We present the results of mol. dynamics calcns. carried out on self-assembled monolayers (SAMs) formed from alkyl thiols chemisorbed on a gold (111) substrate. The alkyl tails are functionalized by polar groups (-NH2) with the potential of forming hydrogen bonds. Particular attention is focused on the prediction of the structural characteristics of the functionalized outer surface of the SAM in an attempt to make contact with scanning tunneling microscopy images. We examine the dependence of the predicted structure on the model used to represent the alkyl chains. [on SciFinder (R)]