The Nitrogen Atom of Vitamin B6 Is Essential for the Catalysis of Radical Aminomutases.

Radical aminomutases are pyridoxal 5'-phosphate (PLP, a B6 vitamer)-dependent enzymes that require the generation of a 5'-deoxyadenosyl radical to initiate the catalytic cycle, to perform a 1,2 amino group shift reaction. The role of the nitrogen atom of PLP in radical aminomutases has not been investigated extensively yet. We report an alternative synthetic procedure to provide easy access to 1-deazaPLP (dAPLP), an isosteric analog of PLP which acts as a probe for studying the role of the nitrogen atom. Our results revealed that lysine 5,6-aminomutase (5,6-LAM), a radical aminomutase, reconstituted with dAPLP cannot turn over a substrate, demonstrating that the nitrogen atom is essential for radical aminomutases. In contrast, biochemical and spectroscopic studies on the S238A variant reconstituted with PLP revealed a minuscule loss of activity. This apparent anomaly can be explained by a water-mediated rescue of activity in S238A, as if mimicking the active site of lysine 2,3-aminomutase. This study leads to a better comprehension of how enzymes harness the optimum capability of PLP to realize catalysis.

4'-CyanoPLP presents better prospect for the experimental detection of elusive cyclic intermediate radical in the reaction of lysine 5,6-aminomutase.

The results of our calculations suggest that the reaction of 4'-cyanoPLP with lysine 5,6-aminomutase offers better prospect for the experimental detection of elusive cyclic azacyclopropylcarbinyl radical (I), which is proposed to be a key intermediate in the reaction of pyridoxal-5'-phosphate dependent radical aminomutases. We have calculated the corresponding hyperfine coupling constants (HFCCs) for (14)N and (13)C of cyano group using several basis sets to help the characterization of 4'-cyanoI.

Large-scale domain motions and pyridoxal-5'-phosphate assisted radical catalysis in coenzyme B12-dependent aminomutases.

Lysine 5,6-aminomutase (5,6-LAM) and ornithine 4,5-aminomutase (4,5-OAM) are two of the rare enzymes that use assistance of two vitamins as cofactors. These enzymes employ radical generating capability of coenzyme B12 (5'-deoxyadenosylcobalamin, dAdoCbl) and ability of pyridoxal-5'-phosphate (PLP, vitamin B6) to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. In spite of all the similarities, these enzymes differ in substrate specificities. 4,5-OAM is highly specific for D-ornithine as a substrate while 5,6-LAM can accept D-lysine and L-ß-lysine. This review focuses on recent computational, spectroscopic and structural studies of these enzymes and their implications on the related enzymes. Additionally, we also discuss the potential biosynthetic application of 5,6-LAM.

Synthesis of 4-thia-[6-(13)C]lysine from [2- (13)C]glycine: access to site-directed isotopomers of 2-aminoethanol, 2-bromoethylamine and 4-thialysine.

4-Thialysine (S-(2-aminoethyl)-L: -cysteine) is an analog of lysine. It has been used as an alternative substrate for lysine in enzymatic reactions. Site-directed isotopomers are often needed for elucidation of mechanism of reactions. 4-Thialysine can be synthesized by reacting cysteine with 2-bromoethylamine, an important reagent in chemical-modification rescue (CMR) of proteins. Here, we present the synthesis of 4-thia-[6-(13)C]lysine, one of the isotopomers of 4-thialysine, from commercially available starting material [2-(13)C]glycine via formation of five intermediates including 2-amino[2-(13)C]ethanol and 2-bromo[1-(13)C]ethylamine. The compounds were characterized using various spectroscopic techniques. Moreover, we discuss that our strategy would provide access to site-directed isotopomers of 2-aminoethanol, 2-bromoethylamine and 4-thialysine. Biological activity of 4-thia-[6-(13)C]lysine was tested in the enzymatic reaction of lysine 5,6-aminomutase.

Electronic structures of ruthenium and osmium complexes of 9,10-phenanthrenequinone.

The reaction of 9,10-phenanthrenequinone (PQ) with [M(II)(H)(CO)(X)(PPh(3))(3)] in boiling toluene leads to the homolytic cleavage of the M(II)-H bond, affording the paramagnetic trans-[M(PQ)(PPh(3))(2)(CO)X] (M = Ru, X = Cl, 1; M = Os, X = Br, 3) and cis-[M(PQ)(PPh(3))(2)(CO)X] (M = Ru, X = Cl, 2; M = Os, X = Br, 4) complexes. Single-crystal X-ray structure determinations of 1, 2·toluene, and 4·CH(2)Cl(2), EPR spectra, and density functional theory (DFT) calculations have substantiated that 1-4 are 9,10-phenanthrenesemiquinone radical (PQ(•-)) complexes of ruthenium(II) and osmium(II) and are defined as trans-[Ru(II)(PQ(•-))(PPh(3))(2)(CO)Cl] (1), cis-[Ru(II)(PQ(•-))(PPh(3))(2)(CO)Cl] (2), trans-[Os(II)(PQ(•-))(PPh(3))(2)(CO) Br] (3), and cis-[Os(II)(PQ(•-))(PPh(3))(2)(CO)Br] (4). Two comparatively longer C-O [average lengths: 1, 1.291(3) Å; 2·toluene, 1.281(5) Å; 4·CH(2)Cl(2), 1.300(8) Å] and shorter C-C lengths [1, 1.418(5) Å; 2·toluene, 1.439(6) Å; 4·CH(2)Cl(2), 1.434(9) Å] of the OO chelates are consistent with the presence of a reduced PQ(•-) ligand in 1-4. A minor contribution of the alternate resonance form, trans- or cis-[M(I)(PQ)(PPh(3))(2)(CO)X], of 1-4 has been predicted by the anisotropic X- and Q-band electron paramagnetic resonance spectra of the frozen glasses of the complexes at 25 K and unrestricted DFT calculations on 1, trans-[Ru(PQ)(PMe(3))(2)(CO)Cl] (5), cis-[Ru(PQ)(PMe(3))(2)(CO)Cl] (6), and cis-[Os(PQ)(PMe(3))(2)(CO)Br] (7). However, no thermodynamic equilibria between [M(II)(PQ(•-))(PPh(3))(2)(CO)X] and [M(I)(PQ)(PPh(3))(2)(CO)X] tautomers have been detected. 1-4 undergo one-electron oxidation at -0.06, -0.05, 0.03, and -0.03 V versus a ferrocenium/ferrocene, Fc(+)/Fc, couple because of the formation of PQ complexes as trans-[Ru(II)(PQ)(PPh(3))(2)(CO)Cl](+) (1(+)), cis-[Ru(II)(PQ)(PPh(3))(2)(CO)Cl](+) (2(+)), trans-[Os(II)(PQ)(PPh(3))(2)(CO)Br](+) (3(+)), and cis-[Os(II)(PQ)(PPh(3))(2)(CO)Br](+) (4(+)). The trans isomers 1 and 3 also undergo one-electron reduction at -1.11 and -0.96 V, forming PQ(2-) complexes trans-[Ru(II)(PQ(2-))(PPh(3))(2)(CO)Cl](-) (1(-)) and trans-[Os(II)(PQ(2-))(PPh(3))(2)(CO)Br](-) (3(-)). Oxidation of 1 by I(2) affords diamagnetic 1(+)I(3)(-) in low yields. Bond parameters of 1(+)I(3)(-) [C-O, 1.256(3) and 1.258(3) Å; C-C, 1.482(3) Å] are consistent with ligand oxidation, yielding a coordinated PQ ligand. Origins of UV-vis/near-IR absorption features of 1-4 and the electrogenerated species have been investigated by spectroelectrochemical measurements and time-dependent DFT calculations on 5, 6, 5(+), and 5(-).

Exploring the mechanism of action of lysine 5,6-aminomutase using EPR and ENDOR spectroscopies.

Radical enzymes orchestrate challenging chemical transformations by devising strategies to tame the highly reactive radical intermediates. Electron paramagnetic resonance (EPR) spectroscopy is the most suitable technique to study various aspects of the radical enzymes. Lysine 5,6-aminomutase (5,6-LAM) is one such radical enzyme and employs coenzyme B12 and pyridoxal 5'-phosphate (PLP) to catalyze the 1,2-amino shift reaction through a radical mechanism. 5,6-LAM accepts either d-lysine or l-ß-lysine as the substrate. EPR and electron nuclear double resonance (ENDOR) spectroscopies have played major roles in deciphering the mechanism of action of 5,6-LAM, while density functional theoretical (DFT) computation and synthetic isotopologues have played supporting roles. This comprehensive toolkit has revealed that 5,6-LAM undergoes large-scale conformational movement to bring PLP and coenzyme B12 close together, which allows the reaction to progress. The conformational change also closes the active site, which protects the radical intermediates and enables their transformation to product without unwanted side reactions. The substrate-related radical (S•), which is spin-coupled with Co2+ generated from homolysis of the CoC bond in coenzyme B12, was unequivocally characterized when a substrate analog, 4-thia-l-lysine, and isotopologues of it were reacted with 5,6-LAM. Studies with substrate analogs revealed a unique "odd-even" correlation with opening of the closed state. Moreover, mutagenesis studies identified the contributions that conserved residues in 5,6-LAM make toward binding of the substrate. Further studies with a cofactor analog, PLP-N-oxide, have shed light on various aspects of the mechanism of action of 5,6-LAM.

Osazone anion radical complex of rhodium(III).

One electron paramagnetic parent osazone complex of rhodium of type trans-Rh(L(NHPh)H(2))(PPh(3))(2)Cl(2) (1), defined as an osazone anion radical complex of rhodium(III), trans-Rh(III)(L(NHPh)H(2)(•-))(PPh(3))(2)Cl(2), 1((t-RhL•)), with a minor contribution (∼2%) of rhodium(II) electromer, trans-Rh(II)(L(NHPh)H(2))(PPh(3))(2)Cl(2), 1((t-Rh•L)), and their nonradical congener, trans-[Rh(III)(L(NHPh)H(2))(PPh(3))(2)Cl(2)]I(3) ([t-1](+)I(3)(-)), have been isolated and are substantiated by spectra, bond parameters, and DFT calculations on equivalent soft complexes [Rh(L(NHPh)H(2))(PMe(3))(2)Cl(2)] (3) and [Rh(L(NHPh)H(2))(PMe(3))(2)Cl(2)](+) (3(+)). 1 is not stable in solution and decomposes to [t-1](+) and a new rhodium(I) osazone complex, [Rh(I)(L(NHPh)H(2))(PPh(3))Cl] (2). 1 absorbs strongly at 351 nm due to MLCT and LLCT, while [t-1](+) and 2 absorb moderately in the range of 300-450 nm, respectively, due to LMCT and MLCT elucidated by TD-DFT calculations on 3((t-RhL•)), [t-3](+), and Rh(I)(L(NHPh)H(2))(PMe(3))Cl (4). EPR spectra of solids at 295 and 77 K, and dichloromethane-toluene frozen glass at 77 K of 1 are similar with g = 1.991, while g = 2.002 for the solid at 25 K. The EPR signal of 1 in dichloromethane solution is weaker (g = 1.992). In cyclic voltammetry, 1 displays two irreversible one electron transfer waves at +0.13 and -1.22 V, with respect to Fc(+)/Fc coupling, due to oxidation of 1((t-RhL•)) to [t-1](+) at the anode and reduction of rhodium(III) to rhodium(II), i.e., [t-1](+) to electromeric 1((t-Rh•L)) at the cathode.

Di-, tri-, tetra-, and hexanuclear copper(II) mono-organophosphates: structure and nuclearity dependence on the choice of phosphorus substituents and auxiliary N-donor ligands.

Reactions of 2,6-dimethylphenyl phosphate (dmppH(2)) and 2,6-diisopropylphenyl phosphate (dippH(2)) with copper(II) precursors have been investigated in the presence of auxiliary N-donor ligands, and new structural types of copper phosphates have been isolated. Copper acetate reacts with dmppH(2) in the presence of either 3,5-di-tert-butyl pyrazole (dbpz) or 3,5-dimethyl pyrazole (dmpz), leading to the isolation of tetrameric complex [Cu(dmpp)(dbpz)](4) 1 and hexanuclear cage complex [Cu(6)(PO(4))(dmpp)(3)(OAc)(3)(dmpz)(9)] 2, respectively. Whereas compound 1 is a cubane-shaped cluster whose Cu(4)O(12)P(4) core resembles the double-4-ring (D4R) zeolite SBU, compound 2 is a novel hexanuclear copper complex with an unprecedented structure in metal phosphate chemistry. Use of bulkier dippH(2) in the above reactions, however, yielded metal-free acid-base complexes [(dippH)(dbpz)(dbpzH)] 3 and [(dippH)(dmpz)(dmpzH)] 4, respectively. The reactions carried out between copper acetate and dmppH(2) or dippH(2) in the presence of chelating ligand 1,10-phenanthroline produced structurally similar dimeric copper phosphates [Cu(phen)(dmpp)(CH(3)OH)](2).2CH(3)OH 5 and [Cu(phen)(dipp)(CH(3)OH)](2).2CH(3)OH 6 with a S4R SBU core. Changing the copper source to [Cu(2)(bpy)(2)(OAc)(OH)(H(2)O)].2ClO(4) and carrying out reactions both with dippH(2) and with dmppH(2) result in the formation of trinuclear copper phosphates [Cu(3)(bpy)(3)(dmpp)(2)(CH(3)OH)(3)].2ClO(4).2CH(3)OH 7 and [Cu(3)(bpy)(3)(dipp)(2)(CH(3)OH)(3)].2ClO(4).2CH(3)OH 8. The three copper ions in 7 and 8 are held together by two bridging phosphate ligands to produce a tricyclic derivative whose core resembles the 4=1 SBU of zeolites. Compounds 1-8 have been characterized by elemental analysis and IR, absorption, emission, and EPR spectroscopic techniques. The crystal structures of compounds 1, 2, 4, 5, 6, and 8 have also been established by single-crystal X-ray diffraction studies.

The molecular mechanism of the open-closed protein conformational cycle transitions and coupled substrate binding, activation and product release events in lysine 5,6-aminomutase.

How a protein domain motion is coupled to the catalytic cycle is a current subject in enzymology. We render down a complicated domain motion in the 5'-deoxyadenosylcobalamin and pyridoxal-5'-phosphate codependent radical enzyme, lysine 5,6-aminomutase, into dominant contributions from Lys370α and Asp298α to the critical Co-C bond cleavage trigger and open-closed cycle transitions.

Stabilization of oxidovanadium(IV) by organic radicals.

o-Imino-p-R'-benzosemiquinone anion radical (L(R')(IS)(˙-)) complexes of oxidovanadium(IV) of type [(L(1)(R-))(VO(2+))(L(R')(IS)(˙-))] (R = H, R' = H, 1; R = H, R' = -CMe(3), 2; R = -CMe(3), R' = H, 3 and R = -CMe(3), R' = -CMe(3), 4) incorporating the redox-innocent tridentate NNO-donor L(1)(R-) ligands (L(1)(R)H = 2,4-di-R-6-{(2-(pyridin-2-yl)hydrazono)methyl}phenol) were isolated and substantiated by elemental analyses, IR, mass, NMR and UV-vis spectra including the single crystal X-ray structure determinations. The V-O(phenolato) (cis to the V=O) lengths spanning 1.905(3)-1.9355(15) Å in 1-4 are consistent with the coordination to the [VO](2+) state. The V-O(IS) (trans to the V=O) lengths, 2.1505(17)-2.1869(15) Å, in 1-4 are longer due to the trans influence of the V=O bond. The V-N(IS) lengths, 1.906(3)-1.924(2) Å, in 1-4 are comparatively shorter due to the higher affinity of the paramagnetic [VO](2+) ion towards the L(R')(IS)(˙-) anion radicals. Density functional theory (DFT) calculations using B3LYP, B3PW91 and PBE1PBE functionals on 1 and 2 authenticated that the closed shell singlet (CSS) solutions (dianionic o-amido-p-R'-phenolates (L(R')(AP)(2-)) coordinated to VO(3+), Type I) of 1-4 are unstable with respect to the open shell singlet (OSS) perturbations. Broken symmetry, BS (1,1) M(s) = 0 (L(R')(IS)(˙-) coordinated to the VO(2+) ion, Type III) solutions of 1-4 are stable and reproduce the experimental bond parameters. Frozen glasses EPR spectra of [1-4](+) ions (e.g. g(||) = 1.948, g(⊥) = 1.978, A(||) = 184 (22 G), A(⊥) = 62(15 G) for [2](+)) and unrestricted DFT calculations on [1](+), [2](+), [1](-) and [2](-) ions using doublet spin state elucidated that the reversible anodic waves at [0.15-0.31] V of 1-4 complexes are due to the oxidation of L(R')(IS)(˙-) generating [(L(1)(R-))(VO(2+))(L(R')(IQ))]+ complexes (L(R')(IQ) = o-imino-p-R'-benzoquinone) coordinated to the [VO](2+) ion (Type V) while the irreversible cathodic waves at -[1.08-1.49] V are due to the formation of unstable [(L(1)(R-))(VO(2+))(L(R')(AP)(2-))](-) complexes (Type II). The second anodic waves at [0.76-0.89] V are assigned to a [VO](3+)-[VO](2+) couple affording diamagnetic [(L(1)(R-))(VO(3+))(L(R')(IQ))](2+), [1-4](2+) complexes (Type VI) which are identified by UV-vis spectra, DFT and time dependent (TD) DFT calculations. Spectro-electrochemical measurements and TD DFT calculations on 1 and 2 disclosed that lower energy electronic absorption bands of 1-4 are due to the LMCT and CSS-OSS perturbation which disappear in [1-4](+) ions. [1-4](+) absorb at 600-650 nm due to d-d transitions and MLCT which are absent in VO(3+) complexes, [1-4](2+).

9,10-phenanthrenesemiquinone radical complexes of ruthenium(III), osmium(III) and rhodium(III) and redox series.

Reactions of 9,10-phenanthrenequinone (PQ) in toluene with [M(II)(PPh3)3X2] at 298 K afford green complexes, trans-[M(PQ)(PPh3)2X2] (M = Ru, X = Cl, 1; M = Os, X = Br, 2) in moderate yields. Reaction of anhydrous RhCl3 with PQ and PPh3 in boiling ethanol affords the dark brown paramagnetic complex, cis-[Rh(PQ)(PPh3)2Cl2] (3) in good yields. Diffusion of iodine solution in n-hexane to the trans-[Os(PQ) (PPh3)2(CO)(Br)] solution in CH2Cl2 generates the crystals of trans-[Os(PQ)(PPh3)2(CO)(Br)](+)I3(-), (4(+))I3(-)), in lower yields. Single crystal X-ray structure determinations of 1·2toluene, 2·CH2Cl2 and 4(+)I3(-), UV-vis/NIR absorption spectra, EPR spectra of 3, electrochemical activities and DFT calculations on 1, 2, trans-[Ru(PQ)(PMe3)2Cl2] (1Me), trans-[Os(PQ)(PMe3)2Br2] (2Me), cis-[Rh(PQ)(PMe3)2Cl2] (3Me) and their oxidized and reduced analogues including trans-[Os(PQ)(PMe3)2(CO)(Br)](+) (4Me(+)) substantiated that 1-3 are the 9,10-phenanthrenesemiquinone radical (PQ(˙-)) complexes of ruthenium(III), osmium(III) and rhodium(III) and are defined as trans/cis-[M(III)(PQ(˙-))(PPh3)2X2] with a minor contribution of the resonance form trans/cis-[M(II)(PQ)(PPh3)2X2]. Two comparatively longer C-O (1.286(4) Å) and the shorter C-C lengths (1.415(7) Å) of the OO-chelate of 1·2toluene and 2·CH2Cl2 and the isotropic fluid solution EPR signal at g = 1.999 of 3 are consistent with the existence of the reduced PQ(˙-) ligand in 1-3 complexes. Anisotropic EPR spectra of the frozen glasses (g11 = g22 = 2.0046 and g33 = 1.9874) and solids (g11 = g22 = 2.005 and g33 = 1.987) instigate the contribution of the resonance form, cis-[Rh(II)(PQ)(PPh3)2Cl2] in 3. DFT calculations established that the closed shell singlet (CSS) solutions of 1Me and 2Me are unstable due to open shell singlet (OSS) perturbation. However, the broken symmetry (BS) (1,1) Ms = 0 solutions of 1Me and 2Me are respectively 22.6 and 24.2 kJ mole(-1) lower in energy and reproduced the experimental bond parameters well prompting the coordination of PQ(˙-) to the M(III) ions. The comparatively shorter C-O lengths, 1.268(4) and 1.266(5) Å and the longer C-C length, 1.466(6) Å, are consistent with the PQ chelation to osmium(II) ion in 4(+). The reversible anodic waves at 0.22, 0.22, and 0.18 V of 1-3, referenced by the Fc(+)/Fc couple, are assigned to the PQ(˙-)/PQ couple forming PQ complexes as trans/cis-[M(III)(PQ)(PPh3)2X2](+) while the cathodic waves at -0.92 and -0.89 V of 2 and 3 are due to formations of PQ(2-) complexes as trans-[M(III)(PQ(2-))(PPh3)2X2](-). 1 displays two overlapping cathodic waves at -0.72(89), -1.0(120) V. EPR spectrum of the frozen glass of 1(-) along with DFT calculations detected the contribution of both the valence tautomers, trans-[Ru(III)(PQ(2-))(PPh3)2Cl2](-) (g1 = g2 = 2.456; g3 = 1.983) and trans-[Ru(II)(PQ(˙-))(PPh3)2X2](-) (g(iso) = 1.999) in the anion. The characteristic lower energy absorption bands of 1 and 2 at 700 nm were assigned to CSS-OSS perturbation MLCT those are absent in paramagnetic 3, 1(+), 2(+), 1(-), 2(-) and 4(+) complexes, investigated by spectro-electrochemical measurements and time dependent (TD) DFT calculations on 1Me, 2Me, 1Me(+) and 1Me(-).

Asymmetric cleavage of 2,2'-pyridil to a picolinic acid anion radical coordinated to ruthenium(II): splitting of water to hydrogen.

The Ru(II)-H and water promoted asymmetric cleavage of 2,2'-pyridil to pyridine-2-carbaldehyde and unprecedented picolinic acid anion radical (PyCOOH(-)˙) complexes, which in solution produce H2 gas and diamagnetic picolinate complexes of ruthenium(II) in moderate yields, is reported.