Adsorption structures of benzene on a Si(5 5 12)-2x1 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.     

Selective adsorption of pyridine at isolated reactive sites on Si(100)

Dative bonding of nitrogen-containing heterocycles offers a strategy for the controlled attachment of aromatic molecules to silicon surfaces. However, while scanning tunneling microscopy shows that pyridine on clean Si(100) initially binds via a dative bonding configuration, slow conversion to a more stable bridging state, destroying the aromaticity, is observed. To restrict adsorption to the dative bonded form, we investigated the interaction of pyridine with isolated reactive sites on partially H-terminated Si(100). While dative bonding on isolated clean dimers is observed, single dangling bonds remain unreacted. This selectivity can be accounted for by the ability of the Si-Si dimers to act as electron acceptors that stabilize the dative bonded species. This observation has important implications for the controlled positioning of single molecules on silicon via dative bonding.     

Thermodynamic factors limiting the preservation of aromaticity of adsorbed organic compounds on Si(100): example of the pyridine

Using pyridine as an example, a thermodynamic analysis of the low temperatures adsorption of aromatic organic molecules with a N atom on the Si(100) surface is presented. This study is restricted to the case of an equilibrium with the gas phase. Dative attachment which is the only way to preserve aromaticity is the more stable form of adsorbed pyridine in dilute solutions at low temperatures. Two factors limit the domain of stability of dative attachment: repulsive interactions between dative bonds prevent them from being present in concentrated solutions while aromaticity contributes to a decrease in the entropy, which explains the vanishing of dative bonds at high temperatures even in dilute solutions.     

Vibrational characterization of different benzene phases on flat and vicinal Si(100) surfaces

Based on high-resolution electron energy loss spectroscopy and temperature-programmable desorption, benzene chemisorption on vicinal and nominally flat Si(100) surfaces has been studied for various adsorption, annealing, and site blocking treatments. Three different chemisorbed benzene (C6H6 and C6D6) phases with distinct thermal desorption characteristics and different vibrational spectra have been separated and characterized on both substrates. All three phases are identified as 1,4-cyclohexadiene-like structures with butterfly geometry. Whereas the dominant phase is di-sigma bonded to the two Si atoms of a single Si-Si dimer, the benzene orientation (double bond orientation) in the other phases is rotated. Di-sigma bonding to Si atoms of adjacent Si-Si dimer for the latter cases is most likely. Coverage and temperature dependent conversions between the different phases have been addressed by vibrational spectroscopy.     

Studies of chemisorbed tetracene on si(111)-7x7

The chemisorption of tetracene on the Si(111)-7x7 surface was studied using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. On the basis of the STM results and dimension analysis, two types of binding configurations were proposed. One of the configurations involves the di-sigma reaction between two C atoms of an inner ring with an adatom-rest atom pair on the substrate to give rise to an unsymmetrical butterfly structure. Tetracene in another configuration possesses four C-Si bonds that are formed via di-sigma reactions between the C atoms at the terminal rings with two center adatom-rest atom pairs within one-half of the surface unit cell. Besides, two other binding modes were proposed based on the dimension compatibility between the tetracene C and the substrate Si dangling bonds even though their identifications through the STM images are nonexclusive. Structural modeling and adsorption energies calculations were carried out using the DFT method. Factors affecting the relative thermodynamic stabilities based on the calculation results and the relative populations of tetracene in the different binding configurations as observed experimentally were discussed.     

Aromaticity: molecular-orbital picture of an intuitive concept

Geometry is one of the primary and most direct indicators of aromaticity and antiaromaticity: a regular structure with delocalized double bonds (e.g., benzene) is symptomatic of aromaticity, whereas a distorted geometry with localized double bonds (e.g., 1,3-cyclobutadiene) is characteristic of antiaromaticity. Here, we present a molecular-orbital (MO) model of aromaticity that explains, in terms of simple orbital-overlap arguments, why this is so. Our MO model is based on accurate Kohn-Sham DFT analyses of the bonding in benzene, 1,3-cyclobutadiene, cyclohexane, and cyclobutane, and how the bonding mechanism is affected if these molecules undergo geometrical deformations between regular, delocalized ring structures, and distorted ones with localized double bonds. We show that the propensity of the pi electrons is always, that is, in both the aromatic and antiaromatic molecules, to localize the double bonds, against the delocalizing force of the sigma electrons. More importantly, we show that the pi electrons nevertheless decide about the localization or delocalization of the double bonds. A key component of our model for uncovering and resolving this seemingly contradictory situation is to analyze the bonding in the various model systems in terms of two interpenetrating fragments that preserve, in good approximation, their geometry along the localization/delocalization modes.     

Self-induced 1-D molecular chain growth of thiophene on Ge(100)

The adsorption of thiophene on Ge(100) has been studied using scanning tunneling microscopy (STM), high-resolution core-level photoemission spectroscopy (HRPES), and density functional theory (DFT) calculations. Until now, thiophene is known to react with the Ge(100) dimer through a [4 + 2] cycloaddition reaction at room temperature, similar to the case of thiophene on Si(100). However, we found that thiophene has two adsorption geometries on Ge(100) at room temperature, such as a kinetically favorable Ge-S dative bonding configuration and a thermodynamically stable [4 + 2] cycloaddition adduct. Moreover, our STM results show that under 0.25 ML thiophene molecules preferentially produce one-dimensional molecular chain structures on Ge(100) via the Ge-S dative bonding configuration.     

Formation of highly ordered organic monolayers by dative bonding: pyridine on ge(100)

The adsorption of pyridine onto the Ge(100) surface has been studied using both real-time scanning tunneling microscopy (STM) and ab initio pseudopotential density functional calculations. The results show that pyridine molecules adsorb on the electron-deficient down-Ge atoms of the Ge=Ge dimers via Ge-N dative bonding, with the pyridine ring tilted to the surface. The electron-rich up-Ge atoms remaining after adsorption of pyridine induce an asymmetric dimer row, which is mainly reconstructed to the c(4 x 2) structure. At pyridine coverage of 0.25 ML, the adsorbed pyridine molecules form a perfectly ordered monolayer. The entire Ge substrate underlying this organic monolayer rearranges into the c(4 x 2) structure.     

Surface reactions of 3-butenenitrile on the Si(001)-2 x 1 surface at room temperature

Using a combination of local -- scanning tunneling microscopy -- and spatially integrated, but chemically sensitive probes -- X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy -- we have examined how 3-butenenitrile reacts with the Si(001)-2 x 1 surface at room temperature. Electron spectroscopies indicate three different nitrogen chemical bonds: a Si-C=N-Si bond, a C=C=N cumulative double bond, and a CN moiety datively bonded to a silicon atom. All molecular imprints detected by scanning tunneling microscopy (STM) involve two adjacent silicon dimers in the same row. The three geometries we propose -- a double di-sigma bonding via the CN and the C=C, a cumulative double bond formation associated with alphaC-H bond dissociation, and a di-sigma vinyl bonding plus a CN datively bonded to a silicon atom -- are all compatible with electron spectroscopies and data. Real-time Auger yield kinetic measurements show that the double di-sigma bonding geometry is unstable when exposed to a continuous flux of 3-butenenitrile molecules, as the Si-C=N-Si unit transforms into a CN moiety. A model is proposed to explain this observation.     

平面五配位硅、 锗XBe5H6(X=Si,Ge)团簇

采用密度泛函理论PBE0方法, 在aug-cc-pVTZ水平上理论预测了含平面五配位硅和锗原子的XBe₅H₆ (X=Si, Ge)团簇. 势能面系统搜索及高精度量化计算表明, 它们均为全局极小结构. XBe₅H₆(X=Si, Ge)团簇整体呈完美的扇形结构: Si/Ge原子被5个金属Be原子配位; 4个H原子以桥基方式与Be原子相键连, 剩余的2个 H原子以端基方式与两端的Be原子成键. 化学键分析表明, XBe₅H₆(X=Si, Ge) 团簇中XBe₅单元具有完全离域的1个π及3个σ键, 外围铍氢间形成4个Be—H—Be 三中心二电子(3c-2e)键及2个定域的Be—H键. XBe₅单元上离域的2π及6σ电子赋予体系π和σ双重芳香性, 并使Si/Ge原子满足八隅律（或八电子规则）. 能量分解-化学价自然轨道分析揭示, Si/Ge和Be₅H₆之间主要为电子共享键.     

Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry

By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two‐step reaction mechanism—1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom—shows that it mirrors acid‐catalyzed ether cleavage in solution. The O−Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell–Evans–Polanyi principle. Electron rearrangement during C−O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular S_N2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained.     

Self-consistent meta-generalized gradient approximation study of adsorption of aromatic molecules on noble metal surfaces

The adsorption of benzene, pyridine, and two nucleobases on the Au(111) surface has been investigated using a fully relaxed, self-consistent meta-generalized gradient approximation (meta-GGA) density functional theory setup with the M06-L functional. The meta-GGA based molecule-surface separations are shortened and the adsorption bond strengths of the molecules are greatly improved over the virtually non-interacting results obtained when using a plain GGA exchange-correlation functional. The nucleobases containing oxygen atoms show higher corrugation with adsorption site and orientation than the other aromatic molecules considered. The adsorption of pentacene is studied on Au, Ag, and Cu surfaces. In agreement with experiment, the adsorption energies are found to increase with decreasing nobleness, but the dependency is underestimated. We point out how the kinetic energy density can discriminate between covalent and non-covalent bonding regions of orbital overlap.     

Coverage‐Dependent Variation of Adsorption Configurations of Methionine on Ge(100)

The adsorption configurations of methionine molecules on the Ge(100) surface have been studied by using DFT calculations, core‐level photoemission spectroscopy (CLPES), and low‐energy electron diffraction (LEED) to scrutinize the adsorption structure as a function of coverage. At first, we obtained two important and stable structures. One is the most stable structure between these structures described as an “O H dissociated‐N dative‐S dative‐bonded structure” and the other is a less stable adsorption structure of these indicating an “O H dissociated‐S dative‐bonded structure” by using DFT calculations. We also performed CLPES to clarify our DFT calculation results. Through the spectral analysis of the S 2p, C 1s, N 1s, and O 1s core‐level spectra, we acquired the reasonable results that also revealed quite different bonding configurations depending on the methionine coverage. At low coverage (ca. 0.30 ML), a single type of sulfur and charged nitrogen peaks, which indicate an “O H dissociated‐N dative‐S dative‐bonded structure”, were observed. On the other hand, two types of sulfur peaks with thiol formation and two nitrogen peaks with neutralized and charged characteristics were monitored at a higher coverage (0.60 ML and above), which can be described as an “O H dissociated‐S dative‐bonded structure”. Hence, we can clearly demonstrate that our results obtained from CLPES spectra and DFT calculations are matched well with each other. Moreover, we additionally confirmed that the relative population of the two types of thiols and amines being included in methionine in between half monolayer induces a surface reorientation in the ordering from 2×1 to 1×1 employing LEED. This interesting variation of the methionine adsorbed on the Ge(100) surface by coverage dependence will be precisely discussed by using DFT calculations, CLPES, and LEED.     

Regioselective cycloaddition reaction of alkene molecules with the asymmetric dimer on Si(100)c(4 x 2)

We investigated the adsorption states of 2-methylpropene and propene on Si(100)c(4 x 2) using low-temperature scanning tunneling microscopy. We have found that regioselective cycloaddition reactions (di-sigma bond formation) occur between the asymmetric alkene molecules and the asymmetric dimers on Si(100)c(4 x 2). First-principles calculations have elucidated that the regioselectivity is closely related to the structures of precursor species and these precursor species have carbocation-like features. Thus, we conclude that Markovnikov's rule is applicable for the cycloaddition of asymmetric alkene with the asymmetric dimer on Si(100)c(4 x 2).     

Double dative bond configuration: pyrimidine on Ge(100)

The adsorption of pyrimidine onto Ge(100) surfaces has been investigated using real-time scanning tunneling microscopy (STM), temperature-programmed desorption (TPD), and density-functional theory (DFT) calculations. Our results show that the adsorbed pyrimidine molecules are tilted about 40 degrees with respect to the Ge surface, and through a Lewis acid-base reaction form bridges between the down-Ge atoms of neighboring Ge dimer rows by double Ge-N dative bonding without loss of aromaticity. For coverages of pyrimidine up to 0.25 ML, a well-ordered c(4x2) structure results from states that appear in STM micrographs as oval-shaped protrusions, which correspond to pyrimidine molecules datively adsorbed on every other dimer. However, above 0.25 ML, the oval-shaped protrusions gradually change into brighter zigzag lines. At 0.50 ML, a p(2x2) structure results from the states that appear in STM as zigzag lines. The zigzag lines are formed by the attachment of pyrimidine molecules to the down-Ge atoms of every Ge dimer. However, the unstable p(2x2) structure eventually reconstructs into a c(4x2) structure due to steric hindrance between the adsorbed pyrimidine molecules after stopping the exposure of pyrimidine to the surface.     

The structure of methyl silatrane (1-methyl-2,8,9-trioxa-5-aza-1-silabicyclo(3.3.3)undecane) as determined by gas phase electron diffraction

The structure of methyl silatrane is investigated by gas-phase electron diffraction at 185° C. The molecule possesses C_3v symmetry. The result obtained for the Si—N distance (2.45(5) Å) indicates essentially no dative bonding between Si and N in the gas phase. This result is quite different from the solid-state result which indicates a Si←N dative bond length of 2.175(4) Å. Other structural parameters compare favorably with both the solid state results and with values obtained in the gas phase for similar molecules.     

Different adsorption structures of pyridine on Si(001) and Ge(001) surfaces

The adsorption and reaction of pyridine on the Si(001) and Ge(001) surfaces are investigated by first-principles density-functional calculations within the generalized gradient approximation. On both surfaces the N atom of pyridine initially reacts with the down atom of the dimer, forming a single bond between the N atom and the down atom. On Ge(001) such an adsorption configuration is most favorable, but on Si(001) a further reaction with a neighboring dimer occurs, resulting in formation of a bridge-type configuration. Especially we find that on Ge(001) the bridge-type configuration is less stable than the gas phase. Our results provide an explanation for a subtle difference in the adsorption structures of pyridine on Si(001) and Ge(001), which was observed from recent scanning tunneling microscopy experiments.     

The intricacies of the stacking interaction in a pyrrole–pyrrole system

Extensive calculations of potential energy surfaces for parallel-displaced configurations of pyrrole–pyrrole systems have been carried out by the use of a dispersion-corrected density functional. System geometries associated with the energy minima have been found. The minimum interaction energy has been calculated as ?5.38 kcal/mol. However, bonding boundaries appeared to be relatively broad, and stacking interactions can be binding even for ring centroid distances larger than 6 Å. Though the contribution of the correlation energy to intermolecular interaction in pyrrole dimers appeared to be relatively small (around 1.6 smaller than it is in a benzene–benzene system), this system’s minimum interaction energy is lower than those calculated for benzene–benzene, benzene–pyridine and even pyridine–pyridine configurations. The calculation of the charges and energy decomposition analysis revealed that the specific charge distribution in a pyrrole molecule and its relatively high polarization are the significant source of the intermolecular interaction in pyrrole dimer systems.     

Chemical structure and orientation of ethylene on Si(114)-(2 x 1)/c(2 x 2)

The basic chemical structure and orientation of ethylene chemisorbed on Si(114)-(2 x 1) at submonolayer coverage is characterized in ultrahigh vacuum using transmission Fourier transform infrared (FTIR) spectroscopy. The spectra are consistent with di-sigma bonding of ethylene to the surface with a preferential molecular orientation over macroscopic lengths. These results are supported by density functional theory (DFT) calculations of vibrational frequencies for optimized ethylene-Si(114) structures occupying the dimer and rebonded atom surface sites. A detailed analysis of the strong angular and polarization dependence of the C-H stretching mode intensities is also consistent with the adsorption structures identified by DFT, indicating that ethylene chemisorbs with the C-C bond axis parallel to the structural rows oriented along the [10] direction on the Si(114)-(2 x 1) surface. The results indicate that the unique structure of this surface makes it an excellent template for elucidating relationships between surface structure and organic reaction mechanisms on silicon.