2.11

Molecular Shapes

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Molecules have characteristic shapes that are important for their functions.

Any diatomic molecule, such as molecular oxygen or hydrogen, is always linear.

As the number of atoms increases, the arrangement of electrons around the central atom influences the shape of the molecule, allowing it to bend and form more complex structures.

Negatively charged electron groups repel one another and try to stay as far apart as possible.

For example, in a water molecule, the oxygen atom forms two bonding pairs of electrons with two hydrogen atoms and has two additional pairs of electrons that are not involved in bonding, called lone pairs of electrons.

These two lone pairs push the bonding pairs around the oxygen atom to about 104.5 degrees, where repulsion is lowest, giving the water molecule a bent shape.

Some biological molecules, such as DNA and proteins, may contain anywhere from a few to millions of atoms.

These large biomolecules are stabilized by intermolecular forces, such as hydrogen bonding, or intramolecular forces, like hydrophobic interactions, allowing them to form long chains and rings that fold into three-dimensional shapes.

They also use structure-specific recognition to interact with other molecules.

For example, opiates with active regions that are structurally similar to endorphins can bind to endorphin receptors and relieve pain.

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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 molecule are oriented linearly on opposite sides of the central atom to minimize repulsions, and three electron groups are arranged in a trigonal planar geometry. Four electron groups form a tetrahedron, five electron groups have trigonal bipyramidal geometry, and six groups are oriented octahedrally.

It is important to note that the electron-pair geometry around a central atom is not always the same as its molecular structure. The electron-pair geometry describes all the regions where electrons are located in a molecule, in bonds and lone pairs. The molecular structure describes the location of the atoms in a molecule, not the electrons. This means that the electron-pair geometry is the same as the molecular structure only when there are no lone electron pairs around the central atom.

A lone pair of electrons occupies a larger space than a bonding pair because a lone pair is bound to only one nucleus, but two nuclei share a bonding electron group. Because of this, lone pair–lone pair repulsions are greater than lone pair–bonding pair and bonding pair–bonding pair repulsions.

Part of this text is adapted from Openstax, Chemistry 2e, Section 7.6: Molecular Structure and Polarity.

Reference:

Flowers, P., Theopold, K., Langley, R., Robinson, W. R., Clark, M. A., Douglas, M., Choi, J. Section 7.6: Molecular Structures. In Chemistry 2e. OpenStax. Houston, TX (2019).

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