Chodkiewicz Michał, Pawlędzio Sylwia, Woińska Magdalena, Woźniak Krzysztof
Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland.
IUCrJ. 2022 Feb 26;9(Pt 2):298-315. doi: 10.1107/S2052252522000690. eCollection 2022 Mar 1.
Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal-organic systems at the cost of only minor differences in the calculated structural parameters when compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of combined with a development version of and . Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time.
赫希菲尔德原子精修（HAR）是从X射线衍射数据中获取氢原子精确结构参数的最有效方法之一。不幸的是，它的计算成本也相对较高，特别是对于较大的分子，这是由于波函数计算的缘故。在此，一种碎片化方法已被测试作为解决此问题的补救措施。对于较大的有机体系，它在计算时间上有一个数量级的提升，对于金属有机体系则快几倍，而与原始的HAR计算相比，所计算的结构参数仅有微小差异。碎片化方法也被应用于聚合物和无序体系，它为应用HAR时出现的问题提供了一种自然的解决方案。碎片化的概念与可转移非球形原子模型（TAAM）密切相关，并有助于深入了解改进TAAM的可能方法。已经测试了将碎片化与化学相似原子之间的原子密度转移相结合的混合方法。对于涉及碎片化的计算，还引入了对分子间相互作用的有效处理。当在（一种用于多肽的碎片化方法）中作为原始方法的替代方法应用时，它实现了更高效的计算。所有计算均使用本地修改版的 与 和 的开发版相结合进行。通过简单实现负载均衡来有效利用多核处理器的能力，发现这对于降低计算时间非常重要。
