The silicate oligomerization reaction is key to sol-gel chemistry and zeolite synthesis. Numerous experimental and theoretical studies have addressed the physical chemistry of silicate oligomers in the prenucleation stage of siliceous zeolite formation. Here we report a study of a silica condensation reaction in aqueous solution in the presence of counter ions (Li+ and NH4+). Ab-initio molecular dynamics simulations have been used to construct reaction energy diagrams including transition state free energies. Contact with Li+ as well as NH4+ increases the activation energies of the dimerization step compared to the situation in the absence of counterions. The presence of NH4+ has no effect on consecutive oligomerization steps. Hence NH4+ will increase the relative formation rate of larger oligomers. © 2009 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim.