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Molecular Models02:00

Molecular Models

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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.
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Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
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Newman Projections02:06

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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...
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VSEPR Theory02:37

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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...
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Molecules with Multiple Chiral Centers02:25

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Molecules that possess multiple chiral centers can afford a large number of stereoisomers. For instance, while some molecules like 2-butanol have one chiral center, defined as a tetrahedral carbon atom with four different substituents attached, several molecules like butane-2,3-diol have multiple chiral centers. A simple formula to predict the number of stereoisomers possible for a molecule with n chiral centers is 2n. However, there can be a lower number where some of the stereoisomers are...
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Related Experiment Video

Updated: Mar 6, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces.

Mahendra Awale1, Daniel Probst1, Jean-Louis Reymond1

  • 1Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland.

Journal of Chemical Information and Modeling
|March 21, 2017
PubMed
Summary

webMolCS is a new web interface for visualizing molecules in 3D chemical spaces. It helps analyze molecular relationships based on properties like composition, shape, and substructures.

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Molecular visualization

Background:

  • Chemical space analysis is crucial for understanding large molecule collections.
  • Existing methods may lack intuitive visualization for diverse molecular properties.
  • Visualizing relationships between molecular properties and structures is challenging.

Purpose of the Study:

  • To introduce webMolCS, a novel web-based interface for visualizing molecules in 3D chemical spaces.
  • To enable analysis of up to 5000 user-defined molecules.
  • To facilitate the exploration of structure-property relationships.

Main Methods:

  • Utilized principal component analysis and similarity mapping for 3D chemical space generation.
  • Incorporated six distinct property spaces: molecular quantum numbers (MQN), SMILES fingerprint (SMIfp), atom pair fingerprint (APfp), extended atom pair fingerprint (Xfp), substructure fingerprint (Sfp), and extended connectivity fingerprint (ECfp4).
  • Developed an interactive interface where molecules are represented as spheres, with structures displayed on mouse-over and color-coded based on user-defined criteria.

Main Results:

  • Successfully visualized up to 5000 molecules in multiple 3D chemical spaces.
  • Demonstrated color-coding capabilities for similarity, rank, or user-defined values to highlight structure-property correlations.
  • Provided a user-friendly platform for exploring complex molecular datasets.

Conclusions:

  • webMolCS offers an effective tool for visualizing and analyzing chemical space.
  • The interface aids in understanding relationships between molecular properties and structural similarities.
  • webMolCS is freely accessible, promoting broader use in chemical research.