Combining experimental and ab initio core-level photoelectron spectroscopy (periodic DFT and quantum chemistry calculations), we elucidated how ammonia molecules bond to the hydroxyls of the (H,OH)-Si(001) model surface at a temperature of 130 K. Indeed, theory evaluated the magnitude and direction of the N 1s (and O 1s) chemical shifts according to the nature (acceptor or donor) of the hydrogen bond and, when confronted to experiment, showed unambiguously that the probe molecule makes one acceptor and one donor bond with a pair of hydroxyls. The consistency of our approach was proved by the fact that the identified adsorption geometries are precisely those that have the largest binding strength to the surface, as calculated by periodic DFT. Real-time core-level photoemission enabled measurement of the adsorption kinetics of H-bonded ammonia and its maximum coverage (0.37 ML) under 1.5 x 10(-9) mbar. Experimental desorption free energies were compared to the magnitude of the adsorption energies provided by periodic DFT calculations. Minority species were also detected on the surface. As in the case of H-bonded ammonia, DFT core-level calculations were instrumental to attribute these minority species to datively bonded ammonia molecules, associated with isolated dangling bonds remaining on the surface, and to dissociated ammonia molecules, resulting largely from beam damage.