Effect of the tert-butiloxycarbonyl protecting group on the adsorption of protected amino-cyclopentene on the Si(100) surface

In this work, we study the effects of the tert-butiloxycarbonyl protecting group at the adsorption coverage of protected 1-amino-3-cyclopentene (ACP) on the Si(100) surface by using a large cluster with a quantum-mechanical/quantum- mechanical hybrid calculation methodology. We find that at lower coverages, the adsorption energies do not vary significantly from the ones obtained previously for the unprotected ACP form. At medium coverages, we find some energetic deviations that are due to counter-intuitive attractive forces between the adsorbed molecules. These attractive forces make it more probable to find groups of two and three protected ACP (BACP) molecules adsorbed right next to each other. Higher surface coverages, however, seem to be severely affected by geometrical restrictions that should be enough to prevent further adsorption. In the end, we conclude that the protecting group works extremely well and can actually increase the final attainable coverage for ACP on the Si(100) surface. © 2007 The American Physical Society.