The frustrated motion of benzene on the surface of Si(111)

Adsorption of 2-vinyl thiophene on Si(100)2 × 1: A van Der Waals corrected DFT study

Oligo- and polythiophenes on surfaces play a fundamental role in building molecular circuits and organic-based electronics and may be assembled via interaction of the monomer units with the surface. In this framework, the nature of interaction of 2-vinyl thiophene (2VTP), a conjugated heteroaromatic monomer unit, with the Si (100) surface was studied by means of density functional theory (DFT). In particular, structural optimizations were performed comparing the effects of the inclusion of van der Waals (VdW) forces. It came out that the adsorption through the double bond is energetically favored, if VdW forces are included, whereas the adsorption through both aromatic ring and double bond simultaneously is more stable, if they are excluded. Physisorbed states were singled out and the barriers between two of them and the corresponding chemisorbed states were calculated along with the imaginary frequencies of the transition states. Also the transition energies have different values if the VdW forces are included.

Mapping the site-specific potential energy landscape for chemisorbed and physisorbed aromatic molecules on the Si(1 1 1)-7 × 7 surface by time-lapse STM

We present a scanning tunnelling microscope study of site-specific thermal displacement (desorption or diffusion) of benzene, toluene, and chlorobenzene molecules on the Si(1 1 1)-7 × 7 surface. Through time-lapse STM imaging and automated image analysis we probe both the chemisorbed and the physisorbed states of these molecules. For the chemisorption to physisorption transition there are distinct site-specific variations in the measured rates, however their kinetic origin is ambiguous. There is also significant variation in the competing rates out of the physisorbed state into chemisorption at the various surface sites, which we attribute to differences in site-specific Arrhenius pre-factors. A prediction of the outcome of the competing rates and pre-factors for benzene over three hours matches experiment.

Preservation of epoxy groups on surfaces in the covalent attachment of butadiene monoxide on Si(111)-(7×7): the effect of a vinyl substituent

A vinyl substituent ensures that butadiene monoxide selectively binds to Si(111)-(7×7) through a [2+2]-like cycloaddition, maintaining an epoxy group in the cycloadduct.

Room temperature discrimination of adsorbed molecules and attachment sites on the Si(111)-7 × 7 surface using a qPlus sensor

In this paper, we show that simultaneous noncontact atomic force microscopy (nc-AFM) and scanning tunneling microscopy (STM) is a powerful tool for molecular discrimination on the Si(111)-7 × 7 surface, even at room temperature. Using density functional theory modeling, we justify this approach and show that the force response allows us to distinguish straightforwardly between molecular adsorbates and common defects, such as vacancies. Finally, we prove that STM/nc-AFM method is able to determine attachment sites of molecules deposited on semiconductor surface at room temperature.

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.

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.

Adsorption-induced desorption of benzene on Si(111)-7 x 7 by substrate-mediated electronic interactions

The process of benzene adsorption on an adjacent adatom-rest atom pair on Si(111)-7 x 7 at room temperature was studied using in-situ scanning tunneling microscopy (STM). Both adsorption and desorption of benzene were observed to take place mostly at adjacent sites during the process. DFT calculation results show that the bond length between the rest atom and the carbon atom in a pre-adsorbed benzene molecule increases due to the charge transfer from a neighboring rest atom in response to an approaching benzene molecule. Such increase in the bond length, when coupled resonantly to the C-Si thermal vibration, could result in bond breakage and desorption of the adsorbate. The studies provide evidence for the desorption of a chemisorbed benzene caused by an adsorbing benzene at a neighboring site through a substrate-mediated electronic interaction.

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).

Formation of Molecular Templates Containing Cumulative Double Bonds (CCC) at Organic/Silicon Hybrid Interfaces

The cumulative double bond (C=C=C), an important intermediate in synthetic organic chemistry, was successfully prepared via the selective attachment of acetylethyne to Si(111)-7 x 7. The experimental observation of the characteristic vibrational modes and electronic structures of the C=C=C group in the surface species demonstrates the [4 + 2]-like cycloaddition occurring between the terminal O and C atoms of acetylethyne and the neighboring Si adatom-rest atom pair, consistent with the prediction of density functional theory calculations. Scanning tunneling microscopy images further reveal that the molecules selectively bind to the adjacent adatom-rest atom pairs on Si(111)-7 x 7.

Selective formation of cumulative double bonds (C[double bond]C[double bond]N) in the attachment of multifunctional molecules on Si(111)-7 x 7

The cumulative double bond (C[double bond]C[double bond]N), an important intermediate in synthetic organic chemistry, was successfully prepared via the selective attachment of acrylonitrile to Si(111)-7 x 7. The covalent binding of acrylonitrile on Si(111)-7 x 7 was studied using high-resolution electron energy loss spectroscopy (HREELS), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), scanning tunneling microscopy (STM) and DFT calculations. The observation of the characteristic vibrational modes and electronic structures of the C[double bond]C[double bond]N group in the surface species demonstrates the [4 + 2]-like cycloaddition occurring between the terminal C and N atoms of acrylonitrile and the neighboring adatom-rest atom pair, consistent with the prediction of DFT calculations. STM studies further show the preferential binding of acrylonitrile on the center adatom sites of faulted halves of Si(111)-7 x 7 unit cells.

Self-directed growth of molecular nanostructures on silicon

Advances in techniques for the nanoscale manipulation of matter are important for the realization of molecule-based miniature devices with new or advanced functions. A particularly promising approach involves the construction of hybrid organic-molecule/silicon devices. But challenges remain--both in the formation of nanostructures that will constitute the active parts of future devices, and in the construction of commensurately small connecting wires. Atom-by-atom crafting of structures with scanning tunnelling microscopes, although essential to fundamental advances, is too slow for any practical fabrication process; self-assembly approaches may permit rapid fabrication, but lack the ability to control growth location and shape. Furthermore, molecular diffusion on silicon is greatly inhibited, thereby presenting a problem for self-assembly techniques. Here we report an approach for fabricating nanoscale organic structures on silicon surfaces, employing minimal intervention by the tip of a scanning tunnelling microscope and a spontaneous self-directed chemical growth process. We demonstrate growth of straight molecular styrene lines--each composed of many organic molecules--and the crystalline silicon substrate determines both the orientation of the lines and the molecular spacing within these lines. This process should, in principle, allow parallel fabrication of identical complex functional structures.

CONTROLLEDMOLECULARADSORPTION ONSILICON: Laying a Foundation for Molecular Devices

This review is about understanding and controlling organic molecular adsorption on silicon. The goal is to provide a microscopic picture of structure and bonding in covalently attached molecule-silicon surface systems. The bias here is that an unprecedented, detailed understanding of adsorbate-surface structures is required in order to gain the control necessary to incorporate organic function into existing technologies or, eventually, to make new molecule-scale devices. A discussion of recent studies of adsorbate structure is presented. This includes simple alkenes, polyenes, benzene, and carene adsorbed on Si(100). Also included is a discussion of wet chemical procedures for forming alkyl and alkoxy covalently functionalized silicon. These discussions are presented together with comments on the related issues of adsorption dynamics and nano-scale manipulation in an effort to point the way toward principles and procedures that will allow the hybrid properties of organic molecules and surfaces to be harnessed.

Isolation of an intrinsic precursor to molecular chemisorption

Over the past 70 years, numerous gas-surface adsorption studies have indicated the existence of a weakly bound, mobile intermediate that is a precursor to chemical bond formation. The direct observation and characterization of such a species are presented. Precursor and chemisorbed benzene on a silicon surface were clearly distinguished with the use of a tunable-temperature scanning tunneling microscope. Precursor decay to chemisorption was observed, allowing the salient features of the potential energy surface to be determined.