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. Author manuscript; available in PMC: 2013 May 26.
Published in final edited form as: J Phys Chem B. 2010 Oct 25;114(46):15092–15105. doi: 10.1021/jp108452y

Chart 1.

Chart 1

Various structures of protonated RGD: (I) charge-solvated (CS) structure; (II) CS structure with neutral guanidine and protonated N-terminus; (III) CS structure with neutral guanidine and Nprotonated Gly-Asp amide bond; (IV) salt-bridge (SB) structure with deprotonated Asp side chain and protonated N-terminal amino group; (V) SB structure with deprotonated Asp side chain and Nprotonated Gly-Asp amide bond; (VI) SB structure with deprotonated Asp side chain and O-protonated Arg-Gly amide bond; (VII) SB structure with deprotonated Asp side chain and O-protonated Gly-Asp amide bond; (VIII) SB structure with deprotonated C-terminus and protonated N-terminal amino group; (IX) SB structure with deprotonated C-terminus and N-protonated Gly-Asp amide bond; (X) SB structure with deprotonated C-terminus and O-protonated Arg-Gly amide bond; (XI) SB structure with deprotonated C-terminus and O-protonated Gly-Asp amide bond. The relative energies are presented for clarity.