Abstract
Basis set superposition error (BSSE) is a significant contributor to errors in quantum-based energy functions, especially for large chemical systems with many molecular contacts such as folded proteins and protein-ligand complexes. While the counterpoise method has become a standard procedure for correcting intermolecular BSSE, most current approaches to correcting intramolecular BSSE are simply fragment-based analogues of the counterpoise method which require many (two times the number of fragments) additional quantum calculations in their application. We propose that magnitudes of both forms of BSSE can be quickly estimated by dividing a system into interacting fragments, estimating each fragment's contribution to the overall BSSE with a simple statistical model, and then propagating these errors throughout the entire system. Such a method requires no additional quantum calculations, but rather only an analysis of the system's interacting fragments. The method is described herein and is applied to a protein-ligand system, a small helical protein, and a set of native and decoy protein folds.
Highlights
The application of quantum chemistry to large molecular systems is a challenging endeavor that is complicated by several factors
Since Basis set superposition error (BSSE) has a strong dependence on the geometric orientation of two interacting fragments, we introduce a simple geometry-dependent model to estimate fragment contributions to BSSE rather than a Gaussian pdf
These fragment-based BSSE estimations can be propagated over a large biomolecule or complex to estimate inter- or intramolecular BSSE
Summary
The application of quantum chemistry to large molecular systems is a challenging endeavor that is complicated by several factors. Large molecular systems contain many different types of chemical interactions, all of which need to be accurately modeled by the energy function in order to reliably estimate the energy of the composite system.. The overall system is broken down into molecular fragments (or in some cases individual atoms14) which are analyzed with and without neighboring basis functions to estimate the energy differences due to IBSSE. These methods (with the exception of the atom-based method) require input from the user about how to fragment the overall system, which is non-unique. By using the fragment BSSE data as a reference set, we can predict systematic and random errors due to BSSE
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