Distortion along reaction coordinate

Figure 29, The effect of the phase-preserving component of the degenerate 2 distorting mode, It may be regarded as a major component of the reaction coordinate that leads to the A] structure (going left, one phase of the mode). Going right, the other phase of the same vibration, the B2 state is formed. (A type-V structure is also obtained along the same coordinate).

A careful distinction must be drawn between transition states and intermediates. As noted in Chapter 4, an intermediate occupies a potential energy minimum along the reaction coordinate. Additional activation, whether by an intramolecular process (distortion, rearrangement, dissociation) or by a bimolecular reaction with another component, is needed to enable the intermediate to react further it may then return to the starting materials or advance to product. One can divert an intermediate from its normal course by the addition of another reagent. This substance, referred to as a trap or scavenger, can be added prior to the start of the reaction or (if the lifetime allows) once the first-formed intermediate has built up. Such experiments are the trapping experiments referred to in Chapters 4 and 5. 

Quantum tunnelling in chemical reactions can be visualised in terms of a reaction coordinate diagram (Figure 2.4). As we have seen, classical transitions are achieved by thermal activation - nuclear (i.e. atomic position) displacement along the R curve distorts the geometry so that the... 

As already noted, in the Born-Oppenheimer approximation, the nuclear motion of the system is subject to a potential which expresses the isotope independent electronic energy as a function of the distortion of the coordinates from the position of the transition state. An analysis of the motions of the N-atom transition state leads to three translations, three rotations (two for a linear molecule), and 3N - 6 (3N- 5 for a linear transition state) vibrations, one which is an imaginary frequency (e.g. v = 400icm 1 where i = V—T), and the others are real vibrational frequencies. The imaginary frequency corresponds to motion along the so-called reaction... 

Ab initio theoretical calculations for the 4-methylpent-2-yl cation by Farca iu et al.115 have shown both a distorted 1 -protonated 1,1,2-trimethylcyclopropane and the open cation to be energy minima along the reaction coordinate at the B3LYP/ 6-31G level. In contrast, only the protonated cyclopropane was found to be an energy minimum in the MP2/6-31G optimization. Whereas the open cation was a transition structure at this level, a coupled cluster geometry optimization (CCSG/6-31G ) showed that the open ion is also a true energy minimum. 

An additional feature revealed by the considerations about molecular distortions is that as the complementary polarities of the addends increases, less distortion of addends will be required to reach the transition state. For example, for a high-lying diene HOMO and low-lying dienophile LUMO, the stabilizing HOMO-LUMO interaction will surpass the destabilizing molecular distortion energy quite early along the reaction coordinate. This will clearly favor the concerted mechanism over the step-... 

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