What hydrogenation does is add more hydrogen atoms to fat and oil molecules, making them more saturated and thus increasing their melting temperature. Hydrogenation is frequently used to convert inexpensive vegetable oils to fats as a substitute for expensive animal fats (e.g. margarine replacing butter & vegetable shortening replacing lard).
This in and of itself is not necessarily nutritionally bad (in a few ways it can be nutritionally better for somepeople), however hydrogenation also has a tendency to create trans-bonds in the carbon backbone of the fat molecules instead of the usual cis-bonds. Cis-bonds are flexible, but trans-bonds are rigid and cause the molecule to kink. These rigid and kinked trans-fat molecules have been shown to correlate with a variety of health problems and thus should be avoided or at least minimized in one's diet.
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