pp. 350-351

Have not the small Particles of Bodies certain Powers, Virtues, or Forces by which they act at a distance, not only upon the Rays of Light for reflecting, refracting and inflecting them, but also upon one another for producing a great part of the Phaenomena of Nature? For it's well know that Bodies act one upon another by the Attractions of Gravity, Magnetism and Electricity; and these Instances shew the Tenor and Course of Nature, and make it not improbable but that there may be more attractive Powers than these. For Nature is very consonant and conformable to her self. How these Attractions may be perform'd, I do not here consider. What I call Attraction may be perform'd by impulse, or by some other means unknown to me. I use that Word here to signify only in general any Force by which Bodies tend towards one another, whatsoever be the Cause. For we must learn from the Phaenomena of Nature what Bodies attract one another, and what are the Laws and Properties of the attraction, before we enquire the Cause by which the Attraction is perform'd, The Attractions of Gravity, Magnetism and Electricity, react to very sensible distances, and so have been observed by vulgar Eyes, and there may be others which reach to so small distances as hitherto escape observation; and perhaps electrical Attraction may reach to such small distances, even without being excited by Friction.

Note that Newton wants first to discover the mathematical form of the attraction law rather than to address the more challenging question of what what makes it have this form.  The source of "action at a distance" where there are no strings connecting the objects involved was not easy to comprehend.

Then follow a dozen pages citing experimental evidence for attraction between particles. For example, increasing attraction between particles might cause them to collide more strongly with one another generating increasing amounts of heat. This could explain the substantial generation of heat when Oil of Vitriol (concentrated sulfuric acid) is mixed with water or is used to dissolve iron

p. 363-4

The Parts of all homogeneal hard Bodies which fully touch one another, stick together very strongly. And for explaining how this may be, some have invented hooked Atoms, which is begging the Question; and others tell us that Bodies are glued together by rest, that is, by an occult Quality, or rather by nothing; and others that they stick together by conspiring Motions, that is, by relative rest amongst themselves. I had rather infer from their Cohesion, that their Particles attract one another by some Force, which in immediate Contact is exceeding strong, at small distances performs the chymical Operations above mention'd, and reaches not far from the Particles with any sensible Effect.

[Perhaps Newton meant that the force that holds particles together is of shorter range than the 1/r^2, or inverse square, force for gravity, electrical attraction, etc.]

p. 369

…By the Table in the second Part of the second Book, wherein the thicknesses of colour'd Plates of Water between two Glasses are set down, the thickness of the Plate where it appears very black, is three eighths of the ten hundred thousandth part of an Inch. And where the Oil of Oranges between the Glasses is of this thickness, the Attraction collected by the foregoing Rule, seems to be so strong, as within a Circle of an Inch in diameter, to suffice to hold up a Weight equal to that of a Cylinder of Water of an Inch in diameter, and two or three Furlongs in length. And where it is of less thickness the Attraction may be proportionally greater, and continue to increase, until the thickness do not exceed that of a single Particle of the Oil. There are therefore Agents in Nature able to make the Particles of Bodies stick together by very strong Attractions. And it is the business of experimental Philosophy to find them out.

The business of the first part of Chemistry 125 is to find out the Agent in Nature that causes atoms to stick together by very strong Attraction, that is, to understand the nature of chemical bonds. We'll see that these bonds are about 20 times stronger that the non-bonded attractions to which Newton was referring.

Note in passing that Newton was able to measure a thickness of "three eighths of the ten hundred thousandth part of an Inch," that is, 3/8 of a millionth of an inch, which works out to about 10 nm or 0.01 microns. Since typical organic molecules are of the order of 1 nm in diameter, this means he could measure thicknesses corresponding to 10 molecules! We'll discuss how he did this when we come to SPM.