High Coordination Sites Research Articles

Adsorption characteristics of atomic nitrogen on ruthenium surfaces

We have studied the adsorption, vibration, and diffusion of N atoms on Ru ( 0 0 0 1 ) , ( 1 0 1 ¯ 0 ) , ( 1 1 2 ¯ 0 ) and ( 1 1 2 ¯ 1 ) surfaces by means of the 5-parameter Morse potential (5-MP) of interaction between atomic nitrogen and a metal surface. The adsorption sites, adsorption geometry, binding energy and eigenvibration of atomic nitrogen on the different ruthenium surfaces are calculated. It is shown that atomic nitrogen always preferably occupies the high coordination sites on Ru surfaces. The 4-fold site is the preferable adsorption site for atomic nitrogen on both open Ru ( 1 1 2 ¯ 0 ) and ( 1 1 2 ¯ 1 ) surfaces while 3-fold site is the most stable adsorption site for atomic nitrogen on both Ru ( 0 0 0 1 ) and ( 1 0 1 ¯ 0 ) surfaces. Moreover, we find the lowest energy pathway of diffusion and diffusion barriers of atomic nitrogen on the surfaces.

Oxides of small Rhodium clusters: Theoretical investigation of experimental reactivities

Density functional theory is used to investigate the structures of cationic rhodium cluster oxides, Rh(6)O(m) (+) (m=1,4). On the monoxide and dioxide, the oxygen atoms occupy bridge sites, while on trioxide and tetroxide clusters, high-coordination sites are favored. A range of spin multiplicities are investigated for each cluster, with high spin multiplicities found to be less favored for the oxides compared with the naked metal clusters. The dissociation of nitric oxide on low-energy isomers of Rh(6)O(4) (+) is investigated and found to be unfavorable compared to molecular adsorption due to a combination of thermodynamic and kinetic factors. These calculations are consistent with, and help to account for, the experimentally observed reactivity of rhodium and rhodium oxide clusters with nitric oxide [M. S. Ford et al., Phys. Chem. Chem. Phys. 7, 975 (2005)].

Both Met(109) and Met(112) are utilized for Cu(II) coordination by the amyloidogenic fragment of the human prion protein at physiological pH

The prion protein is a ubiquitous neuronal membrane protein. Misfolding of the prion protein has been implicated in transmissible spongiform encephalopathies (prion diseases). It has been demonstrated that the human prion protein (PrP) is capable of coordinating at least five CuII ions under physiological conditions; four copper binding sites can be found in the octarepeat domain between residues 61 and 91, while another copper binding site can be found in the unstructured “amyloidogenic” domain between residues 91 and 126 PrP(91–126). Herein we expand upon a previous study [J. Shearer, P. Soh, Inorg. Chem. 46 (2007) 710–719] where we demonstrated that the physiologically relevant high affinity CuII coordination site within PrP(91–126) is found between residues 106 and 114. It was shown that CuII is contained within a square planar (N/O)3S coordination environment with one His imidazole ligand (H(111)) and one Met thioether ligand (either M(109) or M(112)). The identity of the Met thioether ligand was not identified in that study. In this study we perform a detailed investigation of the CuII coordination environment within the PrP fragment containing residues 106–114 (PrP(106–114)) involving optical, X-ray absorption, EPR, and fluorescence spectroscopies in conjunction with electronic structure calculations. By using derivatives of PrP(106–114) with systematic Met→Ile “mutations” we show that the CuII coordination environment within PrP(106–114) is actually comprised of a mixture of two major species; one CuII(N/O)3S center with the M(109) thioether coordinated to CuII and another CuII(N/O)3S center with the M(112) thioether coordinated to CuII. Furthermore, deletion of one or more Met residues from the primary sequence of PrP(106–114) both reduces the CuII affinity of the peptide by two to seven fold, and renders the resulting CuII metallopeptides redox inactive. The biological implications of these findings are discussed.

Structural and Energetic Properties of Ni−Cu Bimetallic Clusters

The lowest-energy structures for all compositions of Ni n Cu m bimetallic clusters with N = n + m up to 20 atoms, N = 23, and N = 38 atoms have been determined using a genetic algorithm for unbiased structure optimization in combination with an embedded-atom method for the calculation of the total energy for a given structure. Comparing bimetallic clusters with homoatomic clusters of the same size, it is shown that the most stable structures for each cluster size are composed entirely of Ni atoms. Among the bimetallic clusters in the size range N = 2-20, the Ni N-1 Cu 1 clusters possess the highest stability. Further, it has been established that most of the bimetallic cluster structures have geometries similar to those of pure Ni clusters. The size N = 38 presents a special case, as the bimetallic clusters undergo a dramatic structural change with increasing atom fraction of Cu. Moreover, we have identified an icosahedron, a double, and a triple icosahedron with one, two, and three Ni atoms at the centers, respectively, as particularly stable structures. We show that in all global-minimum structures Ni atoms tend to occupy mainly high-coordination inner sites, and we confirm the segregation of Cu on the surface of Ni-Cu bimetallic clusters predicted in previous studies. Finally, it is observed that, in contrast to the bulk, the ground-state structures of the 15-, 16-, and 17-atom bimetallic clusters do not experience a smooth transition between the structures of the pure copper and the pure nickel clusters as a function of the relative number of the two types of atoms. For these sizes, the concentration effect on energy is more important than the geometric one.

Effects of different Ti-doping methods on the structure of pure-silica MCM-41 mesoporous materials

Pure-silica mesoporous materials doped by titanium have been prepared by direct synthesis method and post-synthetic impregnation method. The effects of different Ti-doping methods on the structure of pure-silica mesoporous materials have been researched. X-ray diffraction, transmission electron microscopy, scanning electronic microscopy, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, X-ray absorption spectrum and nitrogen adsorption–desorption isotherms have been employed to characterize the products. It has been found that structural properties were strongly related to the amount and the way of titanium introduction. The mesoporous ordering of the samples that have been prepared by direct synthesis method and post-synthetic method became poor with the increasing of titanium amount. The XANES and EXAFS spectra confirmed that the titanium have been inserted into the framework of MCM-41. The titanium grafted in the Ti-MCM-41 in fourfold coordination, and the titanium doped in the Ti/MCM-41 in higher coordination sites.

H2 Adsorption on 3d Transition Metal Clusters: A Combined Infrared Spectroscopy and Density Functional Study

The adsorption of H2 on a series of gas-phase transition metal (scandium, vanadium, iron, cobalt, and nickel) clusters containing up to 20 metal atoms is studied using IR-multiple photon dissociation spectroscopy complemented with density functional theory based calculations. Comparison of the experimental and calculated spectra gives information on hydrogen-bonding geometries. The adsorption of H2 is found to be exclusively dissociative on Sc(n)O+, V(n)+, Fe(n)+, and Co(n)+, and both atomic and molecularly chemisorbed hydrogen is present in Ni(n)H(m)+ complexes. It is shown that hydrogen adsorption geometries depend on the elemental composition as well as on the cluster size and that the adsorption sites are different for clusters and extended surfaces. In contrast to what is observed for extended metal surfaces, where hydrogen has a preference for high coordination sites, hydrogen can be both 2- or 3-fold coordinated to cationic metal clusters.

Vibrational Stark tuning rates from periodic DFT calculations: CO/Pt(1 1 1)

DFT periodic calculations have been used to study the influence of an external electric field on the adsorption of CO on Pt(1 1 1). Particular attention has been focused on the determination of the CO and metal-CO vibrational Stark tuning rates. Stark tuning rates have been calculated at various CO coverages; a linear dependence between the CO Stark tuning rate and the CO surface coverage has been found. We have calculated a value of 68.94 cm −1/(V/Å) for the zero-coverage limit CO Stark tuning rate, in good agreement with the experimental value of 75 ± 9 cm −1/(V/Å). Like the CO Stark tuning rate, the metal-CO vibrational Stark tuning rate also increases as CO surface coverage decreases. In addition, we have found (at 0.25 ML) that the CO Stark tuning rate is similar at different adsorption sites, being only slightly larger at high-coordinated sites. CO vibrational Stark tuning rates of 45.58, 47.96, 47.61 and 48.49 cm −1/(V/Å) have been calculated for ontop, bridge, hcp and fcc hollow sites, respectively. Calculations at high coverage using a (2 × 2)-3CO model yield a CO Stark tuning rate of 21.08 and 25.93 cm −1/(V/Å) for ontop and three-fold hollow CO, respectively. These results show that the CO Stark tuning rate for CO adsorbed at high coordinated sites is only slightly larger than that at ontop sites. This result is in contradiction with experiments, which reported larger CO Stark tuning rates at high-coordinates sites than at ontop sites. Furthermore, the calculated metal-CO stretch is larger for ontop sites than for high-coordinated sites; this result is in disagreement with previous DFT cluster model calculations. Unfortunately, there is not experimental information available to support either result. Finally, we have also studied the CO adsorption site preference dependence on electric fields. We have found that CO adsorbs preferentially at high coordinated sites at more negative fields, and at ontop sites at more positive fields, in agreement with previous experiments and DFT cluster model calculations.

THE ADSORPTION OF Au ON Si(111)-7 × 7 SURFACE: A FIRST-PRINCIPLES STUDY

The initial stage of Au adsorption on the Si (111)-7 × 7 surface has been investigated by the first-principles calculations. Different configurations have been considered and the high coordination sites were determined as the most possible places for the Au adsorption. The diffusion barriers for Au atoms on the Si surface have also been evaluated. The results indicated that the Au atoms could diffuse from the top of the Si rest atoms to the high coordination sites only by overcoming a small barrier of 0.11 eV.

Theoretical study of the Mo–Ru sigma phase

The thermodynamic properties of the Mo–Ru binary σ -phase are investigated using a combination of ab initio calculations and CALPHAD modeling. Total energy calculations have been performed for the complete set of 32 end-member compounds of a 5-sublattice compound energy model. The internal crystallographic parameters for each end-member compound have been determined by minimising the total energy. A simpler, 3-sublattice model of the Mo–Ru σ -phase is formulated on the basis of calculated total energies. The site occupancy is acquired by minimising the free energy given by the compound energy model. A strong preference of Mo and Ru towards high-coordination sites and icosahedral sites in the Mo–Ru σ -phase is found and analysed in terms of the electronic structure.

Preferential site occupancy observed in coexpanded argon-krypton clusters

Free heterogeneous argon-krypton clusters have been produced by coexpansion and investigated by means of x-ray photoelectron spectroscopy. By examining cluster surface and bulk binding energy shifts, relative intensities, and peak widths, we show that in the mixed argon-krypton clusters the krypton atoms favor the bulk and argon atoms are pushed to the surface. Furthermore, we show that krypton atoms in the surface layer occupy high-coordination sites and that heterogeneous argon-krypton clusters produced by coexpansion show the same surface structure as argon host clusters doped with krypton. These observations are supported by site-dependent calculations of chemical shifts.

Initial stages of the adsorption of Ge atoms on theSi(111)−(7×7)surface

Using scanning tunneling microscopy and first-principles density functional calculations, we have investigated systematically the initial stages of single Ge atoms adsorbed on a $\mathrm{Si}(111)\text{\ensuremath{-}}(7\ifmmode\times\else\texttimes\fi{}7)$ surface. When the deposition is at an elevated temperature of $420\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, single Ge atoms are found to substitute for the Si adatoms randomly. When the deposition is at room temperature, single Ge atoms do not replace the Si adatoms but move frequently within half unit cells. When the room temperature prepared sample is imaged at $78\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, the Ge atoms are observed to either adsorb at the stable high coordination sites near the corner Si adatoms or hop among the high coordination sites near the center Si adatoms. The adsorption sites of Ge atoms at high coordination positions have been determined by first-principles calculations and comparisons with measured scanning tunneling microscopic images.

Preferential site occupancy of krypton atoms on free argon-cluster surfaces

Argon clusters have been doped with krypton atoms in a pick-up setup and investigated by means of ultraviolet and x-ray photoelectron spectroscopy (UPS and XPS). The width of the krypton surface feature in the XPS spectra from mixed krypton/argon clusters has been studied and found to be narrower than in the case of homogeneous krypton clusters. By considering known spectral broadening mechanisms of the cluster features and the electron binding energy shift of the cluster surface feature relative to the atomic signal, we conclude that krypton ad-atoms preferentially occupy high-coordination surface sites on the argon host-cluster.

Characterization and catalytic study of Pt [sbnd]Ge/Al 2O 3 catalysts prepared by organometallic grafting

Ge was added to 1% Pt/Al 2O 3 catalyst by controlled surface reaction of Ge( n-C 4H 9) 4 in amounts corresponding nominally to 1/12, 1/8, 1/2, 1, or 2 monolayers. These Pt Ge/Al 2O 3 catalysts were characterized by FTIR of CO, TEM, H 2 chemisorption, and EXAFS as well as tested in catalytic reactions, that is, transformation of hexane, benzene and cyclohexene in the presence of excess hydrogen. Loading of Ge in amounts of 1/12–1/2 monolayers resulted in catalysts with “bimetallic surface.” Loading of 1/12 monolayer of Ge resulted in randomly deposited Ge atoms on the surface of Pt. It hardly affected the catalytic behavior as compared with the Ge-free parent catalyst; 1/8 monolayer of Ge was still located on Pt as single atoms (as shown by EXAFS), but Ge selectively poisoned high coordination sites, active in benzene hydrogenation. This reaction was completely suppressed here, whereas this catalyst was most active in cyclohexene transformation. Pt with 1/8 and 1/2 monolayers of Ge transformed hexane with high selectivity into saturated C 6 products and formed hardly any benzene. The formation of cyclohexane from hexane was also observed, not typical for monofunctional Pt catalysts. Adding 1–2 monolayers of Ge caused a new type of interaction between Pt and Ge containing sites that adsorbed CO but did not adsorb hydrogen. A solid solution of Pt Ge may have arisen here, creating “bulk bimetallic catalysts” with somewhat more surface Pt atoms not interacting with Ge. These catalysts behaved similarly in hydrocarbon transformations as the original parent catalyst. The possible reaction mechanism of hexane transformation is discussed in detail, in terms of thermodynamic limitations of benzene formation and possible surface species.

23Na multiple-quantum MAS NMR of the perovskites NaNbO3and NaTaO3

The distorted perovskites NaTaO(3) and NaNbO(3) have been studied using (23)Na multiple-quantum (MQ) MAS NMR. NaTaO(3) was prepared by high temperature solid state synthesis and the NMR spectra are consistent with the expected room temperature structure of the material (space group Pbnm), with a single crystallographic sodium site. Two samples of NaNbO(3) were studied. The first, a commercially available sample which was annealed at 900 degrees C, showed two crystallographic sodium sites, as expected for the room temperature structure of the material (space group Pbcm). The second sample, prepared by a low temperature hydrothermal method, showed the presence of four sodium sites, two of which match the expected room temperature structure and the second pair, another polymorph of the material (space group P21ma). This is consistent with powder X-ray diffraction data which showed weak extra peaks which can be accounted for by the presence of this second polymorph. Density functional theory (DFT) calculations support our conclusions, and aid assignment of the NMR spectra. Finally, we discuss the measured NMR parameters in relation to other studies of sodium in high coordination sites in the solid state.

Tyr-95 and Ile-172 in Transmembrane Segments 1 and 3 of Human Serotonin Transporters Interact to Establish High Affinity Recognition of Antidepressants

In previous studies examining the structural determinants of antidepressant and substrate recognition by serotonin transporters (SERTs), we identified Tyr-95 in transmembrane segment 1 (TM1) of human SERT as a major determinant of binding for several antagonists, including racemic citalopram ((RS)-CIT). Here we described a separate site in hSERT TM3 (Ile-172) that impacts (RS)-CIT recognition when switched to the corresponding Drosophila SERT residue (I172M). The hSERT I172M mutant displays a marked loss of inhibitor potency for multiple inhibitors such as (RS)-CIT, clomipramine, RTI-55, fluoxetine, cocaine, nisoxetine, mazindol, and nomifensine, whereas recognition of substrates, including serotonin and 3,4-methylenedioxymethamphetamine, is unaffected. Selectivity for antagonist interactions is evident with this substitution because the potencies of the antidepressants tianeptine and paroxetine are unchanged. Reduced cocaine analog recognition was verified in photoaffinity labeling studies using [(125)I]MFZ 2-24. In contrast to the I172M substitution, other substitutions at this position significantly affected substrate recognition and/or transport activity. Additionally, the mouse mutation (mSERT I172M) exhibits similar selective changes in inhibitor potency. Unlike hSERT or mSERT, analogous substitutions in mouse dopamine transporter (V152M) or human norepinephrine transporter (V148M) result in transporters that bind substrate but are deficient in the subsequent translocation of the substrate. A double mutant hSERT Y95F/I172M had a synergistic impact on (RS)-CIT recognition ( approximately 10,000-fold decrease in (RS)-CIT potency) in the context of normal serotonin recognition. The less active enantiomer (R)-CIT responded to the I172M substitution like (S)-CIT but was relatively insensitive to the Y95F substitution and did not display a synergistic loss at Y95F/I172M. An hSERT mutant with single cysteine substitutions in TM1 and TM3 resulted in formation of a high affinity cadmium metal coordination site, suggesting proximity of these domains in the tertiary structure of SERT. These studies provided evidence for distinct binding sites coordinating SERT antagonists and revealed a close interaction between TM1 and TM3 differentially targeted by stereoisomers of CIT.

Experimental and Theoretical Investigation of Single Cu, Ag, and Au Atoms Adsorbed onSi(111)−(7×7)

Using scanning tunneling microscopy and first principles calculations, the adsorption sites of single Cu, Ag, and Au atoms on the Si(111)-(7x7) surface have been systematically investigated and identified. Despite their monovalence, these atoms were found to adsorb at high coordination sites, seeking to saturate the maximum number of dangling bonds. The stable adsorption sites were further observed to be distinctly different in the faulted and unfaulted half unit cells, showing an asymmetry that has never been observed for many other adsorbates.

Bonding Configurations and Collective Patterns of Ge Atoms Adsorbed onSi(111)−(7×7)

We report scanning tunneling microscopy observations of Ge deposited on the Si(111)-(7 x 7) surface for a sequence of submonolayer coverages. We demonstrate that Ge atoms replace so-called Si adatoms. Initially, the replacements are random, but distinct patterns emerge and evolve with increasing coverage, until small islands begin to form. Corner adatom sites in the faulted half unit cells are preferred. First-principles density functional calculations find that adatom substitution competes energetically with a high-coordination bridge site, but atoms occupying the latter sites are highly mobile. Thus, the observed structures are indeed more thermodynamically stable.

Carbon atom adsorption on and diffusion into Fe(110) and Fe(100) from first principles

We employ spin-polarized periodic density functional theory (DFT) to examine carbon atom adsorption on, absorption in, and diffusion into Fe(110) and Fe(100). We find that carbon atoms bind strongly with Fe surfaces and prefer high coordination sites. The carbon atom is predicted to adsorb on the long-bridge site on Fe(110) and the fourfold hollow site on Fe(100). Due to the very short distance between the carbon atom and the subsurface Fe atom of Fe(100), the carbon atom binds more strongly with Fe(100) than with Fe(110). In the subsurface region, the carbon atom prefers the octahedral site, as in bulk Fe. We find that the carbon atom is more stable in the subsurface octahedral site of Fe(110) than that of Fe(100), since the strain caused by the interstitial carbon atom is released by pushing one surface Fe atom towards vacuum by 0.5 \AA{} in Fe(110), while the distortion in Fe(100) propagates far into the lattice. Diffusion of carbon atoms into Fe(110) and Fe(100) subsurfaces goes through transition states where the carbon atom is coordinated to four Fe atoms. The barriers to diffusion into Fe(110) and Fe(100) are 1.18 eV and 1.47 eV, respectively. The larger diffusion barrier into Fe(100) is mainly due to the stronger bonding between carbon and the Fe(100) surface. We predict that the rate-limiting step for $\mathrm{C}$ incorporation into bulk Fe is the initial diffusion to subsurface sites, while the rate-limiting step for absorbed carbon segregation to the surface is bulk diffusion, with no expected difference between rates to segregate to different surfaces. Lastly, we predict that graphite formation will be more favorable on $\mathrm{C}$-covered Fe(110) than $\mathrm{C}$-covered Fe(100).

COMPUTATIONAL STUDY OF TERNARY ALLOY NANOCLUSTER COMPOSITIONAL STRUCTURES: Ni–Cu–Rh VERSUS Ni–Cu–Pd

The Free-energy Concentration Expansion Method (FCEM) was utilized for the prediction of compositional structures in Ni – Cu – Rh cubo-octahedron nanoclusters in comparison to recently reported Ni – Cu – Pd data. While both systems exhibit site-specific, sequentially competitive surface segregation (and resultant core separations), remarkable differences governed by the opposite heteronuclear effective interactions, were noted in the surface compositional patterns. Thus, at relatively low temperatures "mixed" Cu/Pd ordering takes place at the Ni – Cu – Pd cluster surface, whereas in the Ni – Cu – Rh cluster Cu and Ni populate separate low and high-coordinated surface sites, thus forming a kind of "demixed surface order". Dissimilarities in the temperature dependence are discussed in terms of the interplay of segregation and compositional order. Such findings may have implications in heterogeneous catalysis and other technologies based on highly dispersed alloyed particles.

The adsorption sites of rare gases on metallic surfaces: a review

During the past six years, the adsorption geometries of several rare gases in structureshaving several different symmetries on a variety of substrates were determined usinglow-energy electron diffraction (LEED). In most of these studies, a preference is found forthe rare gas atoms to adsorb in the low-coordination sites. Only in the case of adsorptionon graphite has a clear preference for a high-coordination site for a rare gas atom beenfound. This unexpected behaviour is not yet completely understood, although recentdensity functional theory (DFT) calculations for these and similar surfaces suggest thatthis is a general phenomenon. This paper reviews the early studies that were presages ofthe discovery of top site adsorption for rare gases, the discovery itself, and the present stateof understanding of this curiosity. It also details some of the features of the LEEDexperiments and analysis that are specific to the case of rare gas adsorption.