Transition states, structures

This section will describe experimental and theoretical studies of the structure of the transition state with a focus on the extent of bond formation and cleavage. A discussion of chair versus boat transition states is left to the section on stereochemistry. 

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Pedersen S, Herek J L and Zewail A H 1994 The validity of the Diradical hypothesis direct femtosecond studies of the transition-state structures Science 266 1359-64... 

Williams 1 H 1993. Interplay of Theory and Experiment in the Determination of Transition-State Structures. Chemical Society Reviews 1 277-283. 

Dewar s treatment of transition state structure, using reactivity numbers, has the logical defect that in the intermediate kinds of transition states for which it provides evidence the electron localisation is only partial. However, in obtaining the values of the reactivity numbers (which are approximate localization energies), the process of localization is considered to be complete thus, values of parameters which strictly are relevant only to the Wheland type of transition state are incorporated into a different model. ... 

Dashed lines in transition state structures represent partial bonds that is bonds in the process of being made or broken... 

Any reaction w4iich shows a major shift in transition-state structure over the substituent series would be expected to give a nonlinear Hammett plot, since a variation in the extent of resonance participation would then be expected. 

The significance of the concept incorporated in Hammond s postulate is that, in appropriate cases, it permits discussion of transition-state structure in terms of the reactants, inteimediates, or products in a multistep reaction sequence. The postulate indicates that the cases in which such comparison is appropriate are those in which the transition state is close in energy to the reactant, intermediate, or product. Chemists sometimes speak of early or late transition states. An early transition state is reactant-like whereas a late transition state is product-like. 

Because a relates the sensitivity to structural changes that the proton-transfer process exhibits to that exhibited by dissociation of the acid, it is frequently assumed that the value of a can be used as an indicator of transition-state structure. The closer a approaches unity, the greater is the degree of proton transfer in the transition state. There are limits to the generality of this interpretaton, however. ... 

This description provides information, via conventional structures, about the constitution of reactants, products, and the intermediate. Transition state structures are more provisional and may attempt to show the electronic distribution and flow in this region of the reaction path. The curved arrow symbolism is often used, as shown in structure 1 for the first elementary reaction. 

Postulate a transition state structure for the formation of the acetylpyridinium ion from pyridine and acetic anhydride. 

Proposal of transition state structures, stereochemistries, and energetics. 

The Hammond postulate is a valuable criterion of mechanism, because it allows a reasonable transition state structure to be drawn on the basis of knowledge of the reactants and products and of energy differences between the states (i.e., AG and AG°). Throughout this chapter we have located transition states in accordance with the Hammond postulate. 

Curvature in a Br nsted-type plot is sometimes attributed to a change in transition state structure. This is not a change in mechanism rather it is interpreted as a shift in extent of bond cleavage and bond formation within the same mechanistic pattern. Thus, Ba-Saif et al. ° found curvature in the Br nsted-type plot for the identity reactions in acetyl transfer between substituted phenolates this reaction was shown earlier. They concluded that a change in transition state structure occurs in the series. Jencks et al." caution against this type of conclusion solely on the evidence of curvature, because of the other possible causes. 

This discussion of sources of curvature in Br insted-type plots should suggest caution in the interpretation of observed curvature. There is a related matter, concerning particularly item 5 in this list, namely, the effect of a change in transition state structure. Br nsted-type plots are sometimes linear over quite remarkable ranges, of the order 10 pK units, and this linearity has evoked interest because it seems to be incompatible with Marcus theory, which we reviewed in Section 5.3. The Marcus equation (Eq. 5-69) for the plot of log k against log K of the same reaction series requires curvature, the slope of the plot being the coefficient a. given by Eq. (5-67). A Brjinsted plot, however, is not a Marcus plot, because it correlates rates and equilibria of different reactions. The slope p of a Br nsted plot is defined p = d log kobs/d pK, which we can expand as... 

For more difficult cases, Gaussian also provides the QST3 option to Opt, which optimizes a transition state structure based on the reactants, products, and a user-provided guess for the geometry of the transition structure. See the Gaussian 94 User s Reference for more details. 

Another use of frequency calculations is to determine the nature of a stationary point found by a geometry optimization. As we ve noted, geometry optimizations converge to a structure on the potential energy surface where the forces on the system are essentially zero. The final structure may correspond to a minimum on the potential energy surface, or it may represent a saddle point, which is a minimum with respect to some directions on the surface and a maximum in one or more others. First order saddle points—which are a maximum in exactly one direction and a minimum in all other orthogonal directions—correspond to transition state structures linking two minima. 

There are important consequences for this statement. The enzyme must stabilize the transition-state complex, EX, more than it stabilizes the substrate complex, ES. Put another way, enzymes are designed by nature to bind the transition-state structure more tightly than the substrate (or the product). The dissociation constant for the enzyme-substrate complex is... 

Destabilization of the ES complex can involve structural strain, desolvation, or electrostatic effects. Destabilization by strain or distortion is usually just a consequence of the fact (noted previously) that the enzyme is designed to bind the transition state more strongly than the substrate. When the substrate binds, the imperfect nature of the fit results in distortion or strain in the substrate, the enzyme, or both. This means that the amino acid residues that make up the active site are oriented to coordinate the transition-state structure precisely, but will interact with the substrate or product less effectively. 

X-ray crystallographic studies of serine protease complexes with transition-state analogs have shown how chymotrypsin stabilizes the tetrahedral oxyanion transition states (structures (c) and (g) in Figure 16.24) of the protease reaction. The amide nitrogens of Ser and Gly form an oxyanion hole in which the substrate carbonyl oxygen is hydrogen-bonded to the amide N-H groups. 

Examine transition-state structures and bond density surfaces for the Diels-Alder, ene and Cope reactions. 

Solvent effects also depend on the ground-state structure of the substrate and on the transition-state structure, as is shown below. Here let us merely note that A-heterocyclic compounds tend to form a hydrogen bond with hydroxylic solvents even in the ground state. Hydrogen-bond formation in this case is a change in the direction of quaternization of the aza group, as demonstrated by spectral evidence. Therefore, it is undoubtedly a rate-enhancing interaction. 

The latter mechanism is characterized by a transition-state structure of type 64 and by its being (in part) analogous to the mechanism at a saturated carbon. The preference of a two-step mechanism to the apparently simpler one-step mechanism is suggested by the isolation of Meisenheimer complexes and by the kinetics of their formation. The experimental evidence on these... 

A transition-state structure was proposed on the basis of the solid-state structure of [Ni((R,R)-DBF0X)(H20)3](C104)2 (Fig. 1.8). The catalyst-dienophUe complex is thought to be a square-bipyramidal structure containing an octahedral nickel ion. The dienophile adopts an s-cis conformation with the si face shielded by a phenyl group. 

Understanding the importance of the zinc alkoxide, the iodomethylzinc iodide and the zinc sulfonamide allowed Denmark to propose a revised transition state structure xv (Fig. 3.22) [82]. In this picture, the complex, polymetallic aggregate invoked by Rickborn and later by Kobayashi is featured. 

One cannot discuss Lewis acid-catalyzed cycloaddition reactions in the present context without trying to understand the reaction course mechanistically, e.g. using a frontier molecular orbital (FMO) point of reasoning, or theoretical calculations of transition state structures. 

Activation of the Dienophile by Lewis Acids, Interactions, Reaction Course, and Transition-state Structures... 

The carbo-Diels-Alder reaction of acrolein with butadiene (Scheme 8.1) has been the standard reaction studied by theoretical calculations in order to investigate the influence of Lewis acids on the reaction course and several papers deal with this reaction. As an extension of an ab-initio study of the carbo-Diels-Alder reaction of butadiene with acrolein [5], Houk et al. investigated the transition-state structures and the origins of selectivity of Lewis acid-catalyzed carbo-Diels-Alder reactions [6]. Four different transition-state structures were considered (Fig. 8.4). Acrolein can add either endo (N) or exo (X), in either s-cis (C) or s-trans (T), and the Lewis acid coordinates to the carbonyl in the molecular plane, either syn or anti to the alkene. 

Fig. 8.4 The four different transition-state structures considered for the Diels-Alder reaction of acrolein with a diene in the presence of a Lewis acid (BH3). The diene can add...

Both experimental [7] and theoretical [8] investigations have shown that the anti complexes of acrolein and boranes are the most stable and the transition states were located only for these four anti complexes. The most stable transition-state structure was calculated (RHF/3-21G) to be NC, while XT is the least stable of the four located. The activation energy has been calculated to be 21.6 kcal mol for the catalyzed reaction, which is substantially above the experimental value of 10.4 1.9 kcal mol for the AlCl3-catalyzed addition of methyl acrylate to butadiene [4a]. The transition-state structure NC is shown in Fig. 8.5. 

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