Fragmentation and transferability in Hirshfeld atom refinement

Michał Chodkiewicz, Sylwia Pawlȩdzio, Magdalena Woińska, Krzysztof Woźniak

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

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 fragHAR (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 Olex2 combined with a development version of discamb2tsc and ORCA. 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.

Original languageEnglish
Pages (from-to)298-315
Number of pages18
JournalIUCrJ
Volume9
DOIs
StatePublished - Mar 1 2022
Externally publishedYes

Funding

The authors thank the Polish National Science Centre for financial support within OPUS (grant No. 2018/31/B/ST4/ 02142). Calculations were carried out using resources provided by the Wroclaw Centre for Networking and Supercomputing (http://wcss.pl) (grant No. 115). This work was carried out at the Biological and Chemical Research Centre, University of Warsaw, established within the project cofinanced by the European Union from the European Regional Development Fund under the Operational Programme Innovative Economy 2007–2013 and Core Facility for crystallographic and biophysical research to support the development of medicinal products sponsored by the Foundation for Polish Science (FNP).

FundersFunder number
Polish National Science Centre2018/31/B/ST4/ 02142
European Commission
Fundacja na rzecz Nauki Polskiej
European Regional Development Fund
Wroclawskie Centrum Sieciowo-Superkomputerowe, Politechnika Wroclawska115

    Keywords

    • Hirshfeld atom refinement
    • fragmentation
    • quantum crystallography.
    • transferability

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