On the Electronic Structure of [1Fe] Fe−S Complexes from Anionic Photoelectron Spectroscopy

Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH3)4]q, q = -2, -1, +2, +3

Iron-sulfur clusters play important roles in biology as parts of electron-transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron-sulfur cluster of rubredoxin and its cationic counterparts. Specifically, we investigated adiabatic reduction energies, dissociation energies, and bonding properties of the low-lying electronic states of the complexes [Fe(SCH₃)₄]^2-/1-/2+/3+ using multireference (CASSCF, MRCISD), and coupled cluster [CCSD(T)] methodologies. We show that the nature of the Fe-S chemical bond and the magnitude of the ionization potentials in the anionic and cationic [Fe(SCH₃)₄] complexes offer a physical rationale for the relative stabilization, structure, and speciation of these complexes. Anionic and cationic complexes present different types of chemical bonds: prevalently ionic in [Fe(SCH₃)₄]^2-/1- complexes and covalent in [Fe(SCH₃)₄]^2+/3+ complexes. The ionic bonds result in an energy gain for the transition [Fe(SCH₃)₄]^2- → [Fe(SCH₃)₄]^- (i.e., Fe^II → Fe^III) of 1.5 eV, while the covalent bonds result in an energy loss for the transition [Fe(SCH₃)₄]²⁺ → [Fe(SCH₃)₄]³⁺ of 16.6 eV, almost half of the ionization potential of Fe²⁺. The ionic versus covalent bond character influences the Fe-S bond strength and length, that is, ionic Fe-S bonds are longer than covalent ones by about 0.2 Å (for Fe^II) and 0.04 Å (for Fe^II). Finally, the average Fe-S heterolytic bond strength is 6.7 eV (Fe^II) and 14.6 eV (Fe^III) at the RCCSD(T) level of theory.

Assessment of Quantum Mechanical Methods for Copper and Iron Complexes by Photoelectron Spectroscopy

Broken-symmetry density functional theory (BS-DFT) calculations are assessed for redox energetics [Cu(SCH₃)₂]^1–/0, [Cu(NCS)₂]^1–/0, [FeCl₄]^1–/0, and [Fe(SCH₃)₄]^1–/0 against vertical detachment energies (VDE) from valence photoelectron spectroscopy (PES), as a prelude to studies of metalloprotein analogs. The M06 and B3LYP hybrid functionals give VDE that agree with the PES VDE for the Fe complexes, but both underestimate it by ∼400 meV for the Cu complexes; other hybrid functionals give VDEs that are an increasing function of the amount of Hartree–Fock (HF) exchange and so cannot show good agreement for both Cu and Fe complexes. Range-separated (RS) functionals appear to give a better distribution of HF exchange since the negative HOMO energy is approximately equal to the VDEs but also give VDEs dependent on the amount of HF exchange, sometimes leading to ground states with incorrect electron configurations; the LRC-ωPBEh functional reduced to 10% HF exchange at short-range give somewhat better values for both, although still ∼150 meV too low for the Cu complexes and ∼50 meV too high for the Fe complexes. Overall, the results indicate that while HF exchange compensates for self-interaction error in DFT calculations of both Cu and Fe complexes, too much may lead to more sensitivity to nondynamical correlation in the spin-polarized Fe complexes.

Understanding rubredoxin redox sites by density functional theory studies of analogues

Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH(3))(4)](0/1-/2-), [Fe(S(2)-o-xyl)(2)](0/1-/2-), and Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) in different conformations. In particular, the study of Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ∼0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.

Optimization of Spin-Unrestricted Density Functional Theory for Redox Properties of Rubredoxin Redox Site Analogues

Quantum chemical calculations of metal clusters in proteins for redox studies require both computational feasibility as well as accuracies of at least ∼50 mV for redox energies but only ∼0.05 Å for bond lengths. Thus, optimization of spin-unrestricted density functional theory (DFT) methods, especially the hybrid generalized gradient approximation functionals, for energies while maintaining good geometries is essential. Here, different DFT functionals with effective core potential (ECP) and full core basis sets for [Fe(SCH(3))(4)](2-/1-) and [Fe(SCH(3))(3)](1-/0), which are analogs of the iron-sulfur protein rubredoxin, are investigated in comparison to experiment as well as other more computationally intensive electron correlation methods. In particular, redox energies are calibrated against gas-phase photoelectron spectroscopy data so no approximations for the environment are needed. B3LYP gives the best balance of accuracy in energy and geometry compared B97gga1 and BHandH and is better for energies than Møller-Plesset perturbation theory series (MP2, MP3, MP4SDQ) and comparable to coupled cluster [CCSD, CCSD(T)] methods. Of the full core basis sets tested, the 6-31G** basis sets give good geometries, and addition of diffuse functions to only the sulfur significantly improves the energies. Moreover, a basis set with an ECP on only the iron gives a less accurate but still reasonable geometries and energies.

Photoelectron Spectroscopy of the Bis(dithiolene) Anions [M(mnt)2]n- (M = Fe − Zn; n = 1, 2): Changes in Electronic Structure with Variation of Metal Center and with Oxidation

A detailed understanding of the electronic structures of transition metal bis(dithiolene) centers is important in the context of their interesting redox, magnetic, and optical properties. The electronic structures of the series [M(mnt)2]n- (M = Fe - Zn; mnt = 1,2-S2C2(CN)2; n = 1, 2) were examined by a combination of photodetachment photoelectron spectroscopy and density functional theory calculations, providing insights into changes in electronic structure with variation of the metal center and with oxidation. Significant changes were observed for the dianions [M(mnt)2]2- due to stabilization of the metal 3d levels from Fe to Zn and the transition from square-planar to tetrahedral coordination about the metal center (Fe-Ni, D(2h) --> Cu D2 --> Zn, D(2d). Changes with oxidation from [M(mnt)2]2- to [M(mnt)2]1- were largely dependent on the nature of the redox-active orbital in the couple [M(mnt)2](2-/1-). In particular, the first detachment feature for [Fe(mnt)2]2- originated from a metal-based orbital (Fe(II) --> Fe(III)) while that for [Fe(mnt)2]1- originated from a ligand-based orbital, a consequence of stabilization of Fe 3d levels in the latter. In contrast, the first detachment feature for both of [Ni(mnt)2]2- and [Ni(mnt)2]1- originated from the same ligand-based orbital in both cases, a result of occupied Ni 3d levels being stabilized relative those of Fe 3d and occurring below the highest energy occupied ligand-based orbital for both of [Ni(mnt)2]2- and [Ni(mnt)2]1- . The combined data illustrate the subtle interplay between metal- and ligand-based redox chemistry in these species and demonstrate changes in their electronic structures with variation of metal center, oxidation, and coordination geometry.

Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron-containing proteins to be accurately modeled, focussing on iron-sulfur, iron-heme, and iron-only hydrogenases. Data computed at the B3LYP/6-31G* level for a training set of 60 representative complexes have been employed. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure and energetics of molecules both within and outside the training set, and overcome the extensive deficiencies of a B3LYP/STO-3G model. Particularly encouraging is the success of the parameters in describing [4Fe-4S] cubanes. The derived parameter set provides a starting point should greater accuracy for a more restricted range of compounds be required.

Structure and Redox Properties of the Protein, Rubredoxin, and Its Ligand and Metal Mutants Studied by Electronic Structure Calculation

The changes in the structural and electronic properties accompanying metal ionization of the iron-containing protein, rubredoxin, and of some ligand and metal mutants, have been explored using density functional theory (DFT) calculations of the metal atom coordinated to the four immediate residues. Both isolated and embedded cluster studies have been carried out, the latter using the hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The replacement of a cysteine by a serine residue has a considerable effect on both the electronic and geometric structure of the core, which can be qualitatively understood on the basis of the isolated cluster studies. The modulation of these properties caused by the protein environment is quite accurately described by the QM/MM calculations. The predicted core geometries are in good accord with both X-ray and EXAFS data, and the changes in the redox potentials are predicted, at least semiquantitatively, by considering only the core part of the protein.

Development of parameter sets for semi-empirical MO calculations of transition metal systems: Iron parameters for iron–sulfur proteins

A semi-empirical parameter set for iron has been developed which is appropriate for the study of iron-sulfur proteins having a single iron atom, by fitting to density-functional theory (DFT) calculations obtained for a series of small models of iron-containing proteins. These parameters are obtained using a modified BFGS optimisation procedure previously used to obtain semi-empirical parameters for the main group elements. The modifications to this procedure for obtaining parameters for transition metal atoms are outlined. In addition to modifications to the semi-empirical core repulsion function, which yield significant improvements in the calculation of molecular structures, compared to the standard core repulsion function, are outlined. The reported parameters are then tested on a set of model complexes containing a variety of ligands and show good agreement with both DFT and experimental data for these species.

Probing the Electronic Structure of [2Fe-2S] Clusters with Three Coordinate Iron Sites by Use of Photoelectron Spectroscopy

Five series of [2Fe-2S] complexes, [Fe(2)S(2)Cl(2)(-)(x)(CN)(x)](-), [Fe(2)S(2)(SEt)(2)(-)(x)Cl(x)](-), [Fe(2)S(2)(SEt)(2)(-)(x)(CN)(x)](-), [Fe(2)S(2)Cl(2)(-)(x)(OAc)(x)](-) (OAc = acetate), and [Fe(2)S(2)(SEt)(2)(-)(x)(OPr)(x)](-) (OPr = propionate) (x = 0-2), were produced by collision-induced dissociation of the corresponding [4Fe-4S] complexes, and their electronic structures were studied by photoelectron spectroscopy. All the [2Fe-2S] complexes contain a [Fe(2)S(2)](+) core similar to that in reduced [2Fe] ferredoxins but with different coordination geometries. For the first three series, which only involve tricoordinated Fe sites, a linear relationship between the measured binding energies and the substitution number (x) was observed, revealing the independent ligand contributions to the total electron binding energies. The effect of the ligand increases in the order SEt --> Cl --> CN, conforming to their electron-withdrawing ability in the same order. The carboxylate ligands in the [Fe(2)S(2)Cl(2)(-)(x)(OAc)(x)](-) and [Fe(2)S(2)(SEt)(2)(-)(x)(OPr)(x)](-) complexes were observed to act as bidentate ligands, giving rise to tetracoordinated iron sites. This is different from their monodentate coordination behavior in the [4Fe-4S] cubane complexes, reflecting the high reactivity of the unsatisfied three-coordinate iron site in the [2Fe-2S] complexes. The [2Fe-2S] complexes with tetracoordinated iron sites exhibit lower electron binding energies, that is, higher reductive activity than the all tricoordinate planar clusters. The electronic structures of all the [2Fe-2S] complexes were shown to conform to the "inverted energy level scheme".

Electronic Structure and Intrinsic Redox Properties of [2Fe−2S]+ Clusters with Tri- and Tetracoordinate Iron Sites

Using potentially bidentate ligands (-SC2H4NH2), we produced [2Fe-2S]+ species of different coordination geometries by fission of [4Fe-4S]2+ complexes. Even though the ligands are monodentate in the cubane complexes, both mono- and bidentate complexes were observed in the [2Fe] fission products through self-assembly because of the high reactivity of the tricoordinate iron sites. The electronic structure of the [2Fe] species was probed using photoelectron spectroscopy and density functional calculations. It was found that tetracoordination significantly decreases the electron binding energies of the [2Fe] complexes, thus increasing the reducing capability of the [2Fe-2S]+ clusters.

Sequential oxidation of the cubane [4Fe--4S] cluster from [4Fe--4S](-) to [4Fe--4S](3+) in Fe(4)S(4)L(n)(-) complexes

Gaseous Fe(4)S(n)(-) (n = 4-6) clusters and synthetic analogue complexes, Fe(4)S(4)L(n)(-) (L = Cl, Br, I; n = 1-4), were produced by laser vaporization of a solid Fe/S target and electrospray from solution samples, respectively, and their electronic structures were probed by photoelectron spectroscopy. Low binding energy features derived from minority-spin Fe 3d electrons were clearly distinguished from S-derived bands. We showed that the electronic structure of the simplest Fe(4)S(4)(-) cubane cluster can be described by the two-layer spin-coupling model previously developed for the [4Fe] cubane analogues. The photoelectron data revealed that each extra S atom in Fe(4)S(5)(-) and Fe(4)S(6)(-) removes two minority-spin Fe 3d electrons from the [4Fe--4S] cubane core and each halogen ligand removes one Fe 3d electron from the cubane core in the Fe(4)S(4)L(n)(-) complexes, clearly revealing a behavior of sequential oxidation of the cubane over five formal oxidation states: [4Fe--4S](-) --> [4Fe--4S](0) --> [4Fe--4S](+) --> [4Fe-4S](2+) --> [4Fe-4S](3+). The current work shows the electron-storage capability of the [4Fe--4S] cubane, contributes to the understanding of its electronic structure, and further demonstrates the robustness of the cubane as a structural unit and electron-transfer center.

Probing the intrinsic electronic structure of the cubane [4Fe-4S] cluster: nature's favorite cluster for electron transfer and storage

The cubane [4Fe-4S] is the most common multinuclear metal center in nature for electron transfer and storage. Using electrospray, we produced a series of gaseous doubly charged cubane-type complexes, [Fe4S4L4]2- (L = -SC2H5, -SH, -Cl, -Br, -I) and the Se-analogues [Fe4Se4L4]2- (L = -SC2H5, -Cl), and probed their electronic structures with photoelectron spectroscopy and density functional calculations. The photoelectron spectral features are similar among all the seven species investigated, revealing a weak threshold feature due to the minority spins on the Fe centers and confirming the low-spin two-layer model for the [4Fe-4S](2+) core and its "inverted level scheme". The measured adiabatic detachment energies, which are sensitive to the terminal ligand substitution, provide the intrinsic oxidation potentials of the [Fe4S4L4]2- complexes. The calculations revealed a simple correlation between the electron donor property of the terminal thiolate as well as the bridging sulfide with the variation of the intrinsic redox potentials. Our data provide intrinsic electronic structure information of the [4Fe-4S] cluster and the molecular basis for understanding the protein and solvent effects on the redox properties of the [4Fe-4S] active sites.