Natural bond orbital analysis in the ONETEP code: Applications to large protein systems
Louis P. Lee,^{1}
Daniel J. Cole,^{1}
Mike C. Payne,^{1}
ChrisKriton Skylaris,^{2}
^{1}Theory of Condensed Matter Group, Cavendish Laboratory,
University of Cambridge, Cambridge CB3 0HE, UK
^{2}School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
First principles electronic structure calculations are typically
performed in terms of molecular orbitals (or bands), providing a straightforward
theoretical avenue for approximations of increasing sophistication, but do not
usually provide any qualitative chemical information about the system. We can
derive such information via postprocessing using natural bond orbital (NBO) analysis,
which produces a chemical picture of bonding in terms of localized Lewistype bond
and lone pair orbitals that we can use to understand molecular structure and interactions.
We present NBO analysis of largescale calculations with the ONETEP linearscaling
density functional theory package, which we have interfaced with the NBO 5 analysis
program. In ONETEP calculations involving thousands of atoms, one is typically
interested in particular regions of a nanosystem whilst accounting for longrange
electronic effects from the entire system. We show that by transforming the
Nonorthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals,
NBO analysis can be performed within a localized region in such a way that ensures
the results are identical to an analysis on the full system. We demonstrate the
capabilities of this approach by performing illustrative studies of large proteins 
namely, investigating changes in charge transfer between the heme group of myoglobin
and its ligands with increasing system size and between a protein and its explicit
solvent, estimating the contribution of electronic delocalization to the stabilization
of hydrogen bonds in the binding pocket of a drugreceptor complex, and observing,
in situ, the n>pi* hyperconjugative interactions between carbonyl groups that stabilize
protein backbones.
Journal of Computational Chemistry, 34, 429 (2013)
