Green chemistry methods have clearly revealed the definite demands for chemical procedures in performing ecofriendly synthesis using so-called biogenic compounds (BGCs) extracted from biological resources, such as fungi, algae and plantae. These compounds can potentially be used as reducing and stabilizing agents in nanoparticle (NP) synthesis. Modern research in the field of NP synthesis increasingly goes beyond traditional thermodynamic and kinetic approaches. More complex interactions are considered, which are organized according to the analog principle in the environment where nanoparticles with a given morphology are formed. The media state where chemical reactions occur could be viewed as manifestations of specific conformational BGC changes, which influence NP formation with its defined morphology. In this work, the reaction media is considered not only as a chemical system but also as a kind of analog processing unit, where pH, temperature, and spectra (the environment parameters) are the input data, while the size and shape of the nanoparticles formed (the morphology parameters) are the output data. The presented approach allows us to focus on information structure analysis, where each media state transition is associated with a change in the BGC conformational structure which, in turn, affects the size and shape of the NP formed.