Browsing by Subject "Conjugation"
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Item Open Access Poly-cyclodextrin cryogels with aligned porous structure for removal of polycyclic aromatic hydrocarbons (PAHs) from water(Elsevier, 2017-08) Topuz, F.; Uyar, TamerCyclodextrins (CDs) are sugar-based cyclic oligosaccharides, which form inclusion complexes with small guest molecules through their hydrophobic cavity. Here we successfully synthesized highly porous poly-cyclodextrin (poly-CD) cryogels, which were produced under cryogenic conditions by the cross-linking of amine-functional CDs with PEG-based diepoxide cross-linker. The poly-CD cryogels showed aligned porous network structures owing to the directional freezing of the matrix, of which the pore size and architecture exposed variations depending on the composition of the reactants. The cryogels were employed for the removal of genotoxic polycyclic aromatic hydrocarbons (PAHs) from aqueous solutions. They reached PAH sorption capacities as high as 1.25 mg PAH per gram cryogel. This high sorption performance is due to interactions between PAHs and the complete swollen network, and thus, is not restricted by interfacial adsorption. Given that the hydrophilic nature of the components, the sorption performance could only be attributed to the inclusion complex formation of CDs with PAH molecules. The poly-CD cryogels could be recycled with an exposure to ethanol and reused without any significant loss in the sorption capacity of PAHs.Item Open Access Protein folding, misfolding and aggregation: the importance of two-electron stabilizing interactions(Public Library of Science, 2017) Cieplak, A. S.Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions. © 2017 Andrzej Stanisław Cieplak. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Item Open Access Pyramidalized double bonds containing endoperoxide linkages: photooxygenation of dimethyl cis-3,8-dihydroheptalene-3,8, dicarboxylate(American Chemical Society, 1999) Saraçoǧlu, N.; Menzek, A.; Sayan, Ş.; Salzner, U.; Balci, M.Diels-Alder cycloaddition utilizing singlet oxygen as the dienophile with dimethyl cis-3,8-dihydroheptalene-3,8-dicarboxylate (5) has been investigated, and monoaddition product 7 has been isolated. The addition of a second singlet oxygen to the cycloheptatriene unit in 7 gave syn- bis(norcaradiene) bis(endoperoxide) 4. 1H NMR spectral studies and theoretical calculations indicate the increased pyramidalization in syn-4 compared with carbon analogue. The increased pyramidalization results from hyperconjugation between the central π-bond and the four adjacent C-O bonds and by rehybridization at C3, C4, C5, and C6. Furthermore, the increased reactivity for syn-4, which is probably arising from further folding of the central double bond, is also in agreement with theoretical calculations.Item Open Access Theoretical analysis of effects of π-conjugating substituents on building blocks for conducting polymers(American Chemical Society, 1999) Salzner, U.; Lagowski, J. B.; Pickup, P. G.; Poirier, R. A.Geometries of 4-dicyanomethylene-4H-cyclopenta[2,1-b:3,4-b'] dithiophene 1 and its C=O, C=S, C=CH2, C=CF2, and C=C(SR)2 analogues were optimized using density functional theory. Three of the above groups, C=C(CN)2, C=O, and C=S, were also examined on dipyrrole, difuran, dicyclopentadiene, and diborole. Electronic structures were analyzed with respect to their suitability as building blocks for conducting polymers with the natural bond orbital (NBO) method. All bridging groups investigated decrease HOMO-LUMO gaps compared to the unsubstituted parent dimers. Substitution affects HOMO and LUMO energies. Energy gap reduction is caused by a stronger decrease of LUMO energies compared to HOMO energies. The C=S group leads to even smaller energy gaps than the dicyanomethylene group since the HOMO is lowered less in energy with C=S. Compared to unsubstituted dimers, the strongest substituent effects are found with pyrroles and furans. Boroles and thiophenes are least affected. The smallest HOMO-LUMO gaps are obtained for electron-poor systems such as boroles followed by cyclopentadienes. This is analogous to the trend for the unsubstituted parent systems. All of the bridging groups are potential π-acceptors due to their low-lying π*-orbitals, and the corresponding polymers are predicted to be n-dopable. In aromatic structures, the LUMO is localized around the bridging substituent and the coefficients at the α-carbon atoms that reflect electron density are small. This might contribute to the poor conductivity of the n-doped form of poly-1. Electron- poor monomers and polymers tend to switch to quinoid structures. In quinoid repeat units, the HOMO is localized but not as strongly as the LUMO in the aromatic repeat units. The LUMO in quinoid repeat units is delocalized with large coefficients at the α-carbon atoms. Quinoid polymers could therefore be good conductors in the n-doped state.