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Öğe Aromatic versus aliphatic thiols on Au(111) surface: a DFT exploration of adsorption registry and electronic structure(Taylor & Francis Ltd, 2020) Gurdal, YelizSelf-assembled monolayers (SAMs) on metal surfaces have inspired many interesting applications, such as chemical and biological sensors, molecular electronics, magnetism and protective coatings. In this respect, SAMs having different head and tail groups have been synthesised which allow the modification of the material properties by tuning intermolecular, monolayer-metal and/or monolayer-solvent interactions. In this respect, we investigate the adsorption of thiols having aromatic, p-mercaptobenzonitrile (pPhCN) or aliphatic, 2-azidoethanthiol (N3S), tail groups on Au(111) surface by means of Density Functional Theory (DFT). Monomer and dimer adsorption configurations of both pPhCN and N3S molecules as well as the modification of the electronic structures upon adsorption are studied. Our results show that different adsorption mechanisms are observed for the molecules under consideration. While monomer and dimer structures of the pPhCN prefer to adsorb laterally on the surface, for N3S vertical arrangement of the molecules enhances the molecular immobilisation. Although, dominant contributions to the adsorption energy of the laterally adsorbed pPhCN are through S-Au chemical bond, phenyl ring-surface and cyano N-surface interactions, pi-pi stacking of the rings contributes to the stabilisation of the complex in addition to the S-Au chemical bond in the case of vertical attachment. For N3S, on the other hand, only S-Au chemical bond determines the adsorption strength. S-Au interactions result in broad molecular orbital redistribution of the S atoms of both molecules, due to the rehybridisation of S and Au states. Density of cyano-N and cyano-C states present in the pPhCN is affected by the orientation of the rings with respect to each other. In the case of 2N3S, instead, the distribution of the tail group molecular orbitals is not modified by the adsorption.Öğe [CoII(BPyPy2COH)(OH2)2]2+: A Catalytic Pourbaix Diagram and AIMD Simulations on Four Key Intermediates(Swiss Chemical Soc, 2019) Alberto, Roger; Iannuzzi, Marcella; Gurdal, Yeliz; Probst, BenjaminProton reduction by [Co-II(BPyPy2COH)(OH2)(2)](2+)(BPyPy2COH = [2,2'-bipyridin]-6-yl-di[pyridin-2-yllmethanol) proceeds through two distinct, pH-dependent pathways involving proton-coupled electron transfer (PCET), reduction and protonation steps. In this account we give an overview of the key mechanistic aspects in aqueous solution from pH 3 to 10, based on electrochemical data, time-resolved spectroscopy and ab initio molecular dynamics simulations of the key catalytic intermediates. In the acidic pH branch, a PCET to give a Co-III hydride is followed by a reduction and a protonation step, to close the catalytic cycle. At elevated pH, a reduction to Co-I is observed, followed by a PCET to a Co-II hydride, and the catalytic cycle is closed by a slow protonation step. In our simulation, both Co-I and Co-II-H feature a strong interaction with the surrounding solvent via hydrogen bonding, which is expected to foster the following catalytic step.Öğe Combined orbital tomography study of multi-configurational molecular adsorbate systems(Nature Publishing Group, 2019) Kliuiev, Pavel; Zamborlini, Giovanni; Jugovac, Matteo; Gurdal, Yeliz; von Arx, Karin; Waltar, Kay; Schnidrig, StephanMolecular reactivity is determined by the energy levels and spatial extent of the frontier orbitals. Orbital tomography based on angle-resolved photoelectron spectroscopy is an elegant method to study the electronic structure of organic adsorbates, however, it is conventionally restricted to systems with one single rotational domain. In this work, we extend orbital tomography to systems with multiple rotational domains. We characterise the hydrogen evolution catalyst Co-pyrphyrin on an Ag(110) substrate and compare it with the empty pyrphyrin ligand. In combination with low-energy electron diffraction and DFT simulations, we fully determine adsorption geometry and both energetics and spatial distributions of the valence electronic states. We find two states close to the Fermi level in Co-pyrphyrin with Co 3d character that are not present in the empty ligand. In addition, we identify several energetically nearly equivalent adsorption geometries that are important for the understanding of the electronic structure. The ability to disentangle and fully elucidate multi-configurational systems renders orbital tomography much more useful to study realistic catalytic systems.Öğe Comparison of Penta and Tetra-pyridyl Cobalt-based Catalysts for Water Reduction: H2 Production Cycle, Solvent Response and Reduction Free Energy(Wiley-V C H Verlag Gmbh, 2020) Gurdal, Yeliz; Iannuzzi, MarcellaUnderstanding water reduction towards H-2 generation is crucial to overcome today's renewable energy obstacles. Previous studies have shown the superior H-2 production performances of Cobalt based penta-pyridyl (CoaPPy) and tetra-pyridyl (CoaTPy) complexes in solution. We investigate H-2 production cycles of CoaPPy and CoaTPy complexes immersed in water solution by means of Ab-initio Molecular Dynamics and Density Functional Theory. We monitor dynamic properties of the systems, solvent response and structural changes occurring in the catalysts, by simulating all intermediate steps of the H-2 production cycle. Reduction free energies and reorganization energies are calculated. Our results show that, following the first electron injection, H-2 production proceeds with the singlet spin state. Following the first electron insertion, we observe a significant rearrangement of the hydrogen bonding network in the first solvation shell. The cobalt center turns out to be more accessible for the surrounding water molecules in the case of CoaTPy at all the intermediate steps, which explains its higher catalytic performance over CoaPPy. Following the first reduction reaction, a larger gain in reduction free energy is estimated for CoaTPy with respect to CoaPPy, with a difference of 0.14 eV, in line with the experiments. For the second reduction, instead, CoaPPy shows more negative reduction potential, by 0.41 eV.Öğe Design and performance analysis of a PV-assisted alkaline electrolysis for hydrogen production: An experimental and theoretical study(Elsevier Sci Ltd, 2024) Mert, Mehmet Erman; Edis, Cansu; Akyildiz, Senay; Demir, Beyza Nur; Nazligul, Huseyin; Gurdal, Yeliz; Mert, Basak DogruThe PV assisted alkaline electrolysis cell was established for hydrogen generation. Lab-made AgNiCu modified nickel foam cathodes were used in this system. The characterization was achieved using field emission scanning electron microscopy, energy-dispersive X-ray and X-Ray diffraction analysis. The electrochemical performance was investigated via linear sweep voltammetry, cyclic voltammetry, Tafel polarization measurements and electrochemical impedance spectroscopy. The electrolysis potential and time depended efficiency was monitored. The structural theoretical analysis of the electrode surface and hydrogen evolution characteristics were also determined applying Density Functional Theory and Ab-initio Molecular Dynamics simulations which identified the role of Ag decoration and Cu incorporation on the surface against water and proton adsorptions. The modified cathode (AgNiCuF) improved the hydrogen production performance owing to lower hydrogen onset potential (-1.1 V) and charge transfer resistance (0.362 ohm at -1.5 V).Öğe Experimental and theoretical study on hydrogen production by using Ag nanoparticle-decorated graphite/Ni cathode(Wiley, 2021) Yildiz, Resit; Dogru Mert, Basak; Karazehir, Tolga; Gurdal, Yeliz; Toprak Doslu, SerapIn this study, graphite (G) electrode was coated with nickel and decorated with silver nanoparticles (G/Ni/Ag) with the help of galvanostatic method, and electrodes were used as a cathode in alkaline water electrolysis system. The characterization was achieved using X-ray diffraction and field emission scanning electron microscopy. Hydrogen evolution performance of electrodes was investigated via cyclic voltammetry, chronoamperometry, cathodic polarization curves, and electrochemical impedance measurements. Electrochemical results showed that hydrogen production efficiency significantly increased and charge transfer resistance decreased via G/Ni/Ag. The electrochemical water splitting performance of G/Ni/Ag, was established in a joint experimental and computational effort. Water and proton adsorption on Ag-decorated Ni surface were investigated using density functional theory. Electronic structure calculations identified the role of Ag adatom and Ni surface on water and proton adsorptions. From the computational studies, O in water was more reliable to adsorb at the bridge position of the Ag and Ni atoms, leading improved orbital overlap between H and Ni atoms and maximized chemical and physical interactions between the H2O molecules. Therefore, the Ag-decorated Ni(111) surface provides preferable adsorption site for the O atom in water and direct interactions between water Hs and available surface Ni atoms promote water dissociation.Öğe Experimental and theoretical study: Design and implementation of a floating photovoltaic system for hydrogen production(Wiley, 2022) Gullu, Emre; Mert, Basak Dogru; Nazligul, Huseyin; Demirdelen, Tugce; Gurdal, YelizIn this study, lab-made modified graphite cathodes were used to design and implement floating PV assisted alkaline electrolysis cell. The influence of temperature on PV performance was studied both experimentally and theoretically, and the PV module performance was investigated in floating as well as non-floating modes. Power generation of floating PV panel and non-floating PV panel at four different air temperatures was examined. Although there was no substantial improvement in power generation at 6 degrees C or 16 degrees C, values improved by 6.25% and 10.75% at 24 degrees C and 37 degrees C, respectively. For alkaline electrolysis cell part of this system, the graphite (G) cathode was galvanostatically coated with nickel (G/Ni) and decorated with cobalt nano-particles (G/Ni/Co). The characterization of the electrode was achieved using X-Ray diffraction (XRD) and field emission scanning electron microscopy (FESEM). The Co(111)-decorated Ni was determined by XRD, the electrode surface was very rough in FE-SEM micrographs, the detected features provided a larger contact area that supported the formation of simultaneous electrochemical reactions. The electrochemical behavior of electrodes were determined in 1 M KOH by cyclic voltammetry (CV). The modified cathode (G/Ni/Co) enhanced the hydrogen production performance owing to lower hydrogen onset potential. Electronic structure calculations were carried out in order to investigate water as well as proton adsorption on a Co-decorated Ni(111) surface. Density Functional Theory (DFT) calculations identified the role of Co cluster and Ni surface on water and proton adsorptions. According to our knowledge of the literature to date, the practical and theoretical analysis of a floating PV assisted-an alkaline electrolysis system that worked with the laboratory-made electrodes has not been performed before. Results showed that floating PV panels were beneficial than land mounted panels and the G/Ni/Co enhanced the hydrogen generation performance of the system.Öğe Grand Canonical Monte Carlo Modeling of Anesthetic Xe Separation from Exhale Gas Mixtures Using Metal Organic Frameworks(2019) Gurdal, YelizXe has been shown to be a promising candidate for anesthetic applications. However, its high price preventsits usage in clinical industry. An alternative approach is to recover Xe from anesthetic exhale gas mixture andrecycle it to the inhale gas stream. Although, many membranes and/or adsorbents have been proposed forrecovering anesthetic Xe, using metal organic frameworks (MOFs) for adsorption based separation ofanesthetic Xe exhale gas mixtures has been newly studied. MOFs have tunable pore sizes, large surface areas,and high porosities which make them potential candidates for gas separation applications. Currently, very littleis known about anesthetic Xe recovery performances of MOFs. We theoretically investigate adsorption basedseparation of single component and binary mixtures of CO2, Xe, and N2 in three MOFs, namely CECYOY,SUDBOI, and ZUQPOQ. Single component and binary adsorption isotherms and adsorption selectivities arecalculated using Grand Canonical Monte Carlo simulations for each MOF in order to characterize theirperformances as adsorbents. Results suggest that while MOFs prefer adsorption of CO2 for CO2/Xe mixture,Xe adsorption is favorable in the case of Xe/N2 mixture. While SUDBOI shows significantly large CO2adsorption selectivity for CO2/Xe mixture, ZUQPOQ has the largest adsorption selectivity for Xe/N2 mixture.Öğe H2 Evolution Reaction Pathway of a Cobalt Bis-bipyridyl Planar Catalyst Revealed by Ab Initio Simulations(Amer Chemical Soc, 2024) Güçlü, Ipek; Kiser, Ayas; Gurdal, YelizLigand type and ligand coordination around cobalt photocatalysts influence the reaction mechanism of H2 production via water splitting. We investigated the H2 production mechanisms of a cobalt bis-bipyridyl planar water reduction catalyst in an aqueous solution using ab initio molecular dynamics, metadynamics, density functional theory, and free energy perturbation theory. Modeling each intermediate step of the reaction mechanism reveals that the cobalt-based planar catalyst exhibits a preference for a pathway involving two successive reductions, followed by two protonation steps. The reason for this preference is the presence of an energy barrier for the conformational change of water molecules in the first solvation shell following the first reduction. This barrier prevents direct coordination of cobalt with protons, which is necessary for the initial protonation step in the sequential electron- and proton-transfer mechanisms. In the mechanism involving two successive reductions followed by two protonations, however, the second reduction step facilitates direct interaction between cobalt and protons, enabling the initial protonation. Following the second protonation of this mechanism, H2 is produced and released into the solvent. Reduction free energy calculations reveal that, following the first reduction, the singlet spin state of the system is more favorable than the triplet spin state. The reduction free energy of the second electron transfer is 0.19 eV less energetic than that of the first reduction reaction.Öğe Models used for permeability predictions of nanoporous materials revisited for H2/CH4 and H2/CO2 mixtures(Elsevier, 2022) Canturk, Behra; Salih, Ali; Gurdal, YelizHigh throughput screening of new generation nanoporous materials, e.g. metal organic frameworks (MOFs) and zeolitic imidazolate frameworks (ZIFs), for gas mixture separations have produced large amounts of data. Reported gas permeabilities have been mainly calculated using a simplified (approximate) approach. Perme-ability predictions of an alternative method (new method), proposed previously by our group, have shown to significantly improve the predictions of the approximate method for noble gas mixtures. Permeabilities calculated using Onsager coefficients, detailed method, are accepted as correct answers, however constructing Onsager coefficient matrix is computationally cumbersome and not feasible especially for the high throughput screening purposes. In this work, we question in what accuracy the approximate and new methods can predict gas permeabilities and permeation selectivities of gases with respect to the detailed method. We perform Grand Canonical Monte Carlo and Molecular Dynamics simulations for six ZIFs, namely ZIF-6, ZIF-10, ZIF-60, ZIF-69, ZIF-79, and ZIF-81. Permeabilities of H-2/CH4 and H-2/CO(2 )mixtures are selected as cases, since the dominating interactions of the gas species with the pores of the membranes are different. For the H-2/CH4 mixture, approximate and new methods predict H-2 permeability results of the detailed method sufficiently good. CH4 permeabilities of the approximate method reveal deviations from the correct answers, yet the new method improves the predictions of the approximate approach. In the case of H-2/CO2 mixture, H-2 permeabilities calculated by the approximate approach are in agreement with the detailed method, except for ZIF-60 and ZIF-79. For the CO2 permeability, approximate and new methods give significant deviations from the results calculated using the detailed method.Öğe Noncovalent chemistry of xenon opens the door for anesthetic xenon recovery using Bio-MOFs(Royal Society of Chemistry, 2023) Canturk, Behra; Erarslan, Zekiye; Gurdal, YelizDesigning an inexpensive and highly efficient recovery process for xenon (Xe) is gaining importance in the development of sustainable applications. Using metal organic frameworks (MOFs) for separating Xe from anesthetic gas mixtures has been a recent topic studied rarely and superficially in the literature. We theoretically investigated Xe recovery performances of 43 biological MOFs (Bio-MOFs) formed by biocompatible metal cations and biological endogenous linkers. Xe uptakes and Xe permeabilities in its binary mixtures with CO2, O2, and N2 were investigated by applying Grand Canonical Monte Carlo and Molecular Dynamics simulations. Materials with metalloporphyrin, hexacarboxylate, triazine, or pyrazole ligands, dimetallic paddlewheel units, relatively large pore sizes (PLD > 5 Å and LCD > 10 Å), large void fractions (?0.8), and large surface areas (>2900 m2 g?1) have been determined as top performing Bio-MOFs for Xe recovery. By applying Density Functional Theory simulations and generating electron density difference maps, we determined that Xe-host interactions in the top performing Bio-MOFs are maximized mainly due to noncovalent interactions of Xe, such as charge-induced dipole and aerogen-? interactions. Polarized Xe atoms in the vicinity of cations/anions as well as ? systems are fingerprints of enhanced guest-host interactions. Our results show examples of rarely studied aerogen interactions that play a critical role in selective adsorption of Xe in nanoporous materials. © 2023 The Royal Society of Chemistry.Öğe Theoretical investigation of metalated and unmetalated pyrphyrins immobilized on Ag(111) surface(Springer, 2019) Gurdal, YelizInvestigations of interactions between macrocyclic molecules and metal surfaces are crucial for emerging technologies, such as chemical and biological sensors, molecular electronics, read/write/erase memory, and magnetism. Thus, understanding the organic molecule and metal interface gains considerable importance. In this respect, we investigate a relatively unexplored porphyrin-related macrocycle, named as Pyrphyrin (Pyr), on Ag(111) surface by means of density functional theory. Our results show that main contribution to the adsorption energy is the dispersive contribution arising due to the interactions between the molecules and the surface. Optimal coordination of two cyano Ns and Co atoms (for CoPyr) to the surface Ag atoms determine preferred adsorption sites. Cyano ends of the Pyr molecule act as anchoring groups and enhances the stability of the complex by bending towards the Ag(111) surface. Cobalt incorporation into the Pyr core, on the other hand, further increases the adsorption strength by contribution of the attractive interactions between Co and Ag atoms. Selected molecular orbital representations of the complexes reveal the extension of orbitals located on Co and/or on two cyano N towards surface Ag atoms, thus, hybridization between molecular and surface states upon adsorption are confirmed.Öğe Theoretical investigation of mixed-metal metal-organic frameworks as H2 adsorbents: insights from GCMC and DFT simulations(Taylor & Francis Ltd, 2024) Gokdemir, Tugce; Gurdal, YelizMolecular hydrogen (H-2) is a renewable energy carrier, however, its practical applications are limited due to the challenges of developing safe and efficient H-2 storage devices. Metal Organic Frameworks (MOFs) containing at least two different metal ions in their structures are called as mixed-metal MOFs (MM-MOFs) and they could adsorb H-2 in higher amounts compared to structures containing single metal nodes. We theoretically examined the H-2 storage capacities of 26 MM-MOFs having various physical and chemical properties applying Grand Canonical Monte Carlo (GCMC) and Density Functional Theory (DFT) simulations. H-2 adsorption isotherms were calculated using a five-site anisotropic H-2 model. QIXSOG, YOMVIG, OSOYUR, Cu-Mg-BTC, Fe-Mg-BTC, and Cr-Mg-BTC were selected as top-performing MM-MOFs maximising H-2 adsorption gravimetrically and volumetrically at near-ambient conditions (233 K and 100 bar), approaching the DOE targets. YOMVIG has the largest H-2 adsorption enthalpy, calculated as -9.93kJ/mol at 233 K and 100 bar. DFT simulations have been conducted to analyse preferable H-2 adsorption sites as well as identify guest-host interactions. Electron density difference analysis showed that adsorbed H-2 molecules in the OSOYUR, Cr-Mg-BTC, Cu-Mg-BTC, and Fe-Mg-BTC are polarised. Our study challenges existing literature by identifying promising MM-MOFs as potential next-generation hydrogen storage adsorbents at near-ambient conditions.Öğe Theoretical investigation of ZIFs as adsorbents or membranes for separating noble gas mixtures: applying a newer method for predicting performances(Springer, 2021) Gurdal, YelizZeolitic imidazolate frameworks (ZIFs) possess similar topological structures with zeolites, however a number of characteristic properties of the ZIFs, such as easy incorporation of desired linkers to their structures, tunable pore sizes, high porosities, and large surface areas make them better option for targeted engineering applications. In this respect, cheaper, highly efficient, and selective separation of syngas mixtures using ZIFs has been already shown in the literature. Separation and purification of noble gases, on the other hand, have been achieved using energy demanding cryogenic distillation of air and currently we know little about noble gas separation performances of the ZIFs. Replacing energy intensive gas separation techniques with adsorbent and/or membrane based separation technologies, indeed, have been motivated for decreasing the operational costs, price of the pure noble gases, as well as opening new application areas for the noble gases. In this respect, we theoretically investigate Xe/Kr and Xe/Ar separation performances of eight ZIFs, namely ZIF-6, ZIF-11, ZIF-60, ZIF-67, ZIF-69, ZIF-78, ZIF-79, and ZIF-81 using Grand Canonical Monte Carlo and Molecular Dynamics simulations and calculate Xe permeability and permeation selectivity using a newer method suggested previously by our group. While ZIF-11 shows significant Xe uptake from the noble gas mixtures, ZIF-81 and ZIF-79 show exceptional Xe adsorption selectivities for two gas mixtures at low pressures, 22.5 and 21 for the Xe/Kr and 128 and 120 for the Xe/Ar mixture, respectively. ZIF-69 and ZIF-79 show high Xe permeability (4.2x10(5) and 3.2x10(5) Barrers) as well as high Xe permeation selectivity (17.35 and 15.85) for the Xe/Ar mixture at 2 bar feed gas pressure. For the Xe/Kr mixture, on the other hand, we observe high Xe permeability and moderate Xe permeation selectivity, especially at low pressures. Comparing with the limited literature available, these ZIFs show promise for selective separation of Xe from its binary mixtures of Kr and Ar at room temperature. We also compare the permeability and permeation selectivity predictions using different approaches, namely the new method and the approximate approach which is commonly used in the literature. Results reveal significant deviations of the approximate approach with respect to the new method, especially for the permeability calculations. Thus, using the new method for determining membrane performances is highly suggested.Öğe Why the Perfectly Symmetric Cobalt-Pentapyridyl Loses the H2 Production Challenge: Theoretical Insight into Reaction Mechanism and Reduction Free Energies(Wiley-V C H Verlag Gmbh, 2024) Kiser, Ayas; Gurdal, YelizResearchers have extensively investigated photo-catalytic water reduction utilizing Cobalt-based catalysts with polypyridyl ligands. While catalysts exhibiting distorted polypyridyl ligand demonstrate higher H-2 production yields, those with ideal octahedral coordination display poor performance. This outcome suggests the crucial role of ligand framework in catalytic activity, yet reasons behind the disparity in H-2 production rates for catalysts with octahedral geometries remain unclear. We theoretically examined the water reduction mechanism of Co-based poly-pyridyl catalyst, CoPy5, having perfect octahedral coordination. We clarified the effect of octahedral coordination by utilizing each intermediate step of ECEC mechanism. We determined spin states, solvent response, electronic structures, and reduction free energies. CoPy5 with perfect octahedral coordination, alongside its distorted counterparts, exhibit similar spin states as the reaction progresses through each intermediate step. However, the first reduction free energy obtained for the CoPy5 is slightly higher than that of its distorted counterparts. Following the second protonation, resulting H-2 molecule experiences limited diffusion from the Co center due to the compact structure of the CoPy5, which blocks the Co center for the next H-2 production cycle. Catalysts having distorted octahedral geometries facilitate fast removal of H-2 into the solvent. Thus, the reaction center becomes immediately available for subsequent H-2 production.
