Natural bond orbital analysis in the ONETEP code: applications to large protein systems.
Natural bond orbital analysis in the ONETEP code: applications to large protein systems.
复制标题
ONETEP 代码中的自然键轨道分析：在大型蛋白质系统中的应用。
DOI：
10.1002/jcc.23150
复制
发表时间：
2013
影响因子：
3
通讯作者：
Lee LP
中科院分区：
文献类型：
--
作者：
Lee LP
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 theONETEPlinear‐scaling density functional theory package, which we have interfaced with theNBO5 analysis program. InONETEPcalculations 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 ofONETEPto 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, then→ π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.
