diels alder tutorial

The Diels–Alder reaction stands out as one of the most versatile and powerful transformations in organic chemistry. This pericyclic reaction involves the [4+2] cycloaddition of a conjugated diene with an alkene or alkyne—commonly referred to as the dienophile—resulting in the formation of a six-membered ring.

During this reaction, two new carbon–carbon σ-bonds and one carbon–carbon π-bond are formed, while three π-bonds are broken. The net effect is a highly regio- and stereoselective transformation that constructs complex cyclic systems in a single step.

• Step 1: Loading your system into EasyHybrid: File

a) Go to the "File" item on the main menu and select "New".

b) Set your working folder to your custom one. Set the System Type option to "DYFF".

c) Load the coordinate file "diels_alder.mol2".

d) Click "Import System"

• Step 2: Adding the Harmonic Restraints to the system

a) On the toolbar, change the selection mode from "Viewing" to "Picking".

b) Select one of the carbon atoms from the ethylene and the corresponding carbon atom from the butadiene as shown in the figure.

c) Click with the right mouse and select "Add Harmonic Restraint".

d) On the popup tab set the initial distance to 2.8.

e) Click on add.

Afterwards, repeat the process with the other carbon atoms until the system looks like the image below.

• Step 3: Optimize the geometry

a) On the main toolbar, click on the blue "Geometry Optimization" icon.

b) On the popup "Geometry Optimization Window" tab, click on "Run".

c) Click on the "Selection" item on the main menu, then click on "Selections and Restraints".

d) On the popup "Selections" tab, click on right-click on both selections and delete them.

• Step 4: Set the QC theory level

a) On the main toolbar, click on the blue "Quantum Chemistry" icon.

b) On the popup "Quantum Chemistry" tab, adjust the charge, multiplicity and method of the system. For this tutorial we'll use charge 0, multiplicity 1 and the PM6 method.

• Step 5: Configure and run the Reaction Coordinate Scans calculation

a) On the main toolbar, click on the green "Reaction Coordinate Scans" icon.

b) On the popup "Reaction Coordinate Scans" tab, toggle the Reaction Coordinate 2 as shown in the picture below. Both Coordinate Types should be simple distance. If not, toggle "simple distance" on the Coordinate Type option.

c) Using the picking selection mode, pick the RC atoms as shown in the figure below. If everything has gone right the atoms should be the same atoms picked for the Harmonic Restraints on Step 2. On the popup tab, click on "Import from Picking Selection". Repeat this step for RC2.

d) On the popup "Reaction Coordinate Scans" tab, set the step size to -0.1 and the number of steps to 15 in both reaction coordinates.

e) Check if the working folder is still your folder of choice and click "Run". 

• Step 6: Import the data and Analyze

a) On the system header, right-click an select "Import Data".

b) On the popup "Import Data" tab, set the format to pkl folder2d - pDynamo 2D trajectory.

c) Select the folder generated by the scan. Note that, if everything went correctly, EasyHybrid should automatically detect the output.log file associated with the trajectory folder. Click "import".

d) On the main menu, select Analysis then PES Analysis.

e) On the PES Analysis popup, set the reaction path by clicking on the two oposing lower energy spots as shown in the figure below. Then use the scroll bar to change between frames and analyze the reaction.