No, chromatography does not alter the molecular structure of compounds. Chromatography is simply a method for separating mixtures composed of a variety of compounds.
The mixture in question is dissolved in a solvent. The solvent is then allowed to pass through a membrane which has very small holes. The smallest compounds will pass through this membrane more easily than the larger compounds. The smaller compounds thus travel farther faster than the larger compounds. The mixture ends up being separated by size along the length of the membrane. Scientists can then cut the membrane apart and analyze the different compounds individually to determine what was present in the mixture.
None of the compounds are changed by the process of chromatography; they are merely separated from the mixture according to their physical properties (mostly size but sometimes also charge, depending on the membrane material used).
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