  Motivated by recent experiments, we study the variability of the thermal
conductance of single dithiolated alkane molecules of varying length connecting
two gold electrodes. For this purpose, we examine (i) the influence of the
metal-molecule contact and of the electrode orientation on the thermal
conductance of straight alkane chains, (ii) the effect of molecule-internal
disorder realized through torsional gauche defects and the behavior upon
stretching, and (iii) the modifications resulting from temperature-dependent
dynamical variations of the geometry. While we analyze the former two aspects
with a combination of density functional theory (DFT) and nonequilibrium
Green's function (NEGF) methods, in the latter case we use nonequilibrium
molecular dynamics (NEMD). Our calculations show the size of the variation of
the phonon thermal conductance due to changes in contact geometry, that gauche
defects generally reduce the thermal conductance but that they vanish upon
stretching of the junction, and that the thermal conductance at elevated
temperatures results from an average over many junction configurations,
including alkanes with thermally excited gauche defects. Overall we find a good
agreement between the DFT-NEGF and NEMD approaches for our room-temperature
investigations. This confirms that anharmonic effects do not play a major role
in alkane chains containing between four to ten carbon atoms. The phonon heat
transport thus proceeds elastically and phase-coherently through these short
molecular junctions.
