Physisorption of an organometallic platinum complex on silica: an ab initio study

The interaction of trimethyl methylcyclopentadienyl platinum (MeCpPtMe3) with a fully hydroxylated SiO2 surface has been explored by means of ab initio calculations. A large slab model (3 × 3 × 4 supercell) cut out from the hydroxylated β-cristobalite SiO2 (111) surface was chosen to simulate a silica surface. Density functional theory calculations were performed to evaluate the energies of MeCpPtMe3 adsorption to the SiO2 surface. Our results show that the physisorption of the molecule is dependent on both (i) the orientation of the adsorbate and (ii) the adsorption site on the substrate. The most stable configuration was found with the MeCp and Me3 groups of the molecule oriented toward the surface. Finally, we observe that van der Waals corrections are crucial for the stabilization of the molecule on the surface. We discuss the relevance of our results for the growth of Pt-based nanostructured materials via deposition processes such as electron beam-induced deposition.

For most of the deposition processes mentioned above, there is a lack of detailed understanding of the growth mechanism of nanostructures at the molecular level. While for instance in EBID, several Monte Carlo simulations have been performed to study the effects of electron energy, probe size, substrate thickness and deposit composition considering the primary, secondary and backscattered electrons [17,18,19,20,21,22], very little is known about the detailed geometry of adsorption configurations and the possible dissociation processes upon adsorption. If the various deposition processes are to evolve from a set of empirical recipes for producing nanostructures to viable scientific tools for nanofabrication, a complete understanding of the interactions between the substrate, adsorbed precursor molecules, and electrons in the case of EBID, is fundamental and must be developed [4,23,24]. In Ref. [25], a first attempt to investigate the adsorption of tungsten hexacarbonyl (W(CO) 6 ) precursor molecules on a SiO 2 substrate partly modified due to electron irradiation was performed by means of density functional theory (DFT) calculations. In the present work we consider the physisorption process of the more complex molecule MeCpPtMe 3 on a hydroxylated SiO 2 substrate within DFT with and without inclusion of long-range van der Waals (vdW) interactions. This study should serve as the starting point for growth of nanostructures in various deposition processes. SiO 2 is chosen as substrate in our calculations since it is one of the most important substrates in the semiconductor industry, and is widely used for instance in the EBID process.
Physisorption properties have been studied in several systems. For example, Rimola et al. [26] investigated the adsorption of benzene and benzene-1,4-diol on hydrophobic and hydrophilic silica surfaces and found that the adsorption of the aromatic molecules on the hydrophobic silica surface is dictated by vdW interactions and the adsorption energies for the hydrophilic surfaces are almost doubled with respect to the hydrophobic surface due to H-bonding interactions between the substrate and the adsorbate. Mian et al. performed DFT calculations to investigate the catechol adsorption on silica surfaces and indicated that both the hydroxyls and phenylene ring of catechol contribute to its strong adhesion due to hydrogen bonding and vdW interactions [27]. Atodiresei et al. investigated the adsorption mechanism of a single pyridine molecule on Cu(110) and Ag(110) surfaces and found that vdW corrections are very important for the geometry and electronic structure of flat adsorption configurations [28,29]. Our results for MeCpPtMe 3 on SiO 2 show that the adsorption of the molecule is highly sensitive to both (i) the molecule orientation and (ii) the adsorption site on the substrate and we find that only certain geometries are favored in the process. Moreover, inclusion of vdW corrections are crucial for stabilizing the molecule on the surface.
The paper is organized as follows: in the next section the methods used for the DFT calculations are introduced. In Section 3 the electronic properties of the precursor molecule, the substrate as well as the complex molecule-substrate are presented and discussed with special emphasis on the importance of the vdW corrections. Further, we discuss the relevance of our results for the deposition of nanostructures and in Section 4 we provide a summary of our work.

Methods and computational details
Silicon dioxide (SiO 2 ) is a typical polymorphic material with structures ranging from amorphous to various types of crystalline phases. The β-cristobalite crystalline phase and amorphous SiO 2 have a locally similar structure. They have similar densities and refractive indices, and a rather convenient cubic cell. Therefore, β-cristobalite has been frequently used as a model crystal to represent the structure of amorphous SiO 2 [30,31,32,33,34] and will be also considered here as a model substrate.
The β-cristobalite SiO 2 is cubic with eight molecules in the conventional unit cell (Figure 1 (a)). Considering the large size of the precursor molecule MeCpPtMe 3 , we need to find a compromise between computational cost and sufficiently large distances between adsorbates. Thus, a four-layer slab model containing 216 atoms was cut from bulk β-cristobalite (space group F d3m) with the experimental lattice constant 7.16 Å along the [111] direction [25]. We rearranged the resulting structure by adding OH hydroxyl groups to the unsaturated Si atoms exposed at the surface to avoid dangling bond effects. The bottom O atoms resulting from the formation of the surfaces are also saturated with H atoms. In fact, a realistic model for a substrate prepared under nonvacuum conditions is hydroxylated SiO 2 . A vacuum region of approximately 30 Å without considering the adsorbate was placed between slab layers. The geometry is shown in Figure 1 Hydroxyl coverage on silica has been previously measured to be 4.9/nm 2 OH groups at 180-200 • C and 3.6/nm 2 at 300 • C, independent of the structural characteristics [35]. Our model built by a crystalline β-cristobalite [111] facet has a silanol density of 4.5/nm 2 close to that observed on amorphous silica and therefore is a good representation of the experimental environment.
Structure relaxation and electronic properties of the substrate and the complex molecule-substrate were performed in the framework of DFT by using the Vienna ab initio Simulation Package (VASP) [36,37] with a projector augmented wave (PAW) basis set [38,39]. Exchange and correlation effects were treated in the generalized gradient approximation (GGA) in the formulation of Perdew, Burke, and Ernzerhof [40]. The plane wave basis set used to represent the valence electron density was cut off at 400 eV. The Brillouin zone was sampled using a (2 × 2 × 1) Γ-centred mesh. Structural optimizations were performed by minimizing the forces on all atoms to less than 0.01 eV/Å. The two bottom layers, which are expected to be little affected by the adsorption  happening at the surface, were kept fixed in the relaxation process.
In order to compare the calculations of the adsorbed molecule-substrate system where periodic boundary conditions were imposed with those for the isolated molecule in the gas phase, we have also performed calculations for the molecule placed in a slightly distorted cubic cell with a cell parameter of 30 Å. This lengthscale ensures a negligible interaction between the contents of adjacent cells and mimics the properties of the molecule in the gas phase. A slightly distorted cell was used to break the symmetry in the periodic setting. Apart from the number of k-points (a single k-point at Γ was considered for the gas phase), the same parameters were employed for (i) the gas phase calculations (ii) the substrate calculations and (iii) the molecule with substrate calculations.
Van der Waals corrections -also called dispersion corrections-which originate from long-range electron interactions are not captured by the standard DFT. Several approaches have been developed to improve this situation [42,43,44,45]. In our calculations, we consider these effects by using an empirical DFT energy correction scheme (DFT-D) developed by Grimme and implemented in VASP [46]. This implementation has been demonstrated to be very effective for the description of molecular systems such as small molecular adducts, π-stacking, and large complexes where dispersion corrections are relevant [47,48,49].
The dispersion corrected DFT-D energy is calculated by adding an empirical correction E Disp [46] to the Kohn-Sham energy: C ij 6 is a dispersion coefficient for the atom pair ij which is calculated by: where the coefficient C i 6 for atom i is given by C i 6 =0.05N I i p α i , N has values 2, 10, 18, 36, and 54 for atoms from rows one to five of the periodic table, I p is the atomic ionization potential and α are static dipole polarizabilities. R ij denotes the interatomic distance between atoms i and j and s 6 is the global scaling factor for the functional. The term f dmp (R ij ) is a damping function which is given by: The role of the damping function is to scale the force field such as to minimize contributions from interactions within typical bonding distances. Here, R r is the sum of atomic vdW radii. Original values of all atomic and global parameters proposed by Grimme are employed in the present study [46]. The summations are performed over all N atoms in the reference cell and all translations of the unit cell within a cutoff where ∆E ads is the calculated adsorption energy, E system(MCPM+SiO 2 ) corresponds to the total energy of the relaxed system of precursor molecule adsorbed on the substrate, E molecule(MCPM, g) is the total energy of the isolated precursor molecule calculated in the gas phase, and E clean surface(SiO 2 ) is the total energy of the clean hydroxylated SiO 2 substrate.

Isolated precursor molecule
Figure 2 (a) shows the optimized structure of the MeCpPtMe 3 molecule, which has one methyl substituted cyclopentadienyl ring (MeCp) and three methyl ligands (Me 3 ) bound to a central Pt atom. The methylcyclopentadienyl unit is bound to the platinum centre atom in a pentahapto fashion with the typical platinum-carbon distances as found in experiment (2.262 to 2.356 Å) [41]. Table 1 shows selected bond lengths and angles obtained in our calculations compared with experimental data. The agreement between both sets of data is rather good. After relaxation, the distances between the cyclopentadienyl ring carbon and the Pt atom show changes of up to 0.11 Å compared to the experimentally measured distances. The differences for angles between experiment and theory are mostly within 2 • . In order to obtain a first view of how the charge density distributes in the molecule, we have calculated the electronic properties of an isolated molecule with the Gaussian 09 code [50] by considering the standard basis sets. The structure [41] of the isolated precursor molecule MeCpPtMe 3 was first optimized and the resulting structure is consistent with both experimental values and the above GGA calculation for a molecule in the gas phase.
In Figure 2 (b) we show the calculated molecular orbitals for MeCpPtMe 3 . The highest occupied molecular orbital (HOMO) is mostly formed by C 2p-type atomic orbitals from the cyclopentadienyl ring and Pt 5d-type atomic orbitals. The lowest unoccupied molecular orbital (LUMO) is mostly composed of a combination of 2p-type atomic orbitals of C bonded to Pt 5d-type atomic orbitals. Such an orbital configuration indicates that a transition from HOMO to LUMO could happen by charge transfer from the MeCp group to the Me 3 group through Pt. 3.2. Adsorption of MeCpPtMe 3 on the hydroxylated SiO 2 surface Figure 1 shows the structure of bulk β-cristobalite SiO 2 and the employed slab model in this study. This slab has already been relaxed, and the properties analyzed in a previous work [25]. With this slab, a series of adsorption geometry models based on the features of the MeCpPtMe 3 molecule and of the SiO 2 substrate have been evaluated in order to screen for the most stable adsorption configuration. In Figure 3 we show the various configurations. If we consider the molecule as composed of Me 3 and MeCp ligand groups bonding to the central Pt, six different configurations can be considered. In three of them only one of the ligand groups faces the surface (configurations (a)-(c) in Figure 3) and in the other three both of the ligand groups face the surface (configurations (d)-(f) in Figure 3). For each configuration, a set of possible adsorption sites on the substrate are chosen as shown in Figures 4 (a) and (b). For sites 1-5, the orientation of the molecule on the surface is through either the MeCp, Me or Me 3 groups (see Figure 2 (a) and Figure 3 Table 2 lists the calculated adsorption energies where the structure relaxation and the energy calculations were performed without (denoted as E DFT ) and with inclusion of vdW long range interaction effects (denoted as E DFT−D ). We have also included a third column in the table denoted by E DFT * which contains the DFT energy contributions to E DFT−D (i.e. vdW energy corrections have been substracted from E DFT−D ).
In order to analyze these energies, we have plotted in Figure 5  lead to variations in the adsorption energy between 32 and 232 meV. The most stable configuration is significantly modified when vdW corrections are included. In fact, the effect of vdW forces to the weak bonding of MeCpPtMe 3 to a fully hydroxylated SiO 2 surface is to bring the molecule closer to the surface. If we consider the centered Si from the substrate as the topmost Si plane location, the distance between the Pt atom and this Si plane for different configurations in the DFT-D calculation is shown in Figure 5 (b). As we can see, the difference between various configurations follows a similar trend as the adsorption energy calculated in DFT-D ( Figure 5 (a)). The vdW correction brings the adsorbate molecule closer to the substrate when both MeCp and Me 3 groups face the surface, thus enhancing the interaction at the interface. According to Xue et al. [41], it is difficult to see how the platinum can contact the surface in the ground state of the molecule so that some dislocation of the η5-MeCp ring to lower hapticity is required before the platinum atom of the hydrocarbon complex may interact with the surface atoms. In our case, the distance between Pt and the substrate in the geometry where both Me 3 and MeCp groups face the surface is lower than for other orientations (Figure 5), indicating that this configuration enhances Pt-substrate interaction strength.
As shown in Table 2 and Figure 5, the molecule prefers to stay on the surface with both Me 3 and MeCp ligand groups oriented towards the surface (see Figure 3 (d)-(f)) while the orientation with only one of the ligand groups oriented towards the surface is about 154 to 310 meV less stable (see Figure 3 (a)-(c)). Note, that the O Me 2 −MeCp configuration on site 8 is only 19 meV higher in energy, making this structure a close runner-up to the optimal configuration O Me 2 −Cp on site 7; in fact both structures are rather similar and the energies are difficult to distinguish with the precision that we could achieve in our calculations.
In Figure 6 we show the most stable adsorption configuration calculated with inclusion of vdW corrections found in our work with the MeCp group oriented perpendicular to the surface and coupled with one edge of the aromatic ring to the substrate (O Me 2 −Cp ). After relaxation of the molecule-substrate complex, we observe no significant structural deformation of the precursor molecule. The optimized distances between the topmost O atoms on the substrate and the closest atoms of the MeCpPtMe 3 molecule are shown in Figure 6 (a). The spacing is significantly larger than typical covalent or hydrogen bond distances. The structural properties indicate that the precursor molecule is indeed physically adsorbed on the fully hydroxylated SiO 2 surface without formation of covalent bonds with the substrate.
From the calculated binding energies at different sites, we can estimate the surface diffusion barriers, which determine the diffusion ability along different directions [51]. After adsorption, the C-C and C-H bonds of the molecule are slightly weakened, whereas the Pt-C bonds of the Pt-Me 3 group are slightly shortened. The distance between Pt and the MeCp ring are significantly decreased with the length between Pt and C atoms of the MeCp ring shortened by 0.068-0.133 Å. The surface region far from the adsorbate shows almost no changes. However, the O-H bond of the surface silanol and some Si-O bonds close to the adsorbate are weakened after adsorption. This observation indicates that the precursor molecule is loosely bonded to the substrate. We found that Pt d yz and d z 2 orbitals and the C p y orbitals (the orbital notation is given in the local reference frame of the molecule where the xy plane is defined parallel to the MeCp group) play an important role in the interaction between the MeCpPtMe 3 adsorbate and the surface.
The orbital wave function of the HOMO precursor molecule (Figure 2 (b)) indicates that the O Me 2 −Cp orientation has the largest charge density near the substrate orbitals and can thus lead to more interaction than other orientations. This explains why this is the most favorable configuration on the surface. In contrast, the small contribution of the Me from the MeCp ligand to the HOMO orbital explains why the configuration where this ligand group faces the substrate corresponds to the most unstable adsorption configuration (the most unfavorable adsorption energy found in this work (see Table 2). In previous studies on adsorption of molecules containing conjugated π electrons in aromatic rings like cyclopentene (c-C 5 H 8 ) on Ni (111) [52], cyclopentadienyl anion (c-C 5 H 5 − ) on Ni (111) [53] or pyridine on Cu (110) and Ag (110) surfaces [28], the geometric orientation in equilibrium was found to be the one where the cyclic hydrocarbons orient nearly parallel to the surface. In those cases the π systems contribute to the interaction between adsorbate and substrate. This is not the situation in the present more complicated MeCpPtMe 3 precursor molecule. In our case, the p z states of C from the Cp ring are located at about -5 eV deep down in the valence band.
In Fig. 7 we show the total density of states (DOS) of the preferential configuration of MeCpPtMe 3 on SiO 2 as well as the partial contributions of the adsorbate. Results are shown for calculations including vdW corrections. The highest molecular level of the MeCpPtMe 3 adsorbate lies in the gap of the substrate, which pins the Fermi level close to the valence band. The largest contribution at the Fermi level are Pt and MeCp states. We observe that the DOS of the SiO 2 substrate shows only minor modifications with respect to the DOS of the free SiO 2 substrate (compare with Fig. 6 (a) from Ref. [25]). These results confirm the weak interaction between the adsorbate molecule and the SiO 2 substrate.
We can now relate our results to some deposition processes like EBID. Electron irradiation of adsorbed MeCpPtMe 3 produces hydrogen and methane as the only volatile products [3], and the methane could be associated with cleavage of Pt-CH 3 (methyl from Me 3 ) or C-CH 3 (methyl from MeCp). Figure 7 shows that hydrocarbons that contribute to the valence band states near the Fermi level are mainly located in the Me 3 group and the Cp ring of the molecule. This indicates that the methyl on the Me 3 group is more active than that of the MeCp group, therefore theoretically they will be easier to dissociate when external energy is applied. This is in agreement with recent experimental work where the same precursor molecule decomposition on a gold substrate in an EBID process has been investigated with X-ray photoelectron spectroscopy (XPS) and mass spectrometry (MS) [3]. The authors of Ref. [3] find that trimethyl-methylcyclopentadienyl platinum adsorbed on Au substrates at 180 K undergoes electron stimulated decomposition mediated by Pt-CH 3 bond cleavage instead of C-CH 3 .

Summary
Our calculations based on DFT show that the MeCpPtMe 3 molecule is weakly bonded to the fully hydroxylated SiO 2 surface without deformation. The calculated adsorption energy is found to be -0.669 eV where the molecule is located at a nearly hollow site, and the distance of Pt to the topmost -OH surface silanol group is 2.87 Å. Contrary to the adsorption of molecules containing conjugated π electrons in aromatic rings, the preferential configuration of MeCpPtMe 3 corresponds to having the MeCp and Me 3 groups oriented towards the surface. We find that the adsorption is more dependent on the orientation of the adsorbate with respect to the surface than the adsorption site. We also observe that the optimal configuration of the molecule corresponds to a minimum in the Pt-substrate distance, indicating that the interaction between platinum and substrate is maximized in the lowest energy configuration. Moreover, inclusion of vdW corrections contribute to the stabilization of the molecule on the surface. Our calculations provide a theoretical insight on the interfaces between MeCpPtMe 3 and a SiO 2 substrate, which is essential for the growth processes of deposits.