Binding of CO to structural models of the bimetallic subunit at the A-cluster of acetyl coenzyme A synthase/CO dehydrogenase

Trinuclear Ni-Cu-Ni and Ni-Ni-Ni complexes derived from an Ni(ii)-dicarboxamido-dithiolato metallosynthon exhibit redox behavior and CO binding properties similar to those of the A-cluster in acetyl coenzyme A synthase/CO dehydrogenase (ACS/CODH).     

Structural models of the bimetallic subunit at the A-cluster of acetyl coenzyme a synthase/CO dehydrogenase: binuclear sulfur-bridged Ni-Cu and Ni-Ni complexes and their reactions with CO

The Ni(II)-dicarboxamido-dithiolato complexes (Et4N)2[Ni(NpPepS)] (1) and (Et4N)2[Ni(PhPepS)] (2) were used as Nid metallosynthons in the construction of higher nuclearity dinuclear Ni-Cu and Ni-Ni species to model the bimetallic Mp-Nid site of the A-cluster of acetyl coenzyme A synthase/CO dehydrogenase (ACS/CODH). Reaction of 1 with [Cu(neo)Cl] and [Ni(terpy)Cl2] in MeCN affords the dinuclear complexes (Et4N)[Cu(neo)Ni(NpPepS)] (3) and [Ni(terpy)Ni(NpPepS)] (4), respectively. Reaction of 2 with [Ni(dppe)Cl2] in MeCN yields [Ni(dppe)Ni(PhPepS)] (6). The Ni-Cu complex 3 exhibits no redox chemistry at the Nid site and no reaction with CO. In contrast, the Nip sites in 4 and 6 are readily reduced (characterized by their Ni(I) EPR spectra) and bind CO, exhibiting nuco bands at 2044 and 1997 cm-1, respectively, indicating terminal CO binding. The present Ni-Ni systems replicate the structural and chemical properties of the A-cluster site in ACS/CODH and support the presence of Ni at Mp in the catalytically active enzyme.     

Structural and spectroscopic models of the A-cluster of acetyl coenzyme a synthase/carbon monoxide dehydrogenase: Nature's Monsanto acetic acid catalyst

Acetyl coenzyme A synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme present in a number of anaerobic bacteria. The enzyme catalyzes two separate reactions namely, the reduction of atmospheric CO₂ to CO (CODH activity at the C-cluster) and the synthesis of acetyl coenzyme A (ACS activity at the A-cluster) from CO, CH₃ from a corrinoid iron-sulfur protein, and the thiol coenzyme A. The structure(s) of the A-cluster of ACS/CODH from Moorella thermoacetica revealed an unprecedented structure with three different metallic subunits linked to each other through bridging Cys-S residues comprising the active site. In these structure(s) a Fe₄S₄ cubane is bridged via Cys-S to a bimetallic metal cluster. This bimetallic cluster contains a four-coordinate Ni, Cu, or Zn as the proximal metal (to the Fe₄S₄ cluster; designated M_p), which in turn is bridged through two Cys-S residues to a terminal square planar Ni(II) (Ni_d, distal to Fe₄S₄) ligated by two deprotonated carboxamido nitrogens from the peptide backbone. It is now established that Ni is required at the M_p site for the ACS activity. Over the past several years modeling efforts by several groups have provided clues towards understanding the intrinsic properties of the unique site in ACS. To date most studies have focused on dinuclear compounds that model the M_p-Ni_d subsite. Synthesis of such models have revealed that the Ni_p sites (a) are readily removed when mixed with 1,10-phenanthroline (phen) and (b) can be reduced to the Ni(I) and/or Ni(0) oxidation state (deduced by EPR or electrochemical studies) and bind CO in terminal fashion with ν_co value similar to the enzyme. In contrast, the presence of Cu(I) centers at these M_p sites do not bind CO and are not removable with phen supporting a non-catalytic role for Cu(I) at the M_p site in the enzyme. The Ni_d site (coordinated by carboxamido-N/thiolato-S) in these models are very stable in the +2 oxidation state and not readily removed upon treatment with phen suggesting that the source of ‘labile Ni’ and the NiFeC signal arises from the presence of Ni at the M_p site in ACS. This review includes the results and implications of the modeling studies reported so far.     

Cys-Gly-Cys tripeptide complexes of nickel: binuclear analogues for the catalytic site in acetyl coenzyme a synthase

The tripeptide, Ac-CysGlyCys-CONH2, is utilized as a ligand to bind Ni in a fashion identical to that found at the active site of acetyl coenzyme A synthase. The Ni-peptide construct is a suitable metalloligand for the preparation of larger structures formed via bridging Cys side chains. The complexes Ni(CysGlyCys)Ni(dppe) and Ni(CysGlyCys)Ni(depe) serve as close structural representations for the binuclear subcluster, exhibiting electrochemical properties that demonstrate facile access to the reduced mixed valent Ni(II)Ni(I) state, which binds CO.     

The tunnel of acetyl-coenzyme a synthase/carbon monoxide dehydrogenase regulates delivery of CO to the active site

The effect of [CO] on acetyl-CoA synthesis activity of the isolated alpha subunit of acetyl-coenzyme A synthase/carbon monoxide dehydrogenase from Moorella thermoacetica was determined. In contrast to the complete alpha(2)beta(2) enzyme where multiple CO molecules exhibit strong cooperative inhibition, alpha was weakly inhibited, apparently by a single CO with K(I) = 1.5 +/- 0.5 mM; other parameters include k(cat) = 11 +/- 1 min(-)(1) and K(M) = 30 +/- 10 microM. The alpha subunit lacked the previously described "majority" activity of the complete enzyme but possessed its "residual" activity. The site affording cooperative inhibition may be absent or inoperative in isolated alpha subunits. Ni-activated alpha rapidly and reversibly accepted a methyl group from CH(3)-Co(3+)FeSP affording the equilibrium constant K(MT) = 10 +/- 4, demonstrating the superior nucleophilicity of alpha(red) relative to Co(1+)FeSP. CO inhibited this reaction weakly (K(I) = 540 +/- 190 microM). NiFeC EPR intensity of alpha developed in accordance with an apparent K(d) = 30 microM, suggesting that the state exhibiting this signal is not responsible for inhibiting catalysis or methyl group transfer and that it may be a catalytic intermediate. At higher [CO], signal intensity declined slightly. Attenuation of catalysis, methyl group transfer, and the NiFeC signal might reflect the same weak CO binding process. Three mutant alpha(2)beta(2) proteins designed to block the tunnel between the A- and C-clusters exhibited little/no activity with CO(2) as a substrate and no evidence of cooperative CO inhibition. This suggests that the tunnel was blocked by these mutations and that cooperative CO inhibition is related to tunnel operation. Numerous CO molecules might bind cooperatively to some region associated with the tunnel and institute a conformational change that abolishes the majority activity. Alternatively, crowding of CO in the tunnel may control flow through the tunnel and deliver CO to the A-cluster at the appropriate step of catalysis. Residual activity may involve CO from the solvent binding directly to the A-cluster.     

Structural analogues of the bimetallic reaction center in acetyl CoA synthase: a Ni--Ni model with bound CO

Models for the active site of the acetyl CoA synthase (ACS) were synthesized by attachment of Cu+ and Ni(0) to nickel diaminodithiolate (S2N2) and diamidodithiolate (S2N2') complexes. The Ni-Ni species form stable CO adducts, i.e., [{(CO)2Ni}{NiS2N2'}]2-, whereas the Cu-NiS2N2 and Cu-NiS2N2' models do not. These results provide supporting evidence for a biological role for reduced nickel in ACS.     

Lithium fluoroarylamidinates: syntheses, structures, and reactions

Lithium fluoroarylamidinates [(Ar(F)C(NSiMe(3))(2)Li)(n).xD] (Ar(F) = 4-CF(3)C(6)H(4), n = 2, D = OEt(2), x = 1 (2a); n = 1, D = TMEDA, x = 1 (4a); Ar(F) = 2-FC(6)H(4), n = 2, D = OEt(2), x = 1 (2b); Ar(F) = 4-FC(6)H(4), n = 2, D = OEt(2), x = 2 (2c); Ar(F) = 2,6-F(2)C(6)H(3), n = 2, D = OEt(2), x = 1 (2d); n = 2, D = 2,6-F(2)C(6)H(3)CN, x = 2 (3d); Ar(F) = C(6)F(5), n= 2, D = OEt(2), x = 1 (2e), n = 1, D = TMEDA, x = 1 (4e); n = 1, x = 2, D = OEt(2) (5e); D = THF (6e)) were prepared by the well-known method from LiN(SiMe(3))(2) and the corresponding nitrile in diethyl ether or by addition of the appropriate donor D to the respective diethyl ether complexes. Depending on the substituents at the aryl group and on the donors D, three different types of structures were confirmed by X-ray crystallography. Hydrolysis of 2e gave C(6)F(5)C(NSiMe(3))N(H)SiMe(3) (7e) and C(6)F(5)C(NH)N(H)SiMe(3) (8e). The lithium fluoroarylamidinates 2a-2d react with Me(3)SiCl to give the corresponding tris(trimethylsilyl)fluoroarylamidines Ar(F)C(NSiMe(3))N(SiMe(3))(2) (9a-9d). Attempts to prepare C(6)F(5)C(NSiMe(3))N(SiMe(3))(2) from 2e and Me(3)SiCl failed; however, the unprecedented cage [[C(6)F(5)C(NSiMe(3))(2)Li](4)LiF] (10e) in which a fluoride center is surrounded by a distorted trigonal bipyramid of five Li atoms was obtained from this reaction.     

Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase

The catalytic mechanism of molybdenum containing CO dehydrogenase has been studied using hybrid DFT methods with quite large chemical models. The recent high-resolution X-ray structure, showing the surprising presence of copper linked to molybdenum, was used as a starting point. A pathway was initially found with a low barrier for C-O bond formation and CO2 release. However, this pathway did not include the formation of any S-CO2 species, which had been suggested by experiments with an n-butylisocyanide inhibitor. When these SCO2 structures were studied they were found to lead to deep minima, making CO2 release much more difficult. A large effort was spent, including investigations of other spin states, varying the number of protons and electrons, adding water, etc., until a plausible pathway for S-C bond cleavage was found. In this pathway a water molecule is inserted in between molybdenum and the SCO2 group. Full catalytic cycles, including electron and proton transfers, are constructed both with and without S-C bond formation. When these pathways are extended to two full catalytic cycles it can be understood why the formation of the S-C bond actually makes catalysis faster, even though the individual step of CO2 release becomes much more difficult. These results agree well with experimental findings.     

Reduction and methyl transfer kinetics of the alpha subunit from acetyl coenzyme a synthase

Stopped-flow was used to evaluate the methylation and reduction kinetics of the isolated alpha subunit of acetyl-Coenzyme A synthase from Moorella thermoacetica. This catalytically active subunit contains a novel Ni-X-Fe4S4 cluster and a putative unidentified n = 2 redox site called D. The D-site must be reduced for a methyl group to transfer from a corrinoid-iron-sulfur protein, a key step in the catalytic synthesis of acetyl-CoA. The Fe4S4 component of this cluster is also redox active, raising the possibility that it is the D-site or a portion thereof. Results presented demonstrate that the D-site reduces far faster than the Fe4S4 component, effectively eliminating this possibility. Rather, this component may alter catalytically important properties of the Ni center. The D-site is reduced through a pathway that probably does not involve the Fe4S4 component of this active-site cluster.     

Structure and electronic properties of an asymmetric thiolate-bridged binuclear complex: a model for the active site of acetyl CoA synthase

The asymmetric binuclear complex [(dppe)Ni(mu-'S, S')Ni(L)](PF6)2 [L = (N, N'-diethyl-3,7-diazanonane-1,9-dithiolato)2-] shows a reversible one-electron reduction to afford a mixed-valent Ni(II) x Ni(I) species; the reduced complex has been characterised by EPR spectroscopy and mimics the redox active Nip site in the active A-cluster of acetyl coenzyme A synthase.     

Synthetic applications of optically active cyanohydrins. Enantioselective syntheses of the hydroxyamides tembamide and aegeline, the cardiac drug denopamine, and some analogues of the bronchodilator salbutamol

The natural hydroxyamides, (−)-tembamide and (−)-aegeline, and the cardiac drug (−) -denopamine have been prepared in homochiral form in good overall yield (>65%) from para - methoxy or para-allyloxybenzaldehyde by synthetic sequences involving entantioselective hydrocyanation of the aldehydes. Similar chemistry has been used to prepare analogues of the bronchodilator (−)-salbutamol both in high yield and with good enantiomeric excess.     

Transannular reactions of two parallel 1,3-butadiynes: syntheses,structures, and reactions of 1-azacyclotetradeca-3,5,10,12-tetrayne derivatives

The synthesis of 1-alkyl and 1-aryl-1-azacyclotetradeca-3,5,10,12-tetraynes was achieved in a stepwise approach. The key intermediate was 1,13-dibromotrideca-2,4,9,11-tetrayne (18). Reaction with methyl- (19 a), ethyl- (19 b), isopropyl- (19 c), n-butyl- (19 d), and tert-butylamine (19 e) as well as aniline (19 f) and p-methoxyaniline (19 g) gave the corresponding 14-membered tetraynes 20 a-20 g. The ring inversion process of 20 b was studied by variable temperature (1)H NMR spectroscopy. From these measurements a value of 10.6 kcal mol(-1) was calculated for DeltaG(not equal). X-ray investigations on single crystals of 20 b, 20 c, and 20 f revealed the axial position for the substituent at each nitrogen atom. For 20 b we encountered the chair conformation, for 20 c both chair and boat conformations, and for 20 f the boat conformation in the solid state. The reaction of 20 c with concentrated HCl in ethanol yielded 2,10-dichloro-6-isopropyl-6-azatricyclo[9.3.0.0(4,8)]tetradeca-1(11),2,4(8),9-tetraene (25 c). Compound 25 c was oxidized by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) to 27 c. The structure of the latter was confirmed by X-ray investigations. The reaction of 20 c in aqueous HCl lead to the formation of 10-chloro-2-isopropyl-1,3,4,6,7,8-hexahydro-2H-benzo[g]isoquinolin-9-one (37 c). The structure of 37 c was verified by X-ray studies on single crystals.     

Design and synthesis of C5 methylated L-arginine analogues as active site probes for nitric oxide synthase

The role of nitric oxide (NO) as a biological signaling molecule is well established. NO is produced by the nitric oxide synthases (NOSs, EC 1.14.13.39), a class of heme proteins capable of converting l-arginine to NO and l-citrulline. Despite the large body of knowledge associated with the NOSs, mechanistic details relating to the unique oxidative chemistry performed by these enzymes remain to be fully elucidated. Furthermore, a number of disease states are associated with either the over- or underproduction of NO, making the NOS pathway an attractive target for the development of therapeutics. For these reasons, molecular tools capable of providing mechanistic insights into the production of NO and/or the inhibition of the NOSs remain of interest. We report here the stereospecific synthesis and testing of a number of new l-arginine analogues bearing a minimal substitution, methylation at position 5 of the amino acid side chain (such analogues have not been previously reported). The synthetic approach employed a modified photolysis procedure whereby irradiation of the appropriate diacylperoxide precursors at 254 nm gave access to the required unnatural amino acids in good yields. A heme domain construct of the inducible NOS isoform (iNOSheme) was used to assess the binding of each compound to the enzyme active site. The compounds were also investigated as either inhibitors of, or alternate substrates for, the inducible NOS isoform. The results obtained provide new insight into the steric and stereochemical tolerance of the enzyme active site. These findings also further support the role of a conserved active site water molecule previously proposed to be necessary for NOS catalysis.     

Amido/amine triazacyclononane-based zirconium complexes: syntheses, reactivity, and structures

The reactions of [Zr(NMe2)4]2 with triamido-triazacyclonane ligand precursors, {NH(Ph)SiMe2}3tacn (H3N3[9]N3) and {NH(C6H4F)SiMe2}3tacn (H3N3-F[9]N3), led to the formation of complexes [Zr(NMe2)2{N(Ph)SiMe2}2{NH(Ph) SiMe2}tacn], 1, and [Zr(NMe2)2{N(o-C6H4F)SiMe2}2{NH(o-C6H4F)SiMe2} tacn], 2, where the zirconium is coordinated to two remaining dimethylamido ligands and to a dianionic tacn-based ligand, [{N(Ph')SiMe2}2{NH(Ph')SiMe2}tacn]2-, that formed from deprotonation of two amine pendent arms of the ligands' precursors. The third pendent arm of H3N3[9]N3 and H3N3-F[9]N3 remains neutral and not bonded to the zirconium. Treatment of 1 with NaH led to the synthesis of [Zr(NMe2){N(Ph)SiMe2}2tacn], 3, that results from the cleavage of the N-Si bond of the original neutral pendent arm. Complexes [ZrCl{N(Ph')SiMe2}2tacn] (Ph' = C6H5, 4, and C6H4F, 5) have been obtained by reactions of ZrCl4 with {MN(Ph')SiMe2}3tacn.2THF (M = Li, Na). Reactions of 4 and 5 with LiC triple bond CPh led to the syntheses of [Zr(CCPh){N(Ph')SiMe2}2tacn] (Ph' = C6H5, 6, and C6H4F, 7). The solid-state structure of 3 shows a chiral metal center.     

A family of manganese rods: syntheses, structures, and magnetic properties

The reaction of the mixed-valent metal triangles [Mn(3)O(O(2)CR)(6)(py)(3)] (R = CH(3), Ph, C(CH(3))(3)) with the tripodal ligands H(3)thme (1,1,1-tris(hydroxymethyl)ethane) and H(3)tmp (1,1,1-tris(hydroxymethyl)propane) in MeCN, produces a family of manganese rodlike complexes whose structures are all derived from a series of edge-sharing triangles. Variable temperature direct current (dc) magnetic susceptibility data were collected for all complexes in the 1.8-300 K temperature range in fields up to 7.0 T. Complex 1, [Mn(12)O(4)(OH)(2)(PhCOO)(12)(thme)(4)(py)(2)], has an S = 7 ground state with the parameters g = 1.98 and D = -0.13 K. Complex 2, [Mn(8)O(4)((CH(3))(3)CCO(2))(10)(thme)(2)(py)(2)] has a ground state of S = 6, with g = 1.81 and D = -0.36 K. Complex 3, [Mn(7)O(2)(PhCO(2))(9)(thme)(2)(py)(3)], has a spin ground states of S = 7 with the parameters g = 1.78 and D = -0.20 K. The best fit for complex 4, [Mn(6)((CH(3))(3)CCO(2))(8)(tmp)(2)(py)(2)], gave a spin ground state of S = 3 with the parameters g = 1.73 and D = -0.75 K, but was of poorer quality than that normally obtained. The presence of multiple Mn(2+) ions in the structure of 4 leads to the presence of low-lying excited states with energy levels very close to the ground state, and in the case of complex 5, [Mn(6)(CH(3)CO(2))(6)(thme)(2)(H(2)tea)(2)], no satisfactory fit of the data was obtained. DFT calculations on 4 and 5 indicate complexes with spin ground states of S = 4 and S = 0 respectively, despite their topological similarities. Single-crystal hysteresis loop and relaxation measurements show complex 1 to be a SMM.     

Kinetics of CO insertion and acetyl group transfer steps, and a model of the acetyl-CoA synthase catalytic mechanism

Acetyl-CoA synthase/carbon monoxide dehydrogenase is a Ni-Fe-S-containing enzyme that catalyzes the synthesis of acetyl-CoA from CO, CoA, and a methyl group. The methyl group is transferred onto the enzyme from a corrinoid-iron-sulfur protein (CoFeSP). The kinetics of two steps within the catalytic mechanism were studied using the stopped-flow method, including the insertion of CO into a putative Ni(2+)-CH(3) bond and the transfer of the resulting acetyl group to CoA. Neither step had been studied previously. Reactions were monitored indirectly, starting with the methylated intermediate form of the enzyme. Resulting traces were analyzed by constructing a simple kinetic model describing the catalytic mechanism under reducing conditions. Besides methyl group transfer, CO insertion, and acetyl group transfer, fitting to experimental traces required the inclusion of an inhibitory step in which CO reversibly bound to the form of the enzyme obtained immediately after product release. Global simulation of the reported datasets afforded a consistent set of kinetic parameters. The equilibrium constant for the overall synthesis of acetyl-CoA was estimated and compared to the product of the individual equilibrium constants. Simulations obtained with the model duplicated the essential behavior of the enzyme, in terms of the variation of activity with [CO], and the time-dependent decay of the NiFeC EPR signal upon reaction with CoFeSP. Under standard assay conditions, the model suggests that the vast majority of active enzyme molecules in a population should be in the methylated form, suggesting that the subsequent catalytic step, namely CO insertion, is rate limiting. This conclusion is further supported by a sensitivity analysis showing that the rate is most sensitively affected by a change in the rate coefficient associated with the CO insertion step.     

Coordination of methyl coenzyme M and coenzyme M at divalent and trivalent nickel cyclams: model studies of methyl coenzyme M reductase active site

Divalent and trivalent nickel complexes of 1,4,8,11-tetraazacyclotetradecane, denoted as cyclam hereafter, coordinated by methyl coenzyme M (MeSCoM(-)) and coenzyme M (HSCoM(-)) have been synthesized in the course our model studies of methyl coenzyme M reductase (MCR). The divalent nickel complexes Ni(cyclam)(RSCoM)(2) (R = Me, H) have two trans-disposed RSCoM(-) ligands at the nickel(II) center as sulfonates, and thus, the nickels have an octahedral coordination. The SCoM(2-) adduct Ni(cyclam)(SCoM) was also synthesized, in which the SCoM(2-) ligand chelates the nickel via the thiolate sulfur and a sulfonate oxygen. The trivalent MeSCoM adduct [Ni(cyclam)(MeSCoM)(2)](OTf) was synthesized by treatment of [Ni(cyclam)(NCCH(3))(2)](OTf)(3) with ((n)Bu(4)N)[MeSCoM]. A similar reaction with ((n)Bu(4)N)[HSCoM] did not afford the corresponding trivalent HSCoM(-) adduct, but rather the divalent nickel complex polymer [-Ni(II)(cyclam)(CoMSSCoM)-](n) was obtained, in which the terminal thiol of HSCoM(-) was oxidized to the disulfide (CoMSSCoM)(2-) by the Ni(III) center.     

Compound I of nitric oxide synthase: the active site protonation state

A quantum mechanical/molecular mechanical (QM/MM) study of the formation of the elusive active species Compound I (Cpd I) of nitric oxide synthase (NOS) from the oxyferrous intermediate shows that two protons have to be provided to produce a reaction that is reasonably exothermic and that leads to the appearance of a radical on the tetrahydrobiopterin cofactor. Molecular dynamics and energy considerations show that a possible source of proton is the water H-bond chain formed from the surface to the active site, but that a water molecule by itself cannot be the source of the proton; an H3O+ species that is propagated along the chain is more likely. The QM/MM calculations demonstrate that Cpd I and H2O are formed from the ferric-hydrogen peroxide complex in a unique heterolytic O-O cleavage mechanism. The properties of the so-formed Cpd I are compared with those of the known species of chloroperoxidase, and the geometry and spin densities are found to be compatible. The M?ssbauer parameters are calculated and may serve as experimental probes in attempts to characterize NOS Cpd I.