IR and NMR spectroscopic correlation of enterobactin by DFT

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 (HEB) 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 HEB 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 HEB 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 HEB structure. Calculated H andC 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 HEB is described. The matrix-assisted laser desorption/ionization time of the flight mass spectrometry (MALDI-TOF MS) of HEB is also reported of manner to enrich the knowledge about its reactivity.

Experimental and theoretical structural/spectroscopical correlation of enterobactin and catecholamide

“…Unlike the H 6 EB [1] , the calculated [CatFeEB] 3 − shows a unique broad and sharp N-H band at 3547 cm − 1 , coherent with steric restrictions associated to the Fe, and as it is expected the stretching OH bands localized at 3812, 3846, 3747, 3522, 3420, 3371, 3221 and 2880 cm − 1 in H 6 EB disappear in calculated [CatFeEB] 3 . Instead, this band is present in experimental FeEnterobactin, associated to the Fe linked in the Salicylate conformation [SalFeH 3 EB] 0 as it is reported by N.K.…”

“…Raymond [10] , [11] . In the case of stretching and bending C-O bands its intensity decreases, and/or in some cases a signal shift is observed for 1336, 1235, 1175, 1125, 1032, 980, 849, 801, 695, 535 to 1378, 1361, 1094, 1064, 990, 943, 913, 857, 673, 629 and 544 cm − 1 in [CatFeEB] 3 − , details of the H 6 EB IR can be found in [1] . [CatFeEB] 3 − data revels signal shifts for the stretching (C=C) IR bands from 1587, 1544, 1468, 1390, 1343 to 1574, 1555, 1466, 1450, 1370 and 1335 cm − 1 , respectively, this is due to the inductive effect of the Fe attached to the catechol groups, similar to the reports from N.K.…”

“…For the sample preparation of MALDI-TOF MS spectra, 0.5 mL of a saturated solution of a-cyano-4-hydroxycinnamic acid (HCCA) in acetone was deposited on the sample target. A 1 ml aliquot of the sample was injected into a small drop of water previously deposited on the matrix surface [1] . Experimental features Infrared Spectra of [SalFeH 3 EB] 0 was carried out on solid state at RT, instead, a liquid state is performed to capture MALDI-TOF MS spectra.…”

“…Universidad Andres Bello, Facultad de Ciencias Biologicas, Center for Bioinformatic and Integrative Biology (CBIB). Data accessibility Data described here are Supplementary information to the article entitled “IR and NMR Spectroscopic Correlation of Enterobactin by DFT” Spectrochimica Acta A (2018) [1] . Related research article Major details about Enterobactin IR spectra can be found in “IR and NMR Spectroscopic Correlation of Enterobactin by DFT” Spectrochimica Acta A (2018) [1] The Functionalization and characterization of Enterobactin and Fe Enterobactin analogs as well as their affinity prediction with FepA-protein transmembrane using DFT, Molecular Dynamics and Docking will be reported elsewhere.…”

Ironing out pyoverdine’s chromophore structure: serendipity or design?

“…[43][44][45]. The 6-31G* basis set, a verified compromise [46][47][48][49] between accuracy and computational cost in these systems, was used. B3LYP and M06 were found to provide similar results on our systems (RMSD<0.3 Å and Fe 3+ -O distances within 0.03 Å for optimized structures, 2% difference in binding energies).…”