The use of molecular layers to modify the surface and interfaces of solid-state materials while retaining their bulk properties offers great potential. Despite the widespread interest, little work has been undertaken to characterize the growth and surface chemistry of the short-chain alkoxy silane molecular layers. Variable angle spectroscopic ellipsometry, contact angle goniometry, and X-ray photoelectron spectroscopy are used to undertake the work in the present study. Results indicate that 3-mercaptopropyltrimethoxysilane and 2-(trimethoxysilylethyl)pyridine are both unique among the short-chain alkoxy silanes and grow multilayer films in a toluene solution on hydroxylated SiO2 surfaces. In particular, the mercaptan molecular layers show evidence of a changing surface chemistry as a function of growth time. Further, added surface moisture on mercaptan molecular layers yields thicker films of a higher density with more reduced surface sulfur when subsequent growth is resumed as compared to a control sample, Further, the pyridine molecular layers possess negative optical birefringence much like the parylene polymers, polyimides, and phthalocyanine Langmuir-Blodgett films undertaken by previous researchers. In previous cases, the presence of a phenyl group with a large anisotropic molecular polarizability caused the large in-plane polarizability. Further, the pyridine molecular layers exhibited a high index of refraction of 1.567 +/- 0.005 explaining its superior properties as a metallic diffusion barrier at dielectric/metal interfaces from previous research.