  In this work we report the results of theoretical analysis of the effect of
thermal environment on the thermoelectric efficiency of molecular junctions.
The environment is represented by two thermal phonon baths associated with the
electrodes which are kept at different temperatures. The analysis is carried
out using the Buttiker model within the scattering matrix formalism to compute
electron transmission through the system. This approach is further developed,
so that the dephasing parameters are expressed in terms of relevant energies
including the thermal energy, strengths of coupling between the molecular
bridge and the electrodes and characteristic energies of electron-phonon
interactions. It is shown that the latter significantly affect thermoelectric
efficiency by destroying coherency of the electron transport through the
considered system.
