Self-assembled monolayers containing azobenzene groups covalently incorporated into some of the chains are of particular interest because of the photoisomerizable character of the azobenzene unit. A potentially interesting system is one where the terminal groups in the chains that contain azobenzene are different from the other terminal groups. The configurational states of the azobenzene are then expected to control the relative protrusion of the terminal groups and alter the mole fraction of these groups present on the free surface, which directly influences the properties of the monolayer. Molecular dynamics simulations have been performed for mixed systems of a hydrocarbon chain containing azobenzene surrounded by pure hydrocarbon chains on a planar silica substrate. With a surface area assigned roughly three times larger than the usual area for a pure hydrocarbon chain, the azobenzene-containing chain exhibits an observable chain length difference between the trans and the cis configurations. Also the effect of relative positions of the azobenzene group within the chain is studied, and it is found that head and tail connections introduce larger variations in chain length than center connection during the trans reversible arrow cis isomerization. Both effects lead to the alteration of the relative protrusion of functional groups at the chain end, thus the characteristics of the monolayer are altered and controlled at the molecular scale.