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 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...
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
VSEPR Theory and the Basic Shapes02:52

VSEPR Theory and the Basic Shapes

Overview of VSEPR Theory
VSEPR Theory02:37

VSEPR Theory

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...
Molecular Orbital Theory II03:51

Molecular Orbital Theory II

Molecular Orbital Energy Diagrams

You might also read

Related Articles

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

Sort by
Same author

Public Health Nursing and Advocacy for Health Equity.

Public health nursing (Boston, Mass.)·2026
Same author

Bioassay protocol metadata annotation: Proposed standards adoption.

SLAS discovery : advancing life sciences R & D·2024
Same author

The Next Frontier of Environmental Unknowns: Substances of Unknown or Variable Composition, Complex Reaction Products, or Biological Materials (UVCBs).

Environmental science & technology·2022
Same author

Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite.

Environmental health perspectives·2021
Same author

Using Machine Learning to Parse Chemical Mixture Descriptions.

ACS omega·2021
Same author

Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite.

Environmental health perspectives·2021
Same journal

OpenStats: how to combine statistics and research data management (RDM) to leverage efficient scientific data analysis by guided statistics.

Journal of cheminformatics·2026
Same journal

Unified heterogeneity-aware benchmark of drug synergy prediction: a cross-study analysis of traditional machine learning and graph deep learning models.

Journal of cheminformatics·2026
Same journal

Count your bits: fingerprint benchmarking to assess broad chemical space representation.

Journal of cheminformatics·2026
Same journal

Sampling out-of-distribution chemical spaces via Bayesian flow.

Journal of cheminformatics·2026
Same journal

Hold on tight: the kinetic profiling of opioid receptor ligands using the CORAL-MD.

Journal of cheminformatics·2026
Same journal

Transformer-accelerated discovery of inhibitors targeting the RpsA<sub>Δ438</sub> deletion in PZA-resistant tuberculosis.

Journal of cheminformatics·2026
See all related articles

Related Experiment Video

Updated: Jun 8, 2026

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Basic primitives for molecular diagram sketching.

Alex M Clark1

  • 1Molecular Materials Informatics, Inc, Montréal, QC, Canada. aclark@molmatinf.com.

Journal of Cheminformatics
|October 7, 2010
PubMed
Summary
This summary is machine-generated.

A new set of molecular sketching primitives was developed to create 2D molecular diagrams efficiently. These operations minimize input, making them ideal for mobile platforms and reducing bandwidth.

More Related Videos

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

3D Printing of Biomolecular Models for Research and Pedagogy
09:17

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

Related Experiment Videos

Last Updated: Jun 8, 2026

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

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

3D Printing of Biomolecular Models for Research and Pedagogy
09:17

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

Area of Science:

  • Computational chemistry
  • Cheminformatics

Background:

  • Developing user-friendly molecular sketching tools is crucial for chemical research and communication.
  • Existing tools often require precise input devices, limiting accessibility on mobile platforms.

Purpose of the Study:

  • To develop a concise set of primitive operations for molecular diagram sketching.
  • To enable the creation of publication-quality 2D molecular coordinates with minimal input bandwidth.
  • To facilitate the design of user interfaces suitable for mobile devices.

Main Methods:

  • A collection of primitive operations for molecular diagram sketching was created.
  • Algorithmic methods for anticipating probable geometries were employed.
  • Template grafting techniques were utilized to reduce input requirements.

Main Results:

  • The developed primitives allow for the construction of 2D molecular coordinates with minimal input.
  • The system requires only a small number of discrete choices for each operation.
  • This approach is particularly suitable for user interfaces on mobile platforms.

Conclusions:

  • The primitive operations offer an efficient method for molecular sketching, especially on resource-constrained devices.
  • The developed algorithms reduce input bandwidth and enable intuitive molecular diagram creation.
  • This work advances the development of accessible cheminformatics tools for modern platforms.