Which prefix denotes the presence of two atoms in molecular substances?

The prefix that denotes the presence of two atoms in molecular substances is "di." When naming molecular compounds, prefixes are used to indicate the number of atoms of each element in a molecule. In this context, "di" specifically signifies that there are two atoms of a particular element present.

For example, in carbon dioxide (CO₂), the "di" indicates that there are two oxygen atoms bonded to a single carbon atom. This system of nomenclature allows for clear and concise communication about the composition of chemical compounds.

The other prefixes have different meanings: "mono" refers to one atom, "tri" indicates three, and "tetra" corresponds to four. Thus, they do not fit the requirement for indicating two atoms.