Proton transfer direct

Figure 20 Reaction coordinates for the chemicai step of Poi /3 cataiyzed correct nucieotide incorporation and the corresponding structures for each step. Oniy one of three distinct possibie pathways of proton transfer (direct transfer from 03 to 02a(Pa)) is shown. The atoms are shown as coior-coded sticks Mg (green), P (yeiiow), O (red), C (biue), and H (gray). Energies are in kcaimoi Reproduced with permission from M. D. Bojin T. Schiick, J. Phys. Chem. B 2007, 111, 11244-11252. Copyright 2007 American Chemicai Society.

The system was left to evolve at 300 K using a Nose-Hoover thermostat in the NVT ensemble. After about 100 ps, the proton of the Ha acidic glycine moved to N. As also mentioned in the CPMD study [201], a decrease of the water coordination to glycine was observed before and during the transfer (2 waters bound to the acidic OH and to the N atom moved farther away). The proton transferred directly to the amine N without any intermediate bonding with water. 

A. Femdndez-Ramos, J. Rodrfguez-Otero and M.A. Rfos, Intramolecular proton transfer direct dynamics in the glycolate anion Isotope effects, J. Chem. Phys., 107 (1997) 2407. 

Figure A3.8.3 Quantum activation free energy curves calculated for the model A-H-A proton transfer reaction described 45. The frill line is for the classical limit of the proton transfer solute in isolation, while the other curves are for different fully quantized cases. The rigid curves were calculated by keeping the A-A distance fixed. An important feature here is the direct effect of the solvent activation process on both the solvated rigid and flexible solute curves. Another feature is the effect of a fluctuating A-A distance which both lowers the activation free energy and reduces the influence of the solvent. The latter feature enliances the rate by a factor of 20 over the rigid case.

Turning the argument around reactions that do not involve proton transfer steps will only experience a significant effect of the Lewis acids if a direct interaction exists between catalyst and reactant. The conventional Diels-Alder reaction is a representative of this class of reactions. As long as monodentate reactants are used, the effects of Lewis acids on this reaction do not exceed the magnitude expected for simple salt effects, i.e. there are no indications for a direct interaction between Lewis-acid and substrate. 

Depending on experimental parameters, NOE intensities will be affected by spin diffusion (Eig. 8). Magnetization can be transferred between two protons via third protons such that the NOE between the two protons is increased and may be observed even when the distance between the two protons is above the usual experimental limit. This is a consequence of the distance dependence of the NOE. Depending on the conformation, it can be more efficient to move magnetization over intennediate protons than directly. The treatment of spin diffusion during structure refinement is reviewed in more detail in Refs. 31, and 71-73. 

The situation presented in fig. 29 corresponds to the sudden limit, as we have already explained in the previous subsection. Having reached a bend point at the expense of the low-frequency vibration, the particle then cuts straight across the angle between the reactant and product valley, tunneling along the Q-direction. The sudden approximation holds when the vibration frequency (2 is less than the characteristic instanton frequency, which is of the order of In particular, the reactions of proton transfer (see fig. 2), characterised by high intramolecular vibration frequency, are being usually studied in this approximation [Ovchinnikova 1979 Babamov and Marcus 1981]. 

In the El mechanism, the leaving group has completely ionized before C—H bond breaking occurs. The direction of the elimination therefore depends on the structure of the carbocation and the identity of the base involved in the proton transfer that follows C—X heterolysis. Because of the relatively high energy of the carbocation intermediate, quite weak bases can effect proton removal. The solvent m often serve this function. The counterion formed in the ionization step may also act as the proton acceptor ... 

However, as can also be seen in Fig. 11, primary and secondary amines do not perform very effectively as primers, compared to tertiary amines, even though they also contain long alkyl chains. It has been demonstrated that, instead of directly initiating ECA polymerization, primary and secondary amines first form aminocyanopropionate esters, 12, because proton transfer occurs after formation of the initial zwitterionic species, as shown in Eq. 7 [8,9]. 

A catalyst is defined as a substance that influences the rate or the direction of a chemical reaction without being consumed. Homogeneous catalytic processes are where the catalyst is dissolved in a liquid reaction medium. The varieties of chemical species that may act as homogeneous catalysts include anions, cations, neutral species, enzymes, and association complexes. In acid-base catalysis, one step in the reaction mechanism consists of a proton transfer between the catalyst and the substrate. The protonated reactant species or intermediate further reacts with either another species in the solution or by a decomposition process. Table 1-1 shows typical reactions of an acid-base catalysis. An example of an acid-base catalysis in solution is hydrolysis of esters by acids. 

Table 4-1 lists some rate constants for acid-base reactions. A very simple yet powerful generalization can be made For normal acids, proton transfer in the thermodynamically favored direction is diffusion controlled. Normal acids are predominantly oxygen and nitrogen acids carbon acids do not fit this pattern. The thermodynamicEilly favored direction is that in which the conventionally written equilibrium constant is greater than unity this is readily established from the pK of the conjugate acid. Approximate values of rate constants in both directions can thus be estimated by assuming a typical diffusion-limited value in the favored direction (most reasonably by inspection of experimental results for closely related... 

One after the other, step through (or animate) the sequence of structures depicting the SN2 and proton transfer reactions shown above. Compare the two. From what direction does cyanide approach the hydrogen in HCl From the same side as Cl ( frontside ), or from the other side ( backside ) Does the Sn2 reaction follow a similar trajectory ... 

A direct irreversible proton transfer in limiting stage of 1-ethoxybut- l-en-3-yne hydration is confirmed by the value of kinetic isotopic effect k ilk = 2.9. For fast reversible proton transitions this value is less than 1. 

The question arises whether an external electric field will have any large influence on the direction of these proton transfers. In the NH3 molecule all three protons are situated in one hemisphere of the electronic cloud, and so give to the molecule a dipole moment. In the (NH4)+ ion, on the other hand, it is generally accepted that the four protons are placed symmetrically at the corners of a tetrahedron. Accordingly, the (NH4)+ ion will have no dipole moment. 

In their measurements with the cell (195) containing methanol, Non-hebel and Hartley1 verified by direct experiment that the addition of a small drop of water to either side of the cell, sufficient to give a mole fraction of I120 equal to about 0.001, produced a change in the e.m.f. equal to a few millivolts. This was attributed mainly to the proton transfer (44). The curve for HOI in methanol-water mixtures must thus have a very steep slope, as has been sketched on the right-hand side of Fig. 01. 

Although thermodynamics can be used to predict the direction and extent of chemical change, it does not tell us how the reaction takes place or how fast. We have seen that some spontaneous reactions—such as the decomposition of benzene into carbon and hydrogen—do not seem to proceed at all, whereas other reactions—such as proton transfer reactions—reach equilibrium very rapidly. In this chapter, we examine the intimate details of how reactions proceed, what determines their rates, and how to control those rates. The study of the rates of chemical reactions is called chemical kinetics. When studying thermodynamics, we consider only the initial and final states of a chemical process (its origin and destination) and ignore what happens between them (the journey itself, with all its obstacles). In chemical kinetics, we are interested only in the journey—the changes that take place in the course of reactions. 

The major problem in method (a) is that in ion-molecule interchange, considerable momentum in the direction of travel of the incident ion is imparted to both final products. Hence, in a perpendicular type apparatus only transfer of low weight particles can be observed at all and only at very low velocities of the incident ions (1, 9, 10, 11, 12, 13, 19, 20, 23, 27). Cross-sections cannot be measured. The value of these investigations is that some ion-molecule reactions—e.g., proton transfer and hydride ion transfer—can be identified. The energetics and the competition between charge exchange and ion-molecule reactions can be discussed, and by using partially deuterated compounds, one can obtain a detailed picture of the reaction. 

Proton transfers between oxygen and nitrogen acids and bases are usually extremely fast. In the thermodynamically favored direction, they are generally diffusion controlled. In fact, a normal acid is defined as one whose proton-transfer reactions are completely diffusion controlled, except when the conjugate acid of the base to which the proton is transferred has a pA value very close (differs by g2 pA units) to that of the acid. The normal acid-base reaction mechanism consists of three steps ... 

The base in the second step may be water, though it is also possible that in some cases no external base is involved and that the proton is transferred directly to one of the C1O3H oxygens in which case the Cr(IV) species produced would be H2Cr03. 

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