On-top Structure Research Articles

DFT Study on the Interaction of the Smallest Fullerene C20 with Lithium Ions and Atoms

The smallest fullerene C20 with positive electron affinity is considered to be a new organic nano-electronic material. The binding structures and electronic states of lithium ions and atoms (Li+ and Li) trapped on the surface of C20 have been investigated by means of density functional theory (DFT) calculation to elucidate the nature of their interaction. It was found that a Li+ can bind to only one site of C20. This is, specifically, on top of the site where Li+ binds to the carbon atom of C20. On the other hand, in the case of a Li atom, two structures were obtained besides the on-top structure. One was pentagonal structure which included a Li atom on a five-membered ring of C20. The other was a triangular structure in which the Li atom bind to the the carbon–carbon bond of C20. Finally, the nature of the interactions between Li ions or atoms and the C20 cluster was discussed on the basis of theoretical results.

Chemical Reaction of Benzoic Acid with Ge(100): Effect of a Phenyl Substituent

The adsorption of benzoic acid onto Ge (100) was investigated using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. At room temperature, the on-top bidentate structure of benzoate molecules on Ge(100) was the most favorable. After annealing at 420 K, nearly all of the adsorption structures changed into on-top structures. The preference for the on-top structure could be explained in terms of the thermodynamic stability and kinetic considerations. Simulated STM images of the stable configuration could explain the experimentally observed images. The surface ordering of the adsorbed benzoic acid molecules was characterized through an appropriate application of hot surface dosing and annealing of the Ge surface at different coverages. Surface ordering along the dimer row direction was observed at a lower coverage. At saturation coverage, ordered lines with several adsorbed benzoic acid molecules formed along both the dimer row and the dimer direction and were stabilized th...

Surface-Enhanced Raman Scattering Due to Charge-Transfer Resonances: A Time-Dependent Density Functional Theory Study of Ag13-4-Mercaptopyridine

We have used time-dependent density functional theory in conjunction with the CAM-B3LYP functional and MWB28/aug-cc-pVDZ basis set to determine non-, near-, and on-resonance Raman spectra for a complex formed by 4-mercaptopyridine (4-Mpy) binding with a Ag13 cluster via the thiolate Ag–S bond. Geometry optimizations of the Ag13-4-Mpy complex showed an on-top structure directly bound to one Ag atom with the ring of the molecule almost flat with respect to two Ag atoms of the complex. The corresponding B3LYP/MWB28/aug-cc-pVDZ geometry is also an on-top structure directly bound to one Ag atom, but the molecule is directed away from the surface. The near-resonance Raman calculations were carried out in the infinite lifetime approximation, while the on-resonant Raman excitation profiles were calculated with the complex polarization propagator (CPP) approach, introducing a half width at half-maximum spectral broadening of 0.2 eV. Calculation of the UV–vis spectra of the isolated 4-Mpy and of the Ag13-4-Mpy comp...

Simulation of SERS by a DFT study: a comparison of static and near-resonance Raman for 4-mercaptopyridine on small Ag clusters

We have used density functional theory at the B3LYP/LANL2DZ level to calculate the static (DFT) and frequency-dependent (TDDFT) Raman spectra of complexes of 4-mercaptopyridine (4-Mpy) binding with Ag10 and Ag13 clusters via the thiolate Ag-S bond. Geometric optimization of the Ag10-4-Mpy complexes with plus one or neutral charge had a bridging surface structure with the bond between two Ag atoms of the cluster; whereas, the minus charged Ag10-4-Mpy complex had an on-top structure directly bound to one Ag atom. A neutral Ag13-4-Mpy complex showed the on-top structure also. The static (DFT) Raman tensor for these complexes showed the spectra of the structures with bridging geometry were very similar and the static spectra of the on-top structures were also very similar. New assignments for 4-Mpy anion and 4-Mpy bound to the Ag13 cluster were made using the assignment method of Gardner and Wright (2011 J. Chem. Phys. 135 114305) which proves to be more accurate than Wilson numbers. The calculated frequencies of the normal vibrational modes were found to be sufficiently close to several experimental surface enhanced Raman scattering spectra on a variety of different Ag substrates to clarify the previous assignments. The frequency-dependent (TDDFT) Raman calculations were carried out in the infinite life-time approximation. Calculation of the UV–VIS spectra of the isolated 4-Mpy and of the Ag13-4-Mpy complex showed that binding shifts the spectra from deep in the UV to the near-IR and visible region. Calculation of the frequency-dependent (TDDFT) near-resonance Raman spectrum of this complex at 637 nm (resonance at 632 nm) showed a strong enhancement. However, within the infinite life-time approximation, the actual enhancement cannot be estimated. The transition involves a charge transfer from the 4-Mpy molecule to the Ag cluster with a weak oscillator strength, f = 0.0162. The relative intensities for the near-resonance spectrum of Ag13-4-Mpy complex are found to be very different from the static spectrum of the complex. Examination of the integrated enhancement factor, EF, as a function of the vibrational mode symmetry for near-resonance shows the order of relative enhancements to be b2 > b1 > a2 > a1. This order indicates that a charge-transfer resonance mechanism is operating with Herzberg–Teller scattering dominating Franck–Condon scattering for this simulation. Conditions prevailing in such a case are also discussed.

First-principles study of the adsorption and reaction of 2,3-butanediol on Si(001)

The adsorption and reaction of 2,3-butanediol on the Si(001) surface are investigated by first-principles density-functional calculations within the generalized-gradient approximation. We consider the two different reaction pathways forming adsorptions on top of a single dimer (termed the ``on-top'' structure) and across the ends of two adjacent dimers in the same dimer row (termed the ``end-bridge'' structure). For both reaction pathways, the O atom of the hydroxyl group initially bonds to the down Si atom of the buckled dimer and, subsequently, O-H dissociation takes place. However, the reaction of another hydroxyl group shows a drastic difference between the two reaction pathways. Along the former reaction pathway, it is difficult to form the second $\mathrm{Si}\mathrm{O}$ bond because of a repulsive interaction between an O lone pair and a single Si dangling bond, thereby prohibiting formation of the on-top structure. On the other hand, along the latter reaction pathway, an O lone pair of the hydroxyl group is attracted to the down Si atom of a neighboring dimer, proceeding to the formation of the end-bridge structure. These results provide an explanation for a recent scanning tunneling microscope observation that 2,3-butanediol occupies predominantly the end-bridge structure.

Bidentate Structures of Acetic Acid on Ge(100): The Role of Carboxyl Oxygen

The adsorption structures of acetic acid on the Ge(100) surface at room temperature have been investigated by using both scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The conversion of acetic acid to acetate on the Ge(100) surface occurs through dissociation of the O−H bond and the formation of a Ge−O bond. The abstracted hydrogen atom saturates the dangling bond of the other Ge dimer atom or diffuses to a neighboring dimer. Our STM results enable the identification of several adsorption configurations, which arise from bonding involving either one oxygen atom (the monodentate structure) or two oxygen atoms (the bidentate structures). We observe two types of bidentate structures: the end-bridged and on-top structures. The calculations show that the on-top structure is the most stable among many possible adsorption products on the Ge(100) surface considered. Surfaces exposed to acetic acid are annealed to investigate the annealing effect. The end-bridged bidentate and monodentate structures are observed before annealing, while the on-top bidentate structure appears only after annealing. These behaviors are explained in terms of reaction pathways obtained from theoretical calculations.

Initial adsorption structure of ethylene on Si(0 0 1) surface at room temperature

Ethylene (C 2H 4) on the Si(0 0 1) surface has been a subject of numerous investigations over a decade. Despite a wealth of experimental and theoretical studies, the adsorption structures are not clearly understood yet. In order to elucidate this controversial issues clearly, C 2H 4 molecules have been non-dissociatively chemisorbed on Si(0 0 1)-(2 × 1) surface at room temperature with an exposure of 100 L, and C 2H 4 on Si(0 0 1) surface structure has been investigated by coaxial impact collision ion scattering spectroscopy (CAICISS). To determine the adsorption structure of the C 2H 4 molecules definitely, the computer simulation with the two-dimensional trajectory counting method has been performed for the recently proposed most possible two single molecular adsorption configurations (di-σ on-top and di-σ end-bridge). The CAICISS spectra show a better agreement with the simulation results for the di-σ on-top structure than that for the di-σ end-bridge structure. The bond length of Si dimer separation on the Si(0 0 1) surface with the adsorption of 100 L C 2H 4 is found to be 2.35 ± 0.05 Å. This implies that the bonding of Si dimers stays intact. It is also found that the bonding length of C–Si and C–C is 1.81 ± 0.05 Å and 1.61 ± 0.05 Å respectively.

Structure and stability of Al13I clusters

We have performed density functional calculations for the structures and stabilities of Al13I at the scalar relativistic pseudopotential and all-electron levels of theory. The Al13 moiety in Al13I is significantly distorted and structurally similar to an Al13 cation, where the natural population is −0.27e for the I atom. Unlike other Al13-M (M=H, alkali metals, and coinage metals) clusters, a Cs-ontop structure was found to be the most stable form. The Al13I cluster has a large Al13-I binding energy of 3.11 eV and is more stable, as charge transfer to the electronegative I atom is larger.

Collective excitations in alkali metals on Al(111)

The photon-excited multipole and the bulklike modes have been studied in Na/Al(111) and K/Al(111). These collective modes appear for a coverage of ≥2 monolayers. Both the multipole and the bulklike modes exhibit interesting variations in frequency, line shape, and relative intensity with adlayer coverage. The reasons for such behavior are discussed on the basis of existing theoretical results. The substrate Al multipole is found to be attenuated by smooth adlayer growth. Deposition of K on two monolayer Na/Al(111) results in the growth of K related collective excitation at the expense of the Na modes. For complicated surface structures like Al(111)-(√3×√3)R30°:K or the Al(111)-(2×2):Na surface alloy, electron charge-density profiles at the surface are calculated based on ab initio density-functional theory-local-density approximation method to explain the photoyield data. The importance of the shape of the charge-density profile in determining the collective excitations is demonstrated. For Al(111)-(√3×√3)R30°:K, a strong increase in intensity in the energy region of the K plasmons is observed in the on-top structure which is attributed to a mixed plasmon mode. These results show that while the experimental observations for smooth alkali-metal adlayers are in good agreement with existing theory, more theoretical work, especially for the complicated surface structures, is desirable.

The stable configurations for oxygen chemisorption on the diamond (100) and (111) surfaces

The structures resulting from oxygen chemisorption onto the diamond (100) and (111) ideal and reconstructed surfaces have been extensively studied using the SLAB-MINDO molecular orbital method. For the C(100) surface, we find that the lowest energy configuration for monolayer chemisorption is a 1 × 1 on-top structure whilst that for half-monolayer chemisorption is a 2 × 1 dimer bridge site topology. For the C(111) surface, both the single-bond cleavage and triple-bond cleavage surfaces have been studied. Bridge site molecular oxygen chemisorption parallel to the surface is found to be responsible for monolayer oxygen coverage on the single dangling bond C(111) surface. For half-monolayer coverage, chemisorption of atomic oxygen onto the bridge sites of the 2 × 1 π-bonded chain model reconstructed surface is the preferred mechanism. Molecular oxygen is found to be directly dissociative on the triple dangling bond C(111) surface. The lowest energy monolayer configuration on the triple-bond cleavage surface is found to be a tilted on-top model of the single chain reconstructed surface whilst a half-monolayer exposure prefers the bridge sites of the surface single chains. Both the monolayer and half-monolayer minimum energy configurations are found to retain the 2 × 1 topology of the clean C(111) surface. These results are compared with previous studies of oxygen chemisorption onto the Si(100) and (111) surfaces.

A cluster model study of multiple H adsorption on Be(0001)

The different results obtained from slab and cluster calculations are compared. In the clusters we model various H coverages on the Be(0001) surface using a single-layer Be 14 cluster interacting with different numbers of H atoms. With a single H atom the on-top structure is the most stable. Two H atoms are computed to preferentially adsorb at an open site above 3 Be atoms. Caution always needs to be exercised when comparing slab and cluster calculations owing to the different adsorbate coverages being modelled. However, by increasing the number of H atoms in the cluster to simulate a monolayer of H atoms on the Be(0001) surface we obtain results similar to slab calculations with the open and bridging structures close in energy and the on-top structure being least stable. These calculations with H monolayer coverage are noteworthy because they also enable the definition of a desorption energy E des corresponding to the energy of removal for a single H atom from the monolayer. E des differs in value from the average H binding energy D e often used to evaluate the stability of different adsorbate structures on a surface. By using E des, an explanation for the experimentally observed bridging structure for H on the Be(0001) surface is suggested. A similar computation of E des is not possible in a slab calculation owing to limitations on the allowed unit cell size.