RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 32 components of a force field topology database useful for modeling regular DNA and RNA. 76 structures, i. e. Dimethylphosphate (conformation gauche, gauche; 4 mol. orientations), the 4 DNA nucleosides [Deoxyadenosine, Deoxycytidine, Deoxyguanosine and Deoxythymidine (conformations C2'endo and C3'endo; 6 mol. orientations for each conformation) and the 4 RNA nucleosides [Adenosine, Cytidine, Guanosine and Uridine (conformation C3'endo, dihedral constraints were used in the geometry optimization step to avoid intra-molecular hydrogen bonds and transition state type structures: HO3'-O3'-C3'-C4' = 180 deg., HO2'-O2'-C2'-C3' = 290 deg.; 6 mol. orientations) are used in the charge derivation. Procedure automatically carried out using the R.E.D.-III program (mol. orientation controlled using the rigid-body re-orientation algorithm implemented in R.E.D.). Charges are similar that those calculated in the Cornell et al. AMBER force field (and/or its adaptations, see Cieplak et al. J. Comput. Chem. 1995, 16, 1357-1377) althought these new values present the advantage to be highly reproducible. Moreover, no manual adaptation of the total charge of the terminal DNA and RNA fragments is required since the DNA and RNA nucleosides are fitted in a single R.E.D. run. Charge values to be compared with those reported in the projects F-45 and F51 (DNA and RNA force field topology database, respectively).
Authors of the project
F.-Y. Dupradeau & P. Cieplak