Optimized transition states

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

Density functional theory has also been applied successfully to describe the solvent exchange mechanism for aquated Pd(II), Pt(II), and Zn(II) cations (1849 ). Our own work on aquated Zn(II) (19) was stimulated by our interest in the catalytic activity of such metal ions and by the absence of any solvent (water) exchange data for this cation. The optimized transition state structure clearly demonstrated the dissociative nature of the process in no way could a seventh water molecule be forced to enter the coordination sphere without the simultaneous dissociation of one of the six coordinated water molecules. More... 

Figure 7. Optimized transition-states for H2 loss for the 1,5 (16) and 1,6-p-H-bridged (18) 2-heptyl cations showing some of the key geometric parameters at the B3LYP/6-31G level...

Figure 8. Alternative optimized transition-state for H2 loss in 1-6-p-H-bridged 2-heptyl cation, 22, leading to a cyclized secondary cation intermediate at the...

Two extreme epoxidation modes, spiro and planar, are shown in Fig. 9 [33, 34, 53, 54, 76-85]. Baumstark and coworkers had observed that the epoxidation of cis-hexene of dimethyldioxirane was seven to nine times faster than the corresponding epoxidation of tran.y-hexene [79, 80]. The relative rates of the epoxidation of cisitrans olefins suggest that spiro transition state is favored over planar. In spiro transition states, the steric interaction for cw-olefm is smaller than the steric interaction for fran -olefm. In planar transition states, similar steric interactions would be expected for both cis- and trans-olefms. Computational studies also showed that the spiro transition state is the optimal transition state for oxygen atom transfer from dimethyldioxirane to ethylene, presumably due to the stabilizing interactions... 

Figure 2 a-reactants, b-optimized transition state geometry, c-product 1, d-product 2... 

Fig. 8. Optimized transition state for dissociation of Watl (TS[la-2a] ) and the optimized product (2a) upon removal of Watl from the hexacoordinate starting structure. Distances are given in angstroms.

Fig. 13. Optimized transition state for formation of the Fe-0-0-BH4 bridge structure TS[7aM 6-8a] and the accompanying product 8a. Distances are given in angstroms.

Fig. 17. Optimized transition state 8[11 -12 ] leading to the FeIV=0 intermediate with a chelate cofactor 12a. Distances are given in angstroms.

Fig. 22. Optimized transition state for the NIH shift and rotation of Glu 330 (TS[14b-16a] ), which occurs simultaneously for the conformer with the His290 imidazole ring rotated 180° compared to the crystal structure, and the optimized NIH shift product with rotated Glu330 (16a). Distances are given in angstroms.

Fig. 2 Modified More O Ferrall-Jencks diagram for the CH3N02/CH2=N02 system. The curved lines represent the reaction coordinates through the optimized and constrained transition state, respectively. The constrained transition state is less imbalanced as indicated by its location to the left of the optimized transition state.

Fig. 3. Fully optimized transition state (structure 2-3 TS) for H-H bond cleavage in [NiFe] hydrogenase. The oxidation states are Ni(II) and Fe(II). Distances are given in A.

FIGURE 50. B3LYP optimized transition states and activation energies of the Sn(IV)halide-catalyzed cis- and trans-addition of formaldehyde to 4-alkoxyalk-2-enylstannanes. Bond lengths are in A, energies in kcal mol 1. Reproduced by permission of The Royal Society of Chemistry from Reference 169... 

FIGURE 66. Optimized transition states at MP2 for the homolytic substitution reaction of the CH3 substituent in HYCH3 (Y = S, Se, Te) by H3E (E = Si, Ge, Sn). Bond distances are in A, angles in deg. The calculated activation energies (kcalmol-1) at QCISD//MP2 refer to the forward reaction (AE ) and the reverse reaction (A 2 ), respectively (see Figure 65). Reprinted from Reference 187 with permission from Elsevier Science... 

FIGURE 68. Free-radical substitution reactions of hydridotellurides HTeEH3 (E = Si, Ge, Sn) and HTeSi(SiH3)3 with alkyl groups R. The optimized transition states and calculated activation energies are given in Figure 69... 

Fig. 5 Optimized transition states for the reaction of osmium tetroxide with propene via a [2 + 2]-pathway.

---