Similarities and Differences between Cobalamins and Cobaloximes. Accurate Structural Determination of Methylcobalamin and of LiCl- and KCl-Containing Cyanocobalamins by Synchrotron Radiation

Abstract

The accurate crystal structure determinations of MeCbl (1), CNCbl.2LiCl (2), and CNCbl.KCl (3), based on synchrotron diffraction data collected at 100 K and using high-quality single crystals, are reported. Refinements gave R1 indices of 0.0834 (1), 0.0434 (2), and 0.0773 (3). The influence of the water of crystallization and ion content on the crystal packing of these and other cobalamins (XCbl) is discussed, and a relationship between the crystal packing and the corrin side chain conformations is presented. An analysis of the bond lengths within the corrin moiety, based on 13 accurate structures with several X groups, shows that the trend of the C-C and C-N distances can be interpreted in terms of electronic and steric factors. The variation in structural, NMR and IR spectroscopic, and electrochemical properties are compared with those of cobaloximes, the B12 model, when X is varied. This comparison indicates that the pi-back-donation from metal to the CN axial ligand and the transmission of the trans influence of the X ligand are more effective in cobalamins than in cobaloximes. These findings are consistent with a significantly greater availability of electron charge on Co in cobalamins, and, hence, a semiquantitative evaluation of the electronic difference between the cobalt centers in the two systems is allowed.

Spectroscopic Studies of the Corrinoid/Iron−Sulfur Protein from Moorella thermoacetica

“…30 As no crystal structures have yet been reported for Me-Co 3+ CFeSP and free base-off MeCbl (as well as the closely related derivative methylcobinamide, MeCbi + ), an initial model of the enzyme-bound cofactor ( Figure 1) was constructed on the basis of the high-resolution (0.8 Å) crystal structure data available for baseon MeCbl. 31 The nucleotide loop was cleaved at the phosphoester bond proximal to C 17 , and the remaining distal loop fragment was deleted. A water molecule was substituted for the DMB base in the lower axial position, and the geometry of the entire model was optimized using the QM/MM method 32,33 as implemented in the Amsterdam Density Functional (ADF) 2004.01 suite of programs.…”

Theoretical investigations of photophysics and spectroscopic properties in B12 cofactors.

“…In particular, the properties of electronically excited states of CNCbl and MeCbl are analyzed in detail. For both cobalamins, accurate X-ray structures have been reported, 147 and…”

“…According to X-ray crystallographic studies, the Co-C bond in CNCbl (1.868 or 1.886Å) is shorter than in MeCbl (1.979Å) or AdoCbl (2.033Å), respectively. 147,284 These differences have been previously explored by DFT methods, emphasizing the importance of inverse trans influence. 88,164 In the study presented in this chapter geometrical changes associated with electronically excited states of CNCbl were also investigated in order to explain distinct photophysical properties of CNCbl when compared to MeCbl.…”

“…147 To decrease the computational cost associated with the complexity of the system (Figure 1.1), some simplifications to the initial structure were introduced. All side chains of the corrin ring as well as the nucleotide loop were replaced by hydrogen atoms.…”

“…In the present work, such models were also used, based on the highresolution X-ray data of CNCbl and MeCbl cobalamins. 147 To generate the initial structures of the DBI-[Co III (corrin)]-R + models (R = CN or Me), the full CNCbl and MeCbl complexes were simplified by replacing the corrin side chains by hydrogen atoms (Figure 4.1). Full geometry optimization was carried out employing the BP86/6-31G(d) (5d) level of theory, which has been found to be appropriate for structural analysis of cobalt corrinoids.…”