The invention provides a silica nanoparticle comprising a non-porous matrix of silicon-oxygen bonds, wherein the matrix comprises organic agents conjugated to silicon or oxygen atoms in the matrix, the organic agents are conjugated to the matrix through linker L groups, wherein the linker L comprises, for example, an ester, urea, thiourea, or thio ether group, and wherein the diameter of the nanoparticle is about 15 nm to about 200 nm. The invention also provides novel methods of making and using the silica nanoparticles.