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Using intelligent modeling systems for explaining the results of calculations in terms of a particular domain provides more options by contrast with program systems of other classes. A formally described domain ontology that defines the unambiguous interpretation of the terms makes it possible to develop intelligent modeling systems combining knowledge and data of different sections of this domain and program systems for solving application issues. Nanoscience is of a cross-disciplinary nature which implies the necessity to use knowledge of various disciplines, i.e. there are ontologies of other domains in this ontology. The paper proposes a mathematical ontology model of the nanomaterials domain with complicated structures and terms from ontologies of organic chemistry and physical chemistry.