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  1. 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
    Abstract



    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.

  2. 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
    Abstract



    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.

  3. Title: Electric-Field Dependence of the Effective Dieletric Constant in Graphene Materials

    Author(s): Santos E., Kaxiras E.

    American Physical Society, APS March Meeting 2013, March 18-22, 2013, abstract #R6.008 (March 2013)

    doi: 2013APS..MAR.R6008S
    Abstract



    The dielectric constant of a material is one of the fundamental features used to characterize its electrostatic properties such as capacitance, charge screening, and energy storage capability. Here we address the issue of the effective dielectric constant (εG) in a few-layer graphene materials (e.g. graphene, MoS2, WS2, etc.) subjected to an external electric field. In particular for graphene, the value of εG has attracted interest due to contradictory reports from theoretical and experimental studies. Through extensive first-principles electronic structure calculations, including van der Waals interactions, we show that the graphene dielectric constant depends on the value of the external field (Eext): it is nearly constant at εG ~ 3 for low fields (Eext < 0 . 1 V/Å) but increases at higher fields, reaching εG=4.5 at Eext = 1 . 7 V/Å. Further increase of Eext drives the system to an unstable state where the layers are decoupled and can be easily separated. Calculations performed for other layered materials follow the same trend. Our results point to a promising way of understanding and controlling the screening properties of few-layer graphene materials via electrical means. The dielectric constant of a material is one of the fundamental features used to characterize its electrostatic properties such as capacitance, charge screening, and energy storage capability. Here we address the issue of the effective dielectric constant (εG) in a few-layer graphene materials (e.g. graphene, MoS2, WS2, etc.) subjected to an external electric field. In particular for graphene, the value of εG has attracted interest due to contradictory reports from theoretical and experimental studies. Through extensive first-principles electronic structure calculations, including van der Waals interactions, we show that the graphene dielectric constant depends on the value of the external field (Eext): it is nearly constant at εG ~ 3 for low fields (Eext < 0 . 1 V/Å) but increases at higher fields, reaching εG=4.5 at Eext = 1 . 7 V/Å. Further increase of Eext drives the system to an unstable state where the layers are decoupled and can be easily separated. Calculations performed for other layered materials follow the same trend. Our results point to a promising way of understanding and controlling the screening properties of few-layer graphene materials via electrical means. Supported by NSF grant numbers TG-DMR120049, TG-PHY120021, TG-DMR120073 (XSEDE)

  4. Title: Nonlinear optics from an ab initio approach by means of the dynamical Berry phase: Application to second- and third-harmonic generation in semiconductors

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

    Physical Review B, 88, No. 23, pp. 235113- (Dec 11 2013)

    doi: 10.1103/PhysRevB.88.235113
    Abstract



    We present an ab initio real-time-based computational approach to study nonlinear optical properties in condensed matter systems that is especially suitable for crystalline solids and periodic nanostructures. The equations of motion and the coupling of the electrons with the external electric field are derived from the Berry-phase formulation of the dynamical polarization [Souza et al., Phys. Rev. B 69, 085106 (2004)]. Many-body effects are introduced by adding single-particle operators to the independent-particle Hamiltonian. We add a Hartree operator to account for crystal local effects and a scissor operator to correct the independent particle band structure for quasiparticle effects. We also discuss the possibility of accurately treating excitonic effects by adding a screened Hartree-Fock self-energy operator. The approach is validated by calculating the second-harmonic generation of SiC and AlAs bulk semiconductors: an excellent agreement is obtained with existing ab initio calculations from response theory in frequency domain [Luppi et al., Phys. Rev. B 82, 235201 (2010)]. We finally show applications to the second-harmonic generation of CdTe and the third-harmonic generation of Si.

  5. Title: First-Principles Study of the Electronic and Magnetic Properties of Defects in Carbon Nanostructures

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

    Carbon Materials: Chemistry and Physics , 7, pp. 41-76 (24 April 2013)

    doi: 10.1007/978-94-007-6413-2_2
    Abstract



    Understanding the magnetic properties of graphenic nanostructures is instrumental in future spintronics applications. These magnetic properties are known to depend crucially on the presence of defects. Here we review our recent theoretical studies using density functional calculations on two types of defects in carbon nanostructures: substitutional doping with transition metals, and sp3-type defects created by covalent functionalization with organic and inorganic molecules. We focus on such defects because they can be used to create and control magnetism in graphene-based materials. Our main results are summarized as follows: 1. Substitutional metal impurities are fully understood using a model based on the hybridization between the d states of the metal atom and the defect levels associated with an unreconstructed D3h carbon vacancy. We identify three different regimes, associated with the occupation of distinct hybridization levels, which determine the magnetic properties obtained with this type of doping. 2. A spin moment of 1.0 μ B is always induced by chemical functionalization when a molecule chemisorbs on a graphene layer via a single C–C (or other weakly polar) covalent bond. The magnetic coupling between adsorbates shows a key dependence on the sublattice adsorption site. This effect is similar to that of H adsorption, however, with universal character. 3. The spin moment of substitutional metal impurities can be controlled using strain. In particular, we show that although Ni substitutionals are nonmagnetic in flat and unstrained graphene, the magnetism of these defects can be activated by applying either uniaxial strain or curvature to the graphene layer. All these results provide key information about formation and control of defect-induced magnetism in graphene and related materials.

  6. Title: Electric-Field Dependence of the Effective Dielectric Constant in Graphene

    Author(s): Santos E.J.G., Kaxiras E.

    Nano Letters, 13, No. 3, pp. 898-902 (22 January 2013)

    doi: 10.1021/nl303611v
    Abstract



    The dielectric constant of a material is one of the fundamental features used to characterize its electrostatic properties such as capacitance, charge screening, and energy storage capability. Graphene is a material with unique behavior due to its gapless electronic structure and linear dispersion near the Fermi level, which can lead to a tunable band gap in bilayer and trilayer graphene, a superconducting-insulating transition in hybrid systems driven by electric fields, and gate-controlled surface plasmons. All of these results suggest a strong interplay between graphene properties and external electric fields. Here we address the issue of the effective dielectric constant (ε) in N-layer graphene subjected to out-of-plane (Eext⊥) and in-plane (Eext∥) external electric fields. The value of ε has attracted interest due to contradictory reports from theoretical and experimental studies. Through extensive first-principles electronic structure calculations, including van der Waals interactions, we show that both the out-of-plane (ε⊥) and the in-plane (ε∥) dielectric constants depend on the value of applied field. For example, ε⊥ and ε∥ are nearly constant (∼3 and ∼1.8, respectively) at low fields (Eext < 0.01 V/Å) but increase at higher fields to values that are dependent on the system size. The increase of the external field perpendicular to the graphene layers beyond a critical value can drive the system to a unstable state where the graphene layers are decoupled and can be easily separated. The observed dependence of ε⊥ and ε∥ on the external field is due to charge polarization driven by the bias. Our results point to a promising way of understanding and controlling the screening properties of few-layer graphene through external electric fields.

  7. Title: Performance of Nonlocal Optics When Applied to Plasmonic Nanostructures

    Author(s): Stella L., Zhang P., Garcia-Vidal F.J., Rubio A., Garcia-Gonzalez P.,

    The Journal of Physical Chemistry C, 117, No. 17, pp. 8941- 8949 (2 May 2013)

    doi: 10.1021/jp401887y
    Abstract



    Semiclassical nonlocal optics based on the hydrodynamic description of conduction electrons might be an adequate tool to study complex phenomena in the emerging field of nanoplasmonics. With the aim of confirming this idea, we obtain the local And nonlocal optical absorption spectra in a model nanoplasmonic device in which there are spatial gaps between the components at nanometric and subnanometric scales. After a comparison against time dependent. density functional calculations, we conclude that hydrodynamic nonlocal optics provides absorption spectra exhibiting qualitative agreement but not quantitative accuracy. This lack of accuracy, which is manifest even in the limit where induced electric currents are not established between the constituents of the device, is mainly due to the poor description of induced electron densities.

  8. Title: Electrical Spin Switch in Hydrogenated Multilayer Graphene

    Author(s): Santos E.J.G.

    The Journal of Physical Chemistry C, 117, No. 12, pp. 6420-6425 (15 March 2013)

    doi: 10.1021/jp310463k
    Abstract



    Electric field control of magnetism has become increasingly important for the next generation of graphene-based spintronic devices. We predict that the magnetic moment induced by chemisorbed H atoms on the top layer of a few-layer graphene system is tunable by an external electric field. Through accurate first-principles electronic structure calculations, we show that this magnetoelectric effect is negligible in one-layer graphene, but becomes pronounced in bilayer and trilayer graphene, saturating in magnitude in quadrilayer graphene. The effect is due to shifting of the Dirac cone of the pure graphene layers relative to the bands of the hydrogenated layer, induced by the external field. The calculated magnetoelectric coefficient (α) has values comparable to those found for ferromagnetic films or perovskite interfaces. The value of α was also used to identify a half-metallic state at low gate bias, which suggests a new class of spin-polarized materials based on hydrogenated multilayer graphene. Our results point to an experimentally feasible way to create a magnetoelectric coupling in graphene using the interplay between covalent functionalization and electric fields.

  9. Title: Tuning the Electronic and Chemical Properties of Monolayer MoS2 Adsorbed on Transition Metal Substrates

    Author(s): Chen W., Santos E.J.G., Zhu W., Kaxiras E., Zhang Z.

    Nano Letters, 13, No. 2, pp. 509-514 (15 January 2013)

    doi: 10.1021/nl303909f
    Abstract



    Using first-principles calculations within density functional theory, we investigate the electronic and chemical properties of a single-layer MoS2 adsorbed on Ir(111), Pd(111), or Ru(0001), three representative transition metal substrates having varying work functions but each with minimal lattice mismatch with the MoS2 overlayer. We find that, for each of the metal substrates, the contact nature is of Schottky-barrier type, and the dependence of the barrier height on the work function exhibits a partial Fermi-level pinning picture. Using hydrogen adsorption as a testing example, we further demonstrate that the introduction of a metal substrate can substantially alter the chemical reactivity of the adsorbed MoS2 layer. The enhanced binding of hydrogen, by as much as ∼0.4 eV, is attributed in part to a stronger H–S coupling enabled by the transferred charge from the substrate to the MoS2 overlayer, and in part to a stronger MoS2-metal interface by the hydrogen adsorption. These findings may prove to be instrumental in future design of MoS2-based electronics, as well as in exploring novel catalysts for hydrogen production and related chemical processes.

  10. Title: Magnetoelectric effect in functionalized few-layer graphene

    Author(s): Santos E.J.G.

    Physical Review B, 87, No. 15, pp. 155440- (15 April 2013)

    doi: 10.1103/PhysRevB.87.155440
    Abstract



    We show that the spin moment induced by sp3-type defects created by different covalent functionalizations on a few-layer graphene structure can be controlled by an external electric field. Based on ab initio density functional calculations, including van der Waals interactions, we find that this effect has a dependence on the number of stacked layers and concentration of point defects, but the interplay of both with the electric field drives the system to a half-metallic state. The calculated magnetoelectric coefficient α has a value comparable to those found for ferromagnetic thin films (e.g., Fe, Co, Ni) and magnetoelectric surfaces (e.g., CrO2). The value of α also agrees with the universal value predicted for ferromagnetic half-metals and also points to a novel route to induce half-metallicity in graphene using surface decoration.

  11. Title: Carrier-Mediated Magnetoelectric Coupling in Functionalized Graphene

    Author(s): Santos E.J.G.

    ASC Nano, 7, No. 11, pp. 9927-9932 (11 November 2013)

    doi: 10.1021/nn4037877
    Abstract



    Materials in which magnetic order and electric fields can be coupled are of high fundamental and technological interests. Electrical control of magnetism is not only important for ultralow power consumption applications, but also enables control over intrinsic material properties that may have a major step in new developments in spintronic and magnetoelectric devices. Here we show that the magnetism induced by aryl-radicals covalently functionalized on top of multilayer graphene is sensitive to external electric fields which coupled to the interlayer charge-imbalance yields a strong magnetoelectric coupling. We used first-principles simulations, taking into account van der Waals dispersion forces, to show that this effect is thickness-dependent: it increases dramatically to thicker graphene structures reaching magnetoelectric coefficients comparable to perovskite interfaces. The interplay between electric fields and magnetism also leads functionalized graphene layers to a fully polarized spin state (half-metallicity). Efficiency nearly to 100% spin-polarization is observed at low electric bias, and the selection of the spin-conducting channel is determined by the field polarization.

  12. Title: Electrically Driven Tuning of the Dielectric Constant in MoS2 Layers

    Author(s): Santos E.J.G., Kaxiras E.

    ACS Nano, 7, No. 12, pp. 10741-10746 (11 November 2013)

    doi: 10.1021/nn403738b
    Abstract



    The properties of two-dimensional materials, such as molybdenum disulfide, will play an important role in the design of the next generation of electronic devices. Many of those properties are determined by the dielectric constant which is one of the fundamental quantities used to characterize conductivity, refractive index, charge screening, and capacitance. We predict that the effective dielectric constant (ε) of few-layer MoS2 is tunable by an external electric field (Eext). Through first-principles electronic structure calculations, including van der Waals interactions, we show that at low fields (Eext < 0.01 V/Å) ε assumes a nearly constant value ∼4 but increases at higher fields to values that depend on the layer thickness. The thicker the structure, the stronger the modulation of ε with the electric field. Increasing of the external field perpendicular to the dichalcogenide layers beyond a critical value can drive the system to an unstable state where the layers are weakly coupled and can be easily separated. The observed dependence of ε on the external field is due to charge polarization driven by the bias. Implications on the optical properties as well as on the electronic excitations are also considered. Our results point to a promising way of understanding and controlling the screening properties of MoS2 through external electric fields.

  13. 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
    Abstract



    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.

  14. Title: Demonstrating the Transferability and the Descriptive Power of Sketch-Map

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

    J. Chem. Theory Comput. , 9, pp. 1521- (2013)

    Abstract


  15. Title: The Role of Arg228 in the phosphorylation of galactokinase: The mechanism of GHMP kinases by QM/MM studies

    Author(s): Huang M., Li X., Zou J.W., Timson D.J.

    Biochemistry, 52, pp. 4858-4868 (2013)

    doi: 10.1021/bi400228e
    Abstract



    HMP kinases are a group of structurally related small molecule kinases. They have been found in all kingdoms of life and are mostly responsible for catalyzing the ATP-dependent phosphorylation of intermediary metabolites. Although the GHMP kinases are of clinical, pharmaceutical, and biotechnological importance, the mechanism of GHMP kinases is controversial. A catalytic base mechanism was suggested for mevalonate kinase that has a structural feature of the γ-phosphate of ATP close to an aspartate residue; however, for one GHMP family member, homoserine kinase, where the residue acting as general base is absent, a direct phosphorylation mechanism was suggested. Furthermore, it was proposed by some authors that all the GHMP kinases function by a similar mechanism. This controversy in mechanism has limited our ability to exploit these enzymes as drug targets and in biotechnology. Here the phosphorylation reaction mechanism of the human galactokinase, a member of the GHMP kinase family, was investigated using molecular dynamics simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B3LYP-D/AMBER99). The reaction coordinates were localized by potential energy scan using an adiabatic mapping method. Our results indicate that a highly conserved Glu174 captures Arg105 in the proximity of the α-phosphate of ATP, forming a H-bond network; therefore, the mobility of ATP in the large oxyanion hole is restricted. Arg228 functions to stabilize the negative charge developed at the β,γ-bridging oxygen of the ATP during bond cleavage. The reaction occurs via a direct phosphorylation mechanism, and the Asp186 in the proximity of ATP does not directly participate in the reaction pathway. Because Arg228 is not conserved among GHMP kinases, reagents which form interactions with Arg228, and therefore can interrupt its function in phosphorylation, may be developed into potential selective inhibitors for galactokinase.