All organisms are collection of molecules working in an impressive coordinated manner. What are the magical chemistry behind these molecules which made them to associate with each other and undergo darwinism? What made these molecules different from others which still continue to consist lifeless stuff?

your question which is an excellent one, relates to the concept of abiogenesis. If you search this site (top right hand box) or google you will find a goodly amount of relevant information. The bottom line (of course) is we don't know for sure!