The preceding description of the operation of a fuel cell is a simplification because it omits one key feature of the reaction between hydrogen and oxygen. Although hydrogen atoms and oxygen atoms will react spontaneously to form water, both hydrogen and oxygen are found (at room temperature) in the molecular forms H2 and O2. These hydrogen and oxygen molecules must split into atoms before the reaction will proceed, but they will not do so spontaneously because of the chemical bond holding each molecule together, even though these bonds are much weaker than the chemical bonds that will bind them together into a water molecule. The energy needed to cause the individual molecules to dissociate into atoms creates an energy barrier called the activation energy that must be overcome before the highly exothermic reaction between the atoms can take place.

One method of splitting the molecules is to raise their temperature. They will start to dissociate rapidly between 800 oC and 1000 oC. A flame or a spark will be hot enough to split sufficient of the molecules to start the reaction, which then generates so much heat spontaneously that it keeps the reaction going until all the hydrogen or oxygen is used up. Some fuel cell designs use high temperatures to encourage the gas molecules to dissociate, but high temperatures bring their own design and materials problems.

The alternative is to use a catalyst. A catalyst is a component that is needed for a reaction to take place but is not actually consumed during the reaction. As such, it is usually used to accelerate a reaction that will otherwise take place slowly. In the case of the fuel cell the best catalyst for low-temperature acceleration of the reaction is metallic platinum. The platinum acts by attracting the hydrogen and oxygen molecules that will preferentially stick to its surface in dissociated form, generating a supply of the atoms needed for the fuel cell reaction to take place. In its presence, the reaction can take place below 100 oC.

Platinum, even though it is only required in small quantities in a fuel cell, is expensive and this helps to elevate the cost of the cells themselves. A key area of fuel cell research is therefore directed at finding cheaper alternatives. Platinum is also very sensitive to impurities in the gaseous reactants that can poison it, rendering it ineffective. Sulfur dioxide is a particular problem and so is carbon monoxide, both of which can find their way into hydrogen generated by the reforming of natural gas or other fuels. This is another reason why alternative catalysts, which are less sensitive to poisoning, are being sought.

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