Journal
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
Volume -, Issue -, Pages 3826-3834Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpclett.3c00533
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Electronic structure calculations on enzymes with hundreds of atoms can be costly, but fragment-based approximations provide a cost-effective solution. The many-body expansion method allows calculations on enzyme models with 500-600 atoms and compares well with benchmarks. Different boundary conditions can affect the convergence of the calculations, highlighting the need for appropriate assessments of errors in fragment-based approximations. Protocols involving three-body or two-body calculations combined with a full-system correction offer accurate results at a lower computational cost, making high-level quantum chemistry applicable to large systems.
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.
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