Does Hinduism describe about the concept of atoms and molecules? If yes, is there any scientific method by which they came to a conclusion?
Atomism was very prominent among early Hindu schools of thought, including the Jain school. From Wikipedia:
References to the concept of atomism and its atoms are found in ancient India and ancient Greece. In the West, atomism emerged in the 5th century BCE with Leucippus and Democritus. In India the Jain, Ajivika and Carvaka schools of atomism may date back to the 4th century BCE. The Nyaya and Vaisheshika schools later developed theories on how atoms combined into more complex objects. Whether Indian culture influenced Greek or vice versa or whether both evolved independently is a matter of dispute.
Most famous for Hindu Atomism was the Indian philosopher Kanada, who observed the fundamental indestructibility of matter and that matter is in two general states, at rest or in motion. He later developed the ideas of dvyanuka and tryanuka ,which would become diatomic and triatomic molecules.