Abstract

Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree-Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder.

Highlights

  • Ongoing progress in experimental technique development in X-ray crystallography makes this method an excellent tool to observe aspherical electron density deformations that can be attributed to bond formation and other interactions

  • In order to compare the results of the generalized atom refinement (GAR) refinements with the different partitioning schemes, we focused on the structural parameters related to the hydrogen atoms, the lengths of bonds involving hydrogen atoms and hydrogen ADP values, since accurate determination of these with X-ray refinement is more challenging than for heavier atoms

  • The standard deviations for bond lengths from neutron measurements referenced in this work for N—H and O—H bonds lie in the ranges 2–3 and 2.5–6.3 mAfor Hirshfeld atom refinement (HAR) refinement, whereas in the case of C—H bonds in SPAnPS those numbers are 1–5 mAfor neutron data and 3.4– 5.7 mAfor HAR

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Summary

Introduction

Ongoing progress in experimental technique development in X-ray crystallography makes this method an excellent tool to observe aspherical electron density deformations that can be attributed to bond formation and other interactions. The simplest and most popular approach, the only one practically available for many decades is the independent atom model (IAM), which treats the crystal as a set of spherical atomic densities centred on the atomic nuclei. It does not take into account the aspherical nature of atomic electron densities. For this reason, IAM fails to correctly describe those aspects of molecular geometry which are influenced by aspherical electron density deformations, such as the positions and anisotropic displacement parameters of hydrogen atoms.

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