In 1793 Dalton took up his permanent residence in Manchester, and in that year appeared his first book, Meteorological Observations and Essays. Here he deals, among other things, with rainfall, the formation of clouds, evaporation, and the distribution and character of atmospheric moisture. It seemed to him that aqueous vapor always exists as a distinct fluid maintaining its identity among the other fluids of the atmosphere. He thought of atmospheric moisture as consisting of minute drops of water, or globules among the globules of oxygen and nitrogen. He was a disciple of Newton's (to whom, indeed, Dalton had some personal likeness), who looked upon matter as consisting of "solid, massy, hard, impenetrable, movable particles, of such sizes and figures, and with such other properties, and in such proportion, as most conduced to the end for which God formed them." Dalton was so much under the influence of the idea that the physical universe is made up of these indivisible particles, or atoms, that his biographer describes him as thinking corpuscularly. It is probable that his imagination was of the visualizing type and that he could picture to himself the arrangement of atoms in elementary and compound substances.

Now Dalton's master had taught that the atoms of matter in a gas (elastic fluid) repel one another by a force increasing in proportion as their distance diminishes. How did this teaching apply to the atmosphere, which Priestley and others had proved to consist of three or more gases? Why does this mixture appear simple and homogeneous? Why does not the air form strata with the oxygen below and the nitrogen above? Cavendish had shown, and Dalton himself later proved, that common air, wherever examined, contains oxygen and nitrogen in fairly constant proportions.

French chemists had sought to apply the principle of chemical affinity in explaining the apparent homogeneity of the atmosphere. They supposed that oxygen and nitrogen entered into chemical union, the one element dissolving the other. The resultant compound in turn dissolved water; hence the phenomena of evaporation. Dalton tried in vain to reconcile this supposition with his belief in the atomic nature of matter. He drew diagrams combining an atom of oxygen with an atom of nitrogen and an atom of aqueous vapor. The whole atmosphere could not consist of such groups of three because the watery particles were but a small portion of the total atmosphere. He made a diagram in which one atom of oxygen was combined with one atom of nitrogen, but in this case the oxygen was insufficient to satisfy all the nitrogen of the atmosphere. If the air was made up partly of pure nitrogen, partly of a compound of nitrogen and oxygen, and partly of a compound of nitrogen, oxygen, and aqueous vapor, then the triple compound, as heaviest, would collect toward the surface of the earth, and the double compound and the simple substance would form two strata above. If to the compounds heat were added in the hope of producing an unstratified mixture, the atmosphere would acquire the specific gravity of nitrogen gas. "In short," says Dalton, "I was obliged to abandon the hypothesis of the chemical constitution of the atmosphere altogether as irreconcilable to the phenomena."

He had to return to the conception of the individual particles of oxygen, nitrogen, and water, each a center of repulsion. Still he could not explain why the oxygen did not gravitate to the lowest place, the nitrogen form a stratum above, and the aqueous vapor swim upon the top. In 1801, however, Dalton hit upon the idea that gases act as vacua for one another, that it is only like particles which repel each other, atoms of oxygen repelling atoms of oxygen and atoms of nitrogen repelling atoms of nitrogen when these gases are intermingled in the atmosphere just as they would if existing in an unmixed state. "According to this, we were to suppose that atoms of one kind did not repel the atoms of another kind, but only those of their own kind." A mixed atmosphere is as free from stratifications, as though it were really homogeneous.

In his analyses of air Dalton made use of the old nitric oxide method. In 1802 this led to an interesting discovery. If in a tube .3 of an inch wide he mixed 100 parts of common air with 36 parts of nitric oxide, the oxygen of the air combined with the nitric oxide, and a residue of 79 parts of atmospheric nitrogen remained. And if he mixed 100 parts of common air with 72 of nitric oxide, but in a wide vessel over water (in which conditions the combination is more quickly effected), the oxygen of the air again combined with the nitric oxide and a residue of 79 parts of nitrogen again resulted. But in the last experiment, if less than 72 parts of nitric oxide be employed, there will be a residue of oxygen as well as nitrogen; and if more than 72, there will be a residue of nitric oxide in addition to the nitrogen. In the words of Dalton, "oxygen may combine with a certain portion of nitrous gas [as he called nitric oxide], or with twice that portion, but with no intermediate portion."

Naturally these experimental facts were to be explained in terms of the ultimate particles of which the various gases are composed. In the following year Dalton gave graphic representation to his idea of the atomic constitution of chemical elements and compounds.

Much against Dalton's will his method of indicating chemical elements and their combinations had to yield to a method introduced by the great Swedish chemist Berzelius. In 1837 Dalton wrote: "Berzelius's symbols are horrifying: a young student in chemistry might as soon learn Hebrew as make himself acquainted with them. They appear like a chaos of atoms ... and to equally perplex the adepts of science, to discourage the learner, as well as to cloud the beauty and simplicity of the Atomic Theory."

Meantime Dalton's mind had been turning to the consideration of the relative sizes and weights of the various elements entering into combination with one another. He argued that if there be not exactly the same number of atoms of oxygen in a given volume of air as of nitrogen in the same volume, then the sizes of the particles of oxygen must be different from those of nitrogen. His interest in the absorption of gases by water, in the reciprocal diffusion of gases, as well as in the phenomena of chemical combination, stimulated Dalton to determine the relative size and weight of the atoms of the various elements. Dalton said nothing of the absolute weight of the atom. But on the assumption that when only one compound of two elements is known to exist, the molecule of the compound consists of one atom of each of these elements, he proceeded to investigate the relative weights of equal numbers of the two sorts of atoms. In 1803 he pursued this investigation with remarkable success, and taking hydrogen (the lightest gas known to him) as unity, he arrived at a statement of the relative atomic weights of oxygen, nitrogen, carbon, etc. Dalton thus introduced into the study of chemical combination a very definite idea of quantitative relationship. By him the atomic theory of the constitution of matter was made definite and applicable to all the phenomena known to chemistry.