hbond_basicity_predictor.py: Hydrogen Bond Donor Strength and Minimum Detection

The script implements the V_α(r) and V_min methods of Kenny [281] for correlating hydrogen-bond donor and acceptor strengths (association constants) with electrostatic potential (ESP) values. For V_min, local minima determined from a cubic electrostatic potential (ESP) grid around the acceptor atoms is used. The method has been extended to compute the ESP values for halogen bond donors, using a fixed distance that correlates reasonably well with the ESP values obtained by Zou et al [282]. The locations where the ESP values are evaluated are added to each output structure as a dummy atom with the atom property r_user_Kenny_ESP. You can display the values in Maestro—see the Hydrogen Bond Basicity Prediction Panel topic.

The command syntax is as follows:

jaguar run hbond_basicity_predictor.py [options] infile outfile

where infile is a Maestro file that can contain multiple structures, and outfile is the output Maestro file that contains the input structures with the dummy atoms for the ESP values and with the computed property. The script assumes that the input geometries are correct: no attempt is made to optimize them. The job can also be set up and run from Maestro in the Hydrogen Bond Basicity Prediction Panel.

Note: The default r for hydrogen bonds is a lot smaller than its van der Waals radius. The van der Waals radii are used for halogen bonds, so comparison between the H and halogen bonds is not possible.