Functional Groups: The presence and type of functional groups in a molecule can significantly impact its activity. Electronic Properties: The distribution of electrons within a molecule can affect how it interacts with biological systems. Hydrophobicity/Hydrophilicity: The balance between hydrophobic and hydrophilic regions in a molecule can determine its solubility and permeability, influencing its biological activity. Spatial Arrangement: The three-dimensional arrangement of atoms in a molecule, also known as its conformation, can affect how it binds to its target.