Molecular Structure Homepage for First Year Chemistry

Molecular Structure

About this page

This page is dedicated to helping people understand the common geometries in molecular structure, using proteins as examples.

About Geometries

When atoms bond, they arrange in a conformation that will achieve the lowest possible energy. The geometry of the atoms depends both on the nature of the center atom and of the attached atoms. For example, carbon as a center atom tends to have either a tetrahedral, trigonal planar, or linear conformation, depending on the number of multiple bonds. There are a limited number of common conformations due to the fact that there are only a few ways atoms can attach and still remain at relatively low energy.

Angles and distances in a given geometry can vary slightlydepending on atom size and electron interaction. For example, H₂O has an angle of 104.5^o between the hydrogens instead of the expected 109.5^o. When we call two different conformations tetrahedral, in no way do we expect their angles to be identical. At the same time, a knowledgeable person should be able to quickly look at them and recognize them both to be tetrahedral. Really the whole point of knowing the common geometries around an atom is to be able to succinctly describe to someone what the conformation looks like.

Some of the different shapes found in Proteins

Bent
Octahedral
Square Planar
Square Pyramidal
Tetrahedral
Trigonal Bipyramidal
Trigonal Planar
Trigonal Pyramidal

Bent
Both sulfurs of a (2Fe-2S) Ferredoxin are bent. This also is used for electron transport
Bent geometries are really pretty easy to find. One word of caution though, make sure that there would be no hydrogens attached to the center atom. (X-ray diffraction results do not include hydrogens.)

Octahedral
Iron center of hemerythrin An oxygen transport molecule for lower forms of life, worms and molluscs. This iron is always octahedral.
Iron Center of Myoglobin Used for oxygen storage in the tissue The protoporphyrin IX is nearly identical to the same in hemoglobin.

Square Planar
Protoporphyrin IX from hemoglobin Hemoglobin is used for oxygen transport in humans. This is really an incomplete picture, it has a histidine attached to the top.

Square Pyramidal
Protoporphyrin IX and Histidine in hemoglobin Hemoglobin is used for oxygen transport in humans. When it is in this square pyramidal shape it can to pick up an O₂ for transport
Heme-A of Cytochrome-c oxidoreductase. Part of a system that converts O₂ and H⁺ into H₂O in the cell membrane

Tetrahedral
The 4 Iron (Fe) Centers of a (4Fe-4S) Ferredoxin. Used for electron transport. 1blu
The 2 Iron Centers of a (2Fe-2S) Ferredoxin Also used for electron transport
Phosphorus surrounded by 4 oxygen molecules Part of a DNA chain

Trigonal bipyramidal
Iron center of hemerythrin An oxygen transport molecule for lower forms of life, worms and mollusks. This Iron can become octahedral and pick up an O₂

Trigonal Planar
Protoporphyrin IX of hemoglobin Hemoglobin is used for oxygen transport in humans. All around the plane of the protoporphyrin IX there are trigonal planar conformations.

Trigonal Pyramidal
The 4 Sulfur of the (4Fe-4S) Ferredoxin center Used for electron transport Because of the nature of x-ray diffraction, hydrogens do not show up in protein data. So many molecules that might appear to be trigonal pyramidal are in fact tetrahedral.