Can you artificially create molecules with a machine?
This sounds to me like molecular beam chemistry. Within a vacuum chamber, you can create and collimate a focused "beam" of moving atoms or molecules and direct it to hit a stationary target or another beam. You can use spectroscopy to study the species that are formed. The idea is to look for and characterize reactive intermediates or transition states between starting materials and products. But if you were to create a familiar species such as water in this manner, it is not "artificial" water, but the real thing.

Maybe there is a physical chemist out there that can elaborate further on molecular beams.