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. 2012 Aug 20;7(8):e43253. doi: 10.1371/journal.pone.0043253

Figure 1. 2D Structure of the arylamide backbone.

Figure 1

a) hydrogen bonding pattern with free rotation of the third oligomer around the ArCO bond as shown by the arrow. In this case the amide H–H3 and the amide H–H6 can both be in close proximity, but the H–H5 protons can not. This pattern was observed in NMR experiments and dihedral-modified GAFF parameter MD simulations. In b), no hydrogen bond forms leading to free rotation of the third residue around the ArNH bond. In this case the amide H–H3 and the amide H–H5 protons can both be in close proximity, but the amide H–H6 protons can not. This pattern was observed in the unmodified GAFF parameter MD simulations of arylamides, but not in NMR experiments.