Reaction Coordinate SCANS
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 > Reaction coordinate scan
An overview of the window for calculating Reaction coordinate scan can be seen in Figure 1.
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.
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 2: Reaction Coordinate Scan based on simple distance restraints. The reaction coordinate is defined by the distances of two selected atoms, #1 and #2.
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:
r = d(#1 - #2) - d(#2 - #3)
where d(#1 - #2) and d(#2 - #3) are the distances between atoms #1 and #2, and #2 and #3, respectively. If the step size is a positive value, the distance between #1 and #2 decreases, and the distance between atoms #2 and #3 increases, resulting in the tendency for the bond between #1 and #2 to break, and the formation of the bond between #2 and #3. In this case, the harmonic potential is restrictive for both distances that constitute the reaction coordinate simultaneously.
It is important to emphasize that this does not characterize a two-dimensional scan, where each distance comprises a dimension, but rather, when dragging the atoms in the defined reaction coordinate, they will be restricted by the two defined distances simultaneously.
Another important detail is that when atoms #1 and #3 have different masses (and therefore different sizes), the use of the 'Apply Mass Weighted Restraints' flag is recommended. This provides weights for the increments of the distances d(#1 - #2) and d(#2 - #3) based, as the name suggests, on the mass of the involved atoms. So, what happens if the masses of #1 and #3 are different, and I choose not to use the indicated flag? Basically, the scan will require more steps to cover a significant range of the reaction coordinate.
Figure 3: Reaction Coordinate Scan based on multiple distance restraints. The reaction coordinate is defined by a combination of distances obtained from the selection of three atoms, #1, #2, and #3.
Multiple distances *4 atoms - Similar as described before to "Multiple distances", but in this case, the reaction coordinate is defined by a combination of distances obtained from the selection of four atoms, #1, #2, #3 and #4, as shown in Figure 4. In this case, the reaction coordinate is:
r = d(#1 - #2) - d(#3 - #4)
where d(#1 - #2) and d(#3 - #4) are the distances between atoms #1 and #2, and #3 and #4, respectively. If the step size is a positive value, the distance between #1 and #2 decreases, and the distance between atoms #3 and #4 increases, resulting in the tendency for the bond between #1 and #2 to break, and the formation of the bond between #2 and #3. In this case, the harmonic potential is restrictive for both distances that constitute the reaction coordinate simultaneously.
Figure 4: Reaction Coordinate Scan based on multiple distance *4 atoms. The reaction coordinate is defined by a combination of distances obtained from the selection of four atoms, #1, #2, #3 and #4.
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.
For a two-dimensional scan, involving two reaction coordinates simultaneously, the user must activate the togglebox 'Reaction Coordinate 2' located on the right side of the window. The choice of this second reaction coordinate is subject to the same parameters and criteria as the first one. However, in this case, our result will not be a one-dimensional energy profile, as in the case of a one-dimensional scan, but rather an n x m matrix, where n and m are the number of steps defined for the first and second reaction coordinates, respectively.
Finally, the user must define parameters for the geometry optimization routine and storage criteria for the generated data. The data generated by the scan is stored in a folder containing coordinate files in the pkl format, traditional for pdynamo, along with log files. For each frame, a pkl file contaning only cordinates is generated (Not to be confused with pkl files which contain the entire system). The default naming is 'frameX.pkl' for one-dimensional scans and 'frameX_Y.pkl' for two-dimensional scans, where X and Y are integers referring to the indices (step number) along the respective reaction coordinates.
Coordinates: These represent the initial coordinates of the systems. It is recommended that they be the same as those used to define the reaction coordinate and initial distance.
Method: This refers to the geometry optimization method that will be used at each scan relaxation step.
Maximum Interactions: This is the maximum number of interactions allowed at each geometry optimization.
RMS Grad. Tolerance: This is the stopping criterion for geometry optimization.
Number of CPUs: It represents the number of processing units available for parallelizing the scanning process. This option is only available for two-dimensional scans.
Trajectory Name: This is the name of the folder that will contain the coordinate trajectories and log files. The program will reject folder names that already exist in the workplace.
Working Folder: This denotes the location where scan data will be generated.