Browsing by Subject "Nuclear magnetic resonance spectroscopy"

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Open Access
Convergent synthesis and light harvesting properties of dendritic boradiazaindacene (BODIPY) appended perylenediimide dyes
(2010) Bozdemir, O. A.; Yilmaz, M. D.; Buyukcakir, O.; Siemiarczuk, A.; Tutas, M.; Akkaya, E. U.
A convergent synthesis methodology, together with "click- chemistry" between azides and terminal alkynes, allows straighforward access to dendritic light harvesting systems. The novel dendrimer reported in this study has eight boradiazaindacene (BODIPY) units at the periphery and a perylenediimide (PDI) dye at the core. We have demonstrated that visible light is effectively collected as a result of the large absorption cross section of the dendrimer and efficiently channeled to the core PDI unit, resulting in a significant antenna effect. While being one of the very few energy transfer systems with a BODIPY and PDI chromophore pair, this novel dendritic molecule is one of the most efficient in light harvesting. The factors that may play important roles as the generation number increases also become apparent when emission characteristics were analyzed in comparison with a lower generation dendrimer.
Open Access
Double perovskite structure induced by Co addition to PbTiO3: Insights from DFT and experimental solid-state NMR spectroscopy
(American Chemical Society, 2019) Mete, E.; Odabaşı, S.; Mao, H.; Chung, T.; Ellialtıoğlu, Ş.; Reimer, J. A.; Gülseren, Oğuz; Üner, D.
The effects of Co addition on the chemical and electronic structure of PbTiO3 were explored both by theory and through experiment. Cobalt was incorporated into PbTiO3 during the sol–gel process with the X-ray diffraction (XRD) data of the resulting compounds confirming a perovskite structure for the pure samples. The XRD lines broadened and showed emerging cubic structure features as the Co incorporation increased. The changes in the XRD pattern were interpreted as double perovskite structure formation. 207Pb NMR measurements revealed a growing isotropic component in the presence of Co. Consistent with the experiments, density functional theory (DFT)-calculated chemical-shift values corroborate isotropic coordination of Pb, suggesting the formation of cubic Pb2CoTiO6 domains in the prepared samples. Hybrid functional first-principles calculations indicate formation of Pb2CoTiO6 with cubic structure and confirm that Co addition can decrease oxygen binding energy significantly. Experimental UV–vis spectroscopy results indicate that upon addition of Co, the band gap is shifted toward visible wavelengths as confirmed by energy band and absorption spectrum calculations. The oxygen binding energies were determined by temperature-programmed reduction (TPR) measurements. Upon addition of Co, TPR lines shifted to lower temperatures and new features appeared in the TPR patterns. This shift was interpreted as weakening of the oxygen–cobalt bond strength. The change in the electronic structure by the alterations of oxygen vacancy formation energy and bond lengths upon Co insertion is determined by DFT calculations.
Open Access
Drug delivery system based on cyclodextrin-naproxen inclusion complex incorporated in electrospun polycaprolactone nanofibers
(Elsevier, 2014) Canbolat, M. F.; Celebioglu A.; Uyar, Tamer
In this study, we select naproxen (NAP) as a reference drug and electrospun poly (e-caprolactone) (PCL) nanofibers as a fibrous matrix for our drug-delivery system. NAP was complexed with beta-cyclodextrin (βCD) to form inclusion complex (NAP-βCD-IC) and then NAP-βCD-IC was incorporated into PCL nanofibers via electrospinning. The incorporation of NAP without CD-IC into electrospun PCL was also carried out for a comparative study. Our aim is to analyze the release profiles of NAP from PCL/NAP and PCL/NAP-βCD-IC nanofibers and we investigate the effect of CD-IC on the release behavior of NAP from the nanofibrous PCL matrix. The characterization of NAP-βCD-IC and the presence of CD-IC in PCL/NAP-βCD-IC nanofibers were studied by FTIR, XRD, TGA, NMR and SEM. The SEM imaging of the electrospun PCL/NAP and PCL/NAP-βCD-IC nanofibers reveal that the average fiber diameter of these nanofibers is around 300. nm, in addition, the aggregates of CD-IC in PCL/NAP-βCD-IC nanofibers is observed. The release study of NAP in buffer solution elucidate that the PCL/NAP-βCD-IC nanofibers have higher release amount of NAP than the PCL/NAP nanofibers due to the solubility enhancement of NAP by CD-IC.
Open Access
The effect of cucurbit[n]uril on the solubility, morphology, and the photophysical properties of nonionic conjugated polymers in an aqueous medium
(2010) Tuncel, D.; Artar, M.; Hanay, S. B.
The effects of cucurbit[n]uril on the dissolution and the photophysical properties of nonionic conjugated polymers in water are described. For this purpose, a fluorine-based polymer, namely, poly[9,9-bis{6(N,N-dimethylamino) hexyl}fluorene-co-2,5-thienylene (PFT) was synthesized and characterized by spectroscopic techniques including 1D and 2D NMR, UV-vis, fluorescent spectroscopy, and matrix-assisted laser desorption mass spectrometry (MALDI-MS). For the first time, it was demonstrated that a nonionic conjugated polymer can be made soluble in water through an inclusion complex formation with CB8. The structure of the complex was elucidated by NMR experiments including 1H and selective 1D-NOESY. This complex emits green and is highly fluorescent with fluorescent quantum yield of 35%. In contrast, CB6 or water-soluble CB7 although they are chemically identical to CB8 do not have any effect on the dissolution and photophysical properties of PFT. By preparing a protonated version of PFT, the optical properties of PFT in methanol, protonated PFT and PFT@CB8 in water have been studied and compared. It was also observed that the morphology of the polymer PFT was affected by the presence of CB8. Thus CB8-assisted self-assembly of polymer chains leads to vesicles formation; these structures were characterized by DLS, AFM, SEM, and TEM fluorescent optical microscopy.
Open Access
Electronic structure, insulator-metal transition and superconductivity in K-ET2X salts
(1998) Ivanov V.A.; Ugolkova, E.A.; Zhuravlev, M.Ye.; Hakioǧlu, T.
The electronic structure and superconductivity of layered organic materials based on the bis(ethylenedithio)tetrathiafulvalene molecule (BEDT-TTF, hereafter ET) with essential intra-ET correlations of electrons are analysed. Taking into account the Fermi surface topology, the superconducting electronic density of states (DOS) is calculated for a realistic model of K-ET2X salts. A d-symmetry of the superconducting order parameter is obtained and a relation is found between its nodes on the Fermi surface and the superconducting phase characteristics. The results are in agreement with the measured non-activated temperature dependences of the superconducting specific heat and NMR relaxation rate of central 13C atoms in ET. © 1998 John Wiley & Sons, Ltd.
Open Access
Fast-dissolving, prolonged release, and antibacterial cyclodextrin/limonene-inclusion complex nanofibrous webs via polymer-free electrospinning
(American Chemical Society, 2016) Aytac Z.; Yildiz, Z. I.; Kayaci-Senirmak, F.; S. Keskin, N. O.; Kusku, S. I.; Durgun, Engin; Tekinay, T.; Uyar, Tamer
We have proposed a new strategy for preparing free-standing nanofibrous webs from an inclusion complex (IC) of a well-known flavor/fragrance compound (limonene) with three modified cyclodextrins (HPβCD, MβCD, and HPγCD) via electrospinning (CD/limonene-IC-NFs) without using a polymeric matrix. The experimental and computational modeling studies proved that the stoichiometry of the complexes was 1:1 for CD/limonene systems. MβCD/limonene-IC-NF released much more limonene at 37, 50, and 75 °C than HPβCD/limonene-IC-NF and HPγCD/limonene-IC-NF because of the greater amount of preserved limonene. Moreover, MβCD/limonene-IC-NF has released only 25% (w/w) of its limonene, whereas HPβCD/limonene-IC-NF and HPγCD/limonene-IC-NF released 51 and 88% (w/w) of their limonene in 100 days, respectively. CD/limonene-IC-NFs exhibited high antibacterial activity against E. coli and S. aureus. The water solubility of limonene increased significantly and CD/limonene-IC-NFs were dissolved in water in a few seconds. In brief, CD/limonene-IC-NFs with fast-dissolving character enhanced the thermal stability and prolonged the shelf life along with antibacterial properties could be quite applicable in food and oral care applications.
Open Access
Organization of bridging organics in periodic mesoporous organosilicas (PMOs)-polarization micro-raman spectroscopy
(Wiley, 2001) Dag, Ö.; Ozin, G. A.
The organization of bridging organics in oriented periodic mesoporous organosilica film (OPMOF) was demonstrated using the polarization micro-Raman spectroscopy (PMRS) in conjunction with powder x-ray diffraction (PXRD) and polarization optical microscopy (POM). The synthesis and the structural characterization of hexagonal symmetry OPMOF containing bridge-bonded ethane, ethene inside the silica channel walls were described. The mesoscale channels were found to run parallel to the surface of the underlying glass substrates as demonstrated by the PXRD measurements. A hexagonal array of channels with glassy silica organosilica walls was the best description of the structure shown by the PMRS measurements of OPMOF.
Open Access
PH-Responsive polypseudorotaxane synthesized through cucurbit[6]uril catalyzed 1, 3-dipolar cycloaddition
(2006) Tuncel, D.; Tiftik, H. B.; Salih, B.
A pH-responsive polypseudorotaxane has been synthesized via cucurbit[6]uril (CB6)-catalyzed 1,3-dipolar cycloaddition using diazide and dialkyne monomers, which contain a long aliphatic-spacer. The polypseudorotaxane was characterized by spectroscopic techniques (1H, 13C NMR and FT-IR) and matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS). The experimental results reveal that this polypseudorotaxane behaves as a pH-driven polymeric switch. Thus, when amine groups are protonated at an appropriate pH, CB6s are located on the triazole rings due to ion-dipole interaction, whereas at high pH they move onto the hydrophobic aliphatic spacer rather than slipping off the polypseudorotaxane. © The Royal Society of Chemistry 2006.
Open Access
Pideel: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas
(2024-06) Kaynar, Gün
The real-time assessment of tumor characteristics during surgery is crucial, offering the potential to create a feedback mechanism for surgeons. Such feedback enables surgeons to make more informed decisions regarding the extent of tumor resection and whether to adopt a more aggressive or conservative approach. Al-though metabolomics-based tumor pathology prediction methods exist, their predictive performance is often constrained by the limited size of available datasets. Additionally, the feedback about the tumor tissue could be enhanced in terms of content and accuracy. This thesis introduces PiDeeL, a metabolic pathway-informed deep learning model designed to perform survival analysis and pathology assessment based on metabolite concentrations. We demonstrate that integrating pathway information into the model architecture significantly reduces parameter complexity while enhancing survival analysis and pathological classification per-formance. Our results indicate that PiDeeL improves tumor pathology prediction performance over state-of-the-art methods, achieving a 3.38% improvement in the Area Under the ROC Curve and a 4.06% improvement in the Area Under the Precision-Recall Curve. Similarly, regarding the time-dependent concordance index (c-index), PiDeeL exhibits superior survival analysis performance, with a 4.3% improvement compared to current leading methods. Furthermore, importance analyses conducted on input metabolite features and pathway-specific neurons of PiDeeL provide valuable insights into tumor metabolism. Applying this model in the surgical setting will assist surgeons in dynamically adjusting their surgical plans, ultimately leading to more accurate prognosis estimates tailored to the specifics of the surgical procedure.
Open Access
Polyhedral oligomeric silsesquioxane-based hybrid networks obtained via thiol-epoxy click chemistry
(Springer, 2017) Bekin Acar, S.; Ozcelik, M.; Uyar, Tamer; Tasdelen, M. A.
A series of hybrid networks based on polyhedral oligomeric silsesquioxane (POSS) were prepared by thiol-epoxy click reaction using commercially available octakis-glycidyl-POSS (G-POSS), trimethylolpropane triglycidyl ether, and trimethylolpropane tris(3-mercaptopropionate) as monomers. The click reaction was simply catalyzed by lithium hydroxide which proceeded readily at ambient conditions in very good yields. The incorporation of G-POSS into the network was clearly determined by transmission electron microscopy, FTIR, and 1H-NMR spectroscopy techniques performed with a model study using 1-butane thiol and G-POSS molecules. The homogeneous distribution of G-POSS up to 5 wt% in the hybrid network was apparently confirmed by morphological investigations. By increasing G-POSS content higher than 5 wt%, the heterogeneous dispersion of G-POSS was determined from the tensile strength measurements. The significant decrease in tensile strength was possible due to the agglomeration of G-POSS. On the other hand, thermal properties of hybrid networks were compared together by thermogravimetric analyses, where all samples exhibited one-step degradation in the range of 220–500 °C. The thermal decomposition of hybrid network led to complete degradation of the organic part and favored the formation of stable carbonaceous and inorganic residues as char. Thus, the char yields of hybrid networks were increased to 6.2, 7.8, 10.1, 12.7, and 15.1% by G-POSS loadings from 0 to 15 wt%. This improvement was also a proof of the incorporation of G-POSS into the hybrid networks that resulted in high heat-resistant POSS-based hybrid networks compared to a sample without G-POSS.
Open Access
Polymer-free nanofibers from vanillin/cyclodextrin inclusion complexes: high thermal stability, enhanced solubility and antioxidant property
(Royal Society of Chemistry, 2016) Celebioglu A.; Kayaci-Senirmak, F.; Ipek, S.; Durgun, Engin; Uyar, Tamer
Vanillin/cyclodextrin inclusion complex nanofibers (vanillin/CD-IC NFs) were successfully obtained from three modified CD types (HPβCD, HPγCD and MβCD) in three different solvent systems (water, DMF and DMAc) via an electrospinning technique without using a carrier polymeric matrix. Vanillin/CD-IC NFs with uniform and bead-free fiber morphology were successfully produced and their free-standing nanofibrous webs were obtained. The polymer-free CD/vanillin-IC-NFs allow us to accomplish a much higher vanillin loading (∼12%, w/w) when compared to electrospun polymeric nanofibers containing CD/vanillin-IC (∼5%, w/w). Vanillin has a volatile nature yet, after electrospinning, a significant amount of vanillin was preserved due to complex formation depending on the CD types. Maximum preservation of vanillin was observed for vanillin/MβCD-IC NFs which is up to ∼85% w/w, besides, a considerable amount of vanillin (∼75% w/w) was also preserved for vanillin/HPβCD-IC NFs and vanillin/HPγCD-IC NFs. Phase solubility studies suggested a 1:1 molar complexation tendency between guest vanillin and host CD molecules. Molecular modelling studies and experimental findings revealed that vanillin:CD complexation was strongest for MβCD when compared to HPβCD and HPγCD in vanillin/CD-IC NFs. For vanillin/CD-IC NFs, water solubility and the antioxidant property of vanillin was improved significantly owing to inclusion complexation. In brief, polymer-free vanillin/CD-IC NFs are capable of incorporating a much higher loading of vanillin and effectively preserve volatile vanillin. Hence, encapsulation of volatile active agents such as flavor, fragrance and essential oils in electrospun polymer-free CD-IC NFs may have potential for food related applications by integrating the particularly large surface area of NFs with the non-toxic nature of CD and inclusion complexation benefits, such as high temperature stability, improved water solubility and an enhanced antioxidant property, etc.
Open Access
Tetrastyryl-bodipy dyes: convenient synthesis and characterization of elusive near IR fluorophores
(2009) Buyukcakir, O.; Bozdemir, O. A.; Kolemen, S.; Erbas, S.; Akkaya, E. U.
1,3,5,7-Tetramethyl-Bodipy derivatives undergo Knoevenagel-type condensations with aromatic aldehydes to ultimately yield tetrastyryl-Bodipy derivatives. The resulting dyes absorb and emit strongly In the near IR. As the versatility of the Bodipy dyes are fully appreciated, these new tetrastyryl dyes are likely to be featured In a variety of functional supramolecular systems. © 2009 American Chemical Society.
Open Access
Time-resolved XPS analysis of the SiO2/Si system in the millisecond range
(2004) Demirok, U. K.; Ertas, G.; Süzer, Şefik
By applying voltage pulses to the sample rod while recording the spectrum, we show, for the first time, that it is possible to obtain a time-resolved XPS spectrum in the millisecond range. The Si 2p spectrum of a silicon sample containing a ca. 400-nm oxide layer displays a time-dependent charging shift of ca. 1.7 eV with respect to the Au 4f peaks of a gold metal strip in contact with the sample. When gold is deposited as C12-thiol-capped nanoclusters onto the same sample, this time the Au 4f peaks also display time-dependent charging behavior that is slightly different from that of the Si 2p peak. This charging/discharging is related to emptying/filling of the hole traps in the oxide layer by the stray electrons within the vacuum system guided by the external voltage pulses applied to the sample rod, which can be used to extract important parameter(s) related to the dielectric properties of surface structures.