Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, United Kingdom; School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom.
J Comput Chem. 2014 Feb 15;35(5):343-59. doi: 10.1002/jcc.23469. Epub 2013 Oct 29.
Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom-atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom-atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ℓA+ ℓB + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom-atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels are only slightly larger than those calculated at HF/6-31G(d,p) level. This convergence behavior is transferable to the well-known amyloid beta polypeptide Aβ1-42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance.
准确的静电需要使用以原子核为中心的多极矩或远离原子核的额外点电荷。在这里，我们选择前者，并研究先导蛋白 crambin 中原子间静电相互作用的收敛行为。将 crambin 的蛋白质数据库结构中的氨基酸切割成单个氨基酸、二肽或三肽，然后在每一侧用肽键封闭。氨基酸中的原子通过量子化学拓扑学 (QCT) 定义为有限体积电子密度片段。通过使用正则球谐函数的多极展开计算原子间静电能，总相互作用阶数 L=ℓA+ℓB+1=10。基于单个氨基酸计算的 crambin 中所有 15 种可能类型的原子间相互作用的收敛区域中的最小核间距接近从二肽和三肽计算得出的值。在 B3LYP/aug-cc-pVTZ 和 MP2/aug-cc-pVTZ 水平上获得的值仅略大于在 HF/6-31G(d,p)水平上计算的值。这种收敛行为可转移到著名的淀粉样β多肽 Aβ1-42。此外，对于选定的中心原子，还研究了其邻居对其多极矩的影响，以及可以忽略这种影响的距离。最后，随着核间距的增加，Amber 的收敛行为变得更接近 QCT。
