You cannot make the specific compound that is patented, because it is no longer a new compound and someone else has patent protection.
Unless you discover different functional effects for the same compound, if there is no specific compound in the patent, you can make it. After you make it, it will still be considered a new compound and you can publish an article. However, if someone else has been authorized, you can make it. The patent protects such structures but not specific compounds. Then you won't be able to apply for a patent. The things in the article can be regarded as public and owned by everyone, while the patented things are privately owned by others within a certain period of time.
Article 63, paragraph 4 of the Patent Law, “use of relevant patents exclusively for scientific research and experiments” shall not be regarded as infringement of patent rights. Its purpose is to encourage scientific and technological research. However, it is limited to “exclusively” conducting scientific research and scientific experiments, that is, it is limited to scientific research activities that are not for production and operation, and are not for profit.