IR and NMR spectroscopic correlation of enterobactin by DFT

Highlights

• DFT is used to calculate the Infrared and NMR spectra of Enterobactin (H₆EB) structures dependent of dihedral angle with different xc- functionals, like PBE (including long-range corrections) and mPW91, with the standard basis sets QZVP, and 6 31G(d) using fine and ultrafine grid.

• NMR DFT calculations show a strong dependence of the exchange-correlation functional, basis set, grid and dihedral angle.

• The results show significant differences between the OH and NH bands, and the CO amide and O(CO) IR bands in all H₆EB structures, which are often on top of each other.

• The good agreement between the experimental and the calculated spectra using LC-PBE/QZVP and ultrafine grid suggest the possibility of the systems reported here to be considered as a standard set.

• DFT is also utilized to calculate the dependence between dihedral angle with electrostatic potential and frontier orbital. The reactivity of H₆EB is explored by MALDI-TOF MS.

Abstract

Emerging and re-emerging epidemic diseases pose an ongoing threat to global health. Currently, Enterobactin and Enterobactin derivatives have gained interest, owing to their potential application in the pharmaceutical field. As it is known [J. Am. Chem. Soc (1979) 101, 20, 6097–6104], Enterobactin (H₆EB) is an efficient iron carrier synthesized and secreted by many microbial species. In order to facilitate the elucidation of enterobactin and its analogues, here we propose the creation of a H₆EB standard set using Density Functional Theory Infrared (IR) and NMR spectra. We used two exchange-correlation (xc) functionals (PBE including long-range corrections LC-PBE and mPW1), 2 basis sets (QZVP and 6-31G(d)) and 2 grids (fine and ultrafine) for most of the H₆EB structures dependent of dihedral angles. The results show a significant difference between the OH and NH bands, while the CO amide and O(CO) IR bands are often found on top of each other. The NMR DFT calculations show a strong dependence on the xc functional, basis set, and grid used for the H₆EB structure. Calculated ¹H and ¹³C NMR spectra enable the effect of the solvent to be understood in the context of the experimental measurements. The good agreement between the experimental and the calculated spectra using LC-PBE/QZVP and ultrafine grid suggest the possibility of the systems reported here to be considered as a standard set. The dependence of electrostatic potential and frontier orbitals with the catecholamide dihedral angles of H₆EB is described. The matrix-assisted laser desorption/ionization time of the flight mass spectrometry (MALDI-TOF MS) of H₆EB is also reported of manner to enrich the knowledge about its reactivity.