Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds

The van der Waals volume is a widely used descriptor in modeling physicochemical properties. However, the calculation of the van der Waals volume (V_vdW) is rather time-consuming, from Bondi group contributions, for a large data set. A new method for calculating van der Waals volume has been developed, based on Bondi radii. The method, termed Atomic and Bond Contributions of van der Waals volume (VABC), is very simple and fast. The only information needed for calculating VABC is atomic contributions and the number of atoms, bonds, and rings. Then, the van der Waals volume (ų/molecule) can be calculated from the following formula:  V_vdW = ∑ all atom  contributions − 5.92N_B − 14.7R_A − 3.8R_NR (N_B is the number of bonds, R_A is the number of aromatic rings, and R_NA is the number of nonaromatic rings). The number of bonds present (N_B) can be simply calculated by N_B = N − 1 + R_A + R_NA (where N is the total number of atoms). A simple Excel spread sheet has been made to calculate van der Waals volumes for a wide range of 677 organic compounds, including 237 drug compounds. The results show that the van der Waals volumes calculated from VABC are equivalent to the computer-calculated van der Waals volumes for organic compounds.