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Molecular Shapes

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...

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.

Newman Projections

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...

Stereoisomerism of Cyclic Compounds

Stereoisomerism of Cyclic Compounds

In this lesson, we delve into the role of ring conformation and its stability, which determines the spatial arrangement and, consequently, the molecular symmetry and stereoisomerism of cyclic compounds. 1,2-Dimethylcyclohexane is used as a case study to evaluate the possible number of stereoisomers. Here, given the multiple (n = 2) chiral centers, there are 2n = 4 possible configurations that lack a plane of symmetry, as the ring skeleton exists in a non-planar chair conformation. In addition,...

Prochirality

Prochirality

The concept of prochirality leads to the nomenclature of the individual faces of a molecule and plays a crucial role in the enantioselective reaction. It is a concept where two or more achiral molecules react to produce chiral products. A typical process is the reaction of an achiral ketone to generate a chiral alcohol. Here, the achiral reactant reacts with an achiral reducing agent, sodium borohydride, to generate an equimolar mixture of the chiral enantiomers of the product. For example, an...

Two-Dimensional (2D) NMR: Overview

Two-Dimensional (2D) NMR: Overview

The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....

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Updated: May 1, 2026

Interactive Molecular Model Assembly with 3D Printing

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

Two- and three-dimensional rings in drugs.

Matteo Aldeghi¹, Shipra Malhotra, David L Selwood

¹Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK.

Chemical Biology & Drug Design

|January 30, 2014

Summary

3D ring fragments offer diverse structures and shapes crucial for drug discovery, differing significantly from 2D fragments in targeting major drug classes like GPCRs and enzymes.

Keywords:

drug fragment lead optimization ring

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Area of Science:

Medicinal Chemistry
Drug Discovery
Structural Biology

Background:

Flat aromatic rings are standard in fragment-based drug discovery and lead optimization.
Growing interest in three-dimensional (3D) fragments due to novel chemical space exploration and synthetic accessibility.

Purpose of the Study:

To conduct a detailed analysis comparing 3D and 2D ring fragments in marketed drugs.
To investigate the relationship between ring fragment properties (e.g., assembly, shape) and targeted protein classes.

Main Methods:

Analysis of marketed drugs focusing on ring fragment composition.
Evaluation of molecular properties including ring assembly types and molecular shapes.
Correlation of ring fragment characteristics with targeted protein families (e.g., GPCRs, ion channels, enzymes).

Main Results:

Demonstrated high structural and shape diversity within 3D ring systems.
Highlighted the significant importance of 3D ring systems in bioactive compounds.
Identified substantial differences between 2D and 3D fragments in ligands targeting major drug targets.

Conclusions:

3D ring fragments possess considerable structural and shape diversity, essential for bioactive compound development.
Significant distinctions exist in the application of 2D versus 3D fragments for targeting key protein classes like GPCRs, ion channels, and enzymes.