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  1. Title: Multielectron effects in high harmonic generation in N2 and benzene: Simulation using a non-adiabatic quantum molecular dynamics approach for laser-molecule interactions

    Author(s): Dundas D.

    Journal of Chemical Physics, 136, No. 19, pp. 194303-1-194303-17 (MAY 2012)

    doi: 10.1063/1.4718590

    A mixed quantum-classical approach is introduced which allows the dynamical response of molecules driven far from equilibrium to be modeled. This method is applied to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations are possible. The approach is applied to the study of high harmonic generation in N2 and benzene using linearly polarized laser pulses and, to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N2 an enhancement of the cut-off harmonics is observed whenever the laser polarization is aligned perpendicular to the molecular axis. This enhancement is attributed to the symmetry properties of the Kohn-Sham orbital that responds predominantly to the pulse. In benzene we predict that a suppression in the cut-off harmonics occurs whenever the laser polarization is aligned parallel to the molecular plane. We attribute this suppression to the symmetry-induced response of the highest-occupied molecular orbital.

  2. Title: Structure and interactions of ultracold Yb ions and Rb atoms

    Author(s): Lamb H.D.L., McCann J.F., McLaughlin B.M., Goold J., Wells N., Lane I.

    Physical Review A, 86, pp. 022716- (AUG 2012)

    doi: 10.1103/PhysRevA.86.022716

    In order to study ultracold charge-transfer processes in hybrid atom-ion traps, we have mapped out the potential-energy curves and molecular parameters for several low-lying states of the Rb, Yb+ system. We employ both a multireference configuration interaction and a full configuration interaction (FCI) approach. Turning points, crossing points, potential minima, and spectroscopic molecular constants are obtained for the lowest five molecular states. Long-range parameters, including the dispersion coefficients, are estimated from our ab initio data. The separated-atom ionization potentials and atomic polarizability of the ytterbium atom (αd=128.4 atomic units) are in good agreement with experiment and previous calculations. We present some dynamical calculations for (adiabatic) scattering lengths for the two lowest (Yb, Rb+) channels that were carried out in our work. However, we find that the pseudopotential approximation is rather limited in validity and only applies to nK temperatures. The adiabatic scattering lengths for both the triplet and singlet channels indicate that both are large and negative in the FCI approximation.

  3. 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.

  4. Title: Strain-Tunable Spin Moment in Ni-Doped Graphene

    Author(s): Santos E.J.G., Ayuela A., Sánchez-Portal D.

    Journal Physical Chemistry C, 116, No. 1, pp. 1174-1178 (29 November 2012)

    doi: 10.1021/jp2077374

    Graphene, due to its exceptional properties, is a promising material for nanotechnology applications. In this context, the ability to tune the properties of graphene-based materials and devices with the incorporation of defects and impurities can be of extraordinary importance. Here, we investigate the effect of uniaxial tensile strain on the electronic and magnetic properties of graphene doped with substitutional Ni impurities (Nisub). We have found that, although Nisub defects are nonmagnetic in the relaxed layer, uniaxial strain induces a spin moment in the system. The spin moment increases with the applied strain up to values of 0.3–0.4 μB per Nisub, until a critical strain of ∼6.5% is reached. At this point, a sharp transition to a high-spin state (∼1.9 μB) is observed. This magnetoelastic effect could be utilized to design strain-tunable spin devices based on Ni-doped graphene.

  5. Title: Current-induced atomic dynamics, instabilities, and Raman signals: Quasiclassical Langevin equation approach

    Author(s): Lü J.T., Brandbyge M., Hedegård P., Todorov T.N., Dundas D.,

    Physical Review B, 85, pp. 245444- (25 June 2012)

    doi: 10.1103/PhysRevB.85.245444

    We derive and employ a semiclassical Langevin equation obtained from path integrals to describe the ionic dynamics of a molecular junction in the presence of electrical current. The electronic environment serves as an effective nonequilibrium bath. The bath results in random forces describing Joule heating, current-induced forces including the nonconservative wind force, dissipative frictional forces, and an effective Lorentz-type force due to the Berry phase of the nonequilibrium electrons. Using a generic two-level molecular model, we highlight the importance of both current-induced forces and Joule heating for the stability of the system. We compare the impact of the different forces, and the wide-band approximation for the electronic structure on our result. We examine the current-induced instabilities (excitation of runaway “waterwheel” modes) and investigate the signature of these in the Raman signals.

  6. 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.

  7. Title: Magnetism of Single Vacancies in Rippled Graphene

    Author(s): Santos E.J.G., Riikonen S., Sánchez-Portal D., Ayuela A.

    The Journal of Physical Chemistry C, 116, No. 13, pp. 7602-7606 (2 March 2012)

    doi: 10.1021/jp300861m

    Using first-principles calculations, the dependence in the properties of the monovacancy of graphene under rippling controlled by an isotropic strain was determined, with a particular focus on spin moments. At zero strain, the vacancy shows a spin moment of 1.5 μB that increases to ∼2 μB when the graphene is in tension. The changes are more dramatic under compression in that the vacancy becomes nonmagnetic when graphene is compressed more than 2%. This transition is linked to the structural changes that occur around vacancies and is associated with formation of ripples. For compressions slightly greater than 3%, this rippling leads to formation of a heavily reconstructed vacancy structure consisting of two deformed hexagons and pentagons. Our results suggest that any magnetism induced by vacancies that occurs in graphene can be controlled by applying strain.

  8. Title: Universal magnetic properties of sp3-type defects in covalently functionalized graphene

    Author(s): Santos E.J.G., Ayuela A., Daniel Sánchez-Portal D.

    New Journal of Physics, 14, No. 4, pp. 043022- (19 April 2012)

    doi: 10.1088/1367-2630/14/4/043022

    Using density-functional calculations, we study the effect of sp3-type defects created by different covalent functionalizations on the electronic and magnetic properties of graphene. We find that the induced magnetic properties are universal, in the sense that they are largely independent of the particular adsorbates considered. When a weakly polar single covalent bond is established with the layer, a local spin moment of 1.0 μB always appears in graphene. This effect is similar to that of H adsorption, which saturates one pz orbital in the carbon layer. The magnetic couplings between the adsorbates show a strong dependence on the graphene sublattice of chemisorption. Molecules adsorbed at the same sublattice couple ferromagnetically, with an exchange interaction that decays very slowly with distance, while no magnetism is found for adsorbates at opposite sublattices. Similar magnetic properties are obtained if several pz orbitals are saturated simultaneously by the adsorption of a large molecule. These results might open new routes to engineering the magnetic properties of graphene derivatives by chemical means.

  9. 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.

  10. Title: Understanding Adsorption-Induced Structural Transitions in Metal-Organic Frameworks: From the Unit Cell to the Crystal

    Author(s): Triguero C., Coudert F., Boutin A., Fuchs A.H., Neimark A.V.

    The Journal of Chemical Physics, 137, No. 18, pp. 184702- (14 November 2012)

    doi: 10.1063/1.4765369

    Breathing transitions represent recently discovered adsorption-induced structural transformations between large-pore and narrow-pore conformations in bi-stable metal-organic frameworks such as MIL-53. We present a multiscale physical mechanism of the dynamics of breathing transitions. We show that due to interplay between host framework elasticity and guest molecule adsorption, these transformations on the crystal level occur via layer-by-layer shear. We construct a simple Hamiltonian that describes the physics of host-host and host-guest interactions on the level of unit cells and reduces to one effective dimension due to the long-range elastic cell-cell interactions. We then use this Hamiltonian in Monte Carlo simulations of adsorption-desorption cycles to study how the behavior of unit cells is linked to the transition mechanism at the crystal level through three key physical parameters: the transition energy barrier, the cell-cell elastic coupling, and the system size.

  11. Title: Alkylated organic cages: from porous crystals to neat liquids

    Author(s): Giri N, Davidson C.E, Melaugh G.M., Del Pópolo M.G., Jones J.T.A., Hasell T, Cooper A.I., Horton P.N., Hursthouse M.B., James S.L.

    Chemical Science, 3, pp. 2153-2157 (05 April 2012)

    doi: 10.1039/C2SC01007K

    Rigid organic iminospherand cages are rendered meltable by multiple alkylation; below their melting points they can take the form of permanently porous crystals, crystals unstable to desolvation or non-porous glassy solids depending on chain length and branching; melting points as low as 50 °C are observed and a fully Newtonian liquid phase is obtained above 80 °C. Thin glassy fibres can be drawn out from a molten phase.

  12. Title: On transition rates in surface hopping

    Author(s): Escartin J.M., Romaniello P., Stella L., Reinhard P.-G., Suraud E.,

    The Journal of Chemical Physics, 137, No. 23, Art. No. 234113 ( 21 December 2012)

    doi: 10.1063/1.4770280

    Trajectory surface hopping (TSH) is one of the most widely used quantum-classical algorithms for nonadiabaticmolecular dynamics. Despite its empirical effectiveness and popularity, a rigorous derivation of TSH as the classical limit of a combined quantum electron-nuclear dynamics is still missing. In this work, we aim to elucidate the theoretical basis for the widely used hopping rules. Naturally, we concentrate thereby on the formal aspects of the TSH. Using a Gaussian wave packet limit, we derive the transition rates governing the hopping process at a simple avoided level crossing. In this derivation, which gives insight into the physics underlying the hopping process, some essential features of the standard TSH algorithm are retrieved, namely (i) non-zero electronic transition rate (“hopping probability”) at avoided crossings; (ii) rescaling of the nuclear velocities to conserve total energy; (iii) electronic transition rates linear in the nonadiabatic coupling vectors. The well-known Landau-Zener model is then used for illustration.

  13. Title: Nano-indentation of a room-temperature ionic liquid film on silica: a computational experiment

    Author(s): Ballone P., Del Pópolo M.G., Bovio S., Podestà A., Milani.P., Manini N.,

    Physical Chemistry Chemical Physics, 14, pp. 2475-2482 (2012)

    doi: 10.1039/C2CP23459A

    We investigate the structure of the [bmim][Tf2N]/silica interface by simulating the indentation of a thin (4 nm) [bmim][Tf2N] film by a hard nanometric tip. The ionic liquid/silica interface is represented in atomistic detail, while the tip is modelled by a spherical mesoscopic particle interacting via an effective short-range potential. Plots of the normal force (Fz) on the tip as a function of its distance from the silica surface highlight the effect of weak layering in the ionic liquid structure, as well as the progressive loss of fluidity in approaching the silica surface. The simulation results for Fz are in near-quantitative agreement with new AFM data measured on the same [bmim][Tf2N]/silica interface under comparable thermodynamic conditions.

  14. Title: An ignition key for atomic-scale engines

    Author(s): Dundas D., Cunningham B., Buchanan C., Terasawa A., Anthony T Paxton A.T., Todorov T.N.

    Journal of Physics: Condensed Matter, 24, pp. 402203-1-402203-6 (2012)

    doi: 10.1088/0953-8984/24/40/402203

    A current-carrying resonant nanoscale device, simulated by non-adiabatic molecular dynamics, exhibits sharp activation of non-conservative current-induced forces with bias. The result, above the critical bias, is generalized rotational atomic motion with a large gain in kinetic energy. The activation exploits sharp features in the electronic structure, and constitutes, in effect, an ignition key for atomic-scale motors. A controlling factor for the effect is the non-equilibrium dynamical response matrix for small-amplitude atomic motion under current. This matrix can be found from the steady-state electronic structure by a simpler static calculation, providing a way to detect the likely appearance, or otherwise, of non-conservative dynamics, in advance of real-time modelling.

  15. Title: Time-dependent density functional theory study of charge transfer in collisions

    Author(s): Avendaño-Franco G., Piraux B., Gruening M., Gonze X.,

    Theoretical Chemistry Accounts, 131, pp. 1289 - (2012)


  16. Title: Locating binding poses in protein-ligand systems using reconnaissance metadynamics

    Author(s): Soderhjelm P., Tribello G., Parrinello M.

    Proc. Natl. Acad. Sci. U.S.A. , 109, pp. 5170-5175 (2012)


  17. Title: Using sketch-map coordinates to analyze and bias molecular dynamics simulations

    Author(s): Tribello G., Ceriotti M., Parrinello M.

    Proc. Natl. Acad. Sci. U.S.A., 109, pp. 5196-5201 (2012)


  18. Title: Computational Identification of Self-inhibitory Peptides from Envelope Proteins

    Author(s): Xu Y., Rahman N.A.B.D., Othman R., Hu P., Huang M.

    Proteins: Structure, Function and Bioinformatics, 80, pp. 2154- (2012)

    doi: 10.1002/prot.24105

    Fusion process is known to be the initial step of viral infection and hence targeting the entry process is a promising strategy to design antiviral therapy. The self-inhibitory peptides derived from the enveloped (E) proteins function to inhibit the protein–protein interactions in the membrane fusion step mediated by the viral E protein. Thus, they have the potential to be developed into effective antiviral therapy. Herein, we have developed a Monte Carlo-based computational method with the aim to identify and optimize potential peptide hits from the E proteins. The stability of the peptides, which indicates their potential to bind in situ to the E proteins, was evaluated by two different scoring functions, dipolar distance-scaled, finite, ideal-gas reference state and residue-specific all-atom probability discriminatory function. The method was applied to α-helical Class I HIV-1 gp41, β-sheet Class II Dengue virus (DENV) type 2 E proteins, as well as Class III Herpes Simplex virus-1 (HSV-1) glycoprotein, a E protein with a mixture of α-helix and β-sheet structural fold. The peptide hits identified are in line with the druggable regions where the self-inhibitory peptide inhibitors for the three classes of viral fusion proteins were derived. Several novel peptides were identified from either the hydrophobic regions or the functionally important regions on Class II DENV-2 E protein and Class III HSV-1 gB. They have potential to disrupt the protein–protein interaction in the fusion process and may serve as starting points for the development of novel inhibitors for viral E proteins.