  We report a theoretical study of the thermopower of single-molecule
junctions, with focus on phenyl-based molecular junctions. In contrast to prior
studies, thermal fluctuations of the torsional angle between the phenyl rings
and variations in the position of the molecular level alignment with respect to
the electrode Fermi energy were both taken into account. Full thermopower
histograms were obtained, and their dependence on the magnitude of the
fluctuations was studied. We found that at large molecular orbital variations
the thermopower becomes strongly dependent on the torsion angle and can even
change sign. This results in a marked effect of fluctuations on the thermopower
distribution, yielding an average thermopower at high temperatures that differs
(smaller or larger) from the fluctuation-free value, depending on the strength
of fluctuations. We therefore conclude that fluctuations should be taken into
account both when extracting single-molecule parameters, such as the molecular
level-Fermi level offset, and in predictions of the thermopower of molecular
junctions.
