All 3 Uses of

molecule
in
The Hunchback of Notre Dame

Now, at the moment when the door had opened to admit the cardinal, the nine parts of self-esteem in Gringoire, swollen and expanded by the breath of popular admiration, were in a state of prodigious augmentation, beneath which disappeared, as though stifled, that imperceptible molecule of which we have just remarked upon in the constitution of poets; a precious ingredient, by the way, a ballast of reality and humanity, without which they would not touch the earth.†
Chpt 1.1.3

molecule = the smallest amount of a chemical substance that can exist by itself

Each molecule of the gutter bore away a molecule of heat radiating from Gringoire's loins, and the equilibrium between the temperature of his body and the temperature of the brook, began to be established in rough fashion.†
Chpt 1.2.5 *

Each molecule of the gutter bore away a molecule of heat radiating from Gringoire's loins, and the equilibrium between the temperature of his body and the temperature of the brook, began to be established in rough fashion.†
Chpt 1.2.5

Definitions:

(1) (molecule)
the smallest amount of a chemical substance that can exist by itself -- usually consisting of 2 or more atoms
(2) (meaning too rare to warrant focus)
meaning too rare to warrant focus:

Less commonly, molecule is used informally to refer to anything that is very small.