Whether you know it or not, your question is very broad. I'll try to scratch the surface of it.
How does genetically modified/engineered plants relate to chemistry? The DNA that is modified is a molecule. In modifying it, enzymes and chemicals are used in the process. Usually the outcome is a different enzyme, deactivating an enzyme or adding a protein of some sort to the plant.
Process: I'll talk about older techniques and new ones.
Accumulation selection: People don't usually call this genetically modified. This is selectively crossing plants to get the qualities you want. Sometimes you see the word hybrid used in the process.
Good thing - easy to do, has worked for thousands of years
Bad thing - can not add traits (proteins) that are from plants that are too genetically different
Vegetative Propagation: I throught I'd put this in here because people have been cloning plants for years. This is not usually called genetically modified. Just cut off a branch or root and place it in water (more to it with many plants). Easy to make thousands of clones.
Grafting: I just wanted to be complete, so I put this in here too. By splicing two or more plants together, the plant can exhibit qualities of both/all of the previous. Used a lot in fruit trees. Not genetically modified.
Genetically modified- plants have DNA from other organisims inserted into it. This DNA will pass on to it's viable offspring. Examples: Golden Rice - rice is one of the most eaten grains on this planet. Many malnourished areas of the world have access to rice. Malnourished people are more susceptible to blindness. Golden Rice has beta carotine (the DNA is inserted into it) in it. Flavor savor tomato & lipooxygenase free soybeans.
If you want to learn more about them; do a word search on those examples. There are lots of genetically modified plants.
Technique: Different techniques - here's two quick ones
Put DNA fragment of desired trait into a plasmid (extra-cellular bacterial DNA). Get plasmid into a vector (Agrobacterium tumefaciens). Infect plant with vector. The chemistry involved with this is: isolating the DNA for the gene, cutting into the plasmid (restriction enzymes, buffered solutions, more enzymes - etc), and getting the plasmid to be "taken up" by the vector (pH and salt dependent).
Another technique I've seen, but not done. Get desired DNA. Coat pellets with it. Shoot the pellets into the plant. Some of the DNA will transfer. Agricitus (spelling) of Madison, WI, was doing this technique in the mid 90's.
Lots of info here that if you want a specific answer you can do a search on or just post a more specific question.