Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Citation - WoS: 21Citation - Scopus: 23Engineering of Xylanases for the Development of Biotechnologically Important Characteristics(Wiley, 2023) Sürmeli, Yusuf; Şanlı Mohamed, GülşahXylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.Article Citation - WoS: 2Citation - Scopus: 2Tuning the Solid Phase Fluorescence Emission From Long Wavelength Visible To Near-Infrared in Oxazol-5 Derivatives: Structure–property Relationship, Theoretical and Experimental Studies(Springer, 2023) Nazlı, İbrahim Hanif; Yakalı, Gül; Topkaya, Derya; İzmirli, Merve; Uzun, Sema Demirci; Alp, SerapMost of the fluorescent molecules among organic π-conjugated materials show blue or green emission in the solid phase but few of them emit red-shifted visible and near-infrared light in the material science. To create molecules emitting for this feature, two π-conjugated oxazol-5-one derivatives containing donor (OCH3) and acceptor groups (NO2) were synthesized. Their optical and charge-transport properties were investigated through experimental and theoretical methods including the single crystal X-ray crystallography, Hirshfeld Surface Analysis, photophysical studies and Density Functional Theory (DFT), respectively. In addition, FT-IR, 1H-NMR, 13C-NMR spectroscopy, cyclic voltammetry (CV) measurements were performed. According to our results, both molecules may provide the significant pathway of development of long wavelength visible and red emissive features in solid phase with the aggregation induced enhanced emission (AIEE) properties particularly in the fields of OLEDs, optical communication, defence and bioimaging.Article Citation - WoS: 49Citation - Scopus: 54Highly Porous Poly(o-Phenylenediamine) Loaded Magnetic Carboxymethyl Cellulose Hybrid Beads for Removal of Two Model Textile Dyes(Springer, 2022) Arıca, Tuğçe Aybüke; Balcı, Fadime Mert; Balcı, Sinan; Arıca, Mehmet YakupEnsuring the removal of complex dyes from wastewater is a topic of great interest as it is vital for the environment. The present study reports a facile preparation method for poly(o-phenylenediamine) [p(o-PDA)] micro-particles loaded to magnetic carboxymethyl cellulose (CMC) hydrogel beads as adsorbents. The prepared products were characterized by FTIR, TGA, VSM, SEM, BET, and zeta sizer. The Fe3O4@p(o-PDA)@CMC beads were used for the removal of Reactive Blue 4 (RB-4) and Congo Red (CR) textile dyes from an aqueous medium. Different factors, such as adsorbent dose, initial pH, ionic strength, contact time, temperatures, and initial RB-4 and CR concentrations were examined. The maximum adsorption capacities of the RB-4 dye and CR at optimum pH 5 reached 398.7 and 524.6 mg/g in 120 min, respectively. The adsorption of RB-4 and CR on the hybrid magnetic beads can be due to the electrostatic, hydrogen bonding, and π-π interactions. Moreover, the magnetic hybrid beads showed easy regeneration ability and good reusability. The adsorbent can be a very good candidate for the efficient removal of micro-pollutant from wastewater.Article Citation - WoS: 5Citation - Scopus: 5Structural Analysis of Hyperbranched Polyhydrocarbon Synthesized by Electrochemical Polymerization(Royal Society of Chemistry, 2022) Jiang, Yi; Kim, Minhyeok; Nam, Hyunju; Kwak, Sang Kyu; Ruoff, Rodney S.; Lee, Sun Hwa; Seo, Jae Hong; Shin, Eunhye; Joo, Se Hun; Büyükçakır, OnurWe describe a structural analysis method for a hyperbranched polyhydrocarbon (PHC) produced by electrochemical polymerization. Nuclear magnetic resonance (NMR) techniques including 1H-NMR, quantitative 13C-NMR, DEPT 13C-NMR, and 1H-13C HSQC 2D NMR along with elemental analysis and FTIR were used to experimentally assess the likely structure of this complex polymer with random branching. The polymer structure was modeled based on the NMR results. Room temperature density, refractive index, melting temperature, and IR spectrum were good matches to the values, and spectrum, calculated using the simulated structure. Calculated Hildebrand solubility parameters for the simulated structure rationalize the room temperature solubility measured in a range of solvents. The experimental and modeling methods are likely to be applicable to any type of highly branched random branching polymer. To the best of our knowledge, this is the first comprehensive elucidation of the structure of an unknown and randomly hyperbranched polymer by combining experimental results and theoretical simulation, and the methods described should find broad use in the future.Article Citation - WoS: 4Citation - Scopus: 3Hg(ii)-Mediated Intramolecular Cyclization of Alkynyl Hydrazones: Towards a New Reaction-Based Sensing Approach for Hg(ii) Ions(Wiley, 2022) Tütüncü, Büşra Buse; Cebeci, Miray; Emrullahoğlu, MustafaDrawing upon an intramolecular cyclization/annulation reaction sequence mediated by Hg2+ ions, a BODIPY-based fluorescent probe decorated with an alkynyl hydrazone motif responds rapidly and selectively to Hg2+ ions, with a detection limit of 29 nM and a fluorescence turn-on ratio of 15-fold. With the addition of Hg2+ ions, the BODIPY-based alkynyl hydrazone transforms into a pyrazole ring to mediate a turn-on emission response clearly observable to the naked eye under visible light excitation.Article Citation - WoS: 3Citation - Scopus: 5Physically Unclonable Security Patterns Created by Electrospinning, and Authenticated by Two-Step Validation Method(IOP Publishing, 2022) Taşcıoğlu, Didem; Atçı, Arda; Sevim Ünlütürk, Seçil; Özçelik, SerdarCounterfeiting is a growing economic and social problem. For anticounterfeiting, random and inimitable droplet/fiber patterns were created by the electrospinning method as security tags that are detectable under UV light but invisible in daylight. To check the authenticity of the original security patterns created; images were collected with a simple smartphone microscope and a database of the recorded original patterns was created. The originality of the random patterns was checked by comparing them with the patterns recorded in the database. In addition, the spectral signature of the patterns in the droplet/fiber network was obtained with a simple and hand-held spectrometer. Thus, by reading the spectral signature from the pattern, the spectral information of the photoluminescent nanoparticles was verified and thus a second-step verification was established. In this way, anticounterfeiting technology that combines ink formula, unclonable security pattern creation and two-level verification is developed.Article Citation - WoS: 7Citation - Scopus: 7Regio- and Stereo-Chemical Ring-Opening Reactions of the 2,3-Epoxy Alcohol Derivative With Nucleophiles: Explanation of the Structures and C-2 Selectivity Supported by Theoretical Computations(Elsevier, 2022) Gündoğdu, Özlem; Atalay, Abdurrahman; Çelebioğlu, Neslihan; Anıl, Barış; Şahin, Ertan; Şanlı Mohamed, Gülşah; Bozkaya, Uğur; Kara, YunusThe ring-opening reactions of (1aS,2S,6bR)-5-ethyl-2-hydroxyhexahydro-4H-oxireno[2,3-e]isoindole-4,6(5H)-dione were investigated under very mild and nonchelated conditions. C-2 selective ring-opening products were obtained with nucleophilic additions such as Cl−, Br− and N3−. The exact configuration of (3aS,4R,5R,6S,7aS)-5-chloro-2-ethyl-4,6-dihydroxyhexahydro-1H-isoindole-1,3(2H)-dione was determined by X-Ray diffraction analysis which was obtained from the reaction of epoxy alcohol with HCl. On the other hand, theoretical computations were carried out to explain the regioselectivity in the ring opening reaction of epoxy alcohols. The results showed that the ring-opening reaction of both epoxy alcohols proceeds in a kinetically controlled manner and regioselectivity occurs depending on the transition state.Article Citation - WoS: 3Citation - Scopus: 6Hybrid Photonic-Plasmonic Mode-Coupling Induced Enhancement of the Spontaneous Emission Rate of Cds/Cdse Quantum Emitters(Elsevier, 2022) Gökbulut, Belkıs; İnanç, Arda; Topçu, Gökhan; Özçelik, Serdar; Demir, Mustafa Muammern this paper, a hybrid photonic-plasmonic resonator, which comprises an electrospun polymer fiber with a micrometer diameter and a core/shell nanostructure with a gold nanoparticle core, is constructed to investigate the dynamics of the coupled spontaneous emission of CdS/CdSe quantum dots (QDs). The gold nanoparticle core; covered with a silica shell, anchored with individual CdS/CdSe QDs, is placed inside a hollow cylindrical nanocavity formed on the surface of the microfiber to enable integration of the optical mode with the plasmonic effect, which is induced by the localized surface plasmons of the metal nanoparticle being present in the vicinity of the dipoles. The spontaneous emission rate of the QDs, coupled into the hybrid photonic-plasmonic mode, is measured to enhance by a factor of 23 via a time-resolved experimental technique. This result suggests that the regeneration of the optical mode-field inside the photonic-plasmonic resonator through the interaction of the dipoles with the localized surface plasmons of a metal nanoparticle strongly enhances the density of the electromagnetic states of the quantum emitters to facilitate an enhanced spontaneous emission within the host medium of the proposed polymer based-photonic structure.Article Citation - WoS: 8Citation - Scopus: 11The Effect of Protein Bsa on the Stability of Lipophilic Drug (docetaxel)-Loaded Polymeric Micelles(Elsevier, 2021) Polat, Hürriyet; Çevik Eren, Merve; Polat, MehmetPolymeric micelles are promising delivery vehicles for improving the efficacy of anticancer drugs and reducing their side effects. However, considering the binding ability of serum albumin, the possible interaction of micelles with the native plasma components in the bloodstream raises serious questions on micellar stability. The stability of barren or drug-loaded copolymeric micelles was investigated systematically in distilled water (DW) and simulated body fluid (SBF) solutions in the presence of a model protein. The copolymer was a Pluronic® series triblock copolymer (P-123), the drug was strongly lipophilic docetaxel (DOC) and the protein was Bovine Serum Albumin (BSA). The effect of such factors as BSA and DOC concentrations and the aging of the micellar solutions was studied. Both the barren and drug-loaded micelles were quite stable in blank DW and SBF solutions for long times up to 10 days. They lost integrity and showed no inclination to re-assemble when the BSA concentration reached a critical value, which was very close to the plasma Human Serum Albumin (HSA) concentration. The presence of DOC in the micellar cores could not prevent disintegration. The results illustrate clearly that ensuring the stability of polymeric micelles in blood plasma should be an important design factor in their use as drug carriers.Article Gas-Phase Fragmentation Reactions of A7 Ions Containing a Glutamine Residue(Wiley-Blackwell, 2021) Atik, Ahmet; Arslanoğlu, Alper; Yalçın, Talat; Atik, Ahmet; Arslanoğlu, Alper; Yalçın, TalatThe gas-phase fragmentation reactions of the a7 ions derived from glutamine (Q) containing model heptapeptides have been studied in detail with low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). Specifically, the positional effect of the Q residue has been investigated on the fragmentation reactions of a7 ions. The study involves two sets of permuted isomers of the Q containing model heptapeptides. The first set contains the QAAAAAA sequence, and the second set involves of QYAGFLV sequence, where the position of the Q residue is changed from N- to C-terminal gradually for both peptide series. An intense loss of ammonia from the a7 ions followed by internal amino acid eliminations strongly supports forming the imine-amides structure via cyclization/rearrangement reaction for all studied a7 ions. This is in agreement with the pioneering study reported by Bythell et al. (2010, 10.1021/ja101556g). A novel rearrangement reaction is detected upon fragmentation of imine-amide structure, which yields a protonated C-terminal amidated hexapeptide excluding the Q residue. A possible fragmentation mechanism was proposed to form the protonated C-terminal amidated hexapeptide, assisted via nucleophilic attack of the side chain amide nitrogen of the Q residue on its N-protonated imine carbon atom of the rearranged imine-amide structure. Highlights: The gas-phase fragmentation reactions of a7 ions obtained from protonated model peptides containing glutamine residue were studied by ESI-MS/MS. A rearranged imine-amide structure is the predominant even for a7 ions. Novel rearrangement reaction is observed which forms a protonated C-terminal amidated hexapeptide excluding Q residue upon fragmentation of the imine-amide structure.