Alkanedithiols conformation

Gharge Transport in Single Au Alkanedithiol Au Junctions Coordination Geometries and Conformational Degrees of Freedom. Journal of the American Chemical Society, 130, 318-326. 

The nature of the conductance families reported for single alkanedithiol junctions is still under debate. Current interpretations are based on different contact geometries [64, 115, 242], different molecular conformations [64, 244], substrate roughness [245], or the control of tip movement [252],... 

The discrepancies in the reported conductance data of Au-alkanedithiol-Au junctions attracted our attention, and we decided to carry out an in-depth experimental study of the charge transport properties of Au-a,oo-alkanedithiol-Au molecule junctions in a non-conducting solvent. The combination with quantum chemistry ab initio simulations yielded a detailed view of this archetype of molecular junctions, and helped to resolve the puzzle on the role of microscopic geometries at the contacts and in the molecular conformation. 

Independent of the contact geometry, the calculations also demonstrated that the introduction of gauche defects resulted in a decrease of the bridge conductance by a factor of 10, as compared to an all-trans alkanedithiol chain (see Fig. 14b, triangles). Due to variations in the number and positions of gauche defects, as well as various contact geometries, the molecular junctions can exhibit conductance values up to two orders of magnitude below the conductance values of an all-trans conformation of the alkyl chain. 

Comparison of the experimental data with the trends predicted from quantum chemistry ab initio simulations demonstrated that the multiple conductance values of Au-alkanedithiol-Au junctions could be attributed to different Au-sulfur coordination geometries and to different conformations of the alkyl chain. In particular, the medium conductance corresponds to an all-trans conformation of the alkyl chain, with each sulfur atom coordinated in atop position to a single... 

Fig. 29 Three typical arrangements of a single alkanedithiol molecule bridged between Au electrodes as used for the conductance calculations. A 1,9-Nonanedithiol (ND) with one gauche defect and both terminal sulfm atoms coordinated in atop position (low, L), B ND in all-trans conformation and atop-atop coordination (mediiun, M), C all-trans ND in a bridge-bridge coordination (high, H)...

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