Importance of model size in quantum mechanical studies of DNA intercalation

J Comput Chem. 2020 May 5;41(12):1175-1184. doi: 10.1002/jcc.26164. Epub 2020 Feb 3.


The convergence of DFT-computed interaction energies with increasing binding site model size was assessed. The data show that while accurate intercalator interaction energies can be derived from binding site models featuring only the flanking nucleotides for uncharged intercalators that bind parallel to the DNA base pairs, errors remain significant even when including distant nucleotides for intercalators that are charged, exhibit groove-binding tails that engage in noncovalent interactions with distant nucleotides, or that bind perpendicular to the DNA base pairs. Consequently, binding site models that include at least three adjacent nucleotides are required to consistently predict converged binding energies. The computationally inexpensive HF-3c method is shown to provide reliable interaction energies and can be routinely applied to such large models.

Keywords: DFT benchmark; biomolecules; noncovalent interactions.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Pairing
  • DNA / chemistry*
  • Density Functional Theory*
  • Models, Molecular
  • Molecular Structure


  • DNA