Potential Energy Surface Scans
Overview
Scan calculations systematically explore the potential energy surface by varying specific geometric parameters while mapping the energy changes along reaction coordinates. This powerful technique is essential for understanding conformational flexibility, identifying transition states, locating energy minima and maxima, and characterizing reaction pathways.
Scans provide crucial insights into molecular behavior by revealing energy barriers, stable conformations, and the energetic cost of structural changes.
Check the Input and Visualizer section for the allowed input types and how to upload the files.
Available Methods
Two distinct scan methodologies are available, each offering different levels of computational accuracy and speed:
1. Relaxed Scan - High Accuracy All geometric parameters except the scanned coordinate are fully optimized at each scan point, providing the most accurate energy profile along the reaction coordinate.
2. Rigid Scan - High Speed Only the specified parameter is systematically varied while all other atomic positions remain frozen, offering rapid exploration of the energy surface.
Modules Available
Three modules are currently available:
DFT - Density Functional Theory (highest accuracy)
GFN2-XTB - Tight-binding semi-empirical method (fast and reasonably accurate)
Hybrid ML model - Fastest and DFT-accurate using machine learning
Rigid Scan Input Fields
Bond Scans:
When performing a bond scan with the Hybrid ML or DFT module, the following inputs are required:
Total charge of the molecule (e.g., 0)
Spin multiplicity = 2S+1 (e.g., 1 for singlet)
Select the basis set family (e.g., Pople style, Ahlrichs)
Select the basis set (e.g., 6-31G, 6-31+G**)
The functional to be used for the scan (e.g., B3LYP, PBE)
The indices of the two atoms forming the bond to be scanned (e.g., 0, 1). Place 0 in Atom 1 Index and 1 in Atom 2 Index to scan the bond between these two atoms.
The starting length of the bond to be scanned (e.g., 1.0)
The ending length of the bond to be scanned (e.g., 2.0)
The number of points to be calculated along the bond length (e.g., 10)
Note
For the “Bond Angle” scan type, the inputs are similar, but you will specify the indices of three atoms, start angle and end angle in degrees, and the number of points to be calculated along the angle.
Similarly, for the “Dihedral Angle” scan type, user will specify the indices of four atoms, start dihedral angle and end dihedral angle in degrees, and the number of points to be calculated along the dihedral angle.
Relaxed Scan Input Fields
Upon selecting the GFN2-XTB module for running relaxed PES scans, following input parameters must be provided:
Total charge of the molecule (e.g., 0)
Spin multiplicity = 2S+1 (e.g., 1 for singlet)
Select the solvent
The indices of the two atoms forming the bond to be scanned (e.g., 0, 1). Place 0 in Atom 1 Index and 1 in Atom 2 Index to scan the bond between these two atoms.
The starting length of the bond to be scanned (e.g., 1.0)
The ending length of the bond to be scanned (e.g., 2.0)
The number of points to be calculated along the bond length (e.g., 10)
When performing a relaxed scan with the DFT module, see the previous section for the bond scan inputs (e.g., charge, multiplicity, basis set, functional). In addition, the following inputs are required in the “Scan Constraints” section:
Bond Scans:
Syntax:
scan
distance 1 2 1.0 1.5 10
Explanation:
Scans the bond between atoms 1 and 2
From 1.0 Å to 1.5 Å
Calculating 10 equally-spaced points
At each point: bond length is fixed, all other coordinates optimize
Bond Angle Scans:
Syntax:
scan
angle 1 2 3 60.0 120.0 10
Explanation:
Scans the angle formed by atoms 1, 2, and 3
From 60° to 120°
Calculating 10 equally-spaced points
At each point: angle is fixed, all other coordinates optimize
Dihedral Angle Scans:
Syntax:
scan
dihedral 1 2 3 4 30.0 150.0 10
Explanation:
Scans the dihedral angle formed by atoms 1, 2, 3, and 4
From 30° to 150°
Calculating 10 equally-spaced points
Warning
The indices of atoms in the scan command start from 1, not 0. Ensure that you provide the correct atom indices as per your molecular structure. The atom indices is visible on the bottom right corner of the visualiser.
Important
For the 2D relaxed scan, the input fields are similar, but you will specify two parameters to be scanned. Then the “Scan Constraints” section will have two sets of inputs for the parameters. The syntax for the 2D relaxed scan is as follows:
scan
distance 1 2 1.0 1.5 10
angle 3 4 5 60.0 120.0 10
This will scan the bond between atoms 1 and 2 while varying the angle formed by atoms 3, 4, and 5. At each point, the bond length is fixed, and the angle is varied, optimizing all other coordinates. The output will provide the energy profile for the scanned parameters.
*This feature is currently under development and will be available soon.*