Nanostructures exhibit physical properties not predictable by Quantum mechanics, which deals explicitly with energy levels. Trying to work with physical dimensions is a problem not solved from the time of adoption of the Rutherford-Bohr model of hydrogen. Quantum mechanics also does not predict the chemical bond direction, it cannot provide a classical explanation of the spin of leptons and hadrons, why some isotopes are stable and others not, why the neutron has a magnetic moment and the electron has anomalous one, what is the size of the Rydberg state of atoms and so on. Quantum mechanics is also incapable to explain the nuclear transmutations at low temperature or so called LENR processes. These and other problems lead to the conclusion that the Quantum mechanics is not a real physical but a mathematical model only. The reexamination of the scattering experiments also leads to this conclusion, since the spherical shape of the nucleus has been a priory used in the data interpretation. The physical models derived in the Basic Structure of Matter Supergravitation Unified Theory (BSM-SG) provide classical explanations of all these problems. The BSM-SG atomic models provided in the Atlas of Atomic Nuclear Structures are suitable for 3D graphical modeling and analysis of molecules and nanostructures at sub-nanometric scale. A clickable Periodic table of BSM-SG models is available on-line: www.helical-structures.org/Heliconstruct/table.html