  A generalized Green's function theory is developed to simulate the inelastic
electron tunneling spectroscopy (IETS) of molecular junctions. It has been
applied to a realistic molecular junction with an octanedithiolate embedded
between two gold contacts in combination with the hybrid density functional
theory calculations. The calculated spectra are in excellent agreement with
recent experimental results. Strong temperature dependence of the experimental
IETS spectra is also reproduced. It is shown that the IETS is extremely
sensitive to the intra-molecular conformation and to the molecule-metal contact
geometry.
