Adsorption geometry of glycine on Cu（001） determined with low—energy electron diffraction and scanning tunnelling microscopy

Using low-energy electron diffraction (LEED) and scanning tunnelling microscopy (STM) it has been found that glycine molecules adsorbed on Cu(001) can form but only the (2×4) and c(2×4) superstructures. On the basis of the missing LEED spots of the surface, it has been concluded that: each (2×4) unit cell consists of two molecules, one being the mirror image of the other; the C－C axis of both molecules lies in the mirror plane of the Cu substrate without a significant shift and twist from the plane; and the two O atoms of the carboxylate group of both molecules locate at the same height level without significant buckling. According to these conclusions, a structural model has been proposed for the (2×4) superstructure (a model for the c(2×4) superstructure already exists). We argue that the (2×4) and c(2×4) superstructures must have similar specific surface free energy, that their hydrogen bonds must be of N-H-O_II type, and that their local adsorption geometry must be similar or even the same. The advantage of combining STM with LEED to determine surface structures is clearly demonstrated.     

Surface structure of In2O3(111) (1 × 1) determined by density functional theory calculations and low energy electron diffraction

The surface structure of In₂O₃(111) has been investigated by dynamical analysis of low energy electron diffraction data, in conjunction with first principles calculations using density functional theory. The experimental data set consisted of eight independent beams whose intensities were measured for incident energies in the range between 25 eV and 250 eV. In fitting the experimental data it was essential to treat the radii of In and O spheres as variable parameters: following this procedure a final Pendry R factor of 0.31 was obtained. The LEED results are compatible with the calculations and both analyses suggest that the surface structure involves only small vertical relaxations in the outermost of the {[O^2?]₁₂^24?[In³⁺]₁₆⁴⁸⁺[O^2?]₁₂^24?} quadrupolar units that define the (111) surface. The ab initio slab calculations also confirm that lateral relaxations not considered in fitting the experimental data are of very minor importance.     

Co-adsorption of O_2 and H_2O on α-uranium(110) surface:A density functional theory study

First-principles calculations based on density functional theory corrected by Hubbard parameter U(DFT+U) are applied to the study on the co-adsorption of O2 and H_2O molecules to α-U(110) surface. The calculation results show that DFT+U method with Ueff= 1.5 e V can yield the experimental results of lattice constant and elastic modulus of α-uranium bulk well. Of all 7 low index surfaces of α-uranium, the(001) surface is the most stable with lowest surface energy while the(110) surface possesses the strongest activity with the highest surface energy. The adsorptions of O_2 and H_2O molecules are investigated separated. The O_2 dissociates spontaneously in all initial configurations. For the adsorption of H_2O molecule,both molecular and dissociative adsorptionsoccur. Through calculations of co-adsorption, it can be confirmed that the inhibition effect of O_2 on the corrosion of uranium by water vapor originates from the preferential adsorption mechanism,while the consumption of H atoms by O atoms exerted little influence on the corrosion of uranium.     

A density functional theory study of small bimetallic PdnAl (n=1–8) clusters

The geometries, stabilities, and magnetic properties of Pd_nAl (n=1–8) neutral clusters are studied using density functional theory with generalized gradient approximation. The growth pattern for different sized Pd_nAl (n=1–8) clusters is Al-substituted Pd_n+1 clusters and it keeps the similar framework of the most stable Pd_n+1 clusters except n=6 and 8. Al atoms in the ground state Pd_nAl isomers tend to occupy the most highly coordinated position. The analysis of stabilities shows that doping an Al atom can enhance the stabilities of the host Pd clusters and the magic number characteristic of Pd₄ cluster cannot be changed, the Pd₃Al cluster has a higher stability. Charges are transferred from Al atom to Pd atoms in all Pd_nAl clusters, so the Al atom is the electron donor, and Pd atoms are the electron accepters. Doping an Al atom decreases the average atomic magnetic moments of the host Pd clusters.     

A van der Waals density functional theory study of poly(vinylidene difluoride) crystalline phases

Ferroelectric polymers, such as poly(vinylidene difluoride) (PVDF), have many potential applications in flexible electronic devices. PVDF has six experimentally observed polymorphs, three of which are ferroelectric. In this work we use density functional theory to investigate the structural properties, energetics and polarisation of the stable α-phase, its ferroelectric analogue, the δ-phase, and the β-phase, which has the best ferroelectric properties. The results from a variety of exchange and correlation functionals were compared and it was found that van der Waals (vdW) interactions have an important effect on the calculated crystal structures and energetics, with the vdW-DF functional giving the best agreement with experimental lattice parameters. The spontaneous polarisation was found to strongly correlate with the unit cell volumes, which depend on the functional used. While the relative phase energies were not strongly dependent on the functional, the cohesive energies were significantly underestimated using the PBE functional. The inclusion of vdW interactions is, therefore, important to obtain the correct lattice structures, polarisation and energetics of PVDF polymorphs.     

Understanding 4-bromostyrene Adsorption on the Si(001)-(1 × 2) surface: A density functional theory study

Adsorption properties of 4-bromostyrene (Br–Sty) on the Si(001)-(1 × 2) surface are investigated by ab initio calculation based on density functional theory (DFT). For the adsorption of Br–Sty molecule on the Si(001)-(1 × 2) surface, we have assumed two possible cases within: (i) binding on the partially H-terminated surface and (ii) binding on the clean surface. For the first case, we have estimated two different binding sides: (i) Bromine-terminated bindings and (ii) Carbon-terminated binding. The adsorption energies of Br-terminated and C-terminated binding were found as 0.36 eV and 3.76 eV, respectively. In the same manner, we have also assumed two possible binding sides for the clean surface: (i) Br-terminated binding and (ii) ring-shaped binding. We have found adsorption energies for Br-terminated and ring-shaped binding as 0.14 eV and 1.10 eV on the clean surface, respectively. Moreover, the nudged elastic band method (NEB) was used to reveal the adsorption pathway of these binding models. These results serve to understand the possibility of the adsorption of Br–Sty molecules onto different kind of silicon surfaces into different reaction conditions.     

A comparative coupled cluster and density functional theory study of the HOCI → HCIO transition state

The structural features of the HOCl → HClO isomerization mechanism, including all stationary points, and one saddle point, were examined by use of coupled cluster and the B3LYP density functional theory methodology. To improve the results a very large 6–311++G (3df, 3pd) Gaussian-type basis set was employed in the presented calculations. In addition, Gaussian-3 theory was tested against our coupled cluster (with single, double and triple excitations) results, and they were found to correlate closely with one another by around 1–2 kcal mol^?1. The energy change for this isomerization reaction is predicted to be 54.5 kcalmol^?1 and 52.5 kcalmol^?1 with the B3LYP and CCSD (T) methods, respectively, and the activation barrier is 76.1 kcal mol^?1 and 70.1 kcalmol^?1 with the same methods.     

The (2 × 2) reconstructions on the SrTiO3 (001) surface: A combined scanning tunneling microscopy and density functional theory study

Scanning tunneling microscopy study showed that the (2 × 2) reconstruction on the (001) surface of SrTiO₃ should have a surface structure with a 4-fold symmetry. The previously proposed solution for the (2 × 2) reconstruction with the p2gm symmetry only has a 2-fold symmetry. In this study density functional theory study was carried out to propose a possible surface structure with the p4mm surface symmetry which matches the scanning tunneling microscopy images and suggests that two different (2 × 2) surface structures exist. The formation of the (2 × 2) reconstruction with the p4mm symmetry may be due to the kinetics as it has slightly higher surface energy than the one with the p2gm symmetry.     

The electronic structures of commensurate Ru(0001)–(3 × 3)–4Kr and Ru(0001)–(5 × 5)–Kr using density functional theory

We have calculated the minimum energies for each of three positionings of the adatom unit cells for Ru(0001)–(3 × 3)–4Kr (high Kr coverage) and for Ru(0001)–(5 × 5)–Kr (low Kr coverage). The differences between the results for the low and high-coverage cases may clarify puzzles posed by the experimental results of Narloch and Menzel. The low-coverage solution converges to a structure having Kr in the top site at a height of 3.09 Å above the substrate with the adsorption energy 185 meV. In the high-coverage case, adatom unit cells with a corner Kr at top, fcc hollow, and hcp hollow locations are found to have nearly the same adsorption energy of 175 meV. The height of the corner atom above the substrate is found to be 3.35, 3.54, and 3.50 Å for the top, fcc hollow and hcp hollow sites, respectively. These results are explained by demonstrating that there is an enhancement of the substrate electronic density of states at krypton orbital energies in the low-coverage case.     

A density functional theory study on the adsorption of CO and O2 on Cu-terminated Cu2O （111） surface

The adsorptions of CO and 02 molecules individually on the stoichiometric Cu-terminatcd Cu20 （111） surface are investigated by first-principles calculations on the basis of the density functional theory. The calculated results indicate that the CO molecule preferably coordinates to the Cu2 site through its C atom with an adsorption energy of-1.69 eV, whereas the 02 molecule is most stably adsorbed in a tilt type with one O atom coordinating to the Cu2 site and the other O atom coordinating to the Cul site, and has an adsorption energy of -1.97 eV. From the analysis of density of states, it is observed that Cu 3d transfers electrons to 2π orbital of the CO molecule and the highest occupied 5σ orbital of the CO molecule transfers electrons to the substrate. The sharp band of Cu 4s is delocalized when compared to that before the CO molecule adsorption, and overlaps substantially with bands of the adsorbed CO molecule. There is a broadening of the 2π orbital of the 02 molecule because of its overlapping with the Cu 3d orbital, indicating that strong 3d-2π interactions are involved in the chemisorption of the 02 molecule on the surface.     

Adsorption and dissociation of molecular oxygen on α-Pu (0 2 0) surface: A density functional study

Molecular and dissociative oxygen adsorptions on the α-Pu (0 2 0) surface have been systematically studied using the full-potential linearized augmented-plane-wave plus local orbitals (FP-LAPW+lo) basis method and the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional. Chemisorption energies have been optimized for the distance of the admolecule from the Pu surface and the bond length of O-O atoms for four adsorption sites and three approaches of O₂ admolecule to the (0 2 0) surface. Chemisorption energies have been calculated at the scalar relativistic level with no spin-orbit coupling (NSOC) and at the fully relativistic level with spin-orbit coupling (SOC). Dissociative adsorptions are found at the two horizontal approaches (O₂ is parallel to the surface and perpendicular/parallel to a lattice vector). Hor2 (O₂ is parallel to the surface and perpendicular to a lattice vector) approach at the one-fold top site is the most stable adsorption site, with chemisorption energies of 8.048 and 8.415 eV for the NSOC and SOC cases, respectively, and an OO separation of 3.70 Å. Molecular adsorption occurs at the Vert (O₂ is vertical to the surface) approach of each adsorption site. The calculated work functions and net spin magnetic moments, respectively, increase and decrease in all cases upon chemisorption compared to the clean surface. The partial charges inside the muffin-tins, the difference charge density distributions, and the local density of states have been used to investigate the Pu-admolecule electronic structures and bonding mechanisms.     

Influence of the scattering potential model on low energy electron diffraction from Cu(001)−c(2 × 2)-Pb

A dynamical LEED intensity analysis is reported for Cu(001)−c(2 × 2)-Pb. The adsorbate layer distance from the substrate is determined as 2.29 Å, and the topmost interlayer spacing for the substrate is the same as in bulk Cu, in contrast to a contraction for clean Cu(001). This structural result is, within the accuracy reached, insensitive to changes in the assumed scattering potential models. The r-factors suggest a weak preference for an energy-dependent exchange correlation and a moderate one for adding a localized adsorption part inside the muffin-tin spheres. The sensitivity of spectra and r-factors to changes in the assumed isotropic Debye temperature for Pb suggests that vibrational anisotropy should be taken into account in order to improve the accuracy of the analysis. Calculated spin polarization spectra are very sensitive to the exchange approximation, the localized absorption and the Debye temperature. Together with experimental data, they should be useful in particular for determining the vibrational anisotropy.     

Structure and stability of β-Mo2C bulk and surfaces: A density functional theory study

Density functional theory calculations have been performed on the structure and stability of β-Mo₂C bulk and the corresponding low-index surfaces. The eclipse configuration with a Mo-C-Mo-C stacking is the most stable, followed by the structure with a Mo-C-Mo-Mo-C stacking where there is an empty carbon layer every fourth layer. For (0 0 1) and (1 0 0) surfaces, the pure C terminations are more stable than the pure Mo terminations. For (0 1 0) and (1 1 1) surfaces, the Mo terminations are more stable than the C terminations. For the (0 1 1) surface, the mixed Mo/C termination is a little more stable than the Mo termination. Relaxation of these surfaces is moderate with no relaxation degree exceeding 12.8%. Among these surfaces, the mixed Mo/C termination of the (0 1 1) surface is the most stable with the lowest surface free energy, followed by the (1 0 1) surface and the T_Mo-2 termination of the (0 1 0) surface.     

The adsorption and reconstruction of strong electron acceptor tetracyanoethylene (TCNE) on Si(001)-(2 × 1): A density functional theory investigation

The adsorption and reconstruction of strong electron-acceptor TCNE on the Si(001)-(2 × 1) surface are investigated by density functional theory (DFT). The results show that TCNE prefers to adsorb on the trench between two adjacent dimer rows and the CC double bond is parallel to dimer rows. Charge density difference calculation and Bader charge analysis indicate that abundant negative charge transfers from dimer Si to TCNE. Strong interaction makes it difficult for TCNE to move on Si(001), which is confirmed by nudged elastic band (NEB) analysis. In addition, the correlations between simulated STM images and molecular orbitals are discussed and two surface reconstructions of (2 × 1) and (4 × 2) are predicted at different TCNE coverages.     

Electronic structures and coronene on Ru（0001）： vibrational properties of first-principles study

We calculate the configurations,electronic structures,vibrational properties at the coronene/Ru(0001) interface,and adsorption of a single Pt atom on coronene/Ru(0001) based on density functional theory calculations.The geometric structures and electronic structures of the coronene on Ru(0001) are compared with those of the graphene/Ru(0001).The results show that the coronene/Ru(0001) can be a simplified model system used to describe the interaction between graphene and ruthenium.Further calculations of the vibrational properties of coronene molecule adsorbed on Ru(0001) suggest that the phonon properties of differently corrugated regions of graphene on Ru(0001) are different.This model system is also used to investigate the selective adsorption of Pt atoms on graphene/Ru(0001).The configurations of Pt on coronene/Ru(0001) with the lowest binding energy give clues to explain the experimental observation that a Pt cluster selectively adsorbs on the second highest regions of graphene/Ru(0001).This work provides a simple model for understanding the adsorption properties and vibrational properties of graphene on Ru(0001) substrate.     

Effects of shape and dopant on structural,optical absorption,Raman, and vibrational properties of silver and copper quantum clusters: A density functional theory study

We investigate the effects of shape and single-atom doping on the structural, optical absorption, Raman, and vibra- tional properties of Ag13, Ag12CUl, CUl3, and Cul2Agl clusters by using the （time-dependent） density functional the- ory. The results show that the most stable structures are cuboctahedron （COh） for Ag13 and icosahedron （Ih） for CUl3, Agl2CUlcore, and Cul2Aglsur. In the visible-near infrared optical absorption, the transitions consist of the interband and the intraband transitions. Moreover, red shifts are observed as follows： 1） clusters change from Agl2CUlcore to Ag13 to Ag12Culsur with the same motifs, 2） the shapes of pure Agl3 and Agl2CUlcore clusters change from COh to Ih to decahe- dron （Dh）, 3） the shape of Agl2CUlsur clusters changes from Ih to COh to Dh, and 4） the shapes of pure CU13 and Cu12Agl clusters change from Ih to Dh to COb. All of the Raman and vibrational spectra exhibit many significant vibrational modes related to the shapes and the compositions of the clusters. The ranges of vibrational spectra of Ag13, Agl2CUl or CU13, and Cu12Agl clusters become narrower and the vibrational intensities increase as the shape of the clusters changes from Ih to Dh to COh.     

Detection of exhaled gas by γ-graphyne and twin-graphene for early diagnosis of lung cancer: A density functional theory study

In lung cancer, primary diagnosis is quite essential to guarantee human health. In this work, the capability of γ-graphyne and twin-graphene sheets to detect typical breath gases such as benzene, styrene, aniline, and o-toluidine is studied based on density functional theory. The results indicate that these gases are physisorbed on γ-graphyne and twin-graphene. Because of relatively low gas binding strength between gases and γ-graphyne and twin-graphene, these sheets can be proper for the practical gas sensors with a fast recovery rate. Both γ-graphyne and twin-graphene have semiconducting properties before and after gas adsorption. Adsorption of the gases decreases the energy band gap, and increases the electric dipole moment of γ-graphyne and twin-graphene. The electronic properties of twin-graphene are more sensitive than that of γ-graphyne to the presence of the considered gases. Hence, twin-graphene can be desirable and promising material for sensing typical breath gases to diagnose lung cancer.     

Does methanol produce a stable methoxy species on Ru(0001) at low temperatures?

Soft X-ray photoelectron spectroscopy (SXPS) and energy-scanned photoelectron diffraction (PhD) have been used to study the surface species produced by exposure of Ru(0001) to methanol at ~ 150 K. SXPS shows a single surface species is formed at sub-monolayer coverages with an O 1s peak binding energy of ~ 532.6 eV, 2.8 eV greater than that of chemisorbed atomic oxygen. O 1s PhD data from this species shows no significant modulations, in contrast to simulated PhD spectra from a methoxy species occupying a three-fold coordinated hollow site, as predicted by earlier density functional theory calculations, or atop or bridging sites. By contrast, PhD data from the O 1s of the atomic oxygen species in the Ru(0001)(2 × 1)–O phase are consistent with the oxygen atoms occupying ‘hcp’ hollow sites (above second-layer Ru atoms) at a RuO bondlength of 2.01 ± 0.02 Å, essentially identical to previous structure determinations of this phase. O 1s PhD recorded at normal emission from adsorbed CO are also consistent with the known CO atop adsorption species. We conclude that the methanol-derived surface molecular species is not methoxy in a well-defined local site on the surface, but is consistent with clusters of intact methanol identified in a recent infrared spectroscopy investigation.     

Effect of Coulomb repulsion on spin and orbital magnetism of cobalt–benzene complex: A relativistic density functional study

We have demonstrated electronic configurations and magnetic properties of single Co adatom on benzene (Bz) molecule in the framework of relativistic density functional theory. A sequence of fixed spin moment (FSM) calculations were carried out with and without Coulomb repulsion (U). We have investigated that varying the strength of Coulomb repulsion results to different equilibrium positions for the Co adatom on benzene molecule. It was shown that inclusion of the on-site Coulomb repulsion in the Co 3d orbitals affects significantly the geometry of Co–Bz complex. We also found two stable low-spin and high-spin multiplicities for the complex. The nature of the high-spin configuration was explained according to the Hubbard electron–electron correlation in 3d shell of the Co adatom. Our FSM results indicate that the high-spin state is a global minimum in the presence of Hubbard parameter U. The relativistic spin–orbit coupling and using orbital polarization correction induce considerable orbital magnetism in both low and high spin states of the Co–Bz complex. We have also calculated magnetic anisotropy energies for two spin states and we found out that an out-of-plane magnetic orientation of Co adatom is more favorable in the low spin state whereas the Coulomb repulsion (U = 2 eV and U = 4 eV) predicts an in-plane magnetic orientation for Co adatom. Our findings can be implicitly taken into account for the extended system of added single Co atom on graphene.