Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

X-ray Crystallography02:18

X-ray Crystallography

25.8K
The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
25.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Silapropofol: Carbon-Silicon Isosterism in a Key Anesthetic Scaffold.

ACS omega·2026
Same author

Linear-scaling aspherical crystallographic refinement of proteins: a case study for crambin and rubredoxin.

IUCrJ·2025
Same author

Role of restraints on hydrogen atoms in Hirshfeld atom refinement: the case of tri-aspartic acid trihydrate.

Acta crystallographica Section B, Structural science, crystal engineering and materials·2025
Same author

SISYPHOS: An automatic procedure for the serial refinement of single-crystal diffraction data in Olex2.

Structural dynamics (Melville, N.Y.)·2025
Same author

Mitochondria-Targeted Benzoxazole-Based Platinum Photosensitizer Complexes: Photophysical Properties and Photocytotoxicity Evaluation Against Breast and Gastric Cancer Cells.

Journal of medicinal chemistry·2025
Same author

Praseodymium in the formal +5 oxidation state.

Nature chemistry·2025
Same journal

Report of high data rate macromolecular crystallography (HDRMX) meeting, 23 July 2025.

Structural dynamics (Melville, N.Y.)·2026
Same journal

Directional sensitivity of the <math><mrow><mrow><msub><mrow><mi>A</mi></mrow> <mrow><mn>1</mn> <mi>g</mi></mrow></msub></mrow></mrow></math> phonon in biaxially strained bismuth heterofilms studied by transient white light reflectivity.

Structural dynamics (Melville, N.Y.)·2026
Same journal

Erratum: "First experiments with ultrashort, circularly polarized soft x-ray pulses at FLASH2" [Struct. Dyn. <b>12</b>, 034301 (2025)].

Structural dynamics (Melville, N.Y.)·2026
Same journal

<sup>13</sup>C NMR as a foundation for machine learning models of polysaccharides.

Structural dynamics (Melville, N.Y.)·2026
Same journal

Bromodomain dimers: A case study of BRD4 and family-wide AlphaFold predictions.

Structural dynamics (Melville, N.Y.)·2026
Same journal

Integrating metabolomics and histopathology: A method for metabolite recovery from fixed tissue specimens.

Structural dynamics (Melville, N.Y.)·2026
See all related articles

Related Experiment Video

Updated: Jan 18, 2026

Microcrystallography of Protein Crystals and In Cellulo Diffraction
09:35

Microcrystallography of Protein Crystals and In Cellulo Diffraction

Published on: July 21, 2017

9.5K

Benchmarking crystal structure refinement: A systematic study on Hirshfeld atom refinement.

Daniel Brüx1, Florian Meurer2, Florian Kleemiss1

  • 1RWTH Aachen University, Institut für Anorganische Chemie, Landoltweg 1a, 52074 Aachen, Germany.

Structural Dynamics (Melville, N.Y.)
|September 12, 2025
PubMed
Summary
This summary is machine-generated.

This study clarifies wavefunction calculation parameters for Hirshfeld atom refinement (HAR). The pure Hartree-Fock method showed superior performance over density functional theory for polar organic molecules.

More Related Videos

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.6K
Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
06:29

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Published on: March 3, 2021

6.0K

Related Experiment Videos

Last Updated: Jan 18, 2026

Microcrystallography of Protein Crystals and In Cellulo Diffraction
09:35

Microcrystallography of Protein Crystals and In Cellulo Diffraction

Published on: July 21, 2017

9.5K
Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.6K
Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
06:29

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Published on: March 3, 2021

6.0K

Area of Science:

  • Crystallography
  • Computational Chemistry
  • Quantum Chemistry

Background:

  • Hirshfeld atom refinement (HAR) is crucial for accurate crystal structure analysis.
  • Conflicting recommendations exist regarding optimal wavefunction calculation parameters for HAR.
  • Amino acid structures provide reliable benchmarks due to high experimental data quality.

Purpose of the Study:

  • To systematically investigate the impact of wavefunction calculation parameters on HAR.
  • To resolve discrepancies in the literature regarding recommended HAR procedures.
  • To provide guidance on selecting appropriate computational methods for HAR.

Main Methods:

  • Employed a comprehensive permutation of refinement parameters (2496 refinements per amino acid).
  • Utilized high-quality amino acid crystal structures as test cases.
  • Compared gas-phase calculations with solvent models and various quantum chemical methods.

Main Results:

  • Solvent models consistently improved HAR results compared to gas-phase calculations.
  • The pure Hartree-Fock method outperformed all tested density functional theory (DFT) methods.
  • Performance differences were observed across various tested parameters and structures.

Conclusions:

  • Careful selection of the level of theory is critical for successful HAR.
  • The pure Hartree-Fock method is recommended over tested DFT methods for polar organic molecules in HAR.
  • This study offers a clear overview of method and parameter performance in HAR.