Recent Publications

Jorge Kohanoff

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  1. Title: Electron-phonon thermalization in a scalable method for real-time quantum dynamics

    Author(s): Rizzi V., Todorov T.N., Kohanoff J.J., Correa A.A.,

    Physical Review B, 93, No. 2 (27 January 2016)

    doi: 10.1103/PhysRevB.93.024306

    Full Text

    We present a quantum simulation method that follows the dynamics of out-of-equilibrium many-body systems of electrons and oscillators in real time. Its cost is linear in the number of oscillators and it can probe time scales from attoseconds to hundreds of picoseconds. Contrary to Ehrenfest dynamics, it can thermalize starting from a variety of initial conditions, including electronic population inversion. While an electronic temperature can be defined in terms of a nonequilibrium entropy, a Fermi-Dirac distribution in general emerges only after thermalization. These results can be used to construct a kinetic model of electron-phonon equilibration based on the explicit quantum dynamics.

  2. Title: Understanding the Interaction between Low-Energy Electrons and DNA Nucleotides in Aqueous Solution

    Author(s): McAllister M., Smyth, M., Gu B., Tribello G.A., Kohanoff J.,

    Journal of Physical Chemistry Letters, 6, No. 15, pp. 3091-3097 (6 August 2015)

    doi: 10.1021/acs.jpclett.5b01011

    Full Text

    Reactions that can damage DNA have been simulated using a combination of molecular dynamics and density functional theory. In particular, the damage caused by the attachment of a low energy electron to the nucleobase. Simulations of anionic single nucleotides of DNA in an aqueous environment that was modeled explicitly have been performed. This has allowed us to examine the role played by the water molecules that surround the DNA in radiation damage mechanisms. Our simulations show that hydrogen bonding and protonation of the nucleotide by the water can have a significant effect on the barriers to strand breaking reactions. Furthermore, these effects are not the same for all four of the bases.

  3. Title: Cement As a Waste Form for Nuclear Fission Products: The Case of 90Sr and Its Daughters

    Author(s): Dezerald L., Kohanoff J., Correa A., Caro A., Pellenq R., Ulm F., Saúl A.

    Environmental Science & Technology (2015)

    doi: 10.1021/acs.est.5b02609

    Full Text

    One of the main challenges faced by the nuclear industry is the long-term confinement of nuclear waste. Because it is inexpensive and easy to manufacture, cement is the material of choice to store large volumes of radioactive materials, in particular the low-level medium-lived fission products. It is therefore of utmost importance to assess the chemical and structural stability of cement containing radioactive species. Here, we use ab initio calculations based on density functional theory (DFT) to study the effects of 90Sr insertion and decay in C–S–H (calcium-silicate-hydrate) in order to test the ability of cement to trap and hold this radioactive fission product and to investigate the consequences of its β-decay on the cement paste structure. We show that 90Sr is stable when it substitutes the Ca2+ ions in C–S–H, and so is its daughter nucleus 90Y after β-decay. Interestingly, 90Zr, daughter of 90Y and final product in the decay sequence, is found to be unstable compared to the bulk phase of the element at zero K but stable when compared to the solvated ion in water. Therefore, cement appears as a suitable waste form for ,90Sr storage.

  4. 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

    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.

  5. 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

    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.

  6. 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

    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.

  7. 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

    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.

  8. 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

    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.

  9. 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

  10. Title: Organic Synthesis in the Interstellar Medium by Low-Energy Carbon Irradiation

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

    Journal of Physical Chemistry A, 117, No. 39, pp. 9666-9672 (10 May 2013)

    doi: 10.1021/jp312342v

    We present a first principles molecular dynamics (FPMD) study of the interaction of low-energy neutral carbon projectiles with amorphous solid water clusters at 30 K. Reactions involving the carbon atom at an initial energy of 11 and 1.7 eV with 30-molecule clusters have been investigated. Simulations indicate that the formation of hydroxymethylene, an intermediate in formaldehyde production, dominates at the higher energy. The reaction proceeds by fragmenting a water molecule, binding the carbon to the OH radical, and saturating the C valence with a hydrogen atom that can arise from the originally dissociated water molecule, or through a chain of proton transfer events. We identified several possible pathways for the formation of HCOH. When the initial collision occurs at the periphery of the cluster, we observe the formation of CO and the evaporation of water molecules. At the lower energy water fragmentation is not favorable, thus leading to the formation of weakly bound carbon-water complexes.

  11. Title: Dynamics of Excess Electronic Charge in Aliphatic Ionic Liquids Containing the Bis(trifluoromethylsulfonyl)amide Anion

    Author(s): Xu C., Durumeric A., Kashyap H.K., Kohanoff J.J., Margulis C.J.

    Journal of the American Chemical Society, 135, No. 46, pp. 17528-17536 (October 24 2013)

    doi: 10.1021/ja409338z

    In a recent article (J. Am. Chem. Soc. 2011, 133, 20186) we investigated the initial spatial distribution of dry excess electrons in a series of room-temperature ionic liquids (RTILs). Perhaps unexpectedly, we found that in some alkylammonium-based systems the excess negative charge resided on anions and not on the positive cations. Following on these results, in the current paper we describe the time evolution of an excess electronic charge introduced in alkylammonium- and pyrrolidinium-based ionic liquids coupled with the bis(trifluoromethylsulfonyl)amide ([Tf2N–]) anion. We find that on a 50 fs time scale an initially delocalized excess electron localizes on a single [Tf2N–] anion which begins a fragmentation process. Low-energy transitions have a very different physical origin on the several femtoseconds time scale when compared to what occurs on the picosecond time scale. At time zero, these are intraband transitions of the excess electron. However after 40 fs when the excess electronic charge localizes on a single anion, these transitions disappear, and the spectrum is dominated by electron-transfer transitions between the fragments of the doubly charged breaking anion.

  12. Title: Electronic stopping power of H and He in Al and LiF from first principles

    Author(s): Zeb M.A., Kohanoff J., Sanchez-Portal D., Artacho E.

    Nuclear Instruments & Methods in Physics, Research Section B - Beam Interactions with Materials and Atoms, 303, pp. 59-61 (May 15 2013)

    doi: 10.1016/j.nimb.2012.12.022

    Non-linearities in the electronic stopping power of light projectiles in bulk Al and LiF are addressed from first principles using time-evolving time-dependent density functional theory. In the case of Al, the agreement of the calculations with experiments for H and He projectiles is fair, but a recently observed transition for He from one value of the electronic friction coefficient to a higher value at v similar to 0.3 a.u. is not reproduced by the calculations. For LiF, better accuracy is obtained as compared with previously published simulations, albeit the threshold remains overestimated.

  13. Title: Excess Electron Interactions with Solvated DNA Nucleotides: Strand Breaks Possible at Room Temperature

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

    Journal of the American Chemical Society, 134, pp. 9122-9125 (18 May 2012)

    doi: 10.1021/ja303776r

    When biological matter is subjected to ionizing radiation, a wealth of secondary low-energy (<20 eV) electrons are produced. These electrons propagate inelastically, losing energy to the medium until they reach energies low enough to localize in regions of high electron affinity. We have recently shown that in fully solvated DNA fragments, nucleobases are particularly attractive for such excess electrons. The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleavage of the phosphodiester C3′–O3′ bond. Here we present a first-principles study of free energy barriers for the cleavage of this bond in fully solvated nucleotides. We have found that except for dAMP, the barriers are on the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300 K. Such low barriers are possible only as a result of solvent and thermal fluctuations. These findings support the notion that low-energy electrons can indeed lead to strand breaks in DNA.

  14. Title: Nonadiabatic Forces in Ion-Solid Interactions: The Initial Stages of Radiation Damage

    Author(s): Correa A.A., Kohanoff J.J., Artacho E., Sánchez-Portal D, Caro A.,

    Physical Review Letters, 108, No. 21, pp. 213201-213204 (21 May 2012)

    doi: 10.1103/PhysRevLett.108.213201

    The Born-Oppenheimer approximation is the keystone for molecular dynamics simulations of radiation damage processes; however, actual materials response involves nonadiabatic energy exchange between nuclei and electrons. In this work, time dependent density functional theory is used to calculate the electronic excitations produced by energetic protons in Al. We study the influence of these electronic excitations on the interatomic forces and find that they differ substantially from the adiabatic case, revealing a nontrivial connection between electronic and nuclear stopping that is absent in the adiabatic case. These results unveil new effects in the early stages of radiation damage cascades.

  15. Title: Electronic Stopping Power in Gold: The Role of d Electrons and the H/He Anomaly

    Author(s): Zeb M., Kohanoff J.J., Sánchez-Portal D Arnau A, Juaristi J.I., Artacho E.,

    Physical Review Letters, 108, No. 22, pp. 225504-225508 (31 May 2012)

    doi: 10.1103/PhysRevLett.108.225504

    The electronic stopping power of H and He moving through gold is obtained to high accuracy using time-evolving density-functional theory, thereby bringing usual first principles accuracies into this kind of strongly coupled, continuum nonadiabatic processes in condensed matter. The two key unexplained features of what observed experimentally have been reproduced and understood: (i) The nonlinear behavior of stopping power versus velocity is a gradual crossover as excitations tail into the d-electron spectrum; and (ii) the low-velocity H/He anomaly (the relative stopping powers are contrary to established theory) is explained by the substantial involvement of the d electrons in the screening of the projectile even at the lowest velocities where the energy loss is generated by s-like electron-hole pair formation only.

  16. Title: A tight binding model for water

    Author(s): Paxton A.T., Kohanoff J.J.

    Journal of Chemical Physics, 134, No. 4, Art. No. 044130 (2011)

    doi: 10.1063/1.3523983

    Full Text

    We demonstrate for the first time a tight binding model for water incorporating polarizable oxygen atoms. A novel aspect is that we adopt a "ground up" approach in that properties of the monomer and dimer only are fitted. Subsequently we make predictions of the structure and properties of hexamer clusters, ice-XI and liquid water. A particular feature, missing in current tight binding and semiempirical hamiltonians, is that we reproduce the almost two-fold increase in molecular dipole moment as clusters are built up towards the limit of bulk liquid. We concentrate on properties of liquid water, particularly dielectric constant and self diffusion coefficient, which are very well rendered in comparison with experiment. Finally we comment on the question of the contrasting densities of water and ice which is central to an understanding of the subtleties of the hydrogen bond.

  17. Title: Excess Electron Localization in Solvated DNA Bases

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

    Physical Review Letters, 106, pp. 238108- (June 10 2011)

    doi: 10.1103/PhysRevLett.106.238108

    We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

  18. Title: Dry Excess Electrons in Room Temperature Ionic Liquids

    Author(s): Margulis C.J., Annapureddy H.V.R., De Biase P.M., Coker D., Kohanoff J.J., Del Pópolo M.G.

    Journal of the American Chemical Society, 133, pp. 20186- (2011)

    doi: 10.1021/ja203412v

  19. Title: Dispersion interactions in room-temperature ionic liquids: Results from a non-empirical density functional

    Author(s): Kohanoff J.J., Pinilla C., Youngs T.G.A., Artacho E., Soler J.M

    Journal of Chemical Physics, 135, pp. 154505- (2011)


  20. Title: On the treatment of singularities of the Watson Hamiltonian for nonlinear molecule

    Author(s): Scivetti I., Kohanoff J.J., Gidopoulos N.I.

    International Journal of Quantum Chemistry, 111, pp. 307- (2011)


  21. Title: Ab Initio Studies of H-Bonded Systems: The Cases of Ferroelectric KH2PO4 and Antiferroelectric NH4H2PO4

    Author(s): Koval S., Lasave J., Migoni R.L, Kohanoff J.J, Dalal N.S

    Ferroelectrics - Characterization and Modeling (Mickaël Lallart (Ed.)) (2011)


  22. Title: Phonons, Instabilities and Origin of Polarization in KDP

    Author(s): Colizzi G., Lasave J., Kohanoff J.J., Migoni R.

    Ferroelectrics, 401, pp. 200- (2010)


  23. Title: Shell Model Study of Local and Global Energy Barriers in KDP

    Author(s): Koval S., Lasave J., Kohanoff J.J, Migoni R.

    Ferroelectrics, 401, pp. 103 - (2010)


  24. Title: General local and rectilinear vibrational coordinates consistent with Eckart’s conditions

    Author(s): Scivetti I., Kohanoff J., Gidopoulos N.,

    Physical Review A, 79, No. 3, Art. No. 032516 (MAR 2009)

    doi: 10.1103/PhysRevA.79.032516

    We present a general method to construct a set of local rectilinear vibrational coordinates for a nonlinear molecule whose reference structure does not necessarily correspond to a stationary point of the potential-energy surface. We show both analytically and with a numerical example that the vibrational coordinates satisfy Eckart’s conditions. In addition, we find that the Watson Hamiltonian provides a fairly robust description even of highly excited vibrational states of triatomic molecules, except for a few states of large amplitude motion sampling the singular region of the Hamiltonian. These states can be identified through slow convergence.

  25. Title: Self-consistent geometry in the computation of the vibrational spectra of molecules

    Author(s): Scivetti I., Kohanoff J., Gidopoulos N.,

    Physical Review A, 80, No. 2 (2009)

    doi: 10.1103/PhysRevA.80.022516

    An exact and general approach to study molecular vibrations is provided by the Watson Hamiltonian. Within this framework, it is customary to omit the contribution of the terms with the vibrational angular momentum and the Watson term, especially for the study of large systems. We discover that this omission leads to results which depend on the choice of the reference structure. The self-consistent solution proposed here yields a geometry that coincides with the quantum averaged geometry of the Watson Hamiltonian and appears to be a promising way for the computation of the vibrational spectra of strongly anharmonic systems.

  26. Title: A shell model for the H-bonded ferroelectric KH2PO4

    Author(s): Lasave J., Kohanoff J., Migoni R.L., Koval S.,

    Physica B: Condensed Matter, 404, No. 18, pp. 2736-2738 (2009)

    doi: 10.1016/j.physb.2009.06.143

    A shell model for KH2PO4 (KDP), the prototype compound of the family of H-bonded ferroelectric materials, has been constructed by adjusting the interaction parameters to first-principles calculations. Structural properties, energy barriers, phonons, and the relative stability between the ferroelectric (FE) phase and a relevant antiferroelectric metastable structure associated to domain walls, compare very favorably to available first-principles and experimental data. Molecular dynamics simulations show that the model behaves satisfactorily within the FE phase. This model will be used to study the elusive structure of the paraelectric (PE) phase and the nature of the FE-PE phase transition. (C) 2009 Elsevier B.V. All rights reserved.

  27. Title: Structure of warm dense matter via angularly resolved x-ray scatter

    Author(s): Riley D., Gareta J.J.A., Saiz E.G., Khattak F.Y., Kohanoff J., Sahoo S., Naz G.S., Shearer S.F.C., Thornton K.A., Gregory C., Woolsey N.C., Notley M., Neely D.,

    Plasma Physics and Controlled Fusion, 51, No. 12 (2009)

    doi: 10.1088/0741-3335/51/12/124036

    In this paper we describe experimental results on angularly resolved x-ray scatter from a sample of warm dense aluminium that has been created by double sided laser-driven shock compression. The experiment was carried out on the Central Laser Facility of the Rutherford Appleton Laboratory, using the VULCAN laser. The form of the angularly resolved scatter cross-section was compared with predictions based on a series of molecular dynamics simulations with an embedded atom potential, a Yukakwa potential and a bare Coulomb potential. The importance of screening is evident from the comparison and the embedded atom model seems to match experiment better than the Yukawa potential.

  28. Title: Compton scatter profiles for warm dense matter

    Author(s): Sahoo S., Gribakin G.F., Naz G.S., Kohanoff J., Riley D.,

    Physical Review E, 77, No. 4 (2008)

    doi: 10.1103/PhysRevE.77.046402

    In this paper, we discuss the possibility of using x-ray Compton scattering as a probe of the outer electronic structure of ions immersed in warm dense matter. It is proposed that the x-ray free-electron lasers currently under construction will provide an ideal tool for this, with the main pulse being used to create a uniform well-defined sample and the third harmonic providing a clean monochromatic probe. We model the plasma photon scatter spectrum by combining self-consistent finite-temperature electronic structure calculations with molecular dynamics simulations of the ion-ion structure factor. In particular, we present bound-free Compton profiles that are more accurate that those obtained using form factor or impulse approximations.

  29. Title: First-principles molecular dynamics simulations of the interaction of ionic projectiles with liquid water and ice

    Author(s): Kohanoff J., Artacho E.

    5th International Conference on Radiation Damage in Biomolecular Systems (Debrecen, Hyngary, 2008), AIP Conference Proceedings, 1080, pp. 78-87 (JUN 13-15 2008)


    We first present results of first-principles molecular dynamics simulations of the passage of Carbon projectiles through water in the liquid state in the adiabatic regime, where the electrons are always in the instantaneous ground state. We study a range of projectile velocities up to the estimated upper limit for the adiabatic approximation and analyze the different types of collision events. We show that for high projectile velocities collisions are mostly binary, but at lower velocities most trajectories exhibit a continuous energy loss to the medium.. which cannot be properly described as a sequence of independent binary collisions. For the slowest projectiles we observe the formation of new chemical species such as hydronium, H5O2+ and hydrogen peroxide. When C-atoms are completely stopped, then we also see the formation of species like formic acid. By analyzing the generation of secondary fragments, we observe that these are mostly hyperthermal and their spatial rate of generation increases with decreasing projectile energy. The two most numerous species are H and OH. In the second part we study., via electronic dynamics with fixed nuclei, the opposite regime of very fast protons producing only electronic excitation in ice, under channeling conditions. We observe the existence of a threshold velocity for electronic excitation of about 0.2 a.u. By monitoring the rate of increase of the total energy, we calculate the electronic stopping power.

  30. Title: Effect of quantization of vibrations on the structural properties of crystals

    Author(s): Scivetti I., Gidopoulos N., Kohanoff J.,

    Physical Review B, 78, No. 22 (2008)

    doi: 10.1103/PhysRevB.78.224108

    We study the structural effects produced by the quantization of vibrational degrees of freedom in periodic crystals at zero temperature. To this end we introduce a methodology based on mapping a suitable subspace of the vibrational manifold and solving the Schrodinger equation in it. A number of increasingly accurate approximations ranging from the quasiharmonic approximation (QHA) to the vibrational self-consistent field (VSCF) method and the exact solution are described. A thorough analysis of the approximations is presented for model monatomic and hydrogen-bonded chains, and results are presented for a linear H-F chain where the potential-energy surface is obtained via first-principles electronic structure calculations. We focus on quantum nuclear effects on the lattice constant and show that the VSCF is an excellent approximation, meaning that correlation between modes is not extremely important. The QHA is excellent for covalently bonded mildly anharmonic systems, but it fails for hydrogen-bonded ones. In the latter, the zero-point energy exhibits a nonanalytic behavior at the lattice constant where the H atoms center, which leads to a spurious secondary minimum in the quantum-corrected energy curve. An inexpensive anharmonic approximation of noninteracting modes appears to produce rather good results for hydrogen-bonded chains for small system sizes. However, it converges to the incorrect QHA results for increasing size. Isotope effects are studied for the first-principles H-F chain. We show how the lattice constant and the H-F distance increase with decreasing mass and how the QHA proves to be insufficient to reproduce this behavior.

  31. Title: Evidence of short-range screening in shock-compressed aluminum plasma

    Author(s): Saiz E.G., Gregori G., Khattak F.Y., Kohanoff J., Sahoo S., Naz G.S., Bandyopadhyay S., Notley M., Weber R.L., Riley D.,

    Physical Review Letters, 101, No. 7 (2008)

    doi: 10.1103/PhysRevLett.101.075003

    We have investigated the angular variation in elastic x-ray scattering from a dense, laser-shock-compressed aluminum foil. A comparison of the experiment with simulations using an embedded atom potential in a molecular dynamics simulation shows a significantly better agreement than simulations based on an unscreened one-component plasma model. These data illustrate, experimentally, the importance of screening for the dense plasma static structure factor.

  32. Title: Polarization relaxation in an ionic liquid confined between electrified walls

    Author(s): Pinilla C., Del Popolo M.G., Kohanoff J., Lynden-Bell R.M.

    Journal Of Physical Chemistry B, 111, No. 18, pp. 4877-4884 (MAY 10 2007)

    doi: 10.1021/jp067184+

    The response of a room temperature molten salt to an external electric field when it is confined to a nanoslit is studied by molecular dynamics simulations. The fluid is confined between two parallel and oppositely charged walls, emulating two electrified solid-liquid interfaces. Attention is focused on structural, electrostatic, and dynamical properties, which are compared with those of the nonpolarized fluid. It is found that the relaxation of the electrostatic potential, after switching the electric field off, occurs in two stages. A first, subpicosecond process accounts for 80% of the decay and is followed by a second subdiffusive process with a time constant of 8 ps. Diffusion is not involved in the relaxation, which is mostly driven by small anion translations. The relaxation of the polarization in the confined system is discussed in terms of the spectrum of charge density fluctuations in the bulk.

  33. Title: Neutral and charged 1-butyl-3-methylimidazolium triflate clusters: Equilibrium concentration in the vapor phase and thermal properties of nanometric droplets

    Author(s): Ballone P., Pinilla C., Kohanoff J., Del Popolo M.G.

    Journal Of Physical Chemistry B, 111, No. 18, pp. 4938-4950 (MAY 10 2007)

    doi: 10.1021/jp067484r

    Ground state energy, structure, and harmonic vibrational modes of 1-butyl-3-methylimidazolium triflate ([bmim][Tf]) clusters have been computed using an all-atom empirical potential model. Neutral and charged species have been considered up to a size (30 [bmim][Tf] pairs) well into the nanometric range. Free energy computations and thermodynamic modeling have been used to predict the equilibrium composition of the vapor phase as a function of temperature and density. The results point to a nonnegligible concentration of very small charged species at pressures (P similar to 0.01 Pa) and temperatures (T >= 600 K) at the boundary of the stability range of [bmim][Tf]. Thermal properties of nanometric neutral droplets have been investigated in the 0 <= T <= 700 K range. A near-continuous transition between a liquidlike phase at high T and a solidlike phase at low T takes place at T similar to 190 K in close correspondence with the bulk glass point T-g similar to 200 K. Solidification is accompanied by a transition in the dielectric properties of the droplet, giving rise to a small permanent dipole embedded into the solid cluster. The simulation results highlight the molecular precursors of several macroscopic properties and phenomena and point to the close competition of Coulomb and dispersion forces as their common origin.

  34. Title: Clusters, liquids, and crystals of dialkyimidazolium salts. A combined perspective from a initio and classical computer simulations

    Author(s): Del Popolo M.G., Kohanoff J., Lynden-Bell R.M., Pinilla C

    Accounts of Chemical Research, 40, No. 11, pp. 1156-1164 (NOV 2007)

    doi: 10.1021/ar700069c

    We summarize results obtained by a combination of ab initio and classical computer simulations of dialkylimidazolium ionic liquids in different states of aggregation, from crystals to liquids and clusters. Unusual features arising from the competition between electrostatic, dispersion, and hydrogen-bonding interactions are identified at the origin of observed structural patterns. We also discuss the way Bronsted acids interact with ionic liquids leading to the formation of hydrogen-bonded anions.

  35. Title: Simulations of ionic liquids, solutions, and surfaces

    Author(s): Lynden-Bell R.M., Del Popolo M.G., Youngs T.G.A., Kohanoff J., Hanke C.G., Harper J.B., Pinilla C.C.

    Accounts of Chemical Research, 40, No. 11, pp. 1138-1145 (OCT 2007)

    doi: 10.1021/ar700065s

    We have been using atomistic simulation for the last 10 years to study properties of imidazolium-based ionic liquids. Studies of dissolved molecules show the importance of electrostatic interactions in both aromatic and hydrogen-bonding solutes. However, the local structure strongly depends upon ion–ion and solute–solvent interactions. We find interesting local alignments of cations at the gas–liquid and solid–liquid interfaces, which give a potential drop through the surface. If the solid interface is charged, this charge is strongly screened over distances of a few nanometres and this screening decays on a fast time scale. We have studied the sensitivity of the liquid structure to force-field parameters and show that results from ab initio simulations can be used in the development of force fields.

  36. Title: Nuclear quantum effects on the structural properties of solids

    Author(s): Scivetti I., Hughes D., Gidopoulos N., Caro A., Kohanoff J.,

    AIP Conference Proceedings, 963, pp. 212-223 (SEP 25 2007)


  37. Title: Competition of charge density waves and superconductivity in Sulfur

    Author(s): Degtyareva O., Magnitskaya M.V., Kohanoff J., Profeta G., Scandolo S., McMahon M.I., Gregoryanz E.,

    Physical Review Letters, 99, Art. No. 155505 (OCT 15 2007)

    doi: 10.1103/PhysRevLett.99.155505

    Full Text

    A one-dimensional charge-density wave (CDW) instability is shown to be responsible for the formation of the incommensurate modulation of the atomic lattice in the high-pressure phase of sulfur. The coexistence of, and competition between, the CDW and the superconducting state leads to the previously observed increase of Tc up to 17 K, which we attribute to the suppression of the CDW instability, the same phenomenology found in doped layered dichalcogenides.

  38. Title: Molecular electrostatic properties of ions in an ionic liquid

    Author(s): Prado C.E.R., Del Popolo M.G., Youngs T.G.A., Kohanoff J., Lynden-Bell R.M.

    Molecular Physics, 104, No. 15, pp. 2477-2483 (AUG 10 2006)

    doi: 10.1080/00268970600765748

    We have analysed the electronic wave functions from an ab initio simulation of the ionic liquid ( room temperature molten salt) dimethyl imidazolium chloride ([dmim][Cl] or [C(1)mim][CI]) using localized Wannier orbitals. This allows us to assign electron density to individual ions. The probability distributions of the ionic dipole moments for an isolated ion and for ions in solution are compared. The liquid environment is found to polarize the cation by about 0.7D and to increase the amplitude of the fluctuations in the dipole moments of both cation and anion. The relative changes in nuclear and electronic contributions are shown. The implications for classical force fields are discussed.

  39. Title: Solvation structure and transport of acidic protons in ionic liquids: A first-principles simulation study

    Author(s): Del Popolo M.G., Kohanoff J., Lynden-Bell R.M.

    Journal Of Physical Chemistry B, 110, No. 17, pp. 8798-8803 (MAY 4 2006)

    doi: 10.1021/jp0602326

    Ab initio simulations of a single molecule of HCl in liquid dimethyl imidazolium chloride [dmim][Cl] show that the acidic proton exists as a symmetric, linear ClHCl- species. Details of the solvation structure around this molecule are given. The proton-transfer process was investigated by applying a force along the antisymmetric stretch coordinate until the molecule broke. Changes in the free energy and local solvation structure during this process were investigated. In the reaction mechanism identified, a free chloride approaches the proton from the side. As the original ClHCl- distorts and the incoming chloride forms a new bond to the proton, one of the original chlorine atoms is expelled and a new linear molecule is formed.

  40. Title: Development of complex classical force fields through force matching to ab initio data: Application to a room-temperature ionic liquid

    Author(s): Youngs T.G.A., Del Popolo M.G., Kohanoff J.

    Journal Of Physical Chemistry B, 110, No. 11, pp. 5697-5707 (MAR 23 2006)

    doi: 10.1021/jp056931k

    Recent experimental neutron diffraction data and ab initio molecular dynamics simulation of the ionic liquid dimethylimidazolium chloride ([dmim]Cl) have provided a structural description of the system at the molecular level. However, partial radial distribution functions calculated front the latter, when compared to previous classical Simulation results, highlight some limitations in the structural description offered by force field-based simulations. With the availability of ab initio data it is possible to improve the classical description of [dmim]Cl by using the force matching approach, and the strategy for fitting complex force fields in their original functional form is discussed. A self-consistent optimization rnethod for the generation of classical potentials of general functional forill is presented and applied, and a force field that better reproduces the observed first principles forces is obtained. When used in Simulation, it predicts structural data which reproduces more faithfully that observed in the ab initio studies. Some possible refinements to the technique, its application, and the general Suitability of common potential energy functions used within many ionic liquid force fields are discussed.

  41. Title: Electronic structure calculations for solids and molecules: theory and computational methods

    Author(s): Kohanoff J.

    Cambridge University Press (JUN 2006)


    Full Text

    Electronic structure problems are studied in condensed matter physics and theoretical chemistry to provide important insights into the properties of matter. This graduate textbook describes the main theoretical approaches and computational techniques, from the simplest approximations to the most sophisticated methods. It starts with a detailed description of the various theoretical approaches to calculating the electronic structure of solids and molecules, including density-functional theory and chemical methods based on Hartree-Fock theory. The basic approximations are thoroughly discussed, and an in-depth overview of recent advances and alternative approaches in DFT is given. The second part discusses the different practical methods used to solve the electronic structure problem computationally, for both DFT and Hartree-Fock approaches. Adopting a unique and open approach, this textbook is aimed at graduate students in physics and chemistry, and is intended to improve communication between these communities. It also serves as a reference for researchers entering the field.

  42. Title: Structure and dynamics of a confined ionic liquid. topics of relevance to dye-sensitized solar cells

    Author(s): Pinilla C., Del Popolo M.G., Lynden-Bell R.M., Kohanoff J.

    Journal Of Physical Chemistry B, 109, No. 38, pp. 17922-17927 (SEP 29 2005)

    doi: 10.1021/jp052999o

    The behavior of a model ionic liquid (IL) confined between two flat parallel walls was studied at various interwall distances using computer simulations. The results focus both on structural and dynamical properties. Mass and charge density along the confinement axis reveal a structure of layers parallel to the walls that leads to an oscillatory profile in the electrostatic potential. Orientational correlation functions indicate that cations at the interface orient tilted with respect to the surface and that any other orientational order is lost thereafter. The diffusion coefficients of the ions exhibit a maximum as a function of the confinement distance, a behavior that results from a combination of the structure of the liquid as a whole and a faster molecular motion in the vicinity of the walls. We discuss the relevance of the present results and elaborate on topics that need further attention regarding the effects of ILs in the functioning of IL-based dye-sensitized solar cells.

  43. Title: An isothermal-isobaric Langevin thermostat for simulating nanoparticles under pressure: Application to Au clusters

    Author(s): Kohanoff J., Caro A., Finnis M.W.

    Chemphyschem, 6, No. 9, pp. 1848-1852 (SEP 5 2005)

    doi: 10.1002/cphc.200400607

    We present a method for simulating clusters or, molecules subjected to an external pressure, which is exerted by a pressure-transmitting medium. It is based on the canoninical Langevin thermostat, but extended in such a way that the Brownian forces are allowed to operate only from the region exterior to the cluster. We show that the frictional force of the Langevin thermostat is linked to the pressure of the reservoir in a unique way, and that this property manifests itself when the particle it acts upon is not pointlike but has finite dimensions. By choosing appropriately the strength of the random forces and the friction coefficient, both temperature and pressure can be controlled independently. We illustrate the capabilities of this new method by calculating the compressibility of small gold clusters under pressure.

  44. Title: First-principles study of ferroelectricity and isotope effects in H-bonded KH2PO4 crystals

    Author(s): Koval S., Kohanoff J., Lasave J., Colizzi G., Migoni R.L.

    Physical Review B, 71, No. 18, Art. No. 184102 (MAY 2005)

    doi: 10.1103/PhysRevB.71.184102

    By means of extensive first-principles calculations we studied the ferroelectric phase transition and the associated isotope effect in KH2PO4 (KDP). Our calculations revealed that the spontaneous polarization of the ferroelectric phase is due to electronic charge redistributions and ionic displacements which are a consequence of proton ordering, and not vice versa. The experimentally observed double-peaked proton distribution in the paraelectric phase cannot be explained by a dynamics of only protons. This requires, instead, collective displacements within clusters that include also the heavier ions. These tunneling clusters can explain the recent evidence of tunneling obtained from Compton scattering measurements. The sole effect of mass change upon deuteration is not sufficient to explain the huge isotope effect. Instead, we find that structural modifications deeply connected with the chemistry of the H bonds produce a feedback effect on tunneling that strongly enhances the phenomenon. The resulting influence of the geometric changes on the isotope effect agrees with experimental data from neutron scattering. Calculations under pressure allowed us to analyze the issue of universality in the disappearance of ferroelectricity upon compression. Compressing DKDP so that the distance between the two peaks in the deuteron distribution is the same as for protons in KDP, corresponds to a modification of the underlying double-well potential, which becomes 23 meV shallower. This energy difference is what is required to modify the O-O distance in such a way as to have the same distribution for protons and deuterons. At the high pressures required experimentally, the above feedback mechanism is crucial to explain the magnitude of the geometrical effect.

  45. Title: Ab initio molecular dynamics simulation of a room temperature ionic liquid

    Author(s): Del Popolo M.G., Lynden-Bell R.M., Kohanoff J.

    Journal Of Physical Chemistry B, 109, No. 12, pp. 5895-5902 (MAR 31 2005)

    doi: 10.1021/jp044414g

    Ab initio molecular dynamics simulations have been performed for the first time on the room-temperature organic ionic liquid dimethyl imidazolium chloride [DMIM][Cl] using density functional theory. The aim is to compare the local liquid structure with both that obtained from two different classical force fields and from neutron scattering experiments. The local structure around the cation shows significant differences compared to both the classical calculations and the neutron results. In particular, and unlike in the gas-phase ion pair, chloride ions tend to be located near a ring C-H proton in a position suggesting hydrogen bonding. The results are used to suggest ways in which the classical potentials may be improved.

  46. Title: Simulation of interfaces between room temperature ionic liquids and other liquids

    Author(s): Lynden-Bell R.M., Kohanoff J., Del Popolo M.G.

    Faraday Discussions, 129, pp. 57-67 (2005)

    doi: 10.1039/b405514d

    The structure and properties of the interfaces between the room temperature ionic liquid dimethylimidazolium chloride ([dmim]Cl) and different Lennard-Jones fluids and between ionic liquid and water have been studied by molecular dynamics simulations, and compared to the ionic liquid-vapour interface. Two contrasting types of interface were investigated, thermodynamically stable interfaces between ionic liquid and vapour and between ionic liquid and Lennard-Jones fluids, and diffusing interfaces between miscible phases of different compositions involving water. The density profiles of different species through the interface are presented. The cations and water molecules near the former type of interface are aligned relative to the surface, but no orientational preference was found near or in the broad diffusing interface. The ionic liquid has a negative electrostatic potential relative to vapour or Lennard-Jones fluid, but is more positive than pure water. This contrast is explained in terms of the relative importance of orientation and concentration differences in the two types of interface.

  47. Title: Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model

    Author(s): Kohanoff J.J., Cachau R.E.

    Molecular Physics, 102, No. 9-10, pp. 1007-1014 (MAY 10 2004)

    doi: 10.1080/00268970410001725738

    In this paper we study a simple model potential energy surface (PES) useful for describing multiple proton translocation mechanisms. The approach presented is relevant to the study of more complex biomolecular systems like enzymes. In this model, at low temperatures, proton tunnelling favours a concerted proton transport mechanism, while at higher temperatures there is a crossover from concerted to stepwise mechanisms; the crossover temperature depends on the energetic features of the PES. We illustrate these ideas by calculating the crossover temperature using energies taken from ab initio calculations on specific systems. Interestingly, typical crossover temperatures lie around room temperature; thus both concerted and stepwise reaction mechanisms should play an important role in biological systems, and one can be easily turned into another by external means such as modifying the temperature or the pH, thus establishing a general mechanism for modulation of the biomolecular function by external effectors.

  48. Title: Ab-initio investigations of pressure effects on the ferroelectric instabilities in KDP and DKDP

    Author(s): Colizzi G., Kohanoff J., Lasave J., Koval S., Migoni R.L.

    Ferroelectrics, 301, pp. 61-64 (2004)

    doi: 10.1080/00150190490454991

    Results of first-principles calculations are reported for KDP and DKDP as a junction of pressure. The global energy barrier between the two stable (oppositely polarized) equilibrium configurations, and the separation between the corresponding positions of the H-atoms in the O-H-O bridges, are analyzed in terms of a previously proposed, self-consistent double-well model. We argue that the experimentally observed similarity of the H(D) off-centering distance in KDP and DKDP at the transition temperature call be explained only by means of important geometric isotope effects.

  49. Title: Catalytic role of metal oxides in gold-based catalysts: A first principles study of CO oxidation on TiO2 supported Au

    Author(s): Liu Z.P., Gong X.Q., Kohanoff J., Sanchez C., Hu P.

    Physical Review Letters, 91, No. 26, Art. No. 266102 (DEC 31 2003)

    doi: 10.1103/PhysRevLett.91.266102

    CO oxidation on TiO2 supported Au has been studied using density functional theory calculations. Important catalytic roles of the oxide have been identified: (i) CO oxidation occurs at the interface between Au and the oxide with a very small barrier; and (ii) O-2 adsorption at the interface is the key step in the reaction. The physical origin of the oxide promotion effect has been further investigated: The oxide enhances electron transfer from the Au to the antibonding states of O-2, giving rise to (i) strong ionic bonding between the adsorbed O-2, Au, and the Ti cation; and (ii) a significant activation of O-2 towards CO oxidation.

  50. Title: Density Functional Theory: basics, new trends and applications, in Handbook of Molecular Physics and Quantum Chemistry, ed. S. Wilson

    Author(s): Kohanoff J., Gidopoulos N.

    Wiley, Chichester, 2, pp. 532-568 (2003)


  51. Title: Solvation effects on equilibria: Triazoles and N-methyl piperidinol

    Author(s): Murdock S.E., Lynden-Bell R.M., Kohanoff J., Margulis C.J., Sexton G.J.

    Physical Chemistry Chemical Physics, 4, No. 21, pp. 5281-5288 (2002)

    doi: 10.1039/b203429h 10.1039/b203429h

    We have performed calculations of the solvation effects on a number of equilibrium constants in water using a recently proposed hybrid quantum classical scheme in which the liquid environment is modelled using classical solvent molecules and the solute electronic structure is computed using modern quantum chemical methods. The liquid phase space is sampled from a fully classical simulation. We find that solvation effects on both triazole tautomeric equilibrium constants and piperidinol conformational equilibrium constants can be interpreted in terms of subtle differences in the local environment which can be seen in probability densities and radial distribution functions. Lower level calculations were performed for comparison and we conclude that the solvation thermodynamics can be predicted from a good classical model of solvent and solute molecules, but the implicit models that we tried are less successful.

  52. Title: Ferroelectricity and isotope effects in hydrogen-bonded KDP crystals

    Author(s): Koval S., Kohanoff J., Migoni R.L., Tosatti E.

    Physical Review Letters, 89, No. 18, Art. No. 187602 (OCT 28 2002)

    doi: 10.1103/PhysRevLett.89.187602

    Based on an accurate first principles description of the energetics in H-bonded potassium-dihydrogen-phosphate crystals, we conduct a first study of nuclear quantum effects and of the changes brought about by deuteration. Tunneling is allowed only for clusters involving correlated protons and heavy ion displacements, the main effect of deuteration being a depletion of the proton probability density at the O-H-O bridge center, which in turn weakens its proton-mediated covalent bonding. The ensuing lattice expansion couples self-consistently with the proton off-centering, thus explaining both the giant isotope effect and its close connection with geometrical effects.

  53. Title: On the relevance of tunneling for the isotope effect in KDP

    Author(s): Koval S., Kohanoff J., Migoni R.L.

    Ferroelectrics, 268, pp. 659-664 (2002)


    Full Text

    First-principles calculations for KH2PO4 (KDP) show that hydrogen off-center (OC) ordering in the ferroelectric phase is accompanied by electronic charge delocalization from the acceptor and localization at the donor oxygen within the O-H...O bonds. This induces P atoms off-centering in the PO4 tetrahedrons and pairing with K+ ions along the tetragonal axis, thus developing macroscopic polarization. Centered H are collectivelly unstable. However, if the protons are centered, the P and K atoms are stable in their centered positions. In addition, off-centering of a single proton is not energetically favorable. Only correlated proton motions, involving also displacements of heavier atoms, exhibit significant double wells, thus questioning the role of tunneling in isotope effects.

  54. Title: Determining the electronic structure and chemical potentials of molecules in solution

    Author(s): Murdock S.E., Lynden-Bell R.M., Kohanoff J., Sexton G.J.

    Physical Chemistry Chemical Physics, 4, No. 13, pp. 3016-3021 (2002)

    doi: 10.1039/b200991a 10.1039/b200991a

    A simulation scheme is proposed for determining the excess chemical potential of a substance in solution. First, a Monte Carlo simulation is performed with classical models for solute and solvent molecules. A representative sample of these configurations is then used in a hybrid quantum/classical (QM/MM) calculation, where the solute is treated quantum-mechanically, and the average electronic structure is used to construct an improved classical model. This procedure is iterated to self-consistency in the classical model, which in practice is attained in one or two steps, depending on the quality of the initial guess. The excess free energy of the molecule within the QM/MM approach is determined relative to the classical model using thermodynamic perturbation theory with a cumulant expansion. The procedure provides a method of constructing classical point charge models appropriate for the solution and gives a measure of the importance of solvent fluctuations.

  55. Title: Interplay between proton ordering and ferroelectric polarization in H-bonded KDP-type crystals

    Author(s): Koval S., Kohanoff J., Migoni R.L., Bussmann-Holder A.

    Computational Materials Science, 22, No. 1-2, pp. 87-93 (NOV 2001)

    doi: 10.1016/S0927-0256(01)00172-0

    The origin of ferroelectricity in KH2PO4 (KDP) is studied by first-principles electronic structure calculations. In the low-temperature phase, the collective off-centre ordering of the protons is accompanied by an electronic charge delocalization from the near and localization at the far oxygen within the O-H...O bonds. Electrostatic forces. then, push the K+ ions towards off-centre positions, and induce a macroscopic polarization. The analysis of the correlation between different geometrical and electronic quantities, in connection with experimental data. supports the idea that the role of tunnelling in isotopic effects is irrelevant. Instead, geometrical quantum effects appear to play a central role. (C) 2001 Elsevier Science B.V. All rights reserved.

  56. Title: Ab initio simulation of charged slabs at constant chemical potential

    Author(s): Lozovoi A.Y., Alavi A., Kohanoff J., Lynden-Bell R.M.

    Journal Of Chemical Physics, 115, No. 4, pp. 1661-1669 (JUL 22 2001)

    doi: 10.1063/1.1379327

    We present a practical scheme for performing ab initio supercell calculations of charged slabs at constant electron chemical potential mu, rather than at constant number of electrons N-e. To this end, we define the chemical potential relative to a plane (or "reference electrode") at a finite distance from the slab (the distance should reflect the particular geometry of the situation being modeled). To avoid a net charge in the supercell, and thus make possible a standard supercell calculation, we restore the electroneutrality of the periodically repeated unit by means of a compensating charge, whose contribution to the total energy and potential is subtracted afterwards. The "constant mu" mode enables one to perform supercell calculation on slabs, where the slab is kept at a fixed potential relative to the reference electrode. We expect this to be useful in modeling many experimental situations, especially in electro-chemistry. (C) 2001 American Institute of Physics.

  57. Title: The status of the low-temperature phase diagram of hydrogen at the turn of the century

    Author(s): Kohanoff J.

    Journal Of Low Temperature Physics, 122, No. 3-4, pp. 297-311 (FEB 2001)

    doi: 10.1023/A:1004896716926

    Hydrogen. is the simplest element in nature. This simplicity in the atomic state is often assumed to hold also for its condensed phases. Nevertheless; experiments carried out during the past 15 years of the XXth century have shown that this picture is not necessarily a faithful one. Several different low-temperature solid phases have been identified, in contrast with the simplicity idea. These exhibit outstanding features like pressure-independent phonon bands, large isotope effects, and strong infrared activity. In this paper I will give an overview of the current understanding of the low-temperature region of the phase diagram of hydrogen, as emerges from a fruitful cooperative action between diamond anvil cell experiments and first-principles theoretical calculations.

  58. Title: Relevance of heterometallic binding energy for metal underpotential deposition

    Author(s): Sanchez C.G., Leiva E.P.M., Kohanoff J.

    Langmuir, 17, No. 7, pp. 2219-2227 (APR 3 2001)

    doi: 10.1021/la001639j

    We present first-principles calculations for a number of metals adsorbed on several different metallic substrates. Some of these systems are very relevant in electrochemistry, especially in the field of underpotential deposition phenomena. The present studies reveal the existence of a relationship between the excess binding energy and the surface energy difference between substrate and adsorbate. Comparisons with experimental underpotential shifts show that excess binding energies are systematically underestimated. By analyzing experimental information on different systems, we conclude that this discrepancy between our vacuum calculations and experiments carried out in an electrolytic solution is likely to be due to anion adsorption and/or solvent effects.

  59. Title: Linear Scaling DFT Calculations with Numerical Atomic Orbitals

    Author(s): Ordejon P., Artacho E., Cachau R., Gale J., Garcia A., Junquera J., Kohanoff J., Machado M., Sanchez-Portal D., Soler J.M., Weht R.,

    Mat. Res. Soc. Symp. Proc., 667, pp. AA9.6.1-AA9.6.12 (2001)


    Full Text

    We have recently developed a method to perform Density Functional Theory calculations in systems with a very large number of atoms, which is based on the use of numerical atomic orbitals as basis sets. The method incorporates Order-N techniques both in the calculation of the Kohn-Sham hamiltonian matrix elements and in the solution of the wave functions, which make the CPU time and memory to scale linearly with the number of atoms, allowing calculations in very large system. In this work, we present results on several test systems to show that the approach and the basis sets used with our method are able to provide an accuracy similar to that of other standard DFT techniques.

  60. Title: Optimal basis set for electronic structure calculations in periodic systems

    Author(s): Scandolo S., Kohanoff J.

    Physical Review B, 62, No. 23, pp. 15499-15504 (DEC 15 2000)

    doi: 10.1103/PhysRevB.62.15499

    An efficient method for calculating the electronic structure of systems that need a very fine sampling of the Brillouin zone is presented. The method is based on the variational optimization of a single (i.e., common to all points in the Brillouin zone) basis set for the expansion of the electronic orbitals. Considerations from k.p-approximation theory help to understand the efficiency of the method. The accuracy and the convergence properties of the method as a function of the optimal basis set size are analyzed for a test calculation on a 16-atom Na supercell.

  61. Title: Concertedness and solvent effects in multiple proton transfer reactions: The formic acid dimer in solution

    Author(s): Kohanoff J., Koval S., Estrin D.A., Laria D., Abashkin Y.

    Journal Of Chemical Physics, 112, No. 21, pp. 9498-9508 (JUN 1 2000)

    doi: 10.1063/1.481585

    The issue of multiple proton transfer (PT) reactions in solution is addressed by performing molecular dynamics simulations for a formic acid dimer embedded in a water cluster. The reactant species is treated quantum mechanically, within a density functional approach, while the solvent is represented by a classical model. By constraining different distances within the dimer we analyze the PT process in a variety of situations representative of more complex environments. Free energy profiles are presented, and analyzed in terms of typical solvated configurations extracted from the simulations. A decrease in the PT barrier height upon solvation is rationalized in terms of a transition state which is more polarized than the stable states. The dynamics of the double PT process is studied in a low-barrier case and correlated with solvent polarization fluctuations. Cooperative effects in the motion of the two protons are observed in two different situations: when the solvent polarization does not favor the transfer of one of the two protons and when the motion of the two protons is not synchronized. This body of observations is correlated with local structural and dynamical properties of the solvent in the vicinity of the reactant. (C) 2000 American Institute of Physics. [S0021-9606(00)51121-0].

  62. Title: Reply to: "The puzzling stability of monatomic gold wires is the result of small fluctuations"

    Author(s): Torres J.A., Tosatti E., Dal Corso A., Ercolessi F., Kohanoff J.J., Di Tolla F.D., Soler J.M.

    Surface Science, 463, No. 3, pp. 213-214 (2000)


  63. Title: The puzzling stability of monotaomic gold wires

    Author(s): Torres J.A., Tosatti E., Dal Corso A., Ercolessi F., Kohanoff J., di Tolla F.D., Soler J.M.,

    Surf. Science, 426, No. L441 (1999)


  64. Title: Elasticity and mechanical instabilities of diamond at megabar stresses: implications for diamond-anvil-cell research

    Author(s): Ji-Jun Zhao, Scandolo S., Kohanoff J., Chiarotti G.L., TosattiE.,

    Applied Physics Letters, 75, No. 4 (JUL 26 1999)

    doi: 10.1063/1.124424

    We present first-principles calculations of the stress–strain curves for diamond under nonhydrostatic tetragonal compression, in the regime of operation of diamond-anvil cells (DACs). We provide a parametrization of the stress components as a function of strain, which is potentially useful for the controlled design of DACs. A stability analysis shows that a tetragonal-shear mechanical instability sets in in diamond when sigmaz – sigmar = 200 GPa, where sigmaz and sigmar are the axial and radial components of the stress, respectively.

  65. Title: Dipole-quadrupole interactions and the nature of phase III of compressed hydrogen

    Author(s): Kohanoff J., Scandolo S., de Gironcoli S., Tosatti E.,

    Physical Review Letters, 83, No. 20, pp. 4097-4100 (NOV 1999)

    doi: 10.1103/PhysRevLett.83.4097

    A new class of strongly infrared (IR) active structures is identified for phase III of compressed molecular H2 by constant-pressure ab initio molecular dynamics and density-functional perturbation calculations. These are planar quadrupolar structures obtained as a distortion of low-pressure quadrupolar phases, after they become unstable at about 150 GPa due to a zone boundary soft phonon. The nature of the II-III transition and the origin of the IR activity are rationalized by means of simple electrostatics, as the onset of a stabilizing dipole-quadrupole interaction.

  66. Title: An ab initio path integral integral Monte Carlo simulation method for molecules and clusters: application to Li4 and Li5+

    Author(s): Weht R.O., Kohanoff J., Estrin D.A., Chakravarty C.,

    J. Chem. Phys., 108, No. 8848 (1998)


  67. Title: Solid Molecular Phases of Hydrogen via Constant-pressure First-principles Molecular Dynamics

    Author(s): Kohanoff J., Scandolo S.,

    Mat. Res. Soc. Proc. Symp., 499, No. 329 (1998)


  68. Title: Simple Molecular Systems at Very High Pressures: computer simulation studies

    Author(s): Chiarotti G.L., Ancilotto F., Bernasconi M., Bernard S., Cavazzoni C., Focher P., Kohanoff J., Parrinello M., Scandolo S., Serra S., Tosatti E.,

    Rev. High Pressure Sci. Technol., 7, No. 172 (1998)


  69. Title: Molecular dynamics simulation of the a-Al2O3 lattice: dynamic properties

    Author(s): Rambaut C., Jobic H., Jaffrezic H., Kohanoff J., Fayeulle S.,

    J. Phys.: Condens. Matter, 10, No. 4221 (1998)


  70. Title: Solid molecular hydrogen: The broken symmetry phase

    Author(s): Kohanoff J., Scandolo S., Chiarotti G.L., Tosatti E.,

    Phys. Rev. Lett., 78, No. 2783 (1997)


  71. Title: Molecular Dynamics Simulation of Electron Trapping in the Sapphire Lattice

    Author(s): Rambaut C., Oh K.H., Jaffrezic H., Kohanoff J., Fayeulle S.,

    J. Appl. Phys., 81, No. 3263 (1997)


  72. Title: A hybrid quantum and classical mechanical Monte Carlo simulation of the interaction of Hydrogen Chloride with solid water clusters

    Author(s): Estrin D.A., Kohanoff J., Laría D.H., Weht R.O.,

    Chem. Phys. Lett., 280, No. 280 (1997)


  73. Title: Low-temperature atomic dynamics of Si(111)-7x7

    Author(s): Stich I., Kohanoff J., Terakura K.,

    Phys. Rev. B, 54, No. 2642 (1996)


  74. Title: Statistical Properties of the Dense Hydrogen Plasma: an ab initio Molecular Dynamics investigation

    Author(s): Kohanoff J., Hansen J.P.,

    Phys. Rev. E, 54, No. 768 (1996)


  75. Title: Ab initio Molecular Dynamics of metallic hydrogen at high density

    Author(s): Kohanoff J., Hansen J.P.,

    Phys. Rev. Lett., 74, No. 626 (1995)


  76. Title: Porous Silicon: A Silicon Structure with New Optical Properties

    Author(s): Buda F., Kohanoff J.,

    Prog. Quantum Electr., 18, No. 201 (1994)


  77. Title: Phonon Spectra from Short Non-thermally Equilibrated Molecular Dynamics Simulations

    Author(s): Kohanoff J.,

    Comput. Mater. Science, 2, No. 221 (1994)


  78. Title: Ab initio Molecular Dynamics of C70: Intramolecular Vibrations and Zero-point-motion Effects

    Author(s): Onida G., Andreoni W., Kohanoff J., Parrinello M.,

    Chem. Phys. Lett., 219, No. 1 (1994)


  79. Title: Ab initio Molecular Dynamics with Excited Electrons

    Author(s): Alavi A., Kohanoff J., Parrinello M., Frenkel D.,

    Phys. Rev. Lett., 73, No. 2599 (1994)


  80. Title: Effective Li-Li interactions in LixK1-xTaO3

    Author(s): Stachiotti M., Migoni R., Christen H.M., Kohanoff J., Höchli U.T.,

    J. Phys.: Condens. Matter, 6, No. 4279 (1994)


  81. Title: Low Temperature Phase in LixK1-xTaO3

    Author(s): Stachiotti M., Migoni R., Kohanoff J., Höchli U.,

    Ferroelectrics, 157, No. 335 (1994)


  82. Title: Nature of the conduction states in the metallic molecular crystal Li(NH3)4

    Author(s): Kohanoff J., Buda F., Parrinello M., Klein M.L.,

    Phys. Rev. Lett., 73, No. 3133 (1994)


  83. Title: Optical Properties of Porous Silicon: A First-principles Study

    Author(s): Buda F., Kohanoff J., Parrinello M.,

    Phys. Rev. Lett., 69, No. 1272 (1992)


  84. Title: A Possible New Highly Stable Fullerite Cluster: Li12C60

    Author(s): Kohanoff J., Andreoni W., Parrinello M.,

    Chem. Phys. Lett., 198, No. 472 (1992)


  85. Title: Zero-Point-Motion effects on the Structure of C60

    Author(s): Kohanoff J., Andreoni W., Parrinello M.,

    Phys. Rev. B, 46, No. 4371 (1992)


  86. Title: Theoretical Study of LiC6

    Author(s): Kohanoff J., Galli G., Parrinello M.,

    J. Phys. (France) IV, 1, pp. C5-351 (1991)


  87. Title: Interplay Between Ising and Six-vertex Symmetries in a Model for the Roughening of Reconstructed Surfaces

    Author(s): Kohanoff J., Jug G., Tosatti E.,

    J. Phys. A: Math. Gen., 23, No. 5625 (1990)


  88. Title: A model for the Roughening of Reconstructed Surfaces: Finite-size Study and Phase Diagram

    Author(s): Kohanoff J., Jug G., Tosatti E.,

    J. Phys. A: Math. Gen., 23, No. L209 (1990)


  89. Title: Battery Operated STM

    Author(s): Valdés J., Kohanoff J., Lobbe E.E., López Bancalari R., Porfiri M.E., García Cantú R.,

    J. Microsc., 152, No. 675 (1989)


  90. Title: Pulse Method of Measuring Thermal Diffusivity and Optical Absorption Depth for Partially Transparent Materials

    Author(s): Tischler M., Kohanoff J.J., Rangugni G.A., Ondracek G.,

    J. Appl. Phys, 63, No. 1259 (1988)