Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

Proc Natl Acad Sci U S A. 2004 May 4;101(18):6946-51. doi: 10.1073/pnas.0307578101. Epub 2004 Apr 26.


Hydrogen bonding is a key contributor to the exquisite specificity of the interactions within and between biological macromolecules, and hence accurate modeling of such interactions requires an accurate description of hydrogen bonding energetics. Here we investigate the orientation and distance dependence of hydrogen bonding energetics by combining two quite disparate but complementary approaches: quantum mechanical electronic structure calculations and protein structural analysis. We find a remarkable agreement between the energy landscapes obtained from the electronic structure calculations and the distributions of hydrogen bond geometries observed in protein structures. In contrast, molecular mechanics force fields commonly used for biomolecular simulations do not consistently exhibit close correspondence to either quantum mechanical calculations or experimentally observed hydrogen bonding geometries. These results suggest a route to improved energy functions for biological macromolecules that combines the generality of quantum mechanical electronic structure calculations with the accurate context dependence implicit in protein structural analysis.

Publication types

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

MeSH terms

  • Amino Acids / metabolism
  • Hydrogen Bonding
  • Protein Structure, Secondary*
  • Protein Structure, Tertiary*
  • Proteins / chemistry*
  • Proteins / metabolism
  • Quantum Theory*


  • Amino Acids
  • Proteins