On possible influence of different pathways of binding of amides with water on the "pyramidalization" of nitrogen valence bonds of peptide groups
Samchenko, A.A.; Kabanov, A.V.; Komarov, V.M.
Biofizika 55(2): 197-206
2010
ISSN/ISBN: 0006-3029 PMID: 20429270 Document Number: 638891
With the aim to study solvation effects in peptide structure organization, the energy of different types of hydration in simple amines and amides has been analyzed. It was shown based on the quantum-chemical DFT and PM3 calculations of amino derivatives CH3-(CH2)3-NH2, (CH3)2-NH, CH3-NH2, NH3, CH2=CH-NH2, H-CC-NH2, O=C(CH)3-N(CH3)2, O=C(CH3)-NH(CH3), O=C(CH3)-NH2, O=CH-N(CH3)H, and O=CH-NH2 that: (1) in the given set of molecules, the proton acceptor N...H-O variant of hydrogen bonding of NH2-group with a water molecule is dominating only for the simplest amines. Being primordially weaker, the proton donor N-H...OH variant of water H-bonding gradually increases in energy in the given set as the basicity of the compound decreases, and for the case of amides of carbon acids it becomes already a significant channel of the hydration; (2) the intermolecular N-H...O=C bonding of trans-N-methylacetamides, which models the peptide hydrogen bonds in proteins, induces a "planarization" of its initially nonplanar O=C-NH fragments. However, the addition of water molecules to the complex through the proton acceptor N...H-O variant of binding of N atom not only "restores", but even strengthens the "pyramidalization" of valent bonds of peptide groups in this place.