When you get right down to it, molecules are molecules. A man made molecule is the same as a naturally occurring molecule. However, many "vitamins" as they occur in food are really groups of similar molecules, or "complexes." The vitamins in the bottle tend to consist of only one part of the complex and too much of any one molecule can actually be toxic. Hence the warnings about overdosing on Vitamin A or Vitamin D or Vitamin E. Toxicity rarely occurs when the nutrients are derived from food because you are consuming the whole complex of compounds - all of which the body needs.
Vitamins in bottles are truly just supplements.