Intramolecular geometry relaxation

In Equation (4.138) s represents the new intramolecular potential and the constant C = 47T60. As we have already seen, the molecular geometry relaxes in a new minimum under... 

With the geometry relaxation taken into account, the calculated barrier of Eq. (9.15) (using the basis set STO-3G) is lowered from 48kcal/mol to 14kcal/mol. Characteristic is the reduction of the nonvalent distance O - O from 2.73 A in the starting dimer to 2.30 A in the transition state. This trend toward compression of the reactive site and, as a consequence, lowering in the activation barrier was noted earlier in connection with intramolecular proton transfer in malonaldehyde. 

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

Figure 5.2. Grabowski s model of TICT formation in DMABN the locally excited (LE) state with near-planar conformation is a precursor for the TICT state with near perpendicular geometry. The reaction coordinate involves charge transfer from donor D to acceptor A. intramolecular twisting between these subunits, and solvent relaxation around the newly created strong dipole. Decay kinetics of LE and rise kinetics of the TICT state can be followed separately by observing the two bands of the dual fluorescence. For medium polar solvents, well-behaved first-order kinetics are observed, with the rise-time of the product equal to the decay time of the precursor, but for the more complex alcohol solvents, kinetics can strongly deviate from exponentiality, interpretable by time-dependent rate constants. 52 ...

A particularly well studied system which undergoes photochemical cis -> trans isomerization is Pt(gly)2- The work on these compounds through 1969 has already been discussed in detail elsewhere (7), and thus only the major conclusions thereof will be mentioned here. A definitive study by F. Scandola et al. (93) showed that the photochemical cis - trans isomerization of this species occurs with an intramolecular "twisting" mechanism (Fig. 7). The thermally relaxed reactive excited state was proposed to have a pseudo-tetrahedral geometry as shown in Fig. 7. 

In this nonplanar geometry the intramolecular cc resonance is weakened at the expense of the inter-molecular Uq oh interaction, and the radical reverts to a much more localized enol-like form. The NRT description of the relaxed A-state complex exhibits these effects, as shown in the leading a-spin structures 21a to 21c... 

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