Fragmentation and transferability in Hirshfeld atom refinement

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.

X-ray constrained wavefunctions based on Hirshfeld atoms. I. Method and review

“…HAR is particularly significant for molecular biology because hydrogen atoms play such a crucial role in that field, evidenced by the fact that billion-dollar spallation neutron sources have been commissioned in part to detect these atoms (Henderson et al, 2015;Hall-Wilton & Theroine, 2014). In this regard, it is worth mentioning that there have already been recent attempts to extend HAR for use in such macromolecular systems (Malaspina et al, 2019;Bergmann et al, 2020;Chodkiewicz et al, 2022).…”

Accurate crystal structure of ice VI from X-ray diffraction with Hirshfeld atom refinement

“…Such files are then imported into Olex2 and used in the refinement. Details of the implementation are given by Chodkiewicz et al (2022). A density functional method with a B3LYP functional and cc-pVTZ basis set was used for calculation of the electron densities.…”

“…This makes HAR slightly more accurate than the other two methods (at least in the case of smallmolecule structures). Two versions of HAR allow for refinement of structures of disordered crystals (Kleemiss et al, 2021;Chodkiewicz et al, 2022). In this study, a locally developed DiSCaMB version of HAR was used for all HAR refinements (Chodkiewicz et al, 2020).…”

Electron density is not spherical: the many applications of the transferable aspherical atom model

“…The methods based on the molecular wavefunction include Hirshfeld atom refinement (HAR) [18] and the libraries of Extremely Localized Molecular Orbitals (ELMO) [19] . Both approaches are intensively developed and extensively used for the reconstruction of the electron densities and for refinement of crystallographic models, including determination of the hydrogen atom positions [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] .…”