Synthetic analogs of naturally occurring nanoparticles have been studied by a range of X-ray techniques to determine their structure and chemistry, and relate these to their novel chemical properties and physical behavior. ZnS nanoparticles, formed in large concentrations naturally bymicrobial action, have an interesting core-shell structure with a highly distorted and strained outer layer. The strain propagates through the particles and produces unusual stiffness but can be relieved by changing the nature of the surface ligand binding. Weaker bound ligands allow high surface distortion, but strongly bound ligands relax this structure and reduce the overall strain. Only small amounts of ligand exchange causes transformations from the strained to the relaxed state. Most remarkably, minor point contacts between strained nanoparticles also relax the strain. Fe oxyhydroxide nanoparticles appear to go through structural transformations dependent on their size and formation conditions, and display a crystallographically oriented form of aggregation at the nanoscale that alters growth kinetics. At least one Fe oxyhydroxide mineral may only be stable on the nanoscale, and nonstoichiometry observed on the hematite surface suggests that for this phase and possibly other natural metal oxides, chemistry may be size dependent. Numerous questions exist on nanominerals formed in acid mine drainage sites and by reactions at interfaces.