Density derived electrostatic and chemical (DDEC) electron density partitioning

Author:

Louis P. Lee, University of Cambridge

Author:

Daniel J. Cole, University of Cambridge

Atoms-in-molecule electron density partitioning is a useful post-processing analysis tool for computing atomic charges (as well as higher order atomic multipoles) from the total electron density. ONETEP uses the DDEC3 method [1,3] for this purpose, as the computed charges are both chemically meaningful and reproduce the electrostatic potential of the underlying QM calculation. Options are also available for computing Hirshfeld and iterated stockholder atoms (ISA) charges [3,4].

A DDEC3 calculation to partition the electron density and output atomic charges, multipoles and volumes is performed by specifying:

ddec_calculate : T
ddec_multipole : T
ddec_moment : 3

along with the ddec_rcomp block for your system (see below). Iterated stockholder atoms (ISA) partitioning may be performed instead by additionally specifying:

ddec_IH_fraction : 0.00

Classical Hirshfeld partitioning may be performed instead by additionally specifying:

ddec_classical_hirshfeld : T
ddec_IH_fraction : 1.00
ddec_maxit : 1

The reference ion densities for use with DDEC3 are read in from an external library kindly provided by Thomas A. Manz and Nidia Gabaldon Limas (please cite Refs. [1,2]), and are available for download from the ONETEP website:

http://www.onetep.org/pmwiki/uploads/Main/Utilities/ddec_atomic_densities.tar.gz

The paths to the reference densities are specified in the block ddec_rcomp. Specify one core and one total density file for each species in your system (except for hydrogen and helium which do not require a core density file). The example below is for methanol:

%block ddec_rcomp
  H ALL “H_c2.refconf”
  O ALL “O_c2.refconf”
  O CORE “O_c2.coreconf”
  C ALL “C_c2.refconf”
  C CORE “C_c2.coreconf”
%endblock ddec_rcomp

References

For the development of the DDEC method:

\([1]\) T.A. Manz and D.S. Sholl, “Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Non-Periodic Materials,” J. Chem. Theory Comput. 8 (2012) 2844-2867.

\([2]\) T. A. Manz and D. S. Sholl, “Chemically Meaningful Atomic Charges that Reproduce the Electrostatic Potential in Periodic and Nonperiodic Materials”, J. Chem. Theory Comput. 6 (2010) 2455-2468.

And its implementation in ONETEP:

\([3]\) L. P. Lee, N. Gabaldon Limas, D. J. Cole, M. C. Payne, C.-K. Skylaris, T. A. Manz, “Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms”, J. Chem. Theory Comput., 10 (2014) 5377.

\([4]\) L. P. Lee, D. J. Cole, C.-K. Skylaris, W. L. Jorgensen, M. C. Payne, “Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning”, J. Chem. Theory Comput., 9 (2013), 2981.