Geometrical characterization of adenine and guanine on Cu(1 1 0) by NEXAFS, XPS, and DFT calculation

Adsorption of purine DNA bases (guanine and adenine) on Cu(1 1 0) was studied by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine-structure spectroscopy (NEXAFS), and density-functional theory (DFT) calculation. At coverages near 0.2 monolayers, Angular-resolved NEXAFS analysis revealed that adenine adsorbates lie almost flat and that guanine adsorbates are tilted up on the surface with the purine ring parallel to the atom rows of Cu(1 1 0). Referring to the previous studies on pyrimidine DNA bases [M. Furukawa, H. Fujisawa, S. Katano, H. Ogasawara, Y. Kim, T. Komeda, A. Nilsson, M. Kawai, Surf. Sci. 532-535 (2003) 261], the isomerization of DNA bases on Cu(1 1 0) was found to play an important role in the adsorption geometry. Guanine, thymine and cytosine adsorption have an amine-type nitrogen next to a carbonyl group, which is dehydrogenated into imine nitrogen on Cu(1 1 0). These bases are bonded by the inherent portion of -NH-CO- altered by conversion into enolic form and dehydrogenation. Adenine contains no CO group and is bonded to Cu(1 1 0) by participation of the inherent amine parts, resulting in nearly flatly-lying position.     

Adsorption and structure of methyl mercaptoacetate on Cu(1 1 1) surface by XPS and NEXAFS spectroscopy

Methyl mercaptoacetate (MA) on Cu(1 1 1) surface was investigated using synchrotron radiation-based X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. MA adsorbs on the surface via thiolate formation and weak interaction of the carbonyl group with the surface. Two different adsorption states previously reported for methanethiolate and ethanethiolate were confirmed, besides atomic sulfur. NEXAFS measurements support gauche-type conformation of MA whose skeleton lies on the surface.     

RT growth of acetonitrile and acrylonitrile on Si(0 0 1)-2 × 1 studied by XPS and LEED

In this work we show the adsorption of acetonitrile (CH₃CN) and acrylonitrile (CH₂CHCN) on Si(0 0 1)-2 × 1 at room temperature by increasing the molecular doses. Especially, by means of XPS and LEED data, we stress the action of these molecules on the silicon surface locating the dangling-bonds quasi-saturation within 10 L. The shortage of nitrogen XPS signal and some anomalies in carbon spectra point to an invading action from a traditional X-ray source (Al-K_α line) against chemisorbed molecules. In particular, we think that a long exposure to this radiation could break carbon-silicon bonds changing some adsorption geometries and making desorb molecular fragments.     

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.     

Adsorption of nitrogen-containing aromatic molecules on Si(1 1 1)-7 × 7

The adsorption configurations of pyrimidine and triazine on Si(1 1 1)-7 × 7 were investigated using high-resolution electron energy loss spectroscopy (HREELS) X-ray photoelectron spectroscopy and density functional theory calculations. The HREELS spectra of chemisorbed monolayer show the coexistence of the C(sp²)-H and C (sp³)-H stretching modes together with the observation of the unconjugated CN(C) vibrational feature suggesting that the carbon atom and its para-nitrogen atom of pyrimidine and triazine directly participate in binding with the surface to form Si-C and Si-N σ-linkages. The core levels of the C-atom and its opposite nitrogen atom directly binding with Si-atoms experience a down-shifting by 1.8-1.9 and 1.4-1.6 eV, respectively. These experimental findings are consistent with the density functional theory calculations indicating that the carbon atom and its para-nitrogen atom favorably link with the adjacent adatom and rest atom pair to form C-Si and N-Si linkages.     

First-principles study of adsorption and diffusion on Ge/Si(0 0 1)-(2 × 8) and Ge/Si(1 0 5)-(1 × 2) surfaces

Using first-principles total-energy calculations, we have investigated the adsorption and diffusion of Si and Ge adatoms on Ge/Si(0 0 1)-(2 × 8) and Ge/Si(1 0 5)-(1 × 2) surfaces. The dimer vacancy lines on Ge/Si(0 0 1)-(2 × 8) and the alternate S_A and rebonded S_B steps on Ge/Si(1 0 5)-(1 × 2) are found to strongly influence the adatom kinetics. On Ge/Si(0 0 1)-(2 × 8) surface, the fast diffusion path is found to be along the dimer vacancy line (DVL), reversing the diffusion anisotropy on Si(0 0 1). Also, there exists a repulsion between the adatom and the DVL, which is expected to increase the adatom density and hence island nucleation rate in between the DVLs. On Ge/Si(1 0 5)-(1 × 2) surface, the overall diffusion barrier of Si(Ge) along direction is relative fast with a barrier of ∼0.83(0.61) eV, despite of the large surface undulation. This indicates that the adatoms can rapidly diffuse up and down the (1 0 5)-faceted Ge hut island. The diffusion is also almost isotropic along [0 1 0] and directions.     

A study of the interaction between perylene and the TiO2(1 1 0)-(1 × 1) surface-based on XPS, UPS and NEXAFS measurements

The interaction between a semi-large aromatic hydrocarbon compound (perylene) and the TiO₂(1 1 0)-(1 × 1) surface under ultra high vacuum conditions has been probed by X-ray photoemission spectroscopy (XPS), ultraviolet photoemission spectroscopy (UPS) and near-edge X-ray absorption fine structure (NEXAFS) methods. UPS measurements of the adsorbate system have been compared with an experimental UPS spectrum of perylene in the gas phase and a calculated spectrum obtained by means of density functional theory (DFT) methods. NEXAFS results of perylene molecules adsorbed on TiO₂(1 1 0)-(1 × 1) were compared with data from an α-phase perylene single crystal. A novel analysis of the valence data has been employed to show that no strong chemical interaction takes place between perylene and the TiO₂(1 1 0)-(1 × 1) surface. Furthermore, angle-dependent NEXAFS measurements and the growth curve results suggest that the perylene molecules are oriented flat down onto the TiO₂ substrate due to weak van der Waals interactions.     

Assignment of surface IR absorption spectra observed in the oxidation reactions: 2H + H2O/Si(1 0 0) and H2O + H/Si(1 0 0)

Infrared reflection absorption spectroscopy that used buried metal layer substrates (BML-IRRAS) and density functional cluster calculations were employed to investigate the water related oxidation reactions of 2H + H₂O/Si(1 0 0)-(2 × 1), 2D + H₂O/Si(1 0 0)-(2 × 1), and H₂O + H/Si(1 0 0)-(2 × 1). In addition to the oxygen inserted coupled monohydrides, which were previously reported in the former reaction system, we report several other oxidized Si hydride species in our BML-IRRAS experiments. Three new pairs of vibrational bands are identified between 900 and 1000 cm⁻¹. These vibrational frequencies were calculated using Si9 and Si10 cluster models that included all possible structures from zero to five oxygen insertions into the top layer silicon atoms using a B3LYP gradient corrected density functional method with a polarized 6-31G** basis set for all atoms. The three pairs of vibrational modes are assigned to the scissoring modes of adjacent and isolated SiH₂ with zero, one, and two oxygen atoms inserted into the Si back bonds. All the other newly observed vibrational peaks related to Si oxidation are also assigned in this study. The Si-O stretching bands observed in the reaction 2D + H₂O/Si(1 0 0)-(2 × 1) show an isotope effect, which suggests that in the system 2H + H₂O/Si(1 0 0)-(2 × 1) also, hydrogen atom tunneling plays an important role for the insertion of oxygen atoms into Si back bonds that form oxidized adjacent dihydrides.     

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).     

(6 × 2) Reconstruction of the Ag/Si(1 1 1) surface at 77 K

The ground state of the Ag/Si(1 1 1)-(3 × 1) has been investigated by low temperature scanning tunneling microscopy (STM) and density-functional theory. The Fourier transform of the STM image reveals a (6 × 2) reconstruction, which is theoretically found to yield a reconstruction with lower energy than the (3 × 1). The most stable (6 × 2) structural model leads to excellent correspondence between experimental and simulated STM images, and reveals a dimerization of the silver atoms in the channels formed by neighbouring honeycomb Si chains.     

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.     

Resonant Auger spectroscopy study of charge transfer phenomena in N 1s core-excited acetonitrile adsorbates on Si(0 0 1)-2 × 1

Acetonitrile (CH₃CN) adsorbs on Si(0 0 1)-2 × 1 at room temperature under two forms, a cycloaddition-like adduct (Si-CN-Si) and a pendent cyano (Si-CH₂-CN) resulting from the decomposition of the molecule. Resonant Auger spectroscopy has been used to study the excited-state-dependent electron transfer from the N 1s core-excited molecular adsorbate to the silicon substrate, using the core-hole lifetime (∼6 fs) as an internal clock. It is shown that the π_CN^∗ NEXAFS state lies within the silicon bandgap because of a core-excitonic effect. Therefore no charge transfer of the excited electron to the substrate is observed. On the other hand the π_CN^∗ NEXAFS state is placed within the silicon conduction band. Excitation to this orbital leads to valence/Auger spectra in which both resonant and normal Auger contributions are observed. Therefore there is evidence for a charge transfer from the pendent CN to the silicon surface, on a timescale estimated to tens of femtoseconds.     

Conformational isomers of stilbene on Si(1 0 0)

Stilbene (1,2-diphenylethylene) has shown an intriguing isomerisation behavior and may serve as a model system for “molecular switches” incorporating a CC double bond. To evaluate the possible use of such molecules as molecular switches on semiconductor surfaces, the adsorption of cis- and trans-stilbene on Si(1 0 0) has been investigated. Identification of both isomers is achieved by differences in adsorption geometry as revealed by NEXAFS, and differences in electronic structure in the occupied and unoccupied molecular orbitals. For both isomers, bonding takes place via the CC double bond to the Si dimer atoms allowing for free movement of the aromatic rings, a necessary prerequisite for photoinduced isomerisation on the surface. Our experimental results agree well with theoretical calculations.     

Theoretical investigation of the Au/Si(1 1 1)-(5 × 2) surface structure

The atomic structure of the Au/Si(1 1 1)-(5 × 2) surface has been studied by density-functional theory calculations. Two structure models, proposed experimentally by Marks et al. and Hasegawa et al., have been examined on an equal ground. In our total-energy calculations, both models are found to be locally stable and energetically comparable. In our electronic-structure analyses, however, both models fail to reproduce the key features of angle-resolved photoemission spectra and scanning-tunneling-microscopy images, indicating that the considered models need to be modified. Suggestions for the modification are given based on the present calculations.     

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.     

The role of carbon impurities on the Si(0 0 1)-c(4 × 4) surface reconstruction: Theoretical calculations

In this work we employ the state-of-the-art pseudopotential method, within a generalized gradient approximation to the density functional theory, combined with a recently developed method for the calculation of HREELS spectra to study a series of different proposed models for carbon incorporation on the silicon (0 0 1) surface. A fully discussion on the geometry, energetics and specially the comparison between experimental and theoretical STM images and electron energy loss spectra indicate that the Si(1 0 0)-c(4 × 4) is probably induced by Si-C surface dimers, in agreement with recent experimental findings.     

STM study of Si(1 1 3) 3 × 2-Ga surface

The Ga-adsorbed structure on Si(1 1 3) surface at low coverage has been studied by scanning tunneling microscopy (STM). The bright protrusion corresponding to the position of the dimer without the interstitial Si atom of the clean surface disappeared in the filled-state STM image after Ga adsorption, although the protrusion due to the Si adatom still remained. On the basis of the adatom-dimer-interstitial (ADI) model, this result indicates that the Ga atom is adsorbed interstitially at the center of another pentamer that does not have the interstitial Si atom. An ab initio calculation was performed and STM images were simulated.     

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.     

Identification of the vanadyl terminated V2O3(0 0 0 1) surface by NEXAFS spectroscopy: A combined theoretical and experimental study

In this work we present results from density functional theory (DFT) cluster studies to determine polarization-dependent near edge X-ray absorption fine structure (NEXAFS) spectra of the vanadyl termination of the V₂O₃(0 0 0 1) surface. The oxygen K edge spectra are calculated for the relaxed surface geometry where geometric parameters are taken from recent periodic DFT work. A detailed analysis of energetic peak positions, relative intensities, and final state orbitals allows a deep understanding of the complex angular dependence of the calculated spectra on the basis of the local binding environment of differently coordinated oxygen species. Further, our theoretical analysis can assign and explain various spectral details in the experimental NEXAFS data, in particular, those related to vanadyl oxygen. This allows us to support the experimentally suggested vanadyl surface termination.     

Effect of hydrogenation on the electronic structure of the P/Si(0 0 1)-(1 × 2) surface

Ab initio calculations, based on pseudopotentials and density functional theory (DFT), have been performed to investigate the effect of hydrogenation on the electronic properties of P/Si(0 0 1)-(1 × 2) surface. In parallel with this, the electronic band structure of the hydrogenated and non-hydrogenated P/Si(0 0 1)-(1 × 2) surface have been calculated for half- and full-monolayer P. For the mixed Si-P dimer structure, we have identified two occupied and one unoccupied surface state, which correspond to 0.5 ML coverage of P. When this surface is terminated with H, we see that two occupied states completely disappeared and that one unoccupied state is shifted towards the conduction band. A similar calculations for the 1 ML coverage of P have been also carried out. It is seen that the unoccupied state C₁ appeared in the P/Si(0 0 1)-(1 × 2) surface is passivated when this surface is terminated with the H atoms. To explain the nature of the surface states, we have also plotted the total and partial charge densities at the point of the Surface Brillouin Zone (SBZ).