See in SEP the entry on Ancient Atomism :
ancient atomists theorized that the two fundamental and oppositely characterized constituents of the natural world are indivisible bodies—atoms—and void. The latter is described simply as nothing, or the negation of body. Atoms are by their nature intrinsically unchangeable; they can only move about in the void and combine into different clusters.
The changes in the world of macroscopic objects are caused by rearrangements of the atomic clusters. Atoms can differ in size, shape, order and position (the way they are turned); they move about in the void, and—depending on their shape—some can temporarily bond with one another by means of tiny hooks and barbs on their surfaces.
It seems that, at least for Democritus, atoms must be interpreted as in the XVII century mechanicist tradition : only shape, size and motion, devoided of "qualities".
If so, they are not like "modern" chemical" molecules, i.e. differentiated according to the elements they form.
But see also Plato's point of view :
Although the Greek term atomos is most commonly associated with the philosophical system developed by Leucippus and Democritus, involving solid and impenetrable bodies, Plato's Timaeus presents a different kind of physical theory based on indivisibles. The dialogue elaborates an account of the world wherein the four different basic kinds of matter—earth, air, fire, and water—are regular solids composed from plane figures: isoceles and scalene right-angled triangles. Because the same triangles can form into different regular solids, the theory thus explains how some of the elements can transform into one another, as was widely believed.
Extract from GS Kirk & JE Raven, The Presocratic Philosophers (1958), page 406 :
Leucippus and his associate Democritus hold that the elements are the full and the void; They call them being and not-beingrespectively. Being is full and solid, not-being is void and rare. Since the void exists no less than body, it follows that not-being exists not less than being. The two together are the material causes of existing things. And just as those who make the underlying substance one generate other things by its modifications, and postulate rarefaction and condenstaion as the origin of such modifications, in the same way these men too say that the differences in atoms are the causes of other things. They hold that these differences are three - shape, arrangement and position; being, they say, differs only in 'rythm, touching and turning', of which 'rythm' is shape, 'touching' is arrangement and 'turning' is position; for A differs from N in shape, AN form NA in arrangement and Z form N in position. [Aristotle Met A4, 985b4]
Note that we have to "separate" A's interpretation [see : material causes, substance] from the original D's words (very few).
This is , more or less, what you can find in Constantine Vamvacas, The Founders of Western Thought THE PRESOCRATICS (ed or 2001), page 215.
Other possible references :
While atoms themselves had no perceptible qualities (qualities are dependent on atoms forming compounds), they did have different shapes and sizes. Aristotle (Metaphysics 985b15–19 = DK67A6; see also Generation and Corruption 315b6–15 = DK67A9) notes that atoms differ in shape (rusmos), arrangement (diathige), and position (trope) (see also Simplicius, Commentary on Aristotle’s Physics 28.15–26. = DK67A8; 68A38). However, arrangement and position are the sine qua non for the formation of compounds. In the final analysis, only size (megethos) and shape (rhusmos) are intrinsic to the atom themselves [Gerard Naddaf, The Greek Concept of Nature (2005), page 154].
Atomism then involves some sort of ontological reduction. But the fundamental properties need not all be similar in type to the ones which they are invoked to explain; and in some cases (particularly those to do with perceptual properties) the apparent macro-properties are simply emergent upon suitable arrangements and configurations of atomic qualities. Atoms really do possess solidity,resi stivity,and weight as well (On Generation and Corruption 1. 8. 326a9–10; Theophrastus, On Senses 61; Simplicius, On ‘On the Heavens’ 712 = 573–5 KRS);243 and these properties are invoked to explain the creation of macroscopic objects,and their behaviours. By contrast, atoms do not have colour, taste,or temperature in and of themselves (215 above; cf. Lucretius 2. 730–864). We do not know precisely how Democritus accounted for perceptual properties, except in the case of taste, where Theophrastus (On Senses 66 = 591 KRS) reports that bitter flavours are caused by ‘small,smooth, rounded atoms’ while saltiness is the result of larger,jag ged atoms (Epicurus offered fuller explanations along the same lines: To Herodotus 51–4; cf. Lucretius 4. 615–72).
Thus whether or not something tastes sweet depends upon a set of facts about its structure that are not themselves phenomenal at all. This supplies the sense to his claim that things are merely by convention hot and cold,sweet and bitter,and so on. [RJ Hankinson, Cause and Explanation in Ancient Greek Thought (1998), page 203].
