Proteins and organic molecules comprise complex 3D structures responsible for their functions and properties. We analyze the detailed structural mechanisms of proteins and organic molecules using advanced cryogenic electron microscopy (cryo-EM). We also develop related technologies including automated artificial intelligence data collection and analysis for high-resolution and high-precision single particle cryo-EM, electron 3D crystallography and tomography. Our approach thus reveals chemical properties of hydrogen bonds and charges, which are critical in stabilizing structures and fulfilling functions. We also use synchrotron radiation and X-ray free-electron lasers to achieve our goals.