Scalar-relativistic DFT-GGA has been used to study adsorption of water in molecular and dissociative configurations on delta-Plutonium (111) surface. In molecular state, water is physisorbed in an almost flat-lying orientation at a one-fold coordinated on-top site. The interaction of the water 1b1 orbital and the Pu-6d orbital provides the stability of water on the surface, implying that the Pu-5f electrons remain chemically inert. The co-adsorption cases of partially dissociated and fully dissociated products at the three-fold hollow sites yield chemisorption, coupled with rumpling of the surface layer and delocalization of the Pu-5f electrons and formation of strong ionic bonds.
Adsorption of carbon, nitrogen, and oxygen on the (111) surface of delta-Plutonium has been studied within the framework of density functional theory using the full-potential linear augmented plane wave plus local basis (FP-LAPW+lo) method. All adatoms prefer to bind at the higher coordinated hollow sites, with the chemisorption energies for C, N, and O being 6.539 eV, 6.714 eV, and 8.2 eV respectively. The work function and the surface Pu magnetic moments respectively increased and decreased in all cases upon chemisorption. The partial charges inside the muffin tins spheres, difference charge…
Hybrid density functionals, which replaces a fraction of density functional theory (DFT) exchange with exact Hartree-Fock (HF) exchange, have been used to study the structural, magnetic, and electronic properties of delta-Plutonium. The fractions of exact Hartree-Fock exchange used were 25%, 40%, and 55%. Compared to the pure PBE functional, the lattice constants expanded with respect to the experimental value when the PBE-HF hybrid functionals were applied. A non-magnetic ground state was realized for 55% HF contribution; otherwise the ground state was anti-ferromagnetic. The 5f electrons ten…
CO adsorption on Cu(111) and Cu(001) surfaces has been studied within ab-initio density functional theory (DFT). The structural, vibrational and thermodynamic properties of the adsorbate-substrate complex have been calculated. Calculations within the generalized gradient approximation (GGA) predict adsorption in the threefold hollow on Cu(111) and in the bridge-site on Cu(001), instead of on-top as found experimentally. It is demonstrated that the correct site preference is achieved if the underestimation of the HOMO-LUMO gap of CO characteristic for DFT is correct by applying a molecular DFT+…
Oxygen molecule adsorptions on a Pu (100) surface have been studied in detail, using the generalized gradient approximation to density functional theory. Dissociative adsorption with a layer by layer alternate spin arrangement of the plutonium layer is found to be energetically more favorable compared to molecular adsorption. Hor2 approach on a bridge site without spin polarization was found to the highest chemisorbed site with energy of 8.787 eV among all the cases studied. The second highest chemisorption energy of 8.236 eV, is the spin-polarized Hor2 or Ver approach at center site. Inclusio…
DFT calculation of various atomic species on graphene sheet is investigated as prototypes for formation of nano-structures on carbon nanotube (CNT) wall. We investigate computationally adsorption energies and adsorption sites on graphene sheet for a lot of atomic species including transition metals, noble metals, nitrogen and oxygen, using the DFT calculation as a prototype for CNT. The suitable atomic species can be chosen as each application from those results. The calculated results show us that Mo and Ru are bounded strongly on graphene sheet with large diffusion barrier energy. On the oth…
The adsorption geometry of 1,3,5-tris(4-mercaptophenyl)benzene (TMB) on Cu(111) is determined with high precision using two independent methods, experimentally by quantitative low energy electron diffraction (LEED-I(V)) and theoretically by dispersion corrected density functional theory (DFT-vdW). Structural refinement using both methods consistently results in similar adsorption sites and geometries. Thereby a level of confidence is reached that allows deduction of subtle structural details such as molecular deformations or relaxations of copper substrate atoms.
The electronic structure modifications of WSe2 upon NO2-adsorption at room and low temperatures were studied by means of photoelectron spectroscopy. We found only moderate changes in the electronic structure, which are manifested as an upward shift of the WSe2-related bands to the smaller binding energies. The observed effects are modelled within the density functional theory approach, where a weak adsorption energy of gas molecules on the surface of WSe2 was deduced. The obtained experimental data are explained as a valence bands polarisation effect, which causes their energy shift depending …
First-principles DFT levels of calculations have been carried out in order to study the structural stability and electronic properties of hydrogen passivated graphene (H-graphene) clusters. Two different shaped clusters, rectangular and circular, consisting of 6 to 160 carbon atoms and hydrogen termination at the zigzag boundary edges have been studied. The relative stability of rectangular shaped cluster consisting 96 C-atoms found to be 1.5% greater than that of circular shape cluster consisting same number of C-atoms. In comparing circular and rectangular cluster containing same number of C…
We present a comparative Density Functional Theory (DFT) and Density Functional Tight Binding (DFTB) study of geometries and electronic structures of arginine (Arg), arginine adsorbed on the anatase (101) surface of titania in several adsorption configurations, and of an arginine-rich cell penetrating peptide TAT and its adsorption on the surface of TiO2. Two DFTB parameterizations are considered, tiorg-0-1/mio-1-1 and matsci-0-3. While there is good agreement in the structures and relative energies of Arg and peptide conformers between DFT and DFTB, both adsorption geometries and energies are…
Density functional theory $(DFT)$ studies show that doping of $3d TM$ atoms into $Mg_4^{0,+} (TMMg_3^{0,+})$ can alter the endothermic nature of molecular hydrogen adsorption on bare $Mg_4^{0,+}$. $H_2$ adsorption on $TMMg_3^{0,+}$ clusters depends on the $TM(3d)$ orbital contribution to the frontier molecular orbitals of the clusters. In $H_2TMMg_3^{0,+}$ complexes, $H_2$ is adsorbed through donation and back donation of electronic charges with $TMMg_3^{0,+}$ clusters. $H_2$ binding energy is the maximum for $NiMg_3$ (-0.76 eV) and $FeMg_3^+$ (-0.48 eV) among the neutral and cationic $TMMg_3$…
We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the gold-gold distances within the relaxed systems. Consequently, we find that by using different types of LC…
Recently, it was experimentally shown that the performance and thermal stability of the perovskite MAPbI$_3$ were improved upon the adsorption of a molecular layer of caffeine. In this work, we used a hybrid methodology that combines Uncoupled Monte Carlo (UMC) and Density Functional Theory (DFT) simulations to carry out a detailed and comprehensive study of the adsorption mechanism of a caffeine molecule on the surface of MAPbI$_3$. Our results showed that the adsorption distance and energy of a caffeine molecule on the MAPbI$_3$ surface are 2.0 Å and -0.3 eV, respectively. The caffeine/MAPbI…
In this paper, we investigate the adsorption of water monomer on fluorinated graphene using state-of-the-art first principles methods within the framework of density functional theory (DFT). Four different methods are employed to describe the interactions between water and the carbon surface: The traditional DFT calculations within the generalized gradient approximation (GGA), and three types of calculations using respectively the semi-empirical DFT-D2method, the original van der Waals density functional (vdW-DF) method, and one of its variants. Compared with the adsorption on pristine graphen…
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…
Using first-principles calculations based on density-functional theory (DFT) we investigated the effects of the van der Waals (vdW) interactions on the structural and electronic properties of anthracene and pentacene adsorbed on the Ag(111) surface. We found that the inclusion of vdW corrections strongly affects the binding of both anthracene/Ag(111) and pentacene/Ag(111), yielding adsorption heights and energies more consistent with the experimental results than standard DFT calculations with generalized gradient approximation (GGA). For anthracene/Ag(111) the effect of the vdW interactions i…
Approximate semi-local density functional theory (DFT) is known to underestimate surface formation energies yet paradoxically overbind adsorbates on catalytic transition-metal oxide surfaces due to delocalization error. The low-cost DFT+U approach only improves surface formation energies for early transition-metal oxides or adsorption energies for late transition-metal oxides. In this work, we demonstrate that this inefficacy arises due to the conventional usage of metal-centered atomic orbitals as projectors within DFT+U. We analyze electron density rearrangement during surface formation and …
The DFT/vdW-WF method, recently developed to include the Van der Waals interactions in Density Functional Theory (DFT) using the Maximally Localized Wannier functions, is applied to the study of the adsorption of rare-gas atoms (Ne, Ar, Kr, and Xe) on the Cu(111) and Pb(111) surfaces, at three high-symmetry sites. We evaluate the equilibrium binding energies and distances, and the induced work-function changes and dipole moments. We find that, for Ne, Ar, and Kr on the Cu(111) surface the different adsorption configurations are characterized by very similar binding energies, while the favored …
Biomass compounds adsorbed on surfaces are challenging to study due to the large number of possible species and adsorption geometries. In this work, possible intermediates of erythrose, glyceraldehyde, glycerol and propionic acid are studied on the Rh(111) surface. The intermediates and elementary reactions are generated from first 2 recursions of a recursive bond-breaking algorithm. These structures are used as the input of an unsupervised Mol2Vec algorithm to generate vector descriptors. A data-driven scheme to classify the reactions is developed and adsorption energies are predicted. The lo…
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…
The adsorption of 1,4-benzenediamine (BDA) on the Au(111) surface and azobenzene on the Ag(111) surface is investigated using density functional theory (DFT) with a non-local density functional (vdW-DF) and a semi-local Perdew-Burke-Ernzerhof (PBE) functional. For BDA on Au(111), the inclusion of London dispersion interactions not only dramatically enhances the molecule-substrate binding, resulting in adsorption energies consistent with experimental results, but also significantly alters the BDA binding geometry. For azobenzene on Ag(111), the vdW-DF produces superior adsorption energies compa…
We have combined scanning tunneling microscopy with inelastic electron tunneling spectroscopy (IETS) and density functional theory (DFT) to study a tetracyanoethylene monolayer on Ag(100). Images show that the molecules arrange in locally ordered patterns with three non-equivalent, but undeterminable, adsorption sites. While scanning tunneling spectroscopy only shows subtle variations of the local electronic structure at the three different positions, we find that vibrational modes are very sensitive to the local atomic environment. IETS detects sizeable mode frequency shifts of the molecules …
Band Structure Modulation of ZrO2 Nanoparticles for Control of CO Adsorption Properties: A Combined Density Functional Theory - Density Functional Tight Binding Study
School of Materials and Chemical Technology, Institute of Science Tokyo（东京科学大学材料化学技术学院）；RIKEN Center for Computational Science（理化学研究所计算科学中心）；Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada（加查马达大学数学与自然科学学院化学系）
Vacancies in graphene present sites of altered chemical reactivity and open possibilities to tune graphene properties by defect engineering. The understanding of chemical reactivity of such defects is essential for successful implementation of carbon materials in advanced technologies. We report the results of a systematic DFT study of atomic adsorption on graphene with a single vacancy for the elements of rows 1 to 6 of the Periodic Table of Elements (PTE), excluding lanthanides. The calculations have been performed using PBE, long-range dispersion interaction-corrected PBE (PBE+D2 and PBE+D3…
B$_5$Se this work we investigate the Li adsorption properties of a hybrid 2D material, namely monolayer B5Se with first principles calculations. 2 dimensional B$_5$Se was found to have a distorted hexagonal structure with five B atoms and one Se atom at the vertices of each hexagon. The density functional theory (DFT) calculations are performed with the generalized gradient approximation (GGA) and Perdew-Burke-Ernzerhoff (PBE) exchange correlation functional. The results were inclusive of van der Waals corrections with Grimmes DFT-D2 scheme. Electrode performance metrics, as the most preferred…
Understanding the interaction of organic molecules with TiO2 surfaces is important for a wide range of technological applications. While density functional theory (DFT) calculations can provide valuable insight about these interactions, traditional DFT approaches with local exchange-correlation functionals suffer from a poor description of non-bonding van der Waals (vdW) interactions. We examine here the contribution of vdW forces to the interaction of small organic molecules (methane, methanol, formic acid and glycine) with the TiO2 (110) surface, based on DFT calculations with the optB88-vdW…
Sodium, magnesium and aluminum adatoms, which, respectively, possess one, two and three valence electrons in terms of 3s, $3s^2$, and ($3s^2$, 3p) orbitals, are very suitable for helping us understand the adsorption-induced diverse phenomena. In this study, the revealing properties of metal (Na/Mg/Al)-adsorbed graphene systems are investigated by mean of the first-principles method. The single- and double-side chemisorption cases, the various adatom concentrations, the hollow/top/valley/bridge sites, and the buckled structures are taken into account. The hollow and valley adsorptions, which, r…
Chemical adsorption of the species at semiconductor surfaces is analyzed showing the existence of the two contributions to adsorption energy: bond creation and charge transfer. It is shown that the energy of quantum surface states is affected by the electric field at the surface, nevertheless the potential contribution of electron and nuclei cancels out. The charge transfer contribution is Fermi level independent for pinned surfaces. Thus for Fermi level pinned at the surface, the adsorption energy is independent on the Fermi energy i.e. the doping in the bulk. The DFT simulations of adsorptio…
Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions. Herein we present results from quantum Monte Carlo (QMC) for water and meth…
We have studied the adsorption of bisphenol-A-polycarbonate (BPA-PC) on the alpha-Al2O3(0001) surface using density-functional theory (DFT) with van der Waals (vdW) corrections. The BPA-PC polymer can be divided into its chemical fragments which are phenylene, carbonate and isopropylidene groups. We have calculated the adsorption energy and geometry of the BPA-PC segments that consist of two to three adjacent groups of the polymer. Our DFT results show that the adsorption is dominated by the vdW interaction. It is also important to include the interaction of nearest-neighbor groups in order to…
The band gap of periodically-doped graphene with hydrogen is investigated. It is found through a tight-binding model (TB) that for certain periodicities, called here NGPs (non-gap periodicities), no gap is opened at the Dirac point. This result is confirmed by Density Functional Theory (DFT) calculations. DFT results show that a tiny gap is opened for NGPs due to exchange effects, not taken into account in the TB model. However, this tiny gap is one or two orders of magnitude smaller than the gap opened for other periodicities different from NGPs. This finding opens up a new path for band gap …
For carbon-based materials, in contrast to metal surfaces, the relationship between strain and reactivity is not yet established, even though there are literature reports on strained graphene. Knowledge of such relationships would be extremely beneficial for understanding the reactivity of graphene-based surfaces and finding optimisation strategies which would make these materials more suitable for targeted applications. Here we investigate the effects of compressive and tensile strain (up to +/-5%) on the structure, electronic properties and the reactivity of pure, N-doped and P-doped graphen…
Atomic and electronic structures of TiO_2(110) surface with possible adsorptional, substitutional and interstitial Au or Pt elemental impurities at full and one-sixth monolayer concentrations were investigated by density functional theory calculations using the projector augmented wave approach within the plane wave method. Relative thermodynamic stabilities of such phases have been discussed by means of their surface free energies. Our results suggest that tunable photocatalytic activity can be achieved on Pt atom admixed rutile (110) surface at low coverages.
Semiconducting oxides with reducible cations are ideal platforms for various functional applications in nanoelectronics and catalysts. Here we report an ultrathin monolayer alpha-MoO3 where tunable electronic properties and different gas adsorbing behaviors upon introducing the oxygen vacancies (VO). The unique property of alpha-MoO3 is that it contains three different types of oxygen atoms occupying three Wyckoff sites that are absent in other low-dimensional oxides and provides rich electronic hybridized states. The presence of VO triggers intermediate state in the gap at ~0.59 eV below the …
Adsorption geometry and stability of organic molecules on surfaces are key parameters that determine the observable properties and functions of hybrid inorganic/organic systems (HIOSs). Despite many recent advances in precise experimental characterization and improvements in first-principles electronic structure methods, reliable databases of structures and energetics for large adsorbed molecules are largely amiss. In this review, we present such a database for a range of molecules adsorbed on metal single-crystal surfaces. The systems we analyze include noble-gas atoms, conjugated aromatic mo…
Structural and electronic properties comparison between anatase, rutile and monoclinic TiO2(B) titania polymorphs in bulk and related nanostructures simulated by two-dimensional slabs has been performed by means of density functional theory calculations. TiO2(B) was included due to experimental results where it appears as a metastable phase during thermal annealing of low content sodium layered titanate nanostructures obtained via hydrothermal synthesis. Band gaps and surface energies are discussed confronting results obtained by Plane Waves (PW) and Localized Basis Set methods (LCNAO), observ…
We show that a simple first-principles correction based on the difference between the singlet-triplet CO excitation energy values obtained by DFT and high-level quantum chemistry methods yields accurate CO adsorption properties on a variety of metal surfaces. We demonstrate a linear relationship between the CO adsorption energy and the CO singlet-triplet splitting, similar to the linear dependence of CO adsorption energy on the energy of the CO 2$π$* orbital found recently {[Kresse {\em et al.}, Physical Review B {\bf 68}, 073401 (2003)]}. Converged DFT calculations underestimate the CO single…
The effect of vacancy and water adsorption on the electronic structure of semiconducting 2D trichalcogenide material CrPX$_3$ (X: S, Se) is studied using state-of-the-art density functional theory (DFT) approach. It is found that chalcogen vacancies play a minor role on the electronic structure of CrPX$_3$ in the vicinity of the Fermi level leading to the slightly reduced band gap for these materials, however, inducing strongly localised defect states which are placed in the energy gap formed by the valence band states. Our DFT calculations show that the interaction of water molecules with CrP…
We employ first-principles calculations to study the mechanical, geometrical, electronic and magnetic properties of Fe atom embedded s-triazine ($\mathrm{Fe}$@${\mathrm C_6}{\mathrm N_6}$) system under the influence of external environment. Our results show that the binding energy of $\mathrm{Fe}$@${\mathrm C_6}{\mathrm N_6}$ can be modulated by an applied tensile deformation and perpendicular electric field. The non-magnetic semiconducting property of pure s-triazine sheet (${\mathrm C_6}{\mathrm N_6}$) is found to change upon embedding of Fe atom in the porous site of the sheet. It is reveal…
The DFT/vdW-WF2s1 method based on the generation of localized Wannier functions, recently developed to include the van der Waals interactions in the Density Functional Theory and describe adsorption processes on metal surfaces by taking metal-screening effects into account, is applied to the case of the interaction of Xe with noble-metal surfaces, namely Ag(111), Au(111), and Cu(111). The study is also repeated by adopting the DFT/vdW-QHO-WF variant relying on the Quantum Harmonic Oscillator model which describes well many-body effects. Comparison of the computed equilibrium binding energies a…
It is commonly believed that organic molecules are physisorbed on the ideal non-polar surfaces of wide band gap insulators with limited variation of the electronic properties of the adsorbate molecule. On the basis of first principles calculations within density functional theory (DFT) and $GW$ approximation, we show that this is not generally true. We find that the molecular frontier orbitals undergo significant changes when a hydroxy acid (here we chose gluconic acid) is adsorbed on MgSO$_4$$\cdot$H$_2$O(100) surface due to the complex interaction between the molecule and the insulating surf…
Using density-functional theory (DFT), we investigate the selectivity of adsorption of CO2 over N2 and CH4 on planar-type B clusters, based on our previous finding of strong chemisorption of CO2 on the B10-13 planar and quasiplanar clusters. We consider the prototype B8 and B12 planar-type clusters and perform a comparative study of the adsorption of the three molecules on these clusters. We find that, at room temperature, CO2 can be separated from N2 by selective binding to the B12 cluster and not to the B8 cluster. Selective adsorption of CO2 over CH4 at room temperature is possible for both…
It is shown that adsorption energy at semiconductor surfaces critically depends on the charge transfer to or from the adsorbed species. For the processes without the charge transfer, such as molecular adsorption of closed shell systems, the adsorption energy is determined by the bonding only. In the case involving charge transfer, such as open shell systems like metal atoms or the dissociating molecules, the energy attains different value for the Fermi level differently pinned. The DFT simulation of adsorption of ammonia at hydrogen covered GaN(0001) confirms these predictions: the molecular a…
By means of vibrational spectroscopy and density functional theory (DFT), we investigate CO adsorption on phosphorene-based systems. We find stable CO adsorption at room temperature on both phosphorene and bulk black phosphorus. The adsorption energy and vibrational spectrum have been calculated for several possible configurations of the CO overlayer. We find that the vibrational spectrum is characterized by two different C-O stretching energies. The experimental data are in good agreement with the prediction of the DFT model and unveil the unusual C-O vibrational band at 165-180 meV, activate…
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 …
In ceria-based catalysis, the shape of the catalyst particle, which determines the exposed crystal facets, profoundly affects its reactivity. The vibrational frequency of adsorbed carbon monoxide (CO) can be used as a sensitive probe to identify the exposed surface facets, provided reference data on well-defined single crystal surfaces together with a definitive theoretical assignment exist. We investigate the adsorption of CO on the CeO2(110 and (111) surfaces and show that the commonly applied DFT(PBE)+U method does not provide reliable CO vibrational frequencies by comparing with state-of-t…
Recent experiments on the silicon terminated $3\times 2$ SiC(100) surface indicated an unexpected metallic character upon hydrogen adsorption. This effect was attributed to the bonding of hydrogen to a row of Si atoms and to the stabilization of a neighboring dangling bond row. Here, on the basis of Density-Functional calculations, we show that multiple-layer adsorption of H at the reconstructed surface is compatible with a different geometry: besides saturating the topmost Si dangling bonds, H atoms are adsorbed at rather unusual sites, \textit{i.e.} stable bridge positions above third-layer …
