Molecular dynamics (MD) simulations using CHARMM were performed for the solution structures of the pentacoordinate and tetracoordinate PSCS and PRCS adducts of Torpedo californica (Tc) acetylcholinesterase (AChE) formed with 2-(3,3-dimethylbutyl) methylphosphonofluoridate (soman) to assess the molecular origins of stereoselectivity of phosphonylation. MD simulations were also carried out for the PSCS transients in soman-inhibited trypsin to evaluate the differences in the mode of operation of the two enzymes. Parameters for the pentacoordinate phosphonate fragments were constructed from results of an nb initio calculation at the 6-31G* level for a model compound, and those for the tetracoordinate phosphonate fragments were from MNDO calculations. Starting equilibrium structures for the above and for analogous structures for chymotrypsin were generated and energy-optimized in program YETI. The stereoselectivity of AChE for the levorotatory diastereomers of soman amounts to >5.6 kcal/mol difference in transition state free energies and can be rationalized based on the results of the MD calculations : There is a predominant conformation of transient forms of the PsCs diastereomer of soman:inhibited AChE in which every ligand in phosphorus is stabilized by an optimal binding feature of the active site. In contrast, the phosphonyl fragment in the PRCS diastereomer may be accommodated with equal difficulty, at least, two different ways : In the most favorable conformation, the phosphoryl oxygen is engaged in weak interactions with constituents of the oxyanion hole if adjustments in the Ca backbone and substantial motions of Trp84, Trp233, Phe288, and Phe290 are allowed. The remarkable efficiency of F- departure from the pentacoordinate transition states of phosphonylated AChE cannot be explained by general base catalysis by HisH(+)440. Leaving group departure from these structures must be promoted by electrostatic forces, "push" from Glu199 and "pull" from the oxyanion hole, in addition to steric strain. One of the distinguishing features of the crystal structure of TcAChE is the short H-bonds in the catalytic triad. The His440 N delta---OOC beta Asp327 bond distance is 2.5 W (2.8 Angstrom resolution) in AChE and 0.2 Angstrom shorter than the corresponding H-bond in trypsin and chymotrypsin (1.5 Angstrom resolution). This distance increased to 2.7 Angstrom during the dynamics simulation. However, the average H-bond distances are further shortened by 0.05-0.3 Angstrom in energy-minimized structures of the adducts of AChE covalently modified by soman at the pentacoordinate and tetracoordinate intermediate stage. MD simulations of the optimized structures of native AChE and its adducts gave insight into how the skeletal motions accommodate an overcrowded active site particularly in the pentacoordinate adducts. The steric relief is only partial and is balanced by a repositioning of Glu199 toward the catalytic triad and phosphonyl fragment. This subtle reorientation of active-site residues should be relevant to the prominent catalytic efficiency of AChE.