Böttcher et al. Nanoscale Research Letters 2011, 6:214 http://www.nanoscalereslett.com/content/6/1/214 different strengths of interactions (physisorption or chemi- sorption), which appear between the adsorbed molecules and graphene on Ni(111). DFT calculations were used to model different geometries of the adsorbed molecules on top of graphene/Ni(111), and electronic structure calcula- tions were performed for them. The results thus obtained and those of the previous theoretical studies are compared with the present experimental results. The ARPES and XAS studies were performed on the BESSY UE56/2-PGM-1 and UE56/2-PGM-2 beam-lines, and MAX-lab D1011 beam-line, respectively. An ordered set of graphene overlayers was prepared on Ni (111) via thermal decomposition of propene (C3H6) according to the procedure described elsewhere [4-6]. The quality, homogeneity, and cleanliness of the gra- phene/Ni(111) system were verified by means of low- energy electron diffraction and core-level, as well as valence-band photoemission. Water and ammonia were deposited at the partial pressure of p = 5 × 10-8 mbar on the surface of graphene/Ni(111) at 80 K, and the sample was kept at this temperature during spectro- scopic measurements. XAS and XMCD spectra were collected at both Ni L2,3 and C K absorption edges in partial and total electron yield modes with an energy resolution of 80 meV. ARPES experiments were per- formed on experimental station allowing us to obtain 3D data sets of the photoemission intensity I(Ekin,kx,ky), where Ekin is the kinetic energy of the emitted photo- electrons, and kx, and ky are the two orthogonal compo- nents of the wavevector of electron. The energy/angular resolution in ARPES measurements was set to be at 80 meV/0.2°. The base pressure during all the measure- ments was less than 7 × 10-11 mbar. In our DFT studies, the electronic and structural properties of the graphene-substrate system have been obtained using generalized gradient approximation, namely the Perdew-Burke-Ernzerhof (PBE) functional, to the exchange correlation potential. For solving the resulting Kohn-Sham equation, we used the Vienna Ab Initio Simulation Package (VASP) with the projector- augmented wave basis sets [7]. The k-meshes for sam- pling the supercell Brillouin zone are chosen to be as dense as 24 × 24, when folded up to the simple gra- phene unit cell. Plane wave cutoff was set to a value of 875 eV. As was previously found [8] and confirmed in the pre- sent calculations, the most energetically advantageous arrangement is the top-fcc arrangement of carbon atoms on Ni(111) (see Figure 1). For this structure, several high symmetry adsorption positions for molecules are possi- ble. They are T, on-top; B, on-bond; and C, center and are marked by the corresponding capital letters in Figure 1. There are up to 42 and 16 possible configurations of H2O and NH3, respectively, on top of graphene/Ni(111), Page 2 of 7 Figure 1 Geometry of the H2O,NH3/graphene/Ni(111) systems investigated in this study. Graphene layer is arranged in the top- fcc configuration on Ni(111). Adsorbed molecules can be placed in three different highly symmetric adsorption sites: T, on-top; B, on- bond; C, center, with respect to the graphene lattice. Two examples of adsorption are shown: for NH3 in the on-top position with hydrogen atoms directed to the neighboring carbon atoms, and for H2O in the center position with hydrogen atoms directed to the C-C bonds. but in our calculations, the authors restrict the choice to only six arrangements where molecules are placed in the high symmetry positions (T, B, and C) with hydrogen atoms pointing upwards (UP) or downwards (DOWN). Two examples of possible absorption geometries are shown for H2O (C-DOWN–hydrogen atoms are pointed toward the direction of C-C bond) and NH3 (T-UP– hydrogen atoms are pointed toward the direction of the neighboring C atoms) in Figure 1. In these experiments, molecular layers (MLs) of adsorbate with the thicknesses ranging from approximately one third to one fifth of the thickness of ML (corresponding to the dense packing of molecules, when one molecule is placed in every carbon ring) are studied. For simplicity, in the calculations of this study, the concentration of the adsorbed molecules was chosen as 1/3 of ML that corresponds to the (√3 × √3)R30° overstructure with respect to the unit cell of gra- phene (shown in Figure 1 as dashed- and solid-line rhombus, respectively). In order to study the growth modes of water or ammonia, the time sequences of the photoemission maps around the Γ point of the Brillouin zone (sampling angle of ±10° with respect to the normal emission) were recorded. The extracted photoemission intensity map showing the modification of the valence band at the Γ point of the graphene/Ni(111) system upon adsorption of water molecules (t is the deposition time) is shown in Figure 2 (central panel). Photoemission intensity profiles for several time-points demonstrating the main photoe- mission features of spectra [Ni 3d states, graphene π states, and water-induced states (I and II)], as well as intensity profiles as a function of water deposition time