Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions
Paige Bowling, Dustin Broderick, John M. Herbert
Abstract
Electronic structure calculations on enzymes require hundreds of atoms to obtain converged results, but fragment-based approximations offer a cost-effective solution. We present calculations on enzyme models containing 500–600 atoms using the many-body expansion, comparing to benchmarks in which the entire enzyme–substrate complex is described at the same level of density functional theory. When the amino acid fragments contain ionic side chains, the many-body expansion oscillates under vacuum boundary conditions but rapid convergence is restored using low-dielectric boundary conditions. This implies that full-system calculations in the gas phase are inappropriate benchmarks for assessing errors in fragment-based approximations. A three-body protocol retains sub-kilocalorie per mole fidelity with respect to a supersystem calculation, as does a two-body calculation combined with a full-system correction at a low-cost level of theory. These protocols pave the way for application of high-level quantum chemistry to large systems via rigorous, ab initio treatment of many-body polarization.