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The distinction between adiabatic and nonadiabatic reaction mechanisms at an electrode/solution interface is emphasized; in general, only adiabatic or near-adiabatic paths are important in thermally activated reactions. The role of the dielectric in determining the course of such reactions is discussed. A general interpretation of the transfer coefficient and an account of the activation process in simple systems are given in terms of the distribution of electron charge density in the transition state; these are shown to be in good accord with experiment. The conventional approach to these problems, in which an approximate potential-energy path for the reaction is calculated from intersecting potential-energy curves for the initial and final states of the system, is criticized, and an alternative representation in terms of charge variation is proposed.

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Various Green’s-function-based formalisms which express the current I as a function of applied voltage V for an electrode–molecule–electrode assembly are compared and contrasted. The analytical solution for conduction through a Hückel (tight binding) chain molecule is examined and only one of these formalisms is shown to predict the known conductivity of a one-dimensional metallic wire. Also, from this solution we extract the counter-intuitive result that the imaginary component of the self-energy produces a shift in the voltage at which molecular resonances occur, and complete analytical descriptions are provided of the conductivity through one-atom and two-atom bridges. A method is presented by which a priori calculations could be performed, and this is examined using extended-Hückel calculations for two gold electrodes spanned by the dithioquinone dianion. A key feature of this is the use of known bulk-electrode properties to model the electrode surface rather than the variety of more approximate schemes which are in current use. These other schemes are shown to be qualitatively realistic but not sufficiently reliable for use in quantitative calculations. We show that in such calculations it is very important to obtain accurate estimates of both the molecule–electrode coupling strength and the location of the electrode’s Fermi energies with respect to the molecular state energies.

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.