Now showing items 1-20 of 225

    • Synthetic Approaches to C-1 Derivatives of Pancratistatin

      Uppalapati, Bhavana; Department of Chemistry
      The contents of this thesis describe a synthetic approach towards C-1 derivatives of pancratistatin, utilizing a previously published pathway to access a late-stage cis-diol. The key steps of the approach include enzymatic dihydroxylation to provide the C-ring backbone, Myers’ transposition to convert an allylic alcohol into an olefin, and nucleophilic substitution of a tosylate to insert carbon-based nucleophiles at C-1. Experimental and spectral data are provided for the novel compounds.
    • Hydroamidation of Vinyl Ethers by Acid-Catalyzed Multicomponent Isocyanide Addition

      Carlson, Brenden Matthew; Department of Chemistry
      Hydroamidation of carbon–carbon double bonds is an attractive strategy for installing nitrogen functionality into molecular scaffolds and, with it, increasing molecular complexity. To date, metal-based approaches have dominated this area of chemical synthesis despite the drawbacks of air and moisture sensitivity, limited functional group tolerance, toxicity, and/or high cost often associated with using metals. Herein is enclosed an operationally simple, metal-free, one-pot, regioselective, multicomponent synthetic procedure for the hydroamidation of carbon–carbon double bonds. This method features mild reaction conditions and utilizes isocyanides and vinyl ethers for the rapid and modular synthesis of α-oxygenated amide scaffolds. Additional effort was put towards synthesizing reactive natural products as substrates to the developed methodology, and drafting a probable catalytic cycle for the main and side reactions present within this multicomponent procedure.
    • Synthesis and Evaluation of Trans-bilayer Cross Linking Phospholipids Based on Click (Azide-Alkyne) Chemistry

      Hosseini, Yasaman; Department of Chemistry
      This thesis describes the synthesis of two phosphatidylcholine (PC) derivatives that are capable of coupling with each other from the alkyl chain through click reaction to form bola-PC. Successful coupling of monomeric phosphatidylcholine derivatives would lead to synthesis of corresponding phosphatidylinositol molecules as future work. PC derivatives that were synthesized in this work were phosphatidylcholine containing terminal azide and terminal alkyne on the alkyl chain of sn2 position. Sn-glycero-3-phosphocholine (GPC) was used as glycerol back bone with two available hydroxyl groups for esterification. The first esterification was done using dibutyltin oxide as catalyst and palmitoyl chloride as acylating agent on the primary hydroxyl group, sn1 position. Secondary hydroxyl group in the sn2 position of GPC was esterified by terminal alkyne and terminal azide fatty acids through Steglich esterification. PC analogues with suitable functional groups for click chemistry were, then, incorporated in the 100 nm-vesicles in buffer solution and exposed to copper catalyst/L-histidine complex and sodium ascorbate solution at room temperature. Formation of bola-PC were observed in the hydrophobic core of lipid bilayer and this was the main objective of this study.
    • N–Phenyl Pyrroloimidazolone Derivatives for Stereoselective Birch Reduction-Alkylation and Chiral Imidazolylidene-Iridium Complexation

      Tran, Ngan; Department of Chemistry
      This thesis describes the synthesis and use of an N– based proline–derived directing group towards the Birch reduction, diastereoselective alkylation, and the synthesis of NHC–iridium complexes that are precursors for the study of intramolecular aryl C–H activation. A pair of ortho–benzoate esters containing epimeric pyrroloimidazolone chiral auxiliaries underwent sequential Birch reduction and diastereoselective alkylation to provide products ranging from a 50:50 to 95:5 dr for the anti– epimer, and 88:12 to >95:5 diastereomeric ratio (dr) for the syn– epimer. Single crystal X–ray analysis of key anti–epimer–derived products, along with the comparison of the optical rotation measurements of enantiomers that were prepared from the syn–or anti– starting materials to its known enantiomer confirmed the stereoselectivity of the products. This work includes related Schultz stereoselective Birch reduction alkylation of anisole with a chiral benzamide except that the pyrroloimidazolone replaces the achiral methoxy group and serves as the stereodetermining element. In addition, the synthesis and evaluation of the N–phenyl iridium complex derived from the annulated aminal with syn–stereochemistry in the backbone was achieved. Exposure of the neutral Ir–complexes to anionic nucleophiles such as MeLi resulted in an increase of electron density at the Ir atom that initiated C–H bond activation. Lastly, a N–heterocyclic carbene ligand derived from the N–benzyl analogue of the auxiliary was also investigated. Attempts to design a monodentate ligand as well as a bidentate ligand bearing an alcohol side chain were both shown to be unsuccessful at this time.
    • Development of Universal Biosensing Platforms Based on CRISPR/Cas12a systems

      Li, Yongya; Department of Chemistry
      CRISPR/Cas technologies possess the promising potential to affect biosensing field by providing a sensitive, precise, rapid, versatile and cost-effective method for diverse target detections. This thesis focusses on the development of CRISP/Cas12a based biosensing platforms for nucleic acid and protein detection. Two distinct CRISPR/Cas based diagnostic methods were developed. The first developed method is a plasmonic CRISPR Cas12a assay for colorimetric detection of viral nucleic acid. This assay generates colorimetric signals for nucleic acid amplicons by combining the unique target-induced collateral cleavage activity of Cas12a with plasmon coupling of DNA functionalized gold nanoparticles. The practical applications of this assay were successfully demonstrated through the nucleic acid detection of hepatitis B virus (HBV) and Grapevine Red-Blotch Virus (GRBV). The second developed method is a universal proximity CRISPR Cas12a assay for ultrasensitive detection of nucleic acids and proteins. The target recognition is achieved through proximity binding rather than direct CRISPR/Cas 12a recognition, allows the flexible assay design and expansion to target diverse targets. This assay was successfully adapted to detect nucleic acids and antibodies in both buffer and diluted human serum.
    • Synthesis of Heteroleptic Redox-active and Spin-crossover Complexes

      Pelaccia, Mark; Department of Chemistry
      The following research regarding heteroleptic redox-active complexes with the potential for spin-crossover is synthetic in nature. The intent behind incorporating the Schiff base ligand N-(8-quinolyl)salicylaldimine with some redox-active species into a mixed ligand complex featuring a d4-d7 metal ion center was to prime the material for spin-crossover based on strong intermolecular interactions that would enhance cooperativity of the system. Single component systems that display spin-crossover behaviour paired with other physical properties like electrical conductivity hold significance in the field of multifunctional materials, of which there are few examples that feature mixed ligand systems. Information describing this type of chemistry and the magnetic interactions that govern these characteristics is introduced in the first chapter of this work. The synthetic strategies toward mixed ligand complexes in the form of [(Qsal)Fe(RAL)]+X- and [(Qsal)Co(RAL)]+X- have been realized from the use of mononuclear [(Qsal)FeCl2(CH3OH)] and [(Qsal)Co(OAc)]+OAc- species, respectively. The redox-active ligand (RAL) component is an arylazo ligand like 10-(8-quinolylazo)-9-phenanthrol (Qapl) or 1-(2-Pyridylazo)-2-phenanthrol (Papl), which possess a low-lying π* MO that makes them susceptible to multi-step reductions that give rise to radical intermediates. Heteroleptic complexes that were synthesized and isolated like [(Qsal)Fe(Qapl)]+BPh4-, [(Cl-Qsal)Fe(Qapl)]+BPh4-- and homoleptic [Fe(Qapl)2]+BPh4- were diffracted and measured several intermolecular π-π contacts of distances typically between 3.5-3.7 Å, often between the phenanthrene rings of adjacent Qapl ligands. Complexes In the form of [(Qsal)Fe(Qapl)]+X (X= BPh4- or SCN-) showed early onset of spin transition in solution usually beyond 298 K. These complexes were overly reduced in the glovebox which resulted in their deterioration, presumably from the cleavage of the RAL azo bond. The framework developed for the heteroleptic Fe3+ coordination chemistry was applied to cobalt, with some amendments, and afforded several heterleoptic Co3+ complexes using Qsal with the arylazo ligands Qapl and Papl. The heteroleptic cobalt complexes presented here were found to be LS Co3+ which is diamagnetic. However, there is potential under inert atmosphere to produce Co2+ and possibly a phenoxyl radical species with redox-active valence tautomers.
    • Epimeric L-Proline Derived Imidazolone Chiral Auxiliaries for the Stereoselective Alkylative Birch Reduction of Aromatic Esters and Benzonitriles

      Cadwallader, Dusty; Department of Chemistry
      Described in this thesis are several advancements of imidazolidinone chiral auxiliaries. Initially, attempts were made to develop a N-heterocyclic carbene ligand derived from the N-benzyl analog of the auxiliary. Attempts to design a monodentate ligand as well as a bidentate ligand bearing an alcohol side chain were both shown to be unsuccessful. Work on the N-phenyl variant of the auxiliary included expanding upon our recently discovered methodology; a Birch reduction alkylation sequence of an aromatic ester yielding chiral quaternary carbon centres in a stereoselective matter. In substrates that demonstrate poor stereoselectivity, modification of the auxiliary to include a larger neopentoxy directing group gives way to increased selectivity. This work also includes the same Birch reduction alkylation sequence on a series of benzonitrile substrates with up to 64:36 diastereomeric ratio from either epimer of the auxiliary. The low selectivity of the benzonitrile substrates is offset by the resulting diastereomers of the dihydrobenzonitrile products being chromatographically separable. This results in the first preparation of optically pure quaternary carbons alpha to nitrile by Birch-type reductive alkylation. Progress was also made in the manipulation of chiral auxiliaries bearing the chiral alkoxy moiety. These functional groups were transformed into hemiaminals by citric acid hydrolysis in a 3:2 ratio with imidazolone by-products formed by acid mediated elimination of alcohol.
    • The Synthesis of Phosphatidylinositol Bolalipids

      Jewell, Shannon; Department of Chemistry
      This thesis describes the attempted synthesis of phosphatidylinositol bolalipids to be used in the investigation of the mechanism of the phosphatidyl inositol transfer protein, Sec14, and the PI(4)-kinase, Pik1. The synthesis of two unique bolalipids was the goal of this thesis. The esterification of the sn1 position of a protected glycerol unit to stearic acid as well as esterification at the sn2 position to either the C20 or C36 diacid gave the framework of the desired bolalipid. Further success was seen in the coupling of benzyloxybis(diisopropylamino) phosphine to the sn3 position of the deprotected glycerol unit in the generation of a phosphoramidite. However, efforts in the final step of the synthetic method were unsuccessful and did not lead to the complete synthesis of the bola-PI. Though it was possible to couple the 2,3,4,5,6-benzyl protected myo- inositol to the phosphoramidite, the most significant issues in the synthesis of the bola-PI is the oxidation of the phosphite to the phosphonate. Despite multiple attempts with varying oxidizing agents, no oxidation was observed by TLC, P NMR or mass spectrometry data. Two phosphoramidites, precursors to the desired bola-PI molecules, have been synthesized to date. The two phosphoramidites were characterized by H NMR, C NMR, P NMR, mass spectrometry, and optical activity. They are both air and water sensitive and have been observed to decompose with storage, even when placed under nitrogen at -4 oC. Spectral and experimental data are provided for all new compounds.
    • Development and Investigation of the Fluorescence of Cyclopropenium Ions

      Guest, Matt; Department of Chemistry
      The work presented herein employs cyclopropenium ions as a central design element towards the goal of developing fluorescent, superbasic and boronium-substituted compounds. A novel guanidine-cyclopropenimine proton sponge with exceptional basicity is reported that was further utilized to develop a stable tetracoordinate boronium-substituted proton sponge. A large focus of this thesis was also placed on the development of the recently discovered fluorescence of cyclopropenium ions leading to a new class of small molecule organic fluorophores. Among this new platform of fluorescent compounds, a specific fluorophore featured an impressive photophysical profile that bodes well for future applications in fluorescent imaging techniques. Insight into the structure, electronics, bonding and photophysical properties of these derivatives is offered.
    • Synthesizing Self-Healing and Recyclable Silicones Using the Diels-Alder Reaction as a Cross-Linker: Investigation of Various Dienes and Dienophile Systems

      Azadi Namin, Paria; Department of Chemistry
      This thesis focuses on the synthesis of recyclable and self-healing polysiloxane elastomer networks. These features were achieved through the use of thermally reversible Diels-Alder (DA) and retro-Diels-Alder (rDA) reactions. In this work, for the model system, two different dienes (3 and 8) and six dienophile were explored, of which five of the dienophiles are commercially available and one of them was synthesized in the lab (13) to produce a series of model DA adduct. Model systems consisting of diene-functionalized trisiloxanes and bismaleimides as dienophiles were utilized to develop a fundamental understanding of how the electronic differences in the coupling systems would influence the efficiency of the overall reaction. Then for the elastomers, three different methylhydrosiloxane-dimethylsiloxane copolymer, trimethylsiloxane terminated (PDMS) with different molecular weights and Si-H group mole percentages [32 a = 3-4% Si-H and 13000 g/mol; 32 b = 7-9% Si-H and 5500-6500 g/mol; 32 c = 25-30% Si-H and 2000-2600 g/mol] were used and functionalized with two different dienes (3 and 8) to produce six polymeric diene systems (33 a, 33 b, 33 c, 34 a, 34 b and 34 c). After analyzing the model systems, the optimal temperature for adduct formation was determined to be between 60 °C – 70 °C, while the rDA reactions occur were found to occur between 90 °C and 110 °C , depending on the system. The tensile strengths of the elastomer systems correlated well with the cross-link densities of individual elastomers (elastomers were elongated between 0.3 cm and 2.54 cm). Furthermore, the hardness of the elastomers also correlated with the cross-link density of the elastomer (Shore 00 values ranged from 32 to 8 ). However, all of the elastomers displayed a decrease in their Shore 00 values after being damaged and healed. Of particular note in this study are elastomers 35 b and 35 c. Not only were these the only examples of translucent and colourless materials, the elastomers fully cured at room temperature in only 5 h. After mechanical damage the elastomers were heated to 80 °C to induce mobility in the polymer chains, complete healing of the mechanical damage was observed to occur in approximately 3 min and upon cooling to room temperature it cured and got solid again.
    • Synthesis and Investigation of Light Responsive Molecules Containing Cyclopropenium Ions

      Le Sueur, Richard; Department of Chemistry
      The present thesis describes recent advances in the pursuit of novel light-responsive molecules containing cyclopropenium ions. In an effort to understand the underlying factors regarding the photophysical properties of cyclopropenium ions, emphasis was placed on the previously reported “Janus sponge”, where systematic structural modifications to four individual components of the molecule led to measurable and predictable changes in molar extinction coefficients, quantum yields, and Stokes shifts. Using time-dependent density functional theory calculations, the origin of these trends were traced to internal charge transfer. Additionally, modulating hydrogen bonding between intermolecular, bifurcated, and intramolecular interactions by choice of counterion was used to alter the quantum yield of cyclopropenium ion-containing fluorophores. The basis of this switchability was examined using X-ray diffraction analysis, 1H NMR spectroscopy, density functional theory calculations, and fluorescence spectroscopy. Notably, this work led to the development of the first cyclopropenium ion containing “true” proton sponge. As an extension, light responsive molecules are not isolated to fluorescence. This thesis also outlines the development of the first cyclopropenium ion containing an azo group. Key findings include the fact that cyclopropenium ion containing azo compounds are stable and cyclopropenium ions red-shift the absorbance wavelength in comparison to azobenzene by 75 nm. The synthetic, structural, electronic, and photophysical properties of these compounds are discussed.
    • Development of Field-deployable Nucleic Acid Testing Platforms

      Dong, Tianyu; Department of Chemistry
      This thesis is focused on the development of field-deployable nucleic acid testing platforms to allowed rapid detection and quantification of nucleic acids. Two distinct platforms suitable for nucleic acid testing in resource-limited settings were developed. First, a paper-based diagnostic device was developed. The principle of this paper-based device was based on the unique interfacial interaction of DNA and the DNA intercalating dye with cellulose on chromatographic paper. Second, a colorimetric reader was developed. The principle of the reader was based on measuring the absorbance change of a chromogenic substrate which is triggered by DNA and DNA intercalating dyes under light illumination. The performance of both devices was tested using synthetic DNA, nucleic acid amplicons, and actual parasites nucleic acid samples collected from school-age children in rural areas of Honduras.
    • Application of Density Functional Theory to Study the Mechanism of Alkali Metal Enolate Oxidation by N-sulfonyloxaziridines, Umpolung Amide Synthesis from Halo-Amino-Nitro Alkanes, Alkali-Metal Catalyzed Transfer Hydrogenation of Ketones, and Asymmetric Catalyzed Aza-Henry Reactions

      Foy, Hayden; Department of Chemistry
      Density functional theory (DFT) and other computational methods are useful tools for determining reaction mechanisms and the factors governing stereoselectivity. To illustrate the versatility of DFT methods, the following reactions were studied: (1) Li+, Na+, and K+ enolate addition to chiral N-sulfonyloxaziridines, stereoselectivity was found to be controlled by enolate, sulfonyl, and oxaziridine oxygen-cation chelation and steric contacts. From this study it was found that the mechanism proceeded in a SN¬1 rather than SN¬2 like fashion. (2) umpolung amide synthesis working from 1,1,1,1-halo-amino-nitro-alkanes leading to the finding that the amide oxygen originates from the nitro group but also from explicitly interacting water molecules in competing pathways. (3) alkali (Li+, Na+, and K+) metal-catalyzed transfer hydrogenation of acetophenone, the mechanism of which was found to proceed via a six-membered transition state affording direct hydrogen transfer to acetophenone generating the product phenylethanol. The TMEDA ligand had a profound effect in stabilizing the transition state which in turn, lowered the activation energy in comparison to the use of isopropanol ligands. Lastly, (4) asymmetric catalyzed Aza-Henry reactions. Controlling the stereoselectivity of such reactions catalyzed by HMeOQuin((Anth)Pyr)-BAM was an H-bonding manifold of specific hetero- and homonuclear hydrogen bonding motifs (N-H-O and N-H-N respectively) observed in the favored transition state structure (syn-(2S,3R)-TS(eq)). There was a central theme of sterics and other non-covalent interactions, such as - stacking or CH/ interactions, which also played significant roles in determining the stereoselectivity in the investigated reactions.
    • DNA Walkers: Emerging Analytical Applications, Biomolecular-Nanomaterial Probes and Biomolecule Sensors

      Mason, Sean; Department of Chemistry
      DNA walkers are a unique class of dynamic DNA devices that move nucleic acid walkers processively along designated one-, two-, or three-dimensional tracks. Because of the unique mechanical motion, dynamic interaction, and capabilities for signal amplification, programmable signal transduction, high directionality, and predictable analytical performance on the basis of Watson-Crick base paring rules, this class of dynamic DNA nanodevice has gained great attention from the analytical community in the recent years. This includes bioanalytical applications that range from nucleic acid sensing, to protein detection and to cellular imaging and analysis. The research described herein focuses on improving the understanding of biophysical processes involved in the design and operation of DNA walkers. Specifically, we developed a series of stochastic DNA walkers capable of probing dynamic interactions occurring at the biomolecule-nanoparticle (bio-nano) interface. By monitoring dynamics of DNA walkers on spherical nucleic acid (SNA) tracks, we systematically investigated effects of varying interfacial factors, including intramolecular interactions, orientation, cooperativity, steric effect, multivalence, and binding hindrance on enzymatic activities at the bio-nano interface. Leveraging the newly gained knowledge at the interface, we also fabricated ultrasensitive biosensors for amplified detection of nucleic acids and antibodies. Our study revealed critical roles of interfacial factors to enzyme activities and performance of enzyme-driven nanodevices. We also demonstrate that improvement in understanding bio-nano interfaces will facilitate the design and operation of biosensors and inspire new sensing mechanisms.
    • Synthesis of fluorinated nucleosides for probing DNA conformations via 19F NMR spectroscopy

      Solodinin, Andrei; Department of Chemistry
      Work described in this thesis explored the synthesis of 5-fluoro-2’-deoxycytidine and 8-fluoro-2’-deoxyguanosine, and subsequent incorporation of these modified nucleosides into d(CG) repeat oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis, in order to investigate the B-Z junction through 19F NMR spectroscopy. Toward this goal, 5-fluoro-2’-deoxycytidine was successfully synthesized from 5-fluoro-2’-deoxyuridine. Choices of protecting groups for the exocyclic amine of 5-fluoro-2’-deoxycytidine were examined, and N-acetyl was found to be most suitable in terms of the stability of the protected nucleoside and the readiness of its removal. 8-Fluoro-2’-deoxyguanosine was prepared by fluorination of suitably protected 2’-deoxyguanosine using N-fluorobenzenesulfonimide as the fluorinating agent. Circular dichroism and UV/vis spectroscopic studies showed that the fluoro-modification does not affect the overall conformation of the oligonucleotides, both in the B- and Z-form. 19F NMR spectra of single fluoro-modified d(CG)6 sequence at 3’-end (11-FdC) were recorded in solution containing 0.1 – 4 M NaCl. The results supported a theoretical model for B-/Z-DNA transition, where initiation starts from the ends, progressing to eventual transition.
    • Novel Tridentate N,S,N-Metal Compounds of Zinc, Germanium and Phosphorus

      Lortie, John; Department of Chemistry
      A novel ligand based on a flexible NSN tridentate framework, and main group compounds of the general formula M(NSN) were prepared on zinc, germanium, and phosphorus. The compound ZnNSN(dimethylaminopyridine) (III-45a) is fluxional with III-46a in tetrahydrofuran, and its exchange parameters were calculated from NMR measurements. An X-ray structure was obtained for GeNSN (III-47a) crystals isolated from diethylether and exhibits an envelope-like geometry with coordination of the soft sulfur donor to the germanium centre. III-47a was not reactive with CH3I but showed reactivity with 3,6-di-tert-butyl-o-benzoquinone. ClPNSN (III-53) was prepared both by transmetallation of III-46a and by a reaction of an in situ generated Li2NSN and PCl3. HPNSN (III-52) was prepared by halogen exchange of III-53 and L-selectride.
    • Synthesis of 3’, 5’-cyclic diguanylic acid (c-di-GMP) as mucosal vaccine adjuvant and bacterial second messenger

      Milah, Khatma; Department of Chemistry
      The present study describes the synthesis of 3’,5’- cyclic diguanylic acid (c-di-GMP), attempts were made to synthesize guanosine bearing a 2’-O-(hexyn-6-yl)- and 2’-O-(6-azidohexyl)-modification using 2,6-diaminopurine riboside as starting material. The synthesis of 2’-O-(hexyn-6-yl) guanosine started with the alkylation of 2,6-diaminopurine riboside with 6-iodo-1-hexyne, which gave a mixture of 2’- and 3’-O-alkylated 2,6-diaminopurine riboside. Treatment of this product with isobutyryl chloride, followed by ammonium hydroxide gave N2-isobutyryl-2’-O-2’-O-(hexyn-6-yl)-2,6-diaminopurine riboside. Subsequent deamination reaction was carried out with sodium nitrite in a mixed solvent gave the desired N2-isobutyryl-2’-O-2’-O-(hexyn-6-yl) guanosine. N2-Isobutyryl-2’-O-(6-azidohexyl) guanosine was also obtained in the similar manner. Synthesis of a second building block, a suitably protected guanosine H-phosphonate was also attempted using guanosine as starting material. Experimental and spectral data are provided for new compounds.
    • Transient Electron Paramagnetic Resonance Spectroscopy on Photosystem I Reaction Centers

      Shekarsaraei, Setareh; Department of Chemistry
      The reason for the different rates of electron transfer from phylloquinone (PhQ) to the iron-sulfur cluster FX in the two branches of Photosystem I (PSI) is not fully understood. Techniques such as Transient Electron Paramagnetic Resonance (TREPR) have allowed further understanding of the electron transfer rates in these two branches and the role of D575PsaB and Q588PsaA in determining the different rates. Room temperature 9.5 GHz TREPR measurements were performed on PSI from the wildtype and three mutant strains of the cyanobacterium Synechocystis sp. PCC6803, Q588DPsaA (A-mutant), D575QPsaB (B-mutant), Q588DPsaA/ D575QPsaB (AB-mutant) to determine the effects of the mutations on the rates of the electron transfer. The goal of these experiments is to test the model proposed by Ishikita and Knapp, (J. Biol. Chem. 278, 52002–52011 (2003)) that explains the differences in the electron transfer rates as resulting from differences in the amino acid sequences of the two main protein subunits PsaA and PsaB which lead to different midpoint potentials of the two PhQs. The model also proposes that aspartate D575PsaB changes its protonation state during electron transfer. The model suggests that D575PsaB and Q588PsaA play significant roles in determining the potentials, but a previous study found that mutations to D575PsaB caused only small changes in the kinetics (Karyagina, Pushkar, Stehlik, van der Est, Ishikita, Knapp, Jagannathan, Agalarov, Golbeck (Biochemistry 46, 10804-10816 (2007)). It was proposed that this is because the mutations caused similar changes in the potentials of both PhQ and Fx. In this thesis, this proposal is tested using the double mutant Q588DPsaA/ D575QPsaB. Because the two point mutations are symmetrical with respect to FX but not with respect to the quinones, it is postulated that the potentials of the quinones should be changed while that of FX should be unaffected and therefore, the kinetics of the A- and B- branches should be significantly altered. The transient EPR data show evidence that the rates of electron transfer in the two branches have been swapped in the double mutant Q588DPsaA/ D575QPsaB and this indicates the important roles of D575PsaB and Q588PsaA in determining the electron transfer rate.
    • A Step Toward Recyclable Silicone Elastomers

      Nasresfahani, Amin; Department of Chemistry
      This thesis introduces a new strategy for developing polysiloxane networks with the capacity of being recycled. The conventional methods of cross-linking polysiloxanes suffer from lack of self-repair and recyclability. Diels-Alder/retro-Diels-Alder (DA/RDA) equilibrium is a key to establish thermally reversible linkages among polysiloxane chains to enable the material’s recyclability. The equilibrium is optimized to improve the extent of reversibility of the Diels-Alder adduct through functional groups such as carboxyphenyl, ester, and carbon spacers in the structures of maleimide and furan derivatives. The DA/RDA equilibrium is studied by various nuclear magnetic resonance (NMR) spectroscopy experiments and differential scanning calorimeter analyses. The DA reaction is found to be at its highest rate at 50 ͦC while the retro-Diels-Alder reaction is predominant at 110 ͦC. Comparison of the reaction rate constant of the optimized maleimide and furan derivatives at 50 ͦC with the literature suggests that the DA reaction is among those ones described as ultra fast kinetic. Accordingly, series of polysiloxanes are functionalized with the optimized maleimide and furan derivatives to obtain recyclable polysiloxane networks. Dynamic, variable-temperature solid-state 1H NMR experiments are confirmed the rapid, reversible nature of the cross-links within the polysiloxanes. The injured networks are mended to the point that signs of defects were nearly imperceptible even by scanning electron microscopy. The binding strengths of the healed materials are quantified using stress-strain measurements. The healed networks displayed binding strengths that are equal or superior to the undamaged ones.
    • (A) Constructing a Three-Dimensional DNA Nanomachine to Achieve Rapid Isothermal Signal Amplification for Nucleic Acid Detection (B) Regulation of DNA Strand Displacement Using an Allosteric DNA Toehold

      Yang, Xiaolong; Department of Chemistry
      (A) We developed a new strategy to achieve rapid isothermal signal amplification through the construction of DNA nanomachine. DNA nanomachine built from a DNA functionalized gold nanoparticle (DNA−AuNP), which moves a DNA walker along a three-dimensional (3-D) DNA−AuNP track and executes the task of releasing signal reporters (SRs) to generate fluorescence. The movement of the DNA walker is powered by a nicking endonuclease that cleaves specific DNA substrates on the track. During the movement, each DNA walker cleaves multiple substrates, resulting in the rapid release of SRs to achieve signal amplification at a constant temperature. The 3-D DNA nanomachine is highly efficient due to the high local effective concentrations of all DNA components that have been co-conjugated on the same AuNP. Moreover, the activity of the 3-D DNA nanomachine can be controlled by introducing a protecting DNA probe that can hybridize to or dehybridize from the DNA walker in a target-specific manner. This property allows us to tailor the DNA nanomachine into a DNA nanosensor that is able to achieve rapid, isothermal, and homogeneous signal amplification for detection of nucleic acids in both buffer and a complicated biomatrix. (B) Toehold-mediated DNA strand displacement has proven extremely powerful in the construction and operation of DNA devices, including reconfigurable structures, DNA circuits, and amplifications. To achieve the construction of such DNA devices, toeholds are required for controllable activation and regulation. Usually, the complicated strand displacement behaviors and functions are achieved by combining conventional toehold-mediated strand displacement, associative toehold-mediated strand displacement, and remote toehold strand displacement toehold activation mechanisms. We still need to enrich the toolbox of strand displacement techniques with alternative approaches for toehold activation to construct devices of higher complexity. Here we introduce an allosteric DNA toehold (A-toehold) design that allows flexible activation or regulation of DNA strand displacement.