I still quite like our existing icons, but these look great too and have a more cohesive feel.
Amino acids as a puzzle piece works, but I'm not sure about carbon dioxide as a cloud. I also think we should stay away from chemical representations where possible - connected circles can't be differentiated from each other that well. Finding alternatives for ammonia and carbon dioxide without resorting to chemical diagrams will be pretty tricky.
You should be able to edit the game files to test how these icons work. In the GUI folder you'll find ThriveGeneric.png. Replace the existing icons with your versions at the exact same size and overwrite the file, then you'll have your own icons in the game.