Chemistry

3D visualization of organic reactions with CAVOC

3D visualization of organic reactions with CAVOC


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Calculation of the reaction paths

Determination of the transition states

The first important and at the same time time-consuming step in a reaction calculation is to find all transition states involved in the reaction. Transition states correspond to saddle points on the energy hypersurface and are therefore much more difficult to optimize with the methods of numerical mathematics than, for example, the most favorable educt and product conformations, which represent real minima. The numerical calculation of a saddle point is usually only successful if the starting point is already very close to the saddle point. There are several possibilities to get the required good approximations for the transition state geometries. In the simplest method, a transition state of a closely related reaction, e.g. one with slightly different substituents on a part of the molecule that is remote from the reaction center, is used as a pattern characteristic coordinate (e.g. an atomic distance when a bond is formed or a bond is broken) varies in fixed steps and after each step a normal optimization is carried out by defining this coordinate. The structure with the highest energy along this reaction coordinate then represents the approximation for the transition state. Several coordinates can also be varied at the same time, but this is very time-consuming. Furthermore, there are semiautomatic methods that allow a construction of the starting structure for a transition state optimization. These include, for example, the "Linear Synchronous Transit" method implemented in Spartan and the further developed "Synchronous Transit-GuidedQuasi-Newton" method built into Gaussian 94/98.

Reaction paths

When calculating the reaction paths, sets of structures are generated that can be used to visualize reaction processes. In addition, the transition states found are verified in these calculations. The most frequently used method is the IRC calculation (IRC = intrinsic reaction coordinate). An IRC is understood to be an idealized reaction path that always leads with an infinitely small step size on the energetically most favorable (steepest) path from a saddle point on the energy hypersurface to a minimum corresponding to the starting materials or products. In the case of a real reaction, on the other hand, there is always a certain excess of energy when crossing a transition state, which leads to the system oscillating around the most energetically favorable state on its way to the minimum (DRC = dynamic reaction coordinate).

Method

Starting from the transition state, two IRC calculations are carried out, one along the direction given by the imaginary frequency and one opposite to this direction. In order to check whether the calculations have led to the most favorable conformations of the starting materials, products or an intermediate stage, the last of the structures generated in the IRC calculations are compared with those of the optimized target structures. If larger deviations result, either further IRC calculations have to be connected or even new transition states for the necessary conformational changes have to be identified. This must be repeated until the entire path has been calculated.

Literature

Fukui,. (1981):The Path of Chemical Reactions - The IRC Approach. In: Accounts of Chemical Research. 4, 57-64


Video: SN1 Reactions. University Of Surrey (July 2022).


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