On-Surface Assembly of Au-Dicyanoanthracene Coordination Structures on Au(111)

On-surface metal-organic coordination provides a promising way for synthesizing different two-dimensional lattice structures that have been predicted to possess exotic electronic properties. Using scanning tunneling microscopy (STM) and spectroscopy (STS), we studied the supramolecular self-assembly of 9,10-dicyanoanthracene (DCA) molecules on the Au(111) surface. Close-packed islands of DCA molecules and Au-DCA metal-organic coordination structures coexist on the Au(111) surface. Ordered DCA₃Au₂ metal-organic networks have a structure combining a honeycomb lattice of Au atoms with a kagome lattice of DCA molecules. Low-temperature STS experiments demonstrate the presence of a delocalized electronic state containing contributions from both the gold atom states and the lowest unoccupied molecular orbital of the DCA molecules. These findings are important for the future search of topological phases in metal-organic networks combining honeycomb and kagome lattices with strong spin-orbit coupling in heavy metal atoms.     

Imaging in the modern age

This report of the 2011 James L. Waters Symposium at Pittcon 2011 highlights the powerful imaging technologies of electron microscopy (EM) and ion microscopy (IM). The four speakers each provided a window into a specific subset of the field:

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David Bell described the history, development, application, and commercialization of transmission EM (TEM) and scanning TEM (STEM);

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David Martin presented the challenges and methodologies of imaging ordered polymers and biomaterials with TEM;

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Joseph Michael explained the history of the commercialization of scanning EM (SEM) and its modern applications; and,

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David Joy, who submitted his talk in absentia, provided a history of EM and a summary of the advantages of IM versus EM.

     

Ions Can Move a Proton‐Coupled Electron‐Transfer Reaction into Tunneling Regime

The effects of charged species on proton‐coupled electron‐transfer (PCET) reaction should be of significance for understanding/application of important chemical and biological PCET systems. Such species can be found in proximity of activated complex in a PCET reaction, although they are not involved in the charge transfer process. Reported here is the first study of the above‐mentioned effects. Here, the effects of Na⁺, K⁺, Li⁺, Ca²⁺, Mg²⁺, and Me₄N⁺ observed in PCET reaction of ascorbate monoanions with hexacyanoferrate(III) ions in H₂O reveal that, in presence of ions, this over‐the‐barrier reaction entered into tunneling regime. The observations are: a) dependence of the rate constant on the cation concentration, where the rate constant is 71 (at I = 0.0023), and 821 (at 0.5M K⁺), 847 (at 1.0M Na⁺), and 438 M ^?1 s^?1 (at 0.011M Ca²⁺); b) changes of kinetic isotope effect (KIE) in the presence of ions, where k_H/k_D=4.6 (at I = 0.0023), and 3.4 (in the presence of 0.5M K⁺), 3.3 (at 1.0M Na⁺), 3.9 (at 0.001M Ca²⁺), and 3.9 (at 0.001M Mg²⁺), respectively; c) the isotope effects on Arrhenius pre‐factor where A_H/A_D=0.97 (0.15) in absence of ions, and 2.29 (0.60) (at 0.5M Na⁺), 1.77 (0.29) (at 1.0M Na⁺), 1.61 (0.25) (at 0.5M K⁺), 0.42 (0.16) (at 0.001M Ca²⁺) and 0.16 (0.19) (at 0.001M Mg²⁺); d) isotope differences in the enthalpies of activation in H₂O and in D₂O, where ΔΔH^?(D,H)=3.9 (0.4) kJ mol^?1 in the absence of cations, 1.3 (0.6) at 0.5M Na⁺, 1.8 (0.4) at 0.5M K⁺, 1.5 (0.4) at 1.0M Na⁺, 5.5 (0.9) (at 0.001M Ca²⁺), and 7.9 (2.8) (at 0.001M Mg²⁺) kJ mol^?1; e) nonlinear proton inventory in reaction. In the H₂O/dioxane 1 : 1, the observed KIE is 7.8 and 4.4 in the absence and in the presence of 0.1M K⁺, respectively, and A_H/A_D=0.14 (0.03). The changes when cations are present in the reaction are explained in terms of termolecular encounter complex consisting of redox partners, and the cation where the cation can be found in a near proximity of the reaction‐activated complex thus influencing the proton/electron double tunneling event in the PCET process. A molecule of H₂O is involved in the transition state. The resulting ‘configuration’ is more ‘rigid’ and more appropriate for efficient tunneling with Na⁺ or K⁺ (extensive tunneling observed), i.e., there is more precise organized H transfer coordinate than in the case of Ca²⁺ and Mg²⁺ (moderate tunneling observed) in the reaction.     

Simulated annealing‐based optimal control over tunneling process through SDWP and Eckart barrier: A momentum basis representation

For a reaction to proceed via tunneling mechanism, it is essential that the reactants will cross the potential barrier (E_P), where its initial energy (E₀) is below the potential barrier E_P. Tunneling probability τ is defined as the probability of having momentum higher than k_m, where . In the momentum basis representation, τ can be directly calculated by integrating from the limit k_m to infinity, where is the wave function in the momentum space. Instead of the continuous basis, if we chose momentum grid space, τ can be expressed as . Our target here is to increase this τ by applying a polychromatic field, so that the reaction rate can be enhanced. By applying Simulated Annealing technique we have designed some polychromatic electric fields, spatially symmetric and asymmetric type, which enhances the tunneling rate in symmetric double well system and Eckart barrier confined in an infinite well.     

Intermolecular H···O═C bonds induced 2D self‐assembly of thiophene based diketopyrrolopyrrole derivative

Compounds with diketopyrrolopyrrole (DPP) and thiophene moieties have attracted considerable attention because of their promising charge transport properties. The molecular conformation and self‐assembly of 2,5‐dihexadecyl‐3,6‐di(thiophen‐2‐yl)‐2,5‐dihydropyrrolo[3,4‐c]pyrrole‐1,4‐dione (TDPP‐C16) molecule have been investigated by scanning tunneling microscopy and density functional theory alculation. The TDPP‐C16 molecules adsorb with their optimized S‐shaped conformation and form a zipper‐like pattern on highly oriented pyrolytic graphite surface. R and S rotated structures are observed. The nanostructure is dominated by intermolecular double hydrogen bonds between C═O of the DPP units and hydrogen atom of thiophene rings in the neighboring molecules in each row. Atomic force microscopy and density functional theory calculation also display the existence of strong intermolecular hydrogen bonding. The results provide molecular evidence for the intermolecular interactions of the surface structure, which could benefit to the design of the organic semiconducting materials and understanding of underlying principle of charge transfer process. Copyright © 2017 John Wiley & Sons, Ltd.     

Monolayer Rectifiers

Molecular-scale electronics has now been enriched by the discovery that molecules, studied singly by scanning tunneling spectroscopy, or a large array of those molecules, studied in parallel as a Langmuir-Blodgett monolayer between metal electrodes, exhibit rectification, i.e., an asymmetric current as a function of applied voltage.This asymmetry can come, first, from work function differences between two dissimilar metals or the metal-molecule interfaces (Schottky barriers), second from an asymmetric placement of the chromophore between the two metal electrodes, and third, from an asymmetry of the molecular orbitals of the molecule.This third, electronic origin of rectification, first proposed by Aviram and Ratner in 1974, and confirmed in the work reported here, gives us hope that, not too many years from now, molecules can form the basis of ultra-small yet ultra-fast electronic devices and integrated circuits.     

Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer

Recent experimental and theoretical studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying chemical barrier crossing. Here, we have examined portions of a proposed network in dihydrofolate reductase (DHFR) using quantum mechanics/molecular mechanics simulations. The simulations use a hybrid quantum mechanics‐molecular mechanics approach with a recently developed semiempirical AM1‐SRP Hamiltonian that provides accurate results for this reaction. The simulations reproduce experimentally determined catalytic rates for the wild type and distant mutants of E. coli DHFR, underscoring the accuracy of the simulation protocol. Additionally, the simulations provide detailed insight into how residues remote from the active site affect the catalyzed chemistry, through changes in the thermally averaged properties along the reaction coordinate. The mutations do not greatly affect the structure of the transition state near the bond activation, but we observe differences somewhat removed from the point of C? H cleavage that affect the rate. The mutations have global effects on the thermally averaged structure that propagate throughout the enzyme and the current simulations highlight several interactions that appear to be particularly important. © 2014 Wiley Periodicals, Inc.     

Quantum dot resonant tunneling FET on graphene

At this paper a field effect transistor based on graphene nanoribbon (GNR) is modeled. Like in most GNR-FETs the GNR is chosen to be semiconductor with a gap, through which the current passes at on state of the device. The regions at the two ends of GNR are highly n-type doped and play the role of metallic reservoirs so called source and drain contacts. Two dielectric layers are placed on top and bottom of the GNR and a metallic gate is located on its top above the channel region. At this paper it is assumed that the gate length is less than the channel length so that the two ends of the channel region are un-gated. As a result of this geometry, the two un-gated regions of channel act as quantum barriers between channel and the contacts. By applying gate voltage, discrete energy levels are generated in channel and resonant tunneling transport occurs via these levels. By solving the NEGF and 3D Poisson equations self consistently, we have obtained electron density, potential profile and current. The current variations with the gate voltage give rise to negative transconductance.     

Nanoclusters of TiO2 wetted with gold

We combined scanning tunneling microscopy and density functional theory to establish the structure-functionality relationship for nanometer-sized defects on TiO₂(1 1 0). Three-angstrom high topographically distinct dots are ascribed to stoichiometric TiO₂ nanoclusters with low coordination numbers. The under-coordinated O atoms of the nanocluster, with surface O atoms, provide exceptionally strong binding sites for Au nanoparticles. Our atomistic model elucidates a number of characteristics salient to low temperature CO oxidation by Au nanoparticles.