Adsorption of protected and unprotected amino-cyclopentene at the Si(100) surface modeled with a hybrid quantum mechanical cluster technique

Both 1-amino-3-cyclopentene ACP and its protected form N-1-tert-butyloxycarbonylamino-3-cyclopentene BACP were adsorbed at the depassivated Si 100 surface using a hybrid calculation method in a Si197H108 cluster. It was found that the ACP molecule can potentially adsorb in at least eight different modes to the surface. The most stable one connects through both its carbon-carbon double-bond and its amine group, forming a bridge-like structure between two dimers, and has an adsorption energy of −73.9 kcal mol−1. In what concerns the BACP molecule, it was found that the tert-butyloxycarbonil tBOC protecting group does indeed inhibit the reaction of the amine group without affecting energetically the adsorption through the double bond. Its adsorption energy is basically the same as the one for ACP when adsorbed by the same group with both of them having an adsorption energy within 1 kcal mol−1.