7564
J. Phys. Chem. B 2001, 105, 7564-7571
A Density Functional Study on the Effect of the Trans Axial Ligand of Cobalamin on the Homolytic Cleavage of the Co-C Bond Nicole Do1 lker, Feliu Maseras,* and Agustı´ Lledo´ s Unitat de Quı´mica Fı´sica, Edifici C.n, UniVersitat Auto` noma de Barcelona, 08193 Bellaterra, Catalonia, Spain ReceiVed: January 11, 2001; In Final Form: May 29, 2001
Density functional theory (DFT) Becke3LYP calculations including full and restricted geometry optimizations are carried out on the complexes [Co(Cor)(Benz)(CH3)] (Cor ) corrin, Benz ) benzimidazole), [Co(Cor)(Benz)], [Co(Cor)(CH3)], and [Co(Cor)]. These systems, despite the absence of side-chains, constitute the most realistic models used to date for DFT calculations on cofactor B12 and its homolysis product. The calculations prove that both thermodynamics and kinetics of the homolytic bond cleavage of the Co-C bond have very little dependence on the position of the axial benzimidazole ligand. The generality of these results is confirmed by additional calculations on [Co(Cor)(Benz)(CH2R)] (R ) tetrahydrofuran), [Co(Cor)(Im)(CH3)] (Im ) imidazole), and [Co(Cor-CH3)(Benz)(CH3)] (Cor-CH3 ) methylated corrin).
1. Introduction Cobalamins are important cofactors for many enzymatic processes.1,2 Their unique Co-C bond makes them the only known organometallic compounds of biological importance. A key feature of cobalamins is their ability to produce a highly reactive alkyl radical through homolytic cleavage of the covalent Co-C bond. This radical mechanism is the usual operation mode of coenzyme B12, and has also been proposed recently to operate in some biological methylation reactions carried out by methylcobalamins,3 that usually operate through heterolytic cleavage. The homolytic cleavage process has been object of various detailed studies.4-8 It is greatly accelerated by the enzymatic environment, where the Co-C bond dissociation rate is enhanced by a factor of up to 1012 with respect to the value in isolated cobalamins.4,9 The origin of such a strong labilization has always been a challenge to chemists. The X-ray diffraction analysis of coenzyme B12 in 196810 showed that in its active center the cobalt atom is in an octahedral environment, with four equatorial positions occupied by the nitrogen atoms of a corrin ring, and the two axial positions occupied by the 5′-deoxyadenosyl alkyl group and a derivative of the benzimidazole (Figure 1). The eventual effect of this axial base, and in particular of the strain induced through it by the protein chain, on the rate of homolytic cleavage of the Co-C bond has been under discussion almost since that moment. Already in 1969 it was proposed that an upward movement of benzimidazole induces a conformational rearrangement (butterfly distortion) of the corrin ring that as a result interacts with the alkyl group, pushing it away from the Co center, and therefore weakens the Co-C bond.11 This theory of a steric effect of the axial base has afterward been extended and refined.12-16 Recent experimental works have questioned this hypothesis. X-ray studies on several B12-dependent enzymes indicate that in some cases in the enzymatic environment the benzimidazole is replaced by a histidine amino acid from a protein side-chain.17 The importance of this ligand exchange remains quite unclear.18 * Corresponding author. E-mail:
[email protected].
Figure 1. Simplified scheme of cobalamins. R ) CH3, methylcobalamin; R ) 5′-deoxyadenosyl, coenzyme B12. B ) 5,6-dimethylbenzimidazole.
The possible electronic effect of the axial base has also been analyzed from an experimental point of view.19,20 In an extensive study on the Co-C thermolysis in cobalamin derivatives with a variety of different axial bases, Finke and co-workers have found that an increase in the basicity of the axial base does indeed enhance the rate of Co-C bond homolysis but has an even stronger effect on the competing heterolysis,20 an observation that is also shared by other authors.21 On the other hand there is evidence that trans ligand substitution does not necessarily have an important influence on the Co-C bond strength.22 In another recent study by Grabowski and co-workers it is found that the Co-C bond dissociation energy (BDE) is practically the same in the normal base-on form of methylcobalamin as in its derived base-off form.23 It has also been proposed that the axial base has a kinetic effect, stabilizing the transition state of the Co-C bond homolysis.24-27 This effect has been attributed to the competition of effects of σ and π nature in the benzimidazole ligand.28 The correlation between the Co-N(axial) distance and the facility of the Co-C homolytic cleavage remains therefore obscure, and it is a critical variable for understanding the role of the protein in the catalytic process. Interpretation of the experimental results is always complicated by the presence of solvent effects29,30 and other complicating factors, and as a result, definitive conclusions are elusive. The topic is therefore appropriate for theoretical methods. Several molecular mechanics studies on cobaloximes and cobalamins have been carried out31-35 The emerging conclusion35 seems to be that the butterfly distortion induced by a
10.1021/jp010144f CCC: $20.00 © 2001 American Chemical Society Published on Web 07/12/2001
Cobalamin Ligand and the Cleavage of the Co-C Bond shortening of the Co-N(axial) bond is too small to explain the large increase in the Co-C dissociation rate. Standard molecular mechanics force fields are, however, unable to consider the eventual importance of electronic effects, which require specifically tuned force fields or quantum mechanical methods. The application of the latter is complicated by the size of the system and the homolytic nature of the bond dissociation process, but some significant attempts have been made. Early extended Hu¨ckel studies gave support to an influence of the Co-N(axial) bond facilitating the Co-C bond homolysis.36 A study by Lipscomb and Christianson37 with a semiempirical method on the simplified [Co(NH3)3(NH2)(NH3)ax(CH3)] model concluded on the contrary that the axial base does not have an important electronic effect on the Co-C bond strength, a conclusion that is shared by other studies at similar levels.38,39 Later on, much more accurate studies using the density functional theory (DFT) have been carried out on this type of systems. The first of them did not consider the particular topic of the role of the axial base, either because of dealing with the calculation of 14N superfine and nuclear quadrupole coupling constants,40,41 or because of focusing on the mechanism of the B12-dependent rearrangement reactions, without explicit consideration of the cobalt catalyst.42,43 It has not been until very recently that some accurate DFT studies have examined the stereoelectronic properties of cobalamins.44,45,46 These studies concentrated mostly in geometry optimizations with several different axial ligands, and because of this, they could not be conclusive with respect to reaction energetics.47 There are therefore still a number of open questions arising from the experimental studies that have not been answered by previous theoretical studies. We are going to examine in this article whether the eventual strain of the protein environment on the axial ligand can explain the large enhancement of homolysis in a biological environment. To do this we will analyze with a nonlocal DFT method the dependence of both thermodynamics and kinetics of the Co-C bond homolysis on the length of the Co-N(axial) bond length using a large model for cobalamin and full and restricted geometry optimizations. 2. Computational Details All calculations have been carried out using the Becke3LYP method.48-51 The 10 innermost electrons of Co have been replaced by a quasi-relativistic effective core potential and the valence electrons have been described by the corresponding LANL2DZ basis set.52 For the atoms directly attached to the metal center a 6-31G(d) basis53,54 has been used, while all other atoms have been described by a STO-3G basis.55 This basis set was found to be sufficient in preliminary calculations on the smaller [Co(NH3)(NHCH2)3(NHCH2)ax(CH3)] model. The energy profile for the homolytic Co-C bond cleavage has been calculated at the unrestricted Becke3LYP level of theory, using the broken symmetry approach proposed by Noodleman.56 All calculations have been performed with the Gaussian 98 program package.57 Figure 2 shows the models used in the present study. The [Co(Cor)(Benz)(CH3)] (Cor ) corrin, Benz ) benzimidazole) model for methylcobalamin (1) includes the unsubstituted corrin ring and a benzimidazole molecule as the axial base. In the [Co(Cor)(Benz)(CH2R)] (R ) tetrahydrofuran) model for adenosylcobalamin (1′) the adenosyl group has been modeled by a methyl group substituted with a tetrahydrofuran ring. Additional calculations have been performed on [Co(Cor)(Im)(CH3)] (Im ) imidazole) and [Co(Cor-CH3)(Benz)(CH3)]
J. Phys. Chem. B, Vol. 105, No. 31, 2001 7565
Figure 2. The models for methylcobalamin, [Co(Cor)(Benz)(CH3)] (1), and adenosylcobalamin, [Co(Cor)(Benz)(CH2R)] (R ) tetrahydrofuran) (1′), used in this work.
(Cor-CH3 ) methylated corrin) in order to study the influence of different axial ligands and substituents on the corrin ring on the geometry and the Co-C bond dissociation energy of cobalamins. 3. Results and Discussion 3.1. Geometry Optimizations. Starting from the crystal structure of methylcobalamin10 four different structures have been fully optimized: our model for methylcobalamin [Co(Cor)(Benz)(CH3)] (1), its demethylated form [Co(Cor)(Benz)] (2), and their respective base-off forms [Co(Cor)(CH3)] (3) and [Co(Cor)] (4). Species 1 and 3 have been calculated in the singlet electronic state, while 2 and 4 have been calculated as doublets within the unrestricted formalism. In all cases spin contamination was small. Figure 3 shows the equilibrium structures computed at the Becke3LYP level of theory. Selected geometry parameters of the structures in Figure 3 are listed in Table 1. The calculated geometry for 1 is in quite good agreement with the X-ray data for free methylcobalamin.14 The computed bond distances between the metal and the four equatorial nitrogens are within 0.03 Å of the experimental values. The existence of two short bonds, Co-N3 and Co-N6, within the five-membered ring containing the metal, is properly reproduced. The Co-C distance is also well reproduced (1.96 Å vs 1.99 Å). A larger discrepancy appears in the Co-N7 distance, where the computed value (2.288 Å) is 0.1 Å longer than the experimental one (2.18 Å). Similar values for this parameter
7566 J. Phys. Chem. B, Vol. 105, No. 31, 2001
Do¨lker et al. TABLE 1: Selected Geometry Parameters for the Four Optimized Structures of Methylcobalamin and the Corresponding 5- and 4-coordinate Compounds (in Å and Degrees)a compound d(Co-C2) d(Co-N3) d(Co-N4) d(Co-N5) d(Co-N6) d(Co-N7)
1 1.961 (1.99(2)) 1.908 (1.88(2)) 1.948 (1.97(2)) 1.951 (1.93(2)) 1.905 (1.89(2)) 2.288 (2.19(2))
