molecular dynamics simulations of chlorambucildna adducts a structural basis for the 5gnc interstrand dna crosslink formed by nitrogen mustards the alkylation of dna by chlorambucil has been studied using a computational approach molecular dynamics simulations were performed on the fully solvated noncovalent complex two monoadducts and a crosslinked diadduct of chlorambucil with the dcgg3g2cgcdgcg1cccg duplex in which the n7 atoms of g1 g2 and g3 are potential alkylation sites the results provide a structural basis for the preference of nitrogen mustards to crosslink dna duplexes at a 5gnc site a 13 crosslink g1g3 rather than at a 5gc sites a 12 crosslink g1g2 in the noncovalent complex simulation the drug reoriented from a noninterstrand crosslinking location to a position favorable for g1g3 diadduct formation it proved possible to construct a g1g3 diadduct from a structure from the noncovalent simulation and continue the molecular dynamics calculation without further disruption of the dna structure a crosslinked diadduct developed with four bii conformations on the 3 side of each alkylated guanine and of their respective complementary cytosine in the first monoadduct simulation the starting point was the same dna conformation used in the crosslinked diadduct simulation with alkylation at g1 in this simulation the dna deformation was reduced with the helix returning to a more canonical form a second monoadduct simulation was started from a canonical dna conformation alkylated at g3 here no significant motion towards a potential crosslinking conformation occurred collectively the results suggest that crosslink formation is dependent upon the drug orientation prior to alkylation and the required deformation of the dna to permit 13 crosslinking can largely be achieved in the noncovalent complex