Comparison of van der Waals and semiempirical calculations of the molecular volumes of small molecules and proteins.
Molecular volumes for hydrocarbons, amino acids, peptides, and 14 globular proteins were calculated by techniques using van der Waals radii and by semiempirical molecular orbital methods. The resulting values were compared to experimentally determined volumes. The values obtained by methods employing van der Waals radii were found to be up to three times smaller than the experimentally determined values in the case of proteins, 25% smaller than the experimental values for peptides, and up to 50% greater than experimental values for simple hydrocarbons. For the semiempirical calculations, neither the type nor precision of the calculation altered the percentage of the electron density required to reproduce the experimentally observed volumes for any of the different types of molecules tested. For molecules en vacuo, the amount of electron density included was approximately 98.5% of the total calculated value. For solvated molecules, the percentage was closer to 99.5%. From the results of our studies, we conclude that semiempirical techniques are more reliable, less arbitrary, and hence are more accurate for the determination of molecular volumes. The methods by which we employ semiempirical techniques for determination of molecular volume will be described in detail.