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.     

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.     

Ab initio surface reaction energetics of SiH4 and Si2H6 on Si(001)-(2 x 2)

First-principles pseudopotential calculations, within a simple dynamically constrained scheme, have been performed to investigate the reaction of 0.25 ML coverage of SiH4 and Si2H6 with the Si(001)-(2 x 2) surface. The silane molecule (SiH4) is adsorbed on to the surface at a number of different sites (on dimer, interrow, or intrarow) with varying barrier heights. Two distinct structures, which are similar in energy, arise from the initial dissociative reaction SiH4-->SiH3(silyl) + H, where the dissociated species are adsorbed either on the same dimer components or on adjacent dimer components. Several further decays of silyl from SiH4 are presented in two separate regimes of high and low ambient hydrogen coverages. The decomposition of silyl can form two different bridging structures: an on top or an intrarow bridging structure in both of the two hydrogen coverage regimes. The disilane molecule (Si2H6) is also adsorbed upon this surface with varying energy barriers, resulting in a dissociation reaction where two SiH3 species are adsorbed on one dimer or in an adjacent dimer configuration. Plausible energy reaction paths for the above models are presented. The stability of the SiH2 species is also discussed.     

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.     

Surface reaction of alkynes and alkenes with H-Si(111): a density functional theory study

Recent experiments on the addition of alkene and alkyne molecules to H-terminated silicon surfaces have provided evidence for a surface chain reaction initiated at isolated Si dangling bonds and involving an intermediate carbon radical state, which, after abstraction of a hydrogen atom from a neighboring Si-H unit, transforms into a stable adsorbed species plus a new Si dangling bond. Using periodic density functional theory (DFT) calculations, together with an efficient method for determining reaction pathways, we have studied the initial steps of this chain reaction for a few different terminal alkynes and alkenes interacting with an isolated Si dangling bond on an otherwise H-saturated Si(111) surface. Calculated minimum energy pathways (MEPs) indicate that the chain mechanism is viable in the case of C(2)H(2), whereas for C(2)H(4) the stabilization of the intermediate state is so small and the barrier for H-abstraction so (relatively) large that the molecule is more likely to desorb than to form a stable adsorbed species. For phenylacetylene and styrene, stabilization of the intermediate state and decrease of the H-abstraction barrier take place. While a stable adsorbed species exists in both cases, the overall heat of adsorption is larger for the alkyne molecules.     

C59Si on the monohydride Si(100):H-(2 x 1) surface

We propose the use of the Si atom in the experimentally observed C59Si molecule as a possible way to controllably anchor fullerene molecules on a Si surface, due to the formation of a strong bond to one of the Si surface atoms. All our results are based on ab initio total energy density functional theory, and we obtain that the binding energy is on the order of 2.1 eV, approximately 1.4 eV more stable than a C60 bonded in a similar situation. A possible route to obtain such adsorption via a (C59Si)2 dimer is examined, and we find the whole process to be exothermic by approximately 0.2 eV.     

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     

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.     

Initial nitridation of the Ge(100)-2 x 1 surface by ammonia

The reaction of ammonia (NH(3)) on the Ge(100)-2 x 1 surface is investigated using density functional theory (DFT). We find that NH(3) adsorbs molecularly onto Ge(100)-2 x 1 via the formation of a dative bond. The calculations also show that, unlike Si(100)-2 x 1, the activation barrier for subsequent dissociation of NH(3) adsorbed on Ge(100)-2 x 1 is higher than that of reversible desorption, which indicates that NH(3) has a low reactive sticking probability on the Ge(100)-2 x 1 surface. We also predict that nitrogen insertion into the Ge-Ge dimer requires NH(3) overexposure because the activation barrier for NH(2) insertion into the Ge-Ge dimer is significantly above the entrance channel. The nitridation reaction pathway results in the N-H bridge-bonded state, which is found to be 17.4 kcal/mol more stable than the reactants. We find that the reactions of NH(3) on the Ge(100)-2 x 1 surface generally involve higher activation barriers and less stable intermediates than the analogous reactions on the Si(100)-2 x 1 surface.     

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.     

甲醛在CeO2(111)表面吸附的密度泛函理论研究

采用基于第一性原理的密度泛函理论和周期平板模型, 研究了甲醛在以桥氧为端面的CeO2(111)稳定表面上的吸附行为. 通过对不同覆盖度, 不同吸附位的甲醛吸附构型、吸附能及电子态密度的分析发现, 甲醛在CeO2(111)表面存在化学吸附与物理吸附两种情况. 化学吸附结构中甲醛的碳、氧原子分别与表面的氧、铈原子发生相互作用, 形成CH2O2物种; 吸附能随着覆盖度的增加而减小. 与自由甲醛分子相比, 物理吸附的甲醛构型变化不大, 其吸附能较小. 利用CNEB(climbing nudged elastic band)方法计算了甲醛在CeO2(111)表面的初步解离反应活化能(约1.71 eV), 远高于甲醛脱附能垒, 这与甲醛在清洁CeO2(111)表面程序升温脱附实验中产物主要为甲醛的结果相一致.     

Quantum chemical study of adsorption and dissociation of H2S on the gallium-rich GaAs (001)-4 x 2 surface

H(2)S adsorption and dissociation on the gallium-rich GaAs(001)-4 x 2 surface is investigated using hybrid density functional theory. Starting from chemisorbed H(2)S on the GaAs(001)-4 x 2 surface, two possible reaction routes have been proposed. We find that H(2)S adsorbs molecularly onto GaAs(001)-4 x 2 via the formation of a dative bond, and this process is exothermic with adsorption energy of 6.6 kcal/mol. For the first reaction route, one of the H atoms from the chemisorbed H(2)S is transferred to a second-layer As atom and the dissociated SH is inserted into the Ga-As bond with an activation barrier of 8.2 kcal/mol, which is found to be 29.3 kcal/mol more stable than the reactants. For the second case, the dissociated species may insert themselves into the Ga-Ga dimer resulting in the Ga-H-Ga and Ga-HS-Ga bridge-bonded states, which are found to be 29.8 and 22.2 kcal/mol more stable than the reactants, respectively. However, the calculations also show that the activation barrier (16.1 kcal/mol) for chemisorbed H(2)S dissociation through the second route is higher than the transfer of one H atom into a second-layer As atom. As a result, we conclude that sulfur insertion into the Ga-As bond is more kinetically favorable.     

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.     

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.     

The initial step of silicate versus aluminosilicate formation in zeolite synthesis: a reaction mechanism in water with a tetrapropylammonium template

The initial step for silicate and aluminosilicate condensation is studied in water in the presence of a realistic tetrapropylammonium template under basic conditions. The model corresponds to the synthesis conditions of ZSM5. The free energy profile for the dimer formation ((OH)(3)Si-O-Si-(OH)(2)O(-) or [(OH)(3)Al-O-Si-(OH)(3)](-)) is calculated with ab initio molecular dynamics and thermodynamic integration. The Si-O-Si dimer formation occurs in a two-step manner with an overall free energy barrier of 75 kJ mol(-1). The first step is associated with the Si-O bond formation and results in an intermediate with a five-coordinated Si, and the second one concerns the removal of the water molecule. The template is displaced away from the Si centres upon dimer formation, and a shell of water molecules is inserted between the silicate and the template. The main effect of the template is to slow down the backward hydrolysis reaction with respect to the condensation one. The Al-O-Si dimer formation first requires the formation of a metastable precursor state by proton transfer from Si(OH)(4) to Al(OH)(4)(-) mediated by a solvent molecule. It then proceeds through a single step with an overall barrier of 70 kJ mol(-1). The model with water molecules explicitly included is then compared to a simple calculation using an implicit continuum model for the solvent. The results underline the importance of an explicit and dynamical treatment of the water solvent, which plays a key role in assisting the reaction.     

Nitro group as a means of attaching organic molecules to silicon: nitrobenzene on Si(100)-2 x 1

This paper will present the computational and experimental infrared studies of the reactions of nitrobenzene on a Si(100) surface, a prototypical model reaction for understanding the behavior of bifunctional molecules on semiconductor surfaces. The initial reaction of nitrobenzene with the Si(100)-2 x 1 occurs via 1,3-dipolar cycloaddition of the nitro group to the silicon surface dimer. Computational exploration of the initial adsorption configurations suggests that two stable structures can be formed: one with the phenyl ring essentially perpendicular to the surface; the other one with the tilt angle of approximately 113 degrees with respect to the surface normal. The barrier for converting the latter into the former, more stable by approximately 13 kJ/mol, is 19.1 kJ/mol. Further thermal reactions are analyzed, and the reaction pathways are compared for the computational models with fixed vs relaxed subsurface silicon atoms. While all the surface species resulting from nitrobenzene transformations on the Si(100)-2 x 1 surface studied here are thermodynamically stable, most of the reaction pathways can be ruled out on the basis of the analysis of the transition states leading to these species and on the comparison of predicted and measured vibrational spectra. As a result, the exact adsorption configurations can be pinpointed.     

Selective functionalization of the Si(100) surface by a bifunctional alkynylamine molecule: density functional study of the switching adsorption linkage. 2

The reaction of the bifunctional organic molecule 1-(dimethylamino)-2-propyne (DMAP) on the Si(100) surface has been investigated by density functional calculations employing a two-dimer cluster model. We found that, once in the physisorbed dative bonded well (-20.0 kcal mol(-1)), DMAP can proceed via a number of pathways, involving the formation of Si-C sigma bonds, which lead to thermodynamically more stable configurations. We first considered the cycloaddition of the CC triple bond, leading to a Si-C di-sigma bonded product (-58.7 kcal mol(-1)), for which we computed an energy barrier of only 12.5 kcal mol(-1), consistently with the observed switching of DMAP adsorption linkage at 300 K. We also explored the dissociative pathway involving the methylene C-H bond cleavage on the dative bonded DMAP, leading to three adsorption products with one (-57.3 kcal mol(-1)) and three Si-C sigma bonds (-58.7 and -60.6 kcal mol(-1)). The energy barrier for this pathway is computed 24.7 kcal mol(-1) and may therefore compete at temperature above 300 K with the reaction pathway involving the addition of the alkyne unit.     

Adsorption of 3-pyrroline on Si(100) from first principles

The chemisorption of 3-pyrroline (C(4)H(7)N) on Si(100) is studied from first principles. Three different structures can be realized for which, depending on the temperature, the chemisorption process is facile (for two of them it is essentially barrierless); among these configurations the most favored one, from a thermodynamical point of view, is a dissociated structure obtained through an exothermic reaction characterized by the formation of a N-Si bond and a H-Si bond in which the H atom is detached from the molecule. Several other chemisorption structures are possible which, however, require overcoming a significant energy barrier and often breaking multiple bonds. A number of reaction paths going from one stable structure to another have been investigated. We have also generated, for the two basic adsorption structures, theoretical scanning tunneling microscopy images which could facilitate the interpretation of experimental measurements, and we propose a possible reaction mechanism for nitrogen incorporation.     

Diradical mechanism for the [2 + 2] cycloaddition of ethylene on Si(100) surface

Density functional cluster model calculations have been performed to explore the reaction mechanism for the adsorption of ethylene on Si(100). It is shown that the [2 + 2] cycloaddition of ethylene on a Si=Si dimer of Si (100) surface follows a diradical mechanism, via a pi-complex precursor and a singlet diradical intermediate, and the rate-determining step for the overall reaction is the formation of the diradical intermediate.