The microstructural changes in chromophoric self-assembled monolayers induced by modifications in the architecture of the molecular components are studied by X-ray reflectivity and polarized second-harmonic generation (SHG) spectroscopy. Monolayers prepared by chemisorption/quaternization of the chromophore precursor 4-[N,N-bis(3-hydroxypropyl)amino]styryl-4’-pyridine (2a) on preassembled films of the coupling agents (p-ClCH2C6H4)(CH2)(2)SiCl3 (1a), (p-ClCH2C6He4)(CH2)(2)SiCl2CH3 (1b) : and (p-ClCH2C6H4)(CH2)(2)SiCl( CH3)(2) (1c) display a progressive reduction in measured film thickness from 26.4 to 21.8 to 19.6 Angstrom and in optical second-harmonic response, chi((2)) (lambda = 1064 nm), from 3.0 x 10(-7) to 1.7 x 10(-7) to 0.8 x 10(-7) esu, respectively, indicating reduced chromophore surface density with increasing methyl substitution on the silicon of the coupling agent. The chromophoric groups in the film also experience a slight increase in tilt angle with respect to the surface normal, from 37 degrees to 41 degrees to 43 degrees, with increased methylation of Si, indicating that the reduction in thickness is primarily due to microstructural changes in other regions of the film. Monolayers prepared under slightly different conditions with coupling agent 1a and chromophore precursor 2a or the analogous alkynyl chromophore precursor [4-[N,N-bis(3-hydroxypropyl)amino]phenyl]ethynyl-4’-pyridine (2b), and then capped with octachlorotrisiloxane, display a decrease in measured film thickness from 20.5 to 15.1 Angstrom, an increase in monolayer-air interface width, and a reduction in chi((2)) from 2.0 x 10(-7) to 0.6 x 10(-7) esu when 2b is used in place of 2a. Penetration of the capping layer into the film microstructure is suggested by a substantial increase in film electron density to similar to 70% of silicon and an increased measured interface width.