AtoMag Molecular Models

Organic Chemistry Magnetic Models

Chemistry Magnetic Models

Methods of teaching organic chemistry may have changed over the years but the basic concepts are still the same.  Molecular models have been used for decades in teaching chemistry & biochemistry to help visualize the relationship of different atoms in chemical structures. With the advent of more powerful computers, many of the dynamic aspects of chemistry can be demonstrated but hand held models still have their place.

Physical models have the advantage of engaging not only ones visual senses but also tactile especially when strong Nd magnets are used as atom to atom bonds. Some of the most important concepts of organic chemistry can be taught with greater speed & clarity than with standard models & computers and are shown below.

Note: the magnetic model kits shown in the videos are not longer available assembled. If you are interested in building them yourself, please contact us.


The concept of handedness is familiar to everyone but the chemistry definition for this, chirality, is less well known to non-scientists. Nevertheless, it is a fundamental characteristic of many important molecules, especially biological ones. The amino acids that make up the proteins in our body, the sugars such as glucose, & the helix of DNA all exhibit handedness. In fact, the consequences of wrong handedness can be disastrous. Thalidomide is a key example. One version of it functions as a sedative while the other causes deformities during fetal development. LSD (lysergic acid diethylamide) is another. One version passes through you with no effect whereas the other interferes with neurotransmitters & causes hallucinations.

AtoMag chirality molecular models
A pair of subsititued methane models to demonstrate chirality.

By simply changing 3 atoms on our magnetic methane model this simple but critical feature of many organic molecules can be demonstrated elegantly & quickly.

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Chair Boat Flips

The chair boat flip is a concept that is taught very early in organic chemistry to convey the importance of steric hindrance.  In other words, the repulsion caused by the crowding of side groups of atoms within a molecule in turn causes the energy of the system to become higher; i.e. the chair conformation has a lower energy state than the boat conformation of the ring.

Cyclohexane Chair, Skew-Boat, Boat Conformations
Magnetic cyclohexane models to demonstrate chair, skew-Boat, boat conformations

The molecule most commonly used to demonstrate this is cyclohexane but it is equally applicable to glucose. The beauty of the magnetic model is that you can actually feel the resistance to change from the chair to boat conformation & as it accurately mimics what happens when an energy source such as light or heat impinges on the molecule.


Alkanes are the most basic of organic compounds & best demonstrate carbon’s ability to form long chains especially as it relates to biological molecules. In addition to long chains many of these carbon compounds also show extensive branching. Learning how to describe these accurately requires a good understanding of IUPAC nomenclature rules.

Organic Chemistry Teaching-Naming Branched Chain Aklanes
Branched chain alkane nomenclature made easy. Magnetic bonds are also extra strong. Hold one atom and dangle at least 16 more below it.

Magnetic molecular models of alkanes are particularly well suited to teaching these naming conventions. All you need do is simply attach or detach a carbon to the end or the side of the chain & you have a new molecule ready to be named.

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Arene Substitution

This is a fairly basic application of magnetic molecular models. The key advantage is that the difference between the ortho/meta/para configurations can be demonstrated very quickly.

Convert from ortho to meta to para conformation in the blink of an eye.

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Surface Chemistry

In addition to organic chemistry, magnetic molecular models can illustrate some of the principles of solid state chemistry, in particular surface chemistry which can involve  metal coating techniques like chemical vapour deposition or the adsorption of water to salt crystals.

NaCl-H2O magnetic model for surface chemistry
Vapor Deposition “Roulette”

By mounting atoms representing sodium, chlorine, oxygen & hydrogen with properly oriented north & south poles, one can demonstrate this very graphically.

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Other Compounds

Magnetic molecular models are especially useful with biological molecules. The enantiomers of glucose lend themselves especially well to this as do the different types of disaccharide bonds (1-4 & 1-6, etc.). Similarly, the many types of saturated & unsaturated cis & trans fatty acids can be quickly converted from one to the other.

Teaching Organic Chemistry Fundamentals with Magnetic Molecular Models
Article Name
Teaching Organic Chemistry Fundamentals with Magnetic Molecular Models
Teaching some of organic chemistry's basic concepts such as chirality & naming of branched chain alkanes can be done more effectively with magnetic molecular models.
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