Transition structure rearrangements

Just as one may wish to specify the temperature in a molecular dynamics simulation, so may be desired to maintain the system at a constant pressure. This enables the behavior of the system to be explored as a function of the pressure, enabling one to study phenomer such as the onset of pressure-induced phase transitions. Many experimental measuremen are made under conditions of constant temperature and pressure, and so simulations in tl isothermal-isobaric ensemble are most directly relevant to experimental data. Certai structural rearrangements may be achieved more easily in an isobaric simulation than i a simulation at constant volume. Constant pressure conditions may also be importai when the number of particles in the system changes (as in some of the test particle methoc for calculating free energies and chemical potentials see Section 8.9). 

Fig. 6.14. Possible transition structures for [3,3]-sigmatropic rearrangement of 2-cyclohexenyl ester enol ethers. Adapted from J. Org. Chem., 68, 572 (2003), by permission of the American Chemical Society.

The ester 7-1 gives alternative stereoisomers when subjected to Claisen rearrangement as the lithium enolate or as the silyl ketene acetal. Analyze the respective transition structures and develop a rationale to explain these results. 

Scheme 6.24 Corrected B3LYP energies and relevant transition structures and intermediates in the possible rearrangement mechanisms of amidoximes-DMAD adducts 68Z/E.

A theoretical study of degenerate Boulton-Katritzky rearrangements concerning the anions of the 3-hydroxyimi-nomethyl-l,2,5-oxadiazole has been carried out by using semi-empirical modified neglect of diatomic overlap (MNDO) and ab initio Hartree-Fock procedures. Different transition structures and reactive pathways were obtained in the two cases. Semi-empirical treatment shows asymmetrical transition states and nonconcerted processes via symmetrical intermediates. By contrast, ab initio procedures describe concerted and synchronous processes involving symmetrically located transition states <1998JMT(452)67>. 

The framework around which the cause-effect relationships in CSD have been studied is generally referred to as structural evolution. This name has been used, in part, because structural rearrangement at various length scales typically occurs during the transitions from solution species to the final desired him, as outlined in Fig. 2.1.16... 

The conversion of the kinetic data into AAG -values (Table 4.2) assumes that the rate-limiting step is the same in wild type and variant. It also assumes that the mutation does not cause structural rearrangements. Only in very few cases have the kinetic studies on the transition state stabilization by the oxyanion hole contributions been complemented by protein crystallographic studies of the liganded wild-type and mutated variant. One such example, discussed in more detail below, concerns the studies on the Ser42Ala variant of cutinase, in which case it was found that the structural changes are minimal [19]. 

Topologically, one cannot go from B-IMA to Z-IMA by simply turning the helix around the other way. In addition to the rotation of the helix in the opposite direction, the base pairs must "flip over, as they have an orientation relative to the backbone opposite to that which is found in B-IMA. Thus, the transition from B-IMA to Z-IMA is a rather complex procesa involving maiqr structural rearrangements. 

It is important to note that for methyl nitrenium ion the singlet state is not predicted at higher levels of theory to show a potential energy minimum. Rather this species is a transition structure that eliminates H2 without a barrier (Fig. 13.15). It seems likely that the difficulties encountered in attempting to study alkyl nitrenium ions might be traced to their propensity to rearrange or eliminate. 

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