Developing a fundamental understanding of the interactions of chemical warfare agents (CWAs) with surfaces is essential for the rational design of new sorbents, sensors, and decontamination strategies. The interactions of chemical warfare agent simulants, molecules which retain many of the same chemical or physical properties of the agent without the toxic effects, with amorphous silica were conducted to investigate how small changes in chemical structure affect the overall chemistry. Experiments investigating the surface chemistry of two classes of CWAs, nerve and blister agents, were performed in ultrahigh vacuum to provide a well-characterized system in the absence of background gases. Transmission infrared spectroscopy and temperature-programmed desorption techniques were used to learn about the adsorption mechanism and to measure the activation energy for desorption for each of the simulant studied. In the organophosphate series, the simulants diisopropyl methylphosphonate (DIMP), dimethyl methylphosphonate (DMMP), trimethyl phosphate (TMP), dimethyl chlorophosphate (DMCP), and methyl dichlorophosphate (MDCP) were all observed to interact with the silica surface through the formation of a hydrogen bond between the phosphoryl oxygen of the simulant and an isolated hydroxyl group on the surface. In the limit of zero coverage, and after defect effects were excluded, the activation energies for desorption were measured to be 57.9 ± 1, 54.5 ± 0.3, 52.4 ± 0.6, 48.4 ± 1, and 43.0 ± 0.8 kJ/mol for DIMP. DMMP, TMP, DMCP, and MDCP respectively. The adsorption strength was linearly correlated to the magnitude of the frequency shift of the ν(SiO-H) mode upon simulant adsorption. The interaction strength was also linearly correlated to the calculated negative charge on the phosphoryl oxygen, which is affected by the combined inductive effects of the simulants’ different substituents. From the structure-function relationship provided by the simulant studies, the CWA, Sarin is predicted to adsorb to isolated hydroxyl groups of the silica surface via the phosphoryl oxygen with a strength of 53 kJ/mol. The interactions of two common mustard simulants, 2-chloroethyl ethyl sulfide (2-CEES) and methyl salicylate (MeS), with amorphous silica were also studied. 2-CEES was observed to adsorb to form two different types of hydrogen bonds with isolated hydroxyl groups, one via the S moiety and another via the Cl moiety. The desorption energy depends strongly on the simulant coverage, suggesting that each 2-CEES adsorbate forms two hydrogen bonds. MeS interacts with the surface via a single hydrogen bond through either its hydroxyl or carbonyl functionality. While the simulant work has allowed us to make predictions agent-surface interactions, actual experiments with the live agents need to be conducted to fully understand this chemistry. To this end, a new surface science instrument specifically designed for agent-surface experiments has been developed, constructed, and tested. The instrument, located at Edgewood Chemical Biological Center, now makes it possible to make direct comparisons between simulants and agents that will aid in choosing which simulants best model live agent chemistry for a given system. These fundamental studies will also contribute to the development of new agent detection and decontamination strategies.