Data collection techniques used in this study is a library (Library Research) is studying the Quran and studying reading books, journals, textbook, dictionary, and scientific works. To show that the Koran is a guide for mankind, including studying the natural sciences including chemistry, the authors wanted to examine the problem of atoms and molecules based chemistry and the perspective of the Koran which aims to determine the understanding of atoms and molecules according to the concept chemical and Koran, aspects of what is contained in the Koran that can be used as a guide in the learning of atoms and molecules. Atoms and molecules in chemistry teaching in schools is usually not associated with a particular religion of the Qur'an, so as if the atoms and molecules that learning is a science that is separate and has no relations with Al-Quran.
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