Reaction mechanisms experimental molecular study

Experimental Molecular Study of Chemical Reaction Mechanisms... 

One target type for which the molecular mechanism of efficacy has been partly elucidated is the G-protein-coupled receptor (GPCR). It is known that activation of GPCRs leads to an interaction of the receptor with separate membrane G-proteins to cause dissociation of the G-protein subunits and subsequent activation of effectors (see Chapter 2). For the purposes of binding, this process can lead to an aberration in the binding reaction as perceived in experimental binding studies. Specifically, the activation of the receptor with subsequent binding of that... 

The successful mechanism for a reaction is a theory that correlates the many facts which have been discovered and is fruitful for the prediction of new experiments (1). One approach to mechanism is the study of stereochemistry which seeks information concerning the geometrical relationships between the reactants at the critical stages in the reaction. Information is gleaned from the examination of the products, if several isomers differing only in configuration may be formed, or from a study of the reactivity of closely related substances whose molecular shapes are varied in a specific manner. Occasionally a stereochemical fact places a considerable restraint upon the allowable mechanistic postulates, but the most effective employment of stereochemistry generally depends upon its detailed correlation with other experimental methods. 

In 1998, Hasanayn and Streitwieser reported the kinetics and isotope effects of the Aldol-Tishchenko reaction . They studied the reaction between lithium enolates of isobu-tyrophenone and two molecule of beuzaldehyde, which results iu the formation of a 1,3-diol monoester after protonation (Figure 28). They analyzed several aspects of this mechanism experimentally. Ab initio molecular orbital calculatious ou models are used to study the equilibrium and transition state structures. The spectroscopic properties of the lithium enolate of p-(phenylsulfonyl) isobutyrophenone (LiSIBP) have allowed kinetic study of the reaction. The computed equilibrium and transition state structures for the compounds in the sequence of reactions in Figure 28 are given along with the computed reaction barriers and energy in Figure 29 and Table 6. 

However, one should keep in mind that simplified models of the actual physical systems are routinely used and that molecular-level modeling techniques involve various levels of approximations. In principle, computational chemistry can only disprove, and never prove, a particular reaction mechanism. In practice, however, a computational investigation may still, in many cases, be a useful guide as to the likeliness of a given reaction pathway. Comparison to experimental information and to computational studies of alternative reaction mechanisms will help establish the kind of trust (or lack thereof) that should be put into a particular reaction mechanism obtained by computational chemistry. 

In most cases in the real world of chemistry both currently and historically, the reverse order is followed that is, the mechanism is deduced with certainty only after the stereoselectivity has been determined. Because the stereochemical outcome of a chemical reaction is experimentally determined, it provides a powerful tool for examining the intimate spatial details of transition states and for determining how a reaction takes place at the molecular level. As such stereochemical studies have had a huge impact on the elucidation of reaction mechanisms. 

Huge amount of studies by means of molecular orbital (MO) calculations have been reported in the literature, which calculate the structures of reactants, products, reactive intermediates, and TSs of possible reaction pathways, as well as minimum energy paths from the TSs to both the reactant and product sides on the potential energy surface (PES). The information thus obtained, together with experimental findings, has been used to deduce reaction mechanisms. The combined use of experiment and MO calculations has become a common method for physical organic chemists. However, it should be noted that the calculated structures and energies are at OK and that therefore the information obtained from MO calculations may not directly be related to experimental observation at a finite temperature. 

It is likely that theoretical methods, both ab initio and MD simulations, will be needed to resolve the complicated chemical decomposition of energetic materials. There are species and steps in the branching, sequential reactions that cannot be studied by extant experimental techniques. Even when experiments can provide some information it is often inferred or incomplete. The fate of methylene nitramine, a primary product observed by Zhao et al. [33] in their IRMPD/molecular beam experiments on RDX, is a prime example. Rice et al. [99, 100] performed extensive classical dynamics simulations of the unimolecular decomposition of methylene nitramine in an effort to help clarify its role in the mechanism for the gas-phase decomposition of RDX. 

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