Recent Publications

Jorge Kohanoff

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  1. Title: Electron-induced hydrogen loss in uracil in a water cluster environment

    Author(s): Smyth M., Kohanoff J., Fabrikant I.I.

    Journal of Chemical Physics, 140, pp. 184313- (12 May 2014)

    doi: 10.1063/1.4874841
    Abstract



    Low-energy electron-impact hydrogen loss due to dissociative electron attachment (DEA) to the uracil and thymine molecules in a water cluster environment is investigated theoretically. Only the A′-resonance contribution, describing the near-threshold behavior of DEA, is incorporated. Calculations are based on the nonlocal complex potential theory and the multiple scattering theory, and are performed for a model target with basic properties of uracil and thymine, surrounded by five water molecules. The DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster. This growth is due to two effects: the increase of the resonance lifetime and the negative shift in the resonance position due to interaction of the intermediate negative ion with the surrounding water molecules. A similar effect was earlier found in DEA to chlorofluorocarbons.

  2. Title: Universal tight binding model for chemical reactions in solution and at surfaces. III. Stoichiometric and reduced surfaces of titania and the adsorption of water

    Author(s): Lozovoi A.Y., Pashov D.L., Sheppard T.J., Kohanoff J.J., Paxton A.T.

    Journal of Chemical Physics, 141, pp. 044505- (2014)

    doi: 10.1063/1.4890492
    Abstract



    We demonstrate a model for stoichiometric and reduced titanium dioxide intended for use in molecular dynamics and other atomistic simulations and based in the polarizable ion tight binding theory. This extends the model introduced in two previous papers from molecular and liquid applications into the solid state, thus completing the task of providing a comprehensive and unified scheme for studying chemical reactions, particularly aimed at problems in catalysis and electrochemistry. As before, experimental results are given priority over theoretical ones in selecting targets for model fitting, for which we used crystal parameters and band gaps of titania bulk polymorphs, rutile and anatase. The model is applied to six low index titania surfaces, with and without oxygen vacancies and adsorbed water molecules, both in dissociated and non-dissociated states. Finally, we present the results of molecular dynamics simulation of an anatase cluster with a number of adsorbed water molecules and discuss the role of edge and corner atoms of the cluster.

  3. Title: Universal tight binding model for chemical reactions in solution and at surfaces. II. Water

    Author(s): Lozovoi A.Y., Pashov D.L., Sheppard T.J., Kohanoff J.J., Paxton A.T.

    Journal of Chemical Physics, 141, pp. 044504- (2014)

    doi: 10.1063/1.4890343
    Abstract



    A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice—leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point.

  4. Title: Universal tight binding model for chemical reactions in solution and at surfaces. I. Organic molecules

    Author(s): Lozovoi A.Y., Pashov D.L., Sheppard T.J., Kohanoff J.J., Paxton A.T.

    Journal of Chemical Physics, 141, pp. 044503- (2014)

    doi: 10.1063/1.4887095
    Abstract



    As is now well established, a first order expansion of the Hohenberg–Kohn total energy density functional about a trial input density, namely, the Harris–Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

  5. Title: Irradiation of Water Ice by C+ Ions in the Cosmic Environment

    Author(s): McBride E.J., Millar T.J., Kohanoff J.J.

    Journal of PPhysical Chemistry A, 118, No. 34, pp. 6991-6998 (2014)

    doi: 10.1021/jp502738x
    Abstract



    We present a first-principles MD (FPMD) study of the interaction of low-energy, positively charged carbon (C+) projectiles with amorphous solid water clusters at 30 K. Reactions involving the carbon ion at an initial energy of 11 and 1.7 eV with a 30-molecule cluster have been investigated. Simulations indicate that the neutral isoformyl radical, COH•, and carbon monoxide, CO, are the dominant products of these reactions. All of these reactions are accompanied by the transfer of a proton from the reacting water molecule to the ice, where it forms a hydronium ion. We find that COH• is formed either via a direct, “knock-out”, mechanism following the impact of the C+ projectile upon a water molecule or by creation of a COH2+ intermediate. The direct mechanism is more prominent at higher energies. CO is generally produced following the dissociation of COH•. More frequent production of the formyl radical, HCO•, is observed here than in gas-phase calculations. A less commonly occurring product is the dihydroxymethyl, CH(OH)2•, radical. Although a minor result, its existence gives an indication of the increasing chemical complexity that is possible in such heterogeneous environments.

  6. Title: Protection of DNA against low-energy electrons by amino acids: a first-principles molecular dynamics study

    Author(s): Gu B., Smyth M., Kohanoff J.

    Physical Chemistry Chemical Physics, 16, pp. 24350-24358 (2014)

    doi: 10.1039/C4CP03906H
    Abstract