7. How can I simulate a reaction?

The way to set up reactions is by using selections, Setup/Set Velocity and checking Restart in the MD dialog box. Of course you also have to be using a semi-empirical QM method that can handle the system you want to simulate! Thus to set up an SN2 reaction:

1. Set up the initial geometry. Create the methyl chloride molecule and a chlorine atom. Use Edit/Translate, Edit/Rotate and/or Edit/Align Molecules to position them. For instance draw and build methyl chloride, use Align Molecules to align the primary axis with the X axis. Select the carbon and translate it to the origin (assuming whole molecule translation is on in the Tool Preferences dialog box). Then draw the chlorine atom, select it and translate it to -8,0,0. Clear the selection.

2. Choose the calculation options. Set up the semi-empirical options (eg. PM3, charge -1, singlet) and do a single point calculation to make sure all is okay.

3. Define the initial velocities to cause a collision. Select the carbon and use Select/Name Selection to name it as POINT. Clear the selection and then select the isolated chlorine atom. Use Setup/Set Velocity and choose At POINT for direction and 50 for the velocity. Clear the selection.

4. "Fix" the display. To have sphere intersections calculated correctly, draw bonds wherever you think spheres will intersect during the reaction. In this case connect both chlorine atoms to all hydrogens and the carbon. Change to CPK rendering (and perhaps adjust the view.

5. Run dynamics and save snapshots. Use Compute/Molecular Dynamics and choose: Heat time 0, Run time 0.5, Cool time 0, Step size 0.0005 ps, temperature 300, *no* Constant temperature, data collection period 1, screen refresh period 1, and check Restart. Click on Snapshots... and type sn2.hin for the file name (or equivalent but be sure to use hin as the extension!). Then run the simulation! You can Cancel it after the reaction has proceeded as far as you want to follow it.

6. Play back the simulation. Open sn2.hin and it should warn you that modifying the system will cause snapshot data to be lost. You can play back the simulation by checking Playback in the MD dialog box (use Snapshots to choose a subset of of the trajectory).

Obviously there are lots of variables you can play with: initial velocity, "target" location (perhaps off-centre), collection periods, etc.

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