Proton energy profile

These conclusions follow directly from the simulation of a time-dependent proton energy profile along the reaction coordinate. Figure 4.4 demonstrates how random thermal fluctuations cause a temporary lowering of the potential barrier on the line between two extreme positions for a proton. Due to structural fluctuation, at a certain moment of time (t 16.5 ps) there appears the transient configuration for which an oxonium state becomes more stable... 

Fig. 5.9. Energy profile for the scrambling and rearrangement of 4119 cation. A H-bridged B methyl-bridged C Edge protonated methycyclopropane D classical secondary E classical primary F tertiary. Adapted from refs 120 and 121.

These results indicate an energy profile for the 3-methyl-2-butyl cation to 2-methyl-2-butyl cation rearrangement in which the open secondary cations are transition states, rather than intermediates, with the secondary cations represented as methyl-bridged species (comer-protonated cyclopropanes) (Fig. 5.10). 

Outer sphere electron transfer (e.g., [11-19,107,160-162]), ion transfer [10,109,163,164] and proton transfer [165] are among the reactions near electrodes and the hquid/liquid interface which have been studied by computer simulation. Much of this work has been reviewed recently [64,111,125,126] and will not be repeated here. All studies involve the calculation of a free energy profile as a function of a spatial or a collective solvent coordinate. 

FIGURE 8.8. Calculated free-energy profile for the reaction of carbonic anhydrase. g2(a) and g2(b) designate the states where the proton acceptors are water and histidine respectively. 

Fig. 16. Energy profiles of the protonation and propagation reactions of ethene in the gas phase and in solution (CH2C12) starting with 4 monomer units and a free proton...

Figure 13-4. Energy profile for the proton transfer in malonaldehyde enol. 

Despite this fact, acidification of the isolable sodium salt of the carbanion intermediate (35) yields only the less stable aci-form (346)—a colourless solid. This happens because more rapid protonation takes place at the position of higher electron density, i.e. product formation under these conditions is kinetically controlled. The energy profile for the system has the form (Fig. 10.1),... 

Fig. 5. Energy profile (AG/kcal mol-1) of a catalytic cycle of N2 in a Mo-pentaphosphine complex with reduction by decamethylchromocene and protonation by HLut+ obtained by DFT calculations (31).

PROTON TRANSFER REACTION PATHWAY 4.1 Free Energy Profile... 

Figure 8. Total free energy profile for the transfer of the proton as a function of H04...N5 distance.

Table 4. Ab initio energy profile during the proton transfer starting from the reduced tetrahydrofolate. ...

In this study, identification of the critical atomic and molecular determinants pertaining to the mechanism of dihydrofolate to tetrahydrofolate reduction was achieved by (i) ab initio quantum mechanics, (ii) molecular mechanics, and (iii) free energy perturbation techniques. For the first time, the complete free energy profile was calculated for the proton transfer from Asp27 of the enzyme E. Coli DHFR to the N5 position of the dihydropterin moiety of the substrate dihydrofolate. In addition, the free... 

A structure-structure correlation may itself contain some of the necessary information. Note that in Fig. 4 the points are most abundant in the regions where dx and d2 are about 1.0 and 1.5-2 A, respectively, and sparse close to the point where dt and d2 are equal. This distribution is expected if the symmetrical system is of higher energy, so that the energy profile diagram for the proton transfer reaction (5)... 

Ah initio calculations to map out the gas-phase activation free energy profiles of the reactions of trimethyl phosphate (TMP) (246) with three nucleophiles, HO, MeO and F have been carried out. The calculations revealed, inter alia, a novel activation free-energy pathway for HO attack on TMP in the gas phase in which initial addition at phosphorus is followed by pseudorotation and subsequent elimination with simultaneous intramolecular proton transfer. Ah initio calculations and continuum dielectric methods have been employed to map out the lowest activation free-energy profiles for the alkaline hydrolysis of a five-membered cyclic phosphate, methyl ethylene phosphate (247), its acyclic analogue, trimethyl phosphate (246), and its six-membered ring counterpart, methyl propylene phosphate (248). The rate-limiting step for the three reactions was found to be hydroxyl ion attack at the phosphorus atom of the triester. ... 

Figure 2. Free energy profile for converting di hydroxy acetone phosphate, the substrate (abbreviated S) and glyceraldehyde 3-phosphate, the product (abbreviated P), with intermediate formation of the enedi-olate (abbreviated Z). Catalysis occurs either by a free carboxyl group (levels connected by dotted lines) or by triose-phosphate isomerase (levels connected by dashed lines). The vertical arrows show the limits of those states that are less well defined as a result of uncertainty in the experimental data. The transition state marked "e" refers to the exchange of protons between the solvent and the enzyme-bound enediol intermediate (EZ). Reproduced with permission of the authors and the American Chemical Society.

The spectroscopic, kinetic, and thermodynamic data discussed are sufficient to describe semiquantitatively the energy profile of proton transfer to a hydride ligand occurring in solution [29, 35, 36]. Figure 10.10 shows the energy as a function of the proton-hydride distance, varying from the initial state to a final product. The average structural parameters of the initial hydrides and intermediates have been taken from earlier chapters. Since proton-hydride contacts of... 

Figure 10.10 Energy profiles of proton transfer to a hydride ligand of a transition metal complex in solution AEi = + 3 to 4kcal/mol, AE2 = — 5 to — 7 kcal/mol, A 3= + 10 to 14 kcal/mol, and A 4 = —7 kcal/mol the energy is a function of the proton-hydride distance, varying from an initial state (2.5 A) to the final product (0.9 A) conversion of the intimate ion pair to the solvent-separated ion pair is shown as a function of the H+- O" distance. (Reproduced with permission from ref. 29.)...

Figure 10.12 Energy profile obtained for proton transfer from HCl via dihydrogen-bonded complex [A1H4- -HCl] along the reaction coordinate. (Reproduced with permission from ref. 38.)...

Figure 10.13 Energy profile, intermediates, and transition states (TS) obtained by the B3LYP and MP2 (in parentheses) methods for proton transfer from CF3OH to the hydridic hydrogen of the ion [BH4] . (Reproduced with permission from ref. 39.)...

Figure 10.15 Energy profile obtained by DFT calculations for proton transfer to hydridic hydrogen in hydride It from the dimer (CF3COOH)2 (TFA). Energies are given in kcal/mol. (Reproduced with permission from ref. 6.)...

As shown in Figure 2.3, the activation energy of protonation (TSlt) is only 1.9kcal/mol and the proton-transfer reaction exhibits a very flat energy profile. 

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