The PBF Radii File for Jaguar Calculations

The PBF radii file, pbf_radii.ark, determines how van der Waals radii for calculations using the Jaguar PBF solvation module are set according to chemical functional groups. Functional groups are defined in terms of SMARTS patterns (http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html). The file sets radii and solvent accessibility parameters for chosen elements in each SMARTS pattern, using Ark syntax. It is included in the standard data directory, and supersedes the old default.lewis file.

By default (pbf_radii=1), the program obtains a Lewis structure from the Maestro file for the molecule or system, scans the PBF radii file for radius information for each atom and sets radii for relevant atoms, then sets any radii not determined by the PBF radii file according to the atomic section or to the standard default value. Settings for radii not included in the PBF radii file are described in The atomic Section of the Jaguar Input File. If you do not want the atomic radii that determine the dielectric continuum boundary to change according to the chemical environment of the atom (the first shell correction factor), set the solvation keyword isurf to 0 in the gen section. Otherwise, Jaguar alters radii by using the pbf_radii.ark file from the data directory, unless you specify your own file in a PBFRADIIFILE line in the input file, as described in General Description of the Jaguar Input File. If you want Jaguar to determine the Lewis structure from the input coordinates, set pbf_radii=2.

The radius settings in the file pbf_radii.ark (and default.lewis) were optimized for HF and LMP2 solvation calculations in water with Jaguar’s solvation module that included the default correction terms for the cavity and surface area. The molecules used for radius optimization were the molecules containing carbon, hydrogen, oxygen, nitrogen, and sulfur from Reference [221]. All calculations used a 6‑31G** basis set. Geometries were obtained from gas phase optimizations at the HF and LMP2 levels. For both the geometry optimizations and the solvation energy calculations, the LMP2 treatment was restricted to heteroatom pairs.