%0 Journal Article
%A Rovira, Carme
%A Kozlowski, Pawel M.
%D 2007
%T First Principles Study of Coenzyme B12. Crystal Packing Forces Effect on Axial Bond
Lengths
%U https://acs.figshare.com/articles/journal_contribution/First_Principles_Study_of_Coenzyme_B_sub_12_sub_Crystal_Packing_Forces_Effect_on_Axial_Bond_Lengths/3016114
%R 10.1021/jp0660029.s001
%2 https://ndownloader.figshare.com/files/4717417
%K corrin side chains
%K 48 water molecules
%K bond
%K Coenzyme B 12. Crystal Packing Forces Effect
%K coenzyme B 12
%K Axial Bond LengthsIn
%K First Principles Study
%K crystal
%K AdoCbl
%K DFT calculations
%K CPMD
%K model
%X In this work we analyze the structure of coenzyme B12 (AdoCbl) by means of periodic density functional
theory (DFT) in order to elucidate the influence of the corrin side chains and the crystalline environment on
the properties of axial bonds. The Co−Nax axial bond is very weak and its strength of less than 8 kcal/mol
is four times smaller than Co−C which in solution is ∼31 kcal/mol. The proper description of the Co−Nax
distance has been problematic in previous DFT calculations and the source of disagreement between experiment
and theory remained unexplained. To resolve this discrepancy, periodic DFT calculations within the Car−Parrinello molecular dynamics (CPMD) framework were carried out on three different structural models of
increased complexity. The simplest model (DBI-Ado+) contains the naked corrin ring with a total of 96
atoms. The second model is the full coenzyme B12 (AdoCbl) with 209 atoms which has been taken from
crystallographic analysis. To understand the extent to which the crystal packing forces influence the structural
properties of AdoCbl the complete crystal consisting of four AdoCbl molecules plus 48 water molecules
periodically repeated in space was analyzed (1008 atoms). The results show that the properties associated
with the Co−C bond can be well reproduced using truncated models. This does not apply to the Co−Nax
axial bond and the presence of the local environment appears to be essential for the correct prediction of its
bond length. The most interesting outcome of the present analysis is the finding that the actual length of the
Co−Nax bond (2.262 Å) is largely influenced by crystal packing forces.
%I ACS Publications