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Publication Metadata only A NIR-light-driven black phosphorus based nanocomposite for combating bacteria(Wiley-V C H Verlag Gmbh, 2022) Çekçekoğlu, İlknur Aksoy; Sevgi, Fatih; Ersöz, Mustafa; Patır, İmren Hatay; Department of Chemistry; N/A; Department of Chemistry; Eroğlu, Zafer; Küçükkeçeci, Hüseyin; Metin, Önder; Researcher; Researcher; Faculty Member; Department of Chemistry; College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 46962Nanocomposites of semiconducting two-dimensional (2D) materials provide advantageous for combating bacterial infections to overcome antibiotic resistance. In this study, the nanocomposites of 2D black phoshorus (BP) and silver nanoparticles (NPs) were prepared by anchoring as-synthesized Ag NPs on few-layer BP nanosheets via liquid self-assembly method and used as a NIR-light-driven antibacterial agent against Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa), and Gram-positive bacteria (Enterococcus faecalis and Bacillus cereus). The BP/Ag nanocomposites showed excellent photothermal effect and oxidative stress ability to inhibit the initial logarithmic growth phase of E. faecalis and B. cereus. According to the bacterial growth curve, agar plate assay and live/dead viability test, as-synthesized BP/Ag nanocomposites were found to be more effective antibacterial agent for Gram-positive bacteria than Gram-negative bacteria. The presented NIR-light-driven BP-based nanoplatform can open a new avenue for avoiding bacterial resistance and combating pathogenic bacteria and also broad-spectrum disinfection applications.Publication Metadata only Adsorption, folding, and packing of an amphiphilic peptide at the air/water interface(amer Chemical Soc, 2012) N/A; Department of Mechanical Engineering; Engin, Özge; Sayar, Mehmet; Master Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering, College of Engineering; N/A; 109820Peptide oligomers play an essential role as model compounds for identifying key motifs in protein structure formation and protein aggregation. Here, we present our results, based on extensive molecular dynamics simulations, on adsorption, folding, and packing within a surface monolayer of an amphiphilic peptide at the air/water interface. Experimental results suggest that these molecules spontaneously form ordered monolayers at the interface, Adopting a beta-hairpin-like structure within the surface layer. Our results reveal that the beta-hairpin structure can be observed both in bulk and at the air/water interface. However, the presence of an interface leads to ideal partitioning of the hydrophobic and hydrophilic residues, and therefore reduces the conformational space for the molecule and increases the stability of the hairpin structure. We obtained the adsorption free energy of a single beta-hairpin at the air/water interface, and analyzed the enthalpic and entropic contributions. the adsorption process is favored by two main factors: (1) Free-energy reduction due to desolvation of the hydrophobic side chains of the peptide and release of the water molecules which form a cage around these hydrophobic groups in bulk water. (2) Reduction of the total air/water contact area at the interface upon adsorption of the peptide amphiphile. By performing mutations on the original molecule, we demonstrated the relative role of key design features of the peptide. Finally, by analyzing the potential of mean force among two peptides at the interface, we investigated possible packing mechanisms for these molecules within the surface monolayer.Publication Metadata only Aerogel-copper nanocomposites prepared using the adsorption of a polyfluorinated complex from supercritical CO2(Springer, 2012) Kostenko, Svetlana O.; Kurykin, Michael A.; Khrustalev, Victor N.; Khokhlov, Alexei R.; Zhang, Lichun; Aindow, Mark; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Bozbağ, Selmi Erim; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; College of Engineering; N/A; 29633A supercritical deposition method has been used to synthesize aerogel-copper nanocomposites. Carbon, resorcinol-formaldehyde, and silica aerogels (CAs, RFAs, and SAs) were impregnated with a new polyfluorinated copper precursor (CuDI6), which has a high solubility in supercritical carbon dioxide (scCO(2)). Adsorption isotherms of CuDI6 onto various aerogels from scCO(2) were determined at 35 degrees C and 10.6 MPa using a batch method which is based on the measurement of the fluid phase concentration. The relative affinity between CuDI6 and different aerogels changed in the following order: CA > RFA > SA. The effect of temperature on the adsorption isotherms for the CuDI6-CO2-CA system was also studied at 35 and 55 degrees C and at a CO2 density of 736.1 kg/m(3). The CuDI6 uptake at a particular CuDI6 concentration increased with increasing temperature. Adsorbed CuDI6 was found to convert into Cu and Cu/Cu2O nanoparticles on the aerogel supports after chemical or thermal treatments at ambient pressure and at temperatures ranging from 200 to 400 degrees C.Publication Metadata only Anticancer investigation of platinum and copper-based complexes containing quinoxaline ligands(Elsevier, 2022) El-Beshti, Hager Sadek; Yildizhan, Yasemin; Kayi, Hakan; Cetin, Yuksel; Gercek, Zuhal; Ozalp-Yaman, Seniz; Adıgüzel, Zelal; Güngör Topçu, Gamze; Faculy Member; N/A; School of Medicine; N/A; 251865; N/AThis research focuses on synthesis and anticancer activity of trans-[(dichloro)bisdipyridlquinoxalino] and [(dichloro)bisdithienylquinoxalino]copper(II)/platinum(II) compounds as prodrug candidates. The binding interaction of these compounds with calf thymus DNA (CT-DNA) and human serum albumin (HSA) of the complexes were assessed with UV titration, thermal decomposition, viscometric, and fluorometric measurements. The nature of the binding of the complexes on DNA were revealed as electrostatic interaction between the cationic metal complexes ion and the negative phosphate groups of CT-DNA upon removal of the counter ion, chloride. In addition, our complexes induced a surface contact through the hydrophobic region of protein. Antitumor activity of the complexes against human glioblastoma A172, LN229, and U87 cell lines and human lung A549, human breast MDA-231, human cervix HeLa, and human prostate PC-3 cell lines were investigated by examining cell viability, oxidative stress, apoptosis, and migration/invasion. Cytotoxicity of the complexes was evaluated by MTT test. The U87 and HeLa cells were investigated as the cancer cells most sensitive to our complexes. The exerted cytotoxic effect of dipyridlquinoxalino and dithienylquinoxalino copper(II)/platinum(II) complexes was attributed to the formation of the reactive oxygen species in vitro. It is clearly demonstrated that trans-[(dichloro)bisdithenylquinoxalino]copper (II) (Cu(dtq)) has the highest DNA degradation potential and anticancer effect among the tested complexes by leading apoptosis. Wound healing and invasion analysis results also supported the anticancer activity of Cu(dtq).Publication Metadata only Arl2-mediated allosteric release of farnesylated kras4b from shuttling factor pde delta(2018) Jang, Hyunbum; Nussinov, Ruth; N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Özdemir, E. Sıla; Gürsoy, Attila; Keskin, Özlem; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; College of Engineering; College of Engineering; N/A; 8745; 40548Proper localization of Ras proteins at the plasma membrane (PM) is crucial for their functions. To get to the PM, KRas4B and some other Ras family proteins bind to the PDE delta shuttling protein through their farnesylated hypervariable regions (HVRs). The docking of their famesyl (and to a lesser extent geranylgeranyl) in the hydrophobic pocket of PDE delta's stabilizes the interaction. At the PM, guanosine 5'-triphosphate (GTP)-bound Arf-like protein 2 (Arl2) assists in the release of Ras from the PDE delta. However, exactly how is still unclear. Using all-atom molecular dynamics simulations, we unraveled the detailed mechanism of Arl2-mediated release of KRas4B, the most abundant oncogenic Ras isoform, from PDE delta. We simulated ternary Arl2 PDE delta KRas4B HVR complexes and observed that Arl2 binding weakens the PDE delta farnesylated HVR interaction. Our detailed analysis showed that allosteric changes (involving beta 6 of PDE delta and additional PDE delta residues) compress the hydrophobic PDE delta pocket and push the HVR out. Mutating PDE delta residues that mediate allosteric changes in PDE delta terminates the release process. Mutant Ras proteins are enriched in human cancers, with currently no drugs in the clinics. This mechanistic account may inspire efforts to develop drugs suppressing oncogenic KRas4B release.Publication Metadata only Assembly of triblock amphiphilic peptides into one-dimensional aggregates and network formation(amer Chemical Soc, 2016) N/A; N/A; Department of Mechanical Engineering; Özgür, Beytullah; Sayar, Mehmet; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 109820Peptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. a triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: beta-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with <= 1% by weight peptide concentration. in this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall beta-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, Alternative structures such as zero-dimensional aggregates with two beta-sheets oriented orthogonally (which we refer to as a cross-packed structure) and beta-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.Publication Metadata only Bisvinylated [R–Ge9–Ge9–R] 4– cluster dimers(Wiley-V C H Verlag Gmbh, 2015) Benda, Christian B.; He, Haiyan; Klein, Wilhelm; Faessler, Thomas F.; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882The syntheses, crystal structures, and NMR and Raman spectroscopic characterization of two compounds with a new member of the organically functionalized dimeric Ge-9-Ge-9 polyanion [R-Ge-9-Ge-9-R] 4-with R=CH=CH2 are presented. [K([2.2.2] crypt)](4)[(CH2=CH)-Ge-9-Ge-9-(CH=CH2)]center dot 1.76 en (1) was synthesized either at elevated temperature by the reaction of K4Ge9 and bis(trimethylsilyl) acetylene in ethylenediamine or at ambient temperature in the presence of Pt(PPh3)(4). [K([18]crown-6)](4)[(CH2=CH)-Ge-9-Ge-9-(CH=CH2)]center dot 4 en (2) was obtained from the prefabricated monomeric bisvinylated Ge-9 cluster [Ge-9(CH=CH2)(2)](2-) and an ethylenediamine solution of the intermetallic compound K4.79Co0.79Sn9. The reductive cleavage of one or two vinyl groups from [Ge-9(CH=CH2)(2)](2-) - a prerequisite for the latter reaction - could be shown by reacting a solution of the divinylated [Ge-9(CH=CH2)(2)](2-) anion in liquid ammonia with elemental potassium, which resulted in the formation of the ligand-free Ge-9(4-) cluster in the new compound [K-5(OH)]Ge-9(NH3)(11) (3).Publication Metadata only Ca3[BN2]I3: the first halide-rich alkaline earth nitridoborate with isolated [BN2]3 - units(Wiley, 2015) Aydemir, Umut; Drathen, Christina; Akselrud, Lev; Prots, Yurii; Hoehn, Peter; Department of Chemical and Biological Engineering; N/A; Department of Chemistry; Toros, Turna Ezgi; Yahyaoğlu, Müjde; Somer, Mehmet Suat; Undergraduate Student; Master Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 178882The title compound Ca-3[BN2]I-3 was obtained from reactions of mixtures of the starting materials Ca-3[BN2](2) and CaI2 in a 1:4 ratio in sealed Nb tubes at 1223 K. The crystal structure was solved from powder synchrotron diffraction data. Ca-3[BN2]I-3 is the first example of a halide-rich nitridoborate crystallizing in the rhombohedral space group R32 [no. 155, Pearson code: hR96; Z = 12; a = 16.70491(2) angstrom, c = 12.41024(2) angstrom]. The crystal structure is built up by two interpenetrating networks of condensed edge-sharing [BN2]@Ca-6 and [square]@I-6 trigonal antiprisms (square = void). In Ca-3[BN2]I-3 two crystallograhically distinct [BN2](3-) anions are present with d(B1-N) = 1.393(2) angstrom and d(B2-N) = 1.369(9) angstrom. Their bond angles are practically linear, varying only slightly: N-B1-N = 179(1)degrees and N-B2-N = 180 degrees. Vibrational spectra were interpreted based on the D-infinity h symmetry of the discrete linear [N-B-N](3-) moieties, considering the site symmetry reduction and the presence of two distinct [BN2](3-) groups.Publication Open Access Collisional relaxation kinetics for ortho and para NH2- under photodetachment in cold ion traps(Royal Society of Chemistry (RSC), 2018) Gianturco, Francesco A.; Lakhmanskaya, Olga Y.; Vera, Mario Hernandez; Wester, Roland; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129The collisional cooling of the internal rotational states of the nonlinear anion NH2- ((1)A(1)), occurring at the low temperature of a cold ion trap under helium buffer gas cooling, is examined via quantum dynamics calculations and ion decay rate measurements. The calculations employ a novel ab initio potential energy surface that describes the interaction anisotropy and range of action between the molecular anions and the neutral He atoms. The state changing integral cross sections are employed to obtain the state-to-state rate coefficients, separately for the ortho- and the para-NH2- ions. These rates are in turn used to compute the state population evolution in the trap for both species, once photodetachment by a laser is initiated in the trap. The present work shows results for the combined losses of both species after the photodetachment laser is switched on and analyzes the differences of loss kinetics between the two hyperfine isomers.Publication Metadata only Copper(II) and oxidovanadium(IV) complexes of chromone schiff bases as potential anticancer agents(Springer, 2022) Nunes, Patrique; Yıldızhan, Yasemin; Marques, Fernanda; Pessoa, Joao Costa; Correia, Isabel; Adıgüzel, Zelal; Ayhan, Ceyda Açılan; Faculty Member; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; School of Medicine; 251865; 219658We report the synthesis, characterization and biological screening of new chromone Schiff bases derived from the condensation of three 6-substituted-3-formyl-chromones with pyridoxal (HL1-3) and its Cu(II) complexes [Cu(L1-3)Cl], 1-3. For the 6-methyl derivative, HL2, the (VO)-O-IV-complex [VO(L-2)Cl] (5), as well as ternary Cu and (VO)-O-IV complexes with 1,10-phenanthroline (phen), [Cu(L-2)(phen)Cl] (4) and [VO(L-2)(phen)Cl] (6), were also prepared and evaluated. Their stability in aqueous medium and radical scavenging activity toward DPPH are screened, with [Cu(L-2)(phen)Cl] (4) showing hydrolytic stability and [VO(L-2)(phen)Cl] (6) high radical scavenging activity. Spectroscopic studies establish bovine serum albumin (BSA), a model for HSA, as a potential reversible carrier of [Cu(L-2)(phen)Cl] in blood with K-BC approximate to 10(5) M-1. The cytotoxic activity of a group of compounds is evaluated against a panel of human cancer cell lines of different origin (ovary, cervix, brain and breast) and compared to normal cells. Our results indicate that Cu complexes are more cytotoxic than the ligands but not selective towards cancer cells. The most potent complexes (4 and 6) are further evaluated for their apoptotic potential, induction of reactive oxygen species (ROS) and genotoxicity. Both complexes efficiently triggered cell death through apoptosis as evaluated by DNA morphology and TUNEL assay, increased ROS formation as determined by DCFDA (2',7'-dichlorodihydrofluorescein diacetate) analysis, and induced genotoxic damage as visualized via COMET assay in all cancer cells under study. Therefore, 4 and 6 may be potential precursor anticancer molecules, yet they need to be targeted toward cancer cells. [GRAPHICS] .