Transition state environment perturbing

PERTURBING THE TRANSITION STATE ENVIRONMENT 4.1. The Diels-Alder Reaction... 

Most treatments of such double-layer effects assume that the microscopic solvation environment of the reacting species within the interfacial region is unaltered from that in the bulk solution. This seems oversimplified even for reaction sites in the vicinity of the o.H.p., especially since there is evidence that the perturbation of the local solvent structure by the metal surface [18] extends well beyond the inner layer of solvent molecules adjacent to the electrode [19]. Such solvent-structural changes can yield considerable influences upon the reactant solvation and hence in the observed kinetics via the work terms wp and wR in eqn. (7a) (Sect. 2.2). While the position of the reaction site for inner-sphere processes will be determined primarily by the stereochemistry of the reactant-electrode bond, such solvation factors can influence greatly the spatial location of the transition state for other processes. 

Sawaryn and Sokalski (1979) considered the MEP of a few amino-acid residues around the active site and suggested that the Zn24 and OH" ions stabilise the transition state of the reaction. Unfortunately, the mechanism studied involves an attack of water rather than hydroxyl on C02 and the calculation did not treat correctly the protein dielectrics. The crucial role of the Zn2f cation and its local environment was determined quantitatively by the Empirical Valence Bond/Free Energy Perturbation study ofAqvist and Warshel (1992) and Aqvist et al. (1993). This study demonstrated... 

Today, it is indispensable and conunon in modem chemistry to deal with molecules as the quantum systems that consist of a couple of classical mechanical (CM) nuclei and quantum mechanical (QM) electrons, for understanding chemical phenomena deeply. Such QM approaches can provide us the microscopic information such as the stmctural information (e.g. stable state (SS) and transition state (TS)) and chemical properties (e.g. electric or magnetic external fields and internal perturbations such as a nuclear or electron spin) of chemical reaction systems. However, from the point of view of computational efforts, it remains difficult to directly apply the QM approaches to large reaction systems such as the solution (or biological) ones that we are interested in. Thus, to treat these whole reaction systems in solution and biological environment, it is very useful in many cases to employ a multiscale model such as the quantum mechanical/molecular mechanical (QM/MM) methods, which are often combined with molecular dynamics (MD) or Monte Carlo (MC). 

Robinson and Frosch<84,133> have developed a theory in which the molecular environment is considered to provide many energy levels which can be in near resonance with the excited molecules. The environment can also serve as a perturbation, coupling with the electronic system of the excited molecule and providing a means of energy dissipation. This perturbation can mix the excited states through spin-orbit interaction. Their expression for the intercombinational radiationless transition probability is... 

In the case of naphthalene, transitions to the two lowest excited states (again, often indicated with Lb and La) are two-photon forbidden, as in benzene. However, due to vibronic coupling, the Lb band is visible in the 2PA spectrum of naphthalene in the 575-650 nm region (see Fig. 5), while La gains intensity in the IPA spectrum and peaks around 275 nm [44-46], but is basically absent from the 2PA spectrum this is again in line with predictions based on the pseudoparity of the states. Polarization ratio data were used to aid the band assignment. A weak 0-0 peak of the Lb band can actually be seen in the 2PA spectrum (at 630.5 nm for naphthalene in cyclohexane [45] and at 631.8 nm in carbon tetrachloride [47]), probably because of local perturbation of the symmetry due to the solvent environment or other effects [44,45]. The 2PA... 

The calculated excitation energies of the C4v molecules explain the inconsistencies in their MCD spectra. The spectra of these complexes were initially interpreted in terms of a perturbed Oh symmetry (126). The calculations showed that while the higher energy T states are split very little in the C4v symmetry complexes, the l2 state and, in particular, the l2Tlu state are split significantly in the C4v environment (89). The first band in the absorption spectrum thus corresponds to a 2E 2E excitation but the other part of the transition to the 2Tj state, a 2E—>2Ai transition is found in the second band. The 2E—>2E transition is more intense and results in a spectrum with a prominent first band (Fig. 4b). 

The central concern of crystal field theory is what happens to the electronic states of an ion when it is placed in some perturbing symmetric environment. If we assume that a set of ligands placed symmetrically about a transition-metal ion interact only electrostatically with the electrons of that ion, then the answer to this question is relevant to our study of transition-metal compounds. 

---