Acetylene adsorption on Si(1 0 0): A study of the role of surface steps

The focus of this study is on the adsorption of organic molecules onto steps on Si(1 0 0) and acetylene has been chosen as a show-case example. The study is based on a time-dependent quantum mechanical method and is divided into two parts. The first part has a methodological meaning and illustrates the dynamical events occurring when the molecule impinges onto the flat Si(1 0 0) surface. The second part analyzes preferred adsorption sites at steps, which are evaluated under stationary conditions from the minimization of the total energy. Adsorption-desorption events at those sites are analyzed considering temperature-activated motions obtained from the time-dependent representation. The simulation method is based on two Hamiltonians, i.e., semiempirical Hartree-Fock and Density Functional, and uses a cluster to model the exposed surface. Divergences and similarities of the properties of steps with respect to properties of the flat surface, as reported in the literature or obtained from this study, are analyzed and discussed.     

Coverage effects on phenol adsorption on Si(1 0 0)2 × 1 as: A first principle calculation

We investigated the adsorption of a 6-dimers Si(1 0 0)2 × 1 surface as a function of coverage and adsorption type (molecular/dissociative) by first principle calculations. In particular, we performed calculations on models with 2, 3, 4 and 6 phenol molecules, corresponding to coverage Θ = 0.34, 0.5, 0.67 and 1. We found that total adsorption energy, when at least one phenol is in a molecular state is lower than the sum of the corresponding singly adsorbed molecules. The dissociative adsorption of multiple molecules, both in parallel and switched configuration is most favoured for a coverage Θ = 0.34 (2.6 eV per adsorbed molecule). This values decreases to 2.0 eV and remains constant till the coverage 1 is reached.The energy barrier for the molecular-to-dissociated transition of a phenol molecule, in presence of another dissociatively adsorbed molecule is ∼0.008 eV and it is similar to the value in case of single adsorption. Possible hydrogen displacements were also considered.     

Monolayer adsorption of water on NaCl(1 0 0)

Density functional theory calculations have been applied to investigate the adsorption geometry of water overlayers on the NaCl(1 0 0) surface in the monolayer regime. Competition between H-H intermolecular repulsion and the attraction of the polar molecules to the surface ions results in the most stable structure having a 2 × 1 adsorption symmetry with an adsorption energy of 415 meV. Overlayers of 1 × 1 symmetry, as observed in experiment, have slightly lower adsorption energies. The layers are also unstable with respect to rotation of individual molecules. Multiple hydrogens/oxygens interacting with a single substrate ion can pull that ion out of the surface, although the examples considered are energetically very unfavourable. Overlayers of 1 × 1 symmetry with a coverage of one water molecule per NaCl do not have a high enough adsorption energy to wet the surface.     

The chemisorption of pentacene on Si(0 0 1)-2 × 1

Adsorption structures of the pentacene (C₂₂H₁₄) molecule on the clean Si(0 0 1)-2 × 1 surface were investigated by scanning tunneling microscopy (STM) in conjunction with density functional theory calculations and STM image simulations. The pentacene molecules were found to adsorb on four major sites and four minor sites. The adsorption structures of the pentacene molecules at the four major sites were determined by comparison between the experimental and the simulated STM images. Three out of the four theoretically identified adsorption structures are different from the previously proposed adsorption structures. They involve six to eight Si-C covalent chemical bonds. The adsorption energies of the major four structures are calculated to be in the range 67-128 kcal/mol. It was also found that the pentacene molecule hardly hopped on the surface when applying pulse bias voltages on the molecule, but was mostly decomposed.     

Investigation of the interaction of some astrobiological molecules with the surface of a graphite (0 0 0 1) substrate. Application to the CO, HCN, H2O and H2CO molecules

Detailed interaction potential energy calculations are performed to determine the potential energy surface experienced by the molecules CO, HCN, H₂O and H₂CO, when adsorbed on the basal plane (0 0 0 1) of graphite at low temperatures. The potential energy surface is used to find the equilibrium site and configuration of a molecule on the surface and its corresponding adsorption energy. The diffusion constant associated with molecular surface diffusion is calculated for each molecule.     

Reaction mechanism for CO oxidation on Cu(3 1 1): A density functional theory study

The microscopic reaction mechanism for CO oxidation on Cu(3 1 1) surface has been investigated by means of comprehensive density functional theory (DFT) calculations. The elementary steps studied include O₂ adsorption and dissociation, dissociated O atom adsorption and diffusion, as well as CO adsorption and oxidation on the metal. Our results reveal that O₂ is considerably reactive on the Cu(3 1 1) surface and will spontaneously dissociate at several adsorption states, which process are highly dependent on the orientation and site of the adsorbed oxygen molecule. The dissociated O atom may likely diffuse via inner terrace sites or from a terrace site to a step site due to the low barriers. Furthermore, we find that the energetically most favorable site for CO molecule on Cu(3 1 1) is the step edge site. According to our calculations, the reaction barrier of CO + O → CO₂ is about 0.3 eV lower in energy than that of CO + O₂ → CO₂ + O, suggesting the former mechanism play a main role in CO oxidation on the Cu(3 1 1) surface.     

First principles calculations of the adsorption of acetylene on the Si(0 0 1) surface at low and full coverage

The adsorption of acetylene on the Si(0 0 1)-c(2 × 4) surface at low and full coverage is studied by first principles density functional calculations using the generalized gradient approximation. For a single acetylene molecule, the most stable configuration corresponds to the di-σ site, on-top of a silicon dimer. This configuration is 0.36 eV more stable than the end-bridge site between two adjacent Si dimers. However, if there are two acetylene molecules, the paired end bridge configuration becomes the most stable. We have also studied the kinetics of the adsorption of a single acetylene molecule. Our calculations show that the reaction is barrier-free for adsorption in the di-σ configuration, while there is an energy barrier of 0.19 eV for adsorption in the end-bridge site. At monolayer coverage, the most stable configuration corresponds to acetylene molecules in the pair-end bridge configuration, in agreement with previous calculations. We have found a noticeable coverage dependence only for the end-bridge site, but not for the di-σ. Our results show that to have an accurate picture of the adsorption of acetylene on the Si(0 0 1) surface, a large unit cell is needed.     

SiO adsorption on a p(2 × 2) reconstructed Si(1 0 0) surface

We have investigated the adsorption mechanism of SiO molecule incident on a clean Si(1 0 0) p(2 × 2) reconstructed surface using density functional theory based methods. Stable adsorption geometries of SiO on Si surface, as well as their corresponding activation and adsorption energies are identified. We found that the SiO molecule is adsorbed on the Si(1 0 0) surface with almost no activation energy. An adsorption configuration where the SiO binds on the channel separating the dimer rows, forming a Si-O-Si bridge on the surface, is the energetically most favourable geometry found. A substantial red-shift in the calculated vibrational frequencies of the adsorbed SiO molecule in the bridging configurations is observed. Comparison of adsorption energies shows that SiO adsorption on a Si(1 0 0) surface is energetically less favourable than the comparable O₂ adsorption. However, the role of SiO in the growth of silicon sub-oxides during reactive magnetron plasma deposition is expected to be significant due to the relatively large amount of SiO molecules incident on the deposition surface and its considerable sticking probability. The stable adsorption geometries found here exhibit structural properties similar to the Si/SiO₂ interface and may be used for studying SiO_x growth.     

O2 dissociation on Pd(2 1 1) and Cu(2 1 1) surfaces

We have performed ab initio Density Functional Theory (DFT) based calculations to observe the reactivity of the Pd(2 1 1) and Cu(2 1 1) surfaces towards O₂. In order to properly address the adsorption dynamics, the static potential energy surface calculations have been complemented with first principles molecular dynamics calculations, which reveal interesting steering effects that complicate the dissociation dynamics. We have found that on both surfaces the step microfacets are very reactive and the dissociation of the O₂ molecule at room temperature occurs mostly on those sites.     

The conductance of monoatomic As and Ag chains deposited onto silicon steps evaluated using a simplified scattering approach

The purpose of this study is the assessment of the properties of the conductance of deposited atomic chains. Therefore, linear chains of covalent and metallic atoms, i.e. As and Ag, deposited onto monolayer steps of the Si(1 0 0) surface have been considered. The study is based on the extended Hückel theory, used for the evaluation of both the electronic structure and the conductance, and the calculations analyze the binding and adsorption energies of chains of variable length deposited onto SA steps in the light of the similar properties of free standing chains and of chains deposited onto the flat Si(1 0 0) surface. This comparison shows that the stability of the chain depends on its composition, rather than on its length, and increases in the order: free standing, deposited onto SA, deposited onto Si(1 0 0). The central result of the calculations of the conductance is that the dependence of this quantity on the chain length and composition and on the type of substrate parallels the one of the characteristic energies.     

Water adsorption on hydrogenated Si(1 1 1) surfaces

The adsorption of water on the hydrogen terminated Si(1 1 1) surface is studied by means of first-principles calculations as well as contact angle measurements. Possible initial adsorption configurations for single water molecules and the potential energy surface are calculated. Only small adsorption energies of the order of meV are predicted. Calculations for higher coverage show that the water-water interactions are stronger than the water-surface bonding. The contact angle formed between a water droplet on the surface approximated from the total-energy calculations amounts to 88°, while our measured value is 91°.     

Carbide induced reconstruction of monatomic steps on Ni(1 1 1) - A density functional study

We present density functional calculations for carbon adsorption at the two types of monatomic steps on a Ni(1 1 1) surface. We show that it is thermodynamically favourable to make a carbon induced clock-type reconstruction at the close-packed step with a [1 1 1] step geometry, which creates fourfold sites at the step-edge. It is furthermore possible to extend the carbide with the clock reconstructed geometry onto the upper terrace with a net energy gain compared to adsorption of carbon on unreconstructed close-packed steps or terrace sites on Ni(1 1 1). Our findings explain the fact that carbide islands start to grow preferentially on the close-packed steps as has been observed using scanning tunneling microscopy.     

Adsorption of water on TiN (1 0 0), (1 1 0) and (1 1 1) surfaces: A first-principles study

We use first-principles density functional theory-based calculations in the analysis of the interaction of H₂O with (1 0 0), (1 1 0) and (1 1 1) surfaces of TiN, and develop understanding in terms of surface energies, polarity of the surface and chemistry of the cation, through comparison with H₂O adsorption on ZrN. While water molecule physisorbs preferentially at Ti site of (1 0 0) and (1 1 1) surfaces, it adsorbs dissociatively on (1 1 0) surface of TiN with binding stronger than almost 1.32 eV/molecule. Our analysis reveals the following general trends: (a) surfaces with higher energies typically lead to stronger adsorption, (b) dissociative adsorption of H₂O necessarily occurs on a charge neutral high energy surface and (c) lower symmetry of the (1 1 0) plane results in many configurations of comparable stability, as opposed to the higher symmetry (1 0 0) and (1 1 1) surfaces, which also consistently explain the results of H₂O adsorption on MgO available in literature. Finally, weaker adsorption of H₂O on TiN than on ZrN can be rationalized in terms of greater chemical stability of Ti arising from its ability to be in mixed valence.     

Adsorption of V on a hematite (0 0 0 1) surface and its oxidation: Submonolayer coverage

The adsorption of submonolayer V on an idealized model hematite (0 0 0 1) surface and subsequent oxidation under atomic O adsorption are studied by density functional theory. The preferred adsorption sites, adsorption energy and configuration changes due to V and O adsorption are investigated. It is found that in most cases V forms threefold bonds with surface O atoms, inducing a large geometry change at the hematite surface and near surface region and a bond stretch between surface Fe and O. The adsorption energy is mainly decided by interplay between adsorbed metal-surface oxygen bonding and adsorbed metal - subsurface metal interaction. The relative energy of subsequent O adsorption and geometry depends on the reformed V/hematite structure. Electronic properties such as projected densities of states and chemical state change upon V adsorption are studied through both periodic slab and embedded cluster localized orbital calculations; both strong vanadium-oxygen and vanadium-iron interactions are found. While V generally donates electrons to a hematite surface, causing nearby Fe to be partially reduced, the Fe and V oxidization state depends very much on the coverage and detailed adsorption configuration. When the V/hematite system is exposed to atomic O, V is further oxidized and surface/near surface Fe is re-oxidized. Our theoretical results are compared with X-ray surface standing wave and X-ray photoelectron spectroscopic measurements. The influence of d-electron correlation on the predicted structures is briefly discussed, making use of the DFT + U scheme.     

Thin PTCDA films on Si(0 0 1): 1. Growth mode

We have studied the interface and thin film formation of the organic molecular semiconductor 3,4,9,10 perylene tetracarboxylic dianhydride (PTCDA) on clean and on hydrogen passivated Si(0 0 1) surfaces. The studies were made by means of high resolution X-ray photoelectron spectroscopy (HRXPS), near edge X-ray absorption fine structure (NEXAFS), low energy electron diffraction (LEED), and atomic force microscopy (AFM). On the passivated surface the LEED pattern is somewhat diffuse but reveals that the molecules grow in several ordered domains with equivalent orientations to the substrate. NEXAFS shows that the molecules are lying flat on the substrate. The Si 2p XPS line shape is not affected when the film is deposited so it can be concluded that the interaction at the interface between PTCDA and the substrate is weak. The evolution of the film formation appears to be homogeneous for the first monolayer with a nearly complete coverage of flat lying molecules based on the XPS attenuation. For layer thickness of 0.5-2 monolayers (ML) the molecules start to form islands, attracting the molecules in between, leaving the substrate partly uncovered. For thicker films there is a Stranski-Krastanov growth mode with thick islands and a monolayer thick film in between. For the clean surface the ordering of the film is much lower and angle resolved photoelectron spectroscopy (ARPES) of the molecular orbitals have only a small dependence of the emission angle. NEXAFS shows that the molecules do not lie flat on the surface and also reveal a chemical interaction at the interface.     

DFT study of NH3 dissociation on Si(1 1 1)-7 × 7. The role of intermolecular interactions

The adsorption of NH₃ molecule on the Si(1 1 1)-7 × 7 surface modelled with a cluster has been studied using density functional theory (DFT). The results indicate the existence of a precursor state for the non-dissociative chemisorption. The active site for the molecular chemisorption is the adatom; while the NH₃ molecule adsorbs on the Si restatom via this preadsorbed state, the adsorption on the Si adatom is produced practically without an energy barrier. The ammonia adsorption on the adatom induces an electron transfer from the dangling bond of this atom to the dangling bond of the adjacent Si restatom, hindering this site for the adsorption of a second NH₃ incoming molecule. However, this second molecule links strongly by means of two H-bonds. The dissociative chemisorption process was studied considering one and two ammonia molecules. For the dissociation of a lonely NH₃ molecule an energy barrier of ∼0.3 eV was calculated, yielding NH₂ on the adatom and H on the restatom. When two molecules are adsorbed, the NH₃-NH₃ interaction yields the weakening of a N-H bond of the ammonia molecule adsorbed closer the Si surface. As a consequence, the dissociation barrier practically disappears. Thus, the presence of a second NH₃ molecule at the adatom-restatom pair of the Si(1 1 1)-7 × 7 surface makes the dissociative reaction self-assisted, the total adsorption process elapsing with a negligible activation barrier (less than 0.01 eV).     

Adsorption and reactions of HN3 on Si(1 0 0)-2 × 1: A computational study

We have studied the adsorption and decomposition of HN₃ on Si(1 0 0)-2 × 1 surface using the hybrid density functional B3LYP method and effective core potential basis, LanL2DZ, with Si₁₅H₁₆ as a double dimer surface model for cluster calculations. The result shows that the barriers for the dissociative adsorption of HN₃ forming HN(a) + N₂(g) are quite low by stepwise dissociation processes occurring either on a dimer or across the dimers. The low activation energies are consistent with previous experimental observations that the molecularly adsorbed HN₃(a) can undergo decomposition producing HN(a) at low surface temperatures. On the other hand, the predicted activation energies for the N₃(a) + H(a) formation processes are all relatively higher. These results also explain the absence of the N₃(a) species in HREELS measurements following each annealing experiment. Several selected reaction paths were also confirmed with slab model calculations using an optimization approach coupling the energy and gradient calculations by the slab model with the geometrical optimization using Berny algorithm.In addition, the adsorbate effect was examined for the end-on and side-on molecular configurations. For the side-on adsorption configuration, all possible combinations with 1-4 adsorbates can exist on the four surface Si sites of the double dimers, with adsorption energies lying closely to the multiples of that of a single side-on adsorbate (LM2); i.e., adsorption energies are nearly additive. Interestingly, for the end-on adsorption, only 1 and 2 HN₃ molecules can adsorb on a dimer due to the presence of the negative charges on the remaining Si sites in the neighboring dimer. For the two end-on adsorbates on the same dimer, the total adsorption energy is close to two times that of HN₃(a) or LM1. For the mixed end-on/side-on configurations, only one of each type can co-exist on a single dimer pair (Si₁-Si₂ or Si₃-Si₄) sites with adsorption energy close to the sum of those of one end-on and one side-on adsorbate. Finally, the predicted reaction routes and vibrational frequencies showed good agreement with previous experimental results. The stabilities of many ad-species involved in these reactions with end-on and/or side-on configurations have been predicted together with the transition states connecting those species.     

Study of ammonia molecule adsorbing on diamond (1 0 0) surface

The diamond (1 0 0) surface with amino terminations is investigated based on density function theory within the generalized gradient approximation. Our calculated negative electron affinity of diamond (1 0 0) surface with hydrogen termination provides a necessary condition for initiating radical reaction. The results display that the ammonia molecule can form stable C-N covalent bonds on the diamond surface. In addition, due to the lower adsorption energy of one amino group binding on diamond surface, single amino group (SAG) model is easy to be realized in experiment with the comparison of double amino group (DAG) model. The adsorbed ammonia molecule will induce acceptor-like gap states with little change of the valence and conduction band of diamond in SAG model. The adsorption mechanism in the formation of ammonia monolayer on H-terminated diamond (1 0 0) surface, and two possible adsorption structures (SAG and DAG) were especially studied.     

Fabrication of rubrene nanowires on vicinal (0 0 0 1) sapphire surfaces

Morphology of high-vacuum deposited rubrene thin films on the annealed (0 0 0 1) vicinal sapphire surfaces was studied by atomic force microscopy in non-contact mode. Atomic force microscopy images of rubrene thin films indicate that a regular array of steps on the sapphire surface acts as a template for the growth of the arrays of rubrene nanosize wires. To further demonstrate that morphological features of a substrate are crucial in determining the morphology of rubrene layers we have grown rubrene on the sapphire surfaces that were characterized by the terrace-and-step morphology with islands. We have found preferential nucleation of rubrene molecules at the intersection between a terrace and a step, as well as around the islands located on terraces.