The structures of the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers have been fully optimized at B3LYP/6–311++G** level. The intermolecular hydrogen bonding interaction energies have been calculated using the B3LYP/6–311++G**, B3LYP/6–311++G(2df,2p), MP2(full)/6–311++G** and MP2(full)/6–311++G(2df,2p) methods, respectively. The results show that the O–H···O, N–H···O, O–H···N, and C–H···O hydrogen bonding interactions could exist in N-(hydroxymethyl)acetamide dimers, and the O–H···O, N–H···O, and O–H···N hydrogen bonding interactions could be stronger than C–H···O. The three-dimensional network structure formed by ceramide molecules through intermolecular hydrogen bonding interactions may be the main reason why the stratum corneum of skin could prevent foreign substances from entering our body, as is in accordance with the experimental results. The stability of hydrogen-bonding interactions follow the order of (a) > (b) ≈ (c) > (d) > (e) ≈ (f) > (g) > (h). The analyses of the energy decomposition, frequency, atoms in molecules (AIM), natural bond orbital (NBO), and electron density shift are used to further reveal the nature of the complex formation. In the range of 263.0–328.0 K, the complex is formed via an exothermic reaction, and the solvent with lower temperature and dielectric constant is favorable to this process.
Journal of Molecular Modeling – Springer Journals
Published: May 31, 2018
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