Related Experiment Video
Updated: Aug 14, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
Published on: December 1, 2020
How do density functionals affect the Hirshfeld atom refinement?
Bruno Landeros-Rivera1, David Ramírez-Palma2, Fernando Cortés-Guzmán3
1CNRS, UMR 7616, Laboratoire de Chimie Théorique, Paris, France. brunolanderos@hotmail.com.
The amount of Hartree-Fock (HF) exchange in density functionals significantly impacts hydrogen atom refinement in Hirshfeld atom refinement (HAR), but not non-hydrogen bonds. Optimal HF exchange for HAR differs from standard quantum chemistry calculations.
Area of Science:
- Computational chemistry
- Quantum crystallography
- Materials science
Background:
- Hybrid density functionals are widely used in computational chemistry.
- Hirshfeld atom refinement (HAR) is a method for determining molecular structures.
- The influence of Hartree-Fock (HF) exchange on HAR is not well understood.
Purpose of the Study:
- To investigate the effect of varying Hartree-Fock (HF) exchange in hybrid density functionals on the Hirshfeld atom refinement (HAR) of urea and oxalic acid dihydrate.
- To explore the impact of different basis sets, computational methods (MP2, HF), and cluster sizes on HAR results.
- To compare HAR outcomes with neutron diffraction data.
Main Methods:
- Application of hybrid density functionals with varying HF exchange percentages.
- Hirshfeld atom refinement (HAR) on urea and oxalic acid dihydrate.
- Utilizing different basis sets, MP2 and HF methods, and cluster sizes for bulk effect modeling.
Main Results:
- The amount of HF exchange primarily affects the refinement parameters of hydrogen atoms.
- Unlike geometry optimizations, optimal HF exchange mixtures for HAR do not necessarily yield the best agreement with neutron diffraction.
- Non-hydrogen bond lengths are insensitive to method or basis set, while X-H bond lengths increase with HF exchange.
- Thermal ellipsoids tend to shrink with increasing HF exchange, particularly for hydrogen atoms in strong hydrogen bonds.
Conclusions:
- The optimal computational parameters for quantum crystallography via HAR may differ from those used in standard quantum chemistry calculations.
- Development of density functionals and basis sets for quantum crystallography might require a distinct approach.
- Findings suggest a divergence in computational strategies for accurate structural refinement versus electronic property prediction.
Related Concept Videos
Crystal Field Theory - Tetrahedral and Square Planar Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
Molecular Orbital Theory II
Crystal Field Theory - Octahedral Complexes
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
Atomic Orbitals
The Energies of Atomic Orbitals
Hybridization of Atomic Orbitals I

