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Publication Restricted A comparative molecular dynamics study of methylation state specificity of JMJD2A(Koç University, 2009) Ulucan, Özlem; Erman, Burak; 0000-0002-2496-6059; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997
Publication Metadata only A post-HF study on the halogen bonding interaction of pyrene with diatomic halogen molecules(Wiley, 2016) Sütay, Berkay; Yurtsever, Mine; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129We present a detailed SCS-MP2 study on the potential energy curves (PEC) for interactions between diatomic halogen molecules and pyrene. BSSE corrected CCSD[T] energies at equilibrium distances are computed and compared to CCSD(T) energies. The most stable conformation of these weakly bound van der Waals complexes is almost linear in the perpendicular direction to the pyrene plane. The complexes of highly polarizable bromine and iodine molecules with pyrene are very stable and they carry rather large number of vibrational states. Despite its small size, F-2 also forms strong halogen bonding similar to Br-2 and I-2. The interaction between Cl-2 and pyrene is the weakest and it is attributed to the highest polarizability/molar mass ratio of chlorine among the others. I-2-pyrene is found to be the most stable complex due to the strongest mutual polarization effects and is carrying more than 60 vibrational states. Due to the rather large number of electrons in some complexes, the relativistic corrections are also considered.Publication Metadata only Computational screening of ZIFs for CO2 separations(Taylor & Francis Ltd, 2015) N/A; N/A; Department of Chemical and Biological Engineering; Yılmaz, Gamze; Özcan, Aydın; Keskin, Seda; Master Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 40548Using molecular simulations, we studied a diverse collection of zeolite-imidazolate frameworks (ZIFs) to evaluate their performances in adsorption- and membrane-based gas separations. Molecular simulations were performed for both single-component gases (CH4, CO2, H-2 and N-2) and binary gas mixtures (CO2/CH4, CO2/N-2, CO2/H-2 and CH4/H-2) to predict the intrinsic and mixture selectivities of ZIFs. These two selectivities were compared to discuss the importance of multi-component mixture effects on making predictions about the separation performance of a material. Gas separation performances of ZIFs were compared with other nanoporous materials and our results showed that several ZIFs can outperform well-known zeolites and metal-organic frameworks in CO2 separations. Several other properties of ZIFs such as gas permeability, working capacity and sorbent selection parameter were computed to identify the most promising materials in adsorption- and membrane-based separation of CO2/CH4, CO2/N-2, CO2/H-2 and CH4/H-2.Publication Metadata only Computational studies of cyclobutadiene and benzocyclobutene fused to p- and o-quinone(American Chemical Society (ACS), 1998) McKee, Michael L.; Balcı, Metin; Kılıç, Hamdullah; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129Cyclobutadiene and benzocyclobutenes fused to o- and p-quinone have been studied by computational methods. Geometries were optimized at the B3LYP/6-31G* level, and absolute NMR shielding values were calculated using the GIAO method with the HF/6-31G* basis set. NICS values of the compounds 8b,c and 9b,c indicate strong antiaromatic character for cyclobutadiene units. However, 8a and 9a show negative NICS values where the quinodal system reduces the antiaromaticity significantly by forcing these systems to possess a dimethylene-like structure. The calculated C-13 NMR chemical shifts of 6-9 and parent systems are in very good agreement with literature values.Publication Metadata only Conformational similarities in isomerization dynamics of clusters(Amer Chemical Soc, 2003) Department of Chemistry; N/A; Department of Chemical and Biological Engineering; Yurtsever, İsmail Ersin; Palazoğlu, Ahmet; Arkun, Yaman; Faculty Member; N/A; Faculty Member; Department of Chemistry; Department of Chemical and Biological Engineering; College of Sciences; N/A; College of Engineering; 7129; N/A; 108526A method for characterization of the isomerization dynamics from classical trajectories is presented. A measure function describing the topological distance between two clusters of atoms is first developed. Next, this measure is used to identify the regions of the potential energy surface visited by the trajectories. Unlike the commonly used techniques such as simulated annealing or quenching, the proposed method does not require repeated treatment of the trajectory and can be safely used to study the isomerization dynamics of large systems, especially those of monatomic clusters.Publication Restricted Determination of statistical correlations between methylated lysine residues of histone H3 tail by molecular dynamics simulations(Koç University, 2009) Şanlı, Deniz; Keskin, Özlem; 0000-0002-4202-4049; Koç University Graduate School of Sciences and Engineering; Chemical and Biological Engineering; 26605Publication Metadata only Effects of the range of the potential on the structure and dynamics of two-dimensional Coulomb clusters(Taylor & Francis Ltd, 2008) Calvo, Florent; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129The structure, dynamics, and thermodynamics of finite systems of two-dimensional particles interacting mutually through a shielded Coulomb potential, V(r) = e((-kappa r))/r, and bound together by an isotropic parabolic trap, are investigated by means of global optimization and simulation methods. As the range of the potential decreases, or as kappa increases, the number of distinct minima rapidly increases for a given size and the cluster generally shrinks. Looking more specifically at selected sizes below 50, non-monotonic cluster size effects seem to dominate the energetics, chaotic dynamics, and thermodynamics, even though the melting point is weakly affected by the range of the potential.Publication Restricted Efficient ranking of metal organic framework adsorbents and membranes using molecular simulations(Koç University, 2017) Sümer, Zeynep; Keskin, Seda; 0000-0001-5968-0336; Koç University Graduate School of Sciences and Engineering; Chemical and Biological Engineering; 40548Publication Metadata only Energetics and structures of charged helium clusters: comparing stabilities of dimer and trimer cationic cores(Wiley-V C H Verlag Gmbh, 2008) Marinetti, Fabio; Bodo, Enrico; Gianturco, Francesco A.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129We present accurate ab initio calculations of the most stable structures of He-n(+) clusters in order to determine the more likely ionic core arrangements existing after reaching structural equilibrium of the clusters. Two potential energy surfaces are presented: one for the He-2(+) and the other with the He-3(+) linear ion, both interacting with one He atom. The two computed potentials are in turn employed within a classical structure optimization where the overall interaction forces are obtained within the sum-of-potentials approximation described in the main text. Because of the presence of many-body effects within the ionic core, we find that the arrangements with He-3(+) as a core turn out to be energetically preferred, leading to the formation of He-3(+)(He)(n-3) stable aggregates. Nanoscopic considerations about the relative stability of clusters with the two different cores are shown to give us new information on the dynamical processes observed in the impact ionization experiments of pure helium clusters and the importance of pre-equilibrium evaporation of the ionic dimers in the ionized clusters.Publication Metadata only Energy landscapes in photochemical dissociation of small peroxides(Amer Chemical Soc, 2019) N/A; N/A; N/A; Department of Chemistry; Tabriz, Meisam Farzalipour; Çizmeciyan, Melisa Natali; Birer, Özgür; Yurtsever, İsmail Ersin; Master Student; PhD Student; Researcher; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; College of Sciences; N/A; N/A; N/A; 7129Organic peroxides are known to have important roles in many chemical and biochemical processes such as intermediates in the oxidation of various hydrocarbons, as initiators of free-radical polymerization and cross-linking agents, etc. Consequently, the study of the organic peroxides and their radicals are of fundamental interest and importance. Although several reaction pathways after dissociation of organic peroxides have been successfully identified using time-resolved optical absorption spectroscopy, interpretation of the data can be complicated due to spectral overlap of parent molecules, intermediates, and products. Therefore, a reliable theoretical framework is necessary in case of complex or less studied systems. In this study, we investigated the plausible thermal dissociation pathways of diethyl peroxide, ditert butyl peroxide, and dicumyl peroxide by density functional theory with M06-2X hybrid functional and compared its results to coupled cluster single double and perturbative triple, CCSD(T), level energies. Our results indicate that methyl radical elimination is the main dissociation mechanism for all of the studied peroxides after O-O bond cleavage which has been also observed in experiments. The resulting relative energies of the M06-2X functional were found to have reasonable accuracy in comparison with the CCSD(T) method. We also show that time-dependent density functional theory (TD-DFT) with the M06-2X functional provides a suitable guide for interpretation of time-resolved optical absorption spectra of peroxides. The experimental transient absorption spectra of dicumyl peroxide are interpreted using the theoretically predicted pathways and transient radical species. Both results agree within experimental resolution and accuracy. We propose that the traditionally assigned visible absorption is not due to the cumuloxyl radical and the photodissociation of dicumyl peroxide involves other pathways with extremely short-lived radicals.