Theoretical model of the interaction of glycine with hydrogenated amorphous carbon (HAC)

Investigations of adsorption behavior and anti-inflammatory activity of glycine functionalized Al12N12 and Al12ON11 fullerene-like cages

The adsorption behavior of the amino acid, glycine (Gly), via the carboxyl, hydroxyl, and amino groups onto the surfaces of Al₁₂N₁₂ and Al₁₆N₁₆ fullerene-like cages were computationally evaluated by the combination of density functional theory (DFT) and molecular docking studies. It was found that Gly can chemically bond with the Al₁₂N₁₂ and Al₁₆N₁₆ fullerene-like cages as its amino group being more favorable to interact with the aluminum atoms of the adsorbents compared to carboxyl and hydroxyl groups. Oxygen and carbon doping were reported to reduce steric hindrance for Glycine interaction at Al site of Al₁₂ON₁₁/Gly and Al₁₂CN₁₁/Gly complexes. Interaction was further enhanced by oxygen doping due to its greater electron withdrawing effect. Herein, the Al₁₂ON₁₁/Gly complex where two carbonyl groups of Gly are bonded to the aluminum atoms of the Al₁₂N₁₂ fullerene-like cage is the most stable interaction configuration showing ∆_adsH and ∆_adsG values of -81.74 kcal/mol and -66.21 kcal/mol, respectively. Computational studies also revealed the frequency shifts that occurred due to the interaction process. Molecular docking analysis revealed that the Al₁₂N₁₂/Gly (-11.7 kcal/mol) and the Al₁₂ON₁₁/Gly (-9.2 kcal/mol) complexes have a good binding affinity with protein tumor necrosis factor alpha (TNF-α). TNF-α was implicated as a key cytokine in various diseases, and it has been a validated therapeutic target for the treatment of rheumatoid arthritis. These results suggest that the Al₁₂N₁₂/Gly complex in comparison with the Al₁₆N₁₆/Gly, Al₁₂ON₁₁/Gly, and the Al₁₂CN₁₁/Gly complexes could be efficient inhibitors of TNF-α.

Structure and infrared spectra of hydrocarbon interstellar dust analogs

A theoretical study of the structure and mid infrared (IR) spectra of interstellar hydrocarbon dust analogs is presented, based on DFT calculations of amorphous solids. The basic molecular structures for these solids are taken from two competing literature models. The first model considers small aromatic units linked by aliphatic chains. The second one assumes a polyaromatic core with hydrogen and methyl substituents at the edges. The calculated spectra are in reasonably good agreement with those of aliphatic-rich and graphitic-rich samples of hydrogenated amorphous carbon (HAC) generated in our laboratory. The theoretical analysis allows the assignment of the main vibrations in the HAC spectra and shows that there is a large degree of mode mixing. The calculated spectra show a marked dependence on the density of the model solids, which evinces the strong influence of the environment on the strengths of the vibrational modes. The present results indicate that the current procedure of estimating the hydrogen and graphitic content of HAC samples through the decomposition of IR features into vibrational modes of individual functional groups is problematic owing to the mentioned mode mixing and to the difficulty of assigning reliable and unique band strengths to the various molecular vibrations. Current band strengths from the literature might overestimate polyaromatic structures. Comparison with astronomical observations suggests that the average structure of carbonaceous dust in the diffuse interstellar medium lies probably in between those of the two models considered, though closer to the more aliphatic structure.