The vibrational spectrum of a thiolate-based self-assembled monolayer fabricated by the adsorption of benzylmercaptan on a Au(111) substrate is studied using a combined experimental and theoretical approach employing infrared reflection absorption spectroscopy and density functional theory. The vibrational spectra are derived both using a finite differences approach and from ab initio molecular dynamics simulations at various temperatures. In addition, the possibility of adsorbate-induced reconstructions of the Au(111) substrate is taken into account. It turns out that the measured spectra can only be understood by taking finite temperatures into account.