Structure-energy relations in methylcobalamin with and without bound axial base

The properties of the Co-C bond in methylcobalamin (MeCbl) are analyzed by means of first-principles molecular dynamics. The optimized structure is in very good agreement with experiments, reproducing the bent-up deformation of the corrin ring as well as the metal-ligand bond distances. The analysis of the binding energies, bond orders, and vibrational stretching frequencies shows that the axial base slightly weakens the Co-C bond (by 4%), while the alkyl ligand substantially reinforces the Co-axial base bond (by 90%). These findings support several experiments and provide insight into the conversion between the base-on and base-off forms of the MeCbl cofactor.     

Carbon-cobalt bond distance and bond cleavage in one-electron reduced methylcobalamin: a failure of the conventional DFT method

Geometry optimizations at the HF, B3LYP, and CASSCF levels of electronic structure theory have been performed for methylcobalamin (MeCbl) model compounds in both the Co(III) (MeCbl(III)) and Co(II) (MeCbl(II)) formal oxidation states. Since the HOMO-LUMO and C-Co sigma-sigma MO gaps are significantly smaller in the MeCbl(II) compounds compared with MeCbl(III), a pseudo-Jahn Teller effect is possible. CASSCF calculations show that there is strong coupling between C-Co sigma-sigma MOs for the MeCbl(II) models leading to strong state mixing with significant total charge density transfer (approximately 0.4 e-), mainly from the C-Co sigma MO to C-Co sigma MO (approximately 0.3 e-). CASSCF(9:7) calculations show that the strong state mixing leads to an increase in the C-Co bond length for MeCbl(II) model compounds from 1.969 A (DFT and HF calculations) to 2.164 A in the base-on MeCbl(II) model and from 1.938 A to 2.144 A in the base-off MeCbl(II) model. Concomitantly, the Co-N axial bond length increases from 2.121 A (DFT) to 2.344 A in the CASSCF calculation. This coupling interaction between states can be used to explain the much lower Co-C bond dissociation enthalpy and much faster bond cleavage rate for the one-electron reduced methylcobalamin radical anion compared to MeCbl(III). It may also be important for axial bond distances in other Co(II) compounds.     

Spectroscopic studies of the corrinoid/iron-sulfur protein from Moorella thermoacetica

Methyl transfer reactions are important in a number of biochemical pathways. An important class of methyltransferases uses the cobalt cofactor cobalamin, which receives a methyl group from an appropriate methyl donor protein to form an intermediate organometallic methyl-Co bond that subsequently is cleaved by a methyl acceptor. Control of the axial ligation state of cobalamin influences both the mode (i.e., homolytic vs heterolytic) and the rate of Co-C bond cleavage. Here we have studied the axial ligation of a corrinoid iron-sulfur protein (CFeSP) that plays a key role in energy generation and cell carbon synthesis by anaerobic microbes, such as methanogenic archaea and acetogenic bacteria. This protein accepts a methyl group from methyltetrahydrofolate forming Me-Co(3+)CFeSP that then donates a methyl cation (Me) from Me-Co(3+)CFeSP to a nickel site on acetyl-CoA synthase. To unambiguously establish the binding scheme of the corrinoid cofactor in the CFeSP, we have combined resonance Raman, magnetic circular dichroism, and EPR spectroscopic methods with computational chemistry. Our results clearly demonstrate that the Me-Co3+ and Co2+ states of the CFeSP have an axial water ligand like the free MeCbi+ and Co(2+)Cbi+ cofactors; however, the Co-OH2 bond length is lengthened by about 0.2 angstroms for the protein-bound cofactor. Elongation of the Co-OH2 bond of the CFeSP-bound cofactor is proposed to make the cobalt center more "Co1+-like", a requirement to facilitate heterolytic Co-C bond cleavage.     

Spectroscopic and computational studies of Co2+corrinoids: spectral and electronic properties of the biologically relevant base-on and base-off forms of Co2+cobalamin

Co(2+)cobalmain (Co(2+)Cbl) is implicated in the catalytic cycles of all adenosylcobalamin (AdoCbl)-dependent enzymes, as in each case catalysis is initiated through homolytic cleavage of the cofactor's Co-C bond. The rate of Co-C bond homolysis, while slow for the free cofactor, is accelerated by 12 orders of magnitude when AdoCbl is bound to the protein active site, possibly through enzyme-mediated stabilization of the post-homolysis products. As an essential step toward the elucidation of the mechanism of enzymatic Co-C bond activation, we employed electronic absorption (Abs), magnetic circular dichroism (MCD), and resonance Raman spectroscopies to characterize the electronic excited states of Co(2+)Cbl and Co(2+)cobinamide (Co(2+)Cbi(+), a cobalamin derivative that lacks the nucleotide loop and 5,6-dimethylbenzimazole (DMB) base and instead binds a water molecule in the lower axial position). Although relatively modest differences exist between the Abs spectra of these two Co(2+)corrinoid species, MCD data reveal that substitution of the lower axial ligand gives rise to dramatic changes in the low-energy region where Co(2+)-centered ligand field transitions are expected to occur. Our quantitative analysis of these spectral changes within the framework of time-dependent density functional theory (TD-DFT) calculations indicates that corrin-based pi --> pi transitions, which dominate the Co(2+)corrinoid Abs spectra, are essentially insulated from perturbations of the lower ligand environment. Contrastingly, the Co(2+)-centered ligand field transitions, which are observed here for the first time using MCD spectroscopy, are extremely sensitive to alterations in the Co(2+) ligand environment and thus may serve as excellent reporters of enzyme-induced perturbations of the Co(2+) state. The power of this combined spectroscopic/computational methodology for studying Co(2+)corrinoid/enzyme active site interactions is demonstrated by the dramatic changes in the MCD spectrum as Co(2+)Cbi(+) binds to the adenosyltransferase CobA.     

Characterization of Co-C bonding in dichlorovinylcobaloxime complexes

This study combines theory and experiment in an examination of Co-C bonding and reductive Co-C cleavage in cobalt dichlorovinyl complexes. It is motivated by the role of dichlorovinyl complexes as intermediates in the dechlorination of trichloroethylene by cobalamin and cobalamin model complexes. A series of seven cis-1,2-dichlorovinyl(L)cobaloxime complexes were prepared (L = m- and p-substituted pyridines; cobaloxime = bis(dimethylglyoximato)cobalt). The complexes were characterized using 1H NMR, 13C NMR, cyclic voltammetry, and X-ray crystallography. Examination of the metrical parameters of the Co-C=C unit across the series shows very little change in the C=C bond length and a slight increase in the Co-C bond length with increasing electron-donating ability of the pyridine ligand. These structural changes along with electronic structure calculations indicate that Co-C pi-bonding is not important in these complexes. The stronger Co-C bonds of vinylcobaloximes compared to those of alkylcobaloximes are best explained by the higher s character at C. Changes in the reduction potential across the series indicate that the pyridine-bound form is the primary electrochemically active species. Theoretical examination of the Co-C cleavage following reduction supports the direct formation of the cis-1,2-dichlorovinyl anion and not the cis-1,2-dichlorovinyl radical.     

Reductive cleavage mechanism of methylcobalamin: elementary steps of Co-C bond breaking

Density functional theory has been applied to the investigation of the reductive cleavage mechanism of methylcobalamin (MeCbl). In the reductive cleavage of MeCbl, the Co-C bond is cleaved homolytically, and formation of the anion radical ([MeCbl]*-) reduces the dissociation energy by approximately 50%. Such dissociation energy lowering in [MeCbl]*- arises from the involvement of two electronic states: the initial state, which is formed upon electron addition, has dominant pi*corrin character, but when the Co-C bond is stretched the unpaired electron moves to the sigma*Co-C state, and the final cleavage involves the three-electron (sigma)2(sigma*)1 bond. The pi*corrin-sigma*Co-C states crossing does not take place at the equilibrium geometry of [MeCbl]*- but only when the Co-C bond is stretched to 2.3 A. In contrast to the neutral cofactor, the most energetically efficient cleavage of the Co-C bond is from the base-off form. The analysis of thermodynamic and kinetic data provides a rationale as to why Co-C cleavage in reduced form requires prior departure of the axial base. Finally, the possible connection of present work to B12 enzymatic catalysis and the involvement of anion-radical-like [MeCbl]*- species in relevant methyl transfer reactions is discussed.     

Accurate redetermination of the X-ray structure and electronic bonding in adenosylcobalamin

The electronic structure of adenosylcobalamin (B12 coenzyme, AdoCbl) has been calculated by a density functional method, using the orthogonalized linear combination of the atomic orbital method (OLCAO). Since a fixed accurately determined geometry was needed in such calculations, the crystal structure of adenosylcobalamin has been redone and refined to R = 0.065, using synchrotron diffraction data. Comparison with the recently reported electronic structures of cyano- (CNCbl) and methylcobalamin (MeCbl) shows that the net charges and bond orders vary only on the axial donors. The values in the three cobalamins suggest that the Co-C bond in MeCbl has a strength similar to that in AdoCbl, but it is significantly weaker that that in CNCbl. Present results are compared with those previously reported for the analogous corrin derivatives; i.e., simplified cobalamins with the side chains a-f replaced by H atoms. Despite a qualitative agreement, a discrepancy in the calculated HOMO-LUMO gap is found.     

Electronic spectroscopy and computational studies of glutathionylco(III)balamin

We have studied glutathionylcobalamin (GS-Cbl) by optical spectroscopy and with density functional theory (DFT) and time-dependent DFT (TD-DFT) electronic structure methods of truncated geometric models. We examined the geometric structure of the models by comparison of DFT calculations with recent high-resolution experimental X-ray structure data ( Hannibal, L. et al. Inorg. Chem. 2010, 49, 9921) for GS-Cbl, and we examined the TD-DFT excitation simulations by comparison of the models with measured optical spectra. The calculations employed the B3LYP hybrid functional and the nonhybrid BP86 functional in both vacuum and water (conductor polarized continuum model (cpcm)) with the 6-311G(d,p) basis set. The optimized geometric structure calculations for six truncated models were made by varying the chemical structure, solvent model, and the two DFT functionals. All showed similar geometry. Charge decomposition analysis (CDA) and extended charge decomposition analysis (ECDA), especially with BP86 shows the similar charge transfer nature of the Co-S bond in GS-Cbl and the Co-C bond in CH(3)Cbl. Mayer and Wiberg bond orders illustrate the similar covalent nature of the two bonds. Finally, absolute optical spectral simulation calculations were compared with the experimental UV-visible extinction spectrum and the electronic circular dichroism (ECD) differential extinction spectrum. The BP86 method shows more spectral features, and the best fit was found for a GS-Cbl model with 5,6-dimethylbenzimidazole at the BP86/6-311G(d,p) level with a water cpcm solvent model. The excited state transitions were investigated with Martin's natural transition orbitals (NTOs). The BP86 calculations also showed π bonding interactions between Co and the axial S of the GS- ligand in the molecular orbitals (MOs) and NTOs.     

Spectroscopic and computational studies on the adenosylcobalamin-dependent methylmalonyl-CoA mutase: evaluation of enzymatic contributions to Co-C bond activation in the Co3+ ground state

Methylmalonyl-CoA mutase (MMCM) is an enzyme that utilizes the adenosylcobalamin (AdoCbl) cofactor to catalyze the rearrangement of methylmalonyl-CoA to succinyl-CoA. Despite many years of dedicated research, the mechanism by which MMCM and related AdoCbl-dependent enzymes accelerate the rate for homolytic cleavage of the cofactor's Co-C bond by approximately 12 orders of magnitude while avoiding potentially harmful side reactions remains one of the greatest subjects of debate among B(12) researchers. In this study, we have employed electronic absorption (Abs) and magnetic circular dichroism (MCD) spectroscopic techniques to probe cofactor/enzyme active site interactions in the Co(3+)Cbl "ground" state for MMCM reconstituted with both the native cofactor AdoCbl and its derivative methylcobalamin (MeCbl). In both cases, Abs and MCD spectra of the free and enzyme-bound cofactor are very similar, indicating that replacement of the intramolecular base 5,6-dimethylbenzimidazole (DMB) by a histidine residue from the enzyme active site has insignificant effects on the cofactor's electronic properties. Likewise, spectral perturbations associated with substrate (analogue) binding to holo-MMCM are minor, arguing against substrate-induced enzymatic Co-C bond activation. As compared to the AdoCbl data, however, Abs and MCD spectral changes for the sterically less constrained MeCbl cofactor upon binding to MMCM and treatment of holoenzyme with substrate (analogues) are much more substantial. Analysis of these changes within the framework of time-dependent density functional theory calculations provides uniquely detailed insight into the structural distortions imposed on the cofactor as the enzyme progresses through the reaction cycle. Together, our results indicate that, although the enzyme may serve to activate the cofactor in its Co(3+)Cbl ground state to a small degree, the dominant contribution to the enzymatic Co-C bond activation presumably comes through stabilization of the Co(2+)Cbl/Ado. post-homolysis products.     

X-ray structures and homolysis of some alkylcobalt(III) phthalocyanine complexes

The first crystallographic data for sigma-bonded alkylcobalt(III) phthalocyanine complexes are reported. A single-crystal X-ray structure of CH(3)CH(2)Co(III)Pc (Pc = dianion of phthalocyanine) reveals that the solid consists of centrosymmetric face-to-face dimers in which the CH(3)CH(2)Co(III)Pc units retain their square pyramidal geometry. The structure appears to be the first one reported for a five-coordinate RCo(III)(chelate) complex with an electron-deficient equatorial system. The Co-C bond in CH(3)CH(2)Co(III)Pc (2.031(5) A) is the longest found in five-coordinate RCo(III)(chel) complexes (R = simple primary alkyl group). Another X-ray study demonstrates that CH(3)Co(III)Pc(py) has a distorted octahedral geometry with axial bonds of very similar length to those in methylcobalamin. The axial bonds are shorter than those in its octaethylporphyrin analogue, in accordance with a weaker trans axial influence in six-coordinate complexes containing an electron-deficient phthalocyanine equatorial ligand. A different trend has been observed for five-coordinate RCo(III)(chel) complexes: electron-rich equatorial systems seem to make the Co-C axial bond shorter. Kinetic data for the homolysis of RCo(III)Pc complexes (R = Me, Et) in dimethylacetamide are also reported. Homolysis of ethyl derivatives is faster. The Co-C bond dissociation energies (BDEs) for the pyridine adducts of the methyl and the ethyl derivative are 30 +/- 1 and 29 +/- 1 kcal/mol, respectively. The BDE for CH(3)CoPc(py) is considerably lower than that for MeCbl despite the very similar lengths of the axial bonds in the two complexes. The results of this work do not support any correlation between the Co-C bond length and the bond strength as defined by BDE.     

Ultrafast infrared spectral fingerprints of vitamin B12 and related cobalamins

Vitamin B(12) (cyanocobalamin, CNCbl) and its derivatives are structurally complex and functionally diverse biomolecules. The excited state and radical pair reaction dynamics that follow their photoexcitation have been previously studied in detail using UV-visible techniques. Similar time-resolved infrared (TRIR) data are limited, however. Herein we present TRIR difference spectra in the 1300-1700 cm(-1) region between 2 ps and 2 ns for adenosylcobalamin (AdoCbl), methylcobalamin (MeCbl), CNCbl, and hydroxocobalamin (OHCbl). The spectral profiles of all four cobalamins are complex, with broad similarities that suggest the vibrational excited states are related, but with a number of identifiable variations. The majority of the signals from AdoCbl and MeCbl decay with kinetics similar to those reported in the literature from UV-visible studies. However, there are regions of rapid (<10 ps) vibrational relaxation (peak shifts to higher frequencies from 1551, 1442, and 1337 cm(-1)) that are more pronounced in AdoCbl than in MeCbl. The AdoCbl data also exhibit more substantial changes in the amide I region and a number of more gradual peak shifts elsewhere (e.g., from 1549 to 1563 cm(-1)), which are not apparent in the MeCbl data. We attribute these differences to interactions between the bulky adenosyl and the corrin ring after photoexcitation and during radical pair recombination, respectively. Although spectrally similar to the initial excited state, the long-lived metal-to-ligand charge transfer state of MeCbl is clearly resolved in the kinetic analysis. The excited states of CNCbl and OHCbl relax to the ground state within 40 ps with few significant peak shifts, suggesting little or no homolysis of the bond between the Co and the upper axial ligand. Difference spectra from density functional theory calculations (where spectra from simplified cobalamins with an upper axial methyl were subtracted from those without) show qualitative agreement with the experimental data. They imply the excited state intermediates in the TRIR difference spectra resemble the dissociated states vibrationally (the cobalamin with the upper axial ligand missing) relative to the ground state with a methyl in this position. They also indicate that most of the TRIR signals arise from vibrations involving some degree of motion in the corrin ring. Such coupling of motions throughout the ring makes specific peak assignments neither trivial nor always meaningful, suggesting our data should be regarded as IR spectral fingerprints.     

Electronic structure and bonding in hydroxocobalamin

The electronic structure of hydroxocobalamin (OHCbl) has been calculated by a density functional method, using the orthogonalized linear combination of the atomic orbitals method (OLCAO). The X-ray crystal structure has been determined from synchrotron X-ray diffraction data and the geometry determined was used in the calculations. Comparison with the recently reported electronic structures of cyanocobalamin (CNCbl), methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl) shows that Mulliken charges (Q*) and bond orders (BO) vary only on the axial fragment.     

Photolysis of methylcobalamin: identification of the relevant excited states involved in Co-C bond scission

The relevant excited states involved in the photolysis of methylcobalamin (MeCbl) have been examined by means of time-dependent density functional theory (TD-DFT). The low-lying singlet and triplet excited states have been calculated along the Co-C bond at the TD-DFT/BP86/6-31g(d) level of theory in order to investigate the dissociation process of MeCbl. These calculations have shown that the photodissociation is mediated by the repulsive 3(sigmaCo-C --> sigma*Co-C) triplet state. The key metastable photoproduct involved in Co-C bond photolysis was identified as an S1 state having predominantly dCo --> pi*corrin metal-ligand charge transfer (MLCT) character.     

Spectroscopic and computational studies of Co1+cobalamin: spectral and electronic properties of the "superreduced" B12 cofactor

The 4-coordinate, low-spin cob(I)alamin (Co1+Cbl) species, which can be obtained by heterolytic cleavage of the Co-C bond in methylcobalamin or the two-electron reduction of vitamin B12, is one of the most powerful nucleophiles known to date. The supernucleophilicity of Co1+Cbl has been harnessed by a number of cobalamin-dependent enzymes, such as the B12-dependent methionine synthase, and by enzymes involved in the biosynthesis of B12, including the human adenosyltransferase. The nontoxic nature of the Co1+Cbl supernucleophile also makes it an attractive target for the in situ bioremediation of halogenated waste. To gain insight into the geometric, electronic, and vibrational properties of this highly reactive species, electronic absorption, circular dichroism (CD), magnetic CD, and resonance Raman (rR) spectroscopies have been employed in conjunction with density functional theory (DFT), time-dependent DFT, and combined quantum mechanics/molecular mechanics computations. Collectively, our results indicate that the supernucleophilicity of Co1+Cbl can be attributed to the large destabilization of the Co 3dz2-based HOMO and its favorable orientation with respect to the corrin macrocycle, which minimizes steric repulsion during nucleophilic attack. An intense feature in the CD spectrum and a prominent peak in the rR spectra of Co1+Cbl have been identified that may serve as excellent probes of the nucleophilic character, and thus the reactivity, of Co1+Cbl in altered environments, including enzyme active sites. The implications of our results with respect to the enzymatic formation and reactivity of Co1+Cbl are discussed, and spectroscopic trends along the series from Co3+Cbls to Co2+Cbl and Co1+Cbl are explored.     

DFT study of Co-C bond cleavage in the neutral and one-electron-reduced alkyl-cobalt(III) phthalocyanines

Density functional theory (DFT) has been applied to the analysis of the structural and electronic properties of the alkyl-cobalt(III) phthalocyanine complexes, [CoIIIPc]-R (Pc = phthalocyanine, R = Me or Et), and their pyridine adducts. The BP86/6-31G(d) level of theory shows good reliability for the optimized axial bond lengths and bond dissociation energies (BDEs). The mechanism of the reductive cleavage was probed for the [CoIIIPc]-Me complex which is known as a highly effective methyl group donor. In the present analysis, which follows a recent study on the reductive Co-C bond cleavage in methylcobalamin (J. Phys. Chem. B 2007, 111, 7638-7645), it is demonstrated that addition of an electron and formation of the pi-anion radical [CoIII(Pc*)]-Me- significantly lowers the energetic barrier required for homolytic Co-C bond dissociation. Such BDE lowering in [CoIII(Pc*)]-Me- arises from the involvement of two electronic states: upon electron addition, a quasi-degenerate pi*Pc state is initially formed, but when the cobalt-carbon bond is stretched, the unpaired electron moves to a sigma*Co-C state and the final cleavage involves the three-electron (sigma)2(sigma*)1 bond. As in corrin complexes, the pi*Pc-sigma*Co-C states crossing does not take place at the equilibrium geometry of [CoIII(Pc*)]-Me- but only when the Co-C bond is stretched to approximately 2.3 A. The DFT computed Co-C BDE of 23.3 kcal/mol in the one-electron-reduced phthalocyanine species, [CoIII(Pc*)]-Me-, is lowered by approximately 37% compared to the neutral Py-[CoIIIPc]-Me complex where BDE = 36.8 kcal/mol. A similar comparison for the corrin-containing complexes shows that a DFT computed BDE of 20.4 kcal/mol for [CoIII(corrin*)]-Me leads to approximately 45% bond strength reduction, in comparison to 37.0 kcal/mol for Im-[CoIII(corrin)]-Me+. These results suggest some preference by the alkylcorrinoids for the reductive cleavage mechanism.     

辅酶B12模型化合物的研究(Ⅲ)——一类新型烷基钴Schiff碱配合物的合成及Co-C键稳定性

合成与表征了一系列烷基钻Schiff碱配合物RCo(SB)L(R为甲,乙,丙,正丁和异丁基;L为水;SB为双水杨醛缩二甲基丁二胺),它们是一类尚未见报道的新的辅酶B₁₂模型化合物。该配合物的溶液很不稳定,加热或光照促使Co-C键断裂,轴向烷基和平伏面配体对Co-C键稳定性均有影响。经紫外、可见分光光度法及自旋捕集ESR法确定了热分解和光分解反应的产物和超精细分裂常数。     

Interaction of metal porphyrins with fullerene C60: a new insight

The electronic structure and bonding in the noncovalent, supramolecular complexes of fullerene C60 with a series of first-row transition metal porphines MP (M=Fe, Co, Ni, Cu, Zn) have been re-examined with DFT methods. A dispersion correction was made for the C60-MP binding energy through an empirical method (J. Comput. Chem. 2004, 25, 1463). Several density functionals and two types of basis sets were employed in the calculations. Our calculated results are rather different from those obtained in a recent paper (J. Phys. Chem. A 2005, 109, 3704). The ground state of C60.FeP is predicted to be high spin (S=2); the low-spin (S=0), closed-shell state is even higher in energy than the intermediate-spin (S=1) state. With only one electron in the Co-dz2 orbital, the calculated Co-C60 distance is in fact rather short, about 0.1 A longer than the Fe-C60 distance in high-spin C60.FeP. Double occupation of an M-dz2 orbital in MP prevents close association of any axial ligand, and so the Ni-C60, Cu-C60, and Zn-C60 distances are much longer than the Co-C60 one. The evaluated MP-C60 binding energies (Ebind) are 0.8 eV (18.5 kcal/mol) for M=Fe/Co and 0.5 eV (11.5 kcal/mol) for M=Ni/Cu/Zn (Ebind is about 0.2 eV larger in the case of C60-MTPP). They are believed to be reliable and accurate based on our dispersion-corrected DFT calculations that included the counterpoise (CP) correction. The effects of the C60 contact on the redox properties of MP were also examined.