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Contacting a Conjugated Molecule with a Surface Dangling Bond Dimer on a Ge(001):H Surface Allows Imaging of the Hidden Ground Electronic State.
Abstract
Fabrication of single-molecule logic devices requires controlled manipulation of molecular states with atomic-scale precision. Tuning molecule-substrate coupling is achieved here by the reversible attachment of a prototypical planar conjugated organic molecule to dangling bonds on the surface of a hydrogenated semiconductor. We show that the ground electronic state resonance of a Y-shaped polyaromatic molecule physisorbed on a defect-free area of a fully hydrogenated surface cannot be observed by scanning tunneling microscopy (STM) measurements because it is decoupled from the Ge bulk states by the hydrogen-passivated surface. The state can only be accessed by STM if the molecule is contacted with the substrate by a dangling bond dimer. The reversibility of the attachment processes will be advantageous in the construction of surface atomic-scale circuits composed of single molecule devices interconnected by the surface dangling bond wires.
... Similarly, it has been reported that the passivation of semiconducting materials, which removes surface dangling bonds and significantly reduces surface reactivity, may also provide a sufficiently insulating layer for an efficient decoupling of molecular structures from the substrate influence. Among such surfaces, hydrogen-passivated Si(001):H [22,23], Si(111):H [24], and Ge(001):H [25][26][27][28] surfaces are most commonly mentioned. Iron phthalocyanines (FePc) have been studied on Si(111):H [24] and it was concluded that the molecules are weakly coupled to the substrate. ...
... Therefore, our results suggest that the FePc islands are well isolated electronically from the influence of the underlying germanium by the passivating hydrogen layer. This is in line with previous reports showing that other organic compounds are well decoupled from the surface by hydrogen, unless they are contacted with the underlying semiconductor through atomic-scale defects, that is, DBs or DBDs [25]. ...
... This allows us to draw the conclusion that the FePc molecules recorded in Figure 6a were immobilized by DBDs. It is worth noting that the preferred localization of polycyclic molecules on DBDs on Ge(001):H has already been reported for starphenes [25,30,34] and tribiphyenylenes [35]. ...
Self-assembly of iron(II) phthalocyanine (FePc) molecules on a Ge(001):H surface results in monolayer islands extending over hundreds of nanometers and comprising upright-oriented entities. Scanning tunneling spectroscopy reveals a transport gap of 2.70 eV in agreement with other reports regarding isolated FePc molecules. Detailed analysis of single FePc molecules trapped at surface defects indicates that the molecules stay intact upon adsorption and can be manipulated away from surface defects onto a perfectly hydrogenated surface. This allows for their isolation from the germanium surface.
... Indeed, the STM images acquired at voltages above the first negative and positive voltage resonance are dominated by the molecular highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO), respectively. This indicates that the previous assignment of the first observed peak in STS to a lower lying molecular orbital (HOMOÀ2 a, b) and the assumed impossibility to visualize with STM the HOMO/HOMOÀ1 states in ref. 26 were incorrect. Therefore here, we present a new insight into the properties of the weakly adsorbed molecules on a Ge(001):H surface. ...
... We investigate these molecules on the passivated surface to allow comparison with the molecules positioned on a single DB. 26 Molecules on fully passivated surface areas tend to adopt one of two possible planar geometries, which differ only by a small displacement across the surface rows and have been discussed in ref. 26. In both geometries one arm of the molecule is pointing in the direction perpendicular to surface rows (Fig. 3). ...
... However, at liquid helium temperature the molecules manipulated and located on the defect-free Ge(001):H surface areas are sufficiently stable to be imaged. We investigate these molecules on the passivated surface to allow comparison with the molecules positioned on a single DB. 26 Molecules on fully passivated surface areas tend to adopt one of two possible planar geometries, which differ only by a small displacement across the surface rows and have been discussed in ref. 26. In both geometries one arm of the molecule is pointing in the direction perpendicular to surface rows (Fig. 3). ...
Controlling the strength of the coupling between organic molecules and single atoms provides a powerful tool for tuning electronic properties of single-molecule devices. Here, using scanning tunneling microscopy and spectroscopy (STM/STS) supported by theoretical modeling, we study the interaction of a planar organic molecule (trinaphthylene) with a hydrogen-passivated Ge(001):H substrate and a single dangling bond quantum dot on that surface. The electronic structure of the molecule adsorbed on the hydrogen-passivated surface is similar to the gas phase structure and the measurements show that HOMO and LUMO states contribute to the STM filled and empty state images, respectively. Furthermore, we show that the electronic properties are not significantly affected when the molecule is attached to the single dangling bond, which is in contrast with the strong interaction of the molecule with a dangling bond dimer. Our results show that the dangling bond quantum dots could stabilize organic molecules on a hydrogenated semiconductor without affecting their originally designed gas phase electronic properties. Together with the ability to laterally manipulate the molecules on the surface, this will be advantageous in the construction of single-molecule devices, where the coupling and positioning of the molecules on the substrate could be tuned by a proper design of the surface quantum dot arrays, comprising both single and dimerized dangling bonds.
... [35] This is also consistent with the DB being a reactive chemical center on the chemically inert H-Si surface where deposited molecules can selectively adsorb. [36,37] Similar to what was reported previously for the case of gold atoms adsorbed on NaCl over Cu(111), [38,39] the short range electrostatic force due to the localized negative charge on the DB [11,13,14] is most likely the main contributor to the large tip-sample interaction on the DB. (Figure 4-b), each hydrogen atom decorating a silicon atom clearly appears and follows the dimer structure of the 2×1 reconstruction. ...
We report the mechanically induced formation of a silicon-hydrogen covalent bond and its application in engineering nanoelectronic devices. We show that using the tip of a non-contact atomic force microscope (NC-AFM), a single hydrogen atom could be vertically manipulated. When applying a localized electronic excitation, a single hydrogen atom is desorbed from the hydrogen passivated surface and can be transferred to the tip apex as evidenced from a unique signature in frequency shift curves. In the absence of tunnel electrons and electric field in the scanning probe microscope junction at 0 V, the hydrogen atom at the tip apex is brought very close to a silicon dangling bond, inducing the mechanical formation of a silicon-hydrogen covalent bond and the passivation of the dangling bond. The functionalized tip was used to characterize silicon dangling bonds on the hydrogen-silicon surface, was shown to enhance the scanning tunneling microscope (STM) contrast, and allowed NC-AFM imaging with atomic and chemical bond contrasts. Through examples, we show the importance of this atomic scale mechanical manipulation technique in the engineering of the emerging technology of on-surface dangling bond based nanoelectronic devices.
... The insulating layer decouples the molecules electronically from the metal surface while the layer (∼ fewÅ) is still sufficiently thin to allow STM operation without difficulties. Ultrathin layers of conventional insulating materials, for example, alkali-halides [137][138][139], metal-oxides [22,76,140,141], metal-nitrides [142,143], passivated semiconductors [144,145] have been used to study the properties of single atoms, single molecules, and various aspects of molecular electronics in general. Usage of twodimensional films of noble gases [146,147], molecules [148][149][150][151][152] also serve similar purpose of decoupling molecules from the metal surface. ...
Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional materials is a developing field and has already resulted in the discovery of several rich and interesting phenomena. Here, we review this progress with an emphasis on the electronic properties of the adsorbates and the substrate in well-defined systems, as unveiled by scanning tunneling microscopy (STM). We cover three aspects of the self-assembly. The first one focuses on non-covalent self-assembly dealing with site-selectivity due to inherent moire pattern present on 2D materials deposited on substrates. Modification of intermolecular interactions and molecule-substrate interactions influences the assembly drastically and 2D materials can also be used as a platform to carry out covalent and metal-coordinated assembly. The second part deals with the electronic properties of molecules adsorbed on 2D materials. By virtue of being inert and possessing low density of states near the Fermi level, 2D materials decouple molecules electronically from the underlying metal substrate and allow high-resolution spectroscopy and imaging of molecular orbitals. The moire pattern on the 2D materials causes site-selective gating and charging of molecules in some cases. The last section covers the effects of self-assembled organic molecules on the electronic properties of graphene as revealed by spectroscopy and electrical transport measurements. Non-covalent functionalization of 2D materials has already been applied for their application as catalysts and sensors. With the current surge of activity on building van der Waals heterostructures from 2D materials, molecular self-assembly has the potential to add an extra level of flexibility and functionality for applications ranging from flexible electronics and OLEDs to novel electronic devices and spintronics.
... Local hydrogen desorption, induced with the aid of a scanning tunnelling microscope (STM) tip, on the hydrogen-passivated (1×2)-reconstruction of the Si(001) and Ge(001) substrates [hereafter Si/Ge(001):H] can be used to reproducibly and rapidly create dangling-bond (DB) arrays defined with atomic precision. [1][2][3][4] This is a powerful method that allows one to directly pattern planar electronic devices and circuitry made out of DBs, [5][6][7][8][9][10] and to create templates for anchoring molecular networks [11][12][13][14][15] or for selective dopant incorporation. [16][17][18][19] DB arrays have a very rich and complex behaviour, ex-hibiting several metastable charge-and spinstates, 4,[20][21][22][23][24][25][26][27] as well as small polaron and soliton formation. ...
We have theoretically investigated the electronic properties of neutral and n-doped dangling bond (DB) quasi-one-dimensional structures (lines) in the Si(001):H and Ge(001):H substrates with the aim of identifying atomic-scale interconnects exhibiting metallic conduction for use in on-surface circuitry. Whether neutral or doped, DB lines are prone to suffer geometrical distortions or have magnetic ground-states that render them semiconducting. However, from our study we have identified one exception -- a dimer row fully stripped of hydrogen passivation. Such a DB-dimer line shows an electronic band structure which is remarkably insensitive to the doping level and, thus, it is possible to manipulate the position of the Fermi level, moving it away from the gap. Transport calculations demonstrate that the metallic conduction in the DB-dimer line can survive thermally induced disorder, but is more sensitive to imperfect patterning. In conclusion, the DB-dimer line shows remarkable stability to doping and could serve as a one-dimensional metallic conductor on n-doped samples.
... It undergoes a first-order transition from a fluid phase to a solid phase with face-centered cubic packing [15,16]. More complicated shapes such as cubes, rhombohedra [17], or in general three-dimensional regular polyhedra or corner-rounded polyhedra [18][19][20] have been studied as more realistic models for experimental selfassembling systems [21][22][23], applications to drug delivery where shape of the carrier may decide its effectiveness [24], biological material like immunoglobin [25], molecular logic gates [26][27][28], etc. Being able to predict the macroscopic material behavior from knowing its constituent building blocks would help to engineer the synthesis of materials with prescribed properties [29,30]. ...
We study the phase diagram of a lattice gas of 2×2×1 hard plates on the three-dimensional cubic lattice. Each plate covers an elementary plaquette of the cubic lattice, with the constraint that a site can belong to utmost one plate. We focus on the isotropic system, with equal fugacities for the three orientations of plates. We show, using grand canonical Monte Carlo simulations, that the system undergoes two phase transitions when the density of plates is increased: the first from a disordered fluid phase to a layered phase, and the second from the layered phase to a sublattice-ordered phase. In the layered phase, the system breaks up into disjoint slabs of thickness two along one spontaneously chosen Cartesian direction, corresponding to a twofold (Z2) symmetry breaking of translation symmetry along the layering direction. Plates with normals perpendicular to this layering direction are preferentially contained entirely within these slabs, while plates straddling two adjacent slabs have a lower density, thus breaking the symmetry between the three types of plates. We show that the slabs exhibit two-dimensional power-law columnar order even in the presence of a nonzero density of vacancies. In contrast, interslab correlations of the two-dimensional columnar order parameter decay exponentially with the separation between the slabs. In the sublattice-ordered phase, there is twofold symmetry breaking of lattice translation symmetry along all three Cartesian directions. We present numerical evidence that the disordered to layered transition is continuous and consistent with universality class of the three-dimensional O(3) model with cubic anisotropy, while the layered to sublattice transition is first-order in nature.
... For semiconductors, for example, bare silicon or germanium, electronic decoupling of molecules can be achieved by either the growth of ultrathin dielectric layers on top of the surface [34,35] or a chemical modification of the surface to saturate the dangling bonds. In surface-science-based studies, for the latter approach hydrogenation of semiconductor surfaces is frequently applied as effective passivation against chemisorption of adsorbates [36][37][38][39], while also B deposition was shown to result in effective passivation of the Si surface [40,41]. In particular for electronic devices, oxidized semiconductor surfaces (e.g., silicon dioxide layers formed on bare silicon) are mostly used as substrates for fabricating devices [42]. ...
Over the past two decades, organic molecules adsorbed on atomically defined metal surfaces have been intensively studied to obtain an in-depth understanding of their self-assembly behavior, on-surface reactivity, as well as their structural and electronic properties [1-6]. An important aspect to unravel their potential use in electronic and optoelectronic devices is how their functionality can be preserved when adsorbed on surfaces. Unfortunately, the (strong) interaction of the molecules with the metallic surface, for example, due to hybridization of molecular states with electronic bands from the metallic substrate, often alters the electronic properties of the molecules and, moreover, can even turn off their sought-after functionality. As a result of the (strong) interaction, the molecular scaffolds can also become distorted, electronic states may be significantly broadened and shifted, and vibronic states may even be quenched. Decoupling strategies offer unique opportunities to reduce these (strong) interactions. In the following, recent progress to decouple both single molecules and molecular assemblies physically and electronically from a (strongly) interacting support is briefly reviewed.
... It undergoes a first-order transition from a fluid phase to a solid phase with face-centered cubic packing [15,16]. More complicated shapes such as cubes, rhombohedra [17], or in general three-dimensional regular polyhedra or corner-rounded polyhedra [18][19][20] have been studied as more realistic models for experimental selfassembling systems [21][22][23], applications to drug delivery where shape of the carrier may decide its effectiveness [24], biological material like immunoglobin [25], molecular logic gates [26][27][28], etc. Being able to predict the macroscopic material behavior from knowing its constituent building blocks would help to engineer the synthesis of materials with prescribed properties [29,30]. ...
We study the phase diagram of a system of 2×2×2 hard cubes on a three-dimensional cubic lattice. Using Monte Carlo simulations, we show that the system exhibits four different phases as the density of cubes is increased: disordered, layered, sublattice ordered, and columnar ordered. In the layered phase, the system spontaneously breaks up into parallel slabs of size 2×L×L where only a very small fraction cubes do not lie wholly within a slab. Within each slab, the cubes are disordered; translation symmetry is thus broken along exactly one principal axis. In the solidlike sublattice-ordered phase, the hard cubes preferentially occupy one of eight sublattices of the cubic lattice, breaking translational symmetry along all three principal directions. In the columnar phase, the system spontaneously breaks up into weakly interacting parallel columns of size 2×2×L, where only a very small fraction cubes do not lie wholly within a column. Within each column, the system is disordered, and thus translational symmetry is broken only along two principal directions. Using finite-size scaling, we show that the disordered-layered phase transition is continuous, while the layered-sublattice and sublattice-columnar transitions are discontinuous. We construct a Landau theory written in terms of the layering and columnar order parameters which is able to describe the different phases that are observed in the simulations and the order of the transitions. Additionally, our results near the disordered-layered transition are consistent with the O(3) universality class perturbed by cubic anisotropy as predicted by the Landau theory.
... It undergoes a first-order transition from a fluid phase to a solid phase with face centred cubic packing [15,16]. More complicated shapes such as cubes, rhombohedra [17] or in general three dimensional regular polyhedra or cornerrounded polyhedra [18][19][20] have been studied as more realistic models for experimental self-assembling systems [21][22][23], applications to drug delivery where shape of the carrier may decide its effectiveness [24], biological material like immunoglobin [25], molecular logic gates [26][27][28], etc. Being able to predict the macroscopic material behaviour from knowing its constituent building blocks would help to engineer the synthesis of materials with prescribed properties [29,30]. ...
We study the phase diagram of a system of hard cubes on a three dimensional cubic lattice. Using Monte Carlo simulations, we show that the system exhibits four different phases as the density of cubes is increased: disordered, layered, sublattice ordered, and columnar ordered. In the layered phase, the system spontaneously breaks up into parallel slabs of size where only a very small fraction cubes do not lie wholly within a slab. Within each slab, the cubes are disordered; translation symmetry is thus broken along exactly one principal axis. In the solid-like sublattice ordered phase, the hard cubes preferentially occupy one of eight sublattices of the cubic lattice, breaking translational symmetry along all three principal directions. In the columnar phase, the system spontaneously breaks up into weakly interacting parallel columns of size where only a very small fraction cubes do not lie wholly within a column. Within each column, the system is disordered, and thus translational symmetry is broken only along two principal directions. Using finite size scaling, we show that the disordered-layered phase transition is continuous, while the layered-sublattice and sublattice-columnar transitions are discontinuous. We construct a Landau theory written in terms of the layering and columnar order parameters, which is able to describe the different phases that are observed in the simulations and the order of the transitions. Additionally, our results near the disordered-layered transition are consistent with the O(3) universality class perturbed by cubic anisotropy as predicted by the Landau theory.
... Dangling bond (DB) wires formed by STM tip induced hydrogen atom desorption from hydrogenated semiconductor (0 0 1) surfaces of silicon or germanium are candidates for atomic-scale interconnects [37][38][39] addressing atomic [40][41][42][43][44][45] or molecular [46,47] quantum electronic devices. The transport properties of DB wires were subjected to numerous theor etical modeling studies [37][38][39][48][49][50][51], however any direct experimental characterization of these properties have not been reported. ...
Direct characterization of planar atomic or molecular scale devices and circuits on a supporting surface by multi-probe measurements requires unprecedented stability of single atom contacts and manipulation of scanning probes over large, nanometers scale area with atomic precision. In this work, we describe the full methodology behind atomically defined two-probe scanning tunneling microscopy (STM) experiments performed on a model system: dangling bond dimer wire supported on hydrogenated germanium (001) surface. We show that 70 nm long atomic wire can be simultaneously approached by two independent STM scanners with exact probe to probe distance reaching down to 30 nm. This allows direct wire characterization by two-probe I-V characteristics at distances below 50 nm. Our technical results presented in this work open a new area for multi-probe research, which can be now performed with precision so far accessible only by single-probe scanning probe microscopy (SPM) experiments.
... example) is a difference seen, with the DB showing a much larger increase in attractive interaction with the tip. This indicates that short range forces are the main contributor to the interaction force.[35]This is also consistent with the DB being a reactive chemical center on the chemically inert H-Si surface where deposited molecules can selectively adsorb.[36,37]Similar to what was reported previously for the case of gold atoms adsorbed on NaCl over Cu(111),[38,39]the short range electrostatic force due to the localized negative charge on the DB[11,13,14]is most likely the main contributor to the large tip-sample interaction on the DB. ...
We report the mechanically induced formation of a silicon-hydrogen covalent bond and its application in engineering nanoelectronic devices. We show that using the tip of a non-contact atomic force microscope, a single H atom could be vertically manipulated. When applying a localized electronic excitation, a single hydrogen atom is desorbed from the hydrogen passivated surface and can be transferred to the tip apex as evidenced from a unique signature in force curves. In the absence of tunnel electrons and electric field in the STM junction at 0 V, the hydrogen atom at the tip apex is brought very close to a silicon dangling bond, inducing the mechanical formation of a silicon-hydrogen covalent bond and the passivation of the dangling bond. The functionalized tip was used to characterize silicon dangling bonds on the H-Si surface and was shown to enhance the STM image contrast and allowed AFM imaging with atomic and chemical bond contrasts. Through examples, we show the importance of this atomic scale mechanical manipulation technique in the engineering of the emerging technology of on-surface dangling bond based nanoelectronic devices.
... Importantly, DBs provide adsorption sites for single molecule dopants, e. g. phosphine, which after incorporation and activation provides individual phosphorous dopants 3,4 . Also, individual organic molecules can be captured and studied at individual DBs [5][6][7] . ...
Using combined low temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM), we demonstrate hydrogen passivation of individual, selected dangling bonds (DBs) on a hydrogen-passivated Si(100)-21 surface (H-Si) by atom manipulation. This method allows erasing of DBs and thus provides an error-correction scheme for hydrogen lithography. Si-terminated tips (Si tips) for hydrogen desorption and H-terminated tips (H tips) for hydrogen passivation are both created by deliberate contact to the H-Si surface and are assigned by their characteristic contrast in AFM. DB passivation is achieved by transferring the H atom that is at the apex of an H tip to the DB, reestablishing a locally defect-free H-Si surface.
... The insulating layer decouples the molecules electronically from the metal surface while the layer (∼ fewÅ) is still sufficiently thin to allow STM operation without difficulties. Ultrathin layers of conventional insulating materials, for example, alkali-halides [137][138][139], metal-oxides [22,76,140,141], metal-nitrides [142,143], passivated semiconductors [144,145] have been used to study the properties of single atoms, single molecules, and various aspects of molecular electronics in general. Usage of twodimensional films of noble gases [146,147], molecules [148][149][150][151][152] also serve similar purpose of decoupling molecules from the metal surface. ...
Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional materials is a developing field and has already resulted in the discovery of several rich and interesting phenomena. Here, we review this progress with an emphasis on the electronic properties of the adsorbates and the substrate in well-defined systems, as unveiled by scanning tunneling microscopy (STM). We cover three aspects of the self-assembly. The first one focuses on non-covalent self-assembly dealing with site-selectivity due to inherent moire pattern present on 2D materials deposited on substrates. Modification of intermolecular interactions and molecule-substrate interactions influences the assembly drastically and 2D materials can also be used as a platform to carry out covalent and metal-coordinated assembly. The second part deals with the electronic properties of molecules adsorbed on 2D materials. By virtue of being inert and possessing low density of states near the Fermi level, 2D materials decouple molecules electronically from the underlying metal substrate and allow high-resolution spectroscopy and imaging of molecular orbitals. The moire pattern on the 2D materials causes site-selective gating and charging of molecules in some cases. The last section covers the effects of self-assembled organic molecules on the electronic properties of graphene as revealed by spectroscopy and electrical transport measurements. Non-covalent functionalization of 2D materials has already been applied for their application as catalysts and sensors. With the current surge of activity on building van der Waals heterostructures from 2D materials, molecular self-assembly has the potential to add an extra level of flexibility and functionality for applications ranging from flexible electronics and OLEDs to novel electronic devices and spintronics.
... Local hydrogen desorption, induced with the aid of a scanning tunnelling microscope (STM) tip, on the hydrogen-passivated (1×2)-reconstruction of the Si(001) and Ge(001) substrates [hereafter Si/Ge(001):H] can be used to reproducibly and rapidly create dangling-bond (DB) arrays defined with atomic precision. [1][2][3][4] This is a powerful method that allows one to directly pattern planar electronic devices and circuitry made out of DBs, [5][6][7][8][9][10] and to create templates for anchoring molecular networks [11][12][13][14][15] or for selective dopant incorporation. [16][17][18][19] DB arrays have a very rich and complex behaviour, ex-hibiting several metastable charge-and spinstates, 4,[20][21][22][23][24][25][26][27] as well as small polaron and soliton formation. ...
We have theoretically investigated the electronic properties of neutral and n-doped dangling bond (DB) quasi-one-dimensional structures (lines) in the Si(001):H and Ge(001):H substrates with the aim of identifying atomic-scale interconnects exhibiting metallic conduction for use in on-surface circuitry. Whether neutral or doped, DB lines are prone to suffer geometrical distortions or have magnetic ground-states that render them semiconducting. However, from our study we have identified one exception -- a dimer row fully stripped of hydrogen passivation. Such a DB-dimer line shows an electronic band structure which is remarkably insensitive to the doping level and, thus, it is possible to manipulate the position of the Fermi level, moving it away from the gap. Transport calculations demonstrate that the metallic conduction in the DB-dimer line can survive thermally induced disorder, but is more sensitive to imperfect patterning. In conclusion, the DB-dimer line shows remarkable stability to doping and could serve as a one-dimensional metallic conductor on n-doped samples.
... This is unlike some other STM studies of aromatic adlayers. 57 The authors hypothesize that this is because tryptanthrins are smaller molecules, and thus their MO energies are spaced farther apart. This is borne out by gas-phase DFT calculations where, for the parent compound, the HOMO-1 state is 0.52 eV beneath the HOMO energy, and the LUMOþ1 is 1.26 eV above the LUMO energy. ...
A new simulator for scanning tunneling microscopy (STM) is presented based on the linear combination of atomic orbitals molecular orbital (LCAO-MO) approximation for the effective tunneling Hamiltonian, which leads to the convolution integral when applied to the tip interaction with the sample. This approach intrinsically includes the structure of the STM tip. Through this mechanical emulation and the tip-inclusive convolution model, dI/dz images for molecular orbitals (which are closely associated with apparent barrier height, ϕ ap) are reported for the first time. For molecular adsorbates whose experimental topographic images correspond well to isolated-molecule quantum chemistry calculations, the simulator makes accurate predictions, as illustrated by various cases. Distortions in these images due to the tip are shown to be in accord with those observed experimentally and predicted by other ab initio considerations of tip structure. Simulations of the tunneling current dI/dz images are in strong agreement with experiment. The theoretical framework provides a solid foundation which may be applied to LCAO cluster models of adsorbate–substrate systems, and is extendable to emulate several aspects of functional STM operation.
... 1,[25][26][27][28] Surface DBs can also be applied for contacting organic molecules with the substrate. [29][30][31] The ability to manipulate DBs, however, comes at a cost. Often images recorded on DB arrays are difficult to interpret because the underlying tunneling processes are complicated and because the DBs interact in a complex way with the scanning tip. ...
Dangling bond (DB) arrays on Si(001):H and Ge(001):H surfaces can be patterned with atomic precision and they exhibit complex and rich physics making them interesting from both technological and fundamental perspectives. But their complex behavior often makes scanning tunneling microscopy (STM) images difficult to interpret and simulate. Recently it was shown that low-temperature imaging of unoccupied states of an unpassivated dimer on Ge(001):H results in a symmetric butterfly-like STM pattern, despite the fact that the equilibrium dimer configuration is expected to be a bistable, buckled geometry. Here, based on a thorough characterization of the low-bias switching events on Ge(001):H, we propose a new imaging model featuring a dynamical two-state rate equation. On both Si(001):H and Ge(001):H, this model allows us to reproduce the features of the observed symmetric empty-state images which strongly corroborates the idea that the patterns arise due to fast switching events and provides an insight into the relationship between the tunneling current and switching rates. We envision that our new imaging model can be applied to simulate other bistable systems where fluctuations arise from transiently charged electronic states.
... They found that these molecules adsorbed predominantly in a "flat on" configuration. In a completely different system, Godlewski et al. [12] studied the physisorption of aromatic Y-shaped molecules on a Ge (001) surface to characterize the electronic structure of adsorbed molecules that are the basis for single-molecule logic circuits. They found that a flat aromatic molecule interacts strongly with dangling bonds on this surface without any significant alteration of its planar structure. ...
In recent years the statistical mechanics of non-spherical molecules, such as polypeptide chains and protein molecules, has garnered considerable attention as the phase behavior of these systems has important scientific and health implications. More recently, it has been realized that surface binding may have a considerable impact on this behavior. With this in mind, we examine here the role of surface interactions on the phase behavior of Y-shaped molecules (a simplified model of immunoglobulin) using grand-canonical Monte Carlo simulation. In particular, we investigate the critical behavior of a system of such molecules on a hexagonal lattice using histogram reweighting, multicanonical sampling, and finite-size scaling. After obtaining the critical properties of the three-dimensional bulk system, we investigate the impact of a patterned solid surface on these properties as a function of patterning geometry and surface interaction strength. Our results suggest avenues for tailoring phase behavior by selectively controlling surface characteristics.
... However, a major disadvantage of this approach consists in the necessity of rebuilding the circuit with an STM to be able to operate between the logic states, thus considerably reducing the operational speed. In the second approach tri-naphthylene molecules 5,16 were physisorbed on the Si surface for making contact with DBs wires allowing to realize a semi-classical OR gate. Here, the logic operations are supposed to be performed within the molecule itself, while the DB wires served only as a interconnects to metallic nano-pads. ...
Implementing atomic and molecular scale electronic functionalities represents one of the major challenges in current nano-electronic developments. Engineered dangling bond nanostructures on Silicon or Germanium surfaces posses the potential to provide novel routes towards the development of non-conventional electronic circuits. These structures are built by selectively removing hydrogen atoms from an otherwise fully passivated Si(100) or Ge(100) substrate. In this theoretical study, we demonstrate how dangling bond loops can be used to implement different Boolean logic gates. Our approach exploits quantum interference effects in such ring-like structures combined with an appropriate design of the interfacing of the dangling bond system with mesoscopic electrodes. We show how OR, AND, and NOR gates can be realized by tuning either the global symmetry of the system in a multi-terminal setup-by arranging the position of the input and output electrodes-or, alternatively, by selectively applying electrostatic gates in a two-terminal configuration.
Scanning tunneling microscope (STM) has presented a revolutionary methodology to nanoscience and nanotechnology. It enables imaging of the topography of surfaces, mapping the distribution of electronic density of states, and manipulating individual atoms and molecules, all at atomic resolutions. In particular, atom manipulation capability has evolved from fabricating individual nanostructures toward the scalable production of the atomic‐sized devices bottom‐up. The combination of precision synthesis and in situ characterization has enabled direct visualization of many quantum phenomena and fast proof‐of‐principle testing of quantum device functions with immediate feedback to guide improved synthesis. Several representative examples are reviewed to demonstrate the recent development of atomic‐scale manipulation, focusing on progress that addresses quantum properties by design in several technologically relevant materials systems. Integration of several atomically precisely controlled probes in a multiprobe STM system vastly extends the capability of in situ characterization to a new dimension where the charge and spin transport behaviors can be examined from mesoscopic to atomic length scale. The automation of atomic‐scale manipulation and the integration with well‐established lithographic processes further push this bottom‐up approach to a new level that combines reproducible fabrication, extraordinary programmability, and the ability to produce large‐scale arrays of quantum structures. The recent developments of atomic‐scale manipulation with scanning tunneling microscopy (STM) are reviewed. In particular, the review focuses on the progress that addresses quantum properties by design through the precise control of atomic structures in several technologically relevant materials systems. In situ characterization with single‐ and multiprobe STM is discussed, which is utilized for thorough determination of electronic structures.
The synthesis of a threefold symmetric nanographene with 19 cata‐fused benzene rings distributed within six branches is reported. This flat dendritic starphene, which is the largest unsubstituted cata‐condensed PAH that has been obtained to date, was prepared in solution by means of a palladium‐catalyzed aryne cyclotrimerization reaction and it was characterized on surface by scanning probe microscopy with atomic resolution. Nanographenes: The successful synthesis of a dendritic nanographene is reported. [19]Dendriphene, which is the largest unsubstituted cata‐condensed nanographene obtained by solution chemistry, was characterized on‐surface by scanning probe microscopy.
On-surface synthesis represents a successful strategy to obtain designed molecular structures on an ultra-clean metal substrate. While metal surfaces are known to favor adsorption, diffusion, and chemical bonding between molecular groups, on-surface synthesis on non-metallic substrates would allow the electrical decoupling of the resulting molecule from the surface, favoring application to electronics and spintronics. Here, we demonstrate the on-surface generation of hexacene by surface-assisted reduction on a H-passivated Si(001) surface. The reaction, observed by scanning tunneling microscopy and spectroscopy, is probably driven by the formation of Si–O complexes at dangling bond defects. Supported by density functional theory calculations, we investigate the interaction of hexacene with the passivated silicon surface, and with single silicon dangling bonds.
Understanding the mechanisms involved in the covalent attachment of organic molecules to surfaces is a major challenge for nanotechnology and surface science. On the basis of classical organic chemistry mechanistic considerations, key issues such as selectivity and reactivity of the organic adsorbates could be rationalized and exploited for the design of molecular-scale circuits and devices. Here we use tris(benzocyclobutadieno)triphenylene, a singular Y-shaped hydrocarbon containing antiaromatic cyclobutadienoid rings, as a molecular probe to study the reaction of polycyclic conjugated molecules with atomic scale moieties, dangling-bond (DB) dimers on a hydrogen-passivated Ge(001):H surface. By combining molecular design, synthesis, scanning tunneling microscopy and spectroscopy (STM/STS) and computational modeling, we show that the attachment involves a concerted [4+2] cycloaddition reaction that is completely site-selective and fully reversible. This selectivity, governed by the bond alternation induced by the presence of the cyclobutadienoid rings, allows for the control of the orientation of the molecules with respect to the surface DB-patterning. We also demonstrate that by judicious modification of the electronic levels of the polycyclic benzenoid through substituents, the reaction barrier height can be modified. Finally, we show that after deliberate tip-induced covalent bond cleavage, adsorbed molecules can be used to fine tune the electronic states of the DB dimer. This power to engineer deliberately the bonding configuration and electronic properties opens new perspectives for creating prototypical nanoscale circuitry.
We study the different phases and the phase transitions in a system of Y-shaped particles, examples of which include Immunoglobulin-G and trinaphthylene molecules, on a triangular lattice interacting exclusively through excluded volume interactions. Each particle consists of a central site and three of its six nearest neighbours chosen alternately, such that there are two types of particles which are mirror images of each other. We study the equilibrium properties of the system using grand canonical Monte Carlo simulations that implements an algorithm with cluster moves that is able to equilibrate the system at densities close to full packing. We show that, with increasing density, the system undergoes two entropy-driven phase transitions with two broken-symmetry phases. At low densities, the system is in a disordered phase. As intermediate phases, there is a solid-like sublattice phase in which one type of particle is preferred over the other and the particles preferentially occupy one of four sublattices, thus breaking both particle-symmetry as well as translational invariance. At even higher densities, the phase is a columnar phase, where the particle-symmetry is restored, and the particles preferentially occupy even or odd rows along one of the three directions. This phase has translational order in only one direction, and breaks rotational invariance. From finite size scaling, we demonstrate that both the transitions are first order in nature. We also show that the simpler system with only one type of particles undergoes a single discontinuous phase transition from a disordered phase to a solid-like sublattice phase with increasing density of particles.
Using combined low temperature scanning tunneling microscopy and atomic force microscopy (AFM), we demonstrate hydrogen passivation of individual, selected dangling bonds (DBs) on a hydrogen-passivated Si(100)-2 × 1 surface (H–Si) by atom manipulation. This method allows erasing of DBs and thus provides a promising scheme for error-correction in hydrogen lithography. Both Si-terminated tips (Si tips) for hydrogen desorption and H-terminated tips (H tips) for hydrogen passivation are created by deliberate contact to the H–Si surface and are assigned by their characteristic contrast in AFM. DB passivation is achieved by transferring the H atom that is at the apex of an H tip to the DB, reestablishing a locally defect-free H–Si surface.
One of the key challenges in the construction of atomic-scale circuits and molecular machines is to design molecular rotors and switches by controlling the linear or rotational movement of a molecule while preserving its intrinsic electronic properties. Here, we demonstrate both the continuous rotational switching and the controlled step-by-step single switching of a trinaphthylene molecule adsorbed on a dangling bond dimer created on a hydrogen-passivated Ge(001):H surface. The molecular switch is on-surface assembled when the covalent bonds between the molecule and the dangling bond dimer are controllably broken and the molecule is attached to the dimer by long-range van der Waals interactions. In this configuration, the molecule retains its intrinsic electronic properties, as confirmed by combined scanning tunneling microscopy/spectroscopy (STM/STS) measurements, density functional theory (DFT) calculations and advanced STM image calculations. Continuous switching of the molecule is initiated by vibronic excitations, when the electrons are tunneling through the lowest unoccupied molecular orbital (LUMO) state of the molecule. The switching path is a combination of a sliding and rotation motion over the dangling bond dimer pivot. By carefully selecting the STM conditions, control over discrete single switching events is also achieved. Combined with the ability to create dangling bond dimers with atomic precision, the controlled rotational molecular switch is expected to be a crucial building block for more complex surface atomic-scale devices.
Construction of single-molecule electronic devices requires the controlled manipulation of organic molecules and their properties. This could be achieved by tuning the interaction between the molecule and individual atoms by local "on-surface" chemistry, i.e., the controlled formation of chemical bonds between the species. We demonstrate here the reversible attachment of a planar conjugated polyaromatic molecule to a pair of unpassivated dangling bonds on a hydrogenated Ge(001):H surface via a Diels-Alder [4+2] addition using the tip of a scanning tunneling microscope (STM). Due to the small stability difference between the covalently bonded and a nearly undistorted structure attached to the dangling bond dimer by long-range dispersive forces, we show that at cryogenic temperatures the molecule can be switched between both configurations. The reversibility of this covalent bond forming reaction may be applied in the construction of complex circuits containing organic molecules with tunable properties.
Thermally induced aryl halide C-C coupling on surfaces of hydrogen-passivated germanium, Ge(001):H, has been investigated by scanning tunneling microscopy at room temperature. It has been shown that an atomic hydrogen buffer layer is essential for C-C coupling to occur. Competition between dehydrogenation of the passivating layer and dehalogenation of molecular precursors as a function of substrate temperature during the deposition of molecules is discussed.
We show that a dangling bond (DB) dimer on Ge(001):H exhibits a dynamical behavior when the empty states are imaged with scanning tunneling microscopy (STM) at liquid helium temperature. Large amplitude Ge atom vibrations are decisive in facilitating a specific appearance of the structure in the STM images. The underlying mechanism is unraveled using a theoretical model and calculations within the density functional theory framework. Furthermore, we demonstrate the ability to induce controlled switching of the DB dimer with noncontact atomic force microscope and the stabilizing role of the dimer-dimer interaction.
We present a combined experimental and theoretical study of the electronic properties of close-spaced dangling-bond (DB) pairs in a hydrogen-passivated Si(001):H p-doped surface. Two types of DB pairs are considered, called "cross" and "line" structures. Our scanning tunneling spectroscopy (STS) data show that, although the spectra taken over different DBs in each pair exhibit a remarkable resemblance, they appear shifted by a constant energy that depends on the DB-pair type. This spontaneous asymmetry persists after repeated STS measurements. By comparison with density functional theory (DFT) calculations, we demonstrate that the magnitude of this shift and the relative position of the STS peaks can be explained by distinct charge states for each DB in the pair. We also explain how the charge state is modified by the presence of the scanning tunneling microscopy (STM) tip and the applied bias. Our results indicate that, using the STM tip, it is possible to control the charge state of individual DBs in complex structures, even if they are in close proximity. This observation might have important consequences for the design of electronic circuits and logic gates based on DBs in passivated silicon surfaces.
Dangling bond structures created on H-passivated silicon surfaces offer a novel platform for engineering planar nanoscale circuits, compatible with conventional semiconductor technologies. We focus in this investigation on the electronic structure and quantum transport signatures of dangling bond loops built on H-passivated Si(100) surfaces and contacted to carbon nanoribbon leads in a two-terminal planar, nanoscale setup. The computational studies were carried out to rationalize the influence of the local atomic-scale contacts of the dangling bond system to the mesoscopic electrodes as well as the possibility of revealing quantum interference effects in the dangling bond loops. Our results reveal a strong sensitivity of the low-energy quantum transmission to the loop topology and to the atomistic details of the electrode-loop contact. Varying the length of the loop or the spatial position of at least one of the electrodes has a drastic impact on the quantum interference pattern: depending whether constructive or destructive interference within the loop takes place, the conductance of the system can be tuned over several orders of magnitude, thus suggesting the possibility of exploiting such quantum mechanical effects in the design of two-dimensional, atomic-scale electronic devices such as logic gates.
The design and the construction of the first prototypical QHC (Quantum Hamiltonian Computing) atomic scale Boolean logic gate is reported using scanning tunnelling microscope (STM) tip-induced atom manipulation on an Si(001):H surface. The NOR/OR gate truth table was confirmed by dI/dU STS (Scanning Tunnelling Spectroscopy) tracking how the surface states of the QHC quantum circuit on the Si(001):H surface are shifted according to the input logical status.
We analyze self-assembled nanocrystals of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) molecules on hydrogen passivated Ge(001) surface with use of scanning tunneling microscopy (STM) and spectroscopy (STS). At 0.7ML coverage, 2.1 nm high, elongated, hexagonal islands inclined at 37° with respect to the substrate row are mostly observed. By measuring the differential tunneling conductance, we observe an effect of electronic decoupling of the nanocrystals due to the introduced passivating layer. Finally, we shortly discuss the stability of the islands and their interaction with the scanning probe in the ultra-high vacuum (UHV) environment.
Islands composed of perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) molecules are grown on a hydrogen passivated Ge(001):H surface. The islands are studied with room temperature scanning tunneling microscopy and spectroscopy. The spontaneous and tip-induced formation of the top-most layer of the island is presented. Assistance of the scanning probe seems to be one of the factors that facilitate and speed the process of formation of the top-most layer.
Atomically precise dangling-bond (DB) lines are constructed dimer-by-dimer on a hydrogen-passivated Ge(001)-(2×1):H surface by an efficient scanning tunneling microscope (STM) tip-induced desorption protocol. Due to the smaller surface band gap of the undoped Ge(001) substrate compared to Si(001), states associated with individually created DBs can be characterized spectroscopically by scanning tunneling spectroscopy (STS). Corresponding dI/dV spectra corroborated by first-principle modeling demonstrate that DB dimers introduce states below the Ge(001):H surface conduction band edge. For a DB line parallel to the surface reconstruction rows, the DB-derived states near the conduction band edge shift to lower energies with increasing number of DBs. The coupling between the DB states results in a dispersive band spanning 0.7 eV for an infinite DB line. For a long DB line perpendicular to the surface reconstruction rows, a similar band is not formed since the interdimer coupling is weak. However, for a short DB line (2–3 DBs) perpendicular to the reconstruction rows a significant shift is still observed due to the more flexible dimer buckling.
A logic gate has been implemented in a single trinaphthylene molecule. Each logical input controls the position of a surface Au atom that is brought closer or further away from the end of one of the naphthyl branch. Each Au atom carries 1 bit of information and is able to deform nonlocally and to shift in energy the molecular electronic states of the trinaphthylene. Probed at the end of the third naphthyl branch using scanning tunneling spectroscopy, the variations of the tunneling current intensity as a function of the Au atoms position measures the logical output of the gate. We demonstrate both theoretically and experimentally that these variations respect the truth table of a NOR logic gate.
We present an efficient scheme for calculating the Kohn-Sham ground state of metallic systems using pseudopotentials and a plane-wave basis set. In the first part the application of Pulay's DIIS method (direct inversion in the iterative subspace) to the iterative diagonalization of large matrices will be discussed. Our approach is stable, reliable, and minimizes the number of order N-atoms(3) operations. In the second part, we will discuss an efficient mixing scheme also based on Pulay's scheme. A special ''metric'' and a special ''preconditioning'' optimized for a plane-wave basis set will be introduced. Scaling of the method will be discussed in detail for non-self-consistent calculations. It will be shown that the number of iterations required to obtain a specific precision is almost independent of the system size. Altogether an order N-atoms(2) scaling is found for systems up to 100 electrons. If we take into account that the number of k points can be implemented these algorithms within a powerful package called VASP (Vienna ab initio simulation package). The program and the techniques have been used successfully for a large number of different systems (liquid and amorphous semiconductors, liquid simple and transition metals, metallic and semiconducting surfaces, phonons in simple metals, transition metals, and semiconductors) and turned out to be very reliable.
A combined study using density functional calculations and scanning tunneling microscopy experiments shows that individual silver adatoms on ultrathin sodium chloride films on copper surfaces are stable in three different charge states - neutral, negatively, and positively charged adatoms. The charge states of the individual adatoms were manipulated by voltage pulses. The key parameters determining the stability of various charge states are identified and discussed within a simple model.
We investigated dibenzo[a,h]thianthrene molecules adsorbed on ultrathin layers of NaCl using a combined low-temperature scanning tunneling and atomic force microscope. Two stable configurations exist corresponding to different isomers of free nonplanar molecules. By means of excitations from inelastic electron tunneling we can switch between both configurations. Atomic force microscopy with submolecular resolution allows unambiguous determination of the molecular geometry, and the pathway of the interconversion of the isomers. Our investigations also shed new light on contrast mechanisms in scanning tunneling microscopy.
We have spatially resolved the electronic penetration of metallic electronic states through a molecular wire connected to an atomically clean contact. The molecular wire, which is 0.3 nm wide and 1.7 nm long, was electronically connected on one side, and a scanning tunneling microscope tip was used as a second movable electronic counterelectrode. The results reveal a clear exponential decay in the transparency (conductance) of the wire with distance from the contacted end. Analysis of the data shows that electrons are transported along the molecular wire by virtual resonance tunneling with an inverse decay length of 4 nm-1, in excellent agreement with theoretical calculations.
Individual pentacene and naphthalocyanine molecules adsorbed on a bilayer of NaCl grown on Cu(111) were investigated by means of scanning tunneling microscopy using CO-functionalized tips. The images of the frontier molecular orbitals show an increased lateral resolution compared with those of the bare tip and reflect the modulus squared of the lateral gradient of the wave functions. The contrast is explained by tunneling through the p-wave orbitals of the CO molecule. Comparison with calculations using a Tersoff-Hamann approach, including s- and p-wave tip states, demonstrates the significant contribution of p-wave tip states.
We report on the formation of a metal-molecule complex that can be used as a molecular switch. Using a cryogenic scanning tunneling microscope, a covalent bond was formed reversibly between a gold atom and a perylene-3,4,9,10-tetracarboxylic dianhydride molecule supported by a thin insulating film. The bonded and the nonbonded state of the complex were found to be associated with different charge states, and the switching between the two states was accompanied by a considerable change in the tunneling current. Atomic force microscopy molecular imaging was employed to determine precisely the atomic structure of the complex, and the experimental results were corroborated by density functional theory calculations.
Resolving individual atoms has always been the ultimate goal of surface microscopy. The scanning tunneling microscope images
atomic-scale features on surfaces, but resolving single atoms within an adsorbed molecule remains a great challenge because
the tunneling current is primarily sensitive to the local electron density of states close to the Fermi level. We demonstrate
imaging of molecules with unprecedented atomic resolution by probing the short-range chemical forces with use of noncontact
atomic force microscopy. The key step is functionalizing the microscope’s tip apex with suitable, atomically well-defined
terminations, such as CO molecules. Our experimental findings are corroborated by ab initio density functional theory calculations.
Comparison with theory shows that Pauli repulsion is the source of the atomic resolution, whereas van der Waals and electrostatic
forces only add a diffuse attractive background.
The development of electronic devices at the single-molecule scale requires detailed understanding of charge transport through
individual molecular wires. To characterize the electrical conductance, it is necessary to vary the length of a single molecular
wire, contacted to two electrodes, in a controlled way. Such studies usually determine the conductance of a certain molecular
species with one specific length. We measure the conductance and mechanical characteristics of a single polyfluorene wire
by pulling it up from a Au(111) surface with the tip of a scanning tunneling microscope, thus continuously changing its length
up to more than 20 nanometers. The conductance curves show not only an exponential decay but also characteristic oscillations
as one molecular unit after another is detached from the surface during stretching.
A crucial problem in molecular electronics is the control of the electronic contact between a molecule and its electrodes. As a model system, we investigated the contact between the molecular wire group of a C90H98 (Lander) molecule and the edge of a Cu(111) monatomic step. The reproducible contact and decontact of the wire was obtained by manipulating the Lander with a low temperature scanning tunneling microscope. The electronic standing wave patterns on the Cu(111) surface serve to monitor the local electronic perturbation caused by the interaction of the wire end with the step edge, giving information on the quality of the contact.
The nature and control of individual metal atoms on insulators are of great importance in emerging atomic-scale technologies.
Individual gold atoms on an ultrathin insulating sodium chloride film supported by a copper surface exhibit two different
charge states, which are stabilized by the large ionic polarizability of the film. The charge state and associated physical
and chemical properties such as diffusion can be controlled by adding or removing a single electron to or from the adatom
with a scanning tunneling microscope tip. The simple physical mechanism behind the charge bistability in this case suggests
that this is a common phenomenon for adsorbates on polar insulating films.
Ultrathin insulating NaCl films have been employed to decouple individual pentacene molecules electronically from the metallic substrate. This allows the inherent electronic structure of the free molecule to be preserved and studied by means of low-temperature scanning-tunneling microscopy. Thereby direct images of the unperturbed molecular orbitals of the individual pentacene molecules are obtained. Elastic scattering quantum chemistry calculations substantiate the experimental findings.
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.
In recent years, ab initio molecular dynamics (MD) techniques have made a profound impact on the investigation of the structure of the electronic and dynamic properties of liquid and amorphous materials. In this paper, recent developments in this field are reviewed and it is shown that the exact calculation of the electronic groundstate at each MD timestep is feasible using modern iterative matrix diagonalization algorithms. Together with the use of ultrasoft pseudopotentials, ab initio MD simulations can be extended to open-shell transition metals with a high density of states at the Fermi-level. The technique is applied to a number of interesting cases: (a) liquid simple metals (Li, Na, Al, Ge), (b) liquid transition metals (Cu, V), and (c) the transition from a liquid metal to an amorphous semiconductor by the rapid quenching of Ge.
The electronic properties of FePc molecules adsorbed on hydrogen-passivated Si(111) surfaces are investigated by scanning tunneling microscopy at low temperatures. Spatially resolved spectroscopy reveals a significant variation of the electronic states at different positions above the molecule. The highest occupied ligand- and metal-based orbitals of FePc are determined by pronounced peaks in the tunneling spectra and voltage-dependent changes in the microscopic images. Comparison with density functional theory calculations indicates that the electronic ground state is an 3A1g state.
We explore different tip functionalizations for atomic force microscopy (AFM), scanning tunneling microscopy (STM), and Kelvin probe force microscopy (KPFM) of organic molecules on thin insulating films. We describe in detail how tips terminated with single Br and Xe atoms can be created. The performance of these tips in AFM, STM, and KPFM imaging of single molecules is compared to other tip terminations, and the advantages and disadvantages of the different tips are discussed. The Br tip was found to be particularly useful for AFM and lateral manipulation, whereas the Xe tip excelled in STM and KPFM.
Single decastarphene molecules, adsorbed on Cu(111) and on a bilayer of NaCl/Cu(111) are imaged by a combination of low temperature scanning tunneling microscopy (STM) and dynamic atomic force microscopy in the non-contact mode (nc-AFM). This dual imaging technique provides the intramolecular electron density maps of the frontier molecular orbitals via the STM images and the atomic scale skeleton via its constant-height frequency shift nc-AFM images. Recording both images at the same time opens the way to exactly locate the valence states electronic density map of the imaged molecule on its atomic scale skeleton.
A new concept for a single molecule transistor is demonstrated [1]. A single chargeable atom adjacent to a molecule shifts molecular energy levels into alignment with electrode levels, thereby gating current through the molecule. Seemingly paradoxically, the silicon substrate to which the molecule is covalently attached provides 2, not 1, effective contacts to the molecule. This is achieved because the single charged silicon atom is at a substantially different potential than the remainder of the substrate. Charge localization at one dangling bond is ensured by covalently capping all other surface atoms. Dopant level control and local Fermi level control can change the charge state of that atom. The same configuration is shown to be an effective transducer to an electrical signal of a single molecule detection event. Because the charged atom induced shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature. [1] Paul G. Piva1,Gino A. DiLabio, Jason L. Pitters, Janik Zikovsky, Moh'd Rezeq, Stanislav Dogel, Werner A. Hofer & Robert A. Wolkow, Field regulation of single-molecule conductivity by a charged surface atom, NATURE 435, 658-661 (2005)
We present a theoretical formalism specially suited for the simulation of scanning tunneling microscopy (STM) images. The method allows for a realistic description of the STM system, taking fully into account its three-dimensional nature. Bias effects may also be considered since the theory is not restricted to the low-bias limit. The starting point is the previously applied Landauer-Büttiker formula, which expresses the current at the STM junction as a sum of transmission coefficients linking eigenstates at each electrode. The transmission coefficients are directly obtained from the scattering matrix which is, in our approach evaluated through Green-function techniques; in particular, we employ the surface Green-function matching (SGFM) method to find the Green function at the interface, and explicitly derive simple expressions for the current. Additionally, the formalism goes beyond the elastic-scattering limit by considering inelastic effects via an optical potential. We also present a method to analyze the current in terms of contributions arising from individual atomic orbital interactions and their interference with other interactions. To this end, the SGFM method is replaced by a first-order expansion of the interface Green function.
Low-temperature scanning tunneling microscope (STM) images of the Si(100) surface showing apparent (2×1) atom dimer lines have recently been reported. Using experimental and theoretical approaches, it is demonstrated how those (2×1)-like images result from a c(4×2) surface reconstruction imaged at high bias voltages. In the STM junction, the surface contribution of 3px surface-state electronic resonances relative to the 3pz states is bias voltage dependent. The apparent (2×1) STM images result from an increase in the number of bulk Si electronic channels amplifying Si(100)-c(4×2) surface 3px surface states contribution to the tunneling current with respect to the one of 3pz states.
We report on the controlled change of the energetic ordering of molecular orbitals. Negatively charged Copper(II)phthalocyanine on NaCl/Cu(100) undergoes a Jahn-Teller distortion that lifts the degeneracy of two frontier orbitals. The energetic order of the levels can be controlled by Au and Ag-atoms in the vicinity of the molecule. As only one of the states is occupied, the control of the energetic order is accompanied by bistable changes of the charge distribution inside the molecule, rendering it a bistable switch.
We report results of first-principles calculations in terms of which we elucidate the mechanisms for nucleation and initial growth of pentacene films on Si. Pentacene molecules bond in flat, distorted configurations on bare surfaces. On H-passivated surfaces, direct bonding or H replacement are not energetically favored. However, molecules bond in an upright configuration at isolated depassivated Si dangling bonds and film growth continues over the passivated area. The results elucidate generic adsorption issues on inert surfaces and suggest procedures for controlling film growth.
Hybrid density functionals are very successful in describing a wide range of molecular properties accurately. In large molecules and solids, however, calculating the exact (Hartree-Fock) exchange is computationally expensive, especially for systems with metallic characteristics. In the present work, we develop a new hybrid density functional based on a screened Coulomb potential for the exchange interaction which circumvents this bottleneck. The results obtained for structural and thermodynamic properties of molecules are comparable in quality to the most widely used hybrid functionals. In addition, we present results of periodic boundary condition calculations for both semiconducting and metallic single wall carbon nanotubes. Using a screened Coulomb potential for Hartree-Fock exchange enables fast and accurate hybrid calculations, even of usually difficult metallic systems. The high accuracy of the new screened Coulomb potential hybrid, combined with its computational advantages, makes it widely applicable to large molecules and periodic systems.
The adsorption of polyacene molecules on a H-terminated Si(0 0 1)-2 × 1 surface where a few hydrogen atoms have been extracted is presented using the semi-empirical ASED+ method. To scale up the qualitative ASED+ method, the adsorption of benzene and pentacene on a clean silicon surface is first compared with DFT calculations together with their adsorption on a fully hydrogenated Si(1 0 0) surface. When a few hydrogen atoms have been selectively removed from the SiH(0 0 1) surface, ASED+ demonstrates a difficult chemisorption for the polyacenes series on one dangling bond and a large interaction on two dangling bonds compensating for the large molecule deformation required. The influence of the nearest H atoms when the molecule is adsorbed on two dangling bonds of a passivated Si(0 0 1) surface is very small. On a clean and on a partially hydrogenated surface, all the polyacenes need to overcome an energy barrier of 0.3–0.4 eV to reach a chemisorption state.
On a metal–molecule–metal nanojunction, the scanning tunneling microscope (STM) scans at the precise location of the electronic metal–molecule interaction permit a measurement of the contact conductance G0. The conversion curve between the change in the STM contrast Δh due to this interaction and G0 is presented for a series of conjugated molecular wires. At chemisorption distances, the two-valued character of the G0(Δh) function is discussed, indicating experimental ways to evaluate G0 as a function of Δh for different metal–molecule interaction ranges.
On metallic and semiconductor surfaces functional nanostructures can be built with atomic scale precision using the tip of an atomic force microscope/scanning tunneling microscope. In contrast, controlled lateral manipulation on insulators has not been reported. The traditional pushing and pulling based manipulation methods cannot be used for molecules adsorbed on insulating films because of the unfavorable ratio between diffusion barrier and desorption energy. Here, we demonstrate that molecules adsorbed on insulating films can be laterally manipulated in a controlled way by injecting inelastically tunneling electrons at well-defined positions in a molecule. The technique was successfully applied to several different molecules.
We present a detailed description and comparison of algorithms for performing ab-initio quantum-mechanical calculations using pseudopotentials and a plane-wave basis set. We will discuss: (a) partial occupancies within the framework of the linear tetrahedron method and the finite temperature density-functional theory, (b) iterative methods for the diagonalization of the Kohn-Sham Hamiltonian and a discussion of an efficient iterative method based on the ideas of Pulay's residual minimization, which is close to an order N-atoms(2) scaling even for relatively large systems, (c) efficient Broyden-like and Pulay-like mixing methods for the charge density including a new special 'preconditioning' optimized for a plane-wave basis set, (d) conjugate gradient methods for minimizing the electronic free energy with respect to all degrees of freedom simultaneously. We have implemented these algorithms within a powerful package called VAMP (Vienna ab-initio molecular-dynamics package), The program and the techniques have been used successfully for a large number of different systems (liquid and amorphous semiconductors, liquid simple and transition metals, metallic and semi-conducting surfaces, phonons in simple metals, transition metals and semiconductors) and turned out to be very reliable.
We have used scanning tunnelling microscopy (STM) at 77 K to investigate 3,4,9,10-perylene-tetracarboxylic dianhydride (PTCDA) molecules adsorbed on an ultrathin (1-2 monolayer (ML)) film of KBr grown on a c(8 × 2)InSb(001) substrate. The molecules are stabilized both at the KBr steps and on the terraces. On the 1 ML film the PTCDA molecules appear predominantly as single entities, whereas on the 2 ML film formation of molecular clusters is preferred. Differences in the adsorption configurations indicate that the interaction between the molecules and the surface differs significantly for the cases of 1 and 2 ML films. We present images of the molecules obtained with sub-molecular resolution for both filled and empty state sampling modes. We argue that the highest occupied molecular orbital (the lowest unoccupied molecular orbital) is responsible for intramolecular contrast in filled (empty) state images of the molecules, even though they are deformed due to strong interaction with the substrate.
From scanning tunneling microscopy and spectroscopy experiments it is shown that control over the charge-state of individual molecules adsorbed on surfaces can be obtained by choosing a substrate system with an appropriate workfunction. The distribution of the additional charge is studied using difference images. These images show marked intramolecular contrast.
Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted into quantum information throughout the molecule. The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy.
We present scanning tunneling microscopy (STM)-based single-molecule synthesis of linear metal-ligand complexes starting from individual metal atoms (iron or nickel) and organic molecules (9,10-dicyanoanthracene) deposited on an ultrathin insulating film. We directly visualize the frontier molecular orbitals by STM orbital imaging, from which, in conjunction with detailed density functional theory calculations, the electronic structure of the complexes is inferred. Our studies show how the order of the molecular orbitals and the spin-state of the complex can be engineered through the choice of the metal atom. The high-spin iron complex has a singly occupied delocalized orbital with a large spin-splitting that points to the use of these engineered complexes as modular building blocks in molecular spintronics.
Decoupling the electronic properties of a molecule from a substrate is of crucial importance for the development of single-molecule electronics. This is achieved here by adsorbing pentacene molecules at low temperature on a hydrogenated Si(100) surface (12 K). The low temperature (5 K) scanning tunneling microscope (STM) topography of the single pentacene molecule at the energy of the highest occupied molecular orbital (HOMO) tunnel resonance clearly resembles the native HOMO of the free molecule. The negligible electronic coupling between the molecule and the substrate is confirmed by theoretical STM topography and diffusion barrier energy calculations.
We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-density approximation at each molecular-dynamics step. This is possible using conjugate-gradient techniques for energy minimization, and predicting the wave functions for new ionic positions using subspace alignment. This approach avoids the instabilities inherent in quantum-mechanical molecular-dynamics calculations for metals based on the use of a fictitious Newtonian dynamics for the electronic degrees of freedom. This method gives perfect control of the adiabaticity and allows us to perform simulations over several picoseconds.
We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal–amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nosé dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.
Generalized gradient approximations (GGA{close_quote}s) for the exchange-correlation energy improve upon the local spin density (LSD) description of atoms, molecules, and solids. We present a simple derivation of a simple GGA, in which all parameters (other than those in LSD) are fundamental constants. Only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked. Improvements over PW91 include an accurate description of the linear response of the uniform electron gas, correct behavior under uniform scaling, and a smoother potential. {copyright} {ital 1996 The American Physical Society.}
The present work introduces an efficient screening technique to take advantage of the fast spatial decay of the short range Hartree-Fock (HF) exchange used in the Heyd-Scuseria-Ernzerhof (HSE) screened Coulomb hybrid density functional. The screened HF exchange decay properties and screening efficiency are compared with traditional hybrid functional calculations on solids. The HSE functional is then assessed using 21 metallic, semiconducting, and insulating solids. The examined properties include lattice constants, bulk moduli, and band gaps. The results obtained with HSE exhibit significantly smaller errors than pure density functional theory (DFT) calculations. For structural properties, the errors produced by HSE are up to 50% smaller than the errors of the local density approximation, PBE, and TPSS functionals used for comparison. When predicting band gaps of semiconductors, we found smaller errors with HSE, resulting in a mean absolute error of 0.2 eV (1.3 eV error for all pure DFT functionals). In addition, we present timing results which show the computational time requirements of HSE to be only a factor of 2-4 higher than pure DFT functionals. These results make HSE an attractive choice for calculations of all types of solids.
The bistability in the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine molecules constitutes a two-level system that was manipulated and probed by low-temperature scanning tunneling microscopy. When adsorbed on an ultrathin insulating film, the molecules can be switched in a controlled fashion between the two states by excitation induced by the inelastic tunneling current. The tautomerization reaction can be probed by resonant tunneling through the molecule and is expressed as considerable changes in the conductivity of the molecule. We also demonstrated a coupling of the switching process so that the charge injection in one molecule induced tautomerization in an adjacent molecule.