Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules

A continuation of recent studies of the MFCC method for full quantum mechanical computation of the protein-molecule interaction energy when applied to peptides or proteins that have disulfide bonds is presented. The application of the MFCC method in this case requires one to cut the disulfide bond and insert pairs of conjugated molecular caps at the cuts. The cutting of disulfide bond will create peptide fragments with three capped ends. Either the MeS- or HS- cap used at the cut of the S-S bond is found to give excellent results at various levels of ab initio methods.