Theoretical studies of Pd metal deposition on the √3×√3 4-mercaptopyridine self-assembled monolayer

Density Functional Theory Study of Pd Aggregation on a Pyridine‐Terminated Self‐Assembled Monolayer

“…Al ower barrieri sc omputed for the dimerisation when there is one Pd atom intercalated into between the pyridine rings (Figure 6b). The overall process was divided into two segments, i) the Pd diffusion from the on-top- Ns ite into between the pyridine rings, and ii)the Pd 2 dimer formation.T he energetic barrier for the Pd intercalation is approximately 70 meV,w hich agrees with the previousr eport of very low Pd diffusion barrier for the Py0-Aus ystem with ap readsorbed Pd atom in between the rings, [30] although in our case, the initial intercalated Pd atom is below the Np lane. In the second segment,w here the dimerisationo ccurs,ahigher barriero f0 .25 eV is computed.…”

“…It is quite likely that N-bound Pd atoms (or smallerc lusters, see below) will be involved in this process. The energy difference between Pd atoms adsorbed via either Na toms or p-systems of the pyridine could be critically important for the kinetics of diffusion of metal atoms towards cluster formation after discharge.B ased on the above calculations, which show ac lear preference for Pd intercalation (DE = À0.55 eV), diffusiono ft he metal atoms on the PyP1 SAM seems ar ather hindered process, (although even higher barriers between 0.7 eV and1 .6 eV have been reported fors ingle Pd atoms, free or hydrated, on Py0 SAM [30,31] ). In these structures, Pd atoms are well separated and, therefore, have little interaction (Figure 3c).…”

“…Ta king the energetically favoured structure of the PyP1 SAM with ah erringbone packing of planar molecules, the structure involves two Pd atoms per unit cell, that is, a1:1 molecule/Pd ratio. Noting that the presence of solvent molecules has been demonstratedt op revent the metal penetratingt he SAM [31] and also reduce the Pd diffusion barrieri nP y0, [30,31] one H 2 Om olecule per Pd was added to mimict he aqueouse nvironment of the experiments. From model calculations on isolated, neutral [Pd(H 2 O) n ]a nd Pd(py)(H 2 O) n clusters (py = pyridine, see the Supporting Information for details), we confirmed that the neutralP d(py) moiety preferentially binds one additional water molecule (i.e., n = 1) in al inear geometry,s imilar to the preferred coordination mode of the isoelectronic Ag + .…”

“…It should be noted, however,t hat the combined Pd-H 2 Oa nd H 2 O-H 2 Oi nteractions are substantial contributions. We note that direct comparison of theser esultsw ith those of Keith andJ acob [30,31] is difficult because of the different nature of the substrates (Py0 vs. PyP1) and extento fs olvation (most of Keith andJ acob's calculations were performed without water). The calculations agree that Pd 0 should preferentially bind in between the pyridine rings rather than on top of the Na toms, but the precise binding site and interaction strength may depend on the system under scrutiny.…”

“…However,t he complexityo ft he problem involving SAMs with differences in molecular orientation and packing densities, as well as neutrala nd ionic metal speciesi na ne lectrochemically controlled environmentrequiresignificant simplifications. Leaving the electrochemical environmenta side, computational studies performed by Keith and Jacob [30,31] examined diffusion, the prerequisite for nucleation.I nd ensity functional theory (DFT) calculations of single Pd atoms on a4 -mercaptopyridine SAM, activation barriers weref ound to be too high for Pd diffusion. Adding aw ater molecule to the single Pd atom to mimic an aqueous environment did not result in a reduction of the barrier.H owever, in the case of pre-adsorbed Pd atoms, the barriers decreased substantially,t hus greatly facilitating lateral diffusion.…”