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

Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Molecular Shapes01:18

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
MO Theory and Covalent Bonding02:40

MO Theory and Covalent Bonding

The molecular orbital theory describes the distribution of electrons in molecules in a manner similar to the distribution of electrons in atomic orbitals. The region of space in which a valence electron in a molecule is likely to be found is called a molecular orbital. Mathematically, the linear combination of atomic orbitals (LCAO) generates molecular orbitals. Combinations of in-phase atomic orbital wave functions result in regions with a high probability of electron density, while...
Lewis Structures of Molecular Compounds and Polyatomic Ions02:54

Lewis Structures of Molecular Compounds and Polyatomic Ions

To draw Lewis structures for complicated molecules and molecular ions, it is helpful to follow a step-by-step procedure as outlined:
Molecular Comparison of Gases, Liquids, and Solids02:26

Molecular Comparison of Gases, Liquids, and Solids

Particles in a solid are tightly packed together (fixed shape) and often arranged in a regular pattern; in a liquid, they are close together with no regular arrangement (no fixed shape); in a gas, they are far apart with no regular arrangement (no fixed shape). Particles in a solid vibrate about fixed positions (cannot flow) and do not generally move in relation to one another; in a liquid, they move past each other (can flow) but remain in essentially constant contact; in a gas, they move...

You might also read

Related Articles

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

Sort by
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 author

Benchmarking quantum chemical methods with X-ray structures via structure-specific restraints.

IUCrJ·2025
Same author

Nonclassical Zwitterions as a Design Principle to Reduce Lipophilicity without Impacting Permeability.

Journal of medicinal chemistry·2024
Same author

Photochemical C(<i>sp</i>)-C(<i>sp</i><sup>2</sup>) Bond Activation in Phosphaalkynes: A New Route to Reactive Terminal Cyaphido Complexes L<sub></sub>M-C≡P.

Journal of the American Chemical Society·2021
Same author

On modelling disordered crystal structures through restraints from molecule-in-cluster computations, and distinguishing static and dynamic disorder.

IUCrJ·2021

Related Experiment Video

Updated: May 23, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

MoleCoolQt - a molecule viewer for charge-density research.

Christian B Hübschle1, Birger Dittrich

  • 1Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Germany.

Journal of Applied Crystallography
|April 6, 2012
PubMed
Summary

MoleCoolQt is a molecule viewer for charge-density research, aiding in visualizing atomic coordinate systems and topological analysis. It simplifies multipole refinement and supports various file formats for enhanced crystallographic analysis.

More Related Videos

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Related Experiment Videos

Last Updated: May 23, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

  • Crystallography
  • Computational Chemistry
  • Materials Science

Background:

  • Accurate visualization of molecular structures and charge density is crucial for understanding chemical bonding and material properties.
  • Existing tools may lack comprehensive features for multipole refinement and topological analysis.
  • Efficiently handling complex crystallographic data requires specialized software.

Purpose of the Study:

  • To introduce MoleCoolQt, a novel molecule viewer designed for charge-density research.
  • To provide advanced visualization capabilities for multipole refinements and topological analysis.
  • To offer an interactive platform for refining atomic coordinate systems and symmetry in crystallographic studies.

Main Methods:

  • Molecule visualization based on the Hansen and Coppens formalism for multipole refinements.
  • Translation of residual peaks and holes from XDfft for proximity to nearest atoms.
  • Visualization of critical points from charge density topological analysis.
  • Generation of color-mapped isosurfaces via a user-friendly interface.
  • Interactive tools for assigning and altering local atomic coordinate systems and symmetry.
  • On-demand calculation of dummy atoms and automatic updating of XD system files.
  • Interactive dialog for resolving scattering factor assignment issues using the invariom database.

Main Results:

  • Molecule viewer facilitates visualization of local atomic coordinate systems in multipole refinements.
  • Residual peaks/holes and topological critical points are visualized effectively.
  • Interactive features simplify the assignment and modification of local atomic coordinate systems and symmetry.
  • Support for multiple crystallographic file formats including XD, MoPro, SHELX, GAUSSIAN, CIF, and PDB.
  • User-friendly graphical interface developed in C++ with Qt4 library.

Conclusions:

  • MoleCoolQt offers a comprehensive solution for charge-density research, enhancing visualization and analysis.
  • The software streamlines complex crystallographic tasks, including multipole refinement and topological analysis.
  • Its interactive features and broad file format support make it a valuable tool for crystallographers.