Short Bridge Site Research Articles

Density functional study of hydrazine adsorption and its N N bond cleaving on Fe(110) surface

Abstract We report density-functional-theory-based calculations of hydrazine adsorption and its N N bond cleaving on clean Fe(110) surface. It is found that hydrazine may adopt several adsorption configurations among which the most energetically stable is the bridging configuration. Adsorption on short bridge site generally has larger adsorption energies than those on long bridge site. N N bond cleaving is an exothermic process with reaction energies of 1.90 and 1.67 eV on long and short bridge site, respectively. Nudged elastic band method is used to estimate the activation energies of N N bond cleaving. Our results indicate that N N bond cleaving on long bridge site has lower activation energy (0.27 eV) compared to that of short bridge site (0.36 eV). By examining the molecular orbitals of the initial state it is found that this difference stems from stronger bond between the two NH 2 fragments adsorbed on short bridge site as compared to long bridge.

First-principles study of H2S adsorption and dissociation on Mo(1 1 0)

The dissociative adsorption of H2S on perfect and S-covered Mo(110) surfaces have been studied using density functional theory. Adsorption mechanisms of H2S, SH, S and H on both surfaces were analyzed and all possible potential energy profiles of H2S dissociation processes were mapped out. It indicated that H2S, SH, S, and H energetically favor the short bridge, long bridge, hollow, and hollow sites, respectively, on perfect surface, and favor the top, long bridge, hollow, and hollow sites, respectively, on S-covered surface. The first H2S dehydrogenation on clean surface has a barrier of 0.18–0.31eV, while it required a high energy barrier of 0.40–0.88eV on S-covered surface. The second dehydrogenation showed a lower barrier of 85meV on perfect surface, but a higher barrier of 0.29eV on S-covered surface. All these findings indicated that H2S can easily decompose on perfect Mo(110) surface, but the presence of atomic sulfur went against the H–S bond-breaking process both thermodynamically and kinetically. Finally, densities of electronics states and vibrational frequencies have been used to characterize the interactions between adsorbed species and the substrate.

Site-dependent electronic structures of a single molecule on a metal surface studied by scanning tunneling microscopy and spectroscopy

Single-molecule observation of the electronic structures of para-cyanobenzoate (pCB) adsorbed on Cu(110) has been performed using scanning tunneling microscopy (STM) and spectroscopy (STS). We found that pCB has two types of the adsorption site on Cu(110); i.e., two oxygen atoms of pCB are bridged between adjacent Cu atoms at the short- or long-bridge sites. STS and STS mapping revealed that the pCB adsorbed at the short-bridge site has a resonant peak at 2.0V above the Fermi level, which is assigned to the lowest unoccupied molecular orbital (LUMO) of pCB. However, the LUMO state is shifted toward lower voltage (1.2V) when the pCB molecule is adsorbed at the long-bridge site. The energy levels of the LUMO state, depending on the adsorption site of pCB, can thus be ascribed to the degree of the electronic interaction between pCB and the Cu substrate. The site transformation of pCB induced by the injection of tunneling electrons from the STM tip has also been presented.

Configuration change of NO on Cu(110) as a function of temperature.

The bonding structure of nitric oxide (NO) on Cu(110) is studied by means of scanning tunneling microscopy, reflection absorption infrared spectroscopy, and electron energy loss spectroscopy at 6-160 K. At low temperatures, the NO molecule adsorbs at the short bridge site via the N end in an upright configuration. At around 50 K, this turns into a flat configuration, in which both the N and O atoms interact with the surface. The flat configuration is characterized by the low-frequency N-O stretching mode at 855 cm(-1). The flat-lying NO flips back and forth when the temperature increases to ~80 K, and eventually dissociates at ~160 K. We propose a potential energy diagram for the conversion of NO on the surface.

Water adsorption and dissociation on Ni(110): How is it different from its close packed counterparts?

Water adsorption and dissociation on Ni(110) surface is studied in detail and compared with its close packed counterparts using density functional theory calculations. Water adsorption occurs on the top site as found on Ni(100) and Ni(111) but the adsorption is stronger on Ni(110). H and OH preferably adsorb on the short bridge sites (brgshort) opposed to hollow sites on (100) and (111) surfaces. Energy barriers for water molecule dissociation on Ni(110) as obtained from the transition state (TS) calculations were low compared to other Ni low indexed surfaces. TS geometries at different positions of the lattice coordinate, Q, were obtained to study the effect of surface temperature on dissociation of H2O molecules. These calculations revealed that second layer atoms were also involved in the TS. Dissociation probabilities are obtained using a semi-classical approximation by sampling Q for a Boltzmann distribution at different temperatures. Results showed that the increasing surface temperature significantly increases the dissociation probabilities at lower energies and saturates near the barrier for dissociation. Although the contribution from both top and second layers is similar at low surface temperatures, motion of top layer atoms contribute more towards dissociation probability at higher surface temperatures. Dissociation probabilities obtained are more than one order of magnitude higher than that on Ni(100) and Ni(111) surfaces suggesting Ni(110) to be more reactive among the low indexed Ni surfaces.

Oxygen Atom Adsorption on and Diffusion into Nb(110) and Nb(100) from First Principles

To understand the dynamics of oxidation of Nb, we examine the adsorption, absorption, and diffusion of an oxygen atom on, in, and into Nb(110) and Nb(100) surfaces, respectively, using density functional theory. Our calculations predict that the oxygen atom adsorbs on the threefold site on Nb(110) and the fourfold hollow site on Nb(100), and the adsorption energy is −5.08 eV and −5.18 eV, respectively. We find the long and short bridge sites to be transition states for O diffusion on Nb(110), while the on-top site is a rank-2 saddle point. In the subsurface region, the oxygen atom prefers the octahedral site, as in bulk niobium. Our results show also that the O atom is more stable on Nb(110) subsurface than on Nb(100) subsurface. The diffusion of oxygen atoms into niobium surfaces passes through transition states where the oxygen atom is coordinated to four niobium atoms. The diffusion barriers of the oxygen atom into Nb(110) and Nb(100) are 1.81 eV and 2.05 eV, respectively. An analysis of the electronic density of states reveals the emergence of well-localized electronic states below the lowest states of clean Nb surfaces due to d–p orbital hybridization.

Comparative study of phenol and thiophenol adsorption on Cu(110)

Adsorption of phenol and thiophenol (benzenethiol) on Cu(110) is investigated by a scanning tunneling microscope and electron energy loss spectroscopy. Phenol adsorbs intact and forms a cyclic trimer at 78 K. It is dehydrogenated to yield a phenoxy (C6H5O) group at 300 K. On the other hand, thiophenol is dehydrogenated to a thiophenoxy (C6H5S) group even at 78 K. Both products are bonded via chalcogen atom to the short-bridge site with the phenyl ring oriented nearly parallel to the surface. The C6H5O and C6H5S groups are preferentially assembled into the chains along the [001] and [112] directions, respectively. Dipole-dipole interaction is responsible for the chain growth, while the chain direction is ruled by the steric repulsion between chalcogen atoms and adjacent phenyl ring. This work demonstrates a crucial role of chalcogen atom of phenol species in their overlayer growth on the surface.

Theoretical investigation of uranyl ion adsorption on hydroxylated γ-Al2O3 surfaces

We herein report density functional investigations of uranyl adsorption on γ-Al2O3 surfaces. By applying periodic slab models, we report the possible configurations of uranyl adsorbed on the (100) and (110) surfaces of γ-Al2O3 by calculations using density functional theory. The above mentioned two surfaces are expected to be highly reactive and adsorb metal ions preferentially. We explored bidentate inner-sphere adsorption complexes of uranyl at short-bridge sites, AlOO, and long-bridge sites, AlOAlO(H). The results indicate several favorable adsorption configurations which fit the available TRLFS and EXAFS data well. Comparison of key calculated structure parameters with available experimental data suggests an extension of the prevailing interpretation and implies that a set of uranyl complexes may coexist on the edge surfaces of γ-Al2O3.

Theoretical and experimental studies of hydrogen adsorption and desorption on Ir surfaces

We report adsorption and desorption of hydrogen on planar Ir(210) and faceted Ir(210), consisting of nanoscale {311} and (110) facets, by means of temperature programmed desorption (TPD) and density functional theory (DFT) in combination with the ab initio atomistic thermodynamics approach. TPD spectra show that only one H2 peak is seen from planar Ir(210) at all coverages whereas a single H2 peak is observed at around 440 K (F1) at fractional monolayer (ML) coverage and an additional H2 peak appears at around 360 K (F2) at 1 ML coverage on faceted Ir(210), implying structure sensitivity in recombination and desorption of hydrogen on faceted Ir(210) versus planar Ir(210), but no evidence is found for size effects in recombination and desorption of hydrogen on faceted Ir(210) for average facet sizes of 5-14 nm. Calculations indicate that H prefers to bind at the two-fold short-bridge sites of the Ir surfaces. In addition, we studied the stability of the Ir surfaces in the presence of hydrogen at different H coverages through surface free energy plots as a function of the chemical potential, which is also converted to a temperature scale. Moreover, the calculations revealed the origin of the two TPD peaks of H2 from faceted Ir(210): F1 from desorption of H2 on {311} facets while F2 from desorption of H2 on (110) facets.

Ab-initio calculation of C and CO adsorption on the Co (110) surface

The adsorption energies, structural, electrical and magnetic properties of adsorption of C and CO on the fcc Co (110) surface have been investigated using density functional theory. The preferential adsorption site for the fcc Co (110) has been calculated. For the case of C adsorption, the preferential adsorption site is the long-bridge for both the 0.5 and 1.0 monolayers (ML) coverages. Whilst for the CO case, the preferential adsorption sites are at the atop and short-bridge site for 0.5 and 1.0 ML coverages respectively. Structurally, the first two layers of the bare Co (110) surface expand whereas the second and third layers contract. Upon adsorption of either C or CO, however, the degree of expansion and compression reduces. Magnetically, the adsorbates were found to couple ferrimagnetically to the surface and suppress the magnetic moment of the Co layers beneath them. The C adsorbate has a much stronger suppression effect as compared to the CO adsorbate. At 0.5 ML coverage, the C adatom suppresses up to 47% of the magnetic moment in the surface layer compared to a clean Co (110), whereas the CO adsorbate only suppresses up to 16%. For the 1.0 ML coverage case, both the C and CO adsorbates suppress almost equivalently well at 68% and 63% respectively. We also report on a correlation between the amount of charge transfer and the degree of suppression of the surface magnetic moment. Finally, we observe that the electronic charge is shared in the [001] direction for the C adsorbate and in the [11¯0] direction for the CO adsorbate. This anisotropy of surface bonding, in conjunction with the ligand field theory, explains the mechanism behind the spin reorientation transition that occurs uniquely on the CO/Co(110) system.

A first principles study of water adsorption on α-Pu (0 2 0) surface

Adsorptions of water in molecular (H2O) and dissociative (OH+H, H+O+H) configurations on the α-Pu (020) surface have been studied using ab initio methods. The full-potential FP/LAPW+lo method has been used to calculate the adsorption energies at the scalar relativistic with no spin–orbit coupling (NSOC) and fully relativistic with spin–orbit coupling (SOC) theoretical levels. It is found that the SOC effect increases the adsorption energies by ∼0.30eV for the two dissociative adsorptions. Weak physisorptions have been observed for the molecule H2O on the α-Pu (020) surface with primarily a covalent bonding, while the two dissociative adsorptions are chemisorptive with ionic bonding. The one-fold top site with an almost flat-lying orientation is found to be the most stable site for the adsorbed H2O molecule. At the SOC level, the most stable adsorption energy is 0.58eV, the corresponding values being 5.44eV and 5.73eV for the partial dissociation and complete dissociation cases, respectively. The analysis of the local projected density of states shows that the surface Pu-5f electrons remain primarily chemically inert in the molecular water adsorption process. Completely dissociative adsorption at a long bridge site for the dissociated O atom and two short bridge sites for the two dissociated H atoms is the most stable adsorption site. Hybridizations of O(2p)–H(1s)–Pu(5f)–Pu(6d) are observed for the two dissociative adsorptions, implying that some of the Pu-5f electrons become further delocalized and participate in chemical bonding. Work functions decrease for the molecular and the partial adsorption processes while it increases for complete dissociation.

Systematic DFT-GGA study of hydrogen adsorption on transition metals

Computational study of hydrogen adsorption on (111) surface of transition metals with face centered cubic (fcc) lattice is reported and the results are compared with available experimental and theoretical data. In addition, dissociative adsorption of hydrogen on Pt(111), Pt(100) and Pt(110) is studied in the range of coverage from 0.25 to 1 monolayer. In the case of Pt(111) preferential adsorption site was found to be three-coordinated fcc-hollow site, while on Pt(100) and Pt(110) surface hydrogen settles on two-coordinated bridge and short bridge site, respectively. Hydrogen adsorption energy was found to decrease with the increasing coverage. Structural changes of studied Pt surfaces upon hydrogen adsorption have been compared with the experimental data existing in the literature and good qualitative agreement has been obtained.

Imaging sequential dehydrogenation of methanol on Cu(110) with a scanning tunneling microscope

Adsorption of methanol and its dehydrogenation on Cu(110) were studied by using a scanning tunneling microscope (STM). Upon adsorption at 12 K, methanol preferentially forms clusters on the surface. The STM could induce dehydrogenation of methanol sequentially to methoxy and formaldehyde. This enabled us to study the binding structures of these products in a single-molecule limit. Methoxy was imaged as a pair of protrusion and depression along the [001] direction. This feature is fully consistent with the previous result that it adsorbs on the short-bridge site with the C-O axis tilted along the [001] direction. The axis was induced to flip back and forth by vibrational excitations with the STM. Two configurations were observed for formaldehyde, whose structures were proposed based on their characteristic images and motions.

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.

An ab initio study of hydrogen adsorption on the (020) surface of α‐Pu

AbstractAtomic hydrogen adsorptions on the (020) surface of α‐Pu and the effects of surface relaxation on adsorption properties have been studied using a relativistic extension of the full‐potential augmented plane wave with local orbital basis method. The surface has been modeled by a four‐layer periodic slab consisting of 32 Pu atoms with a layer by layer anti‐ferromagnetic arrangement. The adsorption properties for four different adsorption sites, namely the top, hollow, short bridge and long bridge sites have been investigated in detail. All computations have been carried out at two different theoretical levels, namely the scalar relativistic level without spin–orbit interaction (SR‐NSO) and the fully relativistic level with spin–orbit interaction (FR‐SO). The effect of relaxation has also been studied by calculating adsorption properties both on relaxed and non‐relaxed Pu surfaces. Our studies show that the short bridge is the most favorable site for hydrogen adsorption with chemisorptions energies of 2.78 and 2.75 eV, respectively, at the two levels of theory. Neither spin–orbit coupling nor surface relaxation appears to have significant effects on adsorption.

The structure of methoxy species on Cu(110): A combined photoelectron diffraction and density functional theory determination

The local structure of the methoxy species on Cu(110) has been investigated experimentally using chemical-state specific O 1s scanned-energy mode photoelectron diffraction (PhD), and also by density functional theory (DFT) calculations. The PhD data show a clear preference for adsorption with the O bonding atoms in short-bridge sites, though the best fit of multiple-scattering simulations to the experimental data is achieved with two slightly different short-bridge geometries. The DFT calculations also show that not only are the short-bridge sites energetically favoured in isolation, but that coordination to pairs of Cu adatoms has a similar energy. A structure consistent with both the PhD data and the DFT calculations is proposed for the previously-observed (5 × 2)pg ordered phase, based on methoxy species in short-bridge sites on pairs of Cu adatoms and on the underlying surface. Simulated scanning tunnelling microscopy images agree well with those observed experimentally, while the model is also shown to be consistent with the qualitative behaviour seen in early X-ray photoelectron diffraction (XPD) forward-scattering experiments.

Unexpected Deformations Induced by Surface Interaction and Chiral Self‐Assembly of CoII‐Tetraphenylporphyrin (Co‐TPP) Adsorbed on Cu(110): A Combined STM and Periodic DFT Study

In a combined scanning tunnelling microscopy (STM) and periodic density functional theory (DFT) study, we present the first comprehensive picture of the energy costs and gains that drive the adsorption and chiral self-assembly of highly distorted Co(II)-tetraphenylporphyrin (Co-TPP) conformers on the Cu(110) surface. Periodic, semi-local DFT calculations reveal a strong energetic preference for Co-TPP molecules to adsorb at the short-bridge site when organised within a domain. At this adsorption site, a substantial chemical interaction between the molecular core and the surface causes the porphyrin macrocycle to accommodate close to the surface and in a flat geometry, which induces considerable tilting distortions in the phenyl groups. Experimental STM images can be explained in terms of these conformational changes and adsorption-induced electronic effects. For the ordered structure we unambiguously show that the substantial energy gain from the molecule–surface interaction recuperates the high cost of the induced molecular and surface deformations as compared with gas phase molecules. Conversely, singly adsorbed molecules prefer a long-bridge adsorption site and adopt a non-planar, saddle-shape conformation. By using a van der Waals density functional correction scheme, we found that the intermolecular π–π interactions make the distorted conformer more stable than the saddle conformer within the organic assembly. These interactions drive supramolecular assembly and also generate chiral expression in the system, pinning individual molecules in a propeller-like conformation and directing their assembly along non-symmetric directions that lead to the coexistence of mirror-image chiral domains. Our observations reveal that a strong macrocycle–surface interaction can trigger and stabilise highly unexpected deformations of the molecular structure and thus substantially extend the range of chemistries possible within these systems.

Density-functional study of the methoxy intermediates at Cu(111), Cu(110) and Cu(001)surfaces

Although the geometry of the methoxy intermediates on copper surfaces has beeninvestigated in a number of experimental and also in several theoretical papers, thesituation remains controversial for the (110) and (001) surface orientations. In thepresent study, we perform density-functional calculations for the Cu(111), (110)and (001) surfaces. The stress is laid upon the models and ideas proposed in theliterature. At the (111) face, the fcc three-fold adsorption site is found to beslightly more favourable than the hcp one. At the (110) surface, we predict themethoxy to adsorb close to the short-bridge site in a tilted geometry. Metastablelong-bridge positions are less stable by more than 0.3 eV. Since for coverages up toθ = 0.5 the interaction between the methoxy groups is weak, we see no reason for the presence oftwo different adsorbed methoxy forms unless the copper surface is reconstructed. For the(001) surface we obtain almost the same adsorption energy for the upright adsorbedmethoxy in the hollow site, and a tilted methoxy form in a position between the bridgeand the hollow site. The calculations agree semiquantitatively with the availableexperimental data, and admit the presence of two distinct methoxy surface forms.

Density Functional Model Study of Uranyl Adsorption on the Solvated (001) Surface of Kaolinite

We studied the adsorption of uranyl on bare and solvated models of the octahedral (001) surface of kaolinite using first-principles density functional calculations. Inner-sphere bidentate complexes adsorbed at partially deprotonated short-bridge sites AlOO(H) and long-bridge sites AlO−AlO(H) were modeled as the most probable adsorption complexes. The uranyl complex at the doubly deprotonated AlO−AlO long-bridge site exhibits a third contact to the surface, not present in the complex at the corresponding short-bridge site. Adsorption at short-bridge sites is energetically favored compared to complexes at long-bridge sites. We were unable to determine stable adsorption complexes of uranyl at singly deprotonated AlO−AlOH long-bridge sites. Surface solvation, approximated via an adsorbed monolayer of water molecules, hardly affects the adsorption complexes of uranyl. Contacts U−Oeq in the equatorial plane shorten by 2 pm, U−Al distances elongate by up to 4 pm. In contrast to the bare surface, adsorption complexes at long-bridge and short-bridge sites of the solvated surface exhibit similar stabilities.

First-principles study of H on the reconstructed W(100) surface

The first-principles calculations were used to study the hydrogen energetics on the (100) tungsten $(\sqrt{2}\ifmmode\times\else\texttimes\fi{}\sqrt{2})R45\ifmmode^\circ\else\textdegree\fi{}$ surface. Two equilibrium sites for H at the surface are identified, with a low migration barrier from the energetically clearly higher long bridge site to the short bridge site. At low coverages, the majority of H surface diffusion events take place via the short bridge sites. The energetics for H penetration from the surface to the solute site in the bulk was defined, showing that the bulk H diffusion via neighboring tetrahedral sites takes place at depths beyond the second subsurface layer.