New potentially 2D sophisticated nanostructures based on carbon, molybdenum and silicon are generated by the intelligent computing method based on a memetic strategy combining the evolutionary algorithm and the conjugate-gradient optimization technique for the molecular model. The main goal of design is to find stable arrangements of atoms under certain imposed conditions. The objective function is formulated as the total potential energy of an atomic system. The optimized nanostructure is considered as a discrete atomic model. In the case of carbon interactions between atoms are modeled using the AIREBO potential. Validation of the obtained results of new 2D graphene-like materials are presented, along with their mechanical properties. Apart from graphene one of the most prominent 2D material is the Single-Layered Molybdenum Disulfide (SLMoS2), which reveals polymorphism at the nano-level. The paper presents optimization technique which allows to obtain SLMoS2 heterostructures with desired mechanical properties. The behaviour and energy of the atoms is determined by the REAX-FF potential. Examples of such periodic SLMoS2 2H/1T heterostructures are presented. New nanostructures based on silicon are also presented using the presented intelligent methodology and interatomic potentials.