Two different first-principles methods, one based on density functional theory combined with Green's functions and the other on a configuration interaction method, are used to calculate the electronic transport properties of alkane and silane chains terminated by amine end groups in metal-molecule-metal junctions. The lowvoltage conductance is found to decay exponentially with increasing length in both systems, and decay constants are obtained from the different methods. Both methods predict smaller conductance values and steeper decay in the alkane-bridged junctions compared with the silane-bridged junctions, but quantitative differences in the decay constants obtained from the two formalisms arise. These differences are attributed to the treatment of the energy-level alignments in the tunnel junctions as well as the treatment of correlation within the molecular chains. Additionally, end-group effects for both the alkane and the silane chains are studied using both a simple tunnel barrier model and complex band-structure calculations. These results are used to explain differences observed in conductance decay constants in amine-and thiol-linked junctions obtained from the two transport methods; the results further highlight the importance of accurate energy-level alignment between the electrode and molecular states.

Electron transport in a strong coupling regime is investigated by applying the many-electron correlated scattering (MECS) method to an atomic point contact model. Comparing the theoretical calculations to the quantum of conductance obtained experimentally for these systems allows for the error associated with the numerical implementation of the MECS method to be estimated and attributed to different components of the calculations. Errors associated with implementing the scattering boundary conditions and determination of the applied voltage in a finite explicit electrode model are assessed, and as well the impact on the basis set description on predicting the conductance is examined in this weakly correlated limit. The MECS calculation for the atomic point contact results in a conductance of 0.6G(0), in reasonable agreement with measurements for gold point contacts where approximately the conductance quantum G(0) is obtained. The analysis indicates the error attributable to numerical approximations and the explicit electrode model introduced in the calculations should not exceed 40% of the total conductance, whereas the effect of electron-electron correlations, even in this weakly correlated regime, can result in as much as a 30% change in the predicted conductance.

Electronegativity is shown to control charge transfer, energy level alignments, and electron currents in single molecule tunnel junctions, all of which are described through the density matrix. Currents calculated from the one-electron reduced density matrix correct to second order in electron-electron correlation are identical to currents obtained from the one-electron Green's function corrected to second order in electron self-energy. A tight binding model of hexa-1,3,5-triene-1,6-dithiol bonded between metal electrodes is introduced, and the effect of analytically varying electron-electron correlation on electron currents and electronegativity is examined. The model analysis is compared to electronic structure descriptions of a gold-hexatriene (approximated by different exchange-correlation functionals) and Hartree-Fock states as zeroth-order approximations to the one-electron Green's function. Comparison between the model calculations and the electronic structure treatment allows us to relate the ability to describe electronegativity within a single particle approximation to predictions of current-voltage characteristics for molecular tunnel junctions.