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

Determination of Crystal Structures01:29

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
2D NMR: Overview of Heteronuclear Correlation Techniques01:18

2D NMR: Overview of Heteronuclear Correlation Techniques

Heteronuclear correlation spectroscopy is an analytical technique that investigates the coupling between different types of nuclei, often a proton and an X-nucleus, such as carbon-13 or nitrogen-15. This method is commonly used in nuclear magnetic resonance (NMR) spectroscopy to gain insights into complex chemical compounds' structural and compositional aspects. A typical heteronuclear correlation spectrum displays X-nucleus chemical shifts on one axis and a proton spectrum on the other axis.

You might also read

Related Articles

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

Sort by
Same author

Updating direct methods VI. The extended use of the information contained in the Patterson map.

Acta crystallographica. Section D, Structural biology·2026
Same author

MD Simulations of Human Sigma-1 Receptor Trimer Uncover Cholesterol-Dependent Stabilization and Ligand-Specific Dynamics.

Journal of chemical information and modeling·2026
Same author

Atherogenic Index of Plasma Relationship with Cardiovascular Risk Factors and Frailty and Value as Determinant of Mortality in Elderly Patients with Severe Aortic Stenosis.

Metabolites·2026
Same author

From Genome Inspection to Precision Agrochemicals: A Structure-Based Antivirulence Roadmap for Sustainable Crop Protection against <i>Xylella fastidiosa</i>.

Journal of agricultural and food chemistry·2026
Same author

Unveiling the fate of lipid crystalline structures in engineered emulsions during in vitro digestion.

Food chemistry·2026
Same author

Integrative Structural Characterization of <i>Candida glabrata</i> Phosphoglycerate Kinase by Small-Angle X‑ray Scattering and AlphaFold: Implications for Therapeutic Targeting in Candidiasis.

ACS omega·2026

Related Experiment Video

Updated: Jun 7, 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

New computational tools for H/D determination in macromolecular structures from neutron data.

Dritan Siliqi1, Rocco Caliandro, Benedetta Carrozzini

  • 1Institute of Crystallography, CNR, Via G. Amendola 122/O, 70126 Bari, Italy. dritan.siliqi@ic.cnr.it

Acta Crystallographica. Section D, Biological Crystallography
|November 3, 2010
PubMed
Summary

Two new computational methods, n-FreeLunch and DNDM-NDM, accurately determine hydrogen and deuterium positions in macromolecular structures using neutron density maps, especially in ambiguous cases.

More Related Videos

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water
08:48

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

Published on: April 28, 2022

Studying Soft-matter and Biological Systems over a Wide Length-scale from Nanometer and Micrometer Sizes at the Small-angle Neutron Diffractometer KWS-2
11:27

Studying Soft-matter and Biological Systems over a Wide Length-scale from Nanometer and Micrometer Sizes at the Small-angle Neutron Diffractometer KWS-2

Published on: December 8, 2016

Related Experiment Videos

Last Updated: Jun 7, 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

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water
08:48

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

Published on: April 28, 2022

Studying Soft-matter and Biological Systems over a Wide Length-scale from Nanometer and Micrometer Sizes at the Small-angle Neutron Diffractometer KWS-2
11:27

Studying Soft-matter and Biological Systems over a Wide Length-scale from Nanometer and Micrometer Sizes at the Small-angle Neutron Diffractometer KWS-2

Published on: December 8, 2016

Area of Science:

  • Structural biology
  • Computational crystallography
  • Neutron scattering

Background:

  • Accurate determination of hydrogen and deuterium positions is crucial for understanding macromolecular structure and function.
  • Existing X-ray crystallography methods have limitations in resolving light atom positions in neutron density maps.
  • Ambiguities in geometrically predicted hydrogen/deuterium positions necessitate advanced computational approaches.

Purpose of the Study:

  • To develop and validate novel computational methods for precise hydrogen and deuterium localization in macromolecular structures.
  • To leverage neutron density maps for improved atomic resolution in structural studies.
  • To address challenges in determining light atom positions, particularly in cases of geometric ambiguity.

Main Methods:

  • Development of n-FreeLunch, an adaptation of the FreeLunch procedure for neutron crystallography.
  • Implementation of DNDM-NDM, combining difference electron density modification (DEDM) and electron density modification (EDM) for neutron data.
  • Testing and validation of both methods using neutron density map information.

Main Results:

  • Successful application of n-FreeLunch and DNDM-NDM in determining hydrogen and deuterium atom positions.
  • Demonstration of the complementary nature of the two developed methods.
  • Effective resolution of ambiguous hydrogen and deuterium site occupancies in neutron density maps.

Conclusions:

  • n-FreeLunch and DNDM-NDM are effective computational tools for hydrogen and deuterium site determination in neutron crystallography.
  • These methods enhance the accuracy of macromolecular structure determination by precisely locating light atoms.
  • The developed techniques offer significant advancements for structural biology research utilizing neutron diffraction data.