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.     

Empty-state scanning tunneling microscopy image of C2H2 on Si(0 0 1)--new evidence for paired end-bridge di-σ configuration

New evidence of the paired end-bridge configuration in the room-temperature adsorption geometries of C₂H₂ molecules on Si(0 0 1) is presented by scanning tunneling microscopy (STM) and ab initio pseudopotential calculations. The distinct four-leaved feature occupying two adjacent Si dimer sites in the experimental empty-state STM images are well reproduced by simulations of the paired end-bridge adsorption configuration. Calculated energetics suggests that the Si(0 0 1) surface is covered by paired end-bridge structures at the saturation coverage of 1 ML, in agreement with the existing experiments.     

Adsorption of cyclohexadiene, cyclohexene and cyclohexane on Pt(1 1 1)

The adsorption of 1,3-cyclohexadiene, 1,4-cyclohexadiene, cyclohexene and cyclohexane on Pt(1 1 1) was studied using ab initio density functional theory. For 1,3-cyclohexadiene three adsorption modes were distinguished: bridge 1,2-di-σ/3,4-π, hollow 1,4-di-σ/2,3-π and bridge 1,4-di-σ/2,3-π with adsorption energies of −155, −147 and −75 kJ/mol, respectively. Three stable adsorption modes were also identified for 1,4-cyclohexadiene: bridge quadra-σ, hollow di-σ/π and bridge di-π with adsorption energies of −146 kJ/mol, −142 kJ/mol and −88 kJ/mol, respectively. Cyclohexene was found to adsorb in six modes: 4 di-σ and 2 π-adsorption modes. The preferred configuration was found to be boat di-σ with an adsorption energy of −81 kJ/mol. The three other di-σ adsorption modes have comparable adsorption energies, ranging from −64 to −69 kJ/mol. Molecular strain and CPt bonding energies are used to elucidate stability trends. Cyclohexane is found to adsorb only at the hollow site whereby the axial hydrogen atoms are positioned over surface Pt-atoms with an adsorption energy of −37 kJ/mol. The calculations correctly predict the weakening of the axial CH bonds and provide a possible explanation for the large shift in the vibrational frequencies.     

NO adsorption and diffusion on unreconstructed Pt{1 0 0} surface. A density functional theory investigation

Ab initio density functional theory was used to investigate the adsorption and diffusion of a single NO molecule on the unreconstructed Pt{1 0 0}-(1 × 1) surface. To our knowledge this is the first theoretical study of the NO diffusion activation energy on the Pt{1 0 0} surface. The most stable adsorption position for NO corresponds to the bridge site with the axis of the molecule perpendicular to the surface. The bond of the NO molecule to the surface is through the N-atom. We found that there is a low adsorption energy when the NO molecule is bonded through the O-atom and the axis is perpendicular to the surface, for the three high symmetry sites investigated. NO diffusion between bridge-hollow sites, bridge-atop sites, and hollow-atop sites was also investigated. The barrier for NO diffusion is 0.41 eV, which corresponds to the energy difference between the bridge and hollow sites. This value is around 15% of the highest adsorption energy found on this surface. NO stretch frequencies are also calculated for the three high symmetry sites investigated.     

Theoretical study on adsorption of thiophenethiolate molecule on Au(1 1 1) surface

We have theoretically studied the adsorption of a thiophenethiolate (C₄H₃S-S) molecule on the Au(1 1 1) surface by first-principles calculations. It is found that the bridge site is the most stable adsorption site with the adsorption energy of 1.02 eV. In the optimized adsorption geometry, the bond between the head S atom and the connected C atom in the tail thiophene molecule is tilted by 57.2° from the surface normal. In addition, the adsorption of thiophenethiolate induces large relaxations of the surface Au atoms around it. Furthermore, weak interactions between the S atom in the tail thiophene ring and the Au atoms also contribute to the adsorption on the Au surface.     

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.     

Atomic and electronic structure of Sr/Si(0 0 1)-(2 × 2)

The adsorption of Sr on the Si(0 0 1) surface with the semiantiphase dimer (2 × 2) reconstruction is studied, based upon the ab initio pseudopotential calculations. It is calculated that the semiantiphase dimer (2 × 2) reconstruction (2 dimers per unit cell) is more favorable than the (2 × 1) phase (1 dimer per unit cell) by an energy of about 0.24 eV/dimer. Considering the energetically more stable reconstruction, we have assumed four possible locations for 1/4 monolayer (ML) Sr adsorption on this surface: (i) bridge, (ii) cave, (iii) pedestal, and (iv) valley-bridge. We find that Sr adsorption on the valley-bridge site is energetically more favorable than all other cases studied here. Interestingly, one of the dimers becomes symmetric, but the other one is still asymmetric with the buckling angle reduced from 18° to 14°, when compared with the clean Si(0 0 1)-(2 × 2) surface. The calculated bond length between Sr and Si in the case of valley-bridge adsorption site is 3.05 Å, and in good agreement with other theoretical calculations. We also present and compare the electronic band structures for the clean and covered surfaces as well as the corresponding charge density plots.     

Comparative DFT study of the adsorption of 1,3-butadiene, 1-butene and 2-cis/trans-butenes on the Pt(1 1 1) and Pd(1 1 1) surfaces

The interaction of 1,3-butadiene, 1-butene and 2-cis/trans-butenes on the Pt(1 1 1) and Pd(1 1 1) surfaces has been studied with density functional theory methods (DFT). The same most stable adsorption modes have been found on both metal surfaces with similar adsorption energies. For 1,3-butadiene the 1,2,3,4-tetra-σ adsorption structure is shown to be the most stable one, in competition with a 1,4-metallacycle-type mode, which is only less stable by 10-12 kJ mol⁻¹. On Pt(1 1 1) these total energy calculations were combined with simulations of the vibrational spectra. This confirms that the 1,2,3,4-tetra-σ adsorption is the most probable adsorption structure, but cannot exclude the 1,4-metallacycle as a minority species. Although similar in type and energy, the adsorption on the Pd(1 1 1) surface shows a markedly different geometry, with a smaller molecular distortion upon adsorption. The most stable adsorption structure for the butene isomers is the di-σ-mode. Similarly to the case of the 1,3-butadiene, the adsorption geometry is closer to the gas phase one on Pd than on Pt, hence explaining the different spectroscopic results, without the previously assumed requirement of a different binding mode. Moreover the present study has shown that the different selectivity observed on Pt(1 1 1) and Pd(1 1 1) for the hydrogenation reaction of butadiene cannot be satisfactory explained by the single comparison of the relative stabilities of 1,3-butadiene and 1-butene on these metals.     

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.     

Ruthenium adsorption and diffusion on the GaN(0 0 0 1) surface

We report first principles calculations to analyze the ruthenium adsorption and diffusion on GaN(0 0 0 1) surface in a 2×2geometry. The calculations were performed using the generalized gradient approximation (GGA) with ultrasoft pseudopotential within the density functional theory (DFT). The surface is modeled using the repeated slabs approach. To study the most favorable ruthenium adsorption model we considered T₁, T₄ and H₃ special sites. We find that the most energetically favorable structure corresponds to the Ru- T₄ model or the ruthenium adatom located at the T₄ site, while the ruthenium adsorption on top of a gallium atom (T₁ position) is totally unfavorable. The ruthenium diffusion on surface shows an energy barrier of 0.612 eV. The resultant reconstruction of the ruthenium adsorption on GaN(0 0 0 1)- 2×2 surface presents a lateral relaxation of some hundredth of Å in the most stable site. The comparison of the density of states and band structure of the GaN(0 0 0 1) surface without ruthenium adatom and with ruthenium adatom is analyzed in detail.     

A theoretical study of Fe adsorption along Bi-nanolines on the H/Si(0 0 1) surface

We have investigated the energetic stability and equilibrium geometry of the adsorption of transition metal Fe atoms near the self-organized Bi lines on hydrogen passivated Si(0 0 1) surface. Our total energy results show that there is an attractive interaction between Fe adatoms along the Bi-nanolines. For the energetically most stable configuration, the Fe adatoms are seven-fold coordinated, occupying the subsurface interstitial sites aside the Bi-nanolines. With increased coverage, Fe atoms are predicted to form two parallel lines, symmetrically on both sides of the Bi line. Within our local spin-density functional calculations, we find that for the most stable geometries the Fe adatoms exhibit an antiferromagnetic coupling.     

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).     

Diffusion of Pb adatom and ad-dimer on Si(1 0 0) from ab initio studies

The diffusion pathways of Pb adatoms and ad-dimers on Si(1 0 0) are investigated by first-principles calculations. Pb adatoms are found to diffuse on top of the Si(1 0 0) dimer row with an energy barrier of 0.31 eV. However, Pb dimers are energetically more stable. Pb dimers on top of the dimer row have a high energy barrier (0.95 eV) to rotate from the lowest energy configuration to the orientation parallel to the underlying Si(1 0 0) dimer row. Once the ad-dimer is oriented parallel to Si(1 0 0) dimer row, they can diffuse along the dimer row with an energy barrier of only 0.32 eV.     

First-principles study on the catalytic role of Ag in the oxygen adsorption of LaMnO3(0 0 1) surface

In the present paper, the catalytic role of Ag in the oxygen adsorption of LaMnO₃(0 0 1) surface has been theoretically investigated using first-principles calculations based on the density functional theory (DFT) and pseudopotential method. The O₂ adsorption energy is larger for the vertical adsorption and the covalent bond was formed between O₂ molecule and surface Mn. The calculation of electronic properties of interaction between Ag atom and LaMnO₃(0 0 1) surface demonstrates that the most stable position for Ag adsorption is hollow site. The O₂ adsorption energy dramatically increased from 0.298 eV to 1.108 eV due to Ag pre-adsorbed. It is Ag pre-adsorbed that facilitates O₂ adsorption on surface. The bond length and bond population of O₂ molecule indicate that Ag atom facilitates O₂ molecule dissociative adsorption. The Ag atom strengthens LaMnO₃(0 0 1) substrate activity and activity center was formed on surface, which enhances the electrocatalytic activity of LaMnO₃ as solid oxide fuel cells cathode material at low temperature.     

Density functional theory study of selenium adsorption on Fe(1 1 0)

The adsorption of atomic Se on a Fe(1 1 0) surface is examined using the density functional theory (DFT). Selenium is adsorbed in high-symmetry adsorption sites: the -short and long-bridge, and atop sites at 1/2, 1/4, and 1 monolayer (ML) coverages. The long bridge (LB) site is found to be the most stable, followed by the short bridge (SB) and top sites (T). The following overlayer structures were examined, p(2 × 2), c(2 × 2), and p(1 × 1), which correspond to 1/4 ML, 1/2 ML, and 1 ML respectively. Adsorption energy is −5.23 eV at 1/4 ML. Se adsorption results in surface reconstruction, being more extensive for adsorption in the long bridge site at 1/2 ML, with vertical displacements between +8.63 and −6.69% -with regard to the original Fe position-, affecting the 1st and 2nd neighbours. The largest displacement in x or y-directions was determined to be 0.011, 0.030, and 0.021 Å for atop and bridge sites. Comparisons between Se-adsorbed and pure Fe surfaces revealed reductions in the magnetic moments of surface-layer Fe atoms in the vicinity of the Se. At the long bridge site, the presence of Se causes a decrease in the surface Fe d-orbital density of states between 4 and 5 eV below Fermi level. The density of states present a contribution of Se states at −3.1 eV and −12.9 eV. stabilized after adsorption. The Fe-Fe overlap population decrease and a Fe-Se bond are formed at the expense of the metallic bond.     

Adsorption of CO, CO2 and NO molecules on a BaTiO3 (0 0 1) surface

Since the development of Scanning Tunnelling Microscopy (STM) technique, considerable attention has been devoted to various molecules adsorbed on various surfaces. Also, a new concept emerged with molecules on surfaces considered as nano machines by themselves. In this context, a thorough knowledge of surfaces and adsorbed molecules at an atomic scale are thus particularly invaluable. The present work describes the first Density Functional Theory (DFT) study of adsorption of CO, CO₂ and NO molecules on a BaTiO₃ surface following a first preliminary calculation of O and O₂ adsorption on the same surface. In the previously considered work, we found that a (0 0 1) surface with BaO termination is more stable than the one with TiO₂-termination. Consequently, we extended our study to CO, CO₂ and NO molecules adsorbed on a (0 0 1) surface with BaO termination. The present calculation was performed on a (1 × 1) cell with one monolayer of adsorbed molecules. Especially, a series of cases implying CO molecules adsorbed in various geometrical configurations has been examined. The corresponding adsorption energy varies in the range of −0.17 to −0.10 eV. The adsorption energy of a CO₂ molecule directly located above an O surface atom (called O_s) is of the order of −0.18 eV. The O-C distance length is then 1.24 Å and the O-C-O and O-C-O_s angles are 134.0° and 113.0°, respectively. For NO adsorption, the most important induced structural changes are the followings: (i) the N-O bond is broken when a NO molecule is absorbed on a Ba-O_s bridge site. In that case, N and O atoms are located above an O and a Ba surface atom, respectively, whereas the O-Ba-O_s and N-O_s-Ba angles are 106.5° and 63.0°, respectively. The N-O distance is as large as 2.58 Å and the adsorption energy is as much as −2.28 eV. (ii) In the second stable position, the NO molecule has its N atom adsorbed above an O_s atom, the N-O axis being tilted toward the Ba atom. The N-O_s-Ba angle is then 41.1° while the adsorption energy is only −0.10 eV. At last, the local densities of states around C, O as well as N atoms of the considered adsorbed molecules have also been discussed.     

Methanol adsorption on silicon (0 0 1)

Using a first-principles pseudopotential technique, we have investigated the adsorption of CH₃OH on the Si(0 0 1) surface. We have found that, in agreement with the overall experimental picture, the most probable chemisorption path for methanol adsorption on silicon (0 0 1) is as follows: the gas phase CH₃OH adsorbs molecularly to the electrophilic surface Si atom via the oxygen atom and then dissociates into Si-OCH₃ and H, bonded to the electrophilic and nucleophilic surface silicon dimer atoms, respectively. Other possible adsorption models and dissociation paths are also discussed. Our calculations also suggest that the most probable methanol coverage is 0.5 ML, i.e., one molecule per Si-Si dimer, in agreement with experimental evidences. The surface atomic and electronic structures are discussed and compared to available theoretical and experimental data. In addition, we propose that a comparison of our theoretical STM images and calculated vibrational modes for the adsorbed systems with detailed experimental investigations could possibly confirm the presented adsorption picture.     

Study on the adsorption of fluorescein on Ag(1 1 0) substrate

The adsorption of fluorescein on the Ag(1 1 0) surface has been investigated by the first-principles pseudopotential method. Various adsorption geometries have been calculated and the energetically most favorable structure of fluorescein/Ag(1 1 0) was identified. The fluorescein molecule, in most favorable structure, is on hollow site, and the adsorption energy is 2.34 eV. Here the adsorption sites refer to the positions at the first layer of the substrate where the middle carbon atom of the fluorescein molecule is located. The bonding strength of the fluorescein molecule to the Ag substrate is site selective, being determined by electron transfer to the oxygen atoms of the molecule and local electrostatic attraction between the oxygen atoms and the silver atoms.     

First principles calculations of the adsorption and diffusion of Y on the Si(0 0 1)-c(4 × 2) surface

We have studied the adsorption and diffusion of yttrium on the Si(0 0 1)-c(4 × 2) surface in the early stages of growth. Our first principles total energy calculations are based on the density functional theory as implemented in the SIESTA code. The exchange and correlation energies are treated within the generalized gradient approximation according to the Perdew, Burke and Ernzerhof parametrization. Our results demonstrate that the most favorable adsorption site is in the trench between two silicon dimer rows, identified as valley-bridge (V). Our studies show that the diffusion of an Y adatom on Si(0 0 1)-c(4 × 2) surface presents an anisotropic behavior. We found two values for the barriers along the valley (0.54 and 1.07 eV) and one of 1.24 eV in the perpendicular direction, showing that diffusion along the valley is more probable. The analysis of the Mulliken overlap populations shows that the bonding between an Y adatom and the surface is partially covalent. Two Y atoms on the surface do not form dimers instead they are adsorbed as adatoms.     

Effect of hydrogenation on P/Si(0 0 1)-(1 × 2)

Ab initio calculations, based on pseudopotentials and density functional theory, have been performed to investigate the effect of hydrogenation on the atomic geometries and energetics of substitutional phosphorus (P) on the generic Si(0 0 1)-(1 × 2) surface. For the 0.5 ML coverage of P, we have considered three different substitutional sites: (i) the mixed Si-P dimer structure (i.e., the P-nondiffused case), (ii) P-interdiffused to the second layer Si (i.e., intermixed P-Si bond structure) and (iii) P-interdiffused to the third layer Si. We have found that the mixed Si-P dimer structure is 0.79 eV/dimer energetically more favorable than the P-interdiffused case. However, for the hydrogenation of above cases, we have found that the situation is reversed and the interdiffused case is 0.3 eV/dimer energetically more favorable than the P-nondiffused case. Reductions in the number of P-Si is identified as a contributing factor which determines energetically the stable structures during P on Si(0 0 1).