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Motivated by recent experiments, we study the variability of the thermalconductance of single dithiolated alkane molecules of varying length connectingtwo gold electrodes. For this purpose, we examine (i) the influence of themetal-molecule contact and of the electrode orientation on the thermalconductance of straight alkane chains, (ii) the effect of molecule-internaldisorder realized through torsional gauche defects and the behavior uponstretching, and (iii) the modifications resulting from temperature-dependentdynamical variations of the geometry. While we analyze the former two aspectswith a combination of density functional theory (DFT) and nonequilibriumGreen's function (NEGF) methods, in the latter case we use nonequilibriummolecular dynamics (NEMD). Our calculations show the size of the variation ofthe phonon thermal conductance due to changes in contact geometry, that gauchedefects generally reduce the thermal conductance but that they vanish uponstretching of the junction, and that the thermal conductance at elevatedtemperatures results from an average over many junction configurations,including alkanes with thermally excited gauche defects. Overall we find a goodagreement between the DFT-NEGF and NEMD approaches for our room-temperatureinvestigations. This confirms that anharmonic effects do not play a major rolein alkane chains containing between four to ten carbon atoms. The phonon heattransport thus proceeds elastically and phase-coherently through these shortmolecular junctions.

Variability of the thermal conductance of gold-alkane-gold single-molecule junctions studied using ab-initio and molecular dynamics approaches