Diels-Alder Transition State

Usage

The adf.rkf file for this example can be downloaded here:

1. Download DielsAlder_TS.adf.rkf

2. Open the PyOrbb application.

3. Drag the .adf.rkf file to the GUI.

Now the most important interactions will appear. To further study fragment orbitals that interact, the user will want to visualize the orbitals:

4. Select the orbital of interest.

5. Click on the orbital (\(\varphi\)).

Now the PyOrbb viewer window will open with many options for drawing the orbitals.

Once the previous steps have been completed, the user should be able to reproduce the following analysis [1] [2].

Analysis

Diels-Alder cycloadditions are a crucial class of reactions in heterocyclic chemistry, materials chemistry, and total synthesis, and have been extensively studied computationally. In this example, we study the bonding mechanism between the diene, buta-1,3-diene, and the dienophile, ethylene, in the Diels-Alder transition state.

Generally, in pericyclic transition states, two interactions play an important role, namely the normal electron demand (NED) interaction between a filled orbital on the diene and a virtual orbital of the dienophile, and the inverse electron demand (IED), where electrons are donated from a filled orbital on the dienophile to a virtual orbital on the diene. PyOrbb correctly finds both the NED and IED interactions (Figure 9). Additionally, it identifies the Pauli repulsive interaction between the HOMO-1 of the diene and the HOMO of the dienophile, which contributes significantly to the Pauli repulsion term in the EDA computation.

References

[1]

24. Sun, M. V. J. Rocha, T. A. Hamlin, J. Poater, and F. M. Bickelhaupt, “Understanding the differences between iron and palladium in cross-coupling reactions,” Physical Chemistry Chemical Physics 21 (2019): 9651–9664, https://doi.org/10.1039/c8cp07671e.

[2]

Yuman Hordijk, Steven E. Beutick, Xiaobo Sun, Laurens Groot, Tori Gijzen, Jordi Poater, Trevor A. Hamlin, F. Matthias Bickelhaupt, Célia Fonseca Guerra, “PyOrbb – Automated Analyses of Orbital-Interaction Mechanisms” Journal of Computational Chemistry, 2026, e70512, DOI=https://doi.org/10.1002/jcc.70512.