The structure, energetics, and nature of the chemical bonding of phenylthiol adsorbed on the Au(111) surface: Implications for density-functional calculations of molecular-electronic conduction

Abstract

The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111); this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol(-1), indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol(-1). No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3-4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.

Electrochemically controlled self-assembled monolayers characterized with molecular and sub-molecular resolution

“…133 The variety of straight versus singly and doubly branched, otherwise non-functionalized alkanethiols constitutes one system class where computational support has been decisive in the clarification of the highly subtle interplay between Au-S binding sites (hollow sites, bridge, and a-top sites, or intermediates in between), composite lateral interactions, and Au-atom ''mining'' out of the planar Au-electrode surfaces. 124,126,134,135 The latter energetic expenditure is compensated by more favourable Au-S bonding energetics to the now ''loosened'' but still surface-bound Au-atoms.…”

Conductance of a phenylene-vinylene molecular wire: Contact gap and tilt angle dependence

“…Consequently, the coupling at the thiolate-gold interface will be somewhat stronger for the former site. 27 A ͑3 ϫ 3͒ superstructure was employed for the Au͑111͒ surface resulting in nine gold atoms per layer. This represents a moderate 1/9 OPV3 monolayer coverage, which guarantees that the molecules in neighboring cells are sufficiently separated ͑i.e., noninteracting͒.…”

“…This represents a moderate 1/9 OPV3 monolayer coverage, which guarantees that the molecules in neighboring cells are sufficiently separated ͑i.e., noninteracting͒. [27][28][29][30][31][32][33][34] For the geometry optimizations, as well as for the transport computations, the Brillouin zone integrations were performed on a 3 ϫ 3 k-point Monkhorst-Pack mesh in the plane of the surface. For the calculation of the bulk electronic structure of the gold leads the reciprocal space was sampled on a 3 ϫ 3 ϫ 100 grid, with the denser sampling in the direction of transport.…”

“…27 It is commonly assumed that thiols adsorb on gold dissociatively, i.e., by breaking the S-H bond, although both chemisorbed and physisorbed species can be observed at equilibrium. 35 Since dissociation is the dominant mechanism, we have considered the gas phase OPV3 in the dehydrogenated biradical form.…”

Interface electronic structures of reversible double-docking self-assembled monolayers on an Au(111) surface

“…Considerable experimental efforts have been made in order to obtain promising SAMs with expected properties to improve device performances [7][8][9][10]. In past years, great theoretical progress has been achieved in understanding metal-SAM interface electronic structures [11][12][13][14]. By using first-principles calculations, Zojer et al have presented comprehensive studies of various factors impacting on the electronic structures of SAMs, such as the docking group, the backbone, the electron withdrawing/donating ability of polar substituents, the molecular coverage and the mixed ratio of different adsorbed molecules, on work-function modification owing to SAM adsorption and level alignments of the molecular frontier states relative to the metal Fermi level [15][16][17][18][19][20][21][22].…”