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Publication 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.Publication Metadata only HCHO in a cold, quantum solvent: size and shape of its "bubbles" in (4)He droplets from stochastic simulations(Amer Chemical Soc, 2010) Marinetti, Fabio; Gianturco, Francesco A.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129The full interaction between formaldehyde and He-4 atoms has been obtained from a first-principle calculation of the forces at play. In order to describe the nanoscopic features of HCHO being solvated in a quantum liquid, further Monte Carlo calculations for the system HCHO@He-N with N up to 20 have been carried out. The energetics and structure of the systems, as N changes, are extensively analyzed, and the excluded volume ("bubble") created by the inner cage that surrounds the solvated molecule is described and discussed to provide molecular microsolvation details for the title system.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 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 Pi-stack dimers of small polyaromatic hydrocarbons: a path to the packing of graphenes(Amer Chemical Soc, 2009) Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129MP2 calculations of the stacking energy are reported for the dimers of a set of polycyclic aromatic hydrocarbons. The interaction strengths and their dependence on the shape-dependent measures as well as the aromatic character of the monomer are studied. For small systems involving four to six rings, the noncovalent interactions seem to be independent of the shape of the monomers. The most preferred conformations for parallel stacked dimers are not aligned exactly but off-center with small shifts; however, these shifts are on the order of 1 angstrom, and the energy necessary to keep them aligned is less than 0.5 kcal/mol per ring. Small-angle rotations within the molecular planes also do not require much energy, and in some cases they lead to stronger interactions.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 chemical view on the growth mechanisms of odd-sized nitrogen cluster anions(Amer Chemical Soc, 2019) Calvo, Florent; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129The stable structures of odd-numbered anionic nitrogen clusters, N-2n+3(-), have been theoretically investigated in the size range n = 1-9 using a variety of quantum chemistry methods that include perturbation theory, coupled cluster, and density-functional theory with different exchange correlation functionals. We generally find that the clusters are composed of an azide chromophore N-3(-) surrounded by essentially neutral nitrogen molecules. The growth initially proceeds by placing the neutral molecules parallel to the azide anion, completing a first shell at N-13(-), above which the extra molecules arrange on the side but with a significantly lower binding energy. Comparison with the cyclic N-5(-) anionic core shows that the latter is unfavorable, the spectral signatures of both N-5(-) and N2N3- being provided in both the infrared and ultraviolet ranges. The trend of these clusters to be highly stable as (N-2)(n)N-3(-) agrees with recent mass spectrometry experiments under the cryogenic environment of helium droplets. The issues associated with the successful development of a nonreactive force field for such clusters are also highlighted.