Electronic structures,bonding, and spin state energetics of biomimetic mononuclear and bridged dinuclear iron complexes: a computational examination

Structural Chemistry - Mononuclear and dinuclear iron complexes are found as key intermediates in many synthetic and biocatalytic reactions, since many of these species are transient and have high...     

Electronic structure, bonding, spectroscopy and energetics of Fe-dependent nitrile hydratase active-site models

Fe-type nitrile hydratase (NHase) is a non-heme Fe(III)-dependent enzyme that catalyzes the hydration of nitriles to the corresponding amides. Despite experimental studies of the enzyme and model Fe(III)-containing complexes, many questions concerning the electronic structure and spectroscopic transitions of the metal center remain unanswered. In addition, the catalytic mechanism of nitrile hydration has not yet been determined. We now report density functional theory (B3LYP/6-31G) calculations on three models of the Fe(III) center in the active site of NHase corresponding to hypothetical intermediates in the enzyme-catalyzed hydration of acetonitrile. Together with natural bond orbital (NBO) analysis of the chemical bonding in these active-site models and INDO/S CIS calculations of their electronic spectra, this theoretical investigation gives new insight into the molecular origin of the unusual low-spin preference and spectroscopic properties of the Fe(III) center. In addition, the low-energy electronic transition observed for the active form of NHase is assigned to a dd transition that is coupled with charge-transfer transitions involving the metal and its sulfur ligands. Calculations of isodesmic ligand-exchange reaction energies provide support for coordination of the Fe(III) center in free NHase by a water molecule rather than a hydroxide ion and suggest that the activation of the nitrile substrate by binding to the metal in the sixth coordination site during catalytic turnover cannot yet be definitively ruled out.     

Properties of square-pyramidal alkyl-thiolate Fe(III) complexes, including an analogue of the unmodified form of nitrile hydratase

The syntheses and structures of three new coordinatively unsaturated, monomeric, square-pyramidal thiolate-ligated Fe(III) complexes are described, [Fe(III)((tame-N(3))S(2)(Me2))](+) (1), [Fe(III)(Et-N(2)S(2)(Me2))(py)](1-) (3), and [Fe(III)((tame-N(2)S)S(2)(Me2))](2-) (15). The anionic bis-carboxamide, tris-thiolate N(2)S(3) coordination sphere of 15 is potentially similar to that of the yet-to-be characterized unmodified form of NHase. Comparison of the magnetic and reactivity properties of these reveals how anionic charge build up (from cationic 1 to anionic 3 and dianionic 15) and spin-state influence apical ligand affinity. For all of the ligand-field combinations examined, an intermediate S = 3/2 spin state was shown to be favored by a strong N(2)S(2) basal plane ligand field, and this was found to reduce the affinity for apical ligands, even when they are built in. This is in contrast to the post-translationally modified NHase active site, which is low spin and displays a higher affinity for apical ligands. Cationic 1 and its reduced Fe(II) precursor are shown to bind NO and CO, respectively, to afford [Fe(III)((tame-N(3))S(2)(Me))(NO)](+) (18, nu(NuO) = 1865 cm(-1)), an analogue of NO-inactivated NHase, and [Fe(II)((tame-N(3))S(2)(Me))(CO)] (16; nu(CO) stretch (1895 cm(-1)). Anions (N(3)(-), CN(-)) are shown to be unreactive toward 1, 3, and 15 and neutral ligands unreactive toward 3 and 15, even when present in 100-fold excess and at low temperatures. The curtailed reactivity of 15, an analogue of the unmodified form of NHase, and its apical-oxygenated S = 3/2 derivative [Fe(III)((tame-N(2)SO(2))S(2)(Me2))](2-) (20) suggests that regioselective post-translational oxygenation of the basal plane NHase cysteinate sulfurs plays an important role in promoting substrate binding. This is supported by previously reported theoretical (DFT) calculations.     

Redox tuning of mononuclear rhenium(III) complexes containing substituted nitrile andpara-substituted triphenylphosphine ligands

Summary A series of oxorhenium(V) complexes of general formula ReOCl₃[(4-RC₆H₄)₃P]₂ was prepared and converted into rhenium(III) complexes of general formula ReCl₃(MeCN)[(4-RC₆H₄)₃P]₂. Replacement of the coordinated acetonitrile in the complex ReCl₃(MeCN)(Ph₃P)₂ by a series ofpara-substituted benzonitriles yielded complexes of general formula ReCl₃(4-RC₆H₄CN)(Ph₃P)₂. The voltammetric behavior of these oxorhenium(V) and rhenium(III) complexes was characterized. For all three classes of compounds, reversible one-electron oxidations and reductions were observed. The redox potentials were correlated with the pK_a of the substituted phosphine and with the Hammett-Taft constants for both the phosphine and benzonitrile substituent.     

Spectrometric,catalytic, and antimicrobial studies of mononuclear Ru(III) Schiff-base complexes

A series of air stable low spin Ru(III) complexes, [RuX₂(EPh₃)(L)] (where X = Cl or Br; E = P or As; L = monobasic tridentate Schiff-base ligand), have been synthesized by reacting [RuCl₃(PPh₃)₃], [RuCl₃(AsPh₃)₃], and [RuBr₃(PPh₃)₃] with the Schiff base in 1 : 1 molar ratio in benzene. These complexes have been characterized by elemental analysis, FT-IR, UV-Vis, and EPR spectroscopy together with magnetic susceptibility. The redox behaviors of the complexes have been investigated by cyclic voltammetric technique. Catalytic efficiency of the ruthenium complexes was determined for aryl–aryl coupling and the oxidation of primary and secondary alcohols into their corresponding aldehydes and ketones in the presence of molecular oxygen as co-oxidant. All complexes were screened for antibacterial activity.     

Fe (III) complexes of a bis-benzimidazolyl diamide ligand: spectral and catalytic studies

A new tetradentate bis benzimidaozlyl diamide ligand N,N'-Bis (benzimidazol-2-yl-methyl)-hexane-1,6-dicarboxamide (GBSA) has been synthesized and utilized to prepare new Fe(III) complexes with exogenous anionic ligand X=Cl(-) and NO(3)(-). Isomer shift values are in the range found for Iron in the +3 oxidation state while Quadrupole Splitting indicates large distortion from a six coordinate geometry, a finding supported by low temperature EPR work. The E(1/2) values are found to be quite cathodic indicating stability of the Iron (III) complexes. The oxidation of alcohols was investigated using [Fe(GBSA)Cl(3)] as the catalyst with TBHP as an alternate source of oxygen. The respective carbonyl products have been isolated and characterized by (1)H NMR, electronic spectroscopy, mass and IR spectral studies.     

Investigating the structural and electronic properties of nitrile hydratase model iron(III) complexes using projected unrestricted Hartree-Fock (PUHF) calculations

Important structural and mechanistic details concerning the non-heme, low-spin Fe(III) center in nitrile hydratase (NHase) remain poorly understood. We now report projection unrestricted Hartree-Fock (PUHF) calculations on the spin preferences of a series of inorganic complexes in which Fe(III) is coordinated by a mixed set of N/S ligands. Given that many of these compounds have been prepared as models of the NHase metal center, this study has allowed us to evaluate this computational approach as a tool for future calculations on the electronic structure of the NHase Fe(III) center itself. When used in combination with the INDO/S semiempirical model, the PUHF method correctly predicts the experimentally observed spin state for 12 of the 13 Fe(III)-containing complexes studied here. The one compound for which there is disagreement between our theoretical calculations and experimental observation exhibits temperature-dependent spin behavior. In this case, the failure of the PUHF-INDO/S approach may be associated with differences between the structure of the Fe(III) complex present under the conditions used to measure the spin preference and that observed by X-ray crystallography. A preliminary analysis of the role of the N/S ligands and coordination geometry in defining the Fe(III) spin preferences in these complexes has also been undertaken by computing the electronic properties of the lowest energy Fe(III) spin states. While any detailed interpretation of our results is constrained both by the limited set of well-characterized Fe(III) complexes used in this study and by the complicated dependence of Fe(III) spin preference upon metal-ligand interactions and coordination geometry, these PUHF-INDO/S calculations support the hypothesis that the deprotonated amide nitrogens coordinating the metal stabilize the low-spin Fe(III) ground state seen in NHase. Strong evidence that the sulfur ligands exclusively define the Fe(III) spin state preference by forming metal-ligand bonds with significant covalent character is not provided by these computational studies. This might, however, reflect limitations in modeling these systems at the INDO/S level of theory.     

Modeling the active site of nitrile hydratase: synthetic strategies to ensure simultaneous coordination of carboxamido-N and thiolato-S to Fe(III) centers

A general strategy for synthesizing Fe(III) complexes of ligands containing carboxamido-N and thiolato-S donors has been described. Reaction of the doubly deprotonated ligand PyPepS2- (where PyPepSH2=N-2-mercaptophenyl-2'-pyridinecarboxamide) with Fe(III) salts in DMF had previously afforded the Fe(III) complex (Et4N)[Fe(PyPepS)2] without any problem(s) associated with autoredox reactions of the thiolate functionality. In the present work, similar reactions with the doubly deprotonated ligand PiPepS2- (where PiPepSH2=2-mercapto-N-pyridin-2-yl-methylbenzamide) with Fe(III) salts, however, fail to afford any Fe(III) complex because of autoredox reactions. The break in the conjugation in the PiPepSH2 ligand frame is the key reason for this difference in behavior between these two very similar ligands. This is demonstrated by the fact that the same reaction with AqPepS2- (where AqPepSH2=2-mercapto-N-quinolin-8-yl-benzamide), another ligand with extended conjugation, affords the Fe(III) complex (Et4N)[Fe(AqPepS)2] without any synthetic complication. It is therefore evident that ligands in which the carboxamide and thiolate functionalities are kept in conjugation could be used to isolate Fe(III) complexes with carboxamido-N and thiolato-S coordination. This finding will be very helpful in future research work in the area of modeling the active site of Fe-containing nitrile hydratase.     

Conversion of azomethine moiety to carboxamido group at cobalt(III) center in model complexes of Co-containing nitrile hydratase

The Co(III) complex of the Schiff base ligand N-2-mercaptophenyl-2'-pyridylmethyl-enimine (PyASH), namely, [Co(PyAS)(2)]Cl (1), has been synthesized via an improved method and its structure has been determined by X-ray crystallography. The two deprotonated ligands are arranged in mer configuration around the Co(III) center and the overall coordination geometry is octahedral. The coordinated azomethine function in 1 is rapidly converted into carboxamido group upon reaction with OH(-). The product is the bis carboxamido complex (Et(4)N)[Co(PyPepS)(2)] (2), reported by us previously. Reaction of H(2)O(2) with 1 in DMF affords [Co(PyASO(2))(PyPepSO(2))] (3), a species with mixed imine and carboxamido-N donor centers as well as S-bound sulfinates. Further reaction with H(2)O(2) in the presence of NaClO(4) converts 3 into the previously reported bis carboxamido/sulfinato complex Na[Co(PyPepSO(2))(2)] (4). The reaction conditions for the various transformation reactions for complexes 1-4 and the structure of 3 are also reported. The mechanism of the -CH=NR + [O] --> -C(=O)NHR transformation has been discussed. The reactions reported here provide convenient alternate routes for the syntheses of Co(III) complexes with coordinated carboxamide, thiolate, and/or sulfinate donors as models for the Co-site in the Co-containing nitrile hydratase(s).     

Modulation of the pK(a) of metal-bound water via oxidation of thiolato sulfur in model complexes of Co(III) containing nitrile hydratase: insight into possible effect of cysteine oxidation in Co-nitrile hydratase

The Co(III) complexes of N,N'-bis(2-mercaptophenyl)pyridine-2,6-dicarboxamide (PyPSH(4)), a designed pentadentate ligand with built-in carboxamide and thiolate groups, have been synthesized and studied to gain insight into the role of Cys-S oxidation in Co-containing nitrile hydratase (Co-NHase). Reaction of [Co(NH(3))(5)Cl]Cl(2) with PyPS(4)(-) in DMF affords the thiolato-bridged dimeric Co(III) complex (Et(4)N)(2)[Co(2)(PyPS)(2)] (1). Although the bridged structure is quite robust, reaction of (Et(4)N)(CN) with 1 in acetonitrile affords the monomeric species (Et(4)N)(2)[Co(PyPS)(CN)] (2). Oxidation of 2 with H(2)O(2) in acetonitrile gives rise to a mixture which, upon chromatographic purification, yields K(2)[Co(PyPSO(2)(OSO(2))(CN] (3), a species containing asymmetrically oxidized thiolates. The Co(III) metal center in 3 is coordinated to a S-bound sulfinate and an O-bound sulfonate (OSO(2)) group. Upon oxidation with H(2)O(2), 1 affords an asymmetrically oxidized dimer (Et(4)N)(2)[Co(2)(PyPS(SO(2)))(2)] (4) in which only the terminal thiolates are oxidized to form S-bound sulfinate groups while the bridging thiolates remain unchanged. The thiolato-bridge in 4 is also cleaved upon reaction with (Et(4)N)(CN) in acetonitrile, and one obtains (Et(4)N)(2)[Co(PyPS(SO(2)))(CN)] (5), a species that contains both coordinated thiolate and S-bound sulfinate around Co(III). The structures of 1-4 have been determined. The spectroscopic properties and reactivity of all the complexes have been studied to understand the behavior of the Co(III) site in Co-NHase. Unlike typical Co(III) complexes with bound CN(-) ligands, the Co(III) centers in 2 and 5 are labile and rapidly lose CN(-) in aqueous solutions. Since 3 does not show this lability, it appears that at least one thiolato sulfur donor is required in the first coordination sphere for the Co(III) center in such species to exhibit lability. Both 2 and 5 are converted to the aqua complexes [Co(PyPS)(H(2)O)](-) and [Co(PyPS(SO(2))(H(2)O)](-) in aqueous solutions. The pK(a) values of the bound water in these two species, determined by spectrophotometry, are 8.3 +/- 0.03 and 7.2 +/- 0.06, respectively. Oxidation of the thiolato sulfur (to sulfinate) therefore increases the acidity of the bound water. Since 2 and 5 promote hydrolysis of acetonitrile at pH values above their corresponding pK(a) values, it is also evident that a metal-bound hydroxide is a key player in the mechanism of hydrolysis by these model complexes of Co-NHase. The required presence of a Cys-sulfinic residue and one water molecule at the Co(III) site of Co-NHase as well as the optimal pH of the enzyme near 7 suggests that (i) modulation of the pK(a) of the bound water molecule at the active site of the enzyme could be one role of the oxidized Cys-S residue(s) and (ii) a cobalt-bound hydroxide could be responsible for the hydrolysis of nitriles by Co-NHase.     

A computational study of the electronic structure, bonding, and spectral properties of tripodal tetraamine Co(III) carbonate complexes

Density functional calculations have been carried out on the experimentally characterized Co(III) [Co(N4)(O2CO)]+ carbonate complexes containing a tripodal tetraamine ligand (N4 = tpa, Metpa, Me2tpa, Me3tpa, pmea, pmap, tepa) and also the model [Co(NH3)4(O2CO)]+ system. Calculations on the model species, performed using both gas-phase and solvent-corrected procedures, have revealed that the inclusion of a condensed-phase environment is necessary to obtain generally satisfactory results for the structural and bonding properties in these systems. Using the solvent-corrected approach, the observed trends in structural parameters for the metal-ligand bonds, 59Co chemical shifts, and changes in visible absorption wavelengths have been satisfactorily reproduced for the [Co(N4)(O2CO)]+ complexes. A time-dependent density functional analysis of the electronic excitations indicates that the overall composition and character of the relevant (d-d) transitions remain similar throughout the series, indicating that the changes in the Co-N interactions, associated with the structural variations occurring as the N-donor ligand identity and size change, appear most likely responsible for the particular spectroscopic features displayed by these species. These observations are further supported by molecular orbital and energy decomposition analyses. The results from the present calculations confirm recent findings that the inclusion of a treatment for solvent effects plays a critical role in the computational modelling of coordination complexes involving mixed (anionic and neutral) ligands.     

Structural studies and quantum chemical calculations of Cr(III), Fe(III) and Ru(III) bromazepam complexes

The reaction of bromazepam (7‐bromo‐1,3‐dihydro‐5‐(2‐pyridyl)‐2H ‐1,4‐benzodiazepin‐2‐one, BZM) with Cr(III) ( 1 ), Fe(III) ( 2 ) and Ru(III) ( 3 ) salts gives complexes of the type [M(BZM)₃]⋅3X (X = Cl or NO₃). Structural characterization was extensively carried out using various analytical and spectral tools such as infrared, ¹H NMR and UV–visible spectroscopies and magnetic, conductance, elemental and thermal analyses. BZM is a bidentate ligand and interacts with the metal ions via the pyridine and benzodiazepin‐2‐one nitrogen atoms. The magnetic and electronic properties of 2 and 3 are consistent with low‐spin octahedral complexes. The three BZM molecules are non‐isoenergetically coordinated to the metal ions and this is reflected in the values of the second‐order interaction energy. The antibacterial activity was studied using Staphylococcus aureus and Escherichia coli . Coordination of BZM to Cr(III) or Ru(III) ions leads to a marked increase in toxicity with respect to the inactive Fe(III) complex 2 .     

Spectral studies of Fe(III) complexes of dipodal tridentate chelating agents

The dipodal ligands (Im) and (BIm) as well as complexes [FeLCl₃] [L = Im (1) and BIm (2)] have been prepared and studied using spectroscopic techniques. The magnetic moment, IR, electronic (ligand field), FAB-mass and NMR spectral data indicate a hexa-coordinate geometry around high-spin state Fe³⁺ where the ligands coordinate as a tridentate [N,N,N] chelating agent. ⁵⁷Fe-Mössbauer spectral data confirmed the presence of a ligand asymmetry around Fe³⁺ in a high-spin state electronic configuration (t_2g³,e_g², S = 5/2) with nuclear transition Fe(±3/2 → ±1/2) exhibiting Kramer's double degeneracy. The molecular computations provided the optimum energy perspective plots for the molecular geometries giving the important structural data.     

Sulfur K-edge XAS and DFT calculations on nitrile hydratase: geometric and electronic structure of the non-heme iron active site

The geometric and electronic structure of the active site of the non-heme iron enzyme nitrile hydratase (NHase) is studied using sulfur K-edge XAS and DFT calculations. Using thiolate (RS(-))-, sulfenate (RSO(-))-, and sulfinate (RSO(2)(-))-ligated model complexes to provide benchmark spectral parameters, the results show that the S K-edge XAS is sensitive to the oxidation state of S-containing ligands and that the spectrum of the RSO(-) species changes upon protonation as the S-O bond is elongated (by approximately 0.1 A). These signature features are used to identify the three cysteine residues coordinated to the low-spin Fe(III) in the active site of NHase as CysS(-), CysSOH, and CysSO(2)(-) both in the NO-bound inactive form and in the photolyzed active form. These results are correlated to geometry-optimized DFT calculations. The pre-edge region of the X-ray absorption spectrum is sensitive to the Z(eff) of the Fe and reveals that the Fe in [FeNO](6) NHase species has a Z(eff) very similar to that of its photolyzed Fe(III) counterpart. DFT calculations reveal that this results from the strong pi back-bonding into the pi antibonding orbital of NO, which shifts significant charge from the formally t(2)(6) low-spin metal to the coordinated NO.     

Octahedral non-heme oxo and non-oxo Fe(IV) complexes: an experimental/theoretical comparison

Electron-transfer series are described for three ferric complexes of the pentadentate ligand 4,8,11-trimethyl-1,4,8,11-tetraazacyclotetradecane-1-acetate (Me(3)cyclam-acetate) with axial chloride, fluoride, and azide ligands. These complexes can all be reduced coulometrically to their Fe(II) analogs and oxidized reversibly to the corresponding Fe(IV) species. The Fe(II), Fe(III), and Fe(IV) species have been studied spectroscopically and their UV-vis, M?ssbauer, EPR, and IR spectra are presented. The fluoro species [(Me(3)cyclam-acetate)FeF](n+) (n = 0, 1, 2) have been studied computationally using density functional theory (DFT), and the electronic structure of the Fe(IV) dication [(Me(3)cyclam-acetate)FeF](2+) is compared with that of the isoelectronic Fe(IV) oxo cation [(Me(3)cyclam-acetate)FeO](+); the different properties of the two species are mainly due to the significantly covalent Fe=O pi bonds in the latter.     

Mixed-ligand complexes of Ru(III) and Rh(III): ESR studies on some Ru(III) complexes

Reactions of 2-mercapto-3-phenyl-4-quinazolinone (LH) with RuCl₃·xH₂O and RhCl₃·xH₂O afforded the compounds [RuL₂Cl(H₂O)]H₂O, [RuL₂Cl·DMFI and RhL(LH)Cl₂·2H₂O. Reactions of LH with RuCl₃·xH₂O in the presence of N-heterocyclic bases led to the formation of complexes of type [RuL₂ClB]·H₂O (B = pyridine, 3-picoline or imidazole) and [RuLCl₂(o-phen)] H₂O (o-phen = 1, 10-phenanthroline). These complexes were characterized on the basis of analytical, conductivity, magnetic, IR and electronic spectral and ESR studies. Tentative structures for the complexes are proposed.     

Synthesis,structural investigations and antimicrobial studies of hydrazone based ternary complexes with Cr(III), Fe(III) and La(III) ions

A novel series of three trivalent mononuclear ternary complexes of the type, [ML₁L₂] [M = Cr(III), Fe(III) and La(III), HL₁ = 2-((2-(2,4-dinitrophenyl)hydrazone)methyl)phenol, HL₂ = 2-aminophenol] was investigated by various physio-chemical studies. To obtain additional information inside the structure, density functional theory calculation was also carried out. The synthesized complexes showed remarkable antimicrobial activity when tested against A. niger, A. flavus, R. stolonifer, C. albicans, E. coli and Klebsiella sp. microbes. Furthermore, the molecular docking analysis was also carried out to analyze the interactions in protein–ligand complexes. Moreover, the quantitative structure–activity relationship was also investigated to study the biological activity of the ligand.     

Synthesis,crystal structures,spectroscopic studies and antibacterial properties of a series of mononuclear cobalt(III) Schiff base complexes

New complexes of cobalt(III) with the tridentate and tetradentate Schiff base ligands: 3-methoxy-2-{(Z)[(2-hydroxyphenyl)imino]methyl}phenol (H₂L¹), 4-[(2-hydroxyphenyl)imino]-2-pentanone (H₂L²); and 2-((E)-1-(2-((E)-1-(2-hydroxy-4,5-dimethylphenyl)ethylideneamino)ethylimino)ethyl)-4,5 dimethylphenol (H₂L³), namely [Co^III(L¹)(N-MeIm)₃]PF₆ (1), [Co^III(L¹)(py)₃]ClO₄ (2), [Co(L¹)(py)₃][Co(L¹)₂] (3) and [Co^III(L²)(N-MeIm)₃]PF₆ (4) and [Co(L³)(N-MeIm)₂]PF₆ (5), were synthesized and characterized by physico-chemical and spectroscopic methods. The crystal structures of the complexes were determined by X-ray crystallography. In each of these complexes, the cobalt(III) centre has a slightly distorted octahedral environment, utilizing all available coordination centres of the ligands. The complexes were also screened for in vitro antibacterial activities against four human pathogenic bacteria, and their minimum inhibitory concentrations indicated good antibacterial activities.