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From a computational point of view, the fact that no covalent bonds exist between the substrate and the catalytic antibody allows a clear separation between the QM region and the MM region. Problems arising from frontier treatments are thus avoided. This kind of system also permits a clear analysis of the different interaction energy terms between both subsystems.
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[32] plus the substrate (39 atoms) which was was treated by AM1 semiempirical Hamiltonian. Periodic boundary conditions were used in all calculations. Because of its size, only those CA atoms within 30 A of the substrate center of mass were allowed to move (∼11500 atoms, model dependent), and the positions of the remaining atoms were frozen.
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[8] We think that this is a reasonable estimation of the expected error in the catalytic free energy barriers.
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Once the full PMF values were obtained for the oxy-Cope rearrangement (Figure 1) MD trajectories of 1 ns were carried out in the region of the MC and TS (with constraints applied just in the reaction coordinate of the latter), as well as for the TSACA complexes. The values mentioned in the text come from the averaged distances obtained in these long QM/MM trajectories.
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