Chemical bonding knowledge is fundamental and essential to the understanding of almost every topic in chemistry, but it is very difficult to learn. While many studies have characterized some of the central elements of knowledge of this topic, these elements of knowledge have not been systematically organized. We describe the development and testing of a matrix that represents: (A) a systematic organization of the conceptual knowledge on chemical bonding required at high school level and (B) a tool for representing students' conceptual knowledge of this topic. The matrix contains three strands: the structure of matter at the nanoscopic level, electrostatic interactions between charged entities, and energy aspects related to bonding. In each strand there are hierarchically ordered cells that contain fine grain elements of knowledge. Using various instruments, students' conceptual knowledge of chemical bonding was assessed and mapped onto the matrix, generating graphical representations of their knowledge. New computational and online technologies enable automatic data collection and its analysis. Therefore, we believe that this organization and representation of small grain size elements of knowledge can be useful for the development of a detailed diagnostic tool of knowledge of chemical bonding. (Contains 11 tables and 9 figures.)