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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 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 Migration of single iridium atoms and tri-iridium clusters on MgO surfaces: aberration-corrected STEM imaging and ab initio calculations(American Chemical Society (ACS), 2015) Han, Chang Wan; Iddir, Hakim; Curtiss, Larry A.; Browning, Nigel D.; Gates, Bruce C.; Ortalan, Volkan; Department of Chemical and Biological Engineering; Uzun, Alper; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 59917To address the challenge of fast, direct atomic-scale visualization of the migration of atoms and clusters on surfaces, we used aberration-corrected scanning transmission electron microscopy (STEM) with high scan speeds (as little as similar to 0.1 s per frame) to visualize the migration of (1) a heavy atom (Ir) on the surface of a support consisting of light atoms, MgO(100), and (2) an Ir-3 cluster on MgO(110). Sequential Z-contrast images elucidate the surface transport mechanisms. Density functional theory (DFT) calculations provided estimates of the migration energy barriers and binding energies of the iridium species to the surfaces. The results show how the combination of fast-scan STEM and DFT calculations allow visualization and fundamental understanding of surface migration phenomena pertaining to supported catalysts and other materials.Publication Metadata only Modeling ionic reactions at interstellar temperatures: the case of NH2- + H-2 double left right arrow NH3 + H-(Amer Chemical Soc, 2019) Gianturco, F. A.; Satta, M.; Wester, R.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129Structural features and enthalpy details are presented for the title reactions, both for the exothermic (forward) path to NH3 formation and for the endothermic (reverse) reaction to NH2- formation. Both pathways have relevance for the nitrogen chemistry in the interstellar medium (ISM). They are also helpful to document the possible role of H- in molecular clouds at temperatures well below room temperature. The structural calculations are carried out using different ab initio methods and are further employed to obtain the reaction rates down to the interstellar temperatures detected in earlier experiments. The reaction rates are obtained from the computed minimum energy path (MEP) using the variational transition-state theory (VTST) approach. The results indicate very good accord with experiment results at room temperature, while measured low temperature data down to 8 K are well described using an appropriately modified VTST approach. This is done by employing a temperature-dependent scaling, from room temperature conditions down to the lower ISM temperatures, which acknowledges the noncanonical behavior of the fast, barrierless exothermic reaction. The reasons for this behavior and the need for improving on the VTST method when used away from room temperatures are discussed.Publication Metadata only Phase behaviour and dynamics of three-dimensional active dumbbell systems(Royal Society of Chemistry, 2024) Caporusso, C.B.; Negro, G.; Suma, A.; Digregorio, P.; Gonnella G; Cugliandolo, L.F.; Department of Physics; Carenza, Livio Nicola; Department of Physics; College of SciencesWe present a comprehensive numerical study of the phase behavior and dynamics of a three-dimensional active dumbbell system with attractive interactions. We demonstrate that attraction is essential for the system to exhibit nontrivial phases. We construct a detailed phase diagram by exploring the effects of the system's activity, density, and attraction strength. We identify several distinct phases, including a disordered, a gel, and a completely phase-separated phase. Additionally, we discover a novel dynamical phase, that we name percolating network, which is characterized by the presence of a spanning network of connected dumbbells. In the phase-separated phase we characterize numerically and describe analytically the helical motion of the dense cluster.Publication Metadata only Phase-space reconstruction in Hamiltonian systems through multiple time series(Elsevier Science Bv, 1997) Department of Chemistry; Atay, Fatihcan; Yurtsever, İsmail Ersin; Faculty Member; Faculty Member; Department of Chemistry; College of Sciences; 253074A method which combines the various time series originating from a single source in order to reconstruct the phase-space dynamics is applied to a chaotic Hamiltonian system. It is shown that for a large energy range the variation of the maximum Lyapunov exponents can be reproduced more accurately than the results obtained from a single time series, for both clean and noisy signals. Especially in cases where the maximum exponent is close to zero, using multiple series can give better results, providing a more reliable way of detecting chaos.Publication Metadata only Physisorption of h-2 on fullerenes and the solvation of c-60 by hydrogen clusters at finite temperature: a theoretical assessment(American Chemical Society (ACS), 2018) Calvo, F.; Tekin, A.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129The interaction between hydrogen and carbonaceous nanostructures is of fundamental interest in various areas of physical chemistry. In this contribution we have revisited the physisorption of hydrogen molecules and H-2 clusters on fullerenes, following a first-principles approach in which the interaction is quantitatively evaluated for the C-20 system using high-level electronic structure methods. Relative to coupled cluster data at the level of single, double, and perturbative triple excitations taken as a benchmark, the results for rotationally averaged physisorbed H-2 show a good performance of MP2 variants and symmetry-adapted perturbation theory, but significant deviations and basis set convergence issues are found for dispersion-corrected density functional theory. These electronic structure data are fitted to produce effective coarse-grained potentials for use in larger systems such as C-60-H-2. Using path-integral molecular dynamics, the potentials are also applied to parahydrogen clusters solvated around fullerenes, across the regime where the first solvation shell becomes complete and as a function of increasing temperature. For C-60 our findings indicate a sensible dependence of the critical solvation size on the underlying potential. As the temperature is increased, a competition is found between the surface and radial expansions of the solvation shell, with one molecule popping away at intermediate temperatures but getting reinserted at even higher temperatures.Publication Metadata only Possible formation of metastable pah dimers upon pickup by helium droplets(Amer Chemical Soc, 2016) Calvo, F.; Department of Chemistry; N/A; Yurtsever, İsmail Ersin; Birer, Özgür; Faculty Member; Researcher; Department of Chemistry; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; N/A; 7129; N/AUsing path-integral molecular dynamics simulations and two quantum-mechanical-based force fields, we have investigated the conformational stability of dimers of a polycyclic aromatic hydrocarbon, perylene (C20H12), produced under typical experimental conditions of successive pick-up under helium nanodroplet environment. The most stable configurations are found to be of the stacked form with different relative orientations of the main molecular axes, perpendicular or T-shaped dimers being energetically much disfavored; however, in the presence of helium our simulations suggest that the time for rearrangement and pi-stacking may be rather long and exceed hundreds of picoseconds. In addition, highly metastable dimers that are stacked but with a helium monolayer sandwiched between the two molecules are also found as likely products upon successive pickup. This stabilization occurs owing to the stronger localization of the helium atoms facing the aromatic rings, which is further enhanced in the dimer. The implications of the present results are discussed in the perspective of possible identification by spectroscopic methods.Publication Metadata only Quantum features of a barely bound molecular dopant: Cs-2((3)sigma(u)) in bosonic helium droplets of variable size(Amer Chemical Soc, 2011) Perez de Tudela, Ricardo; Lopez-Duran, David; Gonzalez-Lezana, Tomas; Delgado-Barrio, Gerardo; Villarreal, Pablo; Gianturco, Franco A.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129We present in this work the study of small He-4(N)-Cs-2((3)Sigma(u)) aggregates (2 <= N <= 30) through combined variational, diffusion Monte Carlo (DMC), and path integral Monte Carlo (PIMC) calculations. The full surface is modeled as an addition of He-Cs-2 interactions and He-He potentials. Given the negligible strength and large range of the He-CS2 interaction as compared with the one for He-He, a propensity of the helium atoms to pack themselves together, leaving outside the molecular dopant is to be expected. DMC calculations determine the onset of helium gathering at N = 3. To analyze energetic and structural properties as a function of N, PIMC calculations with no bosonic exchange, i.e., Boltzmann statistics, at low temperatures are carried out. At T = 0.1 K, although acceptable one-particle He-Cs-2 distributions are obtained, two-particle He He distributions are not well described, indicating that the proper symmetry should be taken into account. PIMC distributions at T = 1 K already compare well with DMC ones and show minor exchange effects, although binding energies are still far from having converged in terms of the number of quantum beads. As N increases, the He-He PIMC pair correlation function shows a clear tendency to coincide with the experimental boson-liquid helium one at that temperature. It supports the picture of a helium droplet which carries the molecular impurity on its surface, as found earlier for other triplet dimers.Publication Metadata only Quantum mechanical calculations of tryptophan and comparison with conformations in native proteins(amer Chemical Soc, 2006) Department of Chemistry; Department of Computer Engineering; Department of Chemical and Biological Engineering; Yurtsever, İsmail Ersin; Yüret, Deniz; Erman, Burak; Faculty Member; Faculty Member; Faculty Member; Department of Chemistry; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; College of Engineering; 7129; 179996; 179997We report a detailed analysis of the potential energy surface of N-acetyl-L-tryptophan-N-methylamide, (NaTMa) both in the gas phase and in solution. the minima are identified using the density-functional-theory (DFT) with the 6-31g(d) basis set. the full potential energy surface in terms of torsional angles is spanned starting from various initial configurations. We were able to locate 77 distinct L-minima. the calculated energy maps correspond to the intrinsic conformational propensities of the individual NaTMa molecule. We show that these conformations are essentially similar to the conformations of tryptophan in native proteins. for this reason, we compare the results of DFT calculations in the gas and solution phases with native state conformations of tryptophan obtained from a protein library. in native proteins, tryptophan conformations have strong preferences for the, sheet, right-handed helix, tight turn, and bridge structures. the conformations calculated by DFT, the solution-phase results in particular, for the single tryptophan residue are in agreement with native state values obtained from the Protein Data Bank.