Tunnel Currents across Silane Diamines/Dithiols and Alkane Diamines/Dithiols: A Comparative Computational Study Shane McDermott, † Christopher B. George,* ,‡ Giorgos Fagas, † James C. Greer, † and Mark A. Ratner ‡ Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, and Department of Chemistry, Northwestern UniVersity, EVanston, Illinois 60208, USA ReceiVed: September 4, 2008; ReVised Manuscript ReceiVed: NoVember 4, 2008 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 low- voltage 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. I. Introduction As a central problem of molecular electronics, the process of electron transport through single molecules between metallic electrodes has been achieved experimentally and studied theoretically. 1–3 The desire to create junctions with tailored functionalities has led to work examining the roles that end groups, molecular energy levels, and contact geometries play in determining the transport properties of these systems. 4–14 In particular, recent studies have examined physical tunnel junc- tions in which alkanes of varying lengths are bonded between gold electrodes via amine or thiol linkers. 5,10,15–21 These junctions exhibit an exponential decrease in low-voltage conductance, g, with increasing bridging molecular length, l (given in angstroms or the number of methylene units), as is reasonable for conductance far from any injection resonance. This behavior is described by: g(l) ) g C exp(-l) (1) which is characterized by two parameters: the contact resistance R C ) 1/g c and the inverse decay length  22 . The inverse decay length determines how tunnel conductance and resistance scale with increasing molecular length. The contact resistance is obtained in the limit l f 0 and determines the resistance associated with the bonding of the end groups to the metal electrodes or contacts. However, the contact resistance is strongly dependent on the exact configuration of the metal-molecule bonding site, 4,8,9 so it will not be discussed in depth in this article (cf. Supporting Information). Most theoretical treatments of conductance in single-molecule junctions up to this point have been based on density functional theory (DFT) combined with a nonequilibrium Green’s function (NEGF) formalism. 23 The NEGF/DFT formalism recently has been questioned, however, over concerns that exchange-cor- relation effects are leading to spurious conductance values, 24–30 sometimes described incorrectly by orders of magnitude. 24 To avoid issues related to exchange-correlation approximations in DFT, a new transport formalism was recently developed. 31,32 The method uses a configuration interaction (CI) method 33,34 to calculate the electronic structure of the junction, and transport properties are calculated using the Wigner function within open boundary conditions under constraint of the maximum entropy principle. To compare the two methodologies, four test systems were chosen. The amine- and thiol-linked systems were selected as a means to compare the effect of different end groups on conductance, whereas the silane and alkane chains were selected to compare the effects of different chemical backbones and degrees of correlation on the transport. The increased correlation in the silane chains is related to the σ-bond delocalization that has been studied extensively in peralkylated oligosilane chains. 35,36 The photophysics of these oligosilane chains has indicated that their excitation energies are lower than those of alkane chains, and the size of the band gap in silanes may lead to interesting conductance properties such as a decay length between that of alkanes and π-conjugated systems. II. Computational Methods and Theory Junction Geometries. Calculations are performed on tunnel junctions consisting of single molecules spanning a gap between two metal clusters. The molecules considered within this study are alkanes and silanes, and both deprotonated thiol (-S-) and * To whom correspondence should be addressed. E-mail: shane.mcdermott@tyndall.ie (S.M.), c-george@northwestern.edu (C.B.G.), georgios.fagas@tyndall.ie (G.F.), jim.greer@tyndall.ie (J.C.G.), ratner@ chem.northwestern.edu (M.A.R.). † Tyndall National Institute. ‡ Northwestern University. J. Phys. Chem. C 2009, 113, 744–750 744 10.1021/jp8078698 CCC: $40.75  2009 American Chemical Society Published on Web 12/16/2008