Molecular simulations are carried out on amorphous silica systems confined to nanoscale dimensions, in order to elucidate the mechanical properties of nanoporous silica thin films produced by self assembly with surfactant templates. The simulations are carried out in conjunction with experiments led by Jeff Brinker (Sandia National Lab) and continuum modeling by Sal Torquato (Princeton), which show that nanoporous silica exhibits anomalous (and beneficial) modulus-density scaling relations. In particular, the elastic modulus decreases much more slowly with increasing porosity than predicted by continuum theory. The molecular simulations show that this anomalous effect is a consequence of a change in atomic level structure that is induced by the nanoscale architecture. Increased porosity causes the silica framework walls of 1-2 nm thickness to become thinner, which causes the atomic structure to rearrange to stiffer forms; the stiffened framework counteracts the continuum level reduction in elastic modulus, to produce the anomalously slow change in modulus with porosity.