Transferring Protons Atomic Models

ALL-ATOM MODELS FOR PROTON TRANSFER REACTIONS IN ENZYMES... 

Proton transfer reactions, 143-144, 144 activation energy, 149,164 all-atom models for, 146-148 Cys 25-His 159 in papain, 140-143 computer program for EVB calculations, 150-151... 

All-Atom Models for Proton Transfer Reactions in Enzymes, 146... 

Figure 29.19 The reactant (R), transition state (TS) and product (P) configurations for the rate-determining triple proton transfer step of the 58-atom model used to represent the active site of carbonic anhydrase II [18]. The numbers denote bond distances (in A) calculated at two different levels of theory. The arrows in the insert figure represent the tunneling mode and illustrate the degree of synchronicity of the transfer.

So far our discussion of slow proton-transfers and Bronsted exponents has been a qualitative one, apart from the crude electrostatic model represented by Figures 15 and 16. Recently considerable use has been made of a general equation relating the rate of a reaction to its standard free energy change, which was first derived by Marcus for electron-transfer reactions, and later applied by him and by others to reactions involving the transfer of atoms or protons. For present purposes the Marcus equation can be written as ... 

The molecular structure of the CH form in the blue crystal after photo-irradiation resembles that before the irradiation. When the atomic positions of the CH form was refined, additional peaks of the photoproduct and the transferred proton, except for the o-nitro ifitrogen atom, were observed in the difference electron density map. Both of the closely overlapped CH and NH molecules were refined with the isotropic model. The occupancy factor of the photo-produced NH form became 32.8 %. The conversion to the NH form up to 36.4 % was confirmed from the UV-vis spectrum. Under these conditions, the OH form had accumulated to less than 0.5 %. 

Fig. 9.33. Mechanism of fragmentation upon ECD following the hot hydrogen atom model. Here, a protonated lysine residue captures the electron and immediately transfers a hydrogen atom to its neighboring carbonyl-O. Primary and secondary fragmentation pathways of the ions are shown. Adapted from Ref. [150] by permissioiL John Wiley Sons, 2004.

Pulsed source techniques have been used to study thermal energy ion-molecule reactions. For most of the proton and H atom transfer reactions studied k thermal) /k 10.5 volts /cm.) is approximately unity in apparent agreement with predictions from the simple ion-induced dipole model. However, the rate constants calculated on this basis are considerably higher than the experimental rate constants indicating reaction channels other than the atom transfer process. Thus, in some cases at least, the relationship of k thermal) to k 10.5 volts/cm.) may be determined by the variation of the relative importance of the atom transfer process with ion energy rather than by the interaction potential between the ion and the neutral. For most of the condensation ion-molecule reactions studied k thermal) is considerably greater than k 10.5 volts/cm.). 

There have been a number of investigations of the formulation of the problem of electron transfer accompanied by atom transfer particularly with regard to the simultaneous movement of the proton (which, in view of its small mass, may in fact be an atypical case). A possible model for such processes would assume a conservation of bond order along the reaction coordinates (Johnston, 1960). It is of interest that the results of such calculations are similar to those for electron transfer for weak coupling, although the interpretation of the process and parameters (such as a) are different. 

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