Related Experiment Video
Updated: Nov 29, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
Published on: December 1, 2020
Hirshfeld atom like refinement with alternative electron density partitions
Michał Leszek Chodkiewicz1, Magdalena Woińska1, Krzysztof Woźniak1
1Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa, 02-089 Warszawa, Poland.
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.
Related Concept Videos
Atomic Orbitals
Electronic Structure of Atoms
An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum...
The Quantum-Mechanical Model of an Atom
VSEPR Theory
The Aufbau Principle and Hund's Rule
VSEPR Theory and the Basic Shapes

