Christopher Chang - Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases

Version 1

      Publication Details (including relevant citation   information):

      Chang, CH and K Kim (2009) J. Chem. Theory Comput.  5(4): 1137-45

      Abstract:

      We have developed and tested molecular mechanics parameters for   [FeS] clusters found in known [FeFe] hydrogenases. Bond   stretching, angle bending, dihedral and improper torsion   parameters for models of the oxidized and reduced catalytic   H-cluster, [4Fe4S]+,2+Cys4,   [4Fe4S]+,2+Cys3His, and   [2Fe2S]+,2+Cys4, were calculated solely   from Kohn-Sham density functional theory and Natural Population   Analysis. Circumsphere analysis of the cubane clusters in the   energy-minimized structure of the full Clostridium pasteurianum   hydrogenase I showed the resulting metallocluster structures to   be similar to known cubane structures. All clusters were   additionally stable in molecular dynamics simulations over the   course of 1.0 ns in the fully oxidized and fully reduced enzyme   models. Normal modes calculated by quasiharmonic analysis from   the dynamics data show unexpected couplings among internal   coordinate motions, which may reflect the effects of the protein   structure on metallocluster dynamics.

      Address (URL): http://dx.doi.org/10.1021/ct800342w