Inelastic tunneling spectroscopy using scanning tunneling microscopy on trans-2-butene molecule: spectroscopy and mapping of vibrational feature

Inelastic tunneling spectroscopy (IETS) measurement using scanning tunneling microscopy (STM) with a commercially available STM set up is presented. The STM-IETS spectrum measured on an isolated trans-2-butene molecule on the Pd(110) shows a clear vibrational feature in d2I/dV2 at the bias voltage of 360 mV and -363 mV, which corresponds to the nu(C-H) mode (d2I/dV2 approximately 10 nA/V2). In addition, we have obtained an image by mapping the vibrational feature of nu(C-H) in d2I/dV2. The image is obtained by scanning the tip on the surface with the feedback loop activated while the modulation voltage is superimposed on the sample voltage. With the method that is readily performable with conventional software, we have clearly differentiated the molecules of trans-2-butene and butadiene through the mapping of the vibrational feature, demonstrating its capability of chemical identification in atomic scale.     

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.     

Orbital specific chemistry: controlling the pathway in single-molecule dissociation

A scanning tunneling microscope (STM) was used to control the pathway of the dissociation of single O(2) molecules chemisorbed on Ag(110) at 13 K. Tunneling of electrons from the STM tip into the O(2) caused dissociation of the molecule, giving rise to two adsorbed O atoms separated along the [110] direction. In contrast, the ejection of electrons from the O(2) molecule produced adsorbed O atoms separated along the [001] direction. These results illustrate that control of the dissociation pathway and product formation are associated with a specific molecular orbital located at the Fermi level.     

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.     

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 puzzle of contrast inversion in DNA STM imaging

DNA has been at the center of an imaging effort since the invention of the scanning tunneling microscope (STM). In some of the STM imaging reports the molecules appeared with negative contrast, i.e., "submerged" under the metal background and darker. We demonstrate the phenomenon of contrast inversion in DNA STM imaging by controlled and spontaneous contrast inversions and by the dependence of the DNA apparent height with respect to the surface on the imaging bias voltage. Using these characterizations, we formulate a model explaining the above phenomenon by resonant tunneling through virtual states in the vacuum between the STM tip and the DNA molecule.     

Phenyl species formation and preferential hydrogen abstraction in the decomposition of chemisorbed benzoate on Cu(110)

The adsorption and decomposition of benzoic acid on the Cu(110) surface has been investigated using temperature-programmed reaction (TPR) spectroscopy and scanning tunneling microscopy (STM). The benzoate species is found to exist in two conformations--a phase containing upright species at monolayer saturation and a phase containing many lying-down species at lower coverages. Thermal decomposition begins to occur near 500 K, yielding benzene and CO(2). It is found that phenyl species, generated preferentially from the lying-down benzoate species, efficiently abstract H atoms from undecomposed benzoate species to produce benzene in a rate-controlling process with an activation energy of about 29 kcal/mol. Using deuterium-atom substitution at the 4-C position on the benzoate ring it is found that the hydrogen-abstraction reaction is selective for 2,3 and 5,6 C-H bonds. This observation indicates that the mobile phenyl species is surface bound and preferentially attacks C-H bonds which are nearest the Cu surface and bind the benzoate species as either an upright species or a tilted species.     

STM study of morphology and electron transport features in cytochrome c and nanocluster molecule monolayers.

The morphology and electron tunneling through single cytochrome c and nanocluster Pt(5)(CO)(7)[P(C(6)H(5))](4) molecules organized as monolayer Langmuir-Blodgett (LB) films on graphite substrate have been studied experimentally using scanning tunneling microscopy (STM) and spectroscopy techniques with sub-nanometer spatial resolution in a double barrier tunnel junction configuration STM tip-monomolecular film-conducting substrate at ambient conditions. STM images of the films revealed globular structures with characteristic diameters (approximately 3.5 nm for the protein molecule and approximately 1.2 nm for the nanocluster). The spectroscopic study by recording the tunneling current-bias voltage (I-V) curves revealed tunneling I-V characteristics with features as steps of different width and heights that are dependent on the STM tip position over the molecule in the monolayer, giving evidence for sequential discrete electron-tunneling effects with the combination of the single electron Coulomb-charging energy and the electronic energy level separation (molecular spectrum) in such immobilized metalloprotein and nanocluster structures that can be of interest for the development of bioelectronic and hybrid functional nanosystems.     

Theoretical simulations of the tip-induced configuration changes of the 4,4(')-diacetyl-p-terphenyl molecule chemisorbed on Si(001)

We have investigated from a theoretical point of view modifications of the 4,4(')-diacetyl-p-terphenyl molecule chemisorbed on Si(001) induced by the scanning tunneling microscope (STM). In previous experiments, these modifications were observed to occur preferentially at the end of the molecule after a +4.0 V voltage pulse and at the center after a +4.5 V voltage pulse. In the framework of ab initio simulations, we have realized a systematic energetic study of the dissociative chemisorption of one, two, or three phenyl rings of the substituted p-terphenyl molecule. Charge densities were then calculated for the investigated configurations and compared to the STM topographies. Before manipulation with the STM tip, the substituted p-terphenyl molecule is preferentially adsorbed without phenyl ring dissociation, allowing a partial rotation of the central phenyl ring. Our results show that the STM induced modifications observed at the end of the molecule might originate from the dissociation of two phenyl rings (one central and one external ring), while the modifications occurring at the central part of the molecule can be interpreted as a dissociation of the two external rings.     

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.     

Elastic and inelastic electron tunneling spectroscopy of a new rectifying monolayer

Rectification of electrical current was observed in a Langmuir-Schaefer monolayer of fullerene-bis[ethylthio-tetrakis(3,4-dibutyl-2-thiophene-5-ethenyl)-5-bromo-3,4-dibutyl-2-thiophene] malonate, Au electrodes at room temperature (there are two regimes of asymmetry, at lower bias, i.e., between 0 and +/-2 V, and at higher bias), and also between Pb and Al electrodes at 4.2 K. The latter experiment was coupled with second harmonic detection of the second derivative of the current with respect to voltage (d2I/dV2). The d2I/dV2 spectrum shows intramolecular vibrations, and also two antisymmetric broad bands, centered at +/-0.65 V, due to resonant electron tunneling between the Fermi level(s) of the electrodes and the lowest unoccupied molecular orbital of the molecule.     

Current-voltage characteristics of a homologous series of polycyclic aromatic hydrocarbons

A novel alkyl-substituted polycyclic aromatic hydrocarbon (PAH) with D(2h) symmetry and 78 carbon atoms in the aromatic core (C78) was synthesized, thereby completing a homologous series of soluble PAH compounds with increasing size of the aromatic pi system (42, 60, and 78 carbon atoms). The optical band gaps were determined by UV/Vis and fluorescence spectroscopy in solution. Scanning tunneling microscopy (STM) and spectroscopy (STS) revealed diode-like current versus voltage (I-V) characteristics through individual aromatic cores in monolayers at the interface between the solution and the basal plane of graphite. The asymmetry of the current-voltage (I-V) characteristics increases with the increasing size of the aromatic core, and the concomitantly decreasing HOMO-LUMO gap. This is attributed to resonant tunneling through the HOMO of the adsorbed molecule, and an asymmetric position of the molecular species in the tunnel junction. Consistently, submolecularly resolved STM images at negative substrate bias are in good agreement with the calculated pattern for the electron densities of the HOMOs. The analysis provides the basis for tailoring rectification with a single molecule in an STM junction.     

Understanding the contrast mechanism in scanning tunneling microscopy (STM) images of an intermixed tetraphenylporphyrin layer on Ag(111)

The appearance of tetraphenylporphyrins in scanning tunneling micrographs depends strongly on the applied bias voltage. Here, we report the observation and identification of certain features in scanning tunneling microscopy (STM) images of intermixed layers of tetraphenylporphyrin (2HTPP) and cobalt-tetraphenylporphyrin (CoTPP) on Ag(111). A significant fraction of an ordered monolayer of commercially available CoTPP appears as "pits" at negative bias voltages around -1 V. The obvious possibility that these pits are missing molecules within the ordered layer could be ruled out by imaging the molecules at reduced bias voltages, at which the contrast of the pits fades, and at positive bias voltages around +1 V, at which the image contrast is inverted. With the investigation of the electronic structure, in particular the density of states (DOS) close to the Fermi level, of CoTPP and 2HTPP layers by means of ultraviolet photoelectron spectroscopy (UPS) and scanning tunneling spectroscopy (STS), the contrast mechanism was clarified. The correlation of the bias dependent contrast with the UPS data enabled us to interpret the "pits" as individual 2HTPP molecules. Additional evidence could be provided by imaging layers of different mixtures of 2HTPP and CoTPP and by high-resolution STM imaging of the features in CoTPP.     

Selective internal manipulation of a single molecule by scanning tunneling microscopy

We have studied the adsorption of the polyaromatic molecule 1,4"-paratriphenyldimethylacetone, which we have nicknamed Trima. The originality of this linear molecule is that it was designed and synthesized to have two functionalities. First, chemisorb itself to the surface by its two ends rather like a bridge. Second, the central part of the molecule could then be rotated by injecting electrons with the tip of the scanning tunneling microscope (STM). The length of the molecule corresponds exactly to the spacing between five dimers in a row on the Si(100)-2 x 1 surface. We found that the molecule adsorbs as expected on the clean silicon surface by using complementary STM and synchrotron radiation studies. Manipulation of individual molecules with the STM tip showed selective internal modifications that were highly voltage dependent. These manipulations were found to be compatible with an electronic excitation of the pi-pi* transition of the molecule.     

Electronic structures of size-selected single-layered platinum clusters on silicon(111)-7x7 surface at a single cluster level by tunneling spectroscopy

Tunneling spectra of size-selected single-layered platinum clusters (size range of 5-40) deposited on a silicon(111)-7x7 surface were measured individually at a temperature of 77 K by means of a scanning tunneling microscope (STM), and the local electronic densities of states of individual clusters were derived from their tunneling spectra measured by placing an STM tip on the clusters. In a bias-voltage (V(s)) range from -3 to 3 V, each tunneling spectrum exhibits several peaks assignable to electronic states associated with 5d states of a constituent platinum atom and an energy gap of 0.1-0.6 eV in the vicinity of V(s)=0. Even when platinum cluster ions having the same size were deposited on the silicon(111)-7x7 surface, the tunneling spectra and the energy gaps of the deposited clusters are not all the same but can be classified in shape into several different groups; this finding is consistent with the observation of the geometrical structures of platinum clusters on the silicon(111)-7x7 surface. The mean energy gap of approximately 0.4 eV drops to approximately 0.25 eV at the size of 20 and then decreases gradually as the size increases, consistent with our previous finding that the cluster diameter remains unchanged, but the number density of Pt atoms increases below the size of 20 while the diameter increases, but the density does not change above it. It is concluded that the mean energy gap tends to decrease gradually with the mean cluster diameter. The dependence of the mean energy gap on the mean Pt-Pt distance shows that the mean energy gap decreases sharply when the mean Pt-Pt distance exceeds that of a platinum metal (0.28 nm).     

Chemisorbed benzoate-to-benzene conversion via phenyl radicals on Cu(110): kinetic observation of conformational effects

The adsorption and decomposition of benzoic acid on the Cu(110) surface has been investigated using temperature-programmed reaction (TPR) spectroscopy and scanning tunneling microscopy (STM). The benzoate species is found to exist in two conformations: a phase containing upright species at monolayer saturation and a phase containing many tilted species at lower coverages. Thermal decomposition begins to occur near 500 K, yielding benzene and CO2. It is found that phenyl radicals, generated preferentially from the tilted benzoate species, efficiently abstract H atoms from undecomposed benzoate species to produce benzene in a rate-controlling process with an activation energy of about 29 kcal/mol. Using deuterium atom substitution at the 4-C position on the benzoate ring, it is found that the hydrogen abstraction reaction is selective for 2-,3- and 5-,6-C-H bonds. This observation indicates that the mobile phenyl radical is surface bound and preferentially attacks C-H bonds which are nearest the Cu surface binding the benzoate species, either as an upright species or as a tilted species.     

Direct and indirect causes of Fermi level pinning at the SiO/GaAs interface

The correlation between atomic bonding sites and the electronic structure of SiO on GaAs(001)-c(2x8)/(2x4) was investigated using scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and density functional theory (DFT). At low coverage, STM images reveal that SiO molecules bond Si end down; this is consistent with Si being undercoordinated and O being fully coordinated in molecular SiO. At approximately 5% ML (monolayer) coverage, multiple bonding geometries were observed. To confirm the site assignments from STM images, DFT calculations were used to estimate the total adsorption energies of the different bonding geometries as a function of SiO coverage. STS measurements indicated that SiO pins the Fermi level midgap at approximately 5% ML coverage. DFT calculations reveal that the direct causes of Fermi level pinning at the SiO GaAs(001)-(2x4) interface are a result of either local charge buildups or the generation of partially filled dangling bonds on Si atoms.     

Probing the 4f states of ceria by tunneling spectroscopy

Low-temperature scanning tunneling microscopy and spectroscopy have been employed to analyze the local electronic structure of the (111) surface of a ceria thin film grown on Ru(0001). On pristine, defect-free oxide terraces, the empty 4f states of Ce(4+) ions appear as the only spectral feature inside the 6 eV oxide band gap. In contrast, occupied states are detected between -1.0 and -1.5 eV below E(Fermi) in conductance spectra of different point and line defects, such as surface oxygen vacancies, grain boundaries and step edges. They are assigned to partially filled 4f states localized at the Ce(3+) ions. The presence of excess electrons indicates the oxygen-deficient nature of the direct oxide environment. The f state spectroscopy with the STM allows us to probe the spatial distribution of Ce(3+) ions in the ceria surface, providing unique insight into the local reduction state of this chemically important material system.     

Sum frequency generation vibrational spectroscopic and high-pressure scanning tunneling microscopic studies of benzene hydrogenation on Pt(111)

Sum frequency generation (SFG) vibrational spectroscopy and high-pressure scanning tunneling microscopy (HP-STM) have been used in combination for the first time to study a catalytic reaction. These techniques have been able to identify surface intermediates in situ during benzene hydrogenation on a Pt(111) single-crystal surface at Torr pressures. In a background of 10 Torr of benzene, STM is able to image small ordered regions corresponding to the c(2 radical3 x 3)rect structure in which each molecule is chemisorbed at a bridge site. In addition, individual benzene molecules are also observed between the ordered regions. These individual molecules are assumed to be physisorbed benzene on the basis of the SFG results showing both chemisorbed and physisorbed molecules. The surface becomes too mobile to image upon addition of hydrogen but is determined to have physisorbed and chemisorbed benzene present by SFG. It was spectroscopically determined that heating the platinum surface after poisoning with CO displaces benzene molecules. The high-coverage pure CO structure of (radical19 x radical19)R23.4 degrees imaged with STM is a verification of spectroscopic measurements.     

Significance of local density of states in the scanning tunneling microscopy imaging of alkanethiol self-assembled monolayers

A systematic scanning tunneling microscopy (STM) study of alkanethiol self-assembled monolayers (SAMs) is presented as a function of the bias voltage, tunneling current, and tip-termini separation. Stable and etch-pit free SAMs of close-packed undecanethiol/Au(111) were obtained after annealing in ultrahigh vacuum. STM revealed two distinct c(4x2) structures with four nonequivalent molecules per unit cell. For both structures, reversible contrast variations occur upon systematically tuning the bias voltage, the current, and the tip-termini distance. These contrast transitions originate from probing the corresponding local density of states (LDOS) of each molecule and not from the reorientation of the alkanethiol chains. The STM contrast is particularly sensitive to the tip-termini separation in the range of 0.5-2.5 A, reflecting the distance-dependence of LDOS. At a fixed tip elevation, the STM contrast is less sensitive to changes in bias within 0.1-1.2 V. For the first time, we demonstrate that LDOS may override the physical height variations in the STM topographic contrast for alkanethiol SAM systems.