We have studied the interaction of vapor-deposited Al, Cu, Ag, and Au atoms on a methoxy-terminated self-assembled monolayer (SAM) of HS(CH(2))(16)OCH(3) on polycrystalline Au[111]. Time-of-flight secondary ion mass spectrometry, infrared reflection spectroscopy, and X-ray photoelectron spectroscopy measurements at increasing coverages of metal show that for Cu and Ag deposition at all coverages the metal atoms continuously partition into competitive pathways: penetration through the SAM to the S/substrate interface and solvation-like interaction with the -OCH(3) terminal groups. Deposited Au atoms, however, undergo only continuous penetration, even at high coverages, leaving the SAM "floating" on the Au surface. These results contrast with earlier investigations of Al deposition on a methyl-terminated SAM where metal atom penetration to the Au/S interface ceases abruptly after a approximately 1:1 Al/Au layer has been attained. These observations are interpreted in terms of a thermally activated penetration mechanism involving dynamic formation of diffusion channels in the SAM via hopping of alkanethiolate-metal (RSM-) moieties across the surface. Using supporting quantum chemical calculations, we rationalized the results in terms of the relative heights of the hopping barriers, RSAl > RSAg, RSCu > RSAu, and the magnitudes of the metal-OCH(3) solvation energies.

Structural trends for a homologous series of n-alkanethiolate self-assembled monolayers (SAMs), C(n)H(2n+1)S- with 12 < or = n < or = 19, on GaAs(001), studied by a combination of grazing incidence X-ray diffraction and infrared spectroscopy, along with ancillary probes, show an overall decay in organization with decreasing n, with the largest changes occurring below n = 15-16. The long-chain monolayers form a mosaic structure with < or =10 nm domains of molecules organized in an incommensurate pseudo-hcp arrangement with nearest neighbor distances of 4.70 and 5.02 A, a 21.2 A(2) area per chain, two chains per subcell in a herringbone packing with a chain tilt angle of 14 degrees , and preferential domain alignment along the substrate [110]([110]) step edge direction. In contrast, for n < 14 no evidence of translational ordering is seen and the alkyl chains exhibit a loss of conformational ordering and coverage relative to the n > 16 cases. A 4'-methyl-biphenyl-4-thiolate companion SAM shows evidence for ordered structures but with lattice parameters close to those expected for a structure commensurate with the intrinsic GaAs(001) square lattice. These trends are explained on the basis of competitions between lattice, interfacial, and intermolecular forces controlling the nanoscale structures of the SAMs. Overall these results provide an important aspect of understanding the effects of SAM formation on surface properties such as electronic and chemical passivation.

Size-specific interaction of alkali metal ions with aromatic side chains has been proposed as a mechanism for selectivity in some K+ channel proteins. Experiments on gas-phase cluster ions of the form M+(C6H6)n(H2O)m, with M=Na or K, have demonstrated that the interaction between benzene and K+ is sufficiently strong to result in partial dehydration of the ion, i.e., benzene will displace some water molecules from direct contact with the ion. In sharp contrast, there is no evidence that benzene can displace water from the first hydration shell of Na+. The resistance of Na+(H2O)4 towards dehydration in an aromatic environment suggests a molecular-level mechanism for the low permeability of Na+ through the pore region of K+ channel proteins: the hydrated Na+ ion is too large to pass, while K+ can shed enough of its hydration shell to fit through the pore. These results also suggest that it may be possible to design a new class of ionophores that take advantage of the cation–π interaction to confer ion selectivity. This is the first experimental evidence that K+ selectively interacts with an aromatic complex in an aqueous environment, while Na+ does not. A remarkable sidelight from this study was the discovery of a self-assembled cluster ion, Na+(C6H6)8(H2O)4, with a single structure: an inner shell of four water molecules and an outer layer of eight benzene molecules, each of the latter fixed by a π–hydrogen bond to one of the eight interior O–H groups.

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