Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
11 results
Search Results
Publication Metadata only A mixed basis with off-center Gaussian functions for the calculation of the potential energy surfaces for pi-stacking interactions: dimers of benzene and planar C-6(Springer, 2015) Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for pi-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C-6 moieties. Moller-Plesset (MP2, SCS-MP2) and coupled cluster [CCSD(T)] calculations show that such generated basis sets provide an accurate description of p-stacking systems with favorable computation times compared to the standard augmented basis sets. The addition of these off-center functions eliminates the linear dependence of the augmented basis sets, which is one of the most encountered numerical problems during calculation of the oligomers of polyaromatic hydrocarbons (PAH). In this work, we present a comparative study of the general characteristics of the potential energy surfaces for the parallel stacked and T-shape conformations of benzene and planar C6 clusters, using a combination of cc-PVXZ and our optimized functions. We discuss properties, such as the depth and curvature of the potential functions, short and long distance behavior, and the frictional forces between two model monomers.Publication Metadata only Investigation of the factors affecting the photothermal therapy potential of small iron oxide nanoparticles over the 730-840 nm spectral region(Royal Soc Chemistry, 2018) N/A; N/A; N/A; Department of Physics; Department of Chemistry; Bilici, Kübra; Muti, Abdullah; Duman, Fatma Demir; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; N/A; 23851; 178902The use of superparamagnetic iron oxide nanoparticles (SPIONs) as a sensitizer in photothermal therapy (PTT) is relatively new and the origin of such a phenomenon is not known. Usually, large crystals and aggregated particles are preferred in the literature, suggesting that these increase the absorbance of particles at the irradiation wavelength, and hence, provide a larger temperature increase. This study has two major goals: identification of the key factors that affect the photo-induced temperature increase in well-controlled experiments and the influence of laser irradiation on nanoparticle properties. Small, biocompatible poly(acrylic acid) coated SPIONs (PAA/SPIONs) were used since they are more practical for future medical use than large aggregates. We studied the impact of three major laser-dependent variables, namely the wavelength (between 728 and 838 nm), intensity (1.85-9.76 W cm(-2)) and power (105-800 mW) as well as attenuation at the irradiation wavelength, on photothermal heating achieved with PAA/SPIONs. Within the studied range of these variables, only the laser power plays a critical role on the magnitude of photothermal heating in solutions. There is no strong correlation between the attenuation at the excitation wavelength and the temperature increase. In addition, extensive characterization of SPIONs before and after irradiation revealed no significant difference, which supports the re-usability of SPIONs. Lastly, the PTT potential of these small PAA/SPIONs was demonstrated in vitro on HeLa cells. At these low laser powers no temperature increase in SPION-free water or cell death in SPION-free cells was detected. Hence, this study provides a new insight into the photothermal effect of SPIONs, provides a clear and repeatable experimental procedure and demonstrates great potential for small SPIONs to be exploited in PTT.Publication Metadata only Multimodal image-guided folic acid targeted Ag-based quantum dots for the combination of selective methotrexate delivery and photothermal therapy(Elsevier Science Sa, 2020) N/A; N/A; N/A; Department of Physics; Department of Chemistry; Hashemkhani, Mahshid; Muti, Abdullah; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; 23851; 178902Multifunctional quantum dots (QDs) with photothermal therapy (PTT) potential loaded with an anticancer drug and labelled with a targeting agent can be highly effective nano-agents for tumour specific, image-guided PTT/ chemo combination therapy of cancer. Ag-chalcogenides are promising QDs with good biocompatibility. Ag2S QDs are popular theranostic agents for imaging in near-infrared with PTT potential. However, theranostic applications of AgInS2 QDs emitting in the visible region and its PTT potential need to be explored. Here, we first present a simple synthesis of small, glutathione (GSH) coated AgInS 2 QDs with peak emission at 634 nm, 21% quantum yield, and excellent long-term stability without an inorganic shell. Ag2S-GSH QDs emitting in the nearinfrared region (peak emission = 822 nm) were also produced. Both QDs were tagged with folic acid (FA) and conjugated with methotrexate (MTX). About 3-fold higher internalization of FA-tagged QDs by folate-receptor (FR) overexpressing HeLa cells than HT29 and A549 cells was observed. Delivery of MTX by QD-FA-MTX reduced the IC50 of the drug from 10 mu g/mL to 2.5-5 mu g/mL. MTX release was triggered at acidic pH, which was further enhanced with local temperature increase created by laser irradiation. Irradiation of AgInS2-GSH QDs at 640 nm (300 mW) for 10 min, caused about 10 degrees C temperature increase but did not cause any thermal ablation of cells. On the other hand, Ag2S-GSH-FA based PTT effectively and selectively killed HeLa cells with 10 min 808 nm laser irradiation via mostly necrosis with an IC50 of 5 mu g Ag/mL. Under the same conditions, IC50 of MTX was reduced to 0.21 mu g/mL if Ag2S-GSH-FA.Publication Metadata only Preclinical characterization of a novel palladium complex as anticancer drug candidate(Wiley, 2016) Erim, S. Durmuş; İçsel, Ceyda; Yılmaz, Veysel Turan; Ulukaya, Engin; Şahin, Önder; N/A; Department of Chemistry; Department of Chemistry; Ünal, Özlem; Khodadust, Rouhollah; Acar, Havva Funda Yağcı; PhD Student; Other; Faculty Member; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; 178902N/APublication Metadata only Dual laser activatable brominated hemicyanine as a highly efficient and photostable multimodal phototherapy agent(Elsevier Science Sa, 2021) Department of Chemistry; N/A; N/A; N/A; Department of Physics; Department of Chemistry; Department of Chemistry; Gündüz, Hande; Bilici, Kübra; Çetin, Sultan; Muti, Abdullah; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; Kölemen, Safacan; Researcher; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; 224496; N/A; N/A; N/A; 23851; 178902; 272051Dual phototherapy agents have attracted great interest in recent years as they offer enhanced cytotoxicity on cancer cells due to the synergistic effect of photodynamic and photothermal therapies (PDT/PTT). In this study, we demonstrate a brominated hemicyanine (HC-1), which is previously shown as mitochondria targeting PDT agent, can also serve as an effective photosensitizer for PTT for the first time under a single (640 nm or 808 nm) and dual laser (640 nm + 808 nm) irradiation. Generation of reactive oxygen species and photothermal conversion as a function of irradiation wavelength and power were studied. Both single wavelength irradiations caused significant phototoxicity in colon and cervical cancer cells after 5 min of irradiation. However, coirradiation provided near-complete elimination of cancer cells due to synergistic action. This work introduces an easily accessible small molecule-based synergistic phototherapy agent, which holds a great promise towards the realization of local, rapid and highly efficient treatment modalities against cancer.Publication Metadata only Etoposide loaded SPION-PNIPAM nanoparticles improve thein vitrotherapeutic outcome on metastatic prostate cancer cells via enhanced apoptosis(Wiley-V C H Verlag Gmbh, 2020) Erkısa, Merve; Arı, Ferda; Ulukaya, Engin; Department of Chemistry; Department of Chemistry; N/A; Department of Chemistry; Ülkü, İrem; Khodadust, Rouhollah; Yar, Yasemin; Acar, Havva Funda Yağcı; Undergraduate Student; Other; PhD Student; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 178902Prostate cancer is among the leading causes of death worldwide because its metastatic form is a deadly disease. Therefore, the development of new chemotherapeutics is of immense importance. Nanoparticle technology seems to provide diverse options in this regard. Therefore, poly(N-isopropylacrylamide) (PNIPAM) coated superparamagnetic iron oxide nanoparticles (SPION) loaded with Etoposide were prepared in small sizes (57 nm) and with 3.5 % drug content to improve the efficiency of Etoposide in prostate cancer therapy. Sustained release of the drug was achieved, which found to be sensitive to low pH and high temperature. The anti-growth activity of SPION-PNIPAM-Etoposide formulation against metastatic prostate cancer cells (PC-3, LNCaP) were investigated by SRB assay, then, confirmed by ATP assay. Mode of cell death was evaluated by using flow cytometry analyses. A significant improvement of nanoformulated drug was observed at 5-10 mu g/ml doses of the drug in both cell lines. More importantly, this formulation enhanced the cytotoxic effect of Etoposide on PC-3 cells, which is considered more resistant to Etoposide than LNCaP and reduced the IC(50)value by 55 % reaching to 4.5 mu g drug/ml, which is a very significant improvement in the literature. It was clearly shown that nanoformulated drug provided about 3-fold increases in caspase-dependent early apoptotic cells in PC-3 cells. The novel formulation seems to successfully cause cell death of especially PC-3 metastatic prostate cancer cells. It should therefore be taken into consideration for further animal studies as a novel potent anticancer agent.Publication Metadata only Development of a cysteine responsive chlorinated hemicyanine for image-guided dual phototherapy(Elsevier, 2022) Erkısa, Merve; Ulukaya, Engin; N/A; N/A; Department of Chemistry; N/A; N/A; N/A; Department of Physics; Department of Chemistry; Department of Chemistry; Savani, Samira; Onbaşlı, Kübra; Gündüz, Hande; Çelikbaş, Eda; Muti, Abdullah; Khan, Minahil; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; Kölemen, Safacan; Master Student; PhD Student; Researcher; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University AKKİM Boron-Based Materials & High-technology Chemicals Research & Application Center (KABAM) / Koç Üniversitesi AKKİM Bor Tabanlı Malzemeler ve İleri Teknoloji Kimyasallar Uygulama ve Araştırma Merkezi (KABAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; N/A; 365341; 224496; N/A; N/A; N/A 23851; 178902; 272051A cysteine (Cys) activatable chlorinated hemicyanine (Cl-Cys) was introduced as a tumour selective image guided dual phototherapy agent. Cl-Cys exhibited a significant turn on response in its near-IR emission signal and activated its singlet oxygen generation as well as photothermal conversion potentials upon reacting with Cys. The laser irradiation of Cl-Cys induced significant cell death in cancer cells with high Cys level, while it stayed deactivated and non-emissive in a healthy cell line. A profound synergistic PDT/PTT effect was observed at high doses. Remarkably, Cl-Cys marks the first ever example of Cys-responsive small organic-based therapeutic agent and holds a great promise to develop new activity-based photosensitizers for dual phototherapy action.Publication Metadata only Effects of silver sulfide quantum dots coated with 2-mercaptopropionic acid on genotoxic and apoptotic pathways in vitro(Elsevier Ireland Ltd, 2018) Vardar, Deniz Ozkan; Aydin, Sevtap; Hocaoglu, Ibrahim; Basaran, Nursen; Department of Chemistry; Acar, Havva Funda Yağcı; Faculty Member; Department of Chemistry; College of Sciences; 178902Quantum dots (QDs) are highly promising nanomaterials in bioimaging system because of their bright fluorescence, broad UV excitation, narrow emission band, and high photostability. Recently, there is a great activity on Ag2S quantum dots for both imaging and drug/gene delivery due to the potential of having a better cytocompatability and near infrared luminescence. 2-Mercaptopropionic acid (2 MP A)-coated silver sulfide (Ag2S) QDs were reported as the most luminescent, stable, anionic Ag2S QDs in the literature. In this study, we aim to determine the cytotoxicity of 2 MP A/Ag2S in Chinese hamster lung fibroblast (V79) cells. The genotoxic and apoptotic effects of 2 MP A/Ag2S QDs were assessed by the alkaline single cell electrophoresis assay and real time polymerase chain reaction techniques, respectively. The cell viability decreased above 200 mu g/ml and 800 mu g/ml for MTT tetrazolium and neural red uptake assays, respectively. DNA damage was not observed by 2 MP A/Ag2S QDs at the studied concentration levels (5-2000 mu g/ml). The levels of mRNA expression of p53, caspase 3, caspase 9, box, bcl-2, survivin were not changed by 2 MP A/Ag2S QDs below IC50 (around 1000 mu g/ml). Hence, 2 MP A/Ag2S QDs did not show any cytotoxic or genotoxic effects in V79 cells at lower doses. We conclude that the biocompatibility of 2 MP A/Ag2S ODs makes them suitable for cell labeling applications.Publication Metadata only A post-HF study on the interaction of iodine with small polyaromatic hydrocarbons(Springer, 2014) Sutay, Berkay; Yurtsever, Mine; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129In this work, we present a theoretical study of the interaction between a diatomic iodine molecule with planar naphthalene and several other small polyaromatic hydrocarbons (PAHs). Our aim was to understand the general characteristics of the potential energy surface (PES) of this system; that is locating various local minima, finding the variation of PES around these optimum points by means of first principle calculations at MP2, SCS-MP2 and CCSD(T) levels of theory. Two basic orientations of the iodine molecule, i.e., parallel or perpendicular with respect to the naphthalene plane, are discussed. The PES of the former was investigated in detail, including the translation and rotation of I-2 (as a rigid rotor) along the naphtalene surface. It was concluded that, although the perpendicular conformations are usually 1 kcal mol(-1) more stable than the parallel conformation, this small difference does not exclude the presence of both conformations in the gas phase. Both structures were stable enough to hold more than 20 vibrational states. NBO analysis showed that the mutual polarization effects were greater for the perpendicular conformation. It was also observed that the I-2+naphtalene dimer interaction is almost twice of that of I-2+naphtalene, showing the long range character of the interaction.Publication Metadata only Indocyanine green loaded APTMS coated SPIONs for dual phototherapy of cancer(Elsevier Science Sa, 2019) N/A; N/A; Department of Physics; Department of Chemistry; Bilici, Kübra; Muti, Abdullah; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; 23851; 178902Superparamagnetic iron oxide nanoparticles (SPIONs) have been recently recognized as highly efficient photothermal therapy (PTT) agents. Here, we demonstrate, for the first time to our knowledge, dose and laser intensity dependent PTT potential of small, spherical, 3-aminopropyltrimethoxysilane coated cationic superparamagnetic iron oxide nanoparticles (APTMS@SPIONs) in aqueous solutions upon irradiation at 795 nm. Indocyanine green (ICG) which has been recently used for photodynamic therapy (PDT), was loaded to APTMS@SPIONs to improve the stability of ICG and to achieve an effective mild PIT and PDT (dual therapy) combination for synergistic therapeutic effect on cancer cells via a single laser treatment in the near infrared (NIR). Neither APTMS@SPIONs nor ICG-APTMS@SPIONs showed dark toxicity on MCF7 breast and HT29 colon cancer cell lines. A safe laser procedure was determined as 10 min irradiation at 795 nm with 1.8 W/cm(2) of laser intensity, at which APTMS@SPION did not cause a significant cell death. However, free ICG reduced cell viability at and above 10 mu g/ml under these conditions along with generation of reactive oxygen species (ROS), more effectively in MCF7. ICG-APTMS@SPION treated cells showed 2-fold increase in ROS generation and near complete cell death at and below 5 mu g/ml ICG dose, even in less sensitive HT29 cells after a single laser treatment at NIR, which would be safe for the healthy tissue and provide a longer penetration depth. Besides, both components can be utilized for diagnosis and the overall composition may be used for optical-image guided phototherapy in the NIR region.