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In chemistry, geometry generally refers to the spatial relationship of atoms or radicals forming a molecular structure. A good basic example would be the benzene ring that is the basis of the aromatic hydrocarbons. This is a geometric hexagon with the 6 carbon atoms of benzene connected to each other, and each to a hydrogen atom or some other radical.
A more complex configuration is buckminsterfullerine (often called the "buckyball") consisiting of pure carbon as C60 and forming something similar to a geodesic dome.
In any case there is some sort of geometry to all chemical compounds in a sub-microscopic sort of way, and these geometric differences can often make considerable differences in the physical and chemical properties of otherwise similar or nearly identical substances.
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