Running A + BC ==> AB + C

In order to run the reaction you need to start the program and choose the reaction A + BC ==> AB + C


Hit return when you see this screen
 

Click on the A + BC ==> AB + C button and hit return when you see this screen
Click here for detailed instructions for these startup screens


Next you are presented with a dialog which looks like:




For more information about these cases click here


Go dialog

Next machine makes many plots. The plots will be described below. Eventually you are presented with a button labeled "click here to start the trajectories"


You must hit enter or push the button to go on!


Running The Program

Next you get a very complicated looking screen: There are four windows to display the trajectories and many buttons


Let us go through the parts of the screen. First let us consider the various windows. There are four windows labeled "Plot on potential energy surface", "Plot on mass weighted potential energy surface", "animation", "Positions vs time". You can click on each window to bring it forward and watch the plots. Then there are some controls along the top of the screen. We will discuss each part below.


General controls

The Image below shows the general controls


You do not need to use any of the controls to run the program. However, if you click on the buttons you can change how the program performs.


Next it is useful to discuss the plots

Plot on potential energy surface

The first plot is a plot a potential energy surface. Here is a picture of the potential energy surface.


The potential energy surface is a contour plot of the potential energy of the system as a function of r_AB the distance from A to B and r_BC the distance from B to C. The Y axis in the plot is the distance from A to B. The X axis in the plot is the distance from B to C. The reactants are in the upper left of the contour plot; the products are in the lower right of the contour plot. There are contours for E= 9, 15, and 24 kcal/mole. The saddle point is indicated by the red dot. There is also a 45 degree line so you can see whether you have an early or late transition state.

Students sometimes have trouble seeing contour plots of potential energy surfaces. There is a tutorial on contour plots in examples 7G and 8A of R. I. Masel, Kinetics and Catalysis, Wiley 2001. There is also an excel spreadsheet which displays contour plots and allows students to manipulate them. The spreadsheet is available from The wiley website


Trajectories on potential energy surfaces

Here are two trajectories on a potential energy surface.


The trajectories are plots of the A-B and B-C distances versus time when the reactants collide. The black trajectory connects reactants to products so it is a reactive trajectory. The green trajectory goes from the reactants to the transition state and back to the reactants so it is an unreactive trajectory.

There is some other information on the plots of the energy versus time. The additional information includes the date and time in the format day/month/year, the saddle point energy and the collisional energy (i.e. the sum of the kinetic and potential energy for the reactants).


Plot on a mass weighted potential energy surface


There is a subtlety in trajectories on standard potential energy surfaces in that there is some curvature in the trajectories since newton's equation of motion do not separate in r_ab and r_bc coordinates. People use mass weighted coordinates, or the affine transformation to avoid this error. There is a description of the affine transformation in section 8.16 of R. I. Masel, Kinetics and Catalysis, Wiley 2001. We plot the trajectory on mass weighted coordinates in the second window. Once the program is running, you can click anywhere on the window to bring the plot forward.


Animation

We also include an animation of the reaction to help students see the motion. Once the program is running, you can click anywhere on the window to bring the animation forward. Then you can watch the positions of the atoms evolve. Look at the final state. A comes in. Does A scatter away or does C fly away? When does it happen? All of these questions can be answered by looking at the animations.

Positions versus time

Finally we include a plot of the position versus time. Once the program is running, you can click anywhere on the window to bring the animation forward. The plot shows the bond lengths versus time. In the green trajectory, A comes in B and C and eventually C flies away. A discussion of these plots can be found in Chapter 8 of R. I. Masel, Kinetics and Catalysis, Wiley 2001


The ending dialog

After all of the trajectories run you will be presented with a dialog like:


Hit alt-f4 to exit after you are done printing.


There is more information on the ReactMD website.
Click here to visit the ReactMD website

Click here for updates to the documentation

For further information about applications of this program please look in Chapter 9 of R. I. Masel, Principles of Adsorption and Reaction on Solid Surfaces, Wiley 1996 or Chapter 8 of R. I. Masel, Kinetics and Catalysis, Wiley 2001