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13644253325
-
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note
-
We employed a parabolic energy penalty centered on the maximum of the PMF with different values of the force constant allowing a maximum fluctuation of the reaction coordinate of about kT, in terms of the PMF. Sets of initial configurations obtained with different values of the force constant led to the same transmission coefficient. In addition we also used constrained reaction coordinate dynamics and tested that averaged properties were the same that those obtained previously. For example, the averaged absolute gradient with respect to the reaction coordinate differed by less than 2% in the different simulations.
-
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61
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4143062484
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64
-
-
13644253327
-
-
note
-
The averaged charge on the link atom was independent of the reaction coordinate and has a mean value of 0.28 ± 0.02 au. In addition we verified that the charges on the carboxylate group remained unchanged when the link atom was displaced to a more distant position increasing the size of the QM region, both in the reactant and in the transition state.
-
-
-
-
65
-
-
13644268860
-
-
note
-
-1.
-
-
-
-
67
-
-
13644262748
-
-
note
-
The criterion was the distance of the first minimum of the radial distribution function for acetate and chloride anions in water as given in refs 54 and 55, respectively. These distances can lead to a slight underestimation of the coordination number for the neutral atoms.
-
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-
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69
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0001382594
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Tuñón, I.; Martins-Costa, M. T. C.; Millot, C.; Ruiz-López, M. F. Chem. Phys. Lett. 1995, 241, 450-456.
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0001415408
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71
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72
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13644268081
-
-
note
-
The averaged interaction energies were obtained from 10000 structures taken from MD simulations of the transition and reactant states in aqueous solution and in the enzyme. In these calculations we included all the QM region and those water molecules or residues presenting a hydrogen bond with the O2 atom. In the case of the enzyme the side chains of residues Glu56 and Trp125 were not considered in order to avoid the interaction with the chlorine atom.
-
-
-
-
75
-
-
0037450070
-
-
In chorismate mutase, we evaluated this fraction as being less than 10%. Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. Chem. - Eur. J. 2003, 9, 984-991.
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76
-
-
13644259416
-
-
note
-
MM) favours the reaction in solution for this process where one moves from a charge-localized reactant state to a charge-delocalized transition state in which the solvent structure is less distorted. Note that both concepts are different as the reorganization energy also accounts for changes in the interactions.
-
-
-
-
77
-
-
13644255556
-
-
note
-
Estimated as 1/4 of the reorganization energy.
-
-
-
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