Experimental and theoretical structural/spectroscopical correlation of enterobactin and catecholamide

Here we report the IR spectra of FeEnterobactin in catecholate conformations ([CatFeEB]3−) obtained by DFT calculations using PBE/QZVP and their correlation it with its experimental counterpart [SalH3FeEB]0. Fragments of FeEnterobactin and Enterobactin (H6EB) are elucidated from their MALDI-TOF mass spectrometry, and the dependence of the frontier orbitals (HOMO and LUMO) with the catecholamide dihedral angles of H6EB is reported. The frequency distribution of catecholamide dihedral angle of H6EB was carried-out using molecular dynamics (MD). The data presented enriches the understanding of [CatFeEB]3− and H6EB frequency distribution and reactivity.


Subject area
Chemistry and biology. More specific subject area Synthesis, Functionalization, and Characterization of FeEnterobactin and Enterobactin, IR spectra, catecholamide dihedral angles distribution and reactivity. Type of data Plots were done with Origin 6.0 (OriginLab, Northampton, MA). We used Gauss-View to visualize the frontier orbitals, density, electrostatic potentials and vibrational modes. How data was acquired DFT calculations using PBE exchange/correlation functionals and QZVP basis set were used to obtain the infrared spectra (IR) of [SalFeH 3

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 FepAprotein transmembrane using DFT, Molecular Dynamics and Docking will be reported elsewhere.

Value of the data
The elucidation of ([CatFeEB] 3 À ) IR spectra by DFT contrasted with experimental IR leads a greater understanding of the functional group motion which favors the explanation of their chemical modification.
The determination of the frequency distribution of dihedral angles of H 6 EB structures using molecular dynamics (MD) allows to reveal the predominant structure and with this, its prevailing electronic properties; their reactivity parameters leads to predict synthesis of new materials.
The visualization of atomic bond cleavage of FeEnterobactin and Enterobactin obtained by mass spectrometry permit determine the reactivity sites useful for the implementation of functionalization methodologies.  [10,11]. The IR data is used as guide to improve the elucidation of FeEnterobactin and analogs. MALDI-TOF MS data of [CatFeEB] 3 À exhibits a cleavage in C5-C4 instead C4-N in H 6 EB, again, it seems to be that the steric restrictions of the Fe linked to catechol leave the bond C5-C4 more reactive than C4-N in H 6 EB (see Figs. 2 and 3). This is reflected in the dependence of frontier orbitals (HOMO-LUMO) with the frequency distribution of catecholamide dihedral angles of H 6 EB depicted in Figs. 4-8, for five H 6 EB structures. Despite of this wide versatility, the catecholamide arms tend to converge in only one range of frequencies; from À 60°to 60°, granting to H 6 EB a predominant reactive region governed for carbonyl groups (amide and ester). This match with the C4-N scission reveled from the MALDI-TOF MS data [1]. Fig. 8 depicts the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) of H 6 EB structures, where the effects of the dihedral angles are evident. They show an asymmetrical distribution of the ability to donate electrons (HOMO) and accept electrons (LUMO) located in the catecholamides arms.
Based in other analyzes by Vonlanthen et al. [13] and Mishchenko et al. [14] for a study of molecular conductance in a series of organic molecules with fixed dihedral angles, it is expected that the dihedral angles influence the properties of siderophores and their analogs as reported by Raymond et al. [15].
Thus, data here allow us to infer that the IR spectra and the reactivity are strongly influenced by the presence of Fe. These, together with the steric effects between the arms of catecholamide and with the trilactone backbone, as it is showed in data here. The reactive regions in [CatFeEB] 3 À and H 6 EB, where the delocalization of electrons (amide, esters, and catechol groups) is predominant, are like a protein recognition code, giving rise to cellular memory. Nevertheless, this is beyond the scope of this contribution.

Experimental design, materials, and methods
Experimental infrared spectra were recorded at 50000 scans recorded with 2 cm À 1 resolution. Samples, [SalFeH 3 EB] 0 and H 6 EB, were measured using KRS-5 disc. Fifty milligrams of [SalFeH 3 EB] 0 and H 6 EB, separately, was dispersed in 100 ml of dichloromethane, then one drop was placed on a KRS-5 disc to dry. Solid H 6 EB and [SalFeH 3 EB] 0 were characterized. All solvents and H 6 EB were of analytical purity. 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.
Quantum Chemical calculations were performed using Density Functional Theory (DFT) with the PBE exchange-correlation functional including long-range corrections [6] and QZVP [7,8] basis sets, with an ultrafine integral grid. Different starting catechol amide dihedral angles of H 6 EB were considered for the calculations (see data in Figs. [3][4][5][6]. All the results presented correspond to a local minimum for each of the calculated structures. All theoretical results were performed with the Gaussian 09 code [9] and we used Gauss-View to visualize the molecular orbitals, electrostatic potentials, and the vibrational modes. To obtain the frequencies of different dihedral angles values (Arm1, Arm2, and Arm3) from H 6 EB structures over a time lapse, molecular dynamics (MD) simulations (using the Desmond code) of the four structures of H 6 EB were performed, where each structure was embedded into an explicit TIP3P [2] water box. The NPT ensemble was employed with at 300 K and 1.01 bar of pressure and the OPLS-2005 force field [3] was used. Each system was subjected to energy minimization before the MD simulations were carried out for 5 ns. We used a VMD software [5] to calculate the dihedrals angles on catecholamides from H 6 EB structures during the MD trajectories. Plots were done with Origin 6.0 (OriginLab, Northampton, MA). All systems were simulated considering periodic boundary conditions (PBC).