The catalytic Mn2+ sites in the enolase-inhibitor complex: crystallography, single-crystal EPR, and DFT calculations

Determination of ZFS parameters from the EPR spectra of mono-, di- and trinuclear MnII complexes: impact of magnetic coupling

A family of new Mn^II compounds, consisting of seven dinuclear, three mononuclear, and four trinuclear ones, were synthesised using benzoic acid derivatives n-RC₆H₄COOH, where n-R = 2-MeO, 3-MeO, 4-MeO, or 4-^tBu, and 2,2'-bipyridine (bpy) or 1,10-phenantroline (phen) as blocking ligands. The crystal structures of nine of these compounds and the magnetic studies of all of them are reported here. Each type of compound was formed depending on the presence or absence of ClO₄^- ions, the solvent used, and/or the presence of a small amount of water in the reaction medium. The use of the tert-buthylbenzoate ligand gave unexpected results, very likely due to the steric hindrance caused by the voluminous ^tBu groups. The EPR spectra of each type of compound give some peculiar features that allow its identification. Attempts to fit these spectra have been made in order to determine the ZFS parameters, D and E, of the Mn^II ion (for mononuclear and dinuclear systems) or of the ground state (for trinuclear systems). For trinuclear systems, the single-ion ZFS parameters estimated from those of the ground state provided a good simulation of the EPR spectra of these compounds. The EPR signals observed in each case have been rationalised according to the energy level distribution and the plausible population in the excited states. In some particular situations, the sign of D_Mn could be determined from the fit of the EPR spectra of the antiferromagnetic dinuclear compounds, the source of the difference between the spectra lying in the second excited state.

Deciphering the origin of giant magnetic anisotropy and fast quantum tunnelling in Rhenium(IV) single-molecule magnets

Single-molecule magnets represent a promising route to achieve potential applications such as high-density information storage and spintronics devices. Among others, 4d/5d elements such as Re(IV) ion are found to exhibit very large magnetic anisotropy, and inclusion of this ion-aggregated clusters yields several attractive molecular magnets. Here, using ab intio calculations, we unravel the source of giant magnetic anisotropy associated with the Re(IV) ions by studying a series of mononuclear Re(IV) six coordinate complexes. The low-lying doublet states are found to be responsible for large magnetic anisotropy and the sign of the axial zero-field splitting parameter (D) can be categorically predicted based on the position of the ligand coordination. Large transverse anisotropy along with large hyperfine interactions opens up multiple relaxation channels leading to a fast quantum tunnelling of the magnetization (QTM) process. Enhancing the Re-ligand covalency is found to significantly quench the QTM process.

Rhenium(IV) complexes are magnetically anisotropic although the origin of this anisotropy is poorly explored compared to 3d transition metals and lanthanides. Here, the authors computationally examine the effects of ligand donor ability and structural distortion on magnetic anisotropy for a series of rhenium(IV) complexes.

Assigning the EPR fine structure parameters of the Mn(II) centers in Bacillus subtilis oxalate decarboxylase by site-directed mutagenesis and DFT/MM calculations

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals associated with the two Mn(II) centers located in the N- and C-terminal cupin domains of the enzyme. We now report a mutational strategy that has established the assignment of EPR fine structure parameters to each of these Mn(II) centers at pH 8.5. These experimental findings are also used to assess the performance of a multistep strategy for calculating the zero-field splitting parameters of protein-bound Mn(II) ions. Despite the known sensitivity of calculated D and E values to the computational approach, we demonstrate that good estimates of these parameters can be obtained using cluster models taken from carefully optimized DFT/MM structures. Overall, our results provide new insights into the strengths and limitations of theoretical methods for understanding electronic properties of protein-bound Mn(II) ions, thereby setting the stage for future EPR studies on the electronic properties of the Mn(II) centers in OxDC and site-specific variants.

Azurin as a protein scaffold for a low-coordinate nonheme iron site with a small-molecule binding pocket

The apoprotein of Pseudomonas aeruginosa azurin binds iron(II) to give a 1:1 complex, which has been characterized by electronic absorption, Mössbauer, and NMR spectroscopies, as well as X-ray crystallography and quantum-chemical computations. Despite potential competition by water and other coordinating residues, iron(II) binds tightly to the low-coordinate site. The iron(II) complex does not react with chemical redox agents to undergo oxidation or reduction. Spectroscopically calibrated quantum-chemical computations show that the complex has high-spin iron(II) in a pseudotetrahedral coordination environment, which features interactions with side chains of two histidines and a cysteine as well as the C═O of Gly45. In the (5)A(1) ground state, the d(z(2)) orbital is doubly occupied. Mutation of Met121 to Ala leaves the metal site in a similar environment but creates a pocket for reversible binding of small anions to the iron(II) center. Specifically, azide forms a high-spin iron(II) complex and cyanide forms a low-spin iron(II) complex.

Importance of enolase in Giardia lamblia differentiation

The ability of Giardia to differentiate into cysts which survive in the environment and release the virulent trophozoites after ingestion in the small intestine is essential for transmission and disease. We examined the role of enolase, a glycolytic enzyme, in Giardia differentiation. The sequence of Giardia lamblia enolase (gEno) is most similar to enolases in Homo sapiens and Leishmania mexicana, and shows the conserved catalytic and metal-binding residues. We used an integration vector to stably express wild type and mutant gEno. In trophozoites, wild type gEno localized to the cell membrane, caudal flagella and cytosol. gEno is present on the wall of mature cysts, but not in encystation secretory vesicles (ESV). The expression of gEno with a deletion of residues G167-K169, or mutations H389Q/R390S significantly inhibited excystation while mutation of residue D257K had no effect. These results suggest a role for enolase in regulation of Giardia excystation.

Dynamic hydrogen-bonding network in the distal pocket of the nitrosyl complex of Pseudomonas aeruginosa cd1 nitrite reductase

cd(1) nitrite reductase (NIR) is a key enzyme in the denitrification process that reduces nitrite to nitric oxide (NO). It contains a specialized d(1)-heme cofactor, found only in this class of enzymes, where the substrate, nitrite, binds and is converted to NO. For a long time, it was believed that NO must be released from the ferric d(1)-heme to avoid enzyme inhibition by the formation of ferrous-nitroso complex, which was considered as a dead-end product. However, recently an enhanced rate of NO dissociation from the ferrous form, not observed in standard b-type hemes, has been reported and attributed to the unique d(1)-heme structure (Rinaldo, S.; Arcovito, A.; Brunori, M.; Cutruzzolà, F. J. Biol. Chem. 2007, 282, 14761-14767). Here, we report on a detailed study of the spatial and electronic structure of the ferrous d(1)-heme NO complex from Pseudomonas aeruginosa cd(1) NIR and two mutants Y10F and H369A/H327A in solution, searching for the unique properties that are responsible for the relatively fast release. There are three residues at the "distal" side of the heme (Tyr(10), His(327), and His(369)), and in this work we focus on the identification and characterization of possible H-bonds they can form with the NO, thereby affecting the stability of the complex. For this purpose, we have used high field pulse electron-nuclear double resonance (ENDOR) combined with density functional theory (DFT) calculations. The DFT calculations were essential for assigning and interpreting the ENDOR spectra in terms of geometric structure. We have shown that the NO in the nitrosyl d(1)-heme complex of cd(1) NIR forms H-bonds with Tyr(10) and His(369), whereas the second conserved histidine, His(327), appears to be less involved in NO H-bonding. This is in contrast to the crystal structure that shows that Tyr(10) is removed from the NO. We have also observed a larger solvent accessibility to the distal pocket in the mutants as compared to the wild-type. Moreover, it was shown that the H-bonding network within the active site is dynamic and that a change in the protonation state of one of the residues does affect the strength and position of the H-bonds formed by the others. In the Y10F mutant, His(369) is closer to the NO, whereas mutation of both distal histidines displaces Tyr(10), removing its H-bond. The implications of the H-bonding network found in terms of the complex stability and catalysis are discussed.

Predicting the ¹H and ¹³C NMR spectra of paramagnetic Ru(III) complexes by DFT

Nuclear shieldings, including the Fermi-contact and pseudocontact terms, have been calculated with density functional theory (DFT) (nonrelativistic and relativistic) methods in several Ru(III) complexes, thereby predicting (1)H and (13)C paramagnetic shifts. A fair agreement with experimental values is observed. Structural, magnetic and dynamic parameters have also been input to the Solomon-Bloembergen equation in order to predict signal lineshapes. It is shown that DFT-predicted paramagnetic shifts can greatly aid in obtaining and understanding NMR spectra of paramagnetic Ru(III) complexes.

pH-dependent structures of the manganese binding sites in oxalate decarboxylase as revealed by high-field electron paramagnetic resonance

A high-field electron paramagnetic resonance (HFEPR) study of oxalate decarboxylase (OxdC) is reported. OxdC breaks down oxalate to carbon dioxide and formate and possesses two distinct manganese(II) binding sites, referred to as site-1 and -2. The Mn(II) zero-field interaction was used to probe the electronic state of the metal ion and to examine chemical/mechanistic roles of each of the Mn(II) centers. High magnetic-fields were exploited not only to resolve the two sites, but also to measure accurately the Mn(II) zero-field parameters of each of the sites. The spectra exhibited surprisingly complex behavior as a function of pH. Six different species were identified based on their zero-field interactions, two corresponding to site-1 and four states to site-2. The assignments were verified using a mutant that only affected site-1. The speciation data determined from the HFEPR spectra for site -2 was consistent with a simple triprotic equilibrium model, while the pH dependence of site-1 could be described by a single pK(a). This pH dependence was independent of the presence of the His-tag and of whether the preparations contained 1.2 or 1.6 Mn per subunit. Possible structures of the six species are proposed based on spectroscopic data from model complexes and existing protein crystallographic structures obtained at pH 8 are discussed. Although site-1 has been identified as the active site and no role has been assigned to site-2, the pronounced changes in the electronic structure of the latter and its pH behavior, which also matches the pH-dependent activity of this enzyme, suggests that even if the conversion of oxalate to formate is carried out at site-1, site-2 likely plays a catalytically relevant role.

Ab initio and coupled-perturbed density functional theory estimation of zero-field splittings in MnII transition metal complexes

The paper presents a method comparison for the prediction of zero-field splitting (ZFS) parameters in a series of Mn (II) coordination complexes. The test set consists of Mn (II) complexes that are experimentally well-characterized by X-ray diffraction and high-field electron paramagnetic resonance. Their ZFS parameters have been calculated using density functional theory (DFT) as well as complete active space self-consistent field (CASSCF) methods. It is shown that the recently introduced coupled-perturbed spin-orbit coupling (CP-SOC) approach [ Neese, F. J. Chem. Phys. 2007, 127, 164112 ] together with hybrid-DFT functionals leads to a slope of the correlation line (plot of experimental vs calculated D values) that is essentially unity provided that the direct spin-spin interaction is properly included in the treatment. This is different from our previous DFT study on the same series of complexes where a severe overestimation of the D parameter has been found [ Zein, S. ; Duboc, C. ; Lubitz, W. ; Neese, F. Inorg. Chem. 2008, 47, 134 ]. CASSCF methods have been used to evaluate the ZFS in an "ab initio ligand-field" type treatment. The study demonstrates that a substantial part of the relevant physics is lost in such a treatment since only excitations within the manganese d-manifold are accounted for. Thus, a severe underestimation of the D parameter has been found. Because the CASSCF calculations in combination with quasidegenerate perturbation theory treats the SOC to all orders, we have nevertheless verified that second-order perturbation theory is an adequate approximation in the case of the high-spin d (5) configuration.

Calculation of the zero-field splitting tensor on the basis of hybrid density functional and Hartree-Fock theory

The zero-field splitting (ZFS) (expressed in terms of the D tensor) is the leading spin-Hamiltonian parameter for systems with a ground state spin S>12. To first order in perturbation theory, the ZFS arises from the direct spin-spin dipole-dipole interaction. To second order, contributions arise from spin-orbit coupling (SOC). The latter contributions are difficult to treat since the SOC mixes states of different multiplicities. This is an aspect of dominant importance for the correct prediction of the D tensor. In this work, the theory of the D tensor is discussed from the point of view of analytic derivative theory. Starting from a general earlier perturbation treatment [F. Neese and E. I. Soloman, Inorg. Chem. 37, 6568 (1998)], straightforward response equations are derived that are readily transferred to the self-consistent field (SCF) Hartree-Fock (HF) or density functional theory (DFT) framework. The main additional effort in such calculations arises from the solution of nine sets of nonstandard coupled-perturbed SCF equations. These equations have been implemented together with the spin-orbit mean-field representation of the SOC operator and a mean-field treatment of the direct spin-spin interaction into the ORCA electronic structure program. A series of test calculations on diatomic molecules with accurately known zero-field splittings shows that the new approach corrects most of the shortcomings of previous DFT based methods and, on average, leads to predictions within 10% of the experimental values. The slope of the correlation line is essentially unity for the B3LYP and BLYP functionals compared to approximately 0.5 in previous treatments.

A systematic density functional study of the zero-field splitting in Mn(II) coordination compounds

This work presents a detailed evaluation of the performance of density functional theory (DFT) for the prediction of zero-field splittings (ZFSs) in Mn(II) coordination complexes. Eighteen experimentally well characterized four-, five-, and six-coordinate complexes of the general formula [Mn(L)nL'2] with L' = Cl, Br, I, NCS, or N3 (L = an oligodentate ligand) are considered. Several DFT-based approaches for the prediction of the ZFSs are compared. For the estimation of the spin-orbit coupling (SOC) part of the ZFS, it was found that the Pederson-Khanna (PK) approach is more successful than the previously proposed quasi-restricted orbitals (QRO)-based method. In either case, accounting for the spin-spin (SS) interaction either with or without the inclusion of the spin-polarization effects improves the results. This argues for the physical necessity of accounting for this important contribution to the ZFS. On average, the SS contribution represents approximately 30% of the axial D parameters. In addition to the SS part, the SOC contributions of d-d spin flip (alphabeta) and ligand-to-metal charge transfer excited states (betabeta) were found to dominate the SOC part of the D parameter; the observed near cancellation between the alphaalpha and betaalpha parts is discussed in the framework of the PK model. The calculations systematically (correlation coefficient approximately 0.99) overestimate the experimental D values by approximately 60%. Comparison of the signs of calculated and measured D values shows that the signs of the calculated axial ZFS parameters are unreliable once E/D > 0.2. Finally, we find that the calculated D and E/D values are highly sensitive to small structural changes. It is observed that the use of theoretically optimized geometries leads to a significant deterioration of the theoretical predictions relative to the experimental geometries derived from X-ray diffraction. The standard deviation of the theoretical predictions for the D values almost doubles from approximately 0.1 to approximately 0.2 cm-1 upon using quantum chemically optimized structures. We do not find any noticeable improvement in considering basis sets larger than standard double- (SVP) or triple-zeta (TZVP) basis sets or using functionals other than the BP functional.

Origin of the zero-field splitting in mononuclear octahedral dihalide MnII complexes: an investigation by multifrequency high-field electron paramagnetic resonance and density functional theory

The synthesis, structural characterization, and electronic properties of a new series of high-spin six-coordinate dihalide mononuclear MnII complexes [Mn(tpa)X2] (tpa=tris-2-picolylamine; X=I (1), Br (2), and Cl (3)) are reported. The analysis of the crystallographic data shows that in all investigated complexes the manganese ion lies in the center of a distorted octahedron with a cis configuration of the halides imposed by the tpa ligand. By a multifrequency high-field electron paramagnetic resonance investigation (95-285 GHz), the electronic properties of 1-3 were determined (DI=-0.600, DBr=-0.360, DCl=+0.115 cm-1), revealing the important effect of (i) the nature of the halide and (ii) the configuration (cis/trans) of the two halides on the magnitude of D. The spin Hamiltonian parameters obtained by density functional theory calculations initiated from the crystal structure of 1-3 are in reasonable agreement with the experimental values. The absolute value of D is consistently overestimated, but the sign and the trend over the chemical series is well reproduced. Theoretical models (cis- and trans-[Mn(NH3)4X2], X=I, Br, Cl and F) have been used to investigate the different contributions to D and also to understand the origin of the experimentally observed changes in D within the series reported here. This study reveals that the spin-spin coupling contributions to the D tensor are non-negligible for the lighter halides (F, Cl) but become insignificant for the heavier halides (I, Br). The four different types of excitations involved in the spin-orbit coupling (SOC) part of the D tensor contribute with comparable magnitudes and opposing signs. The general trend observed for halide MnII complexes (DI>DBr>DCl) can be explained by the fact that the halide SOC dominates the D value in these systems with a major contribution arising from interference between metal- and halide-SOC contributions, which are proportional to the product of the SOC constants of Mn and X.