Methane (CH₄) is a molecule that is a perfect tetrahedron, and so it is commonly said that no isomerism is possible with methane. However, the carbon-hydrogen bonds of methane constantly vibrate and bend, so that on very short timescales an apparent isomerism can be said to exist. But these structures are not energy minima, and so they do not qualify as isomers.

As complexity increases, isomerism induced by rotations about bonds becomes a bigger factor. In ethane (CH₃CH₃), for example, both carbons are approximately tetrahedral. Thus, there are two limiting structures—staggered ethane, in which the carbon-hydrogen bonds are as far apart as possible, and eclipsed ethane, in which the bonds are as close as possible. These two structures are certainly not the same. Perhaps the best view in which to see the difference is a “Newman projection” (named after American chemist Melvin Newman) in which one sights down the carbon-carbon bond and focuses on the positions of the six hydrogens. In a Newman projection, the front carbon is located at the intersection of the bonds to the three attached hydrogen atoms, and the back carbon is an exploded circle, with the attached bonds emanating from the circumference of the circle.

Immediately, questions of energy arise: Which of the two structures is lower in energy and therefore more stable? The staggered form is lower in energy because in the eclipsed form electrons in carbon-hydrogen bonds on the opposite side of the carbon-carbon bond repel each other. The strain that this repulsion creates increases the potential energy of the eclipsed form. The energy difference is not large, about 3 kilocalories per mole (kcal/mol).

If one plots the energy change as ethane rotates around the carbon-carbon bond, another difficulty is revealed. Like the vibrational and rotational “isomers” of methane mentioned above, eclipsed ethane (E) is not even an energy minimum; it is an energy maximum, a transition state between two staggered ethanes (S). Therefore, ethane, like methane, really has only one form.

If substitutions are made in the ethane molecule—for instance, exchanging some of the hydrogen atoms for deuterium atoms to make 1,2-dideuterioethane—isomeric staggered forms become possible. These staggered forms, called “anti” and “gauche,” of 1,2-dideuterioethane are different but are interconverted through rotations around the central carbon-carbon bond and are called “conformational isomers.”

Whether these different ethanes can be separated depends only on the amount of energy necessary to convert one into the other—that is, to rotate the molecule about the carbon-carbon bond. In the case of 1,2-dideuterioethane, the energy barrier separating the conformational isomers is only 3 kcal/mol, far too low to make them separable under normal conditions.

As stated above in the section Constitutional isomers, butane has two constitutional isomers, butane and isobutane. Isobutane has no conformational isomers, but butane is closely analogous to 1,2-dideuterioethane, in that a pair of anti and gauche conformational isomers is possible for that molecule. Because a methyl group (CH₃) is much larger than hydrogen or deuterium, the plot of energy versus rotational angle is more complex for butane than it is for ethane or 1,2-dideuterioethane.

Ring compounds often have a particularly rich set of conformational isomers. By far the most interesting of the ring compounds is cyclohexane (C₆H₁₂), shown here with cyclopropane (C₃H₆).

Planar cyclohexane contains 12 pairs of eclipsed carbon-hydrogen bonds and is destabilized by these eclipsing interactions, or torsional strain. There are other problems with the planar form. In a flat hexagon, the C―C―C angles must be 120°, quite far from the optimum for tetrahedral carbons (usually quoted as approximately 109.5°; in fact, the real optimum value for cyclohexane is about 112°, the C―C―C angle in propane). In any event, the planar form of cyclohexane is severely destabilized by both torsional and angle strain.

Lower-energy forms can be made as the cyclohexane ring distorts from planarity. This distortion involves no more than rotations about carbon-carbon bonds, just as occurs in ethane or any other acyclic alkane. The energy minimum for cyclohexane is the chair form. In the chair form, carbon-hydrogen bonds are nicely staggered, and the C―C―C bond angle is 111.5°, very close indeed to the optimum.

Note that there are two kinds of carbon-hydrogen bonds in chair cyclohexane. One set of six parallel carbon-hydrogen bonds is perpendicular to the surface on which the chair apparently sits (these are the axial bonds). The other set of six is roughly in the plane of the ring (equatorial bonds). All six axial hydrogens are equivalent, as are all six equatorial bonds.

Rotations about carbon-carbon bonds interconvert two equally energetic chair forms. This process is colloquially called a ring “flip.”

The axial hydrogens in one chair become the equatorial hydrogens in the other as the ring “flips” from one chair to the other. An implication of this change is that there is more than one monosubstituted cyclohexane. In methylcyclohexane, for example, there are two conformational isomers, one with the methyl group axial and one with the methyl group equatorial. The two interconvert through ring flipping.

Which isomer is more stable? For the axial methyl isomer the methyl group interacts unfavourably with nearby methylene groups. This destabilizing interaction is not present in the equatorial isomer. Axial methylcyclohexane is less stable (higher energy) than the equatorial isomer by 1.8 kcal/mol.