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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.

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 conformers.

Conformations of Cyclohexane

Conformations of Cyclohexane

Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...

Chair Conformation of Cyclohexane

Chair Conformation of Cyclohexane

The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...

Fischer Projections

Fischer Projections

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...

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...

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Related Experiment Video

Updated: Jun 27, 2026

Controlling the Size, Shape and Stability of Supramolecular Polymers in Water

Controlling the Size, Shape and Stability of Supramolecular Polymers in Water

Published on: August 2, 2012

A multi-scale framework for predicting α-cyclodextrin assembly on polyethylene glycol axles.

Cameron D Smith¹, Chenfeng Ke², Wenlin Zhang¹

¹Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. wenlin.zhang@dartmouth.edu.

|November 8, 2024

Summary

Controlling alpha-cyclodextrin (αCD) distribution on polyethylene glycol (PEG) is key for robust polymer networks. A new multi-scale model predicts αCD assembly, guiding the design of advanced polyrotaxane materials.

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Controlling the Size, Shape and Stability of Supramolecular Polymers in Water

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Synthesis of Monodisperse Cylindrical Nanoparticles via Crystallization-driven Self-assembly of Biodegradable Block Copolymers

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Single-Molecule Diffusion and Assembly on Polymer-Crowded Lipid Membranes

Single-Molecule Diffusion and Assembly on Polymer-Crowded Lipid Membranes

Published on: July 19, 2022

Area of Science:

Polymer Science
Supramolecular Chemistry
Materials Science

Background:

Controlling ring-on-axle distribution is crucial for slide-ring gels and polyrotaxane networks.
Polymer end functionalization influences alpha-cyclodextrin (αCD) coverage on polyethylene glycol (PEG).

Purpose of the Study:

To develop a multi-scale framework for predicting αCD assembly on bare and functionalized PEG.
To establish design rules for polyrotaxane-based materials with tunable mechanical properties.

Main Methods:

Combined all-atom molecular dynamics and 2D umbrella sampling to calculate free energy landscapes.
Developed a kinetic Monte Carlo (kMC) model incorporating predicted free energies and lattice treatments for diffusion.
Simulated αCD threading onto PEG with various end-functionalizing groups.

Main Results:

The model accurately predicts the number and distribution of αCDs on PEG chains.
Predicted effects of chain length, concentration, and threading barrier on polypseudorotaxane supramolecular structure.
Demonstrated the framework's ability to guide the design of polyrotaxane architectures.

Conclusions:

The multi-scale framework provides a powerful tool for understanding and controlling αCD assembly on polymer axles.
This approach facilitates the rational design of advanced polyrotaxane materials with tailored properties.
The methodology is adaptable for exploring diverse polyrotaxane-based network architectures.