Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Citation - WoS: 2Citation - Scopus: 2Gas Phase Fragmentation Behavior of Proline in Macrocyclic B7 Ions(American Chemical Society, 2023) Taşoğlu, Çağdaş; Arslanoğlu, Alper; Yalçın, TalatThefragmentation characteristics of b (7) ionsproduced from proline-containing heptapeptides have been studiedin detail. The study has utilized the following C-terminally amidatedmodel peptides: PA(6), APA(5), A(2)PA(4), A(3)PA(3), A(4)PA(2), A(5)PA, A(6)P, PYAGFLV, PAGFLVY, PGFLVYA, PFLVYAG,PLVYAGF, PVYAGFL, YPAGFLV, YAPGFLV, YAGPFLV, YAGFPLV, YAGFLPV, YAGFLVP,PYAFLVG, PVLFYAG, A(2)PXA(3), and A(2)XPA(3) (where X = C, D, F, G, L, V, and Y, respectively). The resultshave shown that b (7) ions undergo head-to-tailcyclization and form a macrocyclic structure. Under the collision-induceddissociation (CID) condition, it generates nondirect sequence ionsregardless of the position of the proline and the neighboring aminoacid residues. This study highlights the unusual and unique fragmentationbehavior of proline-containing heptapeptides. Following the head-to-tailcyclization, the ring opens up and places the proline residue in theN-terminal position while forming a regular oxazolone form of b (2) ions for all peptide series. Then, the fragmentationreaction pathway is followed by the elimination of proline with itsC-terminal neighbor residue as an oxazolone (e.g., PXoxa) for all proline-containing peptide series.Article Citation - WoS: 7Citation - Scopus: 6Visceral Leishmaniasis Caused by Leishmania Tropica(Springer, 2023) Özbilgin, Ahmet; Tunalı, Varol; Çavuş, İbrahim; Vardarlı Tetik, Aslı; Dinç, Melike; Yalçın, Talat; Gündüz, Cumhur; Beyaz, Merve; Köse, ŞükranPurposeIn Turkey, the main causative agent of visceral leishmaniasis (VL) is Leishmania. infantum and the main causative agent of cutaneous leishmaniasis (CL) is Leishmania tropica. In this study, we aimed to discuss the possible mechanisms, clinical aspects, and threat of visceralizing L. tropica.MethodsThis study includes seven cases of VL caused by L. tropica.Five patients were male (71%) and four were adults (57%).ResultsAll the VL patients complained of fever and splenomegaly. Fatigue, pancytopenia, and hepatomegaly were present in six patients each (86%), while weight loss and gastrointestinal system (GIS) symptoms were present in 5 patients (71%).ConclusionsIn this study, we have evaluated seven cases of visceralized L. tropica (VLT) in the context of the changing leishmaniasis epidemiology in Turkey. We have evaluated the possible mechanisms of visceralization; inter- and intraspecies genetic exchange with all the old world leishmaniasis agents present in the region, stress induced by inappropriate use of drugs, and possible ongoing adaptation mechanisms of Leishmania spp. The threat posed by VLT is significant as L. tropica is the most widespread and most common cause of leishmaniasis in Turkey. We do not know the vectorial capacity of the sand flies for the transmission of VLT strains or if these strains are in circulation in Turkey. Future studies should be carried out to investigate these issues as the transition of L. tropica from a mild disease-causing agent to a mortal one poses a significant public health concern for Turkey and Europe.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: 1Citation - Scopus: 2A Molecularly Imprinted Polymer as Solid Phase Extraction Sorbent for Ketoprofen Determination in Water and Artificial Serum Prior To Hplc(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2022) Shahwan, Talal; Gürel Özyurt, Elif; Özyurt, Ömer; Ölçer, Yekta Arya; Eroğlu, Ahmet Emin; Boyacı, EzelKetoprofen (KET) is an active pharmaceutical compound that has pain relieving and antipyretic effects. Its determination in body fluids and environmental waters is important due to widespread use of the compound. In this study, a selective and reliable method has been developed for the determination of ketoprofen in water and artificial serum using molecularly imprinted polymers (MIPs) as a solid phase extraction sorbent prior to HPLC-DAD detection. The MIP was synthesized by copolymerization of methacrylic acid (MAA) and trimethylpropane trimethacrylate (TRIM) in the presence of ketoprofen as the template. For the sake of comparison, nonimprinted polymer (NIP) was also synthesized under the same experimental conditions without the addition of ketoprofen under the same experimental conditions. Critical extraction parameters such as sample pH, shaking time and sorbent amount were optimized and adjusted to 8.0, 24 h, and 10.0 mg, respectively, for a sample volume of 10.0 mL. MIP showed higher selectivity than NIP towards ketoprofen in an artificial matrix containing another pain relieving drug, ibuprofen, and a cardiovascular drug, metoprolol. The proposed method was successfully applied for the detection of ketoprofen in spiked drinking water, tap water, and artificial serum samples, and showed satisfactory results with respective recoveries of 96.8 % (± 0.8), 93.7% (± 0.6), 62.2% (± 0.6), and 69.9% (± 0.6).Article Characterization of Yellow Patina on Stone Surfaces by Instrumental Analysis Including Libs(Taylor & Francis, 2022) Badur, Fulya; Aras, Nadir; Yalçın, Şerife; Böke, HasanYellow patina formed on the stone surfaces of historical buildings, monuments, and archaeological structures due to weathering is considered a value of the building in the conservation of cultural heritage studies. Although yellow patina layers can be easily distinguished on white marble surfaces, it is not possible to distinguish them on the yellow travertine surfaces with the naked eye. It should be taken into account in yellow travertines as well as marble surfaces before conservation treatments of the stone. In this study, mineralogical and chemical compositions and the thicknesses of yellow patina layers formed on yellow travertine and marble surfaces in Aizanoi, Aphrodisias, and Hierapolis archaeological sites in Turkey were analyzed in order to constitute a conservation approach in the archaeological sites. In this respect, XRD, FT-IR, SEM-EDX, and LIBS were used in the determination of compositions and thicknesses of yellow patina. Although LIBS analysis is a more convenient method to investigate patina layers on stone surfaces, this technique is not as well known as the others. Yellow patina layers contained calcium oxalate in the form of whewellite (CaC2O4.H2O). Their thicknesses were between 15 and 100 μm and should be protective against weathering on travertine and marble surfaces. Highlights LIBS analysis seems to be the most convenient micro-destructive method to estimate the thickness of the yellow patina layers on the marble and yellow travertine surfaces. The determination of the thickness of the yellow patina is critical to keep irreversible cleaning interventions, especially for the yellow travertines due to their similar colors. Yellow patina is mainly composed of calcium oxalate with clay minerals and organic compounds.Article Citation - WoS: 3Citation - Scopus: 3Structural and Functional Analyses of Gh51 Alpha-L of Geobacillus Vulcani Gs90 Reveal Crucial Residues for Catalytic Activity and Thermostability(Wiley, 2022) Sürmeli, Yusuf; Şanlı Mohamed, GülşahAlpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid–base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C–C bond between C171 and C213 by becoming closer to each other.Article Citation - WoS: 8Citation - Scopus: 7The Use of Mussel Shell as a Bio-Additive for Poly(lactic Acid) Based Green Composites(Lviv Polytechnic National University, 2021) Lap, Metehan Oğulcan; Kanbur, Yasin; Tayfun, ÜmitMussel shell is one of the most hazardous aquaculture wastes and its powder was used as an additive for bio-degradable poly (lactic acid) in this current study. Bio-composites were fabricated via conventional melt mixing technique followed by an injection moulding process. The effects of mussel shell powder inclusion on mechanical, melt-flow, water uptake and morphological performance of poly (lactic acid)-based green composites were reported.Article Citation - WoS: 4Citation - Scopus: 4A Cyclopalladated Bodipy Construct as a Fluorescent Probe for Carbon Monoxide(Wiley, 2022) Çevik Eren, Merve; Eren, Ahmet; Dartar, Suay; Tütüncü, Büşra Buse; Emrullahoğlu, MustafaBy introducing a palladium ion into the backbone of BODIPY, we devised a cyclopalladated BODIPY construct that was almost non-emissive in the absence of any analyte but became highly fluorescent upon interacting with carbon monoxide (CO) in solution and in living cells. A process of ortho-carbonylation and depalladation mediated by the specific binding of CO to palladium, promoted the release of the heavy atom from the fluorophore and consequently generated a fluorescence signal with an exceptionally high (60-fold) enhancement ratio.Article Citation - WoS: 3Citation - Scopus: 1Transition Metal Salt Promoted, Green, and High-Yield Synthesis of Silver Nanowires for Flexible Transparent Conductive Electrodes(Wiley-Blackwell, 2021) Sarısözen, Sema; Tertemiz, Necip Ayhan; Arıca, Tuğçe Aybüke; Polat, Nahit; Kocabaş, Çoşkun; Mert Balcı, Fadime; Balcı, SinanSilver nanowires (AgNWs) have attracted considerable interest from both academia and industry owing to their excellent electrical, optical, and chemical properties. For large-scale synthesis of AgNWs, the polyol method involving ethylene glycol, a toxic alcohol, has been widely used. We herein report on a facile, green, high yield, transition metal salt promoted, open atmosphere method for the synthesis of high quality AgNWs in a glycerol-water mixture. We have shown that transition metal salts have a strong influence on the morphology of AgNWs. Importantly, in the presence of copper(II) chloride, AgNWs with a high aspect ratio of around 400 (length, 36 μm; diameter, 90 nm) were obtained. Additionally, for the first time, we have demonstrated AgNWs based flexible transparent conductive electrodes (TCEs) on poly(sodium 4-styrenesulfonate) (PSS) treated polyethylene terephthalate (PET) substrate with a sheet resistance of 34 Ω/sq and transmittance of 91 % at 550 nm. The PSS layer on the PET substrate generated a highly hydrophilic surface, which boosts interaction of AgNWs with the PET surface. We envision that our results would play a significant role both in the synthesis of AgNWs with high aspect ratio and also in designing new rigid and flexible TCEs having high transmittance and low sheet resistance for applications especially in printable solar cells, organic light emitting diodes, and high performance flexible electronics.Article Citation - WoS: 1Citation - Scopus: 1Rhodium(i)-Catalyzed Co-Gas Arylative Dual-Carbonylation of Alkynes With Arylboronic Acids Via the Formyl C-H Activation of Formaldehyde(Georg Thieme Verlag, 2021) Morimoto, Tsumoru; Wang, Chuang; Tanimoto, Hiroki; Artok, Levent; Kakiuchi, KiyomiThe rhodium(I)-catalyzed reaction of alkynes with aryl-boronic acids in the presence of formaldehyde results in a CO-gas-free arylative dual-carbonylation to produce gamma-butenolide derivatives. The simultaneous loading of phosphine-ligated and phosphine-free rhodium(I) complexes is required for efficient catalysis. The former complex catalyzes the abstraction of a carbonyl moiety from formaldehyde through the activation of its formyl C-H bond (decarbonylation) and the latter catalyzes the subsequent dual-incorporation of the resulting carbonyl unit (carbonylation). The use of larger amounts of the phosphine-ligated rhodium(I) complex generates more carbonyl units, leading to the formation gamma-butenolides via the dual-incorporation of the carbonyl unit.