Natural bond orbital analysis in the ONETEP code: applications to large protein systems.
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 post-processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis-type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large-scale calculations with the ONETEP linear-scaling 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 long-range electronic effects from the entire system. We show that by transforming the Non-orthogonal 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 drug-receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones.
TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom. lpl24@cam.ac.uk
Louis P
LP
Lee
Daniel J
DJ
Cole
Mike C
MC
Payne
Chris-Kriton
CK
Skylaris
D005559:Formamides / Q000737:chemistry; D008744:Methylamines / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D014867:Water / Q000737:chemistry
D005559:Formamides; D008744:Methylamines; D011506:Proteins; D014867:Water; C031066:formamide; C027451:methylamine