PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397

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Citation - WoS: 53
Citation - Scopus: 59
Thickness-Tunable Self-Assembled Colloidal Nanoplatelet Films Enable Ultrathin Optical Gain Media
(Amer Chemical Soc, 2020) Erdem, Onur; Foroutan, Sina; Gheshlaghi, Negar; Guzelturk, Burak; Altintas, Yemliha; Demir, Hilmi Volkan
We propose and demonstrate construction of highly uniform, multilayered superstructures of CdSe/CdZnS core/shell colloidal nanoplatelets (NPLs) using liquid interface self-assembly. These NPLs are sequentially deposited onto a solid substrate into slabs having monolayer-precise thickness across tens of cm(2) areas. Because of near-unity surface coverage and excellent uniformity, amplified spontaneous emission (ASE) is observed from an uncharacteristically thin film having 6 NPL layers, corresponding to a mere 42 nm thickness. Furthermore, systematic studies on optical gain of these NPL superstructures having thicknesses ranging from 6 to 15 layers revealed the gradual reduction in gain threshold with increasing number of layers, along with a continuous spectral shift of the ASE peak (similar to 18 nm). These observations can be explained by the change in the optical mode confinement factor with the NPL waveguide thickness and propagation wavelength. This bottom-up construction technique for thickness-tunable, three-dimensional NPL superstructures can be used for large-area device fabrication.
Citation - WoS: 49
Citation - Scopus: 51
Dicarboxylic Acids Induced Tandem Transformation of Silver Nanocluster
(Amer Chemical Soc, 2023) Wang, Zhi; Gupta, Rakesh Kumar; Alkan, Fahri; Han, Bao-Liang; Feng, Lei; Huang, Xian-Qiang; Sun, Di
Structural transformation of metal nanoclusters (NCs) is of great ongoing interest regarding their synthesis, stability, and reactivity. Although sporadic examples of cluster transformations have been reported, neither the underlying transformation mechanism nor the intermediates are unambiguous. Herein, we have synthesized a flexible 54-nuclei silver cluster (Ag54) by combining soft ((BuC)-Bu-t=C-) and hard ((PrCOO-)-Pr-n) ligands. The existence of weakly coordinated nPrCOO(-) enhances the reactivity of Ag54, thus facilitating the dicarboxylic acid to induce structural transformation. X-ray structural analyses reveal that Ag54 transforms to Ag-28 cluster-based 2D networks (Ag28a and Ag28b) induced by H(2)suc (succinic acid) and H(2)glu (glutaric acid), whereas with H(2)pda (2,2'-(1,2-phenylene)diacetic acid), a discrete Ag-28 cluster (Ag28c) is isolated. The key intermediate Ag17 that emerges during the self-dissociation of Ag54 was isolated by using cryogenic recrystallization and characterized by X-ray crystallography. The "tandem transformation" mechanism for the structure evolution from Ag54 to Ag28a is established by time-dependent electrospray ionization mass spectrometry (ESIMS) and UV-vis spectroscopy. In addition, the catalytic activity in the 4-nitrophenol reduction follows the sequence Ag28c > Ag28b > Ag28a > Ag54 due to more bare silver sites on the surface of the Ag-28 cluster unit. Our findings not only open new avenues to the synthesis of silver NCs but also shed light on a better understanding of the structural transformation mechanism from one cluster to another or cluster-based metal-organic networks induced by dicarboxylates.
Citation - WoS: 53
Citation - Scopus: 54
Cadmium-Free and Efficient Type-II InP/ZnO Quantum Dots and Their Application for Leds
(Amer Chemical Soc, 2021) Eren, Guncem Ozgun; Sadeghi, Sadra; Jalali, Houman Bahmani; Ritter, Maximilian; Han, Mertcan; Baylam, Isinsu; Nizamoglu, Sedat
It is a generally accepted perspective that type-II nanocrystal quantum dots (QDs) have low quantum yield due to the separation of the electron and hole wavefunctions. Recently, high quantum yield levels were reported for cadmium-based typeII QDs. Hence, the quest for finding non-toxic and efficient type-II QDs is continuing. Herein, we demonstrate environmentally benign type-II InP/ZnO/ZnS core/shell/shell QDs that reach a high quantum yield of similar to 91%. For this, ZnO layer was grown on core InP QDs by thermal decomposition, which was followed by a ZnS layer via successive ionic layer adsorption. The small-angle Xray scattering shows that spherical InP core and InP/ZnO core/ shell QDs turn into elliptical particles with the growth of the ZnS shell. To conserve the quantum efficiency of QDs in device architectures, InP/ZnO/ZnS QDs were integrated in the liquid state on blue light-emitting diodes (LEDs) as down-converters that led to an external quantum efficiency of 9.4% and a power conversion efficiency of 6.8%, respectively, which is the most efficient QD-LED using type-II QDs. This study pointed out that cadmium-free type-II QDs can reach high efficiency levels, which can stimulate novel forms of devices and nanomaterials for bioimaging, display, and lighting.
Citation - WoS: 6
Citation - Scopus: 8
Histone Deacetylase Inhibition and Autophagy Modulation Induces a Synergistic Antiproliferative Effect and Cell Death in Cholangiocarcinoma Cells
(Amer Chemical Soc, 2023) Yenigul, Munevver; Akcok, Emel Basak Gencer
Cholangiocarcinoma, also known as biliary tract cancer,is an aggressiveadenocarcinoma arising from epithelial cells lining the intra- andextrahepatic biliary system. The effects of autophagy modulators andhistone deacetylase (HDAC) inhibitors in cholangiocarcinoma are notfully known. It is essential to understand the molecular mechanismsand the effects of HDAC inhibitors in the context of cholangiocarcinoma.The antiproliferative effect of different HDAC inhibitors and autophagymodulation was investigated by the MTT cell viability assay in TFK-1and EGI-1 cholangiocarcinoma cell lines. Combination indexes werecalculated using CompuSyn software. Consequently, apoptosis was detectedby Annexin V/PI staining. The effect of the drugs on the cell cyclewas measured by the propidium iodide staining. The HDAC inhibitionwas confirmed via acetylated histone protein levels by western blotting.HDAC inhibitors, MS-275 and romidepsin, showed a better synergisticeffect with the nocodazole combination. The combination treatmentexerted its growth inhibitory effect by cell cycle arrest and inductionof apoptosis. The cell cycle analysis of the combination treatmentshowed that the S phase and G2/M phase were achieved. Moreover, thenecrotic and apoptotic cell population increased after single HDACinhibitors and combination treatment. The anti-cancer effect of HDACinhibitors is revealed by acetylation levels of histones. While acetylationlevels were increased in response to HDAC inhibitors and autophagymodulator combinations, the HDAC expression decreased. This studyhighlights the importance of the combination of HDAC inhibition andautophagy modulators and demonstrates a synergistic effect, whichcould be a promising therapy and novel treatment approach for cholangiocarcinoma.
Citation - WoS: 36
Citation - Scopus: 38
Effect of Molecular Architecture on Cell Interactions and Stealth Properties of PEG
(Amer Chemical Soc, 2017) Ozer, Imran; Tomak, Aysel; Zareie, Hadi M.; Baran, Yusuf; Bulmus, Volga
PEGylation, covalent attachment of PEG to therapeutic biomolecules, in which suboptimal pharmacokinetic profiles limiting their therapeutic utility are of concern, is a widely applied technology. However, this technology has been challenged by reduced bioactivity of biomolecules upon PEGylation and immunogenicity of PEG triggering immune response and abrogating clinical efficacy, which collectively necessitate development of stealth polymer alternatives. Here we demonstrate that comb-shape poly[oligo(ethylene glycol) methyl ether methacrylate](POEGMA); a stealth polymer alternative, has a more compact structure than PEG and self-organize into nanoparticles in a molecular weight dependent manner. Most notably, we show that comb shape POEGMA promotes significantly higher cellular uptake and exhibits less steric hindrance imposed on the conjugated biomolecule than PEG. Collectively, comb-shape POEGMA offers a versatile alternative to PEG for stealth polymer-biomolecule conjugation applications.
Citation - WoS: 22
Citation - Scopus: 25
Revisiting the Role of Charge Transfer in the Emission Properties of Carborane-Fluorophore Systems: A TDDFT Investigation
(Amer Chemical Soc, 2022) Tahaoglu, Duygu; Usta, Hakan; Alkan, Fahri
In this study, we performed a detailed investigation of the S-1 potential energy surface (PES) of o-carborane-anthracene (o-CB-Ant) with respect to the C-C bond length on o-CB and the dihedral angle between o-CB and Ant moieties. The effects of different substituents (F, Cl, CN, and OH) on carbon- or boron-substituted o-CB, along with a pi-extended acene-based fluorophore, pentacene, on the nature and energetics of S-1 -> S-0 transitions are evaluated. Our results show the presence of a non-emissive S-1 state with an almost pure charge transfer (CT) character for all systems as a result of significant C-C bond elongation (C-C = 2.50-2.56 angstrom) on o-CB. In the case of unsubstituted o-CB-Ant, the adiabatic energy of this CT state corresponds to the global minimum on the S-1 PES, which suggests that the CT state could be involved in emission quenching. Despite large deformations on the o-CB geometry, predicted energy barriers are quite reasonable (0.3-0.4 eV), and the C-C bond elongation can even occur without a noticeable energy penalty for certain conformations. With substitution, it is shown that the dark CT state becomes even more energetically favorable when the substituent shows -M effects (e.g., -CN), whereas substituents showing +M effects (e.g., -OH) can result in an energy increase for the CT state, especially for partially stretched C-C bond lengths. It is also shown that the relative energy of the CT state on the PES depends strongly on the LUMO level of the fluorophore as this state is found to be energetically less favorable compared to other conformations when anthracene is replaced with pi-extended pentacene. To our knowledge, this study shows a unique example of a detailed theoretical analysis on the PES of the S-1 state in o-CB-fluorophore systems with respect to substituents or fluorophore energy levels. Our findings could guide future experimental work in emissive o-CB-fluorophore systems and their sensing/optoelectronic applications.
Citation - WoS: 99
Citation - Scopus: 103
Giant Alloyed Hot Injection Shells Enable Ultralow Optical Gain Threshold in Colloidal Quantum Wells
(Amer Chemical Soc, 2019) Altintas, Yemliha; Gungor, Kivanc; Gao, Yuan; Sak, Mustafa; Quliyeva, Ulviyya; Bappi, Golam; Demir, Hilmi Volkan
As an attractive materials system for high- Record-low optical gain threshold in giant-shell COWs performance optoelectronics, colloidal nanoplatelets (NPLs) benefit from atomic-level precision in thickness, minimizing emission inhomogeneous broadening. Much progress has been made to enhance their photoluminescence quantum yield (PLQY) and photostability. However, to date, layer-by-layer growth of shells at room temperature has resulted in defects that limit PLQY and thus curtail the 0.2 performance of NPLs as an optical gain medium. Here, we introduce a hot-injection method growing giant alloyed shells using an approach that reduces core/shell lattice mismatch and suppresses Auger recombination. Near-unity PLQY is achieved with a narrow full-width-at-half-maximum (20 nm), accompanied by emission tunability (from 610 to 650 nm). The biexciton lifetime exceeds 1 ns, an order of magnitude longer than in conventional colloidal quantum dots (CQDs). Reduced Auger recombination enables record-low amplified spontaneous emission threshold of 2.4 mu J cm(-2) under one-photon pumping. This is lower by a factor of 2.5 than the best previously reported value in nanocrystals (6 /kJ cm(-2) for CdSe/CdS NPLs). Here, we also report single-mode lasing operation with a 0.55 mu J cm(-2) threshold under two-photoexcitation, which is also the best among nanocrystals (compared to 0.76 mu J cm(-2) from CdSe/CdS CQDs in the Fabry-Perot cavity). These findings indicate that hot-injection growth of thick alloyed shells makes ultrahigh performance NPLs.
Citation - WoS: 4
Citation - Scopus: 4
Transparent Films Made of Highly Scattering Particles
(Amer Chemical Soc, 2020) Erdem, Talha; Yang, Lan; Xu, Peicheng; Altintas, Yemliha; O'Neil, Thomas; Caciagli, Alessio; Eiser, Erika
Today, colloids are widely employed in various products from creams and coatings to electronics. The ability to control their chemical, optical, or electronic features by controlling their size and shape explains why these materials are so widely preferred. Nevertheless, altering some of these properties may also lead to some undesired side effects, one of which is an increase in optical scattering upon concentration. Here, we address this strong scattering issue in films made of binary colloidal suspensions. In particular, we focus on raspberry-type polymeric particles made of a spherical polystyrene core decorated by small hemispherical domains of acrylate with an overall positive charge, which display an unusual stability against aggregation in aqueous solutions. Their solid films display a brilliant red color due to Bragg scattering but appear completely white on account of strong scattering otherwise. To suppress the scattering and induce transparency, we prepared films by hybridizing them with oppositely charged PS particles with a size similar to that of the bumps on the raspberries. We report that the smaller PS particles prevent raspberry particle aggregation in solid films and suppress scattering by decreasing the spatial variation of the refractive index inside the film. We believe that the results presented here provide a simple strategy to suppress strong scattering of larger particles to be used in optical coatings.
Citation - WoS: 16
Citation - Scopus: 14
Comparison of Photocatalytic and Adsorption Properties of ZnS@ZnO, CdS@ZnO, and PbS@ZnO Nanocomposites to Select the Best Material for the Bifunctional Removal of Methylene Blue
(Amer Chemical Soc, 2025) Bayram, Umit; Ozer, Cigdem; Yilmaz, Erkan
In this study, photocatalytic- and adsorption-based removal processes were conducted, which are frequently preferred in wastewater treatment due to their ease of control and high removal efficiency. An innovative method aimed at wastewater treatment was developed by combining the advantages of these two distinct approaches within the same material. The study synthesized ZnO, ZnS, CdS, PbS, and their composite structures (ZnS@ZnO, CdS@ZnO, and PbS@ZnO) using a hydrothermal synthesis method. Characterization of the samples was performed through field emission-scanning electron microscopy (FE-SEM), FE-SEM-energy dispersive X-ray (FE-SEM-EDX), X-ray diffraction (XRD), Raman spectroscopy, and Fourier-transform infrared spectroscopy (FTIR) measurement. Additionally, the optical properties of all samples (absorption spectra and band gap) were investigated by using absorbance measurements obtained from ultraviolet (UV)-visible absorption spectroscopy. Although ZnO nanoparticles are among the materials with high photocatalytic properties (exhibiting a photodegradation efficiency of 95.8% in a short duration of 90 min), their adsorption properties are low. Therefore, with the aim of enhancing both the low adsorption values and the photocatalytic properties of pure metal sulfides (ZnS, CdS, PbS), nanocomposites ZnS@ZnO, CdS@ZnO, and PbS@ZnO with different morphologies were synthesized, and their photocatalytic and adsorption-based removal performances on methylene blue (MB) dye were investigated. FE-SEM images indicated that ZnS nanoparticles exhibit a spherical morphology, CdS nanoparticles have a flower-like morphology, and PbS nanoparticles display a dendritic-like structure. The results obtained from experimental studies demonstrated that the highest efficiency in both photocatalytic- and adsorption-based removal was achieved with the ZnS@ZnO nanocomposite. The degradation rates of MB were found to be 95.3, 90.5, and 89.4% for the heterojunction composites ZnS@ZnO, CdS@ZnO, and PbS@ZnO, respectively, over a time range of 0-480 min. The optimal amount of photocatalyst that could effectively degrade MB was determined to be 100 mg, and the reusability studies revealed that the ability of the ZnS@ZnO semiconductor heterojunction photocatalyst to decompose MB into simpler molecules was limited after the fourth cycle. The adsorption-based removal rates were 96.0, 30.5, and 19.4% for the heterojunction composites ZnS@ZnO, CdS@ZnO, and PbS@ZnO, respectively. Finally, parameters influencing the adsorption-based removal of MB, such as pH, mass, and contact time, were examined, indicating that the adsorption capacity of ZnS@ZnO remained unchanged after reaching a value of 40 mgg-1.
Citation - WoS: 61
Citation - Scopus: 62
Effective Neural Photostimulation Using Indium-Based Type-II Quantum Dots
(Amer Chemical Soc, 2018) Jalali, Houman Bahmani; Aria, Mohammad Mohammadi; Dikbas, Ugur Meric; Sadeghi, Sadra; Kumar, Baskaran Ganesh; Sahin, Mehmet; Nizamoglu, Sedat
Light-induced stimulation of neurons via photoactive surfaces offers rich opportunities for the development of therapeutic methods and high-resolution retinal prosthetic devices. Quantum dots serve as an attractive building block for such surfaces, as they can be easily functionalized to match the biocompatibility and charge transport requirements of cell stimulation. Although indium based colloidal quantum dots with type-I band alignment have attracted significant attention as a nontoxic alternative to cadmium-based ones, little attention has been paid to their photovoltaic potential as type-II heterostructures. Herein, we demonstrate type-II indium phosphide/zinc oxide core/shell quantum dots that are incorporated into a photoelectrode structure for neural photostimulation. This induces a hyperpolarizing bioelectrical current that triggers the firing of a single neural cell at 4 mu W mm(-2), 26-fold lower than the ocular safety limit for continuous exposure to visible light. These findings show that nanomaterials can induce a biocompatible and effective biological junction and can introduce a route in the use of quantum dots in photoelectrode architectures for artificial retinal prostheses.
Citation - WoS: 7
Citation - Scopus: 7
Enhancing the Properties of Yttria-Stabilized Zirconia Composites With Zeolitic Imidazolate Framework-Derived Nanocarbons
(Amer Chemical Soc, 2023) Cakan, Niyaz; Issa, Abduselam Abubeker; Alsalman, Hamza; Aliyev, Emin; Duden, Enes Ibrahim; Gurcan Bayrak, Kubra; Sen, Unal
Ceramic matrix composites (CMCs) reinforced with nanocarbon have attracted significant interest due to their potential to enhance mechanical, thermal, and electrical properties. Although the investigation of carbon-based materials such as graphene and carbon nanotubes as additives for advanced ceramics has been widespread, the utilization of metal-organic framework (MOF)-derived nanocarbons in CMCs remains largely unexplored. We extended our previous proof-of-concept investigations by demonstrating the effectiveness of a different type of MOF-derived carbon as a reinforcing phase in an alternative ceramic matrix. We employed spark plasma sintering (SPS) to consolidate yttria-stabilized zirconia (YSZ) and zeolitic imidazolate framework (ZIF-67) powder blends at 1300 degrees C and a uniaxial pressure of 50 MPa. YSZ serves as the ceramic matrix, whereas ZIF-67 serves as the nanocarbon source. The composite exhibits a highly significant improvement in fracture toughness with an increase of up to 13% compared to that of the YSZ monolith. The formation of ZIF-derived nanocarbon interlayers is responsible for the observed enhancement in ductility, which can be attributed to their ability to facilitate energy dissipation during crack propagation and inhibit grain growth. Furthermore, the room-temperature electrical conductivity of the sintered samples demonstrates a substantial improvement, primarily due to the in situ formation of nanocarbon-based fillers, reaching an impressive 27 S/m with 10 wt % ZIF-67 content. Based on the results, it can be inferred that the incorporation of in situ MOF-derived nanocarbons into CMCs leads to a substantial improvement in both the mechanical and electrical properties.
Citation - WoS: 62
Citation - Scopus: 62
Highly Efficient Deep-Blue Electroluminescence Based on a Solution-Processable A-Π Oligo(p-Phenyleneethynylene) Small Molecule
(Amer Chemical Soc, 2019) Usta, Hakan; Alimli, Dilek; Ozdemir, Resul; Dabak, Salih; Zorlu, Yunus; Alkan, Fahri; Can, Ayse
The development of solution-processable fluorescent small molecules with highly efficient deep-blue electroluminescence is of growing interest for organic light-emitting diode (OLED) applications. However, high-performance deep-blue fluorescent emitters with external quantum efficiencies (EQEs) over 5% are still scarce in OLEDs. Herein, a novel highly soluble oligo(p-phenyleneethynylene)-based small molecule, 1,4-bis((2-cyanophenyl)ethynyl)-2,5-bis(2-ethylhexyloxy)benzene (2EHO-CNPE), is designed, synthesized, and fully characterized as a wide band gap (2.98 eV) and highly fluorescent (Phi(PL) = 0.90 (solution) and 0.51 (solid-state)) deep-blue emitter. The new molecule is functionalized with cyano (-CN)/2-ethylhexyloxy (-OCH2CH(C2H5)C4H9) electron-withdrawing/-donating substituents, and ethynylene is used as a pi-spacer to form an acceptor (A)-pi-donor (D)-pi-acceptor (A) molecular architecture with hybridized local and charge transfer (HLCT) excited states. Physicochemical and optoelectronic characterizations of the new emitter were performed in detail, and the single-crystal structure was determined. The new molecule adopts a nearly coplanar pi-conjugated framework packed via intermolecular "C-H center dot center dot center dot pi" and "C-H center dot center dot center dot N" hydrogen bonding interactions without any pi-pi stacking. The OLED device based on 2EHO-CNPE shows an EQE(max) of 7.06% (EQE = 6.30% at 200 cd/m(2)) and a maximum current efficiency (CEmax) of 5.91 cd/A (CE = 5.34 cd/A at 200 cd/m(2)) with a deep-blue emission at CIE of (0.15, 0.09). The electroluminescence performances achieved here are among the highest reported to date for a solution-processed deep-blue fluorescent small molecule, and, to the best of our knowledge, it is the first time that a deep-blue OLED is reported based on the oligo(p-phenyleneethynylene) pi-framework. TDDFT calculations point to facile reverse intersystem crossing (RISC) processes in 2EHO-CNPE from high-lying triplet states to the first singlet excited state (T-2/T-3 -> S-1) (hot-exciton channels) that enable a high radiative exciton yield (eta(r) similar to 69%) breaking the theoretical limit of 25% in conventional fluorescent OLEDs. These results demonstrate that properly designed fluorescent oligo(p-phenyleneethynylenes) can be a key player in high-performance deep-blue OLEDs.
Citation - WoS: 5
Citation - Scopus: 6
Tailored Synthesis of Iron Oxide Nanocrystals for Formation of Cuboid Mesocrystals
(Amer Chemical Soc, 2021) Soran-Erdem, Zeliha; Sharma, Vijay Kumar; Hernandez-Martinez, Pedro Ludwig; Demir, Hilmi Volkan
In this work, we systematically studied the shape- and size-controlled monodisperse synthesis of iron oxide nanocrystals (IONCs) for their use as building blocks in the formation of mesocrystals. For this aim, on understanding the influence of the oleic acid concentration, iron-oleate concentration, and heating rate on the synthesis of robust and reproducible IONCs with desired sizes and shapes, we synthesized highly monodisperse similar to 11 nm sized nanocubes and nanospheres. Magnetic measurements of both cubic and spherical IONCs revealed the presence of mixed paramagnetic and superparamagnetic phases in these nanocrystals. Moreover, we observed that the magnetic moments of the nanocubes are more substantial compared to their spherical counterparts. We then demonstrated a simple magnetic-field-assisted assembly of nanocubes into three-dimensional (3D) cuboid mesocrystals while nanospheres did not form any mesocrystals. These findings indicate that small cubic nanocrystals hold great promise as potential building blocks of 3D magnetic hierarchical structures with their superior magnetic properties and mesocrystal assembly capability, which may have high relevance in various fields ranging from high-density data storage to biomedical applications.
Discovery and in Silico Characterization of Anatolian Water Buffalo Rumen-Derived Bacterial Thermostable Xylanases: A Sequence-Based Metagenomic Approach
(Amer Chemical Soc, 2025) Kurt, Halil; Kaya, Dilek Sever; Akcok, Ismail; Sari, Ceyhun; Albayrak, Ebru; Velioglu, Hasan Murat; Surmeli, Yusuf
This study involved shotgun sequencing of rumen metagenomes from three Anatolian water buffalos, an exploration of the relationship between microbial flora and xylanases, and in silico analyses of thermostable xylanases, focusing on their sequence, structure, and dynamic properties. For this purpose, the rumen metagenome of three Anatolian water buffalos was sequenced and bioinformatically analyzed to determine microbial diversity and full-length xylanases. Analyses of BLAST, biophysicochemical characteristics, phylogenetic tree, and multiple sequence alignment were performed with Blastp, ProtParam, MEGA11 software, and Clustal Omega, respectively. Three-dimensional homology models of three xylanases (AWBRMetXyn5, AWBRMetXyn10, and AWBRMetXyn19) were constructed by SWISS-MODEL and validated by ProSA, ProCheck, and Verify3D. Also, their 3D models were structurally analyzed by PyMOL, BAN Delta IT, thermostability predictor, What If, and Protein Interaction Calculator (PIC) software. Protein-ligand interactions were examined by docking and MD simulation. Shotgun sequence and Blastp analyses showed that Clostridium (Clostridiales bacterial order), Ruminococcus (Oscillospiraceae bacterial family), Prevotella (Bacteroidales bacterial order), and Butyrivibrio (Lachnospiraceae bacterial family) were found as dominant potential xylanase-producer genera in three rumen samples. Furthermore, the biophysicochemical analysis indicated that three xylanases exhibited an aliphatic index above 80, an instability index below 40, and melting temperatures (T m) surpassing 65 degrees C. Phylogenetic analysis placed three xylanases within the GH10 family, clustering them with thermophilic xylanases, while homology modeling identified the optimal template as a xylanase from a thermophilic bacterium. The structural analysis indicated that three xylanases possessed the number of salt bridges, hydrophobic interactions, and T m score higher than 50, 165, and 70 degrees C, respectively; however, the reference thermophilic XynAS9 had 43, 145, and 54.41 degrees C, respectively. BAN Delta IT analysis revealed that three xylanases exhibited lower B '-factor values in the beta 3-alpha 1 loop/short-helix at the N-terminal site compared to the reference thermophilic XynAS9. In contrast, six residues (G79, M123, D150, T199, A329, and G377) possessed higher B '-factor values in AWBRMetXyn5 and their aligned positions in AWBRMetXyn10 and AWBRMetXyn19, relative to XynAS9 including Gln, Glu, Ile, Lys, Ser, and Val at these positions, respectively. MD simulation results showed that the beta 9-eta 5 loop including catalytic nucleophile glutamic acid in the RMSF plot of three xylanases had a higher fluctuation than the aligned region in XynAS9. The distance analysis from the MD simulation showed that the nucleophile residue in AWBRMetXyn5 and AWBRMetXyn10 remained closer to the ligand throughout the simulation compared with XynAS9 and AWBRMetXyn19. The most notable difference between AWBRMetXyn5 and AWBRMetXyn10 was the increased amino acid fluctuations in two specific regions, the eta 3 short-helix and the eta 3-alpha 3 loop, despite a minimal sequence difference of only 1.24%, which included three key amino acid variations (N345, N396, and T397 in AWBRMetXyn5; D345, K396, and A397 in AWBRMetXyn10). Thus, this study provided computational insights into xylanase function and thermostability, which could inform future protein engineering efforts. Additionally, three xylanases, especially AWBRMetXyn5, are promising candidates for various high-temperature industrial applications. In a forthcoming study, three xylanases will be experimentally characterized and considered for potential industrial applications. In addition, the amino acid substitutions (G79Q, M123E, D150I, T199K, A329S, and G377V) and the residues in the beta 3-alpha 1 loop will be targeted for thermostability improvement of AWBRMetXyn5. The amino acids (N345, N396, and T397) and the residues on the beta 9-eta 5 loop, eta 3 short-helix, and eta 3-alpha 3 loop will also be focused on development of the catalytic efficiency.
Citation - WoS: 1
Benefiting From Both Ethanol Oxidation and Bidentate Thiol Groups of DHLA Ligands Under Photoirradiation for Synthesis of Au Nanoparticles With Their Catalytic and Peroxidase Like Activity
(Amer Chemical Soc, 2025) Temur, Nimet; Dadi, Seyma; Dogan, Ayse Nur; Nisari, Mustafa; Avan, Ilker; Ocsoy, Ismail
In this work, we rationally synthesized quite stable gold nanoparticles (AuNPs) using dihydrolipoic acid (DHLA) and DHLA-aspartame (DHLA-Asptm) as both reducing and stabilizing agents in a mixture of water/ethanol at RT under photoirradiation in 10 min. The novelty of this work is that benefiting from both the oxidation of ethanol to ethanal and having the bidentate thiol groups of DHLA, stable DHLA@AuNPs and DHLA-Asptm@AuNPs were successfully and rapidly formed without additional reducing reagents. We systematically examined the formation of DHLA@AuNPs and DHLA-Asptm@AuNPs under different pH values and reaction temperatures. Furthermore, the salt tolerance of DHLA@AuNPs and DHLA-Asptm@AuNPs was tested in a series of sodium chloride solutions. We showed the catalytic and peroxidase-like activities of DHLA@AuNPs against 4-nitrophenol and 3,3 ',5,5 '-tetramethylbenzidine. The AuNPs were characterized by UV-vis spectrophotometry, scanning transmission electron microscopy, zeta potential, and dynamic light scattering.
Citation - WoS: 28
Citation - Scopus: 33
Machine Learning-Aided Inverse Design and Discovery of Novel Polymeric Materials for Membrane Separation
(Amer Chemical Soc, 2024) Dangayach, Raghav; Jeong, Nohyeong; Demirel, Elif; Uzal, Nigmet; Fung, Victor; Chen, Yongsheng
Polymeric membranes have been widely used for liquid and gas separation in various industrial applications over the past few decades because of their exceptional versatility and high tunability. Traditional trial-and-error methods for material synthesis are inadequate to meet the growing demands for high-performance membranes. Machine learning (ML) has demonstrated huge potential to accelerate design and discovery of membrane materials. In this review, we cover strengths and weaknesses of the traditional methods, followed by a discussion on the emergence of ML for developing advanced polymeric membranes. We describe methodologies for data collection, data preparation, the commonly used ML models, and the explainable artificial intelligence (XAI) tools implemented in membrane research. Furthermore, we explain the experimental and computational validation steps to verify the results provided by these ML models. Subsequently, we showcase successful case studies of polymeric membranes and emphasize inverse design methodology within a ML-driven structured framework. Finally, we conclude by highlighting the recent progress, challenges, and future research directions to advance ML research for next generation polymeric membranes. With this review, we aim to provide a comprehensive guideline to researchers, scientists, and engineers assisting in the implementation of ML to membrane research and to accelerate the membrane design and material discovery process.
Citation - WoS: 66
Citation - Scopus: 72
Highly Transparent Au-Coated Ag Nanowire Transparent Electrode With Reduction in Haze
(Amer Chemical Soc, 2014) Kim, Taegeon; Canlier, Ali; Cho, Changsoon; Rozyyev, Vepa; Lee, Jung-Yong; Han, Seung Min
Ag nanowire transparent electrode has excellent transmittance and sheet resistance, yet its optical haze still needs to be improved in order for it to be suitable for display applications. Ag nanowires are known to have high haze because of the geometry of the nanowire and the high light scattering characteristic of the Ag. In this study, a Au-coated Ag nanowire structure was proposed to reduce the haze, where a thin layer of Au was coated on the surface of the Ag nanowires using a mild [Au(en)(2)]Cl-3 galvanic displacement reaction. The mild galvanic exchange allowed for a thin layer of Au coating on the Ag nanowires with minimal truncation of the nanowire, where the average length and the diameter were 13.0 mu m and 60 nm, respectively. The Au-coated Ag nanowires were suspended in methanol and then electrostatically sprayed on a flexible polycarbonate substrate that revealed a clear reduction in haze with a 2-4% increase in total transmittance, sheet resistance ranges of 80-90%, and 8.8-36.8 Ohm/sq. Finite difference time domain simulations were conducted for Au-coated Ag nanowires that indicated a significant reduction in the average scattering from 1 to 0.69 fo Au layer thicknesses of 0-10 nm.
Citation - WoS: 65
Citation - Scopus: 74
Solution-Processable Bodipy-Based Small Molecules for Semiconducting Microfibers in Organic Thin-Film Transistors
(Amer Chemical Soc, 2016) Ozdemir, Mehmet; Choi, Donghee; Kwon, Guhyun; Zorlu, Yunus; Cosut, Bunyemin; Kim, Hyekyoung; Usta, Hakan
Electron-deficient pi-conjugated small molecules can function as electron-transporting semiconductors in various optoelectronic applications. Despite their unique structural, optical, and electronic properties, the development of BODIPY-based organic semiconductors has lagged behind that of other pi-deficient units. Here, we report the design and synthesis of two novel solution-proccessable BODIPY-based small molecules (BDY-3T-BDY and BDY-4T-BDY) for organic thin-film transistors (OTFTs). The new semiconductors were fully characterized by H-1/C-13 NMR, mass spectrometry, cyclic voltammetry, UV-vis spectroscopy, photoluminescence, differential scanning calorimetry, and thermogravimetric analysis. The single-crystal X-ray diffraction (XRD) characterization of a key intermediate reveals crucial structural properties. Solution-sheared top-contact/bottom-gate OTFTs exhibited electron mobilities up to 0.01 cm(2)/V center dot s and current on/off ratios of >10(8). Film microstructural and morphological characterizations indicate the formation of relatively long (similar to 0.1 mm) and micrometer-sized (1-2 mu m) crystalline fibers for BDY-4T-BDY-based films along the shearing direction. Fiber-alignment-induced charge-transport anisotropy (mu?/mu approximate to 10) was observed, and higher mobilities were achieved when the microfibers were aligned along the conduction channel, which allows for efficient long-range charge-transport between source and drain electrodes. These OTFT performances are the highest reported to date for a BODIPY-based molecular semiconductor, and demonstrate that BODIPY is a promising building block for enabling solution-processed, electron-transporting semiconductor films.
Citation - WoS: 13
Citation - Scopus: 13
Tuning the Shades of Red Emission in InP/ZnSe Nanocrystals With Narrow Full Width for Fabrication of Light-Emitting Diodes
(Amer Chemical Soc, 2023) Soheyli, Ehsan; Bicer, Aysenur; Ozel, Sultan Suleyman; Tiras, Kevser Sahin; Mutlugun, Evren
While Cd-based luminescent nanocrystals (NCs) are the most mature NCs for fabricating efficient red light-emitting diodes (LEDs), their toxicity related limitation is inevitable, making it necessary to find a promising alternative. From this point of view, multishell-coated, red-emissive InP-based NCs are excellent luminescent nanomaterials for use as an emissive layer in electroluminescent (EL) devices. However, due to the presence of oxidation states, they suffer from a wide emission spectrum, which limits their performance. This study uses tris-(dimethyl-amino)-phosphine (3DMA-P) as a low-cost aminophosphine precursor and a double HF treatment to suggest an upscaled, cost-effective, and one-pot hot-injection synthesis of purely red-emissive InP-based NCs. The InP core structures were coated with thick layers of ZnSe and ZnS shells to prevent charge delocalization and to create a narrow size distribution. The purified NCs showed an intense emission signal as narrow as 43 nm across the entire red wavelength range (626-670 nm) with an emission quantum efficiency of 74% at 632 nm. The purified samples also showed an emission quantum efficiency of 60% for far-red wavelengths of 670 nm with a narrow full width of 50 nm. The samples showed a relatively long average emission lifetime of 50-70 ns with a biexponential decay profile. To demonstrate the practical ability of the prepared NCs in optoelectronics, we fabricated a red-emissive InP-based LEDs. The best-performing device showed an external quantum efficiency (EQE) of 1.16%, a luminance of 1039 cd m(-2), and a current efficiency of 0.88 cd A(-1).
Citation - WoS: 44
Citation - Scopus: 44
Boronic Acid Moiety as Functional Defect in UiO-66 and Its Effect on Hydrogen Uptake Capacity and Selective Co2 Adsorption: a Comparative Study
(Amer Chemical Soc, 2018) Erkartal, Mustafa; Sen, Unal
Herein, we use linker fragmentation approach to introduce boronic acid moieties as functional defects into Zr-based metal organic frameworks (MOFs, UiO-66). Our findings show that the amount of permanently incorporated boronic acid containing ligand is directly dependent on the synthesis method. The accessible boronic acid moieties in the pore surfaces significantly improve the hydrogen uptake values, which are 3.10 and 3.44 wt % at 21 bar, 77 K for dimethylformamide (DMF)/H2O and DMF/HCI synthesis methods, respectively. Also, CO2 selectivity of the resulting MOFs over N-2 and CH4 significantly increases due to the quadrupolar interaction between active surfaces and CO2 molecules. To the best of our knowledge, both hydrogen storage and selectivity of CO2 for UiO-66 are the highest reported values in the literature to date. Furthermore, another striking result that emerged from the high-pressure hydrogen uptake isotherms is the direct correlation between the defects and hysteric adsorption behavior, which may result in the shift from rigidity to flexibility of the framework due to the uncoordinated sites.

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