We report the synthesis of a novel isotope engineered $^{13}{\rm C}^{12}{\rm C}$ heteronuclear nanostructure: single-wall carbon nanotubes made of enriched clusters which are embedded in natural carbon regions. The material is synthesized with a high temperature annealing from enriched benzene and natural , which are co-encapsulated inside host SWCNTs in an alternating fashion. The Raman 2D line indicates that the isotopes are not distributed uniformly in the inner tubes. A semi-empirical method based modeling of the Raman modes under isotope enrichment shows that experimental data is compatible with the presence of rich clusters which are embedded in a natural carbon containing matrix. This material may find applications in quantum information processing and storage using nuclear spins as qubits.

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