a substitution reaction with a thiol linker 107 with 14.6% yield. The coupling of trisaccharide 90 to spacer-arm linked α-cyclodextrin yielded the desired hexakis-substituted product 110 along with less substituted products. The collected yield of the desired product was 33%, however, we were not able to fully characterize this compound 110 or the hydrolyzed product 111 due to the limited amount available. Our synthesis of persubstituted trisaccharide-branched α-cyclodextrin was one of the first attempts to synthesize persubstituted α-cyclodextrin with relatively large molecules. These compounds will be submitted for binding assays.
https://surface.syr.edu/che_etd/72
oai:surface.syr.edu:che_etd-1072
2010-10-11T18:48:57Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Short strong hydrogen bonds studied by inelastic neutron scattering and computational methods
Jenkins, Timothy Andrew
2003-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Bruce S. Hudson
Hydrogen bonds
Neutron scattering
Bond energies
Potassium hydrogen bistrifluoroacetate
Chemistry
Physical Sciences and Mathematics
Hydrogen bonding can be simply defined as any interaction between molecules that involve the participation of hydrogen, or stated in another fashion: "a hydrogen bond exists when a hydrogen atom H is bonded to more than one other atom". Within this simple definition is a diverse range of interactions that is difficult to explain utilizing conventional ionic and covalent bonding. Hydrogen bonds that exhibit large bond energies are termed short, strong hydrogen bonds and possess unique potential surfaces. These potential surfaces are termed low barrier because the energy barrier that separates the potential wells is lower or equal to the zero point level. Little or no energy is required to move the hydrogen from one well to the other. This potential surface requires special attention in calculating quantum mechanical solutions for these systems due to the quartic shape of these short-strong hydrogen bond potential surfaces.
In this thesis I have examined several short, strong hydrogen bonded systems using inelastic neutron scattering and have calculated the corresponding neutron vibrational spectra. I have also made a detailed investigation into the potential surface of the strong hydrogen bond in potassium hydrogen bistrifluoroacetate. Results have shown that it is possible to calculate accurate structural coordinates and vibrational spectra that agree with the experimental. The calculations give an incorrect energy minimization resulting in incorrect vibrational band placement in the inelastic neutron spectrum from the use of a harmonic fit of an anharmonic potential surface. The anharmonic potential surface resultant from the barrier between double wells positioned below the zero point level is calculated for the hydrogen bond. This can be correctly modeled by calculating the potential surface using a fixed OO distance, and solving the Schrödinger equation along this potential. This is the first comparison of neutron vibrational spectra and calculated spectra to provide an understanding of the limitations of computational methods to examine strong hydrogen bonds. This is a new and powerful tool to accurately examine the strength and structure of strong hydrogen bonds.
https://surface.syr.edu/che_etd/73
oai:surface.syr.edu:che_etd-1074
2010-10-11T19:32:15Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The characterization of two materials for permanent optical memories: Bacteriorhodopsin with its 9-cis retinal containing photoproducts, and fluorinated indolylfulgides with their derivatives
Gillespie, Nathan Bryce
2003-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Robert R. Birge
Memories
Bacteriorhodopsin
Retinal
Photoproducts
Fluorinated
Indolylfulgides
Chemistry
Materials Chemistry
Physical Chemistry
Physical Sciences and Mathematics
The results of studies characterizing the properties and behavior of two photochemically active materials--the protein, bacteriorhodopsin (BR), and fluorinated indolylfulgides (FIFs), along with some of the variants of both--are analyzed and discussed in the frame of the usefulness of these materials in permanent optical memories. Specifically, the two most suitable forms of each system for this purpose and the nature of their photochemical interconversion were studied. For BR, the resting state and its 9- cis retinal containing products are the focus, while cyclizable (Z) and closed (C) forms are targeted for the fluorinated indolylfulgides. In this chapter, the background for each material system is described, followed by a description of their possible implementations in permanent volumetric and holographic optical memories. Each of four chapters in this dissertation following the introduction will be presented in manuscript form--two on bacteriorhodopsin, one on the fulgides, and one that covers a holographic performance analysis of both. Conclusions and recommendations for future work are made at the end of each chapter. They indicate that the work on these materials is very close to generating viable commercial possibilities, and thus in the process of crossing over from pure science into engineering.
https://surface.syr.edu/che_etd/71
oai:surface.syr.edu:che_etd-1075
2010-10-12T13:11:19Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Noninvasive in vivo tissue modulated quantitative Raman spectroscopy of human blood
Finney, William Francis
2002-08-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Joseph Chaiken
Noninvasive
Blood
Glucose monitoring
Medical Biochemistry
We report the first noninvasive in vivo Raman spectrum of human blood. This was accomplished using near infrared Raman and fluorescence spectroscopy and our novel concept of tissue modulation. Tissue modulation is the use of spatiotemporally localized mechanical, thermal, chemical and/or other external influences to manipulate the mobile components of tissue relative to the static components. Tissue modulation allows the use of difference spectroscopy to isolate the spectra of mobile and static tissues. The raw, tissue modulated, noninvasive in vivo Raman spectrum of blood consists of a broad fluorescence component and narrower Raman features. This broad fluorescence component is mainly attributable to hemoglobin and its intensity is proportional to the sampled blood volume. The integral of the fluorescence intensity can be used to normalize the Raman spectrum to the sampled blood volume. The areas of such normalized Raman features are proportional to concentration. The noninvasive Raman spectrum of capillary blood measured in a fingertip is consistent with in vitro spectra. Independent observations supporting the assignment of the spectroscopic signals to blood are needed due to the similar composition and therefore spectra of blood and the surrounding tissues. These independent observations include vasoconstriction and cold induced vasodilatation observed through changes in the fluorescence intensity of fingertips. The optical transmission characteristics of fingertips also change in a manner that is constant with the flow of blood upon tissue modulation. The ability to track the concentration of a blood analyte noninvasively using tissue modulated noninvasive in vivo Raman spectroscopy is of itself further independent proof that the observed spectroscopic signals are attributable to blood. Proof-of-principle clinical studies demonstrating the ability to track blood glucose concentrations noninvasively and in vivo were conducted with the Joslin Diabetes Center at Upstate Medical University in Syracuse, NY.
https://surface.syr.edu/che_etd/81
oai:surface.syr.edu:che_etd-1076
2010-10-12T16:57:18Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The synthesis and structure of novel carborane based and related nonlinear optical materials
Newlon, Amy E.
2003-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James T. Spencer
Carborane
Nonlinear optics
Hydrindacene
Iodoethynylferrocene
Chemistry
Physical Sciences and Mathematics
This work describes the synthesis and characterization of new and unique precursor compounds to nonlinear optical molecular species. Chapter 1 provides a brief introduction to nonlinear optics and also presents some calculations to demonstrate how carborane molecules substituted with charged donor and acceptor species would have exceptionally high β values.
Chapter 2 details the syntheses of various cycloheptatriene- and/or cyclopentadiene-substituted meta -carborane cage compounds. Described is the synthesis and structure of closo -1,7-[1-(1-C 7 H 6 )-7-(2,5-(CH 3 ) 2 -3,4-(C 6 H 5 ) 2 CSH)C 2 B 10 H 10 ] 2 [SnCl 6 ], 32a , as confirmed by spectroscopy and X-ray crystallography. The solid state crystal structure of [(C 6 H 5 ) 3 C][SnCl 5 ]·CH 3 CN, 34 , was also determined and is presented as a comparison to help understand the crystal structure of compound 32a .
Reactions to stabilize the C 5 and C 7 rings attached to the carborane cage by the complexation of metal fragments are described in Chapter 3. The reaction of iodoethynylferrocene with a deprotonated carborane cage, [C 2 B 10 H 11 ] - , produced the compound closo -1,7-[7-(C≡C-{(η 5 -C 5 H 4 )-Fe-(η 5 -C 5 H 5 )})C 2 B 10 H 11 ], 42 . The complete spectroscopic characterization and the X-ray crystal structure are reported for this compound.
The syntheses of nonlinear optical molecular derivatives of the organic compound 1,1,3,3,5,5,7,7-octamethylhydrindacene, 48 , are described in Chapter 4. These reactions involved the bromination of 48 and then the subsequent reaction to attach either the cycloheptatriene or cyclopentadiene rings to the hydrindacene framework.
Chapter 5 provides a brief summary of the work presented here and offers additional detailed explanations concerning some of the reactions described in the previous chapters. Suggestions for potential directions of future work, based on the reactions described here, are offered.
https://surface.syr.edu/che_etd/80
oai:surface.syr.edu:che_etd-1077
2010-10-12T17:02:13Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The Z-selective [2,3] Wittig rearrangement of secondary allylic alpha-stannyl ethers, chiral alpha-alkoxy stannanes, and progress toward the enantiospecific total synthesis of (+)-mycotrieninol I
Giamis, Anthony Martin
2003-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James Kallmerten
Z-selective
Wittig rearrangement
Stannyl ethers-alpha
Alkoxy stannanes-alpha
Mycotrienins
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
A study of the stereochemical consequences of the Still [2,3]-Wittig rearrangement of various related secondary α-lithio ether ethers is the focus of this dissertation. Unique to our work was the observation that trans -disubstituted olefins with a syn -α-alkoxy allylic relationship may rearrange producing cis -homoallylic alcohol products. The ability to prepare compounds stereospecifically with Z-olefins may provide an entry into the total synthesis of several natural products such as the immunosuppressive agent (+)-discodermolide and the tumor cell migration inhibitor (+)-migrastatin.
The basis for our Z-olefin stereocontrol is a reactive conformation that invokes a six-membered chelation between the α-alkoxy group and the lithium cation prior to the [2,3] Wittig rearrangement. This relationship, however, required a transition state model where the stereochemistry at the migrating carbon was maintained contrary to literature precedent. Chiral α-stannyl ethers were prepared in order to observe this stereochemical transfer and to determine whether the Still [2,3] Wittig rearrangement proceeds with retention or inversion of stereochemistry.
A highly convergent asymmetric synthetic approach toward the synthesis of (+)-mycotrienol 1, the core 21-member macrolactam of this family, will also be discussed. Members from the mycotrienin family of novel ansamycin antibiotics were first isolated in 1985 from a culture broth of Streptomyces sp. No. 83-16.
The construction of two key synthons, the C 8 -N 21 aromatic core and the C 1 -C 7 triene precursor will be described. The synthesis of the C 8 -N 21 fragment will explore allenyl and propargyl metal addition to aldehydes in order to prepare a suitable homoallylic alcohol for further functionalization in preparation for a Stille coupling. The planned Stille coupling would complete the carbon framework of the mycotrienol I core. Although calcium-based dissolving metal reduction allowed the cleavage of the C 17 benzyl ether bond in the presence of a terminal acetylene, we found that it was more efficient to introduce the acetylene functionality after the C 17 bond had been cleaved. The C 1 -C 7 synthon, derived from (+)-malic acid, was transformed into a useful ( E,E )-iodo diene in anticipation of the Stille coupling.
https://surface.syr.edu/che_etd/79
oai:surface.syr.edu:che_etd-1078
2010-10-12T18:02:48Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Aminoglycoside binding to the packaging region of HIV-1 RNA
McPike, Mark Patrick
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James C. Dabrowiak
Aminoglycoside
Packaging region
HIV-1
RNA
Immune deficiency
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Chemistry
Life Sciences
The ψ region of HIV-1 spans ∼200 nucleotides (nt) near the 5 ' end of the RNA genome. This region has been shown to play a significant role in encapsidation and transciptional regulation of the viral RNA. As a result, the ψ region has the potential to be a target for drugs. In this study, a 176 nt model (LAI strain) of the ψ region, representing positions 213-388, was investigated with natural aminoglycosides (paromomycin and neomycin) and modified analogues of neomycin (neo-neo, neo-acridine and neo-guanidinium) using footprinting and Circular dichroism (CD) techniques. Footprinting analysis was conducted using the ribonuclease RNase I under optimized "single-hit" kinetic cutting conditions. Intensity data obtained from autogradiograms was used to generate a collection of footprinting plots for each drug. Analysis of the footprinting plots revealed a primary binding site at SL1 for paromomycin and neomycin, with a binding constant of 4.5 × 10 5 M -1 (at 25°C, in 10 mM Tris-HCl, pH 7.5) for neomycin. Analysis of the footprinting plots for neo-acridine and neo-guanidinium also indicated a primary binding site on SL1 having binding constants of 3.4 × 10 5 M -1 and 2.2 × 10 5 M -1 for each drug respectively. Both neo-acridine and neo-guanidinium also interacted with sites on SL2 and SL4. Neo-neo footprinting analysis indicated a single primary binding site on SL2, possibly formed by an intermolecular binding pocket, with a binding constant of 2.5 × 10 5 M -1 . At non-binding sites, each drug produced footprinting plots having an increase in intensity at high drug concentrations. Such effects are a result of structural changes, predominately found in the linker regions of the RNA. Using circular dichroism, the global effects of drug-induced structural change of the 176-mer RNA was measured for each drug. Analysis of plots of CD versus drug concentration revealed an increase in intensity for neomycin, paromomycin and neo-guanidinium at 208 nm and a slight red shift with no intensity change at the same wavelength for neo-neo and neo-acridine. In the drug concentration range of 11 to 20 μM, a decrease in the intensity of the 266 nm band was observed for all the drugs except paromomycin. The intensity changes observed for the 208 nm band are associated with the structural changes in the linker region. By plotting the change in extinction coefficient against drug concentration, CD derived binding constants were calculated for each drug. Results indicated that several binding sites were responsible for the structural changes measured in the CD analysis. This study demonstrates how footprinting and CD methods can be used to identify drug binding sites and drug-induced structural changes associated with drug binding to a large RNA target.
https://surface.syr.edu/che_etd/78
oai:surface.syr.edu:che_etd-1079
2010-10-12T19:04:14Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Computational studies of wavelength selection in cone pigments and cation binding in bacteriorhodopsin
Singh, Deepak
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Robert R. Birge
Wavelength selection
Cone pigments
Cation binding
Bacteriorhodopsin
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Biophysics
Chemistry
Life Sciences
Physical Sciences and Mathematics
Retinal proteins are integral membrane proteins, which bind a co-factor, retinal, via a conserved covalent linkage. Retinal is light-sensitive and can harness light energy, which is used by the protein to perform a variety of physiological functions. Color vision is a direct consequence of the ability of the protein environment to alter the electronic properties of retinal. The violet absorbing pigment from Xenopus laevis (VCOP) has been the subject of much recent experimental characterization. We have developed semi-automated procedures to build three-dimensional models for VCOP and other cone opsins. These models have been used to interpret data from mutagenesis experiments. The chromophore conformation of rhodopsin has also been studied on the basis of recent NMR studies. A minimum energy structure for retinal in rhodopsin adopts a conformation that satisfies NMR data but disagrees with previously published models. MNDO-PSDCI molecular orbital calculations provide strong evidence for the involvement of an arginine residue (R82) as a principle counterion in the bacterial protein, bacteriorhodopsin. A role for R82 in the binding site precludes calcium binding in that region. This led to the study of several crystal structure of bacteriorhodopsin using empirical ion-mapping techniques to identify probable cation binding sites. Molecular dynamics simulations on several promising sites, in conjunction with FTIR studies strongly suggest an interaction between the proton release group and the color-controlling cation binding site.
https://surface.syr.edu/che_etd/77
oai:surface.syr.edu:che_etd-1080
2010-10-12T19:14:30Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Coordination chemistry of rhenium: Design of radiopharmaceuticals for diagnostics and therapeutics in nuclear medicine
Femia, Frank Joseph
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon A. Zubieta
Rhenium
Radiopharmaceuticals
Diagnostics
Therapeutics
Nuclear medicine
Chemistry
Life Sciences
Pharmacology
Pharmacology, Toxicology and Environmental Health
Physical Sciences and Mathematics
A number of rhenium compounds were synthesized and characterized in an attempt to investigate and expand the coordination chemistry of the widely used medicinal imaging radioisotope technetium-99m. Technetium and rhenium are Group VII cogeners with similar hydrazine and oxo-thiolate chemistries. These periodic similarities have allowed for the study of the non-radioactive metal rhenium instead of the synthetically created technetium, which only exists as radioactive isotopes.
In Chapters 1-4 and 6 we address the "3+1" concept of ligand addition to a Group VII metal-oxo species using tridentate ligands carrying the SSS, SOS, ONS, SN(R)S donor atom set (R = various alkyl or aryl substituted pendant groups) and a monodentate thiol. However. Chapter 5 reveals that in the absence of thiolate donors, the {ReO} 3+ core may expand its coordination sphere to accommodate five additional donor groups, an observation suggesting that "3+2" complexes will provide an alternate strategy for the systematic synthesis of materials exploiting the modification of the tridentate and bidentate ligands.
Chapter 7 explores hydrazines as potential tethers, forming two classes of compounds, namely [MCl 3 (η 1 -NNC 5 H 4 NH)(η 2 -HNNC 5 H 4 N)] and [MCl 3 (η 1 -NNC 4 H 3 N 2 H)(η 2 -HNNC 4 H 3 N 2 )] (M = Re or Mo). The study continued with the exploration of the chlorine substitution with potentially useful thiol and alcohol coligands.
Finally. Chapter 8 uses the "3+1" approach in designing long-chain fatty acids for imaging blood perfusion to the heart muscle (myocardium).
https://surface.syr.edu/che_etd/76
oai:surface.syr.edu:che_etd-1081
2010-10-13T14:00:33Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Studies towards the total synthesis of rapamycin
Wang, Tong
2002-06-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James Kallmerten
Rapamycin
Wittig rearrangement-[2
3]
Organic Chemistry
This dissertation describes a stereoselective synthesis of two major fragments of rapamycin. Isolated from Easter Island soil sample in 1975, rapamycin was found to be a potent immunosuppressent and is currently in the phase III of clinical trials as an immunosuppressive therapy.
Previous synthetic efforts including the four total syntheses and degradation studies of rapamycin are presented first.
Considerable effort has focused on the construction of the C1-C21 and C22-C42 sub-units of rapamycin. The synthetic approach to the C1-C21 fragment begins with D -glucose. A [2,3]-Wittig rearrangement of the sugar derivative installs the C11 methyl-bearing center. Subsequent Emmons-Homer olefination introduces the tri-substituted C17-C18. Finally, an aldol addition followed by a Dess-Martin oxidation provides the whole fragment. The C24-C42 fragment of rapamycin is rapidly assembled by serial [2,3]-Wittig and [3,3]-Claisen rearrangements of carbohydrate-derived allylic ethers. An iodolactonization is employed to establish the stereochemistry at C34. Different protecting groups of C28 alcohol are examined. In an alternative synthesis of the C22-C42 fragment, the C23 methyl-bearing center is successfully introduced via an Evans alkylation. Possible routes to the completion of the fragment are also proposed.
https://surface.syr.edu/che_etd/82
oai:surface.syr.edu:che_etd-1082
2010-10-18T18:45:32Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Isotopomers of 2-deoxy-D-ribose: Syntheses and applications in magnetic resonance
Hatala, Paul Joseph
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Philip Borer
Magnetic resonance
Deoxyribonolactones-2
Nucleosides
Regioselective
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
This work demonstrates the chemical synthesis of isotopically labeled 2-deoxyribonolactones--crucial intermediates in the production of isotopically enriched DNA or RNA oligonucleotides. Low-cost, commercially available, one or two-carbon precursors provide carbon-13 labels. Hydrogen isotope labels arise from commercially available materials as well. Previous work from our laboratories has been expanded and improved. The synthetic scheme has been developed to provide increased yields, enantiomerically pure material, different labeling patterns, and conversion to labeled D-ribose.
This work provides the fundamental transformations for creating DNA and RNA oligonucleotides with any combination of carbon ( 14 C, 13 C, and 13 C-depleted 12 C) and hydrogen ( 3 H, 2 H, 1 H) isotopomers. Hundreds of different carbon and hydrogen isotopic combinations are possible for D-ribose, and 2-deoxyribose. Many of these compounds are not available by any other method. Although synthesis utilizing long-lived radioisotopes was not conducted, use of 14 C and 3 H is a trivial expansion of this fundamental work.
A "population labeling" scheme has been devised, where mixing of equimolar amounts of the five 13 C 1 -2-deoxyribonolactones provides a 20-fold increase over natural abundance. A 50-fold increase over natural abundance would be obtained by combination of the 1,3,5- 13 C 3 - and 2,4- 13 C 2 -lactones. Since 13 C- 13 C adjacencies occur only by natural abundance, the population labeling scheme is optimal for NMR relaxation studies of internal motion.
Specific 2 H-labeling is demonstrated by the synthesis of 4- 2 H-2-deoxy-D-ribose. The C4 ' position is the primary site for free-radical attack from ionizing radiation and some DNA cleavage agents.
Other topics are included. Previous synthetic methodology for the incorporation of carbon-13 and deuterium are presented and compared with the methods presented here. Two complete manuscripts are included. Continuing work towards the octalactins is also presented.
https://surface.syr.edu/che_etd/91
oai:surface.syr.edu:che_etd-1083
2010-10-18T19:25:10Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Organic structural influences on metal oxide systems: Vanadium phosphates, vanadium phosphonates, and molybdenum phosphonates
Finn, Robert Clyde
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon Zubieta
Metal oxide
Phosphates
Vanadium phosphonates
Molybdenum phosphonates
Inorganic oxides
Chemistry
Physical Sciences and Mathematics
Rational design synthesis in inorganic/organic hybrid materials has thus far proven elusive. While hydrothermal techniques afford easily characterized single crystalline products, the multitude of reaction variables as well as the inability to view the reaction at maximum temperature, offers little information to mechanistic understanding. With so many variables, attempts to map the entire reaction parameter surface would only be possible combinatorially. As seen in section 2.3 subtle changes in reaction conditions can lead to vastly different structures.
Considering the vastness of the oxide regime, it is important to focus on a few related reaction systems, in this case, vanadium phosphates, vanadium phosphonates, and molybdenum phosphonates. By utilizing subtle changes in starting materials I was able to synthesize numerous compounds with similar building blocks. Perhaps the best example of a recurring building block is seen in section 4 with the Mo 5 O 15 cluster appearing in four separate structures.
All compounds were synthesized hydrothermally and characterized by single-crystal x-ray diffraction. The structures discussed within range from the rather simplistic one-dimensional chain [Zn(bpy)VO 2 PO 4 ] to the much more complex three-dimensional [{Cu(phen)} 2 (V 3 O 5 )(O 3 PCH 2 PO 3 ) 2 (H 2 O)]. Singularly, each structure merely represents a novel compound, together they start to reveal knowledge about the structural preferences, resilient building blocks, and coordination tendencies that are imperative if one expects to someday gain mechanistic control over this regime.
https://surface.syr.edu/che_etd/90
oai:surface.syr.edu:che_etd-1085
2010-10-18T20:14:45Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Structure and function in bacteriorhodopsin and the short-wavelength cone opsins
Kusnetzow, Anakarin
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
John Baldwin
Bacteriorhodopsin
Cone opsins
Rhodopsin
Pigments
Chemistry
Physical Sciences and Mathematics
The nature of the chromophore-binding site of bacteriorhodopsin (bR) has been analyzed by using MNDO-PSDCI molecular orbital theory, and the nature of the calcium binding sites have been studied using difference vibrational spectroscopy coupled with site-directed mutagenesis (FTIR-SDM). In the absence of divalent metal cations in close interaction with Asp-85 and Asp-212, a positively charged amino acid must be present in the same vicinity to stabilize the chromophore binding site. The FTIR-SDM results demonstrate that that cations do not bind near the chromophore. Theoretical models in which Arg-82 is pointed upwards into the chromophore-binding site, and directly stabilizes Asp-85 and Asp-212, successfully rationalize the observed one-photon and two-photon properties of bacteriorhodopsin. The vibrational structure of cation-regenerated bR and two mutants, Glu-194-Gln and Glu-204-Gln, were analyzed and the results implicate the involvement of Glu-194 and Glu-204 as probable cation-binding sites.
The Xenopus violet cone opsin is a member of the short-wavelength cone opsins, and absorbs maximally at 425 nm. The photobleaching pathway of the violet cone opsin purified in delipidated form has been determined. The formation of the intermediates was observed via cryogenic electronic spectroscopy. The protonation state of the chromophore of the short-wavelength cones has been a subject of debate. Vibrational spectroscopy of the violet cone opsin indicates that the chromophore is protonated in the dark. Furthermore, theoretical analysis of the vibrational modes of the protonated and unprotonated 11-cis-retinal support the experimental results obtained and the assignment of a protonated Schiff base linkage in the dark.
https://surface.syr.edu/che_etd/88
oai:surface.syr.edu:che_etd-1089
2010-10-18T20:47:31Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The photocoloration of transition metal oxides
Nash, Fazio Demeatre'
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Joseph Chaiken
Photocoloration
Transition metal oxides
Optical memory
Electrochromic
Chemistry
Physical Sciences and Mathematics
We have introduced a novel hypothesis for describing the reversible photocoloration of WO 3 using sub-bandgap light. Unlike earlier explanations of the well known electrochromism and super-bandgap photochromism, this hypothesis involves a mechanism which is independent of water, i.e. protons, or other cations. Our results demonstrate an independent mechanism in which oxygen exchange between the sample and the ambient atmosphere during the reversible photocoloration process plays the dominant role. Raman, Diffuse Reflectance IR spectroscopies, and electron scattering for chemical analysis (ESCA) were used to characterize our tungsten-oxygen system. We have also identified a set of fundamental parameters and their quantitative relationships. The results of this study are adequately accounted for using our proposed hypothesis.
https://surface.syr.edu/che_etd/84
oai:surface.syr.edu:che_etd-1087
2010-10-18T20:23:49Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Synthesis and thermal automerizations of 4- and 6-exo-deuteriobicyclo[3.1.0]hex-2-enes
Keliher, Edmund John
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
John E. Baldwin
Thermal automerizations
Exo-deuteriobicyclo[3.1.0]hex-2-enes
Vinylcyclopropane
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
Samples of racemic 4- exo -deuteriobicyclo[3.1.0]hex-2-ene (4 x - 1 ) and racemic 6- exo -deuteriobicyclo[3.1.0]hex-2-ene (6 x - 1 ) were synthesized with high incorporation and stereoselectivity of deuterium label. Mole percent concentrations as functions of time profiles for the four isomers were secured from the thermolysis of 4 x - 1 at 224.9, 240.1, and 255.0°C. From this data rate constants for the three isomerization paths ( k r , k i , and k 1,5 ) at the three temperatures were calculated. Relative participation of the three reaction paths was determined; the k r :k i :k 1,5 proportions were 48:11:36. The calculated activation parameters for k r , k i , and k 1,5 were Ea 43.8, 44.8, 44.3 kcal/mole and log A 14.1, 14.1, 14.2, respectively.
Thermolysis of 6 x - 1 at 224.9, 240.1, and 255.0°C provided mole percent concentration as functions of time profiles that were compared with the profiles obtained with 4 x - 1 . This comparison demonstrates that one-centered epimerization, k 6e , plays no kinetically important role at the temperatures and time domains studied.
https://surface.syr.edu/che_etd/86
oai:surface.syr.edu:che_etd-1084
2010-10-18T20:09:45Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Solution conformations of tripeptides and cyclosporins using vibrational circular dichroism and computational methods
Bodack, Louise Ann
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laurie A. Nafie
Solution conformations
Tripeptides
Cyclosporins
Vibrational circular dichroism
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Chemistry
Life Sciences
Pharmacology
Pharmacology, Toxicology and Environmental Health
Physical Sciences and Mathematics
Vibrational circular dichroism (VCD) spectroscopy was used to investigate the solution conformations of a series of protected tripeptides, Z-Ala-Phe-Val-OMe and Z-Ala-Leu-Val-OMe, of DLL, LDL, and LLL configurations, in CCl 4 solutions, at temperatures of 25°C, 5°C, and -5°C in the amide I region, and 25°C and -5°C in the NH-stretching region. Additionally, VCD was used to investigate solution conformations of (1) cyclosporins A, C, D, G, and H in CDCl 3 , in the amide I and NH/OH-stretching regions, and (2) their corresponding magnesium complexes in CD 3 CN, in the amide I region. VCD spectra are sensitive to the chiral arrangement of C=O and NH bonds in intramolecularly hydrogen-bonded conformations. Calculations of geometries and IR and VCD intensities of model cyclosporin fragments, as well as model tripeptides, were carried out at the Hartree-Fock (HF, 6-31G* basis set) and density functional theory (DFT, BPW91 functional/6-31G* basis set) levels. Calculations were also carried out on model dipeptides, only at the HF level.
Solution spectra for the tripeptides indicate that there are multiple conformers present in solution. The LDL tripeptides appear to have only one dominant conformer present as evidenced by similarity in IR and VCD spectra at all temperatures studied. Calculations support that there is only one low energy conformer, a trans C 7 -C 7 ring cis ester orientation. Computational studies on the DLL tripeptides are in agreement with observed data that more than one conformer is present. For the DLL tripeptides, two low energy conformers are present in solution, trans C 7 -C 7 ring cis ester and trans C 5 -C 5 ring cis ester. The VCD spectra provide evidence that the LLL tripeptides aggregate in solution. The appearance of an intense negative low frequency VCD feature in the amide I and NH-stretching regions is indicative of a β-sheet structure. Observed data is reproduced in the DFT calculation for dimer and trimer aggregates. The low energy conformer of the LLL tripeptide is the extended structure, trans C 5 -C 5 ring cis ester, which can undergo self-association.
For the cyclosporins, the good agreement between IR and VCD spectra from experiment and DFT calculation provides evidence that the crystal conformation of cyclosporin A is dominant in CDCl3 solution. Spectra from the NH/OH-stretching region of the free cyclosporins indicate that conformers with both free and hydrogen-bonded NH and OH groups are present in solution. The IR and VCD spectra for the magnesium-complexed cyclosporins are indicative of strong interactions between cyclosporin and magnesium cation.
https://surface.syr.edu/che_etd/89
oai:surface.syr.edu:che_etd-1088
2010-10-18T20:31:52Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The determination of ultra trace levels of mercury in environmental samples in the northeastern United States: Inferring the past, present, and future of atmospheric mercury deposition
Lorey, Peter Michael, Jr.
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Charles Driscoll
Trace levels
Mercury
Environmental samples
Atmospheric mercury deposition
New York
Analytical Chemistry
Chemistry
Environmental Sciences
Physical Sciences and Mathematics
The interest in mercury (Hg) contamination lies primarily in the fact that fish containing high levels of Hg are a part of the human diet. However, the reactions and pathways of Hg before it is assimilated into fish tissue are complex, and in some cases still not well understood. Although Hg is naturally occurring, the concentrations that are measured today, from historical records such as sediment cores and ice cores, are higher than those in preindustrial times. This leads to the conclusion that anthropogenic activities have caused these increases, even in remote areas.
In this study the concentrations of total mercury (Hg T ) were measured in sediment cores from eight lakes in the Adirondack region of New York. Using the results, historical profiles were created for each lake showing the change in flux of Hg T to the sediments over the past 200 years. An increase of 3.5 times above preindustrial values was found, but there has been an evident decline in recent years. The watershed of the lakes was important in the accumulation of Hg in lake sediments.
Another portion of this study involved the analysis of Hg concentrations in water and sediment from 94 lakes in Vermont and New Hampshire. Relationships were developed with physical and chemical data from the lakes in order to elucidate some of the factors that influence the Hg concentrations in lakes in this region. The Hg concentrations were found to be most strongly related to the mean depth, residence time, and pH, and the concentrations of dissolved organic carbon, chloride, and dissolved oxygen of the lakes. The biggest influence of the watershed land use on Hg concentrations was its affect on the chemical characteristics of the lake.
Atmospheric emissions of Hg will be coming under more strict regulations in the forthcoming years. In order to implement regulations with the maximum effectiveness and still be cost effective, a better understanding of Hg behavior is imperative. With an ultimate goal of reducing human health risks from Hg contaminated fish, these results are another step towards shaping the future of atmospheric Hg deposition and its consequences.
https://surface.syr.edu/che_etd/85
oai:surface.syr.edu:che_etd-1086
2010-10-18T20:21:49Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Syntheses, thermal stereomutations, and (1,3)-sigmatropic isomerizations of cis-(1S,2R)- and trans-(1S,2S)-1-(E)-propenyl-2-methylcyclobutanes
Burrell, Richard Charles
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
John E. Baldwin
Sigmatropic isomerizations
Stereomutations
Propenyl-2-methylcyclobutane
Dimethylcyclohexene
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
Samples of trans -3,4-dimethylcyclohexene ( (±)-12 ), cis -3,4-dimethylcyclo-hexene ( (±)-13 ), trans -3,6-dimethylcyclohexene ( (±)-59 ), cis -3,6-dimethylcyclo-hexene ( 60 ), trans -1-( E )-propenyl-2-methylcyclobutane ( (±)-10 ), cis -1-( E )-propenyl-2-methylcyclobutane ( (±)-11 ), trans -1,5-octadiene ( 40 ); cis -1,5-octadiene ( 39 ), 3-ethyl-1,5-hexadiene ( 41 ), and trans -1,6-octadiene ( 80 ) were synthesized and their structures have been correlated with gas chromatographic peak elution order using standard columns. Racemic samples of trans -1-(E)-propenyl-2-methylcyclobutane ((±)-10) and cis -1-(E)-propenyl-2-methylcyclobutane ( (±)-11 ) were heated at 275°C and their thermal stereomutations, fragmentations, and isomerizations to dimethylcyclohexenes were studied. From (±)-10 the ratio of trans -3,4-dimethylcyclohexene ( (±)-12 , ( k si + k ar ), "allowed") to cis -3,4-dimethylcyclohexene ( (±)-13 , ( k sr + k ai ), "forbidden") was determined to be 64:36. From (±)-11 the ratio of trans -3,4-dimethylcyclohexene ( (±)-12 , ( k sr + k ai ), "forbidden") to cis -3,4dimethylcyclohexene ( (±)-13 , ( k si + k ar ), "allowed") was determined to be 71:29.
Samples of trans -(3 S ,4 R )-dimethylcyclohexene ( (-)-(3 S ,4 R )-12) , cis -(3 R ,4 R )-dimethylcyclohexene ( (+)-(3 R ,4 R )-13) , trans -(3 R ,6 R )-dimethylcyclohexene ( (+)(3 R ,6 R )-59) , (1 S ,2 S )- trans -2-methylcyclobutanemethanol ( (+)-(1 S ,2 S )-47) , and (1 S ,2 R )- cis -2-methylcyclobutanemethanol ( (-)(1 S ,2 R )-48) were synthesized and the samples were used to correlate absolute stereochemistry with gas chromatographic peak elution order using columns with chiral stationary phases. Samples of trans -(1 S ,2 S )-1-( E )-propenyl-2-methylcyclobutane ( (+)-(1 S ,2 S )-10) and cis -(1 S ,2 R )-1-( E )-propenyl-2-methylcyclobutane ( (-)-(1 S ,2 R )-11) were synthesized and their thermal stereomutations, fragmentations, and isomerizations to dimethylcyclohexenes were studied at 275°C. From (+)-(1 S ,2 S )-10 the relative importance of the four distinct reaction paths were determined to be 58% si , 5% ar , 33% sr , and 4% ai . From (-)-(1 S ,2 R )-11 the relative importance of the four distinct reaction paths were determined to be 18% si , 11% ar , 51% sr , and 20% ai . These results show that the vinylcyclobutane rearrangements of (+)-(1 S ,2 S )-10 and (-)-(1 S ,2 R )-11 are not under orbital symmetry control. These vinylcyclobutane rearrangements most likely proceed through a short-lived conformationally flexible diradical traversing relatively flat transition regions under dynamic control much like the vinylcyclopropane rearrangement.
https://surface.syr.edu/che_etd/87
oai:surface.syr.edu:che_etd-1090
2010-10-18T20:53:14Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The synthesis and characterization of new metallaborane and carborane derivatives on the way to novel nonlinear optical materials and molecular nanosystems
Taylor, Jesse W.
2001-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James T. Spencer
Metallaborane
Carborane
Nonlinear optical
Molecular nanosystems
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
The work described here consists of the synthesis and characterization of new borane cluster compounds, including large metallaboranes and substituted carboranes that are intermediates to new nonlinear optical materials and molecular nanosystems.
The first chapter of this work describes the synthesis of two new nineteen-vertex metallaborane compounds, [(CH 3 ) 4 N][B 18 H 20 Ni(η 5 -C 5 H 5 )] ( 1.4b ) and [B 18 H 19 (2-THF)Ni(η 5 -C 5 H 5 )] ( 1.5 ). The reaction of anti -B 18 H 22 with nickelocene affords the new compounds 1.4b and 1.5 . Complete spectroscopic analysis and a single crystal X-ray study are reported and discussed for both compounds. This chapter also contains a discussion of the synthesis and spectroscopic characterization of the first exo -bound organometallic fragment to an anti -B 18 H 22 cluster, [9-(Fe(CO) 2 (η 5 -C 5 H 5 )) anti -B 18 H 21 ] ( 1.3 ). Also presented are some photochemical reactions of these non- closo macropolyhedral metallaborane clusters.
The synthesis and complete characterization of a new linked bis- ortho -carborane species, 1,1 ' -bis( ortho -carborane)-3-fluorenol ( 2.3 ), is reported in the second chapter of this work. The synthesis of compound 2.3 begins with bis- ortho -carborane, which is first deprotonated and then reacted with methyl formate to afford 1,1 ' -bis( ortho -carborane)-3-fluorenol ( 2.3 ). The complete spectroscopic characterization and the X-ray crystal structure of 2.3 are reported here. This new compound contains a five-membered ring that is comprised completely of carbon atoms.
The third chapter of this work discusses the synthesis and characterization of a series of compounds that should lead to the preparation of new boron-based nonlinear optical materials with para -carborane as the primary structural unit. Complete spectroscopic characterization is presented for six previously unknown substituted para -carborane compounds, including: [1-(1-C 7 H 7 )-12-(H)-C 2 B 10 H 10 ] ( 3.3 ), [1-(1-C 7 H 7 )-12-(C 5 H 4 -1-(OH)-3,4-(CH 3 ) 2 )-C 2 B 10 H 10 ] ( 3.5 ), [1-(1-C 7 H 7 )-12-(C 5 H 3 -3,4-(CH 3 ) 2 )-C 2 B 10 H 10 ] ( 3.6 ), [1-(4-C 7 H 7 )-12-(C 5 H 3 -3,4-(CH 3 ) 2 )-C 2 B 10 H 10 ] ( 3.7 ) [1-(4-C 7 H 7 )-12-(C 5 H 2 -3-(CN)-3,4-(CH 3 ) 2 )-C 2 B 10 H 10 ] ( 3.10 ), and [1-(4-C 7 H 7 )-12-(C 5 H-3,5-(CN) 2 -3,4-(CH 3 ) 2 )-C 2 B 10 H 10 ] ( 3.11 ). The X-ray crystal structure analyses of compounds 3.3 , 3.7 , and 3.10 , are also provided in this chapter.
https://surface.syr.edu/che_etd/83
oai:surface.syr.edu:che_etd-1091
2010-10-19T13:39:14Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Design and synthesis of fluorinated derivatives of indolyl fulgides and fulgimides
Thomas, Craig Joseph
2000-10-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Watson J. Lees
Fluorinated derivatives
Indolyl fulgides
Fulgimides
Photochromic compounds
Optical storage media
Organic Chemistry
Two of the more intensely studied classes of photochromic compounds are the fulgides and fulgimides. A large amount of interest exists due to the lack of a thermal reversion of the photochromic event, making fulgides ideal candidates for optical storage media. We set out to design novel fulgides that utilize the lessons learned from the vast number of variously substituted fulgides and fulgimides that already exist in the chemical literature. Combining the advantageous trends perceived from electronic effects and steric bulk we have designed and synthesized novel fulgides and fulgimides maximizing photochromic properties such as quantum yield, cyclicity and the wavelength of the absorption maximum. In addition to the rational design of numerous derivatives of these molecules, modifications to existing synthetic protocols and new synthetic methodologies have been designed and incorporated. Among these are new methods providing for the necessary acyl ketones and the opening of the previously inert cis indole lactones. With improvements to the synthesis and photochromic properties of the fulgides and fulgimides, the reality of a molecular based memory device is becoming more conceivable. Furthermore, with the new patterns between structure and function established, the design and synthesis of further, novel fulgides and fulgimides will be explored.
https://surface.syr.edu/che_etd/92
oai:surface.syr.edu:che_etd-1092
2010-10-20T14:31:10Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
HIV-1 Psi RNA: Dimerization and nucleocapsid protein binding studies
Shubsda, Michael Frederick
2000-12-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James C. Dabrowiak
Immune deficiency
HIV-1
Psi RNA
Dimerization
Nucleocapsid
Protein binding
Biochemistry
The monomer-dimer equilibrium of three RNAs (19, 27, and 41-mers) containing the dimer initiation site (DIS) from the HIV-1 Ψ-element are studied by non-denaturing polyacrylamide gel electrophoresis and the equilibrium constants are reported. To aid in interpreting experiments differential equations for diffusion, migration, and reaction were solved to simulate gel patterns, showing that if only monomer and dimer peaks were present the equilibrium constant K could be calculated from the spot intensities. If the pattern was more complicated, having streaks, a load-and-run gel was needed to give the value of K . Since equilibrium was rapid in the gel well, a dilution factor was used to estimate the sample concentration in the well. To test our technique, a study of DNA 12-mers was done, which yielded K s comparable to literature values. The dimerization constants, at 5°C, for the 19, 27, and 41-mer RNAs were ∼10 8 , ∼10 6 , and ∼10 5 M -1 at an ionic strength of ∼100 mM. The decrease in K with length is attributed partly to changes in rotational entropy of rigid rod type molecules and conformational entropy of the monomers. The equilibrium between stem-loop 3 (SL3, also from the HIV-1 Ψ-element) and the nucleocapsid protein (NCp7) was also studied by gel electrophoresis, showing at least two different RNA-protein complexes are formed. The gel intensity data was fit to several models, differing in species stoichiometries, giving the best fit for a 2:1 complex (RNA:NCp7 ratio) that self-associates to an 8:4 tetramer. For the dilution experiments, at 5°C and ionic strength of 28 mM, K 1 for the 2:1 complex is ∼10 11 M -2 and K 2 for the 8:4 complex is ∼10 16 M -3 . The titration experiments gave K 1 ∼ 10 7 M -2 (poorly determined) and K 2 ∼ 10 19 M -3 . Considering the importance of RNA dimerization and NCp7 binding to HIV proliferation in vivo, these studies could lay the groundwork to new therapies.
https://surface.syr.edu/che_etd/94
oai:surface.syr.edu:che_etd-1093
2010-10-20T15:12:43Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Influences of organonitrogen components or organonitrogen-heterometal complexes on molybdenum- and vanadium-oxide composite materials: Hydrothermal syntheses and structural characterization
Hagrman, Pamela Jayne
2000-05-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon A. Zubieta
Molybdenum oxides
Vanadium oxide
Organonitrogen
Chemistry
The influences of organonitrogen components on the solid state structures of molybdenum and vanadium oxides, some with secondary metal sites present, were investigated by utilizing hydrothermal techniques to synthesize related materials. All syntheses presented were carried out with either a molybdate or a vanadate starting material, appropriate ligand, and, in some cases, a precursor containing the secondary metal of choice. These components were reacted in either polytetrafluoroethylene-lined stainless steel acid digestion bombs or borosilicate glass tubes. Reaction conditions were varied by adjusting reaction components, temperature, fill volume, time, and precursor concentrations. The organonitrogen ligands utilized for this study included bidentate, tridentate and bis-tridentate, as well as bridging moieties. Careful examination of the crystalline products of these reactions will help further understanding of the complex relationships between ligand choice, metal oxide selection and the presence of secondary metal components.
https://surface.syr.edu/che_etd/93
oai:surface.syr.edu:che_etd-1094
2010-10-22T14:28:51Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Modification of the extended solid structure of cuprous cyanide using polyimines
Chesnut, Douglas James
2000-12-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon A. Zubieta
Cuprous cyanide
Polyimines
Cyanide
Composites
Chemistry
Design of extended solid-state materials and their subsequent preparation has been an empirical process due to the complexity of parameter space. Further complicating the design of desired materials is the variation in not only elemental composition, but also structural composition of chemical building blocks from which extended solids can be derived.
The exploration of parameter space of the set of systems Cu-CN-LL-LL ' (LL and LL ' = polyimines) was initiated to provide markers for a structural informatics data base. Compounds of the general formulas {Cu x (CN) x (LL) y } and {Cu x (CN) y (LL ' )(LL)} were prepared in hydrothermal media. They were structurally characterized via single crystal x-ray diffraction experiments and FTIR-microscopy.
The polyimines employed functioned in one of three general modes in the composite materials: (i) truncation of the propagation of the cuprous cyanide substructure, (ii) linking of the cuprous cyanide substructure in a linear fashion, and (iii) tethering of the cuprous cyanide substructure in a non-linear fashion. The additional property of templation was associated to varying degrees with each of the three general modes.
All copper species were formally assigned a unipositive oxidation state in agreement with charge balance requirements and observed metal center coordination geometries. The presence of close contacts between cuprous centers was estimated to be dominantly determined by the structure directing properties, or lack thereof, of the polyimines employed.
https://surface.syr.edu/che_etd/95
oai:surface.syr.edu:che_etd-1095
2010-10-25T13:38:20Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Raman optical activity: Theory, instrumentation and measurements. Electron transition current density: Ab initio calculation of vibrational transition current density in selected molecules
Lee, Eunah
2000-05-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laurence A. Nafic
Raman optical activity
Electron transition current
Vibrational transition current
Chemistry
Physical Chemistry
In the part I of this thesis, the theory of natural Raman optical activity (ROA) is summarized within the far-from-resonance approximation and the strong resonance approximation. Improvements in a dual circular polarization (in-phase) ROA instrument are reported with a summary of the changes in the optics. The ROA spectra of selected proteins measured in the backscattering DCP I configuration are reported. The pH dependence of ROA spectra of captopril is reported. Improved resonance ROA spectra of naproxen are also presented.
In the part II of this thesis, vibrational transition current density (TCD) is reported as a new theoretical method to visualize the flow of electron current density caused by nuclear motions during a vibration. TCD is related to vibrational circular dichroism (VCD) through the integrand of electronic contribution to the velocity-form electric dipole transition moment.
A TCD map is a vector field plot over a grid of points; each vector represents the magnitude and direction of the electron density velocity for the volume element centered at the grid point. Visual interpretation of these TCD maps provides information about the magnetic dipole transition moment and electric quadruple transition moment as well as the electric dipole transition moment.
The calculations on formaldehyde and ethylene demonstrate the theoretical and computational methodology and visual interpretation with respect to requirements of symmetry. The calculation of the methine stretching modes of ( S )-methyl- d 3 lactate- Cd 3 conformers demonstrates how a TCD map can provide insight into the origin of IR and VCD spectral intensities. The calculation of (2 S , 3 S )-oxirane- d 2 demonstrates the effect of basis set size on the TCD map.
https://surface.syr.edu/che_etd/98
oai:surface.syr.edu:che_etd-1096
2010-10-25T17:57:56Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Applications of tellurium in synthesis of alkenes, allylic alcohols, allylic amines and heterocyclic compounds
Chao, Bin
1999-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Donald C. Dittmer
Alkenes
Tellurium
Allylic alcohols
Allylic amines
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
A novel methodology for the stereospecific syntheses of alkenes from 1,2 cyclic sulfates via tellurium chemistry has been discovered. meso -2,3-Diphenylethane-2,3-diol [arrow right] cis stilbene; d,l -2,3-diphenylethane-2,3-diol [arrow right] trans -stilbene. Compared with other procedures, advantages of this method include (1) the use of mild temperatures (0°C to room temperature), (2) the rapidity of the reaction (10 min to 2 h), (3) stereo specificity, (4) the recovery of Te o , and (5) the adaptability of the reaction to the use of catalytic amount of Te (0.1 equiv).
Tellurium mediated nucleophilic reduction under "no-solvent" conditions have been investigated systematically. Secondary and tertiary allylic alcohols were synthesized with different substitution patterns by "no-solvent" reactions in excellent yields.
A new telluride phase transfer catalysis process has been developed and successfully applied to the syntheses of secondary and tertiary allylic alcohols. A catalytic amount of Te o can be used. Previous regiochemistry problems were overcome by this procedure: epoxycinnamyl tosylate gave 1-phenyl-2-propen-1-ol exclusively in 98% yield. One of the attractive features is easy workup--the toluene organic phase is removed and concentrated to give pure allylic alcohols. A chiral phase transfer catalyst was tried but no asymmetric induction was found from racemic starting materials.
A general efficient procedure has been found to synthesize racemic and non-racemic secondary and tertiary allylic amines via tellurium chemistry from activated aziridines. The syntheses of racemic allylic amines involve three steps starting from allylic alcohols. The synthesis of chiral allylic amines was completed using Sharpless' aminohydroxylation or asymmetric epoxidation procedure.
A new domino tellurium mediated nucleophilic reduction and Michael addition has been discovered for the synthesis of oxygen-containing heterocycles. A synthesis of a highly functionized racemic isohydrobenzofuran has been completed through five steps. Chiral heterocycles can be conveniently prepared using Sharpless' asymmetric epoxidation.
https://surface.syr.edu/che_etd/97
oai:surface.syr.edu:che_etd-1097
2010-10-25T18:44:31Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
An enantiospecific synthetic approach to the ansatrienin family of ansamycin antibiotics
Dintzner, Matthew Richard
1998-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James Kallmerten
Ansamycin
Antibiotics
Enantiospecific
Organic Chemistry
Pharmacology
Progress towards an enantiospecific synthetic route to the ansatrienin family of naturally-occurring ansamycin antibiotics is presented herein. Synthetic design was originally based on the Emmons-Horner coupling of C9-N and C1-C8 synthons of the target system. Construction of the C9-N intermediate was motivated by a novel strategy for intramolecular protection of the C13- hydroxyl group as part of a pyranosidic ring system with C17. The pyran ring system was efficiently generated through an asymmetric hetero-Diels Alder reaction, which additionally served to impart chirality to the system as well as dictate C14-C15 olefin geometry and set the stage for sigmatropic development of the C11-C13 contiguous stereocenters. Mukaiyama aldol technology was successfully employed as an alternative to the ester enolate Claisen rearrangement for generating relative stereochemistry at C11-C13. The C3 stereocenter was derived from R-(+)-malic acid, which was successfully employed to generate the C1-C8 intermediate. Failure to effect convergence via the originally intended Emmons-Horner protocol necessitated investigation of several alternative synthetic pathways to the target system. Linear extension of the C9-N intermediate via sequential Emmons-Horner olefinations to install the all- trans triene moiety, followed by an aldol condensation with ethyl acetate, served to complete the carbon skeleton, not accounting for C3-stereochemistry. Attempts to install the requisite stereochemistry at C3 via an asymmetric aldol were unsuccessful. Several synthetic approaches to the ansatrienin target system are described.
https://surface.syr.edu/che_etd/96
oai:surface.syr.edu:che_etd-1098
2010-10-26T13:45:32Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The synthesis and structural study of organically templated copper molybdenum oxides
Hagrman, Douglas Earl
2000-05-01T07:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon A. Zubieta
Organonitrogen
Copper
Molybdenum oxides
Chemistry
An investigation into the structural motifs developed by applying batch hydrothermal synthetic techniques to organonitrogen-templated copper molybdenum oxides was undertaken. All reactions were carried out with molybdenum trioxide, a copper(II) starting material (CuSO 4 ·5H 2 O, Cu(NO 3 )·2.5 H 2 O) and the organonitrogen in 10ml of water contained in a 23ml Parr acid digestion bomb. Variations in reaction conditions included temperature (120-220°C), concentration of precursors, and the type of organoamine incorporated into the metal oxide framework. The organonitrogen ligands utilized are mono-, di-, tri- and tetradentate ligands varying in size and geometry. By characterizing all crystalline products with single crystal x-ray diffraction, one can gain some understanding of the synergistic relationships between the formation of the metal oxide framework and the organonitrogen template. This understanding can further the development of new metastable materials combining microporosity and selectivity for catalytic reactions.
https://surface.syr.edu/che_etd/106
oai:surface.syr.edu:che_etd-1099
2010-10-26T15:09:40Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Fourier transform vibrational circular dichroism: Step-scan instrumentation and biological applications
Long, Fujin
1998-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laurence A. Nafie
Teresa B. Freedman
Fourier transform
Vibrational circular dichroism
Step-scan instrumentation
Analytical Chemistry
Chemistry
In this dissertation, the instrument design and optimization of two step-scan Fourier transform vibrational circular dichroism (FT-VCD) spectrometers are described and several applications of VCD spectroscopy using this instrumentation are reported. The solution conformation and absolute configuration of a number of pharmaceutical and biological molecules are determined, and in addition, several analyses of optical purity measurements using the VCD spectroscopic method are illustrated.
The development of FT-VCD spectrometers based on a Nicolet Magna 850 FTIR for the mid-IR region and a Bruker IFS-55 FTIR for the near-IR region is described. It is demonstrated that using concentric optical elements with careful alignment, VCD spectra for single enantiomers of a chiral sample can be obtained with low levels of interfering artifacts and high signal-to-noise ratio. In the mid-IR region, the comparison of traditional sequential rapid-scan, new simultaneous rapid-scan and step-scan shows that the simultaneous rapid-scan method gives the highest quality, and sequential rapid-scan and the step-scan mode follow closely. In the step-scan method, a wide range of step speeds and lock-in-amplifier time constants can be used, and the VCD noise level is proportional to the actual data-averaging time. In the near-IR region, although VCD spectra can be collected in the rapid-scan mode, higher signal-to noise ratios are achieved for step-scan measurements by a factor of 2. It is shown that an InSb detector with very high D* only improves the signal-to-noise ratio slightly comparing to an MCT detector, and both Nicolet-based and Bruker based instruments give the same spectral quality using the same InSb detector.
FT-VCD spectra of the small pharmaceutical molecules propranolol, ibuprofen, naproxen and a series of cyclosporins and four β-turn peptides have been measured. Ab initio molecular orbital calculations were used in interpreting the spectra. Solution conformational structures of propranolol, the cyclosporins and the peptides are characterized. The positive VCD features for the S-configuration of the chiral center common to ibuprofen and naproxen are identified. It is demonstrated that optical purity can be measured with a precision of 1% ee by VCD measurements without enantiomeric separation or chemical modification of the sample.
https://surface.syr.edu/che_etd/105
oai:surface.syr.edu:che_etd-1100
2010-10-26T15:42:05Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
I. Kinetic analysis of anticancer drug cleavage of closed-circular and intracellular DNA. II. Binding studies of the HIV-1 nucleocapsid protein to the SL3 stem-loop of the HIV-1 packaging signal
Kirk, Chris Allen
1998-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James C. Dabrowiak
Immune deficiency
DNA cleavage
Anticancer drug
HIV-1
Nucleocapsid
SL3
Stem-loop
Packaging signal
Biochemistry
Chemistry
Genetics
I. Anticancer drug efficacy is dependent on the kinetics of DNA cleavage by the drug exceeding the rate of repair by cellular repair enzymes. As such, study of kinetics of cleavage by a drug may actually be of greater importance than examination of its specificity. A kinetic analysis of cleavage of simian virus 40 (SV40) DNA inside and outside green monkey BSC-1 cells by the enediyne antiobiotic C-1027 and its free chromophore is described. The ratio of single-strand to double-strand cutting for the holoantiobiotic and its free chromophore is approximately 1.8 for extracellular SV40 DNA. For intracellular DNA, double-strand cutting is much more probable than single-strand. Also, the overall rate of cleavage of form I DNA inside the cell is much larger than the rate outside. Cleavage rate constants are also discussed for cutting of pBR322, SV40 and PM2 DNAs by the nonspecific cutter Fe-EDTA and the antitumor agent bleomycin.
II. A binding study of the HIV-1 nucleocapsid protein (NCp7) for a stem-loop (SL3) in the HIV-1 packaging signal region using native polyacrylamide gel electrophoresis is reported. The binding constant, averaged for all pertinent experiments, is 490 $\pm$ 300 mM$\sp{-2}$, with the stoichiometry being 1 NCp7 to 2 SL3 molecules. Values for K calculated for assays run at ambient temperature are in close agreement with those obtained from assays performed at 4$\sp\circ$C. Since the SL3-NCp7 interaction has been proven to be integral to viral propagation, study of the complexation process may have ramifications in development of future anti-HIV drugs.
https://surface.syr.edu/che_etd/104
oai:surface.syr.edu:che_etd-1101
2010-10-26T18:20:22Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Preparation, characterization and exploitation of novel self-assembled nanostructured thin films
Guerin, Frederic
1999-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Janos H. Fendler
Self-assembled
Nanostructured
Thin films
Microcrystallization
Langmuir-Blodgett
Chemistry
Materials Chemistry
Physical Sciences and Mathematics
Novel nanostructured thin multilayer films composed of surfactants (DHP, DODAB), polyelectrolytes (PSS, PVS, PDDA, PEI), dyes (ruthenium complexes), J-aggregates (cyanine dye) and metallic or semiconducting nanoparticles (Au, TiO 2 ) were prepared by the techniques of Langmuir-Blodgett and self-assembly. The structure of the self-assembled films, their interactions at interfaces and surfaces, their modification and the role they play were investigated by surface plasmon spectroscopy (SPS), quartz crystal microbalance (QCM), atomic force microscopy (AFM), absorption and emission spectroscopies, near-field scanning optical microscopy (NSOM) and electron microscopies (TEK, SEM).
Microcrystallization, photoluminescence, charge transport, and electron transfer were examined in the layer-by-layer self-assembled films using a variety of characterization techniques. QCM was developed and used in conjunction with simultaneous SPS to assess the nature of the self-assembly process and measure the thickness of multilayered thin films. NSOM was assembled as a complementary technique for the rapid, sensitive and non-destructive optical imaging and local spectroscopy of the supramolecular architecture work at surfaces and interfaces composed of submicron sized structures.
High resolution near-field optical imaging and spectroscopy have been used to provide a valuable insight into the microcrystallization of cationic [Ru(bby) 3 ] 2+ complexes under anionic dihexadecyl phosphate (DHP) monolayers as functions of the surface pressure and the conditioning of the monolayer. It was possible to spatially and spectrally resolve, at a submicron resolution, the presence of isolated seed crystals and their growth into differently shaped [Ru(bpy) 3 ] 2+ microcrystallites in the various phases of the monolayer.
Surface pressure (II) vs . surface area (A) isotherms, Brewster angle microscopy and AFM images provided evidence for a controllable two-dimensional crystal growth of an amphiphile [Ru(bpy) 3 ] 2+ -C 60 dyad molecule at the air-water interface and the existence of a truly monolayered structure. It suggested that the dyad fibers were composed of close-packed clusters with diameters of 100 ± 20 nm.
Finally NSOM was extended to allow single nanoparticle imaging and to probe the enhanced excitonic fluorescence of J-aggregates, attached to a monolayer of gold nanoparticles in a layer-by-layer self-assembled ultra thin film.
https://surface.syr.edu/che_etd/103
oai:surface.syr.edu:che_etd-1102
2010-10-26T18:53:08Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Membrane processes for gas separations: Part I. Removal of carbon dioxide and hydrogen sulfide from low-quality natural gas. Part II. Enrichment of krypton in air
Hao, Jibin
1998-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
S. A. Stern
P. A. Rice
Membrane processes
Gas separations
Natural gas
Krypton
Carbon dioxide
Hydrogen sulfide
Chemical Engineering
Chemistry
The objective of this study was to determine the process design characteristics and economics of membrane separation processes for reducing the concentrations of H 2 S and CO 2 in low-quality natural gas containing substantial amounts of the two acid gases to pipeline specifications ([Special characters omitted.] 2 mole-% CO 2 and [Special characters omitted.] 4 ppm H 2 S). The new processes considered the simultaneous use of two different types of polymer membranes for the above application, namely, one with higher CO 2 /CH 4 selectivity and the other with higher H 2 S/CH 4 selectivity.
The performance and economics of membrane process configurations comprising one, two, and three permeation stages, with and without recycle streams, were examined and optimized via extensive computer simulations. Most computations assumed as a "base-case", the processing of a medium-size natural gas stream of 35 MMSCFD at 800 psia. The natural gas was taken to contain [Special characters omitted.] 10 mole-% H 2 S and [Special characters omitted.] 40 mole-% CO 2 . The most economical process configuration was two permeation stages in series, with H 2 S-selective membranes in the first stage and CO 2 -selective membranes in the second stage . The most economical process configurations for upgrading natural gas containing either only substantial amounts of H 2 S or of CO 2 were also determined. The sensitivity of the process economics to feed flow rate, feed pressure, membrane module cost, and wellhead cost of natural gas was studied. A comparison of the processing cost of membrane processes with that of conventional gas absorption processes utilizing diethanolamine as solvent was also investigated.
II . A membrane process for enrichment of Kr in air was studied experimentally as a technique of improving the accuracy of Kr analysis. "Asymmetric" silicone rubber membranes were found to be most suitable for this application. The study was investigated with a feed gas mixture containing 0.99 mole-% Kr, 20.70 mole-% O 2 , and 78.30 mole-% N 2 . The Kr concentration could be increased from 0.99 to 2.23 mole-% in a single membrane stage and further raised to 3.73 mole-% in two stages in cascade. Computer simulations of "cross-flow" model yielded results in general agreement with experimental data.
https://surface.syr.edu/che_etd/102
oai:surface.syr.edu:che_etd-1103
2010-10-26T19:17:31Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Tellurium-triggered reactions of 5-hydroxymethyl-2-oxazolidinone tosylates, aziridinemethanol tosylates, and oxiranemethanol tosylates: Synthesis of allylic amines and no-solvent synthesis of allylic alcohols via ultrasound and microwave irradiations
Xu, Qinyu
1999-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Donald C. Dittmer
Tellurium-triggered
Aziridinemethanol tosylates
Oxiranemethanol tosylates
Allylic amines
Ultrasound
Microwave irradiations
Chemistry
Organic Chemistry
Physical Sciences and Mathematics
A novel methodology for the stereospecific syntheses of allylic amines from 5-hydroxymethyl 2-oxazolidinone tosylates via tellurium chemistry has been discovered. These are the first reactions between 5-hydroxymethyl 2-oxazolldinone tosylates and telluride ions. Compared with other procedures, the advantages of this method include (1) The use of mild temperatures (room temperature), (2) oxazolidinones; are readily available from aminodiols (derived from allylic alcohols), and triphosgene, methyl chloroformate, and dimethyl carbonate, (3) either enantiomer of the non-racemic allylic amine can be obtained since the starting enantiomeric oxiranernethanols are available via Sharpless asymmetric epoxidation of allylic alcohols, (4) the problem of regioselectivity in the telluride reaction that is observed with some aziridinemethanol derivatives reported previously was avoided in this process.
Tellurium-mediated nucleophilic reduction under "no-solvent" conditions via ultrasound and microwave irradiation has been investigated systematically. Secondary and tertiary allylic alcohols were synthesized with different substitution patterns by "no-solvent" reactions in excellent yields. Compared with the use of a mortar and pestle, the use of ultrasound and microwave has the following advantages: (1) The "no-solvent" synthesis of allylic alcohols is an environmentally benign organic reaction, which excludes the usage of non-environmentally friendly organic solvent, (2) more efficient and much more convenient, (3) avoid the contact of chemicals with personnel that the trituration process involved, (4) the yields of all the "no-solvent" reactions are from good to excellent.
An improved phase transfer system was discovered by changing the reducing agent in the aqueous phase. Rongalite and sodium hydroxide (NaOH) were replaced by NaBH 4 to reduce the elemental tellurium to telluride ions. The advantage of this new system is that the potential problem of decomposition of the phase transfer catalyst under basic conditions can be avoided.
https://surface.syr.edu/che_etd/101
oai:surface.syr.edu:che_etd-1104
2010-10-26T19:39:19Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Theoretical and applied studies of rhodopsin and bacteriorhodopsin
Tallent, Jack R.
1999-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Robert R. Birge
Retinal
Holographic memory
Rhodopsin
Bacteriorhodopsin
Biochemistry, Biophysics, and Structural Biology
Biophysics
Chemistry
Life Sciences
Physical Sciences and Mathematics
Part I . The conformational and electronic properties of the 12-s-cis and 12-s-trans conformers of 11-cis retinal are analyzed. Our models confirm that the 12-s-cis isomer is more stable in vacuum and the 12-s-trans conformer is more stable in polar and nonpolar solvent environments due to dispersive and electrostatic interactions. Electronic analysis indicates that the features in the absorption spectrum are due to a complex set of overlapping transitions. Assignments are made for all four band systems.
Ground- and excited-state surfaces connecting rhodopsin and bathorhodopsin along the [Special characters omitted.] dihedral reaction path are partially adiabatically mapped. Forward and reverse photochemistry is simulated via molecular dynamics. The activated complex is reached in ∼375 fs following excitation. Best results for quantum yields and product formation times are obtained by including both dynamic and phased (partitioned) nonadiabatic coupling: [Special characters omitted.] ps; [Special characters omitted.] ps. The lower quantum yield of the B [arrow right] R isomerization is due to a sign change in the nonadiabatic coupling term at [Special characters omitted.] = 92° and to the rapid arrival of the trajectory into the activated complex which prevents equilibration of the excited state and lowers the dynamic coupling term. The [Special characters omitted.] excited singlet state spectrum is calculated as a function of time following excitation of rhodopsin.
A model of thermal noise in rods is proposed whereby thermal isomerization occurs when the retinal Schiff base is unprotonated. This model accounts for the low activation energy of 23-27 kcal mol -1 and is supported by both molecular models and experimental measurements.
Part II . A prototype holographic memory is described which demonstrates simultaneous storage and retrieval of ten holographic images in the same volume of a bacteriorhodopsin(BR)/polyvinylalcohol(PVA) film. The suitability of BR as a volume holographic memory medium is discussed.
Photochemistry in dried PVA films of the blue membrane form of BR is demonstrated. As in solution, blue[Lef-right arrow]pink interconversion occurs, but with much lower quantum yield. Additionally, a species absorbing maximally at 450 nm appears as a photoproduct of blue membrane.
https://surface.syr.edu/che_etd/100
oai:surface.syr.edu:che_etd-1105
2010-10-27T19:37:42Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The primary event of visual opsins
Vought, Bryan William
1999-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Robert R. Birge
Primary event
Opsins
Vision
Biochemistry
Biochemistry, Biophysics, and Structural Biology
Biophysics
Life Sciences
Opsin proteins are responsible for capturing light during the initial steps of vision. Opsins have a characteristic cofactor, retinal, which harnesses light energy. Color vision is possible because different groups of opsins tune the spectral sensitivity of retinal from 350 nm to greater than 600 nm. The origins of this spectral tuning remain a mystery. The primary event describes the transformation of opsin from its initial state to the first trappable (by temperature) intermediate, bathorhodopsin, after retinal absorbs a quantum of light. During this event, as much as 60% of the light energy is chemically trapped by the protein. This energy is then used in subsequent steps to alter the conformation of the protein to a state which binds and activates a G-protein. I have studied the primary event in two poorly characterized but important classes of opsins: the short-wavelength sensitive and invertebrate opsins. These proteins have not been studied extensively biochemically due to experimental limitations in obtaining significant quantities. Using heterologous expression systems, I have demonstrated that significant quantities of these proteins can be produced for cryogenic UV-Vis spectroscopy. By analyzing the primary event in short-wavelength sensitive opsins, I report that the mechanism used to adjust the spectral sensitivity of the violet opsins is the same as the other visible-absorbing pigments. Computer simulations combined with experimentally derived primary event data, indicate that the primary mechanism responsible for spectral tuning is modulation of the Schiff base--counterion distance. Furthermore, spectral tuning of the UV-sensitive opsins must be different. An investigation of the primary event of Drosophila rhodopsin1 reveals that the retinal binding site is similar to the vertebrate binding sites. The binding site must contain a single counterion stabilizing a protonated Schiff-base. This is contrary to previous resonance Raman experiments which have shown that the vertebrate counterion equivalent position is neutral in a cephalopod opsin.
https://surface.syr.edu/che_etd/99
oai:surface.syr.edu:che_etd-1106
2010-10-28T14:26:29Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Studies toward the total synthesis of octalactin A and B
Sherer, Brian A.
1998-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
James Kallmerten
Cytotoxin
Lactone ring
Octalactin
Chemistry
An attempted linear synthesis of the cytotoxic marine metabolites octalactin A and B is reported. Isolated in 1991 from a microorganism growing on an ocean sponge, octalactin A was found to be modestly cytotoxic while octalactin B exhibited significantly less bioactivity. Spectroscopic studies have provided details of a unique structural array including an unusual eight-membered lactone ring while single crystal X-ray analysis has described the three dimensional structure.
Previous successful synthetic efforts as well as some preliminary work towards the octalactins has been presented. All of the reported syntheses of the octalactins accomplished rely on a common convergent strategy utilizing a Ni(II)/Cr(II) coupling of a vinyl halide and an aldehyde.
A racemic, stereoselective synthesis of the entire carbon framework of the octalactins is described. A linear sequence utilizing a series of sigmatropic rearrangements is employed to establish the carbon framework as well as the key stereochemistry. Chirality at C13 is installed through an allyl Grignard addition to isobutyraldehyde. (2,3) -Wittig rearrangement of an $\alpha$-tertiary allylic ether develops asymmetry at C7 and C8. A novel S$\sb{\rm N}\sp\prime$ lactonization establishes the stereocenter at C9 while a (3,3) -Claisen rearrangement of a glycolate ester creates chirality at C3 and C4. Possible routes to the completion of the natural product are also discussed.
https://surface.syr.edu/che_etd/110
oai:surface.syr.edu:che_etd-1107
2010-10-28T14:33:35Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
Vibrational circular dichroism spectroscopy and its applications to conformational study of bifunctional chiral molecules
Qu, Xinhua
1995-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Laurence Nafie
Analytical chemistry
Chemistry
Analytical Chemistry
This dissertation is concerned with the solution conformations of selected bifunctional chiral molecules by experimental measurement and calculation of vibrational circular dichroism (VCD). In addition, the optical design for a Fourier transform vibrational circular dichroism (FT-VCD) instrument and improvements to this system have been evaluated. Included in the appendices of this dissertation are a comparison study of Fourier transform vibrational circular dichroism (FT-VCD) and multichannel detected Raman optical activity (ROA) and experimental VCD measurements of other chiral molecules.
The instrumental development study describes modifications for the FT-VCD instrument based on a Nicolet Magna 550 FT-IR spectrometer. The mirrors have been replaced by infrared lenses in the new optical designs for this system. High signal-to-noise (S/N) ratio, minimized artifacts and flat baselines have been achieved in raw VCD spectra for single enantiomer samples obtained on the upgraded FT-VCD instrument with much less collection time than before.
In the molecular conformation study, the OH-, NH- and CH-stretching absorbance and VCD spectra of (R,R)-(+)-hydrobenzoin (I), (1S,2R)-(+)-2-amino-1,2-diphenylethanol (II), (1R,2R)-(+)-1,2-diphenylethylenediamne (III), (S)-(+)-1-amino-2-propanol (IV) and (S)-(+)-2-amino-1-propanol (V), in dilute CCl$\sb4$ or $\rm C\sb2Cl\sb4$ solutions, have been measured. The mid infrared (IR) region absorbance and VCD spectra of molecules IV and V, in concentrated CDCl$\sb3$ solution, have also been recorded. Ab initio molecular orbital calculations of geometries, vibrational frequencies and VCD intensities far a number of conformers of these molecules have been carried out. The recently developed locally distributed origin gauge model (LDO) for VCD was used for first time to calculated the rotational strengths for the conformers of large size molecules I, II and III at a 3-21G basis set level. The calculate results have been found to give good agreement with experiment in the OH- and NH-stretching frequency regions. The solution conformations of this group of molecules have been identified through comparison of experimental and calculated results. The VCD spectra were interpreted based on previous research for small chiral diol, amino alcohol and amine molecules with the coupled oscillator model and the local chirality concepts.
https://surface.syr.edu/che_etd/109
oai:surface.syr.edu:che_etd-1108
2010-10-28T14:56:11Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The chemistry of rhenium with hydrazines and thiols
Maresca, Kevin P.
1998-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon Zubieta
http://libezproxy.syr.edu/login?url=http://proquest.umi.com/pqdweb?did=732845311&sid=1&Fmt=2&clientId=3739&RQT=309&VName=PQD
Chemistry
A number of rhenium compounds were synthesized and characterized in attempts to investigate and expand the coordination chemistry of the widely used medicinal imaging radioisotope technetium-99m. Rhenium and technetium are Group VII cogeners whose hydrazine and oxo-thiolate chemistries are very similar. The periodic similarities have allowed for the study of the non-radioactive metal rhenium instead of the synthetically created technetium, which exists only as radioactive isotopes. Influencing the chemistry were two schools of thought for delivering the potential radiopharmaceutical agents. The first concept, the conjugation technique tethers the metal to a biomolecule with specific biodistribution patterns. In this case, we explored hydrazines as potential tethers, forming the class of compounds (MCl$\sb3(\eta\sp1$-NNC$\sb5$H$\sb4$NH)($\eta\sp2$-H$ \sb{\rm x}$NNC$\sb5$H$\sb4$N)) (M = Re, Tc, or Mo). The study continued with the exploration of the chlorine substitution with potentially useful thiol coligands.
The second approach, the "integration technique," utilizes small molecules to incorporate the metal. Here, we designed rhenium-mixed-thiolate complexes, aiming to improve biodistribution by varying steric requirements and charges. Thiolate complexes were evaluated because of their high yields, ease of isolation and characterization, and the ability to synthesize and derivatize novel thiols with relative ease. We systematically synthesized and characterized numerous metal-thiolate complexes, with a heavy emphasis on investigating the coordination chemistry.
https://surface.syr.edu/che_etd/108
oai:surface.syr.edu:che_etd-1109
2010-10-28T16:48:28Z
publication:etd
publication:che
publication:coscde
publication:che_etd
publication:cas
publication:dche
The synthesis and structural study of oxovanadium phosphites, phosphates, and phosphonates
Bonavia, Grant Howard
1998-01-01T08:00:00Z
Dissertation
Doctor of Philosophy (PhD)
Chemistry
Jon Zubieta
Oxovanadium
Phosphates
Phosphites
Organophosphonates
Chemistry
The synthesis and structural studies of a number of oxovanadium phosphites, phosphates, and organophosphonates were undertaken. Utilization of alternative phosphorous polyoxoanion units allowed the isolation of solid state materials with novel structural motifs: (i) Oxovanadium phosphites with and without organoammonium structure directing agents have been produced with two- and three-dimensional frameworks. (ii) Investigations in the oxofluorovanadium phosphate system have produced solid state materials with organoammonium cation structure directors and alkali metal cation space fillers. (iii) The oxovanadium organophosphonate system has produced a novel cylindrical structure type. (iv) Furthermore, the structural diversity of the oxovanadium organodiphosphonate system permits the formation of a series of materials with frameworks ranging from zero- to three-dimensional.
Synthesis of these materials is achieved by hydrothermal methods. The hydrothermal technique provides a means to the isolation of meta-stable materials which would be unattainable by high-temperature ceramic methods. The study of V/P/O open-framework solids may provide a route to the synthesis of a catalytic material with high selectivity in addition to possessing extended catalytic mechanisms.
https://surface.syr.edu/che_etd/107
1460069/simple-dublin-core/100//