Geometry Optimization

Reaction coordinate scans are the simplest procedures when starting to model a chemical reaction in computational chemistry. Allows exploring the potential energy surface (PES) associated with the reaction of interest. It basically consists of dragging one or more atoms so that chemical bonds are broken and formed, transforming reactants into products. In EasyHybrid this procedure is done by applying a harmonic restraint potential so that, at each increment of distance attributed to the atoms of the reaction coordinate, the system is relaxed, avoiding undue collisions.

On the main toolbar, this is the icon that represents Reaction Coordinate Scans (either in one or two dimensions).

In EasyHybrid, the reaction coordinate scans can also be performed by accessing:

Main Menu > Simulate > XXX

An overview of the window for calculating Reaction coordinate scan can be seen in Figure 1.

Chair

Twisted boat

Reaction Coordinates

The selection of atoms that will compose the reaction coordinate 'r' must be done by importing the information of atoms selected using the picking mode, using the 'Importing from Picking Selection' button. As a distance criterion, we have two options:

Simple distance - This is the simplest definition of the reaction coordinate, based on the distance between two selected atoms, #1 and #2 (Figure 2).

r = d(#1 - #2)

If the step size used is a positive value, the distance between atoms will increase at each scan step. In this case, the harmonic potential restraint applies only to the simple distance between atoms #1 and #2.

Figure 1: Reaction Coordinate Scan window overview. The window is divided into three sections: 1) assignment of the first reaction coordinate, 2) assignment of the second reaction coordinate (this is optional), and finally, 3) configuration of the geometry optimization parameters and storage of the generated trajectories.

Multiple distances - This reaction coordinate is defined by a combination of distances obtained from the selection of three atoms, #1, #2, and #3, as shown in Figure 3. In this case, the reaction coordinate is:

After defining which atoms will be part of the reaction coordinate, the user must also define:

Step Size: It represents the increment of distance, measured in angstroms, that will be applied during the propagation of the reaction coordinate.
Number of Steps: This indicates the total number of steps that will be performed. For a simple distance-based reaction coordinate, the product of the number of steps and the step size equals the final distance between the two selected atoms.
Force Constant: This value corresponds to the force associated with the harmonic restraint potential, measured in newtons per mole.
Initial Distance: It denotes the initial distance, measured in angstroms, obtained from the coordinates of the selected atoms and how the reaction coordinate is defined.