Formation of Di-σ Bond in Benzene Chemisorption on Si(111)-7×7

Surface-Induced Keto-Enol Tautomerization of DNA Base Molecules and Consequent [4 + 2]-like Cycloaddition on Si(111)7×7

Adsorption and film growth of deoxyribonucleic acid (DNA) base molecules (cytosine, guanine, thymine, and adenine) on Si(111)7×7 have been studied by combining X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). Multiple tautomeric forms and keto-enol tautomerization are revealed by the O 1s, N 1s, and C 1s XPS spectra of the O-containing DNA bases: cytosine, guanine, and thymine. While the carbonyl group-containing keto tautomer is more stable in a thick film and in powder, the hydroxyl group-containing enol tautomer is found at the interface. The keto-enol tautomerization, as induced by the reactive Si(111)7×7 surface, leads to the formation of a conjugated aromatic six-membered ring with a delocalized π electron system and to the consequent [4 + 2]-like cycloaddition between the enol tautomer and the 7×7 surface. The DFT calculation suggests that the enol tautomer exhibits a kinetic advantage over the keto one for the [4 + 2]-like cycloaddition. Among the several plausible pathways for the cycloaddition provided by the enol tautomer, the experimentally determined one involves a ring N and ring C atom (a polar pair), rather than two ring C atoms (a nonpolar pair), to better match the polar Si adatom-restatom pair of the 7×7 surface. Furthermore, the reacted ring C atom does not have any attached terminal functional group (e.g., -NH₂ and -OH). Further deposition leads to continuous film growth in the keto tautomeric form for cytosine and guanine. For the only O-free DNA base molecule, adenine, dative bonding N → Si, rather than the [4 + 2]-like cycloaddition, is observed on the 7×7 surface. Of the four DNA base molecules, adenine is also the only one with its aromaticity maintained when adsorbed on the Si(111)7×7 surface. A reactive surface like the 7×7 surface could therefore provide a new control to trigger tautomerization that is often associated with genetic mutation.

Guided Molecular Assembly on a Locally Reactive 2D Material

Atomically precise engineering of the position of molecular adsorbates on surfaces of 2D materials is key to their development in applications ranging from catalysis to single-molecule spintronics. Here, stable room-temperature templating of individual molecules with localized electronic states on the surface of a locally reactive 2D material, silicene grown on ZrB₂ , is demonstrated. Using a combination of scanning tunneling microscopy and density functional theory, it is shown that the binding of iron phthalocyanine (FePc) molecules is mediated via the strong chemisorption of the central Fe atom to the sp³ -like dangling bond of Si atoms in the linear silicene domain boundaries. Since the planar Pc ligand couples to the Fe atom mostly through the in-plane d orbitals, localized electronic states resembling those of the free molecule can be resolved. Furthermore, rotation of the molecule is restrained because of charge rearrangement induced by the bonding. These results highlight how nanoscale changes can induce reactivity in 2D materials, which can provide unique surface interactions for enabling novel forms of guided molecular assembly.

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.

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.

Atomic Structures of Benzene and Pyridine on Si(5 5 12)-2 × 1

The adsorption structures of benzene and pyridine on Si(5 5 12)-2 x 1 were studied at 80 K by using a low-temperature scanning tunneling microscope and density functional theory calculations. These structures are different from those observed on low-index Si surfaces: benzene molecules exclusively bind to two adatoms, that is, with di-sigma bonds between carbon atoms and silicon adatoms, leading to the loss of benzene aromaticity; in contrast, pyridine molecules interact with adatom(s) through either Si-N dative bonding or di-sigma bonds. Dative bonding configurations with pyridine aromaticity are the dominant adsorption features and are more stable than di-sigma bonding configurations. Thus the dative bonding of nitrogen-containing heteroaromatic molecules provides a strategy for the controlled attachment of aromatic molecules to high-index surfaces.

Adsorption structures of benzene on a Si(5512)-2×1 surface: A combined scanning tunneling microscopy and theoretical study

In the first ever attempt to study the adsorption of organic molecules on high-index Si surfaces, we investigated the adsorption of benzene on Si(5 5 12)-(2x1) by using variable-low-temperature scanning tunneling microscopy and density-functional theory (DFT) calculations. Several distinct adsorption structures of the benzene molecule were found. In one structure, the benzene molecule binds to two adatoms between the dimers of D3 and D2 units in a tilted butterfly configuration. This structure is produced by the formation of di-sigma bonds with the substrate and of two C[Double Bond]C double bonds in the benzene molecule. In another structure, the molecule adsorbs on honeycomb chains with a low adsorption energy because of strain effects. Our DFT calculations predict that the adsorption energies of benzene are 1.03-1.20 eV on the adatoms and 0.22 eV on the honeycomb chains.

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).

Binding Mechanisms of Methacrylic Acid and Methyl Methacrylate on Si(111)-7×7Effect of Substitution Groups

The interaction of methacrylic acid and methyl methacrylate with Si(111)-7 x 7 has been investigated using high-resolution electron energy loss spectroscopy (HREELS) and X-ray photoelectron spectroscopy (XPS). While methacrylic acid chemisorbs dissociatively through O-H bond cleavage, methyl methacrylate is covalently attached to the silicon surface via a [4+2] cycloaddition. The different reaction pathways of these two compounds on Si(111)-7 x 7 demonstrate that the substitution groups play an important role in determining the reaction channels for multifunctional molecules, leading to the desired flexibility in the organic modification of silicon surfaces.

Selective bonding of pyrazine to silicon(100)-2×1 surfaces: The role of nitrogen atoms

The covalent binding of pyrazine on Si(100) have been investigated using high-resolution electron energy loss spectroscopy (HREELS) and x-ray photoelectron spectroscopy. Experimental results clearly suggest that the attachment occurs exclusively through the bonding of the two para-nitrogen atoms with the surface without the involvement of the carbon atoms, as evidenced from the retention of the (sp2) C-H stretching mode in HREELS and a significant down shift of 1.6 eV in the binding energy of N 1s. The binding mechanism for pyrazine on Si(100) demonstrates that reaction channels for heteroatomic aromatic molecules are strongly dependent on the electronic properties of the constituent atoms.