The chemical effects on the adhesion and friction between alkanethiol self-assembled monolayers (SAMs) on gold are studied using molecular dynamics simulations. Alkanethiol SAMs (S(CH2)(n)X) are investigated as a function of the terminal group (X = CH3, OH, COOH) and chain length n. The adhesive force is calculated as a function of the separation between two SAMs with the same terminal group. The maximum attraction for methyl-terminated SAMs is much weaker than for the OH- and COOH-terminated SAMs which form interlayer hydrogen bonds. The COOH-terminated SAMs have the strongest attraction. For the COOH- and OH-terminated SAMs, the adhesion-separation curves depend strongly on n. In both cases the change in the position of the attractive minimum is large as a function of n. The magnitude of the attractive minimum varies little for OH-terminated SAMs, and the variation is also small for COOH-terminated SAMs once the odd:even effect is considered. The source of the n dependence is structural changes within the SAMs. For separations within the attractive region of the adhesion curve, the interlayer hydrogen bond interactions pull the chains to a more upright tilt angle than the equilibrium, single-monolayer tilt angle. Longer chains have more upright tilt angles for separations in the attractive region. For COOH SAMs with n less than or equal to 13 the maximum adhesion is significantly larger for odd n in comparison to even n - 1. The difference between even and odd cases decreases with n, and for n > 13 the difference is smaller than our uncertainty. Friction simulations between two SAMs with the same n show that the shear stress is significantly larger for X = COOH than for CH3.