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

Electronic Structure of Atoms02:28

Electronic Structure of Atoms

21.5K

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...
21.5K
Atomic Orbitals02:44

Atomic Orbitals

34.4K
An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.
34.4K
Hybridization of Atomic Orbitals II03:35

Hybridization of Atomic Orbitals II

36.4K
sp3d and sp3d 2 Hybridization
36.4K
Hybridization of Atomic Orbitals I03:24

Hybridization of Atomic Orbitals I

51.5K
The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
51.5K
Atomic Structure01:17

Atomic Structure

82.5K
The Greek philosopher Democritus proposed that everything on Earth is made up of tiny particles called atomos, Greek for "indivisible," from which the modern term "atom" is derived. In the 19th century, John Dalton proposed the atomic theory that is still largely correct today. He put forth five postulates to explain how atoms made up the world around us. (1) All matter is composed of infinitely small particles or atoms. (2) All atoms of a given element are identical to one...
82.5K
Atomic Structure01:33

Atomic Structure

162.7K
Overview
162.7K

You might also read

Related Articles

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

Sort by
Same author

Oxidovanadium(v) coordination compounds based on 1,5-bis(2-hydroxy-3-methoxybenzylidene)carbohydrazide: from discrete to polymeric assemblies.

RSC advances·2026
Same author

Periodic Hirshfeld Atom Refinement.

The journal of physical chemistry letters·2026
Same author

Stable 1,3,2-Benzodithiazolyl Radicals: Modification of Reactivity, Crystal Packing, and Solid State Magnetic Properties by Fluorination.

ChemistryOpen·2026
Same author

Interplay between geometry, electron density, and polarizability of the controversial drug atoxyl in crystal and biological environments.

RSC advances·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

Cooperative Free Energy: Induced Protein-Protein Interactions and Cooperative Solvation in Ternary Complexes.

Journal of chemical theory and computation·2025
Same journal

Towards light-coupled sample preparation for time-resolved cryoEM studies.

IUCrJ·2026
Same journal

Cryo-EM analysis of cooperative conformational changes in the SARS-CoV-2 spike protein trimer.

IUCrJ·2026
Same journal

Towards time-resolved MicroED grid preparation using mix-and-inject gas dynamic virtual nozzles.

IUCrJ·2026
Same journal

How cryoEM has advanced our understanding of bacteriophages and bacteriocins targeting Clostridioides difficile.

IUCrJ·2026
Same journal

CryoEM structures reveal allosteric regulation of the catalytic activity of the multi-protein human MAT enzyme complexes.

IUCrJ·2026
Same journal

Cryo-EM-guided subtractive optimization of a novel VCP/p97 inhibitor.

IUCrJ·2026
See all related articles

Related Experiment Video

Updated: Apr 22, 2026

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

5.3K

Hirshfeld atom refinement.

Silvia C Capelli1, Hans-Beat Bürgi2, Birger Dittrich3

  • 1Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milan, Italy.

Iucrj
|October 9, 2014
PubMed
Summary
This summary is machine-generated.

This study introduces an enhanced Hirshfeld atom refinement (HAR) method using iterative quantum mechanical calculations. The refined HAR method accurately determines hydrogen atom positions and displacements from X-ray diffraction data, matching neutron diffraction precision.

Keywords:
X-ray structure refinementanisotropic displacement parametersaspherical atom partitioninghydrogen atom modellingquantum mechanical molecular electron densities

More Related Videos

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
13:28

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

Published on: May 16, 2017

51.2K
Subnanometer-resolution Structural Determination of Hemagglutinin from Cryo-electron Tomography of Influenza Viruses
08:19

Subnanometer-resolution Structural Determination of Hemagglutinin from Cryo-electron Tomography of Influenza Viruses

Published on: November 7, 2025

1.0K

Related Experiment Videos

Last Updated: Apr 22, 2026

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

5.3K
High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
13:28

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

Published on: May 16, 2017

51.2K
Subnanometer-resolution Structural Determination of Hemagglutinin from Cryo-electron Tomography of Influenza Viruses
08:19

Subnanometer-resolution Structural Determination of Hemagglutinin from Cryo-electron Tomography of Influenza Viruses

Published on: November 7, 2025

1.0K

Area of Science:

  • Crystallography
  • Quantum Chemistry
  • Materials Science

Background:

  • Hirshfeld atom refinement (HAR) refines structural parameters using X-ray diffraction data and quantum mechanical electron densities.
  • Existing HAR methods lack iterative refinement for improved accuracy.

Purpose of the Study:

  • To enhance the Hirshfeld atom refinement (HAR) method with an iterative procedure.
  • To assess the accuracy of the improved HAR method for determining structural parameters, including hydrogen atoms, from X-ray diffraction data.

Main Methods:

  • Implemented an iterative process involving electron density calculations, Hirshfeld atom scattering factor calculations, and least-squares refinements.
  • Applied the iterative HAR method to X-ray diffraction data of the dipeptide Gly-l-Ala at various temperatures.
  • Compared HAR results with neutron diffraction data.

Main Results:

  • The iterative HAR method accurately determined structural parameters, including hydrogen atom positions and anisotropic displacement parameters (ADPs).
  • Hydrogen bond lengths and ADPs determined by HAR showed high agreement with neutron diffraction data, achieving precision comparable to neutron measurements.
  • The method demonstrated high accuracy, with bond lengths better than 0.009 Å and ADPs better than 0.006 Ų for hydrogen atoms at lower temperatures.

Conclusions:

  • The iterative Hirshfeld atom refinement (HAR) method significantly improves the accuracy of structural determination from X-ray diffraction data.
  • This enhanced HAR technique provides precision for hydrogen atom parameters comparable to neutron diffraction, even with routine X-ray data resolution.