Quantum mechanical investigation of aqueous desferrioxamine B metal complexes: Trends in structure, binding, and infrared spectroscopy

Efficient density functional theory directed identification of siderophores with increased selectivity towards indium and germanium

Siderophores are promising ligands for application in novel recycling and bioremediation technologies, as they can selectively complex a variety of metals. However, with over 250 known siderophores, the selection of suiting complexants in the wet lab is impractical. Thus, this study established a density functional theory (DFT) based approach to efficiently identify siderophores with increased selectivity towards target metals on the example of germanium and indium. Considering 239 structures, chemically similar siderophores were clustered, and their complexation reactions modeled utilizing DFT. The calculations revealed siderophores with, compared to the reference siderophore desferrioxamine B (DFOB), up to 128 % or 48 % higher selectivity for indium or germanium, respectively. Experimental validation of the method was conducted with fimsbactin A and agrobactin, demonstrating up to 40 % more selective indium binding and at least sevenfold better germanium binding than DFOB, respectively. The results generated in this study open the door for the utilization of siderophores in eco-friendly technologies for the recovery of many different critical metals from various industry waters and leachates or bioremediation approaches. This endeavor is greatly facilitated by applying the herein-created database of geometry-optimized siderophore structures as de novo modeling of the molecules can be omitted.

Biosynthesis of iron-chelating terramides A-C and their role in Aspergillus terreus infection

Fungal natural products from various species often feature hydroxamic acid motifs that have the ability to chelate iron. These compounds have an array of medicinally and ecologically relevant activities. Through genome mining, gene deletion in the host Aspergillus terreus, and heterologous expression experiments, this study has revealed that a nonribosomal peptide synthetase (NRPS) TamA and a specialized cytochrome P450 monooxygenase TamB catalyze the sequential biosynthetic reactions in the formation of terramides A-C, a series of diketopiperazines (DKPs) with hydroxamic acid motifs. Feeding experiments showed that TamB catalyzes an unprecedented di-hydroxylation of the amide nitrogens in the diketopiperazine core. This tailoring reaction led to the formation of two bidentate iron-binding sites per molecule with an unusual iron-binding stoichiometry. The structure of the terramide A-Fe complex was characterized by liquid chromatography-mass spectrometry (LC-MS), Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy and electron paramagnetic resonance spectroscopy (EPR). Antimicrobial assays showed that the iron-binding motifs are crucial for the activity against bacteria and fungi. Murine infection experiments indicated that terramide production is crucial for the virulence of A. terreus and could be a potential antifungal drug target.

Reduction-cleavable desferrioxamine B pulldown system enriches Ni(ii)-superoxide dismutase from a Streptomyces proteome

Two resins with the hydroxamic acid siderophore desferrioxamine B (DFOB) immobilised as a free ligand or its Fe(iii) complex were prepared to screen the Streptomyces pilosus proteome for proteins involved in siderophore-mediated Fe(iii) uptake. The resin design included a disulfide bond to enable the release of bound proteins under mild reducing conditions. Proteomics analysis of the bound fractions did not identify proteins associated with siderophore-mediated Fe(iii) uptake, but identified nickel superoxide dismutase (NiSOD), which was enriched on the apo-DFOB-resin but not the Fe(iii)-DFOB-resin or the control resin. While DFOB is unable to sequester Fe(iii) from sites deeply buried in metalloproteins, the coordinatively unsaturated Ni(ii) ion in NiSOD is present in a surface-exposed loop region at the N-terminus, which might enable partial chelation. The results were consistent with the notion that the apo-DFOB-resin formed a ternary complex with NiSOD, which was not possible for either the coordinatively saturated Fe(iii)-DFOB-resin or the non-coordinating control resin systems. In support, ESI-TOF-MS measurements from a solution of a model Ni(ii)-SOD peptide and DFOB showed signals that correlated with a ternary Ni(ii)-SOD peptide-DFOB complex. Although any biological implications of a DFOB-NiSOD complex are unclear, the work shows that the metal coordination properties of siderophores might influence an array of metal-dependent biological processes beyond those established in iron uptake.

Elucidation of crude siderophore extracts from supernatants of Pseudomonas sp. ZnCd2003 cultivated in nutrient broth supplemented with Zn, Cd, and Zn plus Cd

This research aimed to study siderophores secreted from Pseudomonas sp. PDMZnCd2003, a Zn/Cd tolerant bacterium. The effects of Zn and/or Cd stress were examined in nutrient broth to achieve the actual environmental conditions. Acid and alkali supernatants and liquid-liquid extraction with ethyl acetate and butanol were carried out to obtain crude extracts containing different amounts of the metals. The bacterial growth, UV-visible spectra of the supernatants and siderophore production indicated that the production of siderophores tended to be linked to primary metabolites. Pyocyanin was produced in all treatments, while pyoverdine was induced by stress from the metals, especially Cd. FT-IR spectra showed C=O groups and sulfur functional groups that were involved in binding with the metals. LC-MS revealed that pyocyanin, 1-hydroxy phenazine, pyoverdine, and pyochelin were present in the crude extracts. S K-edge XANES spectra showed that the main sulfur species in the extracts were the reduced forms of sulfide, thiol, and disulfide, and their oxidation states were affected by coordination with Zn and/or Cd. In addition, Zn K-edge EXAFS spectra and Cd K-edge EXAFS spectra presented Zn-O and Cd-O as coordination in the first shell, in case the extracts contained less metal. Although the mix O/S ligands had chelation bonding with Zn and Cd in the other extracts. For the role of S groups in pyochelin binding with the metals, this was the first report. The results of these experiments could be extended to Pseudomonas that respond to metal contaminated environments.

Mobilization and partitioning of rare earth elements in the presence of humic acids and siderophores

Developing rare earth elements (plus yttrium, REY) as a group of environmental tracer requires comprehensive understandings in their geochemical behaviors associated with natural organic matter. Recent work highlighted the promotions on REY mobilization and cerium oxidation by siderophores during silicate dissolution, but the mechanism remained ambiguous. Here, we performed batch fluid-rock interaction experiments to explore the functions of siderophore desferrioxamine B (DFOB) and humic acids (HA) towards REY mobility and partitioning during REY-bearing ferrihydrite dissolution. To acquire in-depth knowledge of organic controls on REY, we used multiple strategies, including elemental, multispectral, and electrochemical analyses, to investigate the organic regulation on REY geochemistry. This study sheds light on the function of ligand-specific selectivity and solid-fluid organic molecular fractionation, primarily dependent on hydrochemical settings (pH, organic compounds, ionic strength, and oxicity). Our results confirm the catalytic oxidation ability of ligand, which forms DFOB-Ce(IV) (K = 10⁴², electrochemistry), producing positive Ce anomalies in solutions by ligand-driven redox shifting. Both HA and DFOB showed high affinities to HREY, and facilitated LREY/HREY partitioning. The mobilization of REY and the development of Ce anomalies were limited by HA coatings that modified surface properties and disturbed the approach of DFOB. Excess siderophores attack inert HA coatings, facilitating REY liberation and Ce redox activities. The release of REY and catalytic oxidation of Ce can be inhibited at high ionic strength or under oxygen deficiency. Our study reveals that natural organic matter significantly influences the fate of REY in iron oxides, and crucial for the biogeochemical cycles of REY in nature.

Predicting the Thermodynamic Stability of Zirconium Radiotracers

The thermodynamic stability of a metal-ligand complex, as measured by the formation constant (log β), is one of the most important parameters that determines metal ion selectivity and potential applications in, for example, radiopharmaceutical science. The stable coordination chemistry of radioactive ⁸⁹Zr⁴⁺ in an aqueous environment is of paramount importance when developing positron-emitting radiotracers based on proteins (usually antibodies) for use with positron emission tomography. Desferrioxamine B (DFO) remains the chelate of choice for clinical applications of ⁸⁹Zr-labeled proteins, but the coordination of DFO to Zr⁴⁺ ions is suboptimal. Many alternative ligands have been reported, but the challenges in measuring very high log β values with metal ions such as Zr⁴⁺ that tend to hydrolyze mean that accurate thermodynamic data are scarce. In this work, density functional theory (DFT) calculations were used to predict the reaction energetics for metal ion complexation. Computed values of pseudoformation constants (log β') are correlated with experimental data and showed an excellent linear relationship (R² = 0.97). The model was then used to estimate the absolute and relative formation constants of 23 different Zr⁴⁺ complexes using a total of 17 different ligands, including many of the alternative bifunctional chelates that have been reported recently for use in ⁸⁹Zr⁴⁺ radiochemistry. In addition, detailed computational studies were performed on the geometric isomerism and hydration state of Zr-desferrioxamine. Collectively, the results offer new insights into Zr⁴⁺ coordination chemistry that will help guide the synthesis of future ligands. The computational model developed here is straightforward and reproducible and can be readily applied in the design of other metal coordination compounds.

Computational Tools for Calculating log β Values of Geochemically Relevant Uranium Organometallic Complexes

Uranium (U^VI) interacts with organic ligands, subsequently controlling its aqueous chemistry. It is therefore imperative to assess the binding ability of natural organic molecules. We evidence that density functional theory (DFT) can be used as a practical protocol for predicting the stability of U^VI organic ligand complexes, allowing for the development of a relative stability series for organic complexes with limited experimental data. Solvation methods and DFT settings were benchmarked to suggest a suitable off-the-shelf solution. The results indicate that the IEFPCM solvation method should be employed. A mixed solvation approach improves the accuracy of the calculated stability constant (log β); however, the calculated log β are approximately five times more favorable than experimental data. Different basis sets, functionals, and effective core potentials were tested to check that there were no major changes in molecular geometries and Δ_r G. The recommended method employed is the B3LYP functional, aug-cc-pVDZ basis set for ligands, MDF60 ECP and basis set for U^VI, and the IEFPCM solvation model. Using the fitting approach employed in the literature with these updated DFT settings allows fitting of 1:1 U^VI complexes with root-mean-square deviation of 1.38 log β units. Fitting multiple bound carboxylate ligands indicates a second, separate fitting for 1:2 and 1:3 complexes.

Increased Solubility and Bioavailability of Hydroxy-Cr(III) Precipitates in the Presence of Hydroxamate Siderophores

Siderophores are a diverse group of low molecular weight biogenic metallophores with a particular affinity for Fe(III) but they also have potential to complex a number of other polyvalent metal cations, including Cr(III). Here we show that two hydroxamate siderophores, desferrioxamine B and rhodotorulic acid, at environmentally relevant concentrations, facilitate the dissolution of hydroxy-Cr(III) precipitates from a common layer silicate. Desferrioxamine B and rhodotorulic acid induced maximum initial Cr dissolution rates of 11.3 ± 1.7 × 10^- 4  and 9.03 ± 0.68 × 10^- 4 µmol m^- 2 h^- 1, respectively, yielding maximum solution Cr concentrations of 0.26 ± 0.01 and 0.20 ± 0.02 µmol m^- 2, respectively. These data demonstrate that hydroxamate siderophores may play an important role increasing the dispersal of Cr in natural environments, thus facilitating greater bioavailability of this potential toxin.

Copper isotope fractionation during equilibration with natural and synthetic ligands

As copper (Cu) stable isotopes emerge as a tool for tracing Cu biogeochemical cycling, an understanding of how Cu isotopes fractionate during complexation with soluble organic ligands in natural waters and soil solutions is required. A Donnan dialysis technique was employed to assess the isotopic fractionation of Cu during complexation with the soluble synthetic ligands ethylenediaminetetraacetic acid (EDTA), nitrilotriacetic acid (NTA), iminodiacetic acid (IDA) and desferrioxamine B (DFOB), as well as with Suwannee River fulvic acid (SRFA). The results indicated enrichment of the heavy isotope ((65)Cu) in the complexes, with Δ(65)Cu complex-free values ranging from +0.14 to +0.84‰. A strong linear correlation was found between the logarithms of the stability constants of the Cu complexes and the magnitudes of isotopic fractionation. These results show that complexation of Cu by organic ligands can affect the isotopic signature of the free Cu ion. This free Cu is considered the most bioavailable species, and hence, our results highlight the importance of understanding fractionation processes in the uptake medium when using Cu isotopes to study the uptake mechanisms of organisms. These data contribute a vital piece to the emerging picture of Cu isotope cycling in the natural environment, as organic complexation plays a key role in the Cu cycle.