Advanced reaction coordinate scans

The Reaction Coordinate Scans window (see PES Scans) has two additional modes for more complex reaction coordinates.

Advanced mode (weighted distance list)

Open Simulate > Advanced RC Scans, or check Advanced mode (weighted distance list) at the top of the Reaction Coordinate Scans window (Figure 1). In this mode each reaction coordinate is an arbitrary linear combination of interatomic distances,

RC = Σ wk dk

which is useful for reactions with several bonds forming and breaking at the same time (for example concerted proton transfers or cycloadditions).

• Defining the coordinate: pick two atoms in the 3D view (picking selection) and click Import from Picking Selection: a row with the two atoms (atm1/idx1, atm2/idx2), the weight and the current distance is added to the list. Repeat for every distance. The cells are editable (double-click), so the weights can be changed; select a row and press Delete to remove it.

• Step Size (default 0.1 Å), Number of Steps (default 30), Force Constant (default 4000 kJ mol-1 Å-2) and Initial Distance (the starting value of the combined coordinate) have the same meaning as in the simple mode.

• Reaction Coordinate 2 can be enabled to scan a two-dimensional surface; the Number of CPUs field is enabled for two-dimensional scans.

TS-centered mode

In the simple mode, the option TS-centered mode (scan in both directions from a transition state) starts the scan from a structure near the transition state and scans the coordinate both forward and backward. Each reaction coordinate then has two numbers of steps, F > (forward) and B < (backward), so that the scan covers both sides of the starting structure. This mode is not available in advanced mode.

The remaining parameters (Coordinates, optimization Method, Maximum iterations, RMS Grad. Tolerance, Trajectory Name and Working Folder) are the same as in the simple scans. Export Script writes a Python/pDynamo script that reproduces the scan outside the interface.