Protonation of biologically relevant sulfur ligands

PhD ThesisA variety of metalloenzymes contain iron-sulfur clusters (e.g. nitrogenases, aconitase and carbon monoxide dehydrogenase) or nickel-thiolate components (e.g. urease, hydrogenase, CO-dehydrogenase (CODH), methyl coenzyme M reductase, Ni-superoxide dismutase, and glyoxalase I) as the catalytic site where substrates are bound and transformed. The ways in which substrates bind and are transformed at these natural iron and nickel sites remain poorly defined. Studying the natural metalloenzymes is inherently difficult because the complexity of the biological systems, but studies of the protonation on synthetic iron-sulfur and nickel-thiolate complexes allow us to establish possible mechanisms of these natural catalysts. This thesis describes the kinetics and mechanisms of the protonation of synthetic Fe-S clusters and simple Ni-thiolate complexes. The first part of the thesis describes the protonation and binding of substrates to synthetic Fe-S-based clusters. The [NBun4]2[Fe4S4X4] (X= SPh or Cl) were synthesised and characterised by 1H NMR spectroscopy. The kinetics of the acid-catalyzed substitution reactions of the teminal chloro-ligands in [Fe4S4Cl4]2- by PhS− to form [Fe4S4(SPh)4]2- in the presence of the acids NHR3+ (R = Me, Prn or Bun) in MeCN have been studied. Although these acids have very similar pKas (17.6–18.4) the reactions show a variety of different kinetics, some of which are inconsistent with a mechanism involving simple protonation of the cluster followed by substitution of a terminal ligand. The observed behaviour is more consistent with the recently proposed mechanism in which a Fe–(μ3-SH) bond elongation/cleavage occurs upon protonation of a μ3-S, and suggests that both the acidity and bulk of the acid is important in the protonation step. Other studies have determined the activation parameters (ΔH‡ and ΔS‡) for both the protonation and substitution steps of the acid-catalyzed substitution reactions of [Fe4S4X4]2− (X = Cl or SEt). A significantly negative ΔS‡ is observed for the substitution steps of both clusters indicating associative pathways. This is inconsistent with earlier interpretation of the kinetics of these reactions (based exclusively on the dependence of the rate on the concentration of nucleophile) and indicates that there is no dissociative substitution mechanism and the pathway VI associated with a zero-order dependence on the concentration of PhS− involves associative substitution with the solvent (MeCN) being the nucleophile. The mechanism of the acid-catalyzed substitution reaction of the terminal chloro-ligands in [NBun4]2 [Fe4S4Cl4] by PhS− in the presence of NHBun3+ involves rate-limiting proton transfer from NHBun3+ to the cluster (k0 = 490 ± 20 dm3 mol−1 s−1). A variety of small molecules and ions (L = substrate = Cl−, Br−, I−, RNHNH2 (R = Me or Ph), Me2NNH2, HCN, NCS−, N3−, ButNC or pyridine) bind to [Fe4S4Cl4]2− and this affects the rate of subsequent protonation of [Fe4S4Cl4(L)]n−. Where the kinetics allow, the equilibrium constants for the substrates binding to [Fe4S4Cl4]2− (KL) and the rates of proton transfer from NHBun3+ to [Fe4S4Cl4(L)]n− (kL0) have been determined. The results indicate the following general features. (i) Bound substrates increase the rate of protonation of the cluster, but the rate increase is modest (kL0/k0 = 1.6 to ≥72). (ii)When KL is small, so is kL0/k0. (iii) Binding substrates which are good σ-donors or good π-acceptors lead to the largest kL0/k0. This behaviour is discussed in terms of the recent proposal that protonation of [Fe4S4Cl4]2− at a μ3-S, is coupled to concomitant Fe–(μ3-SH) bond elongation/cleavage. The clusters [NHR3]2[Fe4S4X4] (X= PhS, R= Et or Bun; X= Cl, R= Bun) were synthesised and characterised by1H NMR spectroscopy and X-ray crystallography. The crystallography shows NH…X interactions between the cation and the cubanoid cluster. Comparison of the cluster dimensions in [NHR3]2[Fe4S4X4] with those reported earlier for [NR′4]2[Fe4S4X4] (R′ = Me, X = PhS; R′ = Et, X = Cl) indicates that N–H…X interactions have a negligible effect on the dimensions of the cluster. The relevance of these structures to understanding where on [Fe4S4X4]2- protonation labilises the cluster to substitution is discussed. The second part of the thesis describes the protonation of [Ni(SAr){PhP(CH2CH2PPh2)2}]+ complexes. The complexes of [Ni(SC6H4R-2)(triphos)]BPh4 (R= Me, MeO or Cl; triphos = PhP(CH2CH2PPh2)2) and [Ni(SC6H3Me2-2,6)(triphos)]BPh4 were synthesised and structurally characterised by X-ray crystallography. The crystallography of [Ni(SC6H4R-2)(triphos)]BPh4 (R= Me or MeO) and [Ni(SC6H3Me2-2,6)(triphos)]BPh4 shows that the geometry at Ni is square planar and Ni is 4-coordinate; but the geometry for [Ni(SC6H4Cl-2)(triphos)]BPh4 is a square-based pyramid with the chloro-group occupying the apical position and Ni is 5-coordinate. The protonation of all synthesised complexes with both lutH+ (lut= 2,6-dimethylpyridine) and picH+ (pic= 4-methylpyridine) in MeCN were studied using stopped-flow spectrophotometry. These studies show that proton transfer reactions are slow and, in many cases, the hydrogen bonded VII precursor intermediate {[Ni(thiolate)(triphos)]…Hlut}2+ can be detected. For [Ni(SC6H4Cl-2)(triphos)]BPh4, the rates of protonation with lutH+ and picH+ are significantly different (kpic/klut = 2 x 103). However, for [Ni(SC6H4R-2)(triphos)]BPh4 (R= H, Me or MeO) and [Ni(SC6H3Me2-2,6)(triphos)]BPh4 complexes, the differences in the rates with lutH+ and picH+ are much less marked (kpic/klut = 2 - 15) because the thiolate ligand can undergo relatively unhindered Ni-S rotation, allowing protonation from either side of the square plane. Protonation by picH+ is substantially faster than with (the more sterically-demanding) lutH+ because proton transfer in this complex must occur through a cavity in the surrounding phenyl substituents of triphos which is too small for lutH+ to penetrate. DFT calculations support this proposal and allow further exploration of the effects that steric interactions between the phenyl groups for triphos and lutH+ have on the rates of proton transfer to [Ni(thiolate)(triphos)]+.Higher Committee for Education Development in Iraq (HCED) and Iraqi Ministry of Higher Education and Scientific Research (MOHE