The question of how molecules arrange their atoms in space is an important one in chemistry. The way a molecule sits in space affects its chemical properties, such as how it bonds with other molecules.
Conformation refers to the spatial arrangement of the atoms in a molecule. A conformation is defined by the positions of two atoms within the molecule, usually the central atom and the atom attached to one side of it.
There are two main categories of conformations: staggered and eclipsed. Staggered conformations have alternating positions of higher and lower energy, while eclipsed conformations have both atoms in the same state of energy.
The question of which conformation is most stable, or spends more time in equilibrium, is an interesting one that has been studied extensively. Central to this question is determining whether one conformation is higher in energy than the other, or if they are equal in energy.
Chair conformations
Conformational isomerism deals with the spatial arrangement of atoms in a molecule. In cyclohexane chemistry, this refers to how the six carbons in the ring are arranged relative to each other.
There are two major conformational arrangements of cyclohexane rings in molecules. These are called chair conformations, named after the way the ring sits as if it were a chair.
In one conformation, called syn-1,3-dimethylcyclohexane, the two methyl groups (CH3 groups) sit above and below the plane of the ring. In the other conformation, called anti-1,3-dimethylcyclohexane, the two methyl groups sit on opposite sides of the plane of the ring.
Which conformation(s) exist in equilibrium with each other depends on several factors including temperature and pressure.(www.pennstateclimatechange.
Axial conformations
When cyclohexane molecules assume an axial conformation, one carbon atom is oriented perpendicular to the plane of the ring, and one is oriented parallel to the plane of the ring.
The atom that is oriented perpendicular to the ring is referred to as the axial carbon, and the two atoms that are parallel to each other are referred to as the end carbons of the molecule.
When cyclohexane molecules assume an axial conformation, one carbon atom is oriented perpendicular to the plane of the ring, and one is oriented parallel tothe plane ofthe ring. Theatom thatisis referredtoasthe axialcarbon,andthetwoarereferredtoas theeend carbonsofof themolecule. Axial conformations can be in equilibrium with both chair conformations. Cyclohexane rings can switch between these two conformational preferences depending on environmental factors.
Equilibrium between conformations
When there is an equilibrium between two different conformations, the molecule can switch back and forth between the two configurations. This happens when one configuration is more stable than the other.
In the case of cis-1,3-dimethylcyclohexane, both conformations are equally stable. When this happens, the molecule does not settle into one conformation or the other; instead, it moves back and forth between the two.
By studying these molecules in detail using theoretical chemistry methods such as quantum chemistry and molecular dynamics, researchers can determine which of these conformations is most stable. This information can then be used in industrial applications involving these molecules.
Conformational analysis also has applications in research on pharmaceuticals. Some drugs work by binding to a molecule in a particular conformation; determining whether a drug does this depends on knowledge of conformationally dynamic molecules.
Helpful tips
When drawing conformation structures, it is best to always draw the simplest structure possible. More elaborate structures may look nicer, but they do not represent the molecule as accurately as simple ones do.
When drawing cis-1,3-dimethylcyclohexane, only draw six carbon atoms and six hydrogen atoms. Do not add extra bonds or atoms to make it look different than the default shape!
When drawing trans-1,3-dimethylcyclohexane, only draw eight carbon atoms and six hydrogen atoms. Again, do not add extra bonds or atoms to make it look different than the default shape!
Conformations can be categorized into two major groups: rotamers and conformers. Conformers stay in a specific geometry relative to each other, whereas rotamers can twist around each other. Conformers cannot twist around each other, so all of its angles and geometries stay the same.
Use of molecular models
Another way to determine conformational equilibrium is by using molecular models. These models can be 3D models, like atoms glued together to form a molecule, or they can be physically modeled like putting a ball and stick model of the molecule into a jar with water.
Both of these simulations test whether the molecule moves freely or not in liquid. If it does, then the molecule is in equilibrium between two conformations.
Simulations like these are less time consuming than NMR and IR tests, but require more advanced knowledge of chemistry and physics to construct them. They are also more easily fooled by incorrect atom placement or lack of fluidity in the model.
For cis-1,3-dimethylcyclohexane, both 3D and ball and stick models show that both chair conformations are in equilibrium.
Cis-1,3-dimethylcyclohexane chair conformation
The cis conformation is one of the most prevalent conformations in organic chemistry. A conformation is a spatial arrangement of atoms or groups of atoms in a molecule.
This particular conformation is referred to as a chair shape because the molecule rests on two keto groups, similar to a chair with legs and a back. This conformation is in equilibrium with the trans conformation, where the molecule does not have a back and the legs are switched.
The cis-1,3-dimethylcyclohexane exists partially as each conformational isomer, or enantiomer, which are mirror images of each other. Enantiomers cannot coexist due to their lack of symmetry, which makes one of them more stable than the other. In this case, it is theorized that the S(-)-enantiomer is more stable due to its interaction with water.
Cis-1,3-dimethylcyclohexane axial conformation
Cis-1,3-dimethylcyclohexane is a molecule with twelve carbons. It has an odd number of carbons, meaning it has one ring structure. It also has three methyl groups, or CH 3 groups.
The stability of cis-1,3-dimethylcyclohexane is dependent on the interaction between its two distinct chair conformations. The difference between these two conformations is the rotation of the methyl groups around the cyclohexane ring.
In one conformation, the methyl groups face each other, whereas in the other conformation, they do not. This difference in orientation determines whether the molecule is cis or trans; if the molecules are oriented in opposite directions, they are cis. Trans molecules are oriented in the same direction as their counterpart molecule.
What determines the equilibrium?
In this case, the equilibrium is determined by the energy required to convert from one conformation to the other. The more difficult this transition is, the less likely it is that conformational equilibrium will be biased in either direction.
Conformational equilibrium can also be influenced by temperature. As temperature increases, molecular vibrations increase as well. These molecular vibrations can interact with the conformational equilibrium, making one conformation more likely than the other.
When calculating conformational equilibrium for cyclohexane derivatives, you must remember to take into account both internal and external hydrogen bonds. If there are no external hydrogen bonds, then only internal ones must be taken into account when calculating stability of each conformation.
