Mechanisms of molecular manipulation with the scanning tunneling microscope at room temperature: chlorobenzene/si(111)-(7 x 7)

A self-consistent model to link surface electronic band structure to the voltage dependence of hot electron induced molecular nanoprobe experiments

Understanding the ultra-fast transport properties of hot charge carriers is of significant importance both fundamentally and technically in applications like solar cells and transistors. However, direct measurement of charge transport at the relevant nanometre length scales is challenging with only a few experimental methods demonstrated to date. Here we report on molecular nanoprobe experiments on the Si(111)-7 × 7 at room temperature where charge injected from the tip of a scanning tunnelling microscope (STM) travels laterally across a surface and induces single adsorbate toluene molecules to react over length scales of tens of nanometres. A simple model is developed for the fraction of the tunnelling current captured into each of the surface electronic bands with input from only high-resolution scanning tunnelling spectroscopy (STS) of the clean Si(111)-7 × 7 surface. This model is quantitatively linked to the voltage dependence of the molecular nanoprobe experiments through a single manipulation probability (i.e. fitting parameter) per state. This model fits the measured data and gives explanation to the measured voltage onsets, exponential increase in the measured manipulation probabilities and plateau at higher voltages. It also confirms an ultrafast relaxation to the bottom of a surface band for the injected charge after injection, but before the nonlocal spread across the surface.

Electron stimulated desorption of vanadyl-groups from vanadium oxide thin films on Ru(0001) probed with STM

Low-temperature scanning tunnelling microscopy (STM) is employed to study electron-stimulated desorption of vanadyl groups from an ultrathin vanadium oxide film. The vanadia patches are prepared by reactive vapour deposition of V onto a Ru(0001) surface and comprise a highly ordered network of six and twelve membered V-O rings, some of them terminated by upright V[double bond, length as m-dash]O groups. The vanadyl units can be desorbed via electron injection from the STM tip in a reliable fashion. From hundreds of individual experiments, desorption rates are determined as a function of bias voltage and tunnelling current. Data analysis reveals a distinct threshold behaviour with bias onsets at +3.3 V and -2.6 V for positive and negative polarity, respectively. The desorption rate varies quadratically (cubically) with the tunnelling current at positive (negative) sample bias, indicating that V[double bond, length as m-dash]O desorption is a many-electron process. Based on our findings, a mechanism for desorption is proposed that includes resonant tunnelling into anti-bonding or out of bonding orbitals, followed by vibrational ladder climbing in the binding potential of the V[double bond, length as m-dash]O ad-system. The underlying electronic states can be identified directly in the STM conductance spectra taken on the oxide surface.

Metal-Organic Framework Hybrids Aid Metabolic Profiling for Colorectal Cancer

Colorectal cancer (CRC) is the third most common fatal cancer worldwide, accounting for ≈10% of cancer-related mortality. Metabolic shift occurs from the very early stage during the development of CRC, which is of significant etiological and diagnostic importance toward precision medicine. Here, an advanced molecular tool to characterize the metabolic alterations in CRC, based on metal-organic framework (MOF) hybrids is reported. Consuming only 500 nL of plasma without any sample pretreatment, MOF hybrids yield direct metabolic fingerprints by laser desorption/ionization mass spectrometry in seconds. A diagnostic prediction model by a machine learning algorithm is constructed, to discriminate CRC patients from normal controls with an average area under the curve of 0.947 for the discovery cohort and 0.912 for the independent validation cohort. In addition, CRC-specific metabolic signature consisting of 34 potential biomarkers, based on the aforementioned diagnostic model is identified. The results advance the design of nanomaterial-based platforms for metabolic analysis and establish a new liquid biopsy tool for CRC screening compatible with the current clinical workflow in practice.

Effect of Hydrophilic Monomer Distribution on Self-Assembly of a pH-Responsive Copolymer: Spheres, Worms and Vesicles from a Single Copolymer Composition

A series of copolymers containing 50 mol % acrylic acid (AA) and 50 mol % butyl acrylate (BA) but with differing composition profiles ranging from an AA-BA diblock copolymer to a linear gradient poly(AA-grad-BA) copolymer were synthesized and their pH-responsive self-assembly behavior was investigated. While assemblies of the AA-BA diblock copolymer were kinetically frozen, the gradient-like compositions underwent reversible changes in size and morphology in response to changes in pH. In particular, a diblock copolymer consisting of two random copolymer segments of equal length (16 mol % and 84 mol % AA content, respectively) formed spherical micelles at pH >5, a mix of spherical and wormlike micelles at pH 5 and vesicles at pH 4. These assemblies were characterized by dynamic light scattering, cryo-transmission electron microscopy and small angle neutron scattering.

The nanometre limits of ballistic and diffusive hot-hole mediated nonlocal molecular manipulation

We report an experimental investigation into the surface-specific and experimental limits of the range of STM induced nonlocal molecular manipulation. We measure the spot-size of the nonlocal manipulation of bromobenzene molecules on the Si(111)-7 × 7 surface at room temperature at two voltages and for a wide range of charge-injection times (number of hot charge-carriers) from 1 s up to 500 s. The results conform to an initially ballistic, 6-10 nm, and then hot-hole diffusive, 10-30 nm, transport away from the localised injection site. This work gives further confirmation that nonlocal molecular manipulation by STM directly reveals the ultrafast transport properties of hot-charge carriers at surfaces.

Desorption of CO from individual ruthenium porphyrin molecules on a copper surface via an inelastic tunnelling process

The coordination of CO to metalloporphyrins changes their electronic and magnetic properties. Here we locally desorb CO molecules from a single ruthenium tetraphenylporphyrin carbonyl (CO-RuTPP) on Cu(110) using STM. The desorption is triggered by the injection of holes into the occupied states of the adsorbate using an unusual two-carrier process.

Molecular and atomic manipulation mediated by electronic excitation of the underlying Si(111)-7x7 surface

We report the local atomic manipulation properties of chemisorbed toluene molecules on the Si(111)-7x7 surface and of the silicon adatoms of the surface. Charge injected directly into the molecule, or into its underlying bonding silicon adatom, can induce the molecule to change bonding site. The voltage dependence of the rates of these processes match closely with scanning tunnelling spectroscopy of the toluene and adatom species. The branching ratio between toluene molecules which are moved to a neighbouring site, or those that travel further is invariant to voltage, suggesting a common final manipulation step for both injection into the molecule and into the bonding adatom site. At low temperatures the rate of silicon adatom manipulation matches that of toluene manipulation, further suggesting that all these manipulation processes are driven by electronic excitation of the underlying silicon surface. Our results therefore suggest that a common non-adiabatic process mediates atomic and molecular manipulation induced by the STM on the Si(111)-7x7 surface and may also mediate similar manipulation induced by the laser irradiation of the Si(111)-7x7 surface.

Current-Driven Hydrogen Desorption from Graphene: Experiment and Theory

Electron-stimulated desorption of hydrogen from the graphene/SiC(0001) surface at room temperature was investigated with ultrahigh vacuum scanning tunneling microscopy and ab initio calculations in order to elucidate the desorption mechanisms and pathways. Two different desorption processes were observed. In the high electron energy regime (4-8 eV), the desorption yield is independent of both voltage and current, which is attributed to the direct electronic excitation of the C-H bond. In the low electron energy regime (2-4 eV), however, the desorption yield exhibits a threshold dependence on voltage, which is explained by the vibrational excitation of the C-H bond via transient ionization induced by inelastic tunneling electrons. The observed current independence of the desorption yield suggests that the vibrational excitation is a single-electron process. We also observed that the curvature of graphene dramatically affects hydrogen desorption. Desorption from concave regions was measured to be much more probable than desorption from convex regions in the low electron energy regime (∼2 eV), as would be expected from the identified desorption mechanism.

Probing Single-Molecule Dissociations from a Bimolecular Complex NO-Co-Porphyrin

Axial coordinations of diatomic NO molecules to metalloporphyrins play key roles in dynamic processes of biological functions such as blood pressure control and immune response. Probing such reactions at the single molecule level is essential to understand their physical mechanisms but has been rarely performed. Here we report on our single molecule dissociation experiments of diatomic NO from NO-Co-porphyrin complexes describing its dissociation mechanisms. Under tunneling junctions of scanning tunneling microscope, both positive and negative energy pulses gave rise to dissociations of NO with threshold voltages, +0.68 and -0.74 V at 0.1 nA tunneling current on Au(111). From the observed power law relations between dissociation rate and tunneling current, we argue that the dissociations were inelastically induced with molecular orbital resonances by stochastically tunneling electrons, which is supported with our density functional theory calculations. Our study shows that single molecule dissociation experiments can be used to probe reaction mechanisms in a variety of axial coordinations between small molecules and metalloporphyrins.

Concerted Thermal-Plus-Electronic Nonlocal Desorption of Chlorobenzene from Si(111)-7 × 7 in the STM

The rate of desorption of chemisorbed chlorobenzene molecules from the Si(111)-7 × 7 surface, induced by nonlocal charge injection from an STM tip, depends on the surface temperature. Between 260 and 313 K, we find an Arrhenius thermal activation energy of 450 ± 170 meV, consistent with the binding energy of physisorbed chlorobenzene on the same surface. Injected electrons excite the chlorobenzene molecule from the chemisorption state to an intermediate physisorption state, followed by thermal desorption. We find a second thermal activation energy of 21 ± 4 meV in the lower temperature region between 77 and 260 K, assigned to surface phonon excitation.

Non-local atomic manipulation on semiconductor surfaces in the STM: the case of chlorobenzene on Si(111)-7×7

Control over individual atoms with the scanning tunnelling microscope (STM) holds the tantalising prospect of atomic-scale construction, but is limited by its "one atom at a time" serial nature. "Remote control" through non-local STM manipulation-as we have demonstrated in the case of chlorobenzene on Si(111)-7×7-offers a new avenue for future "bottom-up" nanofabrication, since hundreds of chemical reactions may be carried out in parallel. Thus a good understanding of the non-local manipulation process, as provided by recent experiments, is important. Comparison of scanning tunnelling spectroscopy (STS) measurements of the bare Si(111)-7×7 surface and chemisorbed chlorobenzene molecules with the voltage dependence of the non-local STM-induced desorption of chlorobenzene proves particularly instructive. For example, the chlorobenzene LUMO appears at +0.9 V with respect to the Fermi level, whereas non-local manipulation thresholds are found at +2.1 V and +2.7 V. This difference supports a picture in which the voltage thresholds for non-local electron-induced desorption depend principally on the energies of the electronic states of the surface. Furthermore, the demonstration that the non-local process is largely insensitive to surface steps up to five layers in height suggests that either the electron transport in this process is subsurface in character or surface charge transport is responsible but is in some way unaffected by the steps.

Atom-by-atom assembly

Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to 'see' individual atoms by means of imaging, but is also a tool that is used to 'touch' and 'take' the atoms, or to 'hear' their movements. Therefore, the STM can be considered as the 'eyes', 'hands' and 'ears' of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed.

How nanoscience translates into technology: the case of self-assembled monolayers, electron-beam writing, and carbon nanomembranes

One of the great quests in nanotechnology is to translate nanoprecision materials science into practical manufacturing processes. The paper by Angelova et al. in this issue of ACS Nano, which discusses the production of functional carbon-based membranes with a thickness of 0.5 to 3 nm, provides instructive insight into how researchers are pulling together complementary strands from a quarter century of nanoscience research to develop novel, hybrid processing schemes. In this Perspective, we reflect on the progress that is taking place in the two principal component technologies combined in this scheme, namely, (i) control of self-assembled monolayers, including their detailed atomic structures, and (ii) electron-induced manipulation and processing of molecular layers, as well as considering (iii) remaining challenges for thin membrane production in the future.

Preparing and regulating a bi-stable molecular switch by atomic manipulation

We present a scanning tunneling microscopy (STM) investigation into the influence of the STM tip on the adsorption site switching of polychlorinatedbiphenyl (PCB) molecules on the Si(111)-7 × 7 surface at room temperature. From an initially stable adsorption configuration, atomic manipulation by charge injection from the STM tip prepared a new bi-stable configuration that switched between two bonding arrangements. No switching rate bias dependence was found for +1.0 to +2.2 V. Assuming a thermally driven switching process we find that the measured energy barriers to switching are influenced by the exact location of the STM tip by more than 10%. We propose that this energy difference is due the dispersion interaction between the tip and the molecule.

Assembling and disassembling Ag clusters on Si(111)-(7×7) by vertical atomic manipulation

Atomic manipulation has been rarely used in the studies of complex structures and a low temperature requirement usually limits its application. Herein we have demonstrated a vertical manipulation technique to reproducibly and reversibly manipulating Ag atoms on an Si(111)-(7×7) surface by a scanning tunneling microscope tip at room temperature. Simple and complex Ag nanoclusters were assembled and disassembled with a precise control of single Ag atoms, which provided critical information on the size of these nanoclusters. The manipulation showed the growth processes of these Ag clusters and even partly unveiled their atomic structures. This technique can form a fundamental basis for further studies of the Ag/Si(111)-(7×7) system and for fabricating functional nanodevices in various metal-semiconductor systems.

Site- and energy-selective intramolecular manipulation of polychlorinated biphenyl (PCB) molecules

We demonstrate the conversion of an adsorbed precursor state of polychlorinated biphenyl (PCB) molecules on the Si(111)-7 × 7 surface at room temperature into a more stable configuration via site- and energy-selective atomic manipulation in the scanning tunneling microscope (STM). Whereas molecular desorption is maximized by electron injection into the chemisorbed molecular ring at low voltage, injection into the physisorbed molecular ring above a threshold voltage (2.5 V) favors the reconfiguration of the bonding. The results clearly demonstrate both intramolecular charge localization and intramolecular charge transportation as key ingredients in the atomic manipulation of individual polyatomic molecules.

A new mechanism of atomic manipulation: bond-selective molecular dissociation via thermally activated electron attachment

We report a new mechanism of (bond-selective) atomic manipulation in the scanning tunneling microscope (STM). We demonstrate a channel for one-electron-induced C-Cl bond dissociation in chlorobenzene molecules chemisorbed on the Si(111)-7 × 7 surface, at room temperature and above, which is thermally activated. We find an Arrhenius thermal energy barrier to one-electron dissociation of 0.8 ± 0.2 eV, which we correlate explicitly with the barrier between chemisorbed and physisorbed precursor states of the molecule. Thermal excitation promotes the target molecule from a state where one-electron dissociation is suppressed to a transient state where efficient one-electron dissociation, analogous to the gas-phase negative-ion resonance process, occurs. We expect the mechanism will be obtained in many surface systems, and not just in STM manipulation, but in photon and electron beam stimulated (selective) chemistry.

Nonlocal desorption of chlorobenzene molecules from the Si(111)-(7×7) surface by charge injection from the tip of a scanning tunneling microscope: remote control of atomic manipulation

We report the nonlocal desorption of chlorobenzene molecules from the Si(111)-(7×7) surface by charge injection from the laterally distant tip of a scanning tunneling microscope and demonstrate remote control of the manipulation process by precise selection of the atomic site for injection. Nonlocal desorption decays exponentially as a function of radial distance (decay length ∼100  A) from the injection site. Electron injection at corner-hole and faulted middle adatoms sites couples preferentially to the desorption of distant adsorbate molecules. Molecules on the faulted half of the unit cell desorb with higher probability than those on the unfaulted half.

Time-resolved scanning tunnelling microscopy for molecular science

Time-resolved scanning tunnelling microscopy (STM) and its application in molecular science are reviewed. STM can image individual atoms and molecules and thus is able to observe the results of molecular processes such as diffusion, desorption, configuration switching, bond-breaking and chemistry, on the atomic scale. This review will introduce time-resolved STM, its experimental limitations and implementations with particular emphasis on thermally activated and tunnelling current induced molecular processes. It will briefly examine the push towards ultrafast imaging. In general, results achieved by time-resolved STM demonstrate the necessity of both space and time resolution for fully characterizing molecular processes on the atomic scale.

Modelling components of future molecular devices

We discuss challenges involved in modelling different components of molecular devices and give several examples that demonstrate how computer modelling evolved over the last few years to become a comprehensive tool for designing molecules, predicting their adsorption and diffusion at surfaces, simulating atomic force microscopy imaging and manipulation of atoms and molecules at insulating surfaces and studying electron conduction in prototype molecular devices. We describe some of the computational techniques used for modelling adsorption, diffusion, imaging and manipulation of organic molecules at surfaces and challenges pertaining to these studies, give several examples of applications and discuss further prospects for theoretical modelling of complex organic molecules at surfaces.

Calibrating thermal and scanning tunnelling microscope induced desorption and diffusion for the chemisorbed chlorobenzene/Si(111)7 × 7 system

The precise calibration of thermally driven processes in scanning tunnelling microscope (STM) manipulation experiments, especially at room temperature and above, is necessary to uncover an accurate picture of non-thermal dynamical processes such as desorption induced by electronic transitions, driven by the STM current. Here we probe the displacement (the sum of desorption and diffusion) of chlorobenzene molecules chemisorbed on the Si(111)-7 × 7 surface, induced both by the STM electrical current and by heat. We also establish truly passive imaging inspection parameters. The activation energy for pure thermal displacement is 580 ± 20 meV, possibly associated with excitation to a physisorbed precursor state. STM induced displacement shows a marked decrease with increasing temperature, once the thermal effects are removed.

First-principles study of thermal and electron-activated dissociation of acetone on Si(001)

Using first-principles density-functional calculations, we investigate the reaction of acetone on the Si(001) surface, which exhibits the conversion from a kinetically controlled reaction to thermodynamically controlled one by means of thermal anneal or the highly confined electron beam of the scanning tunneling microscopy (STM) tip. We identified the four different reaction pathways forming not only two kinds of di-sigma structures on top of a single Si dimer (termed as the [2+2] cycloaddition structure) and across the ends of two adjacent Si dimers but also two bridge-bonded dissociative structures (termed the "end-bridge" and "dimer-bridge" structures) involving two adjacent Si dimers. Our calculated energy profiles for the reaction pathways show not only that formation of the [2+2] cycloaddition structure is kinetically favored because of its low-energy barrier, but also that, as temperature increases, the kinetically favored [2+2] cycloaddition structure is converted to the more thermodynamically stable end-bridge and dimer-bridge structures via an intermediate state where the O atom forms a dative bond to the down Si atom of the buckled dimer. In addition, we find that the Si-C bonding (antibonding) states of the [2+2] cycloaddition structure appear at about 1-2 (2-3) eV below (above) the Fermi level, in which injected holes (electrons) through the STM tip can be created (trapped) to give rise to a Si-C bond breakage. These results manifest that the kinetically controlled reaction of acetone on Si(001) is associated with the [2+2] cycloaddition structure, rather than the alpha-H cleavage structure proposed by a recent STM experiment.

Electronic Switching of Single Silicon Atoms by Molecular Field Effects

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

Quantifying desorption of saturated hydrocarbons from silicon with quantum calculations and scanning tunneling microscopy

Electron stimulated desorption of cyclopentene from the Si(100)-(2 x 1) surface is studied experimentally with cryogenic UHV STM and theoretically with transport, electronic structure, and dynamical calculations. Unexpectedly for a saturated hydrocarbon on silicon, desorption is observed at bias magnitudes as low as 2.5 V, albeit the desorption yields are a factor of 500 to 1000 lower than previously reported for unsaturated molecules on silicon. The low threshold voltage for desorption is attributed to hybridization of the molecule with the silicon surface, which results in low-lying ionic resonances within 2-3 eV of the Fermi level. These resonances are long-lived, spatially localized, and displaced in equilibrium with respect to the neutral state. This study highlights the importance of nuclear dynamics in silicon-based molecular electronics and suggests new guidelines for the control of such dynamics.

Surface Chemistry of Monochlorinated and Dichlorinated Benzenes on Si(100)2×1: Comparison Study of Chlorine Content and Isomeric Effects

Using X-ray photoelectron spectroscopy (XPS) and temperature-programmed desorption (TPD), the room temperature (RT) adsorption and thermal evolution of monochlorobenzene (MCB) and 1,3-dichlorobenzene (1,3-DCB) on Si(100)2x1 have been investigated and compared with that of 1,2-dichlorobenzene (1,2-DCB) reported previously. Like 1,2-DCB, the C 1s features observed at 284.6 (C(1)) and 286.0 eV (C(2)) for both MCB and 1,3-DCB could be attributed to the C-H and C-Cl bonds, respectively. The C(1)/C(2) intensity ratios for MCB (5.0) and 1,3-DCB (2.0) are found to follow the stoichiometric ratios of the C-H to C-Cl bonds for MCB and 1,3-DCB, respectively, indicating that both MCB and 1,3-DCB adsorb on Si(100)2x1 molecularly with negligible C-Cl dissociation at RT, in marked contrast to the partial C-Cl dissociation found for 1,2-DCB. Unlike 1,2-DCB with two discernible Cl 2s features at 270.3 and 271.2 eV, a single Cl 2s feature at 271.2 eV is observed for MCB and 1,3-DCB, in accord with the single local chemical environment for Cl. The TPD results show that MCB undergoes molecular desorption exclusively, similar to that found for benzene. Both molecular desorption and recombinative HCl desorption are found for 1,3-DCB, similar to that for 1,2-DCB. Despite the different Cl contents and relative Cl locations on the benzene ring, both MCB and 1,3-DCB exhibit RT adsorption behavior remarkably similar to that of benzene. To explain the C-Cl dissociation observed for 1,2-DCB, we propose a possible transition state involving the Cl atoms located at more physically compatible positions with the surface Si dimers in order to facilitate the conversion of 1,2-DCB (preferentially over 1,3-DCB) to dissociated products at RT. However, the thermal evolution of 1,3-DCB is closer to that of 1,2-DCB than that of MCB and benzene. The breakage of C-Cl bonds is found to occur at a relatively low temperature of 425 K, which suggests a relatively low activation barrier for the dechlorination of 1,3-DCB adspecies. Calculated energetics for 1,4-DCB on Si(100)2x1 shows that double dechlorination is not as favorable a process as those for 1,2-DCB and 1,3-DCB.

A reversible molecular switch based on pattern-change in chlorobenzene and toluene on a Si(111)-(7x7) surface

A reversible molecular switch is proposed, based on an observed change in a physisorbed pattern of chlorobenzene or toluene at Si(111)-(7x7), from "triangles" to "circles". Electronic excitation, at an applied surface voltage of Vs = -2.0 V, caused molecular migration, by one atomic site, from under the tip (switch "off"). Thereafter, the adsorbate pattern reverted thermally from circles to triangles (switch "on") across a measured activation barrier of Ea = 0.3 eV for chlorobenzene and 0.2 eV for toluene.

STM Study of the Conformation and Reaction of Long-Chain Haloalkanes at Si(111)-7 × 7

Scanning tunneling microscopy (STM) has been used to study the adsorption of 1-fluoro-, 1-chloro-, and 1-bromo-substituted C(12) alkanes at the Si(111)-7 x 7 surface, at temperatures from 300 to 500 K. We report self-assembly of these physisorbed adsorbates, C(12)H(25)X, to form approximately circular corrals, (C(12)H(25)X)(2), with charge transfer to a corralled adatom in each case (cf. Dobrin et al. Surf. Sci. 2006, 600, L43). The corrals comprised pairs of semicircular horizontal long-chain molecules stable to approximately 100 degrees C. At > or =150 degrees C, the corrals desorbed or reacted locally to imprint a halogen atom, X-Si, and an adjacent alkane residue, R-Si. The corral height profiles, together with the location of the imprinted X-Si resulting from thermal or electron-induced surface reaction, led to a picture of the molecular configurations in these haloalkane corrals, (C(12)H(25)X)(2), X = F, Cl, Br, and the dichloro corrals, 1,12-dichlorododecane, (ClC(12)H(24)Cl)(2).

Reaction of 1,2-Dibromobenzene with the Si(111)-7×7 Surface, a DFT Study

Reaction between 1,2-dibromobenzene and the Si(111)-7x7 surface has been studied theoretically on the DFT(B3LYP/6-31G(d)) level. A 12-atom silicon cluster, representing two adatoms and one rest atom of the faulted half of the unit cell, was used to model the silicon surface. The first step of the reaction was a covalent attachment (chemisorption) of an intact 1,2-dibromobenzene molecule to the silicon cluster. Binding energies were calculated to be between 1.04 and 1.14 eV, depending on the orientation of the molecule. A second step of the reaction was the transfer of the Br atom to the silicon cluster. Activation energies for the transfer of the Br atom were calculated to be between 0.4 and 0.6 eV, suggesting that the thermal bromination reaction occurs on a microsecond time scale at room temperature. A third step of the reaction could be the transfer of the second Br atom of the molecule, the desorption of the organic radical, or the change of the adsorption configuration of the radical, depending on the original orientation of the adsorbed intact molecule. A novel, aromatic, two-sigma-bound adsorbed configuration of the C6H4 radical, in which a carbon ring of the radical is perpendicular to the silicon surface, has been introduced to explain previous experimental observations (Surf. Sci. 2004, 561, 11).

Picometer-Scale Electronic Control of Molecular Dynamics Inside a Single Molecule

Tunneling electrons from a low-temperature (5 kelvin) scanning tunneling microscope were used to control, through resonant electronic excitation, the molecular dynamics of an individual biphenyl molecule adsorbed on a silicon(100) surface. Different reversible molecular movements were selectively activated by tuning the electron energy and by selecting precise locations for the excitation inside the molecule. Both the spatial selectivity and energy dependence of the electronic control are supported by spectroscopic measurements with the scanning tunneling microscope. These experiments demonstrate the feasibility of controlling the molecular dynamics of a single molecule through the localization of the electronic excitation inside the molecule.

Tip-state control of rates and branching ratios in atomic manipulation

We report the atomic manipulation properties of two distinct, stable, and reproducible states of a scanning tunneling microscope tip applied to chlorobenzene/Si(111)-(7x7). We show that the tip state influences the rates of (current-driven) molecular desorption and C-Cl dissociation as well as the branching ratio between these processes, but does not change the mediating electronic channel or the required number of electrons. These manipulation properties combined with the imaging properties of the two tip-states suggest the major difference between tip-states is their coupling efficiency to the pi-states of the chlorobenzene molecule.

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.

Two-electron dissociation of single molecules by atomic manipulation at room temperature

Using the tip of a scanning tunnelling microscope (STM) to mechanically manipulate individual atoms and molecules on a surface is now a well established procedure. Similarly, selective vibrational excitation of adsorbed molecules with an STM tip to induce motion or dissociation has been widely demonstrated. Such experiments are usually performed on weakly bound atoms that need to be stabilized by operating at cryogenic temperatures. Analogous experiments at room temperature are more difficult, because they require relatively strongly bound species that are not perturbed by random thermal fluctuations. But manipulation can still be achieved through electronic excitation of the atom or molecule by the electron current tunnelling between STM tip and surface at relatively high bias voltages, typically 1-5 V. Here we use this approach to selectively dissociate chlorine atoms from individual oriented chlorobenzene molecules adsorbed on a Si(111)-7 x 7 surface. We map out the final destination of the chlorine daughter atoms, finding that their radial and angular distributions depend on the tunnelling current and hence excitation rate. In our system, one tunnelling electron has nominally sufficient energy to induce dissociation, yet the process requires two electrons. We explain these observations by a two-electron mechanism that couples vibrational excitation and dissociative electron attachment steps.

Decoration of surfaces with size-selected clusters and molecular manipulation at room temperature: precision and uncertainty in organizing atoms

The deposition onto surfaces of clusters of atoms, prepared and size-selected in the gas phase, is, like atomic or molecular manipulation with the scanning tunnelling microscope, an appealing (but parallel) route to the creation of nanoscale surface features. Both of these seemingly orthogonal approaches allow, in principle, a selected number of atoms to be organized, and both are strongly affected by the lateral thermal diffusion of the constituent atoms, molecules or clusters over the surface. In this sense, the room-temperature (as opposed to cryogenic-temperature) regime can be regarded as a hostile environment for organizing atoms. In this paper we review recent achievements in size-selected cluster deposition and molecular manipulation at room temperature and thus address the fundamental question: with what precision can we organize atoms at room temperature?