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In this work, we have computationally modeled the adsorption of 1,3-diiodobenzene ( meta-diiodobenzene or m-DIB) on Cu(1 1 0) by means of density functional theory including van der Waals interaction using Grimme's method. We have compared the adsorption energies and structures of 23 possible configurations of the physisorbed molecule. Furthermore, we have simulated STM images for the four most stable configurations using the Tersoff-Hamann approach at different bias voltages. We find that all the adsorption orientations have comparable energy, and we discuss the relative probabilities of experimental observation. We find that the adsorption induces small distortions in the molecular structure of the adsorbate and in some cases an adsorption-induced symmetry breakdown occurs. We also find evidence that the most stable arrangement is actually a bistable system with interesting symmetry properties. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

We propose an atom-superposition-based method for simulating spin-polarized scanning tunneling microscopy (SP-STM) from first principles. Our approach provides bias-dependent STM images in high spatial resolution, with the capability of using either constant current or constant height modes of STM. In addition, topographic and magnetic contributions can clearly be distinguished, which are directly comparable to results of SP-STM experiments in the differential magnetic mode. Advantages of the proposed method are that it is computationally cheap, it is easy to parallelize, and it can employ the results of any ab initio electronic structure code. Its capabilities are illustrated for the prototype frustrated hexagonal antiferromagnetic system, Cr monolayer on Ag(111) in a noncollinear magnetic 120° Néel state. We show evidence that the magnetic contrast is sensitive to the tip electronic structure, and this contrast can be reversed depending on the bias voltage. [ABSTRACT FROM AUTHOR]

Based on a simple model for spin-polarized scanning tunneling spectroscopy (SP-STS), we study how tip magnetization and electronic structure affects the differential conductance (dI/dV) tunneling spectrum of an Fe(001) surface. We take into account energy dependence of the vacuum decay of electron states and tip electronic structure either using an ideal model or based on ab initio electronic structure calculation. In the STS approach, topographic and magnetic contributions to dI/dV can clearly be distinguished and analyzed separately. Our results suggest that the sensitivity of STS on a magnetic sample can be tuned and even enhanced by choosing the appropriate magnetic tip and bias set point, and the effect is governed by the effective spin polarization. [ABSTRACT FROM AUTHOR]

n equation proposed by Levy, Perdew and Sahni (Phys. Rev. A 30:2745, ) is an orbital-free formulation of density functional theory. However, this equation describes a bosonic system. Here, we analyze on a very fundamental level, how this equation could be extended to yield a formulation for a general fermionic distribution of charge and spin. This analysis starts at the level of single electrons and with the question, how spin actually comes into a charge distribution in a non-relativistic model. To this end we present a space-time model of extended electrons, which is formulated in terms of geometric algebra. Wave properties of the electron are referred to mass density oscillations. We provide a comprehensive and non-statistical interpretation of wavefunctions, referring them to mass density components and internal field components. It is shown that these wavefunctions comply with the Schrödinger equation, for the free electron as well as for the electron in electrostatic and vector potentials. Spin-properties of the electron are referred to intrinsic field components and it is established that a measurement of spin in an external field yields exactly two possible results. However, it is also established that the spin of free electrons is isotropic, and that spin-dynamics of single electrons can be described by a modified Landau-Lifshitz equation. The model agrees with the results of standard theory concerning the hydrogen atom. Finally, we analyze many-electron systems and derive a set of coupled equations suitable to characterize the system without any reference to single electron states. The model is expected to have the greatest impact in condensed matter theory, where it allows to describe an N-electron system by a many-electron wavefunction Ψ of four, instead of 3 N variables. The many-body aspect of a system is in this case encoded in a bivector potential. [ABSTRACT FROM AUTHOR]

Abstract: It has been shown that electron transitions, as measured in a scanning tunnelling microscope, are related to chemical interactions in a tunnelling barrier. Here, we show that the shape and apparent height of subatomic features in both, measurements of the attractive forces in an atomic force microscope, and measurements of the tunneling current between the Si(111) surface and an oscillating cantilever, depend directly on the available electron states of the silicon surface and the silicon tip. Simulations and experiments confirm that forces and currents show similar subatomic variations for tip-sample distances approaching the bulk bonding length. [Copyright &y& Elsevier]

Over the last few years it has become increasingly important to keep track of single electron processes on the atomic scale. The reason for this trend is the ultimate goal of building and testing molecular devices. The combination of scanning tunneling microscopy with powerful modeling is now capable of treating some of the most important issues in this regime. Issues like spin polarization and magnetization, imaging of single electron states, chemical bonding, and energy transport on the single electron scale. We expect that the ultimate goal of understanding and measuring most processes on the level of single electrons can be reached within the near future.Events on the atomic level are governed by electron properties. This fact has profound implications on the direction materials research takes, once it focuses on single molecules and atoms. [ABSTRACT FROM AUTHOR]

We propose a computationally efficient atom-superposition-based method for simulating spin-polarized scanning tunneling spectroscopy (SP-STS) on complex magnetic surfaces based on the sample and tip electronic structures obtained from first principles. We go beyond the commonly used local density of states (LDOS) approximation for the differential conductance dI/dV. The capabilities of our approach are illustrated for a Cr monolayer on a Ag(111) surface in a noncollinear magnetic state. We find evidence that the simulated tunneling spectra and magnetic asymmetries are sensitive to the tip electronic structure, and we analyze the contributing terms. Related to SP-STS experiments, we show a way to simulate two-dimensional differential conductance maps and qualitatively correct effective spin-polarization maps on a constant current contour above a magnetic surface. [ABSTRACT FROM AUTHOR]

Abstract: The aim of this work is to revisit the problem of acetylene adsorption on silicon (100). Extending previous theoretical work and including van der Waals forces explicitly in the simulations we remove existing ambiguities about the adsorption sites. The simulated adsorption energies and scanning tunneling microscopy contours are in good agreement with experimental data, they support the interpretation of a two-dimer feature at the surface as resulting from the adsorption of two individual molecules. It is also found that the simulated apparent heights agree with experimental values, if the actual bandgap of silicon is taken into account. [Copyright &y& Elsevier]

The adsorption of semifluorinated alkanethiols on Au/mica was studied by scanning tunneling microscopy (STM). The adlayer structure produced is based on a p(2×2) structure though lines of molecules displayed extensive kinks and bends. In addition, a considerable variation in the contrast of molecular features is found. Molecular modeling calculations confirm that, for the fluorinated thiols, inequivalently adsorbed molecules within a p(2×2) registry are present, an aspect that endows the local structure of the adlayer with a higher flexibility in comparison to nonfluorinated thiols, where one adsorption site is strongly favored in a ([Square_Root]3×[Square_Root]3)R30° structure. Simulated STM imaging on the optimized systems successfully recovered the effects on the molecular feature contrast induced by the flexibility of the fluorinated thiol adlayer. [ABSTRACT FROM AUTHOR]

Scanning probe instruments in conjunction with a very low temperature environment have revolutionized the ability of building, functionalizing, and analysing two dimensional interfaces in the last twenty years. In addition, the availability of fast, reliable, and increasingly sophisticated methods to simulate the structure and dynamics of these interfaces allow us to capture even very small effects at the atomic and molecular level. In this review we shall focus largely on metal surfaces and organic molecular compounds and show that building systems from the bottom up and controlling the physical properties of such systems is no longer within the realm of the desirable, but has become day to day reality in our best laboratories. [ABSTRACT FROM AUTHOR]

Balancing catalytic efficiency and stability is always a critical and challenge issue for energy related research. Here we propose a reaction reconstruction strategy to create active sites in the sub-layer of sulfur-modified transition metal-based catalysts, which can both achieve a high efficiency and exhibit an excellent stability for overall water splitting. The sub-layer active sites of S-Fe and S-Ni are evidenced by the bulk-sensitive X-ray absorption spectroscopy (XAS), while they cannot be observed by the surface-sensitive X-ray photoelectron spectroscopy. Theoretical calculations reveal that the sub-layer active sites can promote the water dissociation and accelerate the formation of high-energy peroxyl groups in anodes to achieve a high efficiency, while the surface layer can protect the sub-layer sites for excellent stability. The high stability is also confirmed by in-situ XAS. As a result, the obtained bi-functional catalyst as both cathode and anode can achieve a current density of 10 mA cm−2 for overall water splitting at a low cell voltage of 1.53 V (1.81 V for 100 mA cm−2), with an excellent stability over 200 h, which outperforms the benchmark Pt/C-RuO 2 /NF electrodes. [Display omitted] • Active sub-layer sites were created to both achieve a high efficiency and obtain an excellent stability. • Sub-layer sites were directly identified by X-ray absorption spectroscopy in-situ at each reaction stage. • Sub-layer sites can accelerate the formation of high-energy peroxyl groups to improve the performance. • The catalysts can achieve 10 mA cm−2 at a low cell voltage of 1.53 V for overall water splitting over 200 h. [ABSTRACT FROM AUTHOR]

The site-dependent g factor of a single magnetic molecule, with intramolecular resolution, is demonstrated for the first time by low-temperature, high-magnetic-field scanning tunneling microscopy of dehydrogenated Mn-phthalocyanine molecules on Au(111). This is achieved by exploring the magneticfield dependence of the extended Kondo effect at different atomic sites of the molecule. Importantly, an inhomogeneous distribution of the g factor inside a single molecule is revealed. Our results open up a new route to access local spin properties within a single molecule. [ABSTRACT FROM AUTHOR]

Abstract: In this work we provide a density functional theory (DFT) study of high coverage metastable benzene adsorption on a Si(100) surface. We examine intra- and inter-dimer interactions, phase ordering and in-dimer-row directional stability. From comparison of transition barriers (nudged elastic band calculations) and energetic stability between the single adsorptions and their high coverage cases we conclude that molecular interactions at high coverage neither influence the relative stability of metastable adsorption nor their reaction barrier. We investigate inter-dimer adsorption of benzene on the C-type defect and discuss its relevance to high coverage. It is found that the high coverage inter-dimer (ID) adsorption has increased stability, similar to C-defect adsorption, while the other mixed cases of ID are less likely to occur. All of the presented calculations are performed in an extended framework with newly implemented Grimme corrections to account for van der Waals interactions (DFT-D), which are benchmarked against standard DFT results. Additionally we present a scanning tunneling microscopy study for the high coverage adsorptions together with its structural analysis, through which we aid high coverage STM identification. [Copyright &y& Elsevier]

Silicene, a two-dimensional (2D) honeycomb structuresimilar tographene, has been successfully fabricated on an Ir(111) substrate.It is characterized as a (√7×√7) superstructurewith respect to the substrate lattice, as revealed by low energy electrondiffraction and scanning tunneling microscopy. Such a superstructurecoincides with the (√3×√3) superlattice of silicene.First-principles calculations confirm that this is a (√3×√3)silicene/(√7×√7)Ir(111)configuration and that it has a buckled conformation. Importantly,the calculated electron localization function shows that the siliconadlayer on the Ir(111) substrate has 2D continuity. This work providesa method to fabricate high-quality silicene and an explanation forthe formation of the buckled silicene sheet. [ABSTRACT FROM AUTHOR]

Adsorbates on metals, but not previously on semiconductors, have been observed to display long-range repulsive interactions. On metals, due to efficient dissipation, the repulsions are weak, typically on the order of S meV at 10 A. On the 7 x 7 reconstruction of the Si(111) surface, charge transport through the surface has been demonstrated by others using charge injection by STM tips. Here we show that for both physisorbed brominated molecules, and for chemisorbed Br-atoms, induced charge- transfer in the Si(111) -7 × 7 surface can lead to a strong repulsive interaction between adsorbates, calculated as 200 meV at 13.4 Å. This large repulsive interaction must be channeled through the surface since it causes widely spaced "one-per-corner-hole" patterns of physisorption (three cases-directly observed here) and subsequent chemi- sorption (four cases observed). The patterns were observed by ultrahigh vacuum scanning tunneling microscopy for four different brominated hydrocarbon adsorbates; 1,2-dibromoethane, 1 -bromopropane, 1 -bromopentane, and bromobenzene, deposited individually on the surface. In every case, adsorbates were overwhelmingly more likely to be found singly than multiply adjacent to a corner-hole, constituting a distinctive pattern having a probability p = 7 × 10-5 compared to a random distribution. [ABSTRACT FROM AUTHOR]

The recoil of adsorbates away (desorption) and towards (reaction) surfaces is well known. Here, we describe the long-range recoil of adsorbates in the plane of a surface, and accordingly the novel phenomenon of reactions occurring at a substantial distance from the originating event. Three thermal and three electron-induced surface reactions are shown by scanning tunnelling microscopy to propel their physisorbed ethylenic products across the rough surface of Si(100) over a distance of up to 200 Å before an attachment reaction. The recoil energy in the ethylenic products comes from thermal exoergicity or from electronic excitation of chemisorbed alkenes. We propose that the mechanism of migration is a rolling motion, because the recoiling molecule overcomes raised surface obstacles. Electronic excitation of propene causes directional recoil and often end-to-end inversion, suggesting cartwheeling. Ab initio calculations of the halogenation and electron-induced reactions support a model in which asymmetric forces between the molecule and the surface induce rotation and therefore migration. [ABSTRACT FROM AUTHOR]

The fabrication of nano devices at surfaces makes conflicting demands of mobility for self-assembly (SA) and immobility for permanence. The solution proposed in earlier work from this laboratory involved pattern formation in physisorbed molecules by SA, followed by localized reaction to chemically imprint the pattern substantially unchanged, a procedure we termed molecu- lar-scale imprinting (MSl). Here, as proof of generality we ex- tended this procedure, previously applied to imprinting circles on Si(111)-7x7, to SA lines of 1-chioropentane (CP) on Si(100)-2x1. The physisorbed lines consisted of pairs of CP that grew perpendi- cular to the Si dimer rows, as shown by scanning tunneling micro- scopy and ab initio theory. Chemical reaction of these lines with the surface was triggered in separate experiments by three different modes of energization: heat, electrons, or light. In all cases the CP molecules underwent MSI with a Si atom beneath so that the physisorbed lines of CP pairs were imprinted as chemisorbed lines of Cl pairs. [ABSTRACT FROM AUTHOR]

Oxygen vacancies on metal oxide surfaces have long been thought to play a key role in the surface chemistry. Such processes have been directly visualized in the case of the model photocatalyst surface TiO2(110) in reactions with water and molecular oxygen. These vacancies have been assumed to be neutral in calculations of the surface properties. However, by comparing experimental and simulated scanning tunneling microscopy images and spectra, we show that oxygen vacancies act as trapping centers and are negatively charged. We demonstrate that charging the defect significantly affects the reactivity by following the reaction of molecular oxygen with surface hydroxyl formed by water dissociation at the vacancies. Calculations with electronically charged hydroxyl favor a condensation reaction forming water and surface oxygen adatoms, in line with experimental observations. This contrasts with simulations using neutral hydroxyl where hydrogen peroxide is found to be the most stable product. [ABSTRACT FROM AUTHOR]

The controlled imprinting of surfaces with specified patterns is important in the development of nanoscale devices. Previously, such patterns were created using self-assembled physisorbed adsorbate molecules that can be stabilized on the surface by subsequent chemical bonding. Here we show a first step towards use of the bonding within a surface to propagate reactions for patterning, namely the cooperative reaction of adjacent silicon atoms. We exploit the double-bonded silicon dimer pairs present on the surface of Si(100)-2×1 and show that the halogenation of one silicon atom (induced by electrons or heat) results in cooperative halogenation of the neighbouring silicon atom with unit efficiency. The reactants used were two 1-halopentane molecules physisorbed over a pair of silicon atoms. This cooperative pair of halogenation reactions was shown by ab initio calculation to be sequential on a timescale of femtoseconds. [ABSTRACT FROM AUTHOR]

Molecule-based functional devices on surfaces may take advantage of bistable molecular switches. The conformational dynamics and efficiency of switches are radically different on surfaces compared to the liquid phase. We present a design of molecular layers which enables bistable switching on a surface and, for the first time, demonstrate control of a single switch in a dense and ordered array at the spatial limit. Up and down motion of a central Sn ion through the frame of a phthalocyanine molecule is achieved via resonant electron or hole injection into molecular orbitals. [ABSTRACT FROM AUTHOR]

One-dimensional nanostructures at silicon surfaces have potential applications in nanoscale devices. Here we propose a mechanism of dipole-directed assembly for the growth of lines of physisorbed dipolar molecules. The adsorbate chosen was a halide, in preparation for the patterned imprinting of halogen atoms. Using scanning tunnelling microscopy, physisorbed 1,5-dichloropentane on Si(100)-2×1 was shown to self-assemble at room temperature into molecular lines that grew predominantly perpendicular to the Si-dimer rows. Line formation was triggered by the displacement of surface charge by the dipolar adsorbate. Experimental and simulated scanning tunnelling microscopy images were in agreement for a range of positive and negative bias voltages. The geometry of the physisorbed molecules and nature of their binding were evident from the scanning tunnelling microscopy images, as interpreted by scanning tunnelling microscopy simulation. [ABSTRACT FROM AUTHOR]

The controlled anchoring of molecular building blocks on appropriate templates is a major prerequisite for the rational design and fabrication of supramolecular architectures on surfaces. We report on a particularly selective adsorption process of hexa-peri-hexabenzocoronene on Au(111), which leads to well-controlled adsorption position and orientation of the polycyclic aromatic hydrocarbons. Scanning tunneling microscopy reveals selective adsorption on monatomic steps in the fcc stacking regions with a specific orientation of 18° between the molecular axis and the step normal. Ab initio calculations for various adsorption sites reveal the lowest total energy for adsorption on a kink site. Energy considerations and the excellent agreement between experimental and simulated images show that adsorption on kink sites is responsible for the specific adsorption angle. [ABSTRACT FROM AUTHOR]

We have observed on-off switching of scanning tunneling microscope current flow to silicon adatoms of the Si(111)-(7 × 7) surface that are enclosed within a bistable dimeric corral of self-assembled chlorododecane molecules. These thermally activated oscillations amounted to an order of magnitude change in the current. Theory showed that small changes in molecular configuration could cause alterations in the corralled adatom's electronic energy by as much as 1 eV due to local field effects, accounting for the observed current switching. [ABSTRACT FROM AUTHOR]

With the approach presented herein, a large aromatic π-system is synthesized, which shows extraordinarily high solubility and an effective suppression of aggregation. This was due to a distortion of the aromatic core by bulky tert-butyl groups and the solubilizing effects of alkyl chains in the corona of the aromatic core. Therefore not only the processing and cleaning of the materials with standard laboratory techniques became possible, but moreover the first structure-rich UV/vis and a resolved ¹H NMR spectra for an aromatic system two times larger than hexa-peri-hexabenzocoronene were recorded. The bulk properties in an extruded fiber as well as on the surface showed a columnar self-assembly including a phase in which a homeotropic alignment on a substrate was observed, which turns the material into an interesting candidate for future applications in electronic devices. [ABSTRACT FROM AUTHOR]

By means of scanning tunneling microscopy and density functional theory calculations, we studied the water formation reaction on the Rh(110) surface when exposing the (2 × 1 )p2mg-O structure to molecular hydrogen, characterizing each of the structures that form on the surface during the reaction. First the reaction propagates on the surface as a wave front, removing half of the initial oxygen atoms. The remaining 0.5 monolayers of O atoms rearrange in pairs, forming a c(2 × 4) structure. Second, as the reaction proceeds, areas of an intermediate structure with c(2 × 2) symmetry appear and grow at the expense of the c(2 × 4) phase, involving all the oxygen atoms present on the surface. Afterward, the c(2 × 2) islands shrink, indicating that complete hydrogenation occurs at their edges, leaving behind a clean rhodium substrate. Two possible models for the c(2 × 2) structure, where not only the arrangement but also the chemical identity is different, are given. The first one is a mixed H + O structure, while the second one resembles the half-dissociated water layer already proposed on other metal surfaces. In both models, the high local oxygen coverage is achieved by the formation of a hexagonal network of hydrogen bonds. [ABSTRACT FROM AUTHOR]

Electrical transport through molecules has been much studied since it was proposed that individual molecules might behave like basic electronic devices, and intriguing single-molecule electronic effects have been demonstrated. But because transport properties are sensitive to structural variations on the atomic scale, further progress calls for detailed knowledge of how the functional properties of molecules depend on structural features. The characterization of two-terminal structures has become increasingly robust and reproducible, and for some systems detailed structural characterization of molecules on electrodes or insulators is available. Here we present scanning tunnelling microscopy observations and classical electrostatic and quantum mechanical modelling results that show that the electrostatic field emanating from a fixed point charge regulates the conductivity of nearby substrate-bound molecules. We find that the onset of molecular conduction is shifted by changing the charge state of a silicon surface atom, or by varying the spatial relationship between the molecule and that charged centre. Because the shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature. [ABSTRACT FROM AUTHOR]

Thermal (300 K) and electron-induced reactions of benzene (Bz), chlorobenzene (ClPh), 1,2-dichlorobenzene (1,2-diClPh) and 1,4-dichlorobenzene (1,4-diClPh) with Si(1 0 0)2 × 1 have been examined by scanning tunneling microscopy (STM). Thermal reactions of Bz yielded predominantly the quadruply-σ-bound tight bridge, TB, configuration on top of the Si dimer-rows, For ClPh and 1,2-diClPh, which resembled one another, thermal reaction led with 45–50% yield to the doubly-σ-bound butterfly, BF, configuration, also on top of the dimer-row, and with 20% yield to a novel ‘displaced’, D, configuration to one side of a dimer-row. The adsorbate 1,4-diClPh was alone in favouring a configuration in which neighbouring dimer-rows were ‘linked’ (L) by a bright-feature centrally located between the dimer-rows. By ab initio calculation, we interpret D as due to the rupture of one C–Cl bond per adsorbate molecule, and L to the rupture of two C–Cl’s. The breaking of this weak bond is followed in the former case by attachment of the aromatic ring to one dimer-row, and in the latter to attachment to two adjacent dimer-rows. Application of a −5 V voltage pulse to the STM tip substantially increased the percentage of row-linking structures, L, for 1,4-diClPh, but neither −5 V nor +4–6 V volt pulses resulted in L-type binding of Bz. The postulated L product of 1,4-diClPh, with an aromatic ring linking the two inner Si atoms of adjacent dimer-rows and the two Cl’s on the outer Si atoms of the dimer-rows, is shown to be in accord with ab initio simulation of the observed STM image. [Copyright &y& Elsevier]

Describes the behavior of a chiral molecule with a defined nickel (110) surface. Creation of highly enantioselective heterogeneous catalysts; Use of the reflection absorption infrared spectroscopy; Emphasis in surface science research.

Chloropentane forms asymmetric (‘A’) and symmetric (‘S’) pairs on Si(100)-2×1, differing in the direction of curvature of one pentane tail. Surprisingly this renders the rate of thermal reaction of ‘A’ fifteen times greater than ‘S’ in chlorinating room-temperature silicon. Correspondingly, for electron-induced reaction the energy threshold for Ais 1 eV less than for S. [ABSTRACT FROM AUTHOR]

The article presents a study which determines the supramolecular patterns during electron interference and direct intermolecular interactions. It indicates that surface-state electrons of (111) surfaces of noble metals are considered as model systems for two-dimensional free electron gases. The study has fabricated two-dimensional crystals of CoPc with plane symmetry groups by using a combination of quantum interference of surface state electrons.