Person: FINDIKÇI, Ilknur Eruçar
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Ilknur Eruçar
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FINDIKÇI
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ArticlePublication Metadata only Zinc(II) and cadmium(II) coordination polymers containing phenylenediacetate and 4,4′-azobis(pyridine) ligands: Syntheses, structures, dye adsorption properties and molecular dynamics simulations(Elsevier, 2017) Sezer, G. G.; Arıcı, M.; Fındıkçı, İlknur Eruçar; Yeşilel, O. Z.; Özel, H. U.; Gemici, B. T.; Erer, H.; Mechanical Engineering; FINDIKÇI, Ilknur EruçarTwo new coordination polymers (CPs) – [Zn(µ4-ppda)(µ-abpy)0.5]n(1) and [Cd(μ3-opda)(µ-abpy)0.5(H2O)]n(2) (o/ppda = 1,2/1,4-phenylenediacetate, abpy = 4,4′-azobis(pyridine)) – have been synthesized by using Zn(II)/Cd(II) salts in the presence of o- and p-phenylenediacetic acid and abpy under hydrothermal conditions. Their structures have been characterized by FT-IR spectroscopy, elemental analysis, X-ray powder diffraction and single crystal X-ray diffraction techniques. The structural diversities were observed depending on anionic ligands and metal centers in the synthesized complexes. Complex 1 consists of a 2-fold interpenetrated 3D+3D→3D framework with pcu topology while complex 2 has a 2D structure with sql topology. The adsorption of methylene blue (MB) was studied to examine the potential of the title CPs for removal of dyes from aqueous solution. Molecular dynamics (MD) simulations were also performed to examine diffusion of MB in 1 and 2. Thermal and optical properties of two complexes were also discussed.ArticlePublication Metadata only Molecular simulations of COFs, IRMOFs and ZIFs for adsorption-based separation of carbon tetrachloride from air(Elsevier, 2019-01) Gülçay, Ezgi; Fındıkçı, İlknur Eruçar; Mechanical Engineering; FINDIKÇI, Ilknur Eruçar; Gülçay, EzgiCovalent organic frameworks (COFs), metal organic frameworks (MOFs) and zeolitic imidazolate frameworks (ZIFs) have been widely studied gas separation applications due to their large surface areas, high pore volumes, tunable pore sizes and chemical stabilities. In this study, separation performances of 153 COFs, 14 IRMOFs and 8 ZIFs were assessed for efficient removal of carbon tetrachloride (CCl4) from CCl4/Ar, CCl4/N-2, CCl4/O-2 mixtures at 298 K and infinite dilution. The top performing three materials in each group, namely, borazine-linked polymer (BLP-2H-AA), IRMOF-11 and ZIF-6 were identified. Single-component, binary mixture and quaternary mixture adsorption isotherms of argon (Ar), CCl4, nitrogen (N-2) and oxygen (O-2) in these materials were computed at 298 K and various total pressures from 10(-3) to 1.5 x 10(4) kPa. Mixture adsorption selectivities and separation potentials were then calculated and the effect of relative humidity on the performance of adsorption-based CCl4 separation was examined. Single-component and quaternary mixture diffusion coefficients of Ar, CCl4, N-2 and O-2 were finally computed. Our results showed that ZIF-6 exhibits the highest adsorption selectivity and the highest separation potential for CCl4/Ar, CCl4/N-2 and CCl4/O-2 mixtures, followed by IRMOF-11 and BLP-2H-AA. Results of this computational study will be highly useful to identify the promising materials for removal of CCl4 from air.ArticlePublication Metadata only Combining tensile test results with atomistic predictions of elastic modulus of graphene/polyamide-6,6 nanocomposites(Elsevier, 2023-06) Batyrov, Merdan; Dericiler, K.; Palabıyık, Büşra Akkoca; Okan, B. S.; Öztürk, Hande; Fındıkçı, İlknur Eruçar; Mechanical Engineering; KAYMAKSÜT, Hande Öztürk; FINDIKÇI, Ilknur Eruçar; Batyrov, Merdan; Palabıyık, Büşra AkkocaIn this work, we combined tensile test results with atomistic simulations to investigate the effect of filler parameters including distribution, stacking, loading and lateral graphene size on elastic moduli of graphene/PA-6,6 nanocomposites. Stacked and randomly distributed atomistic models were adapted in Molecular Dynamics (MD) simulations to establish the limits of stiffness enhancement in graphene reinforced PA-6,6 nanocomposites with loading ratios changing from 0 to 1 wt%. Experimental results showed that incorporating of 0.3–0.4 wt% graphene loading improved the elastic modulus of the neat polymer by 41.7%−43.5%. While the test sample behaved close to the computational results of the stacked atomistic model at low graphene loadings up to 0.4 wt%, it overshot the predictions of the randomly distributed model at all considered loadings up to 1 wt%. Elastic moduli of graphene-based PA-6,6 nanocomposites increased linearly with graphene loading in the stacked model, however, no such relation was detected in the randomly distributed model. The lower stiffness enhancement provided by the randomly distributed model compared to the stacked model was revealed as the small lateral size of graphene plates in PA-6,6 matrix. As the graphene size increased, the elastic modulus of the graphene dramatically increased, directly improving the elastic modulus of the nanocomposite. The developed computational approach is highly useful to estimate the boundaries of stiffness enhancement provided by graphene dispersions in macroscale nanocomposite samples.ArticlePublication Metadata only Computational investigations of Bio-MOF membranes for uremic toxin separation(Elsevier, 2022-01-15) Palabıyık, Büşra Akkoca; Batyrov, Merdan; Fındıkçı, İlknur Eruçar; Mechanical Engineering; FINDIKÇI, Ilknur Eruçar; Palabıyık, Büşra Akkoca; Batyrov, MerdanDeveloping new and efficient methods as an alternative to hemodialysis is important due to the challenges associated with poor efficiency of membranes and long dialysis sessions. Recently, metal organic frameworks (MOFs) have attracted interest in the membrane community due to their tunable physical and chemical properties. However, their potential in uremic toxin separations is still unknown and it is not practical to test each synthesized MOF for uremic toxin separations. The main objective of this study is to computationally assess membrane-based uremic toxin separation performances of 60 bio-compatible MOFs (bio-MOFs). Combining grand canonical Monte Carlo (GCMC) and equilibrium molecular dynamics (EMD) simulations, we predicted urea, creatinine, and water permeabilities of bio-MOFs and their membrane selectivities for urea/water and creatinine/water separations. Results showed that OREZES, a carboxylate-based MOF exhibited the highest membrane selectivity (347.94) for urea/water separation whereas BEPPIX, an amino-based MOF gave the highest creatinine/water selectivity (1.5 × 105) at infinite dilution and 310 K. Guest-guest and host–guest interaction energies for uremic toxins were also computed during EMD simulations and van der Waals interactions were found to be much stronger than the coulombic interactions. We finally examined the effect of MOF's flexibility on the predicted membrane performance and membrane selectivities of bio-MOFs for urea/water separation significantly enhanced when the structural flexibility was considered in simulations. Our results will be a guide for further studies to design novel bio-MOF membranes for uremic toxin separations.ArticlePublication Open Access Computational investigation of dual filler-incorporated polymer membranes for efficient CO2 and H2 separation: MOF/COF/Polymer mixed matrix membranes(American Chemical Society, 2023-01-26) Aydın, S.; Altintas, C.; Fındıkçı, İlknur Eruçar; Keskin, S.; Mechanical Engineering; FINDIKÇI, Ilknur EruçarMixed matrix membranes (MMMs) composed of two different fillers such as metal-organic frameworks (MOFs) and covalent-organic frameworks (COFs) embedded into polymers provide enhanced gas separation performance. Since it is not possible to experimentally consider all possible combinations of MOFs, COFs, and polymers, developing computational methods is urgent to identify the best performing MOF-COF pairs to be used as dual fillers in polymer membranes for target gas separations. With this motivation, we combined molecular simulations of gas adsorption and diffusion in MOFs and COFs with theoretical permeation models to calculate H2, N2, CH4, and CO2 permeabilities of almost a million types of MOF/COF/polymer MMMs. We focused on COF/polymer MMMs located below the upper bound due to their low gas selectivity for five industrially important gas separations, CO2/N2, CO2/CH4, H2/N2, H2/CH4, and H2/CO2. We further investigated whether these MMMs could exceed the upper bound when a second type of filler, a MOF, was introduced into the polymer. Many MOF/COF/polymer MMMs were found to exceed the upper bounds showing the promise of using two different fillers in polymers. Results showed that for polymers having a relatively high gas permeability (≥104 barrer) but low selectivity (≤2.5) such as PTMSP, addition of the MOF as the second filler can have a dramatic effect on the final gas permeability and selectivity of the MMM. Property-performance relations were analyzed to understand how the structural and chemical properties of the fillers affect the permeability of the resulting MMMs, and MOFs having Zn, Cu, and Cd metals were found to lead to the highest increase in gas permeability of MMMs. This work highlights the significant potential of using COF and MOF fillers in MMMs to achieve better gas separation performances than MMMs with one type of filler, especially for H2 purification and CO2 capture applications.ArticlePublication Unknown Computational investigation of metal organic frameworks for storage and delivery of anticancer drugs(Royal Society of Chemistry, 2017-08-14) Fındıkçı, İlknur Eruçar; Keskin, S.; Mechanical Engineering; FINDIKÇI, Ilknur EruçarMetal organic frameworks (MOFs) have been recently used in biomedical applications such as drug storage and drug delivery due to their large surface areas, high pore volumes, and tunable physical and chemical characteristics. In this study, we investigated MOF-74 materials for efficient storage and delivery of two anticancer drug molecules, methotrexate (MTX) and 5-fluorouracil (5-FU). We initially compared the results of our molecular simulations with the available experimental data for the MTX and 5-FU uptakes of various MOFs. Motivated by the good agreement between experiments and simulations, we computed MTX and 5-FU uptakes in 10 different MOF-74 materials having various physical and chemical properties. At low fugacity, MTX adsorption is favored over 5-FU since MTX has stronger interactions with the MOFs whereas at high fugacity, 5-FU adsorption is favored over MTX due to the entropic effects. Our results showed that MOF-74 materials outperform the MTX and 5-FU storage capacities of traditional materials such as polymeric nanoparticles and two dimensional layered nanomaterials. We also examined the diffusion of drug molecules in MOFs considering both single-component and mixture transport for the first time in the literature. Both drug molecules diffuse slowly in MOFs suggesting that MOF-74 materials are strong alternatives to traditional porous materials for delivery of MTX and 5-FU. This computational study will be useful to effectively identify the most promising MOFs for target drug delivery applications prior to experiments. Our results will also guide the experiments for the design and development of MOFs as anticancer drug carrier systems.ArticlePublication Open Access Computational screening of covalent organic frameworks for hydrogen storage(Turkish Chemical Society, 2020) Gülçay, Ezgi; Fındıkçı, İlknur Eruçar; Mechanical Engineering; FINDIKÇI, Ilknur Eruçar; Gülçay, EzgiCovalent Organic Frameworks (COFs) have been considered as promising materials for gas storage applications due to their highly porous structures and tunable characteristics. In this work, high-throughput molecular simulations were performed to screen the recent Computation-Ready Experimental COF Database (CoRE-COF) for H2 storage a first time in the literature. Predictions for H2 uptakes were first compared with the experimental data of several COFs. Motivated from the good agreement between simulations and experiments, we performed Grand Canonical Monte Carlo (GCMC) simulations to compute volumetric H2 uptakes of 296 COFs at various temperatures and pressures and identified the best candidates which exhibit a superior performance for H2 storage. COFs outperformed several well-known MOFs such as HKUST-1, NU-125, NU-1000 series, NOTT-112 and UiO-67 at 100bar/77K adsorption and 5bar/160K desorption conditions. We also examined the effect of Feynman-Hibbs correction on simulated H2 isotherms and H2 working capacities of COFs to consider quantum effects at low temperatures. Results showed that the Feynman-Hibbs corrections do not affect the ranking of materials based on H2 working capacities, but slightly affect the predictions of H2 adsorption isotherms. We finally examined the structure-performance relations and showed that density and porosity are highly correlated with the volumetric H2 working capacities of COFs. Results of this study will be highly useful in guiding future research and focusing experimental efforts on the best COF adsorbents identified in this study.ArticlePublication Open Access An extensive comparative analysis of two MOF databases: high-throughput screening of computation-ready MOFs for CH4 and H2 adsorption(Royal Society of Chemistry, 2019-04-28) Altintas, C.; Avci, G.; Daglar, H.; Azar, A. N. V.; Fındıkçı, İlknur Eruçar; Velioglu, S.; Keskin, S.; Mechanical Engineering; FINDIKÇI, Ilknur EruçarComputation-ready metal-organic framework (MOF) databases (DBs) have tremendous value since they provide directly useable crystal structures for molecular simulations. The currently available two DBs, the CoRE DB (computation-ready, experimental MOF database) and CSDSS DB (Cambridge Structural Database non-disordered MOF subset) have been widely used in high-throughput molecular simulations. These DBs were constructed using different methods for collecting MOFs, removing bound and unbound solvents, treating charge balancing ions, missing hydrogens and disordered atoms of MOFs. As a result of these methodological differences, some MOFs were reported under the same name but with different structural features in the two DBs. In this work, we first identified 3490 common MOFs of CoRE and CSDSS DBs and then performed molecular simulations to compute their CH4 and H-2 uptakes. We found that 387 MOFs result in different gas uptakes depending on from which DB their structures were taken and we identified them as problematic' MOFs. CH4/H-2 mixture adsorption simulations showed that adsorbent performances of problematic MOFs, such as selectivity and regenerability, also significantly change depending on the DB used and lead to large variations in the ranking of materials and identification of the top MOFs. Possible reasons of different structure modifications made by the two DBs were investigated in detail for problematic MOFs. We described five main cases to categorize the problematic MOFs and discussed what types of different modifications were performed by the two DBs in terms of removal of unbound and bound solvents, treatment of missing hydrogen atoms, charge balancing ions etc. with several examples in each case. With this categorization, we aimed to direct researchers to computation-ready MOFs that are the most consistent with their experimentally reported structures. We also provided the new computation-ready structures for 54 MOFs for which the correct structures were missing in both DBs. This extensive comparative analysis of the two DBs will clearly show how and why the DBs differently modified the same MOFs and guide the users to choose either of the computation-ready MOFs from the two DBs depending on their purpose of molecular simulations.ArticlePublication Metadata only Hydrothermal synthesis and characterization of two dimensional coordination polymers with 2,2′-dimethylglutarate and 1,2-bis(imidazol-1-ylmethyl)benzene(Elsevier, 2019-03-24) Yaman, P. K.; Erer, H.; Arici, M.; Fındıkçı, İlknur Eruçar; Yesilel, O. Z.; Mechanical Engineering; FINDIKÇI, Ilknur EruçarThe hydrothermal reactions of some metal ions with 2,2'-dimethylglutaric acid (22dmgH(2)) and 1,2-bis(imidazol-1-ylmethyl)benzene (obix) newly afford four coordination polymers are called, {[Co-2 (mu-22dmg)(2)(mu-obix)(2)]center dot 1.5H(2)O}(n) (1), {[Cu(mu-22dmg)(mu-obix)]center dot H2O}(n) (2), {[Zn-2(mu-22dmg)(2)(mu-obix)(2)]center dot 2H(2)O}(n) (3) and [Cd-2(mu-22dmg)(2)(mu-obix)(2)(H2O)](n) (4). All of the complexes were characterized by elemental analysis, IR spectra, single crystal X- ray diffraction, powder X-ray diffraction (PXRD), and thermal analysis techniques. Furthermore, photoluminescence and topological properties were studied. The X-ray single crystal study shows that complexes 1, 3 and 4 display 3-fold parallel interpenetrating networks with hcb topology showing an unusual 2D + 2D + 2D -> 2D structures. Topological analysis reveals that complex 2 has an uninodal 4-c net sql topology with the point symbol of 4(4).6(2). Atomically-detailed simulations were finally performed to compute hydrogen (H-2) uptake in these complexes at 77 K.ArticlePublication Open Access Metal-organic framework glasses with permanent accessible porosity(Nature Publishing Group, 2018-11-28) Zhou, C.; Longley, L.; Krajnc, A.; Smales, G. J.; Qiao, A.; Fındıkçı, İlknur Eruçar; Doherty, C. M.; Thornton, A. W.; Hill, A. J.; Ashling, C. W.; Qazvini, O. T.; Lee, S. J.; Chater, P. A.; Terrill, N. J.; Smith, A. J.; Yue, Y.; Mali, G.; Keen, D. A.; Telfer, S. G.; Bennett, T. D.; Mechanical Engineering; FINDIKÇI, Ilknur EruçarTo date, only several microporous, and even fewer nanoporous, glasses have been produced, always via post synthesis acid treatment of phase separated dense materials, e.g. Vycor glass. In contrast, high internal surface areas are readily achieved in crystalline materials, such as metal-organic frameworks (MOFs). It has recently been discovered that a new family of melt quenched glasses can be produced from MOFs, though they have thus far lacked the accessible and intrinsic porosity of their crystalline precursors. Here, we report the first glasses that are permanently and reversibly porous toward incoming gases, without post-synthetic treatment. We characterize the structure of these glasses using a range of experimental techniques, and demonstrate pores in the range of 4 – 8 Å. The discovery of MOF glasses with permanent accessible porosity reveals a new category of porous glass materials that are elevated beyond conventional inorganic and organic porous glasses by their diversity and tunability.