The authors present the results of an IR study of the effect of temperature on the formation of Au-monolayer-Si molecular junctions by using a flip-chip lamination approach. Carboxylic acid-terminated alkanethiols self-assembled on an ultrasmooth gold substrate have been laminated to H-Si(111) at 0.8 MPa as a function of temperature. p-polarized-back-side reflection absorption infrared spectroscopy of the alkanoic acids within the molecular junction indicates increasing disorder, likely near the carboxylic acid (-COOH) terminus, of the all-trans chain up to 60 degrees C, followed by a propagation of these defects down the molecular length. The low frequency region of the IR spectra as a function of temperature indicates that the -COOH group is interacting with the H-Si(111) surface. The IR spectra indicate that the reaction is largely due to the availability of the COOH groups to react. Flip-chip lamination is an effective approach to form molecular junctions. Unlike direct metal evaporation, it ensures the formation of robust structures where the organic monolayer is chemically bonded to both surfaces with no signs of metal penetration.