The control of material assembly on the nano-meter scale [1–4] as well as their self-assembly [5–7] are the two extremes of the most intensely studied subjects in the fields of nano-science and nano-technology. Self-assembly is characterized by high yields but often chaotic organization of nano-particles, whereas absolute control leads to accurate positioning, usually at the expense of yield. Controlled or tuneable self-assembly  balances the two extremes and is the most pursued subject for attainment of controlled properties and, at the same time, maintain mass production.
As the dimensions of metal particles decrease, novel properties different from those of the bulk counterparts are observed and ultimately resulted in the miniaturization of electronic devices . Shrinking the size of devices drastically leads to the manifestation of unexpectedly enhanced electronic, optical, magnetic, chemical, and geometric properties [6, 10, 11].
On relatively inert substrates, such as graphite, many nano-structures can be fabricated in a nearly free-standing state by various deposition techniques such as thermal evaporation [12–14]. These structures can be characterized by popular analytical techniques such as scanning probe microscopy and X-ray photoelectron spectroscopy (XPS).
On a fundamental level, there are two recognized design strategies for the fabrication of supported nano-scale materials. These are classified as top-down approach, which entails various lithographic methods (working from the macroscopic to the nano-scopic), and bottom-up approach which involves the self-assembly of atoms or molecules on the surface into large structures [9, 11]. This, for example, can be done by surface segregation. In general terms, bottom-up assembled nano-scale structures could provide unparalleled processing speed and size reductions, and hold the promise of powering future electronic devices. This approach totally opens up new opportunities beyond the limits of top-down technology through self assembly [9, 15, 16].
Highly oriented pyrolytic graphite (HOPG) has been extensively used as a prototypical inert and atomically flat model system in many nucleation and growth studies of silver (Ag) clusters and islands [11, 17–20]. The use of HOPG as a substrate is advantageous in a sense that metallic properties of HOPG allow electron spectroscopy and microscopy experiments to be conducted without surface charging problems. For instance, atomic resolution scanning tunneling microscopy (STM) images can be easily obtained on HOPG.
Studies on properties of deposited silver nano-clusters and particles are not only of fundamental interest but also related to various technologically important fields such as catalysis, electronic devices, and gas sensors [21, 22]. These metal clusters can be regarded as the precursors to a new generation of nano-structured materials and devices [10, 13, 23].
In the field of catalysis, ordered arrays of metal clusters show catalytic properties dependent upon cluster size and shape. The reactivity and catalytic activity can be very dependent upon geometry arrangement and electronic structure of the supported cluster [2, 6]. STM is a very promising tool to study the supported metal clusters as it gives the complementary information about the particle/support morphology.
The nucleation and growth dynamics of Ag particles on an inert HOPG substrate is generally portrayed as in a three-dimensional (3-D) islanding mode (Volmer-Weber type of growth) which is often thermodynamically favored over uniform films or random-distributed adatoms as established by STM [23, 24].
This article presents an investigation by STM and XPS of individual self-assembled Ag nano-clusters grown by thermal evaporation of Ag atoms on HOPG surfaces at room temperature. Density function theory (DFT) ab initio calculations are conducted to determine the site selective adsorption of Ag on the hexagonal graphene layer.
Noting that the experimental variables that influence the dynamics of Ag nano-particles are temperature, deposition rate and the residual vacuum [20, 25], the present experiments were carried out in two different ultra-high vacuum chambers. The first chamber was equipped with a Ag effusion cell, Omicron variable temperature (VT) STM (Omicron NanoTechnology GmbH, Taunusstein, Germany), low energy electron diffraction and Auger electron spectroscopy (AES) optics in UHV.
Before deposition, clean HOPG (0001) samples were prepared by cleaving in air and immediately transferring substrate into the VT-STM UHV chamber through a load lock. The cleanness of HOPG was confirmed by STM and AES prior to evaporation. Silver was evaporated by thermal evaporation (base pressure < 10-10 Torr) of the solid material (99.9999% purity) from a Knudsen cell which gives a flux of atoms onto the HOPG substrate maintained at room temperature. The average deposition rate was 0.1 monolayer/sec and constitute a current flux of 1.04 μA that was allowed to flow for approximately 5 s. The flux of Ag atoms was kept constant by controlling the emission current between the W filament and the Ag source. Nano-meter-size Ag particles were spontaneously formed by diffusion and aggregation of the deposited material on the surface. AES confirmed the presence of Ag on the carbon dominated surface after growth. The samples were then studied by STM, operated in the constant current mode using electrochemically etched W tips as probes. Height, as a function of lateral position, represents the surface image. The STM-image scales were calibrated using Si(111)-7 × 7 and HOPG.
Electronic and chemical properties of deposited Ag clusters were studied using the second UHV chamber equipped with a XPS spectrometer. The Ag on HOPG samples was mounted in a PHI 5400 XPS vacuum chamber with a base pressure of < 8 × 10-9 Torr. Angle-resolved XPS was performed using a non-monochromatic magnesium Kα source (1,253.6 eV) and a concentric hemispherical sector analyzer with pass energy of 178.95 eV and a scan rate of 5 eVs-1. The X-ray source was operated at a power of 300 W at various electron take-off angles. The binding energy scale was calibrated with the Cu 3p3/2 (933 eV) and Au 4f7/2 (84 eV) peaks.
Within the framework of density function theory, density functional calculations were carried out using the generalized gradient approximations/PBE  exchange correlation potential embedded within the DMol3 . The interaction between the ionic cores and the valence electrons is modeled using the ultra-soft pseudopotentials of Vanderbilt .
Energetics and electronic properties, density of states and band structures were computed for the pristine (pure) graphene surface, silver adsorbed on the hollow site, bridge site of the hexagonal ring as well as on the top site of the carbon atom in the hexagon of the 33-atom graphene sheet. A kinetic energy cutoff of 350 eV was employed, and this choice gave fully converged calculations. Brillouin zone sampling was done using the 2 × 2 × 1 special k-point mesh employing the Monkhorst-Pack scheme .