Theoretical study of the reaction of acrylonitrile on Si(001)

Two recent experiments for adsorbed acrylonitrile on the Si(001) surface reported different adsorption structures at 110 and 300 K. We investigate the reaction of acrylonitrile on Si(001) by first-principles density-functional calculations. We find that the so-called [4+2] structure in which acrylonitrile resides between two dimer rows is not only thermodynamically favored over other structural models but also easily formed via a precursor where the N atom of acrylonitrile is attached to the down atom of the Si dimer. The additional initial-state theory calculation for the C 1s core levels of adsorbed acrylonitrile provides an interpretation for the observed low- and room-temperature adsorption configurations in terms of the precursor and [4+2] structures, respectively.     

Structure and binding energies of unsaturated hydrocarbons on Si(001) and Ge(001)

The adsorption of acetylene, ethylene, and benzene on the Si(001) and Ge(001) surfaces is investigated by first-principles density-functional calculations within the generalized-gradient approximation. We find that the adsorption energies of the three hydrocarbons containing a triple bond, a double bond, and a pi-conjugated aromatic ring decrease as the sequence of C2H2>C2H4>C6H6. We also find that the bondings of acetylene, ethylene, and benzene to Ge(001) are much weaker than those to Si(001). As a result, benzene is weakly bound to Ge(001) while it is chemisorbed on Si(001), consistent with temperature-programmed desorption data.     

Initial stage of Si(001) surface oxidation from first-principles calculations

A comprehensive density-functional theory (DFT) study of the atomic structure, electronic properties, and optical response of the Si(001) surface at the initial stages of oxidation is presented. The most favored adsorption position of a single O atom on top of the (4 x 2)-reconstructed Si(001) surface is found at the back-bond of the "down" Si dimer atom. There is no energy barrier for oxygen insertion into this bond. The ionization energy of the surface reaches a maximum when the oxidation of the second Si monolayer starts. Oxidation leads to an increase of the energy gap between occupied and empty surface states. The calculated reflectance anisotropy spectroscopy (RAS) data in comparison with experiment suggest a considerable amount of surface disorder already after oxidation of the first monolayer.     

Density functional theory study of one-dimensional growth of styrene on the hydrogen-terminated Si(001)-(3 x 1) surface

Recent experimental work has shown that the addition of styrene molecules to hydrogen-terminated Si(001) surfaces leads to the formation of one-dimensional molecular structures through a radical-initiated surface chain reaction mechanism. These nanometric structures are observed to be directed parallel to the dimer rows on the H-Si(001)-(2 x 1) surface and perpendicular to the same rows on H-Si(001)-(3 x 1). Using periodic density functional theory (DFT) calculations, we have studied the initial steps of the radical chain mechanism on the H-Si(001)-(3 x 1) surface and compared them to analogous results for H-Si(001)-(2 x 1). On the H-Si(001)-(3 x 1) surface, one of the crucial steps of the surface chain reaction, namely, the abstraction of a H atom from a nearby surface hydride unit, is found to have a somewhat smaller activation energy in the direction perpendicular to the dimer rows (H abstraction from the nearest dihydride site) than along the rows (H abstraction from a neighboring dimer). Additionally, due to the steric repulsion between the styrene molecules and the SiH2 subunits, growth along the dimer rows is not thermodynamically favorable on the (3 x 1) surface. On the other hand, due to the absence of the SiH2 subunits, growth parallel to the Si dimer rows becomes favored on the H-Si(001)-(2 x 1) surface.     

Purely site-specific chemisorption and conformation of trimethylamine on Si(100)c(4 x 2)

One of the fundamental points of interest on the Si(100) surface is how the spatial localization of electron density on the buckled silicon dimer controls the site-specific reaction toward different Lewis acid and Lewis base molecules. We have investigated the adsorption of trimethylamine (TMA) on Si(100)c(4x2) using scanning tunneling microscopy (STM) at 80 K. The adsorbed TMA appears as a triangle-shaped bright protrusion in the occupied-state STM image. The triangle-shaped protrusion is ascribed to three methyl groups in the adsorbed TMA. The center of the protrusion is located on the down atom site, which indicates that the adsorption of TMA occurs only on the down dimer atom. Thus, TMA adsorption on Si(100)c(4x2) is found to be purely site-specific on the down dimer atom and can be categorized in Lewis acid-base reaction.     

The chemisorption of coronene on Si(001)-2 x 1

Coronene (C24H12) adsorption on the clean Si(001)-2 x 1 surface was investigated by scanning tunneling microscopy and by density-functional calculations. The coronene adsorbed randomly at 25 degrees C on the surface and did not form two-dimensional islands. The scanning tunneling microscopy measurements revealed three adsorption sites for the coronene molecule on the Si(001) surface at low coverage. The major adsorption configuration involves coronene bonding to four underlying Si atoms spaced two lattice spacings apart in a dimer row. The two minor adsorption configurations involve asymmetrical bonding of a coronene molecule between Si dimer rows and form surface species with a mirror plane symmetry to their chiral neighbor species. The two minor bonding arrangements are stabilized by a type-C defect on the Si(001) surface.     

Self-directed growth of benzonitrile line on H-terminated Si(001) surface

Using first-principles density-functional calculations we predict a self-directed growth of benzonitrile molecular line on a H-terminated Si(001) surface. The C[triple bond]N bond of benzonitrile reacts with a single Si dangling bond which can be generated by the removal of a H atom, forming one Si-N bond and one C radical. Subsequently, the produced C radical can be stabilized by abstracting a H atom from a neighboring Si dimer, creating another H-empty site. This H-abstraction process whose activation barrier is 0.65 eV sets off a chain reaction to grow one-dimensional benzonitrile line along the Si dimer row. Our calculated energy profile for formation of the benzonitrile line shows its relatively easier formation compared with previously reported styrene and vinylferrocene lines.     

乙炔在Ge(001)表面吸附的反应路径

采用第一性原理方法研究了乙炔分子在Ge(001)表面的吸附反应.通过系统考察0.5和1.0ML覆盖度时形成di-σ和end-bridge构型的反应路径,研究在表面形成di-σ和paired-end-bridge构型的反应几率.除了表面反应以外,本文还涉及了亚表层Ge原子参与的吸附反应,乙炔在亚表层原子上吸附形成的亚稳态结构sub-di-σ,是形成end-bridge结构的第二条途径,此反应机理对于表面吸附结构的形成起重要的作用.与乙炔分子不同的是,表面以下原子参与时乙烯分子的吸附反应为吸热反应.综合热力学和动力学的分析表明,paired-end-bridge构型是乙炔分子吸附的主要构型,此结论解释了乙炔分子在Ge(001)表面吸附构型的实验结果.对于乙烯和乙炔两分子在Ge(001)表面吸附的分析比较揭示了导致两者之间差异的原因.     

Study of adsorption and decomposition of H2O on Ge(100)

The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of H2O on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, H2O molecules are bound to the surface via Ge-O dative bonds between the O atom of H2O and the electrophilic down atom of the Ge dimer. In the dissociative adsorption geometry, the H2O molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in an H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the H2O coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the H2O molecule from the molecular adsorption to the dissociative adsorption geometry.     

Complex Surface Chemistry of an Otherwise Inert Solvent Molecule: Tetrahydrofuran on Si(001)

The reaction of tetrahydrofuran (THF), an otherwise inert solvent molecule, on Si(001) was experimentally studied in ultra‐high vacuum. Using scanning tunneling microscopy (STM) and photoelectron spectroscopy at variable temperature, we could both isolate a datively bound intermediate state of THF on Si(001), as well as the final configuration that bridges two dimer rows of the Si(001) surface after ether cleavage. The latter configuration implies splitting of the O?C bond, which is typically kinetically suppressed. THF thus exhibits a hitherto unknown reactivity on Si(001).     

Two dissociation pathways of water and ammonia on the Si(001) surface

Using first-principles density-functional calculations, we investigated two competing pathways for the dissociation of water and ammonia on a Si(001) surface. For both systems, we found that, in addition to the conventionally accepted intradimer transfer of the H atom, the interdimer transfer of the H atom can be equally probable with the same reaction mechanism. Our analysis shows that the two dissociation pathways occur through the Lewis acid-base reaction between the partially positive H ion and the electron-abundant up atom of the buckled Si dimer. The result of the interdimer H transfer not only supports a recently proposed model for C-defect on Si(001) but also corresponds to the recent scanning tunneling microscopy data of ammonia dissociation on Si(001).     

Electronic effects induced by single hydrogen atoms on the Ge(001) surface

The properties of an isolated dangling bond formed by the chemisorption of a single hydrogen atom on a dimer of the Ge(001) surface are investigated by first-principles density functional theory (DFT) calculations, and scanning tunneling microscopy (STM) measurements. Two stable atomic configurations of the Ge-Ge-H hemihydride with respect to the neighboring bare Ge-Ge dimers are predicted by DFT. For both configurations, the unpaired electron of the HGe(001) system is found to be delocalized over the surface, rendering the isolated dangling bond of the hemihydride unoccupied. However, local surface charge accumulation, such as may occur during STM imaging, leads to the localization of two electrons onto the hemihydride dangling bond. The calculated surface densities of states for one of the charged Ge-Ge-H hemihydride configurations are found to be in good agreement with atomic-resolution STM measurements on n-type Ge(001). Comparison with a Si-Si-H hemihydride of the Si(001) surface shows similarities in structural properties, but substantial differences in electronic properties.     

Density functional study of XH4 (XSi and Ge) reactivity upon dissociative adsorption onto the Si(100) surface

Total energy calculations based on density functional theory (DFT) with generalized gradient approximation (GGA) and ultrasoft pseudopotential approximation and an analysis tool of atom‐resolved density of states (ADOS) have been used to investigate (1) the energetic profiles for the possible initial dissociative adsorption of XH₄ (X?Si and Ge) onto the Si(100)? (2 × 2) surface to evaluate their reactivity and (2) the effect of surface electronic states of Si(100)? (2 × 2) on gaseous molecular precursors XH₄ (X?Si and Ge) during initial dissociative adsorption to understand the factors governing their reactivity. Our calculated lower‐energy barrier for initial dissociative adsorption of GeH₄ is due to the forming of stronger bond of Si? H between H within GeH₄ and buckled‐down Si atom on the Si(100)? (2 × 2) surface accompanying the larger extent of unbuckling of the buckled Si?Si dimer on the Si(100)? (2 × 2) surface at the transition state. Our evaluated better reactivity for GeH₄ than SiH₄ (a factor of around 14.6) is slightly larger than observed higher reactivity for GeH₄ than SiH₄ (a factor of between 2 and 5 depending on the incident kinetic energy) employed supersonic molecular bean techniques. Finally, our calculated ADOS indicate that the surface electronic states of buckled Si?Si dimer on the Si(100)? (2 × 2) surface energetically favorably participate in the transition state during GeH₄ initial dissociative adsorption to reduce the energy barrier, i.e., enhance its reactivity, in comparison with SiH₄ initial dissociative adsorption onto the Si(100)? (2 × 2) surface under the same reaction conditions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

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.     

Initial hydrogenations of pyridine on MoP(001): a density functional study

The initial hydrogenations of pyridine on MoP(001) with various hydrogen species are studied using self-consistent periodic density functional theory (DFT). The possible surface hydrogen species are examined by studying interaction of H(2) and H(2)S with the surface, and the results suggest that the rational hydrogen source for pyridine hydrogenations should be surface hydrogen atoms, followed by adsorbed H(2)S and SH. On MoP(001), pyridine has two types of adsorption modes, i.e., side-on and end-on; and the most stable η(5)(N,C(α),C(β),C(β),C(α)) configuration of the side-on mode facilitates the hydrogenation of pyridine. The optimal hydrogenation path of pyridine with surface hydrogen atoms in the Langmuir-Hinshelwood mechanism is the formation of 3-monohydropyridine, followed by producing 3,5-dihydropyridine, in which the two-step hydrogenations take place on the C(β) atoms. When adsorbed H(2)S is considered as the source of hydrogen, slightly higher hydrogenation barriers are always involved, while the energy barriers for hydrogenations involving adsorbed SH are much lower. However, the hydrogenation of pyridine should be suppressed by the adsorption of H(2)S, and the promotion effect of adsorbed SH is limited.     

Phosphine dissociation and diffusion on Si(001) observed at the atomic scale

A detailed atomic-resolution scanning tunneling microscopy (STM) and density functional theory study of the adsorption, dissociation, and surface diffusion of phosphine (PH(3)) on Si(001) is presented. Adsorbate coverages from approximately 0.01 monolayer to saturation are investigated, and adsorption is performed at room temperature and 120 K. It is shown that PH(3) dissociates upon adsorption to Si(001) at room temperature to produce both PH(2) + H and PH + 2H. These appear in atomic-resolution STM images as features asymmetric-about and centered-upon the dimer rows, respectively. The ratio of PH(2) to PH is a function of both dose rate and temperature, and the dissociation of PH(2) to PH occurs on a time scale of minutes at room temperature. Time-resolved in situ STM observations of these adsorbates show the surface diffusion of PH(2) adsorbates (mediated by its lone pair electrons) and the dissociation of PH(2) to PH. The surface diffusion of PH(2) results in the formation of hemihydride dimers on low-dosed Si(001) surfaces and the ordering of PH molecules along dimer rows at saturation coverages. The observations presented here have important implications for the fabrication of atomic-scale P dopant structures in Si, and the methodology is applicable to other emerging areas of nanotechnology, such as molecular electronics, where unambiguous molecular identification using STM is necessary.     

Maleic anhydride adsorption on silicon (001)

The adsorption of maleic anhydride on the Si(001) surface has been investigated using the first-principles pseudopotential formalism. Our total-energy calculations suggest that maleic anhydride (C2H2-C2O3) adsorbs preferentially through a [2+2] cycloaddition of the C=C bond ([2+2]) with an adsorption energy of around 42 kcal/mol. Besides the [2+2] configuration we have also considered other possible coverages and adsorption models, including the adsorption on inter-row and intrarow dimer sites. Based on the analysis of the relative stability of different adsorption models, we propose the formation of mixed domains, containing the [2+2] unit and an interdimer unit. The comparison of our calculated electronic band structure, vibrational modes, and scanning tunneling microscopy images for the [2+2] and the favored interdimer adsorbed structures corroborate our proposed mixed domain model.     

Surface S(N)2 reaction by H2O on chlorinated Si(100)-2 x 1 surface

The potential energy surfaces of one, two, and three water molecule sequential adsorptions on the symmetrically chlorinated Si(100)-2 x 1 surface were theoretically explored with SIMOMM:MP2/6-31G(d). The first water molecule adsorption to the surface dimer requires a higher reaction barrier than the subsequent second water molecule adsorption. The lone pair electrons of the incoming water molecule nucleophilically attack the surface Si atom to which the leaving Cl group is bonded, yielding an S(N)2 type transition state. At the same time, the Cl abstracts the H atom of the incoming water molecule, forming a unique four-membered ring conformation. The second water molecule adsorption to the same surface dimer requires a much lower reaction barrier, which is attributed to the surface cooperative effect by the surface hydroxyl group that can form a hydrogen bond with the incoming second water molecule. The third water molecule adsorption exhibits a higher reaction barrier than the first and the second water molecule adsorption channels but yields a thermodynamically more stable product. In general, it is expected that the surface Si-Cl bonds can be subjected to the substitution reactions by water molecules, yielding surface Si-OH bonds, which can be a good initial template for subsequent surface chemical modifications. However, oversaturations can be a competing side reaction under severe conditions, suggesting that the precise control of surface kinetic environments is necessary to tailor the final surface characteristics.     

Adsorption of acrylonitrile on diamond and silicon (001)-(2 x 1) surfaces: effects of dimer structure on reaction pathways and product distributions

Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) are used to compare the reaction of acrylonitrile with Si(001) and C(001) (diamond) surfaces. Our results show that reaction with Si(001) and C(001) yield very different product distributions that result from fundamental differences in the ionic character of these surfaces. While acrylonitrile reacts with the C(001) surface via a [2 + 2] cycloaddition reaction in a manner similar to nonpolar molecules such as alkenes and disilenes, reaction with the Si(001) surface occurs largely through the nitrile group. This work represents the first experimental example of how differences in dimer structure lead to very different chemistry for C(001) compared to that for Si(001). The fact that Si(001) reacts with the strongly polar nitrile group of acrylonitrile indicates that the zwitterionic character of this surface controls its reactivity. C(001) dimers, on the other hand, behave more like a true molecular double bond, albeit a highly strained one. Consequently, while alternative strategies will be necessary for chemical modification of Si(001), traditional schemes from organic chemistry for functionalization of alkenes and disilenes may be available for building molecular layers on C(001).     

Thiophene adsorption and activation on MoP(001), gamma-Mo2N(100), and Ni2P(001): density functional theory studies

The adsorption and dissociation of thiophene on the MoP(001), gamma-Mo(2)N(100), and Ni(2)P(001) surfaces have been computed by using the density functional theory method. It is found that thiophene adsorbs dissociatively on MoP(001), while nondissociatively on gamma-Mo(2)N(100) and Ni(2)P(001). On MoP(001), the dissociation of the C-S bonds is favored both thermodynamically and kinetically, while the break of the first C-S bond on gamma-Mo(2)N(100) has an energy barrier of 1.58 eV and is endothermic by 0.73 eV. On Ni(2)P(001) there are Ni(3)P(2)- and Ni(3)P-terminated surfaces. On the Ni(3)P(2)-terminated surface, the dissociation of the C-S bonds of adsorbed thiophene is endothermic, while it is exothermic on the Ni(3)P-terminated surface.