We have studied the adsorption of the protected form of amino-cyclopentene on the Si(100) surface at several coverage densities, using a very large cluster of 21 silicon dimers and a hybrid QM/QM (ONIOM) methodology. We performed linear transit scans for the study, and have understood the process at a microscopic detail. The work has answered all doubts that remained from previous studies, including the fact that the stabilization provided by the carboxylic groups is not due to the formation of hydrogen bonds as previously hypothesized, but to dipole-dipole attractions. (c) 2007 Elsevier B.V. All rights reserved.