We investigated students' knowledge constructions of basic quantum chemistry concepts, namely atomic orbitals, the Schrödinger equation, molecular orbitals, hybridization, and chemical bonding. Ausubel's theory of meaningful learning provided the theoretical framework and phenomenography the method of analysis. The semi-structured interview with 19 second-year chemistry students supplied the data. We identified four levels of explanations in the students' answers. In addition, the scientific knowledge claims reflected three main levels of models. By combining levels of explanations with levels of models, we derived four categories. Two of the categories are shades of variation in the rote-learning part of a continuum, while the other two categories are in the meaningful-learning part. All students possessed alternative conceptions some of which occurred within certain categories, while others spanned more categories. The insistence on the deterministic models of the atom, the misinterpretation of models, and the poor understanding of the current quantum concepts are main problems in the learning of the basic quantum chemistry concepts. © 2009 Wiley Periodicals, Inc. J Res Sci Teach 46: 520–536, 2009