Molecular Studies of Siderophores in Aqueous Solutions and at the Mineral Oxide - Organic Interface

Siderophores in the natural environment

Siderophores are organic macromolecules (400-1000 Da) released by bacteria in iron limiting situations to complex ferric iron and prevent precipitation of iron oxyhydroxides in the natural environment. They are composed of hydroxamate and phenolate derivatives (Figure 1), which provide high affinity complexation sites for ferric iron. Pioneering studies by the groups of Neilands and Raymond characterized siderophore properties including binding constants [1], mechanisms of cellular uptake [2], and structure [3]. Farkas et al. have discussed the redox chemistry of several siderophores [4], and surface dissolution studies by Holmen and Kraemer [5] have elucidated adsorption processes at the metal oxide-organic interface. The past research has provided a library of information concerning siderophores, but few studies have analyzed siderophore-surface or aqueous solution interactions at a molecular level.


Figure 1
Figure 1: Two examples of siderophores common in the environment.



The objective of this project is to gain a better understanding of the molecular properties of siderophores in both aqueous solution and on mineral surfaces. The properties (coordination chemistry and local bonding environment) of siderophores will be evaluated using vibrational (IR and Raman) and X-ray absorption spectroscopy (XAS). This molecular-level investigation of siderophores will test hypotheses provided by theoretical models and help gain insight into geochemical processes such as contaminant transport, weathering influenced by mineral adsorbed organics, and actinide sequestration processes.


Complementary instrumentation (IR and Raman/ NEXAFS and EXAFS) will be used to evaluate the siderophores in aqueous solution and on mineral surfaces. The IR work is done in our home lab at Princeton University using a Bruker Attenuated Total Reflectance – Fourier Transform Infrared (ATR-FTIR) spectrometer. The Raman studies are completed in the Department of Chemistry. The NEXAFS studies are performed at the Advanced Light Source at the Lawrence Berkeley National Lab (LBNL) and the EXAFS studies were performed at the Stanford Synchrotron Radiation Laboratory (SSRL). To date, the aqueous solution studies have been completed and preliminary studies on mineral surfaces are now being performed.

Experimental and theoretical results

To model the larger siderophore desferrioxamine B (desB), an oxime, acetohydroxamic acid (aHa) (Figure 2), was used. Infrared studies of aHa and desB at different pH values show definite shifts in certain frequencies as the compound goes above the pKa. To illustrate these shifts, Figure 3 shows the IR spectra above and below the pKa, along with the density functional theory (DFT) theoretical models.

Figure 2
Figure 2: Cis and trans forms of acetohydroxamic acid. The O-deprotonated resonance forms are shown for the cis molecule.


Figure 3
Figure 3: Experimental and Theoretical IR spectra of aHa. a) Experimental spectra at pH = 4.98, b) Theoretical spectra of the neutral aHa model, c) Experimental spectra at pH = 12.35, d) the theoretical spectra of N-deprotonated aHa and, e) O-deprotonated aHa.


Similar peaks occur when aHa complexes with iron. Figure 4 shows the IR and Raman (plus theoretical) of the Fe(aHa) complex.


Figure 4
Figure 4: a) Experimental Raman spectra of the Fe(aHa) complex. The excitation peak is at 407 nm. b) Theoretical Raman spectra, c) experimental IR spectra, and d) theoretical IR spectra of the Fe(aHa) complex.

Future work

In the future, studies on minerals will be completed with both vibrational and x-ray absorption spectroscopy. Once the Fe-complexation of siderophores are completed, synthetic siderophores will be made that can selectively complex actinides in DOE nuclear contaminated sites.


  1. Brink, C.P. & Crumbliss, A.L. (1984). Kinetics, Mechanism, and Thermodynamics of Aqueous Iron (III) Chelation and Dissociation: Influence of Carbon and Nitrogen Substituents in Hydroxamic acid Ligands. Inorganic Chemistry 23, 4708-4718.
  2. Matzanke, B.F., Muller-Matzanke, G. & Raymond, K.N. (1989). Siderophore Mediated Iron Transport. In Iron Carriers and Iron Proteins (Loehr, T.M., ed.). pp. 124, VCH: New York.
  3. Neilands, J.B. (1995). Siderophores: Structure and Function of Microbial Iron Transport Compounds. Journal of Biological Chemistry, 270 26723-26726.
  4. Farkas, E., Enyedy, E.A. & Csoka, H. (1999). A comparison between the chelating properties of some dihydroxamic acid, desferrioxamine B and acetohydroxamic acid. Polyhedron 18, 2391-2398.
  5. Holmen, B.A. & Casey, W.H. (1996). Hydroxamate ligands, surface chemistry, and the mechanism of ligand promoted dissolution of goethite (alpha -FeOOH(s)). Geochimica et Cosmochimica Acta 60, 4403-4416.