Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Conference Object Citation - WoS: 3Citation - Scopus: 3Halloysite Nanotube Loaded Polyamide Nanocomposites: Structural, Morphological, Mechanical, Thermal and Processing Behaviors(American Institute of Physics, 2023) Akar, Alinda Öykü; Yıldız, Ümit Hakan; Tayfun, Ümit; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn this study, the polyamide 6 (PA) matrix was reinforced with the purified, fine ground and amino-silane treated halloysite nanotubes (HNT) at different concentrations. The preparation of composites was carried out using a lab-scale twin-screw micro-compounder with loading ratios at 0.5, 1, 3, and 20% by weight, and the test samples were prepared by the injection-molding process. According to mechanical test results, additions of HNT to the PA matrix caused slight improvements in tensile strength and Youngs' modulus parameters. The optimum concentrations for all of the additives used were estimated by comparison of mechanical test data. The addition of aminosilane-modified HNT resulted in a higher impact performance at high loading levels up to 3% concentrations. Further addition of HNT caused a reduction in the mechanical parameters of composites. Thermal studies revealed that the glass transition temperature of PA shifted to higher values after HNT mineral inclusions. Thermo-mechanical results showed that storage moduli of PA exhibited improvement with an increase in HNT content. The distributions of HNT clay into the PA phase were visualized with SEM images. Based on these observations, a high level of dispersion homogeneity was achieved for lower filling ratios. According to melt-flow and force measurements, composites filled with 20% of HNT displayed a remarkable increase in exerted force during melt-blending. © 2023 Author(s).Article Citation - WoS: 4Citation - Scopus: 4Colorimetric Assaying of Exosomal Metabolic Biomarkers(MDPI, 2023) Yan, Evelias; Yıldız, Ümit Hakan; Yıldız, Ümit Hakan; Boehm, Bernhard O.; Palaniappan, Alagappan; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyExosomes released into the extracellular matrix have been reported to contain metabolic biomarkers of various diseases. These intraluminal vesicles are typically found in blood, urine, saliva, breast milk, cerebrospinal fluid, semen, amniotic fluid, and ascites. Analysis of exosomal content with specific profiles of DNA, microRNA, proteins, and lipids can mirror their cellular origin and physiological state. Therefore, exosomal cargos may reflect the physiological processes at cellular level and can potentially be used as biomarkers. Herein, we report an optical detection method for assaying exosomal biomarkers that supersedes the state-of-the-art time consuming and laborious assays such as ELISA and NTA. The proposed assay monitors the changes in optical properties of poly(3-(4-methyl-3'-thienyloxy) propyltriethylammonium bromide) upon interacting with aptamers/peptide nucleic acids in the presence or absence of target biomarkers. As a proof of concept, this study demonstrates facile assaying of microRNA, DNA, and advanced glycation end products in exosomes isolated from human plasma with detection levels of ~1.2, 0.04, and 0.35 fM/exosome, respectively. Thus, the obtained results illustrate that the proposed methodology is applicable for rapid and facile detection of generic exosomal biomarkers for facilitating diseases diagnosis.Research Project Çeşitli ilaç etken maddelerinin kapiler elektrokromatografi ile tayini için yeni kapiler kolonlar geliştirilmesi(2018) Eroğlu, Ahmet Emin; Çağır, Ali; Karabudak, Engin; Yıldız, Ümit Hakan; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyProjenin amacı, üç farklı ilaç etken madde grubundan beta-blokerler (metoprolol ve atenolol), anti-kanser ilaçları (5-florourasil ve azasitidin) ve diüretik ilaçların (bendroflumetiazid, klorotiazid ve hidroklorotiazid), kapiler elektroforez ve kapiler elektrokromatografi ile tayini için yeni metotlar gelistirilmesidir. Ilk çalısmada, anti kanser ilaçların etken maddesi olan 5- florourasil ve 5-azasitidin için farklı formülasyonlara (farklı fonksiyonel monomerler, porojenler ve monomer:çapraz baglayıcı oranları) sahip moleküler baskılanmıs polimerler (MIP) sentezlendi. Çözelti pH?sı, çalkalama süresi, sorbent miktarı gibi parametreler optimize edildi ve bu kosullarda 5-FU ve 5AC için dedeksiyon limit (LOD) degerleri sırasıyla 0.40 mg/L ve 0.28 mg/L ve tayin limit (LOQ) degerleri 1.33 mg/L ve 0.92 mg/L olarak hesaplandı. Ikinci çalısmada, analit grubu olarak seçilen tiazidlerin belirlenmesinde kullanılacak kapiler elektrokromatografi kolonu hazırlanması için sol-jel kimyası ve moleküler baskılama teknigi kullanıldı. Modifiye silika sol-jeller (amin- ve fenil-modifiye) ve farklı MIP materyalleri (inorganik- ve organik-bazlı) duragan faz kaplama malzemesi olarak kullanılmak için sentezlendi. Kolon içine yüklenecek maddenin seçimi için kapiler elektroforez (CE) öncesinde sorpsiyon çalısması yapıldı. Kritik deneysel parametreler optimize edildi; elektrolit çözeltisi olarak pH?sı 9.4?e ayarlanmıs 10.0 mM borat seçildi. Çalısma voltajı 25 kV, kaset sıcaklıgı 30.0 °C?ye sabitlendi. LOD degerleri 0.20 mg/L ile 0.30 mg/L, LOQ degerleri 0.44 mg/L ile 0.99 mg/L arasında bulundu. Çalısmanın üçüncü kısmında, ß-blokerlerin tayini için moleküler baskılanmıs organik-inorganik polimerler ve sol-jel metoduyla silikat nanopartikülleri sentezlendi ve kapiler elektrokromatografi kolonunda kaplama/dolgu malzemesi olarak kullanıldı. Sentezlenen üç farklı sorbentin sorpsiyon performansı kıyaslandı. Moleküler baskılanmıs organik polimerlerin metoprolole yüksek sorpsiyon kapasitesi ve seçicilik gösterdigi belirlendi. Duragan faz optimizasyon çalısmalarından sonra CEC kolonu gelistirildi ve analitik performansı incelendi. Söz konusu kolonla yapılan çalısmalarda metoprolol için LOD ve LOQ degerleri sırasıyla 10.0 mg/L ve 32.0 mg/L olarak hesaplandı.Conference Object Citation - WoS: 1Citation - Scopus: 1Biomimetic Peptide-Conjugated Membranes for Developing an Artificial Cornea(IEEE, 2022) Sunal, Gülşah; Yıldız, Ümit Hakan; Akgün, İsmail Hakkı; Güven, Sinan; Yıldız, Ümit Hakan; Karaman, Ozan; Horzum, Nesrin; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyThe corneal endothelium is composed of a single layer of specialized endothelial cells, protecting, and nourishing the inner surface of the cornea. Corneal endothelial cells do not proliferate after birth and their number decrease with age. Trauma, inflammation, or surgical intervention can cause cell loss. When damage is extensive and the density of corneal endothelial cells decreases to a critical level, it results in corneal edema and vision loss. Besides them, when corneal endothelium has irreversible damage, the only treatment way is corneal transplantation. But there are some drawbacks such as finding donors, immune reactions, and the number of patients waiting on the transplantation lists for years. Tissue engineering approaches can provide promising alternatives for the regeneration of corneal endothelium tissue. Peptides can be used to modify and functionalize the scaffolds, allowing for the production of bioactive and biomimetic surfaces. Peptide-modified scaffold surfaces might direct and enhance the behaviors of cells. In this study, the aim was to functionalize the polycaprolactone (PCL) membranes with tissue-specific peptides and to characterize the peptide-conjugated membranes by Fourier-Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), and X-ray Photoelectron Spectroscopy (XPS) analysis. The synthesized peptides were successfully conjugated on the PCL biomembranes.Article Citation - WoS: 14Citation - Scopus: 13Investigations of Polyamide Nano-Composites Containing Bentonite and Organo-Modified Clays: Mechanical, Thermal, Structural and Processing Performances(Walter de Gruyter GmbH, 2021) Yıldız, Ümit Hakan; Yıldız, Ümit Hakan; Tayfun, Ümit; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyPolyamide 6 (PA) matrix was reinforced with Na-activated bentonite, amino functional silane treated bentonite and organo-modified clays at different concentrations. The preparation of composites was carried out using melt-blending method and the test samples were prepared by injection-molding process. Mechanical, thermal, structural and processing investigations of PA based composites were reported performing via tensile, hardness, and impact tests, differential scanning calorimetry (DSC), thermal gravimetric analysis (TGA), scanning electron microscopy (SEM), X-ray diffraction analysis (XRD) and force measurements, respectively. According to mechanical test results, additions of fillers to PA matrix caused slight improvements for tensile strength and modulus parameters. Silane treated BNT exhibited improvement in mechanical results compared to Na-activated bentonite additions. Thermal studies revealed that decomposition and melting temperatures of PA shifted to higher values after inclusion of clay into polymer matrix. Results confirmed that organo-clay and bentonite additions with their lower filling ratios yielded enhancements for the mechanical and thermal performance of polyamide.Article Citation - WoS: 1Citation - Scopus: 1Gadolinium and Polythiophene Functionalized Polyurea Polymer Dots as Fluoro-Magnetic Nanoprobes(MDPI, 2022) Karabacak, Soner; Palaniappan, Alagappan; Yıldız, Ümit Hakan; Karabacak, Soner; Gulyás, Balázs; Padmanabhan, Parasuraman; Yıldız, Ümit Hakan; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyA rapid and one-pot synthesis of poly 3-thiopheneacetic acid (PTAA) functionalized pol-yurea polymer dots (Pdots) using polyethyleneimine and isophorone diisocyanate is reported. The one-pot mini-emulsion polymerization technique yielded Pdots with an average diameter of ~20 nm. The size, shape, and concentration of the surface functional groups could be controlled by al-tering the synthesis parameters such as ultrasonication time, concentration of the surfactant, and crosslinking agent, and the types of isocyanates utilized for the synthesis. Colloidal properties of Pdots were characterized using dynamic light scattering and zeta potential measurements. The spherical geometry of Pdots was confirmed by scanning electron microscopy. The Pdots were post-functionalized by 1,4,7,10 tetraazacyclododecane-1,4,7,10-tetraacetic acid for chelating gadolinium nanoparticles (Gd3+) that provide magnetic properties to the Pdots. Thus, the synthesized Pdots possess fluorescent and magnetic properties, imparted by PTAA and Gd3+, respectively. Fluorescence spectroscopy and microscopy revealed that the synthesized dual-functional Gd3+-Pdots ex-hibited detectable fluorescent signals even at lower concentrations. Magnetic levitation experiments indicated that the Gd3+-Pdots could be easily manipulated via an external magnetic field. These findings illustrate that the dua-functional Gd3+-Pdots could be potentially utilized as fluorescent reporters that can be magnetically manipulated for bioimaging applications.Article Citation - WoS: 43Citation - Scopus: 46Glucuronoxylan-Based Quince Seed Hydrogel: a Promising Scaffold for Tissue Engineering Applications(Elsevier, 2021) Güzelgülgen, Meltem; Güzelgülgen, Meltem; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu; Arslan Yıldız, Ahu; 04.01. Department of Chemistry; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 04. Faculty of ScienceNatural gums and mucilages from plant-derived polysaccharides are potential candidates for a tissue-engineering scaffold by their ability of gelation and biocompatibility. Herein, we utilized Glucuron-oxylanbased quince seed hydrogel (QSH) as a scaffold for tissue engineering applications. Optimization of QSH gelation was conducted by varying QSH and crosslinker glutaraldehyde (GTA) concentrations. Structural characterization of QSH was done by Fourier Transform Infrared Spectroscopy (MR). Furthermore, morphological and mechanical investigation of QSH was performed by Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). The protein adsorption test revealed the suitability of QSH for cell attachment. Biocompatibility of QSH was confirmed by culturing NIH-3T3 mouse fibroblast cells on it. Cell viability and proliferation results revealed that optimum parameters for cell viability were 2 mg mi(-1)of QSH and 0.03 M GTA. SEM and DAPI staining results indicated the formation of spheroids with a diameter of approximately 300 pm. Furthermore, formation of extracellular matrix (ECM) microenvironment was confirmed with the Collagen Type-I staining. Here, it was demonstrated that the fabricated QSH is a promising scaffold for 3D cell culture and tissue engineering applications provided by its highly porous structure, remarkable swelling capacity and high biocompatibility. (C) 2021 Published by Elsevier B.V.Article Citation - WoS: 5Citation - Scopus: 6Toward Single-Layer Janus Crystals: Off-Balance Materials From Synthesis To Nanotechnology Applications(American Institute of Physics, 2021) Yıldız, Ümit Hakan; Şahin, Hasan; Sözen, Yiğit; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Şahin, Hasan; 04.01. Department of Chemistry; 01. Izmir Institute of Technology; 04.04. Department of Photonics; 04. Faculty of ScienceThe existence of things is directly related to their structural symmetry in a broad framework ranging from atoms to crystalline materials and from simple cells to complex organisms like humans. However, structural imbalance that occurs through natural or artificial means can provide completely different advantages. Molecules, crystals, and complex structures with structural imbalance constitute the family of Janus-type materials. This perspective provides a comprehensive discussion on the synthesis techniques of Janus-type materials, their use in fields from biology to materials science, and very recent studies on the family of 2D ultrathin graphene-like structures. We believe that, thanks to the advances in experimental techniques, the few-atom-sized off-balanced materials will be indispensable parts of the nanotechnology products that soon will be used in our daily lives.Article Citation - WoS: 2Citation - Scopus: 2Transition-Metal Direct C-H Arylation of Thiophene in Aqueous Media Via Potassium Peroxymonosulfate(John Wiley and Sons Inc., 2019) Özenler, Sezer; Özenler, Sezer; Kaya, Hakan; Yıldız, Ümit Hakan; Elmacı, Nuran; Elmacı Irmak, Nuran; Yıldız, Ümit Hakan; 04.01. Department of Chemistry; 01. Izmir Institute of Technology; 04. Faculty of ScienceThis study covers the use of potassium peroxymonosulfate (PPS) which, is a mild and inexpensive catalyst, for direct coupling of C-H/C-H for water soluble thiophene. The 3-(4-methyl-3 '- thienyloxy)propyltriethylammonium bromide (M1) has been selected as model monomer that reacted PPS in 2.0, 0.20 and 0.020 monomer to PPS ratio. The reaction has been monitored via NMR spectroscopy revealing the monomer consumption and formation of dimers to tetramers as well as completion of reaction within 15 minutes. Resultant product is easily collected without tedious work up steps. The computational calculation has optimized the regularity of the coupling as head to tail, tail to tail, head to tail (HT-TT-HT) for tetramer. The regularity of tetramer which is further satisfied via NMR analysis showing emergence of new peaks at 3.56 and 4.48. The shifts in the UV maximum of reactive species have been monitored by absorbance spectroscopy showing time dependent red shift corresponds to growing from monomer to tetramers. The reaction has self-stopped due to low solubility of moderate condensates (higher than trimer), however further experiments have performed in water-organic mixtures showed great promises to obtain higher condensates.Article Citation - WoS: 39Citation - Scopus: 37Flow-Through Colorimetric Assay for Detection of Nucleic Acids in Plasma(Elsevier, 2019) Ammanath, Gopal; Yıldız, Ümit Hakan; Yeasmi, Sanjida; Srinivasulu, Yuvasri; Vats, Mukti; Cheema, Jamal Ahmed; Nabilah, Fairuz; Liedberg, Bo; Yıldız, Ümit Hakan; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyA flow-through colorimetric assay for detection of nucleic acids in plasma is reported. The proposed assay features an array of four polyvinylidene fluoride (PVDF) membranes impregnated with cationic poly (3-alkoxy-4-methylthiophene) (PT) as an optical reporter. The sensing strategy is based on monitoring the changes in optical properties of PT, upon complexation with target nucleic acids in the presence and in the absence of their corresponding complementary peptide nucleic acids (PNAs). As a proof of concept, the proposed methodology is validated using two biomarkers; lung cancer associated microRNA (mir21) and hepatitis B virus DNA (HBV-DNA). The flow-through colorimetric assay enabled detection of mir21 and HBV-DNA in plasma without requiring tedious sample pre-treatment and clean up protocols. Colorimetric responses for mir21 and HBV-DNA were obtained at nanomolar concentrations over five orders of magnitudes (from 1 nM to 10 mu M), with a limit of detection of -0.6 nM and -2 nM in DI water and plasma, respectively. A logic gate system was developed to utilize the colorimetric assay responses as inputs for discrimination of mir21 and HBV-DNA and subsequently to obtain a profile of nucleic acids in samples that exceed respective clinical threshold limits, thereby enabling rapid and point of care (POC) disease diagnosis. Furthermore, the proposed methodology can be utilized for detection of a large number of nucleic acids in plasma by extending the array of PT impregnated membranes incorporated with their corresponding complementary PNAs. (C) 2019 Elsevier B.V. All rights reserved.
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