Proton dynamical effects

Quantum Mechanical Dynamical Effects for an Enzyme Catalyzed Proton Transfer Reaction... 

A similar simplification is commonly used in the description of the dynamic effects observed for protons which are attached to carbon atoms which in turn are bonded to an ammonium group where the ammonium protons are exchanging with the environment. (87)... 

The enzyme mechanism, however, remains elusive. Quantum mechanical models generally disfavor C6-protonation, but 02, 04, and C5-protonation mechanisms remain possibilities. Free energy computations also appear to indicate that C5-protonation is a feasible mechanism, as is direct decarboxylation without preprotonation O-protonation mechanisms have yet to be explored with these methods. Controversy remains, however, as to the roles of ground state destabilization, transition state stabilization, and dynamic effects. Because free energy models do take into account the entire enzyme active site, a comprehensive study of the relative energetics of pre-protonation and concerted protonation-decarboxylation at 02, 04, and C5 should be undertaken with such methods. In addition, quantum mechanical isotope effects are also likely to figure prominently in the ultimate identification of the operative ODCase mechanism. 

Some examples which show the dynamic effects of alkyl and silyl substituents on barriers to rotation in allyllithium compounds 26 to 32 are listed in Table 7. These results were obtained from proton NMR line shape data. The procedure for compounds 26, 28, 29 and 32, which exhibited rotation around their C — CH2 bonds, is diagrammed by structure 33 in which hydrogens A, B and X are all nonequivalent and each couples to the others. Rotation averages the A and B shifts as well as the coupling constant between them and 3./(Ha.Hx) averages with 37(HB,HX), (Figure 15). At the same time, the Hx resonance... 

It is interesting to note that, for malonic acid (which is structurally related to DMMA), the activation energy measured from XH NMR Tx measurements [170] is 5.6 kj mol-1, which is significantly lower than in DMMA and is assigned to proton jumps between the two minima of an asymmetric double well potential. This emphasises the importance of the effect of the crystal packing on the asymmetry of the potential function, which defines the mechanism of the proton dynamics in carboxylic acid dimers. 

The interiors of proteins are more densely packed than liquids [181], and so the participation of the atoms of the protein surrounding the reactive system in an enzyme-catalysed reaction is likely to be at least as important as for a reaction in solution. There is experimental evidence which indicates that protein dynamics may modulate barriers to reaction in enzymes [10,11]. Ultimately, therefore, the effects of the dynamics of the bulk protein and solvent should be included in calculations on enzyme-catalysed reactions. Dynamic effects in enzyme reactions have been studied in empirical valence bond simulations Neria and Karplus [180] calculated a transmission coefficient of 0.4 for proton transfer in triosephosphate isomerase, a value fairly close to unity, and representing a small dynamical correction. Warshel has argued, based on EVB simulations of reactions in enzymes and in solution, that dynamical effects are similar in both, and therefore that they do not contribute to catalysis [39]. 

Results from these CP-MD calculations show that we in fact have a more complicated situation than dealing with simple hydrogen bond or ion-pair complex formation as methanol interacts with a zeolite acidic proton. Stich and coauthors conclude that the zeolite reactivity can be understood only by taking three factors into account simultaneously zeolite topology, sorbate loading, and dynamic effects. The examples above illustrate that the capabilities of modern modeling techniques will allow us to accept this challenge. 

Vibrational spectroscopy measures atomic oscillations practically on the scale as the scale of proton dynamics, 10-15 to 10 12 s. Fillaux et al. [110] note that optical spectroscopies, infrared and Raman, have disadvantages for the study of proton transfer that preclude a complete characterization of the potential. (However, the infrared and Raman techniques are useful to observe temperature effects inelastic neutron spectra are best observed at low temperature.) As mentioned in Ref. 110, the main difficulties arise from the nonspecific sensitivity for proton vibrations and the lack of a rigorous theoretical framework for the interpretation of the observed intensities. 

As opposed to this riding effect, the rather modest intensity observed for lattice modes is clear evidence that protons are almost totally decoupled from carbonate entities. Consequently, conventional force fields must be abandoned. Proton dynamics are better represented with localized modes defined with respect to a "fixed" (laboratory) referential frame. From both viewpoints of spectroscopy and quantum chemistry, this is a dramatic change. 

Fitting procedures give information on wave functions via mean-square displacements (ufj for each vibration and effective oscillator masses. It transpires that proton dynamics for bending modes correspond very closely to isolated harmonic oscillators with a mass of 1 amu [Ikeda 2002], They are largely de-... 

As a conclusion for this section, INS studies of KHCOs single-crystals provide the most detailed, and hopefully the most tutorial, view of proton dynamics ever obtained. The limitation of optical techniques to establishing an unambiguous representation of proton dynamics is emphasized. Effective oscillator masses of 1 amu are determined for each normal mode. Then arises a new fundamental question which mechanisms can account for the decoupling of proton dynamics from the lattice ... 

Neutron scattering experiments shed a new light on proton dynamics in the extended arrays of hydrogen bonded centrosymmetric dimer entities of the KHCO3 crystal. Proton dynamics are decoupled from the lattice. Measurements of effective oscillator masses (namely, 1 amu) contribute to full determination of normal coordinates. 

It was hypothesised that as the proton moves off-centre the planarity of the ring is lost and the donor carboxylate group rotates out of the plane, relaxing the strain energy [56]. The effective potential along the stretching coordinate presented in Fig. 7.16 is a snapshot of the proton dynamics before the rotation of the carboxylic group creates asymmetry in the potential surface. 

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