We use a first-principles calculation and small-angle neutron scattering (SANS) to investigate the mechanism and the nanosize products of the sol-gel reaction with diphenylsilanediol (DPD) and 3-methacryloxypropyltrimethoxysilane (MEMO) precursors in synthesizing a hybrid waveguide material. It is predicted that switching between a DPD hydroxyl and a MEMO methoxy with a reaction rate of 6.8 x 10^{-6 s-1 at 300 K is the fastest process for the first reaction step, thus generating diphenylmethoxysilanol (DPM) and 3-methacryloxypropyldimethoxysilanol (MEDO) as products. However, we determine that this reaction pathway could be modified by the presence of the H}2^{O released from a catalyst such as Ba(OH)}2^.H2^{O. Next, switching between the DPM hydroxyl and the MEDO methoxy is followed to generate diphenyldimethoxysilane (DPDM) and 3-methacryloxypropylmethoxysilanediol (MEMDO). However, condensation between a MEMDO hydroxyl and a DPDM methoxy is found to be most favorable for the third reaction step, which generates the DPDM-MEMDO dimer and CH}3OH molecule as products. In a similar fashion, a DPDM methoxy of the DPDM-MEMDO dimer can condense with a MEMDO hydroxyl of the second DPDM-MEMDO dimer to increase the chain, but its reaction rate of 2.8 x 10-11 s-1 is predicted to be about 5 times smaller than that between a DPDM methoxy and a MEMDO hydroxyl. This implies that the reaction rate for the larger nanostructures becomes smaller. Additionally, our SANS measurements determine that the final products from our sol-gel reaction are on the nanometer scale, at sizes from 1.76 to 2.36 nm.