This study examined high school chemistry students' understandings of big ideas--matter and energy, how these understandings are related to macro and submicro representations and fine-grained distinguishing characteristics of students' explanations. The study was conducted in the context of computer-based models and model-based assessments. Qualitative analysis, descriptive statistics and a stepwise Regression model was run to examine students' explanations to assessment questions and their relationship to quantitative measures of students' understandings of big ideas. Students' explanations revealed consistent level 1 and 2 understandings for each big idea. When we examined the relationship between explanations and students' understandings of big ideas, the step-wise regression model was statistically significant for matter and energy. At the fine-grained level, students' explanations revealed distinct clusters--knowledge components that students used to construct descriptive and explanatory explanations for each level of understanding. These findings have implications for effective instructional approaches, targeted enactment of computer-based models and understandings of the range of novice chemistry understanding.