Theoretical and experimental investigation of the electronic and magnetic structure of transition metal atoms on an insulating interface with a metallic substrate at low temperatures is quite challenging. In this paper, we show a density functional theory plus Hubbard $U$ based protocol to study an Mn adatom on three symmetrically allowed absorption sites, namely on O, hollow (between two Mg and two O) and on Mg on MgO(001). We added a thick enough(bulk-like) metallic Ag slab beneath MgO for faithful replication of scanning tunneling microscopy (STM) experiments. Our study reveals that to determine the stable most binding site, we need to obtain a Hubbard $U$ value from the density functional theory(DFT) calculations, and our results show agreement with STM experiments. Our calculated Hubbard $U$ values for the three adatom sites are different. When Mn sits on O, it retains 2.4 $μ_B$ spin moment, close to its atomic spin moment. However, when Mn sits on other adatom sites, the spin moment decreases. Using the atom projected density of states, we find Mn on O atom shows very narrow crystal field splitting among \textit{d} orbitals, whereas on other adatom sites Mn \textit{d} orbitals show significant splitting. We calculate charge and spin densities and show vertical and horizontal propagation of charge and spin density varies widely between sites. Mn on Mg top shows an unusual feature, that Mn pushes Mg below, to make a coplanar of Mn geometry with the four oxygen atoms. In addition, we explained the reason for spin leaking down to the Ag layers. Mn on MgO/Ag does not show any spin-flip behavior in the STM, an unusual phenomenon, and we used our first principles-based approach to explain this unique observation.
We use Ca doping during growth of one and two monolayer thick MgO films on Ag(100) to identify the adsorption sites of individual adatoms with scanning tunneling microscopy. For this we combine atomic resolution images of the bare MgO layer with images of the adsorbates and the substitutional Ca atoms taken at larger tip-sample distance. For Ho atoms, the adsorption sites depend on MgO thickness. On the monolayer, they are distributed on the O and bridge sites according to the abundance of those sites, 1/3 and 2/3 respectively. On the MgO bilayer, Ho atoms populate almost exclusively the O sit…
The adsorption of MgO molecules on a Fe(001) surface was studied using density functional theory (DFT) and projector augmented wave methods. The energetically most favored configurations for different adsorption sites considered were identified. The most preferable adsorption geometry is when the MgO molecules are parallel to the surface, with Mg in the interstitial site and O in on-top of the Fe atom. During the adsorption of subsequent MgO molecules in this geometry, a sharp, non-oxidized interface is formed between the MgO adlayer and Fe(001) surface. The adsorption of MgO perpendicular to …
Scanning tunneling microscopy (STM) provides real-space electronic state information at the atomic scale that is most commonly used to study materials surfaces. An intriguing extension of the method is attempt to study the electronic structure at an insulator/conductor interface by performing low-bias imaging above the surface of an ultrathin insulating layer on the conducting substrate. We use first-principles theory to examine the physical mechanisms giving rise to the formation of low-bias STM images in the MgO/Ag system. We show that the main features of the low-bias STM contrast are compl…
We investigate the adsorption of a single tetracyanoethylene (TCNE) molecule on the silver (001) surface. Adsorption structures, electronic properties, and scanning tunneling microscopy (STM) images are calculated within density-functional theory. Adsorption occurs most favorably in on-top configuration, with the C=C double bond directly above a silver atom and the four N atoms bound to four neighboring Ag atoms. The lowest unoccupied molecular orbital of TCNE becomes occupied due to electron transfer from the substrate. This state dominates the electronic spectrum and the STM image at moderat…
We have studied the adsorption of NO, and the coadsorption of N and O, on four physical and hypothetical systems: unstrained and strained Rh(100) surfaces and monolayers of Rh atoms on strained and unstrained MgO(100) surfaces. We find that as we go from Rh(100) to Rh/Mg0(100), via the other two hypothetical systems, the effective coordination progressively decreases, the $d$-band narrows and its center shifts closer to the Fermi level, and the strength of adsorption and co-adsorption increases. Both strain and the presence of the oxide substrate contribute significantly to this. However, char…
By means of density functional theory we have undertaken a structural, electronic and magnetic survey of the adsorption of the Fe_xPt_y(x,y=<4) clusters on MgO (001) surface under the generalized gradient approximation. We have tested different atomic adsorption geometries with the aim of scan a wider range of adsorption sites in order to determine the preferential surface covering. Our main conclusion in this respect is that the FePt wets the surface. The intracluster (before and after the adsorption) and cluster-to-surface binding mechanisms were investigated via the adsorption energy, charg…
The interface between FePt--L1$_0$ and MgO(001) alloys has been studied using density functional calculations. Because the stacking of the face-centered tetragonal L1$_0$ phase is formed by alternating Fe and Pt planes, both the Fe- and Pt-terminated contact layers were studied. Furthermore, due to the large mismatch between the in-plane lattice constants of both systems, we have chosen some common $a$ values for both alloys in order to explore in detail the adsorption energy, the electronic structure and the interface magnetism. The adsorption energy has been calculated by subtracting the ene…
Improving reactivity on an insulating surface is crucial due to their important applications in surface catalytic reactions. In this work, we carried out first-principles calculations to investigate the adsorption of O2 on a single-layer MgO(100) film deposited on metal substrate. The adsorption configurations, reaction pathways, molecular dynamics simulations, and electronic properties are reported. We reveal that O2 can completely dissociate on the surface, which is in sharp contrast to that on MgO(100) films thicker than one monolayer. The dissociated O2 tends to penetrate into the interfac…
We present a density functional study of the structural and electronic properties of small Cu_n (n=1,4) aggregates on defect-free MgO(100). The calculations employ a slab geometry with periodic boundary conditions, supercells with up to 76 atoms, and include full relaxation of the surface layer and of all adsorbed atoms. The preferred adsorption site for a single Cu adatom is on top of an oxygen atom. The adsorption energy and Cu-O distance are E_S-A = 0.99 eV and d_S-A = 2.04 Angstroems using the Perdew-Wang gradient corrected exchange correlation functional. The saddle point for surface diff…
We present a general computational scheme based on molecular dynamics (m.d.) simulation for calculating the chemical potential of adsorbed molecules in thermal equilibrium on the surface of a material. The scheme is based on the calculation of the mean force in m.d. simulations in which the height of a chosen molecule above the surface is constrained, and subsequent integration of the mean force to obtain the potential of mean force and hence the chemical potential. The scheme is valid at any coverage and temperature, so that in principle it allows the calculation of the chemical potential as …
Using density functional theory, we investigate the possible adsorption sites of CO molecules on the recently discovered Pt induced Ge nanowires on Ge(001). Calculated STM images are compared to experimental STM images to identify the experimentally observed adsorption sites. The CO molecules are found to adsorb preferably onto the Pt atoms between the Ge nanowire dimer segments. This adsorption site places the CO in between two nanowire dimers, pushing them outward, blocking the nearest equivalent adsorption sites. This explains the observed long-range repulsive interaction between CO molecul…
Chemisorption of CO on the stepped Cu(211) surface is studied within ab-initio density functional theory (DFT) and scanning tunneling microscopy (STM) imaging as well as manipulation experiments. Theoretically we focus on the experimentally observed ordered (2x1) and (3x1) CO-phases at coverages 1/3, 1/2 and 2/3 monolayer (ML). To obtain also information for isolated CO molecules found randomly distributed at low coverages, we also performed calculations for a hypothetical (3x1) phase with 1/3 ML. The adsorption geometry, the stretching frequencies, the work functions and adsorption energies o…
We present a systematic theoretical investigation of the surface properties, stability and reactivity, of rock-salt type alkaline-earth metal oxides including MgO, CaO, SrO, and BaO. The accuracy of commonly used exchange-correlation density functionals (LDA, PBE, RPBE, PBEsol, BEEF-vdW and hybrid HSE) and random-phase approximation (RPA) is evaluated and compared to existing experimental values. Calculated surface energies of the four most stable surface facets under vacuum conditions: the (100) surface, the metal and oxygen terminated octopolar (111), and the (110) surfaces exhibit a monoton…
Doping of Si using the scanning probe hydrogen depassivation lithography technique has been shown to enable placing and positioning small numbers of P atoms with nanometer accuracy. Several groups have now used this capability to build devices that exhibit desired quantum behavior determined by their atomistic details. What remains elusive, however, is the ability to control the precise number of atoms placed at a chosen site with 100% yield, thereby limiting the complexity and degree of perfection achievable. As an important step towards precise control of dopant number, we explore the adsorp…
Electron paramagnetic resonance (EPR) can provide unique insight into the chemical structure and magnetic properties of dopants in oxide and semiconducting materials that are of interest for applications in electronics, catalysis, and quantum sensing. Here, we demonstrate that EPR in combination with scanning tunneling microscopy (STM) allows for probing the bonding and charge state of alkali metal atoms on an ultrathin magnesium oxide layer on a Ag substrate. We observe a magnetic moment of $1μ_\mathrm{B}$ for Li$_2$, LiNa, and Na$_2$ dimers corresponding to spin radicals with a charge state …
Molybdenum supported thin films of ScN, MgO and NaF with a Cu adatom have been studied in the framework of density functional theory. We have observed a charge transfer from the metal/film interface to the Cu atom and investigated its relation to surface and interface deformations. We find that a weak interaction between the metal and the film is a promising prerequisite for adatom charging. The detailed study of Cu/NaF/Mo and NaF/Mo indicates that the distortion of the NaF film caused by the Cu adsorption has essentially anharmonic character, as it is coupled to a strong charge redistribution…
The adsorption of iron phthalocyanine (FePc) on the passivated H/Si(111) surface is explored from first principles. We find that the organic molecule is predominantly physisorbed with a distance to the surface of $2.6 \pm 0.1$ Angstrom, but also exhibits sizable resonance with the underlying substrate. This establishes the present system as interesting mixed covalent-van-der-Waals-bound test case, which we use to compare the impact of different approaches to van-der-Waals interactions. (Spin-polarized) scanning tunneling microscopy (SP STM) images are simulated, selectively accessing different…
The adsorption of CO molecules at the Ca3Ru2O7(001) surface was studied using low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT). Ca3Ru2O7 can be easily cleaved along the (001) plane, yielding a smooth, CaO-terminated surface. The STM shows a characteristic pattern with alternating dark and bright stripes, resulting from the tilting of the RuO$_6$ octahedra. At 78,K, CO adsorbs at an apical surface O at the channel edge with a predicted binding energy of $E_{ads} = -0.85$eV. After annealing at room temperature, the CO forms a strong bond ($E_{ads}= -2.04$eV…
We examine the adsorption of a single Ni atom on a monolayer of MgO on a Ag substrate using DFT and DFT+U computational approaches. We find that the electronic and magnetic properties vary considerably across the three binding sites of the surface. Two of the binding sites are competitive in energy, and the preferred site depends on the strength of the on-site Coulomb interaction U. These results can be understood in terms of the competition between bonding and magnetism for surface adsorbed transition metal atoms. Comparisons are made with a recent experimental and theoretical study of Co on …
Electron paramagnetic resonance (EPR) spectroscopy is widely employed to characterize paramagnetic complexes. Recently, EPR combined with scanning tunneling microscopy (STM) achieved single-spin sensitivity with sub-angstrom spatial resolution. The excitation mechanism of EPR in STM, however, is broadly debated, raising concerns about widespread application of this technique. Here, we present an extensive experimental study and modelling of EPR-STM of Fe and hydrogenated Ti atoms on an MgO surface. Our results support a piezoelectric coupling mechanism, in which the EPR species oscillate adiab…
The interaction of water with oxide surfaces is of great interest for both fundamental science and applications. We present a combined theoretical [density functional theory (DFT)] and experimental [Scanning Tunneling Microscopy (STM), photoemission spectroscopy (PES)] study of water interaction with the two-dimensional titania overlayer that terminates the SrTiO$_3$(110)-(4$\times$1) surface and consists of TiO$_4$ tetrahedra. STM, core-level and valence band PES show that H$_2$O neither adsorbs nor dissociates on the stoichiometric surface at room temperature, while it dissociates at oxygen …
Nickel and Rhodium (001) surfaces display a similar - as from STM images - clock reconstruction when half a monolayer of C/Ni, N/Ni or O/Rh is adsorbed; no reconstruction is observed instead for O/Ni. Adsorbate atoms sit at the center of the black squares of a chess-board, $c(2\times 2)$, pattern and two different reconstructions are actually compatible with the observed STM images - showing a $(2\times 2)p4g$ pattern - according to whether a rotation of the black or white squares occurs. We report on a first - principles study of the structure of X/Ni(001) and X/Rh(001) surfaces (X=C,N,O) at …
The adsorption of methanol (CH3OH) at the Fe3O4(001)-c(2x2) surface was studied using X-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and temperature-programmed desorption (TPD). CH3OH adsorbs exclusively at surface defects sites at room temperature to form hydroxyl groups and methoxy (CH3O) species. Active sites are identified as step edges, iron adatoms, antiphase domain boundaries in the c(2x2) reconstruction, and above Fe atoms incorporated in the subsurface. In TPD, recombinative desorption is observed around 300 K, and a disproportionation reaction to form me…
We used DFT to study the energetics of the decomposition of alane, AlH3, on the Si(001) surface, as the acceptor complement to PH3. Alane forms a dative bond with the raised atoms of silicon surface dimers, via the Si atom lone pair. We calculated the energies of various structures along the pathway of successive dehydrogenation events following adsorption: AlH2, AlH and Al, finding a gradual, significant decrease in energy. For each stage, we analyse the structure and bonding, and present simulated STM images of the lowest energy structures. Finally, we find that the energy of Al atoms incorp…
Herein, we invesgate the consequence of local voltage pulses on the adsorption state of single indigo molecules on the Cu(111) surface as well as on the atomic structure underneath the molecule. With a scanning tunneling microscope, at 5 K, intact molecules are imaged as two lobes corresponding to the electron density of each indoxyl moiety of the molecule which are connected by a carbon double bond. Then, two short successive voltage pulses with the tip placed above the molecule generate irreversible modifications, as revealed by consecutive scanning tunneling microscopy (STM) imaging. Densit…
Density functional calculations with a large unit cell have been conducted to investigate adsorption, segregation and magnetization of Mn monomer on GaAs(110). The Mn adatom is rather mobile along the trench on GaAs(110), with an energy barrier of 0.56 eV. The energy barrier for segregation across the trenches is nevertheless very high, 1.67 eV. The plots of density of states display a wide gap in the majority spin channel, but show plenty of metal-induced gap states in the minority spin channel. The Mn atoms might be invisibl in scanning tunneling microscope (STM) images taken with small bias…
We investigate an anthracene derivative, 3(5)-(9-anthryl) pyrazole (ANP), self-assembled on the Au (111) surface by means of scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. A chessboard-like network structure composed of ANP molecules is found, covering the whole Au (111) substrate. Our STM results and DFT calculations reveal that the formation of chessboard-like networks originates from a basic unit cell, a tetramer structure, which is formed by four ANP molecules connected through C-H-N hydrogen-bonds. The hydrogen bonds inside each tetramer and the mole…
Isolated hydrogen atoms absorbed on graphene are predicted to induce magnetic moments. Here we demonstrate that the adsorption of a single hydrogen atom on graphene induces a magnetic moment characterized by a ~20 meV spin-split state at the Fermi energy. Our scanning tunneling microscopy (STM) experiments, complemented by first-principles calculations, show that such a spin-polarized state is essentially localized on the carbon sublattice complementary to the one where the H atom is chemisorbed. This atomically modulated spin-texture, which extends several nanometers away from the H atom, dri…
We investigate Co nanostructures on Bi$_{2}$Se$_{3}$ by means of scanning tunneling microscopy and spectroscopy [STM/STS], X-ray absorption spectroscopy [XAS], X-ray magnetic dichroism [XMCD] and calculations using the density functional theory [DFT]. In the single adatom regime we find two different adsorption sites by STM. Our calculations reveal these to be the fcc and hcp hollow sites of the substrate. STS shows a pronounced peak for only one species of the Co adatoms indicating different electronic properties of both types. These are explained on the basis of our DFT calculations by diffe…
We investigate the electronic and magnetic properties of single Fe, Co, and Ni atoms and clusters on monolayer graphene (MLG) on SiC(0001) by means of scanning tunneling microscopy (STM), x-ray absorption spectroscopy, x-ray magnetic circular dichroism (XMCD), and ab initio calculations. STM reveals different adsorption sites for Ni and Co adatoms. XMCD proves Fe and Co adatoms to be paramagnetic and to exhibit an out-of-plane easy axis in agreement with theory. In contrast, we experimentally find a nonmagnetic ground state for Ni monomers while an increasing cluster size leads to sizeable mag…
Adsorption of benzoic acid on the (110) surface of rutile, both unreconstructed and (1x2)- reconstructed ones, at saturation coverage of one benzoate per two adjacent five-coordinated Ti5c sites has been studied using DFT simulations, as implemented through the Vienna Ab initio Simulations Package (VASP). In order to study the effects of hydrogen bonding and Van der Waals forces in influencing the relative stabilities of different adsorbate overlayer superstructures, these studies were performed through Local Density Approximation (LDA), Generalized Gradient Approximation(GGA) and DFT-D2. Thro…
We report on a first-principles study of the structure of O/Rh(001) at half a monolayer of oxygen coverage, performed using density-functional theory. We find that oxygen atoms sit at the center of the black squares of a chess-board, $c(2\times 2)$, pattern. This structure is unstable against a rhomboid distortion of the black squares, which shortens the distance between an O atom and two of the four neighboring Rh atoms, while lengthening the distance with respect to the other two. We actually find that the surface energy is further lowered by allowing the O atom to get off the short diagonal…
Realization of graphene moiré superstructures on the surface of 4d and 5d transition metals offers templates with periodically modulated electron density, which is responsible for a number of fascinating effects, including the formation of quantum dots and the site selective adsorption of organic molecules or metal clusters on graphene. Here, applying the combination of scanning probe microscopy/spectroscopy and the density functional theory calculations, we gain a profound insight into the electronic and topographic contributions to the imaging contrast of the epitaxial graphene/Ir(111) syste…
Adsorption of CO at the Sr$_3$Ru$_2$O$_7$(001) surface was studied with low-temperature scanning tunneling microscopy (STM) and density functional theory. In situ cleaved single crystals terminate in an almost perfect SrO surface. At 78 K, CO first populates impurities and then adsorbs above the apical surface O with a binding energy E$_\mathrm{ads}$=-0.7 eV. Above 100 K, this physisorbed CO replaces the surface O, forming a bent CO2 with the C end bound to the Ru underneath. The resulting metal carboxylate (Ru-COO) can be desorbed by STM manipulation. A low activation (0.2 eV) and high bindin…
The evolution of titanyl-phthalocyanine (TiOPc) thin films on Ag(111) has been investigated using IRAS, SPA-LEED and STM. In the (sub)monolayer regime various phases are observed that can be assigned to a 2D gas, a commensurate and a point-on-line phase. In all three phases the non-planar TiOPc molecule is adsorbed on Ag(111) in an oxygen-up configuration with the molecular pi-conjugated backbone oriented parallel to the surface. The commensurate phase reveals a high packing density, containing two molecules at inequivalent adsorption sites within the unit cell. Both molecules assume different…
Decagonal quasiperiodic ordering of Sn thin film on $d$-Al-Ni-Co, is shown based on scanning tunneling microscopy (STM), low-energy electron diffraction and density functional theory (DFT). Interestingly, the decagonal structural correlations are partially retained up to a large film thickness of 10 nm grown at a 165$\pm$10 K. The nucleation centers called 'Sn white flowers' identified by STM at submonolayer thickness are recognized as valid patches of the decagonal clathrate structure with low adsorption energies. Due to the excellent lattice matching (to within 1%) between columns of Sn dode…
We identify the atomic structure of the Au/Si(111)-5x2 surface by using density functional theory calculations. With seven Au atoms per unit cell, our model forms a bona fide 5x2 atomic structure, which is energetically favored over the leading model of Erwin, Barke, and Himpsel [Phys. Rev. B 80, 155409 (2009)] and well reproduces the Y- and V-shaped 5x2 STM images. This surface is metallic with a prominent half-filled band of surface states, mostly localized around the Au-chain area. The correct identification of the atomic and band structure of the clean surface further clarifies the adsorpt…
Catalysis has entered everyday life through a number of technological processes relying on different catalytic systems. The increasing demand for such systems requires rationalization of the use of their expensive components, like noble metal catalysts. As such, a catalyst with low noble metal concentration, in which each one of the noble atoms is active, would reach the lowest price possible. Nevertheless, there are no reactivity descriptors outlined for this type of low coordinated supported atoms. Using DFT calculations, we consider three diverse systems as models of single atom catalysts. …
We present a Scanning Tunneling Microscopy (STM) investigation of gold deposited at the magnetite Fe3O4(001) surface at room temperature. This surface forms a reconstruction with (\surd2\times\surd2)R45° symmetry, where pairs of Fe and neighboring O ions are slightly displaced laterally, forming undulating rows with 'narrow' and 'wide' adsorption sites. At fractional monolayer coverages, single Au adatoms adsorb exclusively at the narrow sites, with no significant sintering up to annealing temperatures of 400 °C. The strong preference for this site is possibly related to charge and orbital ord…
The tunnelling anisotropic magnetoresistance (TAMR) effect describes the sensitivity of spin-polarized electron transport to the orientation of the magnetization with respect to the crystallographic axes. As the TAMR effect requires only a single magnetic electrode, in contrast to the tunnelling magnetoresistance effect, it offers an attractive route towards alternative spintronics applications. In this work we consider the TAMR effect at the single-atom limit by investigating the anisotropy of the local density of states in the vacuum above transition-metal adatoms adsorbed on a noncollinear …
