Single-molecule chemistry and analysis: mode-specific dehydrogenation of adsorbed propene by inelastic electron tunneling

A single propene molecule, located in the junction between the tip of a scanning tunneling microscope (STM) and a Cu(211) surface can be dehydrogenated by inelastic electron tunneling. This reaction requires excitation of the asymmetric C-H stretching vibration of the ═CH(2) group. The product is then identified by inelastic electron tunneling action spectroscopy (IETAS).     

The initiation and characterization of single bimolecular reactions with a scanning tunneling microscope

A scanning tunneling microscope (STM) operating at 9 K in ultrahigh vacuum was used to initiate a bimolecular reaction between isolated hydrogen sulfide and dicarbon molecules on the Cu(001) surface. The reaction products ethynyl (CCH) and sulfhydryl (SH) were identified by inelastic electron tunneling spectroscopy (STM-IETS) and by sequentially removing hydrogen atoms from an H2S molecule using energetic tunneling electrons. For comparison, the thermal diffusion and reaction of H2S and CC at 45 K and H2O and CC at 9 K were also observed.     

Imaging and vibrational spectroscopy of single pyridine molecules on Ag(110) using a low-temperature scanning tunneling microscope

A scanning tunneling microscope (STM) was used to extract the images of single, isolated pyridine molecules adsorbed on Ag(110) and to record their vibrational spectrum at 13 K. On the STM image, the pyridine molecule appears as an elongated protrusion along the [001] direction on top of a silver atom, indicating that it is bonded through its nitrogen lone pair electrons. STM inelastic electron tunneling spectroscopy of the adsorbed pyridine revealed C-D and C-H stretch modes at 282 and 378 meV, respectively.     

Chemical imaging of single 4,7,12,15-tetrakis[2.2]paracyclophane by spatially resolved vibrational spectroscopy

Single 4,7,12,15-tetrakis[2.2]paracyclophane were deposited on NiAl(110) surface at 11 K. Two adsorbed species with large and small conductivities were detected by the scanning tunneling microscope (STM). Their vibrational properties were investigated by inelastic electron tunneling spectroscopy (IETS) with the STM. Five vibrational modes were observed for the species with the larger conductivity. The spatially resolved vibrational images for the modes show striking differences, depending on the coupling of the vibrations localized on different functional groups within the molecule to the electronic states of the molecule. The vibrational modes are assigned on the basis of ab initio calculations. No IETS signal is resolved from the species with the small conductivity.     

Monolayer structure of tetracene on Cu (100) surface: parallel geometry

The geometrical arrangement of tetracene on Cu (100) surface at monolayer coverage is studied by using scanning tunneling microscopy measurement and density functional theory (DFT) calculations. Tetracene molecule is found to be oriented with its molecular plane parallel to the substrate surface, and no perpendicular geometry is observed at this coverage. The molecule is aligned either in the [011] or [011] direction due to the fourfold symmetry of the Cu (100) surface. DFT calculations show that the molecule with the "flat-lying" mode has larger adsorption energy than that with the "upright standing" mode, indicating that the former is the more stable structure. With the flat-lying geometry, the carbon atoms prefer to be placed between surface Cu atoms. The molecular center prefers to be located at the bridge site between two nearest surface Cu atoms.     

Vibronic states in single molecules: C60 and C70 on ultrathin Al2O3 films

Vibronic states are observed in single C(60) and C(70) molecules by scanning tunneling microscopy. When single fullerene molecules are adsorbed on a thin layer of Al(2)O(3) grown on a NiAl(110) substrate, equally spaced features are observed in the differential conductance (dI/dV), which are clearly resolved in d(2)I/dV(2) spectra. These features are attributed to the vibronic states of the molecule. The vibronic progressions are sensitive to the molecular orientations and can have different spacings in different electronic bands of the same molecule. For C(60,) these vibronic states are associated with the intramolecular A(g) and H(g) vibrational modes. Vibronic states are not resolved in molecules adsorbed on the metal surface. However, inelastic electron tunneling spectroscopy exhibits a vibrational mode at 64 meV for C(60) and 61 meV for C(70) adsorbed on NiAl(110).     

Direct observation of C2 hydrocarbon-oxygen complexes on Ag(110) with a variable-low-temperature scanning tunneling microscope

A variable-low-temperature scanning tunneling microscope (STM) was used to observe oxygen (O2), ethylene (C2H4), and acetylene (C2H2) molecules on a Ag(110) surface and the various complexes that were formed between these two hydrocarbons and oxygen at 13 K. Ethylene molecule(s) were moved to the vicinity of O2 either by STM tunneling electrons at 13 K or thermally at 45 K to form (C2H4)x-O2 (x = 1-4) complexes stabilized by C-H...O hydrogen bonding. Acetylene-oxygen complexes involving one or two acetylene molecules were observed.     

Gate-controlled current and inelastic electron tunneling spectrum of benzene: a self-consistent study

We use density functional theory based nonequilibrium Green's function to self-consistently study the current through the 1,4-benzenedithiol (BDT). The elastic and inelastic tunneling properties through this Au-BDT-Au molecular junction are simulated, respectively. For the elastic tunneling case, it is found that the current through the tilted molecule can be modulated effectively by the external gate field, which is perpendicular to the phenyl ring. The gate voltage amplification comes from the modulation of the interaction between the electrodes and the molecules in the junctions. For the inelastic case, the electron tunneling scattered by the molecular vibrational modes is considered within the self-consistent Born approximation scheme, and the inelastic electron tunneling spectrum is calculated.     

Local chemical reaction of benzene on Cu110 via STM-induced excitation

We have investigated the mechanism of the chemical reaction of the benzene molecule adsorbed on Cu(110) surface induced by the injection of tunneling electrons using scanning tunneling microscopy (STM). With the dosing of tunneling electrons of the energy 2-5 eV from the STM tip to the molecule, we have detected the increase of the height of the benzene molecule by 40% in the STM image and the appearance of the vibration feature of the nu(C-H) mode in the inelastic tunneling spectroscopy (IETS) spectrum. It can be understood with a model in which the dissociation of C-H bonds occurs in a benzene molecule that induces a bonding geometry change from flat-lying to up-right configuration, which follows the story of the report of Lauhon and Ho on the STM-induced change of benzene on the Cu(100) surface. [L. J. Lauhon and W. Ho, J. Phys. Chem. A 104, 2463 (2000)]. The reaction probability shows a sharp rise at the sample bias voltage at 2.4 V, which saturates at 3.0 V, which is followed by another sharp rise at the voltage of 4.3 V. No increase of the reaction yield is observed for the negative sample voltage up to 5 eV. In the case of a fully deuterated benzene molecule, it shows the onset at the same energy of 2.4 eV, but the reaction probability is 10(3) smaller than the case of the normal benzene molecule. We propose a model in which the dehydrogenation of the benzene molecule is induced by the formation of the temporal negative ion due to the trapping of the electrons at the unoccupied resonant states formed by the pi orbitals. The existence of the resonant level close to the Fermi level ( approximately 2.4 eV) and multiple levels in less than approximately 5 eV from the Fermi level, indicates a fairly strong interaction of the Cu-pi(*) state of the benzene molecule. We estimated that the large isotope effect of approximately 10(3) can be accounted for with the Menzel-Gomer-Redhead (MGR) model with an assumption of a shallow potential curve for the excited state.     

Chemisorption and dissociation of single oxygen molecules on Ag110

The chemisorption of single oxygen molecules on Ag110 and the dissociation of the adsorbed molecules induced by tunneling electrons were studied at 13 K using a variable-low-temperature scanning tunneling microscope. Two predominant types of chemisorbed O2 molecules were identified, one with the O2 molecular axis aligned along the [001] direction of the substrate [O2(001)], and the other with the molecular axis aligned along the [110] direction [O2(110)]. Tunneling of electrons between the scanning tunneling microscope tip and O2(001) caused the molecule either to rotate or dissociate, depending on the direction of electron tunneling. In contrast, electron tunneling caused O2(110) to dissociate regardless of tunneling direction. In addition to O2(001) and O2(110), several other oxygen species and their dynamical behaviors were observed.     

Simulation of single molecule inelastic electron tunneling signals in paraphenylene-vinylene oligomers and distyrylbenzene[2.2]paracyclophanes

Inelastic resonances in the electron tunneling spectra of several conjugated molecules are simulated using the nonequilibrium Greens function formalism. The vibrational modes that strongly couple to the electronic current are different from the infrared and Raman active modes. Spatially resolved inelastic electron tunneling (IET) intensities are predicted. The simulated IET intensities for a large distyrylbenzene paracyclophane molecule are in qualitative agreement with recent experimental results.     

A theoretical rationalization of a total inelastic electron tunneling spectrum: the comparative cases of formate and benzoate on Cu(111)

Inelastic electron tunneling spectroscopy (IETS) performed with the scanning tunneling microscope (STM) has been deemed as the ultimate tool for identifying chemicals at the atomic scale. However, direct IETS-based chemical analysis remains difficult due to the selection rules that await a definite understanding. We present IETS simulations of single formate and benzoate species adsorbed in the same upright bridge geometry on a (111)-cleaved Cu surface. In agreement with measurements on a related substrate, the simulated IET-spectra of formate/Cu(111) clearly resolve one intense C-H stretching mode whatever the tip position in the vicinity of the molecular fragment. At variance, benzoate/Cu(111) has no detectable IET signal. The dissimilar IETS responses of chemically related molecules--formate and benzoate adsorbates--permit us to unveil another factor that complements the selection rules, namely the degree of the vacuum extension of the tunneling active states perturbed by the vibrations. As a consequence, the lack of a topmost dangling bond orbital is entirely detrimental for STM-based inelastic spectroscopy but not for STM elastic imaging.     

Single-molecule vibrations, conformational changes, and electronic conductivity of five-membered heterocycles

Using an ultrahigh vacuum scanning tunneling microscope (STM), we have explored the interactions of isolated five-membered heterocycles, pyrrole, thiophene, pyrrolidine, and tetrahydrothiophene, with the Cu(001) surface at 9 K. Pyrrolidine was also studied on the Ag(001) surface. Important distinctions in bonding, vibrational spectra, and vibrationally mediated negative differential resistance were observed with the aid of single-molecule inelastic electron tunneling spectroscopy (STM-IETS).     

2H‐Tetrakis(3,5‐di‐tert‐butyl)phenylporphyrin on a Cu(110) Surface: Room‐Temperature Self‐Metalation and Surface‐Reconstruction‐Facilitated Self‐Assembly

The adsorption behavior of 2H‐tetrakis(3,5‐di‐tert‐butyl)phenylporphyrin (2HTTBPP) on Cu(110) and Cu(110)–(2×1)O surfaces have been investigated by using variable‐temperature scanning tunneling microscopy (STM) under ultrahigh vacuum conditions. On the bare Cu(110) surface, individual 2HTTBPP molecules are observed. These molecules are immobilized on the surface with a particular orientation with respect to the crystallographic directions of the Cu(110) surface and do not form supramolecular aggregates up to full monolayer coverage. In contrast, a chiral supramolecular structure is formed on the Cu(110)–(2×1)O surface, which is stabilized by van der Waals interactions between the tert‐butyl groups of neighboring molecules. These findings are explained by weakened molecule–substrate interactions on the Cu(110)–(2×1)O surface relative to the bare Cu(110) surface. By comparison with the corresponding results of Cu–tetrakis(3,5‐di‐tert‐butyl)phenylporphyrin (CuTTBPP) on Cu(110) and Cu(110)–(2×1)O surfaces, we find that the 2HTTBPP molecules can self‐metalate on both surfaces with copper atoms from the substrate at room temperature (RT). The possible origins of the self‐metalation reaction at RT are discussed. Finally, peculiar irreversible temperature‐dependent switching of the intramolecular conformations of the investigated molecules on the Cu(110) surface was observed and interpreted.     

Inelastic electron tunneling spectroscopy by STM of phonons at solid surfaces and interfaces

Inelastic electron tunneling spectroscopy (IETS) combined with scanning tunneling microscopy (STM) allows the acquisition of vibrational signals at surfaces. In STM-IETS, a tunneling electron may excite a vibration, and opens an inelastic channel in parallel with the elastic one, giving rise to a change in conductivity of the STM junction. Until recently, the application of STM-IETS was limited to the localized vibrations of single atoms and molecules adsorbed on surfaces. The theory of the STM-IETS spectrum in such cases has been established. For the collective lattice dynamics, i.e., phonons, however, features of STM-IETS spectrum have not been understood well, though in principle STM-IETS should also be capable of detecting phonons. In this review, we present STM-IETS investigations for surface and interface phonons and provide a theoretical analysis. We take surface phonons on Cu(1?1?0) and interfacial phonons relevant to graphene on SiC substrate as illustrative examples. In the former, we provide a theoretical formalism about the inelastic phonon excitations by tunneling electrons based on the nonequilibrium Green’s function (NEGF) technique applied to a model Hamiltonian constructed in momentum space for both electrons and phonons. In the latter case, we discuss the experimentally observed spatial dependence of the STM-IETS spectrum and link it to local excitations of interfacial phonons based on ab-initio STM-IETS simulation.     

Electron Transport through Single π‐Conjugated Molecules Bridging between Metal Electrodes

Understanding electron transport through a single molecule bridging between metal electrodes is a central issue in the field of molecular electronics. This review covers the fabrication and electron‐transport properties of single π‐conjugated molecule junctions, which include benzene, fullerene, and π‐stacked molecules. The metal/molecule interface plays a decisive role in determining the stability and conductivity of single‐molecule junctions. The effect of the metal–molecule contact on the conductance of the single π‐conjugated molecule junction is reviewed. The characterization of the single benzene molecule junction is also discussed using inelastic electron tunneling spectroscopy and shot noise. Finally, electron transport through the π‐stacked system using π‐stacked aromatic molecules enclosed within self‐assembled coordination cages is reviewed. The electron transport in the π‐stacked systems is found to be efficient at the single‐molecule level, thus providing insight into the design of conductive materials.     

Theoretical Study on Adsorption and Diffusion of N Atoms on Cu Low-index Surface

The adsorption and diffusion of N atoms on the three low-index Cu planes were studied using 5-parameter Morse potential (5-MP) method, and the best theory-experiment agreement was obtained. N atoms of Cu(100) surface sit on the fourfold hollow site with the vertical height of 0.018 nm closely coplanar with the topmost copper layer, and the four Cu-N bond lengths are 0.182 nm and the fifth Cu-N distance is 0.199 nm. For Cu(111) system, the existence of aberrant Cu(100) reconstructed structure is approved at higher coverage, and at low coverage the structure is almost an ideal Cu(111) surface structure. With respect to Cu(110) system, the N atoms are adsorbed at LB and H3 sites, not at SB site. The diffusion passage and diffusion barrier of adsorbed N atoms were also studied.     

一氧化碳共吸附法确定叔丁胺分子在Cu(111)表面的吸附位

采用扫描隧道显微镜(STM)和密度泛函理论(DFT)研究了78 K时单个叔丁胺分子在Cu(111)表面的吸附位. 我们提出以共吸附的一氧化碳√3 ×√3 超结构为基底铜原子的标识方法, 确定了低覆盖度的叔丁胺分子在Cu(111)表面的吸附位为顶位. 而采用单个一氧化碳分子标识基底铜原子的位置, 同样得出了叔丁胺分子的吸附位为顶位. 此外, 还采用DFT计算叔丁胺分子在Cu(111)表面的优势吸附构型. 理论计算结果表明顶位吸附构型为能量最稳定的构型, 与实验结果相吻合.     

Molecular assembly of rubrene on a metal/metal oxide nanotemplate

We investigated the adsorption properties and self-assembly of rubrene molecules on the copper oxide nanotemplate formed by high-temperature exposure of Cu(110) to molecular oxygen. Using high-resolution scanning tunneling microscopy under ultrahigh-vacuum conditions, we observed a complex variety of self-assembled motifs, driven by competing effects such as the chemical affinity between the organic molecule and the surface, surface coverage, and spatial confinement of the rubrene molecules within the rows of the template.     

Adsorption geometry of 4-picoline chemisorbed on the Cu(110) surface: a study of forces controlling molecular self-assembly

The adsorption of 4-picoline (4-methylpyridine) on the Cu(110) surface has been studied with time-of-flight electron stimulated desorption ion angular distribution (TOF-ESDIAD) and other methods. Using deuterium labeling in the methyl group and hydrogen labeling on the aromatic ring, it has been possible to separately monitor by TOF-ESDIAD the C-D bond directions and the C-H bond directions in the adsorbed molecule. These triangulation measurements have led to a detailed understanding of the conformation of the adsorbed molecule relative to the Cu(110) crystal lattice, allowing one to witness changes in the molecular conformation as adsorbate-adsorbate interactional effects take place for increasing coverages. At low coverages, the molecule adsorbs by the N atom at an atop Cu site with the aromatic ring parallel to the <001> azimuth and with the molecular axis inclined 33 (+/- 5) degrees along the <001> azimuth. As rows of 4-picoline molecules form long range ordered chain structures oriented along the <112> azimuth, the aromatic ring twists 29 degrees about the inclined molecular axis as a result of forces between the adsorbate molecules. The initial tilting of the molecular axis at low coverage is likely due to the interaction of the positive-outward dipole with its image in the substrate. The ring twist may result from dipoleminus signdipole forces between the adsorbate molecules in the rows formed tending to form nested parallel pyridine rings. These studies are the first to apply the TOF-ESDIAD method for the measurement of the direction of chemical bonds at more than one molecular location within an adsorbed molecule and the new method is named electron stimulated desorption-molecular triangulation (ESD-MT). The results obtained give information of importance in understanding the factors which control conformational effects during the molecular self-assembly of complex adsorbed molecules on surfaces.