Structure and property of glycine’s derivatives bound by multications (H+, Li+, and Na+): A theoretical study

Abstract

The calculations using several different methods (B3P86, MP2, MP3, MP4SDQ, and CCSD) and basis sets [6-31G*, 6-31+G*, and 6-311+G(2df,2pd)] have been first performed for 15 glycine derivatives (one Gly–2H+, one Gly–3H+, five Gly–H+Li+ isomers, three Gly–H+Na+ isomers, three Gly–Li+Na+ isomers, and two Gly–2Na+ isomers) formed by multications (H+, Li+ or Na+) and different active sites of a glycine molecule. These calculations yield accurate geometric structures, relative energies, bond energies, vibrational frequencies, infrared intensities, and charge distributions. The comparisons of relative energy for each isomer show that both Gly–2H+ and Gly–3H+ derived from the most stable neutral glycine hold the lowest energies among their respective corresponding isomers. For the Gly–2H+, two protons are, respectively, bound to the amino nitrogen and the syn carbonyl oxygen of the most stable neutral glycine molecule. On the basis of the Gly–2H+, the derivative Gly–3H+ can be generated when the third proton binds to the hydroxyl oxygen. For five Gly–H+Li+ isomers, three Gly–H+Na+ isomers, three Gly–Li+Na+ isomers, and two Gly–2Na+ isomers, each of their corresponding ground state possesses the structure with the heavier cation coordinated to carbonyl oxygen and the lighter one to the anti-amino nitrogen of another kinds of neutral glycine molecule. The bond energies first reveal that some of these derivatives must surmount an activation energy barrier in the course of some cation (proton) dissociating from it. The origin of these barriers are investigated and discussed. Finally characteristic frequency calculations imply that the study is very important in the search of the glycine derivatives by rotational spectroscopy, or for the identification of their isomers by their infrared bands.

The binding site dependence of binding energy in both metalated and protonated diglycine and triglycine peptides

“…For example, the differences between G 2 H + Li1 + and G 2 H + Li2 + , between G 2 H + Na1 + and G 2 H + Na2 + , and between G 2 H + K1 + and G 2 H + K2 + are 10.3, 10.5 and 10.1 kcal/mol, respectively, almost constant values. The results agree well with our previous reports [6,7] that the binding mode with protonation at the terminus nitrogen and metalation at the carboxyl oxygen of the C-terminus will decrease the electrostatic repulsion effect between them (like the case in G 2 H + M2 +/2+ ), and thus strengthen the stability of G 2 H + M2 +/2+ over the G 2 H + M1 +/2+ . Consequently, the BE of the M-O bond is also reduced, as described below.…”

“…The positive BE values were reported previously in the double cationized glycine (G) systems [6][7][8][9]. Columbic repulsion contributes the positive BE mainly [7,22].…”

“…Previous studies [6,9] showed that it was more readily to produce a stable GH + Na + /Li + in thermodynamics by following binding order, i.e., Na + /Li + was first bound at the carbonyl oxygen of a glycine then the amino-terminus nitrogen was protonized. The opposite binding order would involve higher activation energy.…”

“…Therefore, some small peptides are often used to probe those properties, such as the proton affinity [2,3] and the metalation [4], because of their experimental tractability and relative simplicity. In fact, protonated and metalated amino acids, taken as simpler models to simulate and predict the behaviors of peptides and even proteins, had already been comprehensively investigated previously [5][6][7][8][9].…”

Study of metal ions (Na+, K+) interaction with different conformations of glycine molecule

“…They also calculated the proton affinities for the bidentate complexes. Ai et al [19] studied the multication derivatives for glycine molecule. Moision and Armentrout [20] calculated sodium affinities for glycine using experimental and theoretical methods.…”