Motivated by a revision of the classical equations of electromagnetism that allow for the inclusion of solitary waves in the solution space, the material collected in this book examines the consequences of adopting the modified model in the description of atomic structures. The possibility of handling "photons" in a deterministic way indeed gives a chance to review the foundations of quantum physics. Atoms and molecules are described as aggregations of nuclei and electrons joined through organized photon layers resonating at various frequencies, explaining how matter can absorb or emit light quanta. Some established viewpoints are subverted, offering an alternative scenario. The analysis seeks to provide an answer to many technical problems in physical chemistry and, at the same time, to raise epistemological questions.