Transition states geometry optimization

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],... 

In 1983 the first MOPAC program was written and contained both the MlNDO/3 and MNDO models. This program allowed geometry optimization, transition state location by use of a reaction coordinate, gradient minimizations, and vibrational frequency calculations. MNDO has been applied with success to the prediction of polarizabilities, hyperpolarizabilities, ESCA, nuclear quadrupole resonance, and numerous other properties. ... 

Geometry Optimizations, Transition States, and Reaction Paths... 

Schlegel H B 1982 Optimization of equilibrium geometries and transition states J. Comput. Chem. 3 214... 

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

Ab initio calculations at HF/6-31+G level of theory for geometry optimization and MP2/6-31+G //HF/6-31+G level for single-point total energy calculations were reported for lenthionine (1,2,3,5,6-pentathiepane). The unsymmetrical twist-chair conformation is the most stable conformation of lenthionine. The unsymmetrical twist-boat form is 33.0 kj mol-1 less stable. Conformational racemization of twist-chair conformation can take place via plane symmetrical chair geometry as transition state and requires 50.7 kj mol 1 <2003JMT225>. 

Figure 4.23 MP2/6-31G optimized geometries of transition states for Reactions...

The variationally optimized transition state geometries were found to be different for transfer of a proton or a deuteron, the first indication of such a difference for an enzyme reaction [67]. Quantum treatment of vibrations was found to be important for the calculation of the rate constant, and variational transition state theory was important for calculating kinetic isotope effects. The... 

Adamantanone is more rigid than cyclohexanone and less able to distort to achieve an optimal transition state geometry. The system avoids the problem present in studies of cyclohexanone of compaiison of C-C and C-H. 

Figure 6 Optimized geometries for transition states 7 and 8. Bond lengths in A, angles in degrees. Phosphine groups omitted for clarity. BLYP regular font B3LYP italics font MP2 bold font.

Fig. 18. The optimized geometries of transition states computed at the B3LYP/6-311+G(3df, 2p) level for the HO-CIO system [75],...

Aryl halides are much less reactive than alkyl halides in nucleophilic substitution reactions. The carbon-halogen bonds of aryl halides are too strong, and aryl cations are too high in energy, to permit aryl halides to ionize readily in S l-type processes. Furthermore, as Figure 12.7 shows, the optimal transition-state geometry required for 8 2 processes... 

Interesting from methodological point of view investigations have been performed by Glad and Jensen [33], They have calculated deuterium a-secondaiy kinetic isotope effects (SKIE) as an example of oxirane interaction with nucleophiles and compared them with optimized transition state geometries (Table 10.1). 

Using redtmdant internal coordinates to optimize equilibrium geometries and transition states. Journal of Computational Chemistry,... 

Using Redundant Internal Coordinates to Optimize Equilibrium Geometries and Transition States. 

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