Theses and Dissertations from UMD
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Item REVERSIBLE QUINONE METHIDE ALKYLATION OF DNA(2009) Wang, Huan; Rokita, Steven E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Alkylation of DNA has been found to cause cancer and also to serve as its treatment. Quinone methides (QMs) are highly electrophilic molecules implicated in numerous metabolism processes. Studies of QM's reversible reaction with nucleophiles of DNA are important to understand the mechanism of its biological activity. Reversible alkylation of QMs can extend their lifetime under aqueous conditions. The repeated capture and release of QM from dA adduct can help QM equivalents escape the irreversible trapping and extend QM's lifetime by 100-fold. This effect of dA saturates at a concentration of about 6 mM. In contrast, dG, dC, and dT do not have the ability to preserve QM under aqueous conditions. Oligonucleotides can also preserve QM equivalents by forming labile intrastrand adducts. An oligonucleotide has now been shown to transfer bisQM to its complementary sequences to form interstrand crosslinking. Non-complementary sequences can not be alkylated by bisQM-oligonucleotide adducts. The nucleotide composition of oligonucleotides affects their ability to transfer QM as well. A G rich sequence showed a strong ability for crosslinking a complementary sequence. However, C rich and A rich sequences did not have such an ability. Excess alkylation of C rich and A rich oligonucleotides relative to that of G rich oligonucleotide may interrupt the hybridization of complementary sequences and suppress the formation of DNA crosslinking. The reversibility of crosslinking by QM within duplex DNA has been demonstrated by a strand displacement system. The reversible QM-DNA bond does not prevent strand displacement and allows bisQM to migrate within a series of changing DNA structures by forming crosslinking. The reactivity of bisQM is preserved beyond 11 days in duplex DNA by forming labile DNA cross-links under aqueous conditions. The migration of QM is found to be under thermodynamic control and bisQM preferentially retain cross-links in the most stable DNA duplexes.Item Visible Light Photorelease of Carboxylate Anions by Mediated Photoinduced Electron Transfer to Pyridinium-based Protecting Groups(2009) Borak, John Brian; Falvey, Daniel E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The use of sensitized photoinduced electron transfer (PET) to trigger release of redox-active photoremovable protecting groups (PRPGs) allows a broad range of chromophores to be selected that absorb in difference wavelength ranges. Mediated electron transfer (MET) is particularly advantageous as sub-stoichiometric amounts of the often costly sensitizer (relative to the amount of protected substrate) can be combined with an excess amount of an inexpensive electron donor. Thus, the sensitizer acts as an electron shuttle between the donor and the protecting group to initiate release. The development of improved MET release systems using visible light as the trigger is the focus of the current work. The N-alkylpicolinium (NAP) group has demonstrated its utility as an aqueous-compatible PET-based PRPG, releasing protected substrates upon one electron reduction. Adaptation of MET PRPG release to visible light absorbing mediators began with employing ketocoumarin dyes that primarily form excited triplet states. These chromophores demonstrated high rates of release of NAP-protected carboxylates using sub-stoichiometric concentrations of mediator. Subsequently, nanomolar concentrations of gold nanoparticles were used to mediate electron transfer to NAP-protected compounds. This system exhibited rapid deprotection with very high release quantum efficiencies. In an effort to use highly stable visible-light-absorbing metal-centered dyes with modest redox properties, the NAP group has been synthetically modified to adjust its reduction potential to more positive values. Photolysis of solutions containing the protected substrate, a large excess of an electron donor, and substoichiometric amounts of the dye tris(bipyridyl)ruthenium(II) released the free carboxylates in high yields while photodegradation of the chromophore was minimal. To demonstrate the utility of the NAP group, a quasi-reversible photorheological fluid has been developed based on the formation and disruption of aqueous micelles. In solutions containing the surfactant cetyltrimethylammonium bromide, visible light photorelease of a carboxylate additive from the NAP-ester derivative induces a 105 increase in solution viscosity due to the formation of an interpenetrating micelle network. Subsequent irradiation of the viscoelastic fluid with UV light induces a cis-trans isomerization within the released carboxylate thereby disrupting the micelle network and decreasing solution viscosity by 102.5.Item Catechols as Membrane Anion Transporters(2009) Berezin, Sofya; Davis, Jeffery T.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)ABSTRACT Title of Document: CATECHOLS AS MEMBRANE ANION TRANSPORTERS Sofya Berezin, Doctor of Philosophy, 2009 Directed By: Professor, Jeffery T. Davis, Department of Chemistry and Biochemistry Synthetic anion transporters have potential as antimicrobials, extractants, sensors, etc. Anionophores may also help us understand how natural systems move ions across hydrophobic barriers. While bacterial siderophores and synthetic analogues use catecholates for Fe3+ uptake, this work reports of catechols facilitating biomembrane transport of anions. We demonstrate that simple bis-catechol III-25 is an anion transporter whose activity depends on catechol's substitution and amphiphilicity. We also describe liposomal assays and devised quantitative description that allows one to study facilitated anion transport. These assays indicate that selectivity of III-25 follows the Hofmeister bias: anions which are easier to dehydrate are made more permeable to the membrane by this bis-catechol. We believe that our description of the ion selectivity and mechanism for III-25 opens an outstanding opportunity for those interested in determining the selectivity and mechanism for other synthetic and natural biomembrane ion transporters. In the beginning of this project we investigated number of simple amides and phenols to evaluate their relative affinity and stoichiometry of interaction with Cl- anion. ESI-MS and 1H NMR analysis showed that a dimer, catechol2*Cl-, was the major complex formed when TBA+Cl- was mixed with excess catechol. Based on this finding we attached two catechols to a TREN scaffold. A hydrophobic alkyl amide groups were linked to TREN's third position. Surprisingly, this simple design led to the active analogs III-23 - III-26. A medium-length, III-25, was the most active compound, indicating that ion transport ability depends on the ability to partition into the biomembrane. Finally, we noticed that the experimentally observed weak dependence of the transport rates on the anion's hydration energy, namely, kAnion decreasing in the order ClO4- > I- > NO3- > Br- > Cl-, is also seen for some of Nature's anion transporters. Thus, anion permeation into the CFTR chloride channel shows a similar trend. We also observed a nonlinear dependence of kAnion on the concentration of bis-catechol. These findings led us to believe that self-association of III-25 provides transient pores that allow permeation without requiring complete dehydration of the inorganic anions. Future efforts will include incorporating selectivity filters into these bis-catechols to help overcome the Hofmeister bias.Item Intact bacterial hopanoids as specific tracers of bacterial carbon in marine and estuarine environments(2009) Taylor, Karen Ann; Harvey, H. Rodger; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Intact bacteriohopanepolyols (BHPs) and their degrative products were investigated in surface sediments and particulate organic matter from the Bering Sea, Western Arctic Ocean and Chesapeake Bay to trace the inputs of bacterial carbon sources and the dominant microbial processes operative during organic matter recycling. Despite cold temperatures and the dominance of diatoms, cyanobacteria are ubiquitous and inhabit the deeper layers of the euphotic zone in the Bering Sea, where their contributions to sediments were directly traced. As a small but important contribution to the total system chlorophyll, cyanobacteria represent a previously undocumented fraction of the organic carbon pool in this region. In the Western Arctic, soil derived bacterial sources were abundant and include a fraction that likely degraded on land prior to being transported into the Arctic Ocean. Bacterial signatures in Chesapeake Bay transition along the salinity gradient with intact hopanoids reflecting a diverse range of potential bacterial sources.Item USING "SMALL" MOLECULES AS TRANSMEMBRANE ANION TRANSPORTERS(2009) Okunola, Oluyomi Adeola; Davis, Jeffery T; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Functional, "small" molecule anion transporters have been identified and developed from natural products and synthetic organic compounds. The major discoveries include the design of a transmembrane Cl- transporter whose activity is pH-tunable, a NO3- transporter that displays unique selectivity for NO3- over Cl- anions, and a series of small molecules that efficiently transport HCO3- across liposomal membranes via a HCO3-/Cl- exchange mechanism. An assay for detecting transmembrane HCO3- transport using paramagnetic Mn2+ and 13C NMR is also described. Modulated Cl- transport was achieved by lipophilic calix[4]arene amides 2.2-2.4, all in the cone conformation. Modulation was achieved through functional group modification to one of the four side-chains. The cone conformation was confirmed by both 1H NMR and X-ray crystallography. Significantly, Cl- transport was gated by pH in the presence of triamido calixarene TAC-OH 2.3, which possesses a phenolic hydroxyl group. Using fluorescence assays, the rate of Cl- transport by TAC-OH 2.3 across liposomal membranes decreased with increasing pH, while transport rate by cone-H 2.2a, lacking an OH group, was not affected by pH. Nitrate was selectively transported over Cl- in the presence of nitro tripod 3.1, a small molecule receptor for both anions. The selective transport of NO3- by 3.1 is a significant discovery as most known synthetic Cl- transporters also transport NO3- ions and vice versa. Nitrate transport across liposomal membranes was confirmed by enzyme-coupled and fluorescence assays. Tripod 3.1 induced an increase in the intravesicular pH of liposomes that were not experiencing a pH gradient, while no pH changes occurred in the presence of calixarene 2.1 a known Cl- and NO3- transporter. This result suggests that 3.1 is an H+/NO3- symporter. Transmembrane HCO3- transport was achieved using the natural product, prodigiosin, 4.1, and synthetic isophthalamides 4.2-4.4. The Cl-/HCO3- exchange mechanism by which compounds 4.1-4.4 transport HCO3- was elucidated by ISE and NMR assays. The 13C NMR assay provided direct evidence for HCO3- transport in the presence of paramagnetic Mn2+ ions, and was adaptable to various assay conditions.Item Discrete and Polymeric Complexes Comprising Bis-nor-seco-CB[10] and Oligoammonium Ions(2009) Nally, Regan; Isaacs, Lyle; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)ABSTRACT Title of Document: DISCRETE AND POLYMERIC COMPLEXES COMPRISING BIS-NOR-SECO-CB[10] AND OLIGOAMMONIUM IONS Regan C. Nally, Ph.D., 2009 Directed By: Professor Lyle D. Isaacs Department of Chemistry and Biochemistry Supramolecular architectures composed of multiple components are challenging to produce, as the enthalpic gain must be greater than the entropic penalty of strict geometrical arrangements. Therefore, it is the goal of supramolecular chemists to strategically design and synthesize molecules that will exhibit selectivity toward formation of a particular complex. This dissertation describes the formation of supramolecular architectures of increasing size and is organized in the following way. Chapter 1 introduces the reader to the field of supramolecular polymer chemistry. Chapter 2 describes the synthesis of a series of monovalent ditopic guests (II-1 - II-6) and their complexation properties toward double cavity cucurbituril host bis-ns-CB[10]. We observed the preferential formation of 1:1, 2:2, and oligomeric complexes rather than the desired n:n supramolecular polymers. Guest II-7 which contains a longer biphenyl spacer successfully precludes the formation of the 1:1 complex but results in the formation of the 2:2 complex (bis-ns-CB[10]2*II-72) rather than supramolecular polymer. Guest II-8 is heterovalent and ditopic and is shown to reversibly form 2:2 and 1:2 complexes (bis-ns-CB[10]2*II-82 and bis-ns-CB[10]*II-82) in response to changes in host:guest stoichiometry. Lastly, this equilibrium can be manipulated by the addition of exogenous CB[6] which selectively targets the hexanediammonium ion binding region of II-8 and delivers the penta-molecular complex bis-ns-CB[10]*II-82*CB[6]2. Chapter 3 describes the formation of a main chain supramolecular polymer from a mixture of poly(diallyldimethylammonium chloride) (III-1) and bis-ns-CB[10]. The bis-ns-CB[10] molecular container behaves as a molecular handcuff, bringing together two ends of individual polymers to form III-1n* bis-ns-CB[10]m, resulting in an extension of the length of polymer. The effect of bis-ns-CB[10] on the physical properties of the polymer was investigated using viscometry in aqueous solution. A decrease in the ηrel was observed upon increasing concentrations of bis-ns-CB[10] to a solution of III-1. Atomic force microscopy (AFM), and diffusion-ordered spectroscopy (DOSY) were performed to probe the mode of interaction between polymer III-1 and bis-ns-CB[10]. Collectively, the data supports the two roles for bis-ns-CB[10]: 1) as a deaggregation agent, and 2) as a molecular handcuff that non-covalently links individual polymer strands resulting in overall extension of the polymer.Item Ketyl Radical Recombination Reaction in Various Ionic Liquids(2009) Pierson, Megan Christina; Falvey, Daniel; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Ten ionic liquids were made for a series of experiments meant to help characterize the usefulness of room temperature ionic liquids (RTILs) in various settings. This series of experiments used laser flash photolysis to study the effect of ionic liquids on the rate constants of the recombination of ketyl radicals, created from flash photolysis of benzophenone in the presence of benzhydrol. From the RTILs, the data showed that most ionic liquids had a faster rate constant than the diffusion limit predicted by the Einstein-Stokes-Smoluchowski equation. The main exception was that EMIM-NTf2 where the reaction was slower than its predicted diffusion limit.Item Synthetic Ion Channels From Lipophilic Guanosine Derivatives(2009) Ma, Ling; Davis, Jeffery T; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Synthetic ion channels and pores not only represent models of natural transmembrane ion channels, but also demonstrate their potential applications in the areas of drug delivery, biosensors, antimicrobial agents and other molecular devices. In this thesis, lipophilic guanosine derivatives that combine both "molecular recognition" and "membrane soluble" features are utilized for the development of the self-assembled synthetic ion channels. The potential of lipophilic G-quadruplexes to function as synthetic ion channels has been investigated by tracing the cation exchange process between free cations and G-quadruplex bound cations. Cation exchange between bulk cations (K+, NH4+) in solution and the bound cations in G-quadruplexes (G 1)16*4Na+*4DNP- was investigated by electrospray ionization mass spectrometry and by 1H , 15N NMR spectroscopy. The ESI-MS and 1H NMR data showed that G-quadruplexes containing "mixed cations" formed through a sequential ion exchange process. The use of NMR-"visible" 15NH4+ cations in the NMR titration experiments allowed the determination of two "mixed-cation" intermediates by 15N-filtered 1H NMR and selective NOE spectroscopy. A "central insertion" pathway was proposed for the cation exchange process from (G 1)16* 4Na+* 4DNP- to (G 1)16* 4NH4+* 4DNP-. In the lipophilic G-quadruplex, the "central" Na+, bound between the 2 symmetry related G8-Na+ octamers, is bound less strongly than are the 2 "outer" Na+ ions sandwiched within the G8-octamers. These results demonstrated the dynamic nature of lipophilic G-quadruplex in solution and directed the design of a ditopic guanosine-sterol conjugate as an approach toward making synthetic ion channels. Guanosine-sterol conjugate 3-1 was prepared by coupling 2', 3'-bis-TBDMS, 5'-amino guanosine with a bis-lithocholic acid derivative. Voltage clamp experiments demonstrated a series of stable, single ion channel conductances when compound 3-1 was incorporated into a planar phospholipid membrane. These channels are large; with nanoSiemens conductance values and they last for seconds of "open" time. This feature distinguishes them from most synthetic channels, which typically conduct in the picosiemens range with millisecond lifetimes. The structural studies using the bis-lithocholamide linker demonstrated that the guanosine moiety plays an essential role in the self-assembly of the transmembrane ion channels. The sizes of the most prevalent single channels calculated by Hille's equation are much larger than the diameter of a G-quartet, which suggested that the ion transport proceeded through larger pore(s) that form upon self-assembly of lipophilic guanosine-lithocholate 3-1 within the phospholipid membrane. The large transmembrane pore(s) could be envisioned as a supramolecular structure with hydrophobic walls of bis-lithocholate linker and a central pillar of a cation-filled G-quadruplex. The use of a bis-urea functionality in the bis-lithocholic acid linker generated guanosine-sterol conjugate 4-1. The ion channel activity of 4-1 was demonstrated by voltage clamp experiment. Large ion channels formed from 4-1 had longer life-times than those formed from compound 3-1. The extra stabilization of self-assembled ion channels attributed to the bisurea hydrogen bonding is consistent with the structural hypothesis of ion channels. The stable large transmembrane ion channels self-assembled by lipophilic guanosine derivatives have potential for delivery of drugs or biomolecules.Item Efforts Toward Synthesis of Novel Analogs of the Bacterial Second-Messenger, c-di-GMP(2009) Shurer, Andrew Joseph; Sintim, Herman O; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The formation of bacterial biofilms is a common mechanism for antibiotic resistance. It has been shown that bis-(3'-5')-cyclic dimeric guanosine monophosphate, c-di-GMP, plays a key role in bacterial biofilm formation; therefore, the proteins that regulate the metabolism or adaptive response of c-di-GMP are favorable targets for novel antimicrobials. We herein describe a solid-support methodology developed in the Sintim Laboratory and efforts toward its application to the synthesis of novel c-di-GMP analogs. Our selected targets are a series of analogs bearing various substitutions at the 2'-position of the ribose backbone. Syntheses of 2'-deoxy and 2'-methoxy analogs were achieved as well as that of key intermediates toward the 2'-fluoro and conformationally flexible analogs.Item PALLADIUM-CATALYZED ALLYLIC-ARYLATION: MECHANISTIC STUDIES AND APPLICATION TO THE TOTAL SYNTHESIS OF (+/-)-7-DEOXYPANCRATISTATIN DERIVATIVES(2009) Shukla, Krupa; DeShong, Philip; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Palladium-catalyzed carbon-carbon bond formation is one of the most widely used reactions for the synthesis of biologically active substances. The DeShong group has demonstrated that hypervalent silicates can be employed for allyl-aryl carbon-carbon bond couplings in the presence of a Pd(0) catalyst. The goals of this dissertation are (1) to demonstrate application of palladium-catalyzed allylic-arylation coupling to the total synthesis of (+/-)-7-deoxypancratistatin and its analogues, and (2) to study the mechanism of allyl-aryl cross coupling reactions. In spite of the potent antitumor and antiviral activity of (+)-7-deoxypancratistatin, the use of this compound is limited in clinical applications because of its low natural abundance and lack of a practical scalable synthetic route. In order to test the feasibility of siloxane-based coupling in the synthesis of 7-deoxypancratistatin, a simplified analogue of (+/-)-7-deoxypancratistatin was synthesized. The key reaction in the synthesis involved stereoselective construction of a carbon-carbon bond between A and C rings via coupling of an aryl siloxane with an allylic carbonate. While siloxane methodology was successfully applied to the synthesis of a (+/-)-7-deoxypancratistatin analogue, application of this methodology to the natural product (+/-)-7-deoxypancratistatin proved to be a significant challenge. To understand the causes of the failure of the coupling reaction, a detailed mechanistic study was undertaken. Hammett analysis of the allyl-aryl coupling reaction demonstrated that the rate of the coupling reaction was enhanced by electron-withdrawing groups on the aryl siloxane. The positive slope of the Hammett plot indicated a charged transition state in which negative charge on the aryl ring was stabilized inductively. Furthermore, this study provided useful information regarding the nature of ligands on the palladium. Based on this study, a new family of Pd(0) olefin catalysts was developed. These catalysts were found to be highly efficient and formed carbon-carbon bond even at ambient temperature. Novel Pd(0) olefin complexes were successfully employed in the synthesis of (+/-)-7-deoxypancratistatin. The key coupling reaction of allylic carbonate with aryl siloxane produced Hudlicky's intermediate, thus constituting formal total synthesis of the actual product. Though the reaction required higher catalytic loading and proceeded in moderate yields, the ability of the reaction to work at ambient temperature is advantageous for practical synthesis of the natural product. Future studies shall aim at optimization of the key coupling reaction and application of this methodology to the synthesis of pancratistatin and related derivatives.