Non-covalent interactions play an important role in structure and reactivity of biological molecules. The large size of the molecules as well as the complexity and diversity of biochemical pathways makes biological processes challenging for quantum chemistry. Ab-initio based fragmentation approaches, such as fragment molecular orbital (FMO) and effective fragment potential (EFP) methods offer a viable alternative to conventional quantum chemistry methods, enabling modeling of non-covalent interactions in large systems, while retaining comparable accuracy. Natural partitioning of the interaction energy into Coulomb, polarization, dispersion, and exchange-repulsion terms make them an attractive choice for analysis and interpretation of intermolecular forces. The application of these methods for the investigation of non-covalent interactions in amide-stacked conformations of γ-peptides, hydrogen bonding and staking in DNA bases, and ligand binding to DNA is presented. The non-covalent contributions to the stabilization of such conformations of γ-peptides, DNA bases stacks, and binding affinities of ligands to DNA have been determined.

Modeling non-covalent interactions in biomolecules: An ab initio based fragmentation approach

249th National Meeting (2015)

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