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Molecular Models

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.

Fischer Projections

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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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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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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.

Molecular Shapes

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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...

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According to the theory of resonance, if two or more Lewis structures with the same arrangement of atoms can be written for a molecule, ion, or radical, the actual distribution of electrons is an average of that shown by the various Lewis structures.
Resonance Structures and Resonance Hybrids
The Lewis structure of a nitrite anion (NO2−) may actually be drawn in two different ways, distinguished by the locations of the N–O and N=O bonds.

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Related Experiment Video

Updated: Jun 10, 2026

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

Generative models for chemical structures.

David White¹, Richard C Wilson

¹Software Technologies Research Group, University of Bamberg, 96047 Bamberg, Germany.

Journal of Chemical Information and Modeling

|July 30, 2010

Summary

This summary is machine-generated.

This study introduces a new generative model for chemical structures using pattern recognition. The model creates novel, valid molecules likely active against a specific biological target.

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Published on: December 25, 2021

Area of Science:

Computational chemistry
Cheminformatics
Drug discovery

Background:

Generative models are crucial for de novo drug design.
Developing models that generate chemically valid and novel structures remains a challenge.

Purpose of the Study:

To develop a generative model for chemical structures using pattern recognition techniques.
To enable ligand-based de novo design of novel molecules.
To ensure the generation of chemically valid molecular structures.

Main Methods:

Utilized pattern recognition techniques to build a statistical model of chemical structure variations.
Employed an implicit hydrogen model to maintain chemical validity.
Implemented a projection method to ensure generated samples map to valid chemical structures.

Main Results:

Successfully constructed a generative model for chemical structures.
Demonstrated the ability to generate novel, structurally similar molecules.
Showcased that seeding the model with active molecules yields new likely active compounds.

Conclusions:

The developed generative model effectively supports ligand-based de novo design.
The method ensures chemical validity of generated molecules.
This approach holds promise for accelerating the discovery of new drug candidates.