Spectroscopic second-harmonic generation (SHG) and reflectance-anisotropy spectroscopy (RAS) are used to probe molecular adsorption on clean reconstructed single-domain stepped Si(001) in ultra-high vacuum (UHV). We implement a simplified bond hyperpolarizability model (SBHM) as a common microscopic analysis for SHG and RAS. Three different scenarios are studied: (i) The dissociative adsorption of molecular hydrogen on dangling bonds of D[subscript B] step-edges. (ii) Structural changes to rebonded r-D[subscript B] steps induced by exposure to atomic hydrogen. (iii) The adsorption of cyclopentene on Si(001)(2x1) terrace dimers in a [2+2] cycloaddition pathway. Using the SBHM we develop a new optical fingerprinting method to isolate, identify and monitor individual types of bonds (e.g. dimers, rebonds, dangling bonds, backbonds) and their chemical activity on a single-domain stepped Si(001) surface using nonresonant, but rotationally-anisotropic, second-harmonic generation (RA-SHG). The methods presented here will be applicable to many material systems and allow to track, in-situ and in real-time, the chemical action of adsorbates on surfaces. / text