Noncovalent interactions in biochemistry

Authors

  • Kevin E. Riley,

    1. Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico
    Search for more papers by this author
  • Pavel Hobza

    Corresponding author
    1. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
    2. Department of Physical Chemistry, Palacky University, Olomouc, Czech Republic
    • Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
    Search for more papers by this author

Abstract

Noncovalent interactions are known to play a key role in biochemistry. The knowledge of stabilization (relative) energies and their components is very important for understanding the nature of these interactions. Accurate and benchmark data on interaction (relative) energies and structures can be obtained from coupled-cluster with single and double and perturbative triple excitations [CCSD(T)] calculations with extended basis of atomic orbitals or even at the complete basis set limit. These methods cannot be, however, used for systems larger than about 50 atoms. In this contribution, the applicability and performance of various recently introduced wavefunction and density functional methods are examined in detail. It is shown that a very good performance by some of these methods is obtained only by introducing empirical parameters fitted mostly to CCSD(T) benchmark data. Among the methods described, special attention is paid to two techniques. First, the symmetry-adapted perturbation technique that allows obtaining not only accurate values of total interaction energies but also their components. Results of these calculations reveal a key role of dispersion energy in stabilizing the structures of biomolecular systems. Second, the semiempirical quantum chemical parameterized model 6 method (PM6) augmented by empirical terms describing the dispersion and H-bonding energies. The method is suitable for much extended systems having several thousands of atoms and can be thus used, e.g., in the drug design. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 3-17 DOI: 10.1002/wcms.8

Ancillary