DFT and TD-DFT studies to elucidate the configurational isomers of ferric aerobactin, ferric petrobactin, and their ferric photoproducts

Sasha Gardner, Carl J. Carrano, Yuezhi Mao, Frithjof C. Kuepper, Andrew L. Cooksy (Corresponding Author)

Research output: Contribution to journalArticlepeer-review

Abstract

Iron-chelating siderophores such as aerobactin and petrobactin are produced by marine bacteria to sequester iron under low iron stress. Those that contain a citrate moiety undergo light-catalyzed ligand-tometal charge transfer, inducing decarboxylation and formation of photoproducts. In this work, we employed density functional theory to obtain the optimized geometries and determine the relative energies and geometric parameters of different configurations of Fe(III)-coordinated aerobactin, petrobactin, and their photoproducts. Time-dependent density functional theory was then used to compute the UV-vis absorption spectra of these species, and the comparison against experimental spectra further elucidated the structural configurations most likely to be adopted by these compounds. Frequency calculations provided Fe-O force constants on the same order as other siderophores. The relative energies and predicted spectra support the cis-cis C-fac configuration for ferric aerobactin and the cis-trans C-mer configuration for its photoproduct, while only mild support is found for specific configurations of the ferric petrobactin structures (meta-mer and meta-fac for the precursor, cis-cis para-fac for the photoproduct). The predicted ferric petrobactin spectra are found to be fairly insensitive to the configuration of the ferric complex.
Original languageEnglish
Number of pages17
JournalBiometals
DOIs
Publication statusAccepted/In press - 10 Sept 2024

Bibliographical note

Author contributions: Sasha Gardner carried out all calculations and composed the original draft of the manuscript including tables and figures. Carl J. Carrano suggested the project, provided the original experimental data, and provided early guidance on the interpretation of the experimental work. Yuezhi Mao and Andrew Cooksy provided guidance and resources for the calculations. Frithjof Küpper provided guidance on the context of the work and on the original experimental work and drafted relevant sections of the manuscript. All authors save Carrano edited the manuscript.

Data Availability Statement

Input and output files for DFT, TD-DFT calculations in Q-chem. Python files for extracting excitation data from TD-DFT output files and python files for plotting
spectra from excitation data are all available from the Zenodo repository at https://doi.org/10.5281/zenodo.13308919. https://zenodo.org/ records/11054797.

Keywords

  • siderophores
  • aerobactin
  • petrobactin
  • DFT
  • TD-DFT
  • UV-vis
  • absorbance
  • decarboxylation

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