Parameterization of the DFTB3 method for Br, Ca, Cl, F, I, K, and Na in organic and biological systems

J Chem Theory Comput. 2015 Jan 13;11(1):332-42. doi: 10.1021/ct5009137.


We present an extension to the recent 3OB parametrization of the Density Functional Tight Binding Model DFTB31,2 for biological and organic systems. Parameters for the halogens F, Cl, Br, and I have been developed for use in covalently bound systems and benchmarked on a test set of 106 molecules (the ‘OrgX’ set), using bonding distances, bonding angles, atomization energies, and vibrational frequencies to assess the performance of the parameters. Additional testing has been done with the X40 set of 40 supramolecular systems containing halogens,3 adding a simple correction for the halogen bonds that are strongly overbound in DFTB3. Furthermore, parameters for Ca, K, and Na as counterions in biological systems have been created. To benchmark geometries as well as ligand binding energies a test set ‘BioMe’ of 210 molecules has been created that cover coordination to various functional groups frequently occurring in biological systems. The new DFTB3/3OB parameter set outperforms DFT calculations with a double-ζ basis set in terms of energies and can reproduce DFT geometries, with some minor deviations in bond distances and angles due to the use of a minimal basis set.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Products / chemistry*
  • Calcium / chemistry*
  • Halogens / chemistry*
  • Metals, Alkali / chemistry*
  • Organic Chemicals / chemistry*
  • Quantum Theory*


  • Biological Products
  • Halogens
  • Metals, Alkali
  • Organic Chemicals
  • Calcium