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My question is based upon the statement found here:
an element may be homogeneous on a larger scale, compared to being heterogeneous on a smaller scale. This is known as an effective medium approach, or effective medium approximations.
So, is it acceptable to say that water molecule is a heterogeneous molecule?
I think you are confused. Heterogenous and homogeneous are words that are used to describe mixtures (of substances). In homogenous mixtures, the substances exist only in one phase, while heterogeneous mixtures the substances exist in two or more phases.
A molecule is homonuclear if it consists of atoms of a single chemical element ($\ce{O2}$). A molecule is heteronuclear if it is composed of more than one element ($\ce{H2O}$). Note that any pure molecule is considered a substance, and it is the combinations of these substances that form mixtures, either homogeneous, heterogeneous, or colloidal.
No. "Element" in the article cited doesn't mean a chemical element or molecule but the it is considering the "volume of stuff" under consideration. The "element" could be a solution, the ocean, or a galaxy sized masses. Also heterogeneity/homogeneity are typically applied on a "macroscale" sample meaning large enough that the sample isn't quantum sized.
Thus for water (or some solution) the heterogeneity is really a concept of the volume of solution under consideration not the water molecule itself. So a liter of salt water would be homogeneous, but clam chowder would be heterogeneous.
If we were considering homogenized milk then yes/no gets a bit tricky. We'd have to consider how we define homogeneous since 1 ml sized samples would be the same but the homogenized milk really has two phases mixed together. (I'd guess that you could centrifuge homogenized milk and get it to separate.)
As another example the oceans are heterogeneous. The surface water will have a different chemical composition (pH, salt concentration) as compared to the water in the deep parts.
