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  1. 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.

  2. Title: Binding modes of diketo-acid inhibitors of HIV-1 integrase: A comparative molecular dynamics simulation study

    Author(s): Huang M., Grant G.H., Richards W.G.

    Journal of Molecular Graphics and Modelling, 29, No. 1, pp. 956- (JUN 2011)

    doi: 10.1016/j.jmgm.2011.04.002

    HIV-1 integrase (IN) has become an attractive target since drug resistance against HIV-1 reverse transcriptase (RT) and protease (PR) has appeared. Diketo acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN: however the action mechanism is not well understood. Here, to study the inhibition mechanism of DKAs we performed 10 ns comparative molecular dynamics simulations on HIV-1 IN bound with three most representative DKA inhibitors: Shionogi inhibitor, S-1360 and two Merck inhibitors L-731,988 and L-708,906. Our simulations show that the acidic part of S-1360 formed salt bridge and cation–π interactions with Lys159. In addition, the catalytic Glu152 in S-1360 was pushed away from the active site to form an ion–pair interaction with Arg199. The Merck inhibitors can maintain either one or both of these ion–pair interaction features. The difference in potencies of the DKA inhibitors is thus attributed to the different binding modes at the catalytic site. Such structural information at atomic level, not only demonstrates the action modes of DKA inhibitors but also provides a novel starting point for structural-based design of HIV-1 IN inhibitors.

  3. Title: Electronic states and spin-forbidden cooling transitions of AlH and AlF

    Author(s): Wells N., Lane I.

    Physical Chemistry Chemical Physics, 13, pp. 19018- (AUG 2011)

    doi: 10.1039/c1cp21313j

    The feasibility of laser cooling AlH and AlF is investigated using ab initio quantum chemistry. All the electronic states corresponding to the ground and lowest two excited states of the Al atom are calculated using multi-reference configuration interaction (MRCI) and the large AV6Z basis set for AlH. The smaller AVQZ basis set is used to calculate the valence electronic states of AlF. Theoretical Franck–Condon factors are determined for the A1Π → X1Σ+ transitions in both radicals and found to agree with the highly diagonal factors found experimentally, suggesting computational chemistry is an effective method for screening suitable laser cooling candidates. AlH does not appear to have a transition quite as diagonal as that in SrF (which has been laser cooled) but the A1Π → X1Σ+ transition transition of AlF is a strong candidate for cooling with just a single laser, though the cooling frequency is deep in the UV. Furthermore, the a3Π → X1Σ+ transitions are also strongly diagonal and in AlF is a practical method for obtaining very low final temperatures around 3 μK.

  4. Title: Computational Verification of Two Universal Relations for Simple Ionic Liquids. Kinetic Properties of a Model 2:1 Molten Salt

    Author(s): Armstrong J.A, Ballone P.

    Journal of Physical Chemistry B, 115, No. 17, pp. 4927-4938 (April 8 2011)


  5. Title: A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. II. Coulomb interaction effects in single conjugated polymer chains

    Author(s): Miranda R.P., Fisher A.J, Stella L., Horsfield A.P.,

    The Journal of Chemical Physics, 134, No. 24, Art. No. 244102 (28 June 2011)

    doi: 10.1063/1.3600404

    Conjugated polymers have attracted considerable attention in the last few decades due to their potential for optoelectronic applications. A key step that needs optimisation is charge carrier separation following photoexcitation. To understand better the dynamics of the exciton prior to charge separation, we have performed simulations of the formation and dynamics of localised excitations in single conjugated polymer strands. We use a nonadiabatic molecular dynamics method which allows for the coupled evolution of the nuclear degrees of freedom and of multiconfigurational electronic wavefunctions. We show the relaxation of electron-hole pairs to form excitons and oppositely charged polaron pairs and discuss the modifications to the relaxation process predicted by the inclusion of the Coulomb interaction between the carriers. The issue of charge photogeneration in conjugated polymers in dilute solution is also addressed.

  6. Title: A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. I. General formalism and application to open-shell states

    Author(s): Miranda F.P., Fisher A.J., Stella L., Horsfield A.P.,

    The Journal of Chemical Physics, 134, No. 24, Art. No. 244101 (28 June 2011)

    doi: 10.1063/1.3600397

    The solution of the time-dependent Schrodinger equation for systems of interacting electrons is generally a prohibitive task, for which approximate methods are necessary. Popular approaches, such as the time-dependent Hartree-Fock (TDHF) approximation and time-dependent density functional theory (TDDFT), are essentially single-configurational schemes. TDHF is by construction incapable of fully accounting for the excited character of the electronic states involved in many physical processes of interest; TDDFT, although exact in principle, is limited by the currently available exchange-correlation functionals. On the other hand, multiconfigurational methods, such as the multiconfigurational time-dependent Hartree-Fock (MCTDHF) approach, provide an accurate description of the excited states and can be systematically improved. However, the computational cost becomes prohibitive as the number of degrees of freedom increases, and thus, at present, the MCTDHF method is only practical for few-electron systems. In this work, we propose an alternative approach which effectively establishes a compromise between efficiency and accuracy, by retaining the smallest possible number of configurations that catches the essential features of the electronic wavefunction. Based on a time-dependent variational principle, we derive the MCTDHF working equation for a multiconfigurational expansion with fixed coefficients and specialise to the case of general open-shell states, which are relevant for many physical processes of interest.

  7. Title: Mechanism of Breathing Transitions in Metal–Organic Frameworks

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

    Journal of Physical Chemistry Letters, 2, No. 16, pp. 2033-2037 (22 July 2011)

    doi: 10.1021/jz2008769

    We present a multiscale physical mechanism and a stochastic model of breathing transitions, which represent adsorption-induced structural transformations between large-pore and narrow-pore conformations in bistable metal–organic frameworks, such as MIL-53. We show that due to interplay between host framework elasticity and guest molecule adsorption, these transformations on the level of the crystal occur via layer-by-layer shear. We construct a simple Hamiltonian that describes the physics of host–host and host–guest interactions and show that a respective Monte Carlo simulation model qualitatively reproduces the experimentally observed features of breathing transitions.

  8. Title: Analog of Rabi oscillations in resonant electron-ion systems

    Author(s): Stella L., Miranda R.P., Horsfield A.P., Fisher A.J.,

    The Journal of Chemical Physics, 134, No. 19, Art. No. 194105 (21 May 2011)

    doi: 10.1063/1.3589165

    Quantum coherence between electron and ion dynamics, observed in organic semiconductors by means of ultrafast spectroscopy, is the object of recent theoretical and computational studies. To simulate this kind of quantum coherent dynamics, we have introduced in a previous article [L. Stella, M. Meister, A. J. Fisher, and A. P. Horsfield, J. Chem. Phys. 127, 214104 (2007)] an improved computational scheme based on Correlated Electron-Ion Dynamics (CEID). In this article, we provide a generalization of that scheme to model several ionic degrees of freedom and many-body electronic states. To illustrate the capability of this extended CEID, we study a model system which displays the electron-ion analog of the Rabi oscillations. Finally, we discuss convergence and scaling properties of the extended CEID along with its applicability to more realistic problems

  9. Title: Structural Transitions in MIL-53 (Cr): View from Outside and Inside

    Author(s): Neimark A.V., Coudert F., Triguero C., Boutin A., Fuchs A.H., Beurroies I., Renaud Denoyel R.

    Langmuir, 27, No. 8, pp. 4734-4741 (18 March 2011)

    doi: 10.1021/la200094x

    We present a unified thermodynamic description of the breathing transitions between large pore (lp) and narrow pore (np) phases of MIL-53 (Cr) observed during the adsorption of guest molecules and the mechanical compression in the process of mercury porosimetry. By revisiting recent experimental data on mercury intrusion and in situ XRD during CO2 adsorption, we demonstrate that the magnitude of the adsorption stress exerted inside the pores by guest molecules, which is required for inducing the breathing transition, corresponds to the magnitude of the external pressure applied from the outside that causes the respective transformation between lp and np phases. We show that, when a stimulus is applied to breathing MOFs of MIL-53 type, these materials exhibit small reversible elastic deformations of lp and np phases of the order of 2−4%, while the breathing transition is associated with irreversible plastic deformation that leads to up to ∼40% change of the sample volume and a pronounced hysteresis. These results shed light on the specifics of the structural transformations in MIL-53 (Cr) and other soft porous crystals (SPC).

  10. Title: Strong electronic correlation in the hydrogen chain: A variational Monte Carlo study

    Author(s): Stella L., Attaccalite C., Sorella S., Rubio A.,

    Physical Review B, 84, No. 24, Art. No. 245117 (14 December 2011)

    doi: 10.1103/PhysRevB.84.245117

    In this paper, we report a fully ab initio variational Monte Carlo study of the linear and periodic chain of hydrogen atoms, a prototype system providing the simplest example of strong electronic correlation in low dimensions. In particular, we prove that numerical accuracy comparable to that of benchmark density-matrix renormalization-group calculations can be achieved by using a highly correlated Jastrow-antisymmetrized geminal power variational wave function. Furthermore, by using the so-called "modern theory of polarization" and by studying the spin-spin and dimer-dimer correlations functions, we have characterized in detail the crossover between the weakly and strongly correlated regimes of this atomic chain. Our results show that variational Monte Carlo provides an accurate and flexible alternative to highly correlated methods of quantum chemistry which, at variance with these methods, can be also applied to a strongly correlated solid in low dimensions close to a crossover or a phase transition.

  11. Title: Electron detachment from negative ions in a short laser pulse

    Author(s): Shearer S. F. C. , Smyth M., and Gribakin G. F.

    Physical Review A, 84, pp. 033409- (12 September 2011)

    doi: 10.1103/PhysRevA.84.033409

    We present an efficient and accurate method to study electron detachment from negative ions by a few-cycle linearly polarized laser pulse. The adiabatic saddle-point method of Gribakin and Kuchiev [ Phys. Rev. A 55 3760 (1997)] is adapted to calculate the transition amplitude for a short laser pulse. Its application to a pulse with N optical cycles produces 2(N+1) saddle points in complex time, which form a characteristic “smile.” Numerical calculations are performed for H− in a 5-cycle pulse with frequency 0.0043 a.u. and intensities of 1010, 5×1010, and 1011 W/cm2, and for various carrier-envelope phases. We determine the spectrum of the photoelectrons as a function of both energy and emission angle, as well as the angle-integrated energy spectra and total detachment probabilities. Our calculations show that the dominant contribution to the transition amplitude is given by 5–6 central saddle points, which correspond to the strongest part of the pulse. We examine the dependence of the photoelectron angular distributions on the carrier-envelope phase and show that measuring such distributions can provide a way of determining this phase.

  12. Title: Is the pinning of ordinary dislocations in γ-TiAl intrinsic or extrinsic in nature? A combined atomistic and kinetic Monte Carlo approach.

    Author(s): Katzarov I.H., Paxton A.T.

    Acta Materialia, 59, No. 3, pp. 1281-1290 (2011)

    doi: 10.1016/j.actamat.2010.10.060

    Full Text

    We address the question of the observed pinning of 1/2 <110] ordinary screw dislocations in γ-TiAl which leads to the characteristic trailing of dipoles in the microstructure. While it has been proposed that these may be variously intrinsic or extrinsic in nature, we are able to rule out the former mechanism. We do this by means of very large scale, three dimensional atomistic simulations using the quantum mechanical bond order potential. We find that the kink-pair formation energy is large: 6eV, while the single kink migration energy is conversely very small: 0.13eV. Using these, and other atomistically derived data, we make kinetic Monte Carlo simulations at realistic time and length scales to simulate dislocation mobility as a function of stress and temperature. In the temperature range of the stress anomaly in γ-TiAl, we determine whether one or several of the pinning and unzipping processes associated with generation of jogs are observed during our simulations. We conclude that the pinning of ordinary dislocations and anomalous mechanical behaviour in γ-TiAl must be attributed to a combination of extrinsic obstacles and extensive cross-slip in a crystal containing impurities.

  13. 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.

  14. Title: Effect of hydrophobic nanopatches within an ionic surface on the structure of liquids

    Author(s): Youngs T.G.A., Hardacre C.,

    Physical Chemistry Chemical Physics, 13, No. 2, pp. 582-585 (2011)


    The structures of liquid water and isopropanol have been studied as a function of the size of a hydrophobic patch present in a model hydrophilic surface via molecular dynamics simulations. A significant anisotropy extending into the first few solvent layers is found over the patch which suggests implications for many real-world systems in which nanoscale heterogeneity is found.

  15. Title: Nonconservative current-induced forces: A physical interpretation

    Author(s): Todorov T.N., Dundas D., Paxton A.T., Horsfield A.P.

    Beilstein Journal of Nanotechnology, 2, pp. 727-733 (2011)

    doi: 10.3762/bjnano.2.79

    Full Text

    We give a physical interpretation of the recently demonstrated nonconservative nature of interatomic forces in current-carrying nanostructures. We start from the analytical expression for the curl of these forces, and evaluate it for a point defect in a current-carrying system. We obtain a general definition of the capacity of electrical current flow to exert a nonconservative force, and thus do net work around closed paths, by a formal noninvasive test procedure. Second, we show that the gain in atomic kinetic energy over time, generated by nonconservative current-induced forces, is equivalent to the uncompensated stimulated emission of directional phonons. This connection with electron–phonon interactions quantifies explicitly the intuitive notion that nonconservative forces work by angular momentum transfer.

  16. 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

  17. 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)


  18. 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)


  19. 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)


  20. Title: Implementation and testing of Lanczos-based algorithms for Random-Phase Approximation eigenproblems

    Author(s): Gruening M., Marini A., Gonze X.

    Computational Materials Science, 50, pp. 2148-2156 (2011)


  21. Title: Local-field and excitonic effects in the optical response of α-alumina

    Author(s): Marinopoulos A.G., Gruening M.,

    Phys. Rev. B, 83, pp. 195129- (2011)


  22. Title: Real-time approach to the optical properties of solids and nanostructures: Time-dependent Bethe-Salpeter equation

    Author(s): Attaccalite C., Gruening M., Marini.A.,

    Phys. Rev. B, 84, pp. 245110 - (2011)


  23. Title: Exploring the free energy surfaces of clusters using reconnaissance metadynamics

    Author(s): Tribello G., Cuny J., Eshet H., Parrinello M.

    J. Chem. Phys., 135, pp. 114109 - (2011)


  24. Title: Simplifying the representation of complex free-energy landscapes using sketch-map

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

    Proc. Natl. Acad Sci. U.S.A , 108, pp. 13023-13028 (2011)


  25. Title: Isomorhpism between ice and silica

    Author(s): Tribello G., Slater B., Zwijnenburg M., Bello R.

    Phys. Chem. Chem. Phys. , 12, pp. 8597-8606 (2011)


  26. Title: Surface energy and surface proton order of the ice Ih basal and prism surfaces

    Author(s): Pang D., Liu L., . Tribello G., Slater B., Michaelides A., Wang E.

    J Phys. Condens. Matter, 22, pp. 074209- (2011)


  27. Title: Prospects for ultracold carbon via charge exchange reactions and laser cooled carbides

    Author(s): Wells N., Lane I.

    Physical Chemistry Chemical Physics, 13, pp. 19036- (2011)

    doi: 10.1039/c1cp21304k

    Strategies to produce an ultracold sample of carbon atoms are explored and assessed with the help of quantum chemistry. After a brief discussion of the experimental difficulties using conventional methods, two strategies are investigated. The first attempts to exploit charge exchange reactions between ultracold metal atoms and sympathetically cooled C+ ions. Ab initio calculations including electron correlation have been conducted on the molecular ions [LiC]+ and [BeC]+ to determine whether alkali or alkaline earth metals are a suitable buffer gas for the formation of C atoms but strong spontaneous radiative charge exchange ensure they are not ideal. The second technique involves the stimulated production of ultracold C atoms from a gas of laser cooled carbides. Calculations on LiC suggest that the alkali carbides are not suitable but the CH radical is a possible laser cooling candidate thanks to very favourable Frank-Condon factors. A scheme based on a four pulse STIRAP excitation pathway to a Feshbach resonance is outlined for the production of atomic fragments with near zero centre of mass velocity.

  28. Title: Magnetism of covalently functionalized carbon nanotubes

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

    Applied Physics Letters, 99, No. 6, pp. 062503- (2011)

    doi: 10.1063/1.3623755

    We investigate the electronic structure of carbon nanotubes functionalized by adsorbates anchored with single C-C covalent bonds. We find that despite the particular adsorbate, a spin moment with a universal value of 1.0 μ B per molecule is induced at low coverage. Therefore, we propose a mechanism of bonding-induced magnetism at the carbonsurface. The adsorption of a single molecule creates a dispersionless defect state at the Fermi energy, which is mainly localized in the carbon wall and presents a small contribution from the adsorbate. This universal spin moment is fairly independent of the coverage as long as all the molecules occupy the same graphenic sublattice. The magnetic coupling between adsorbates is also studied and reveals a key dependence on the graphenic sublattice adsorption site.