Nanocrystal gels have structural complexity that spans length scales, which has so far hampered the use of simulations to predict or rationalize their structure-dependent optical properties. Although plasmonic nanoparticle gels have been reported to exhibit spectrally shifted and broadened extinction spectra compared to their constituent nanoparticles, these effects vary widely and unpredictably for different nanoparticle compositions and gel preparation strategies. We demonstrate the value of MPM for understanding gel structure and optical properties by considering networks of ITO nanocrystals (a ≈ 6 nm, 6.0% Sn) linked by dynamic covalent bonding 26 (Fig. , S10, and S11).