John Cockcroft and Ernest Walton: 1932 paper on the disintegration of lithium by fast protons: artificial transmutation. This paper is at Nature. (Link to a biographical sketch of Cockcroft and one of Walton.)
Hans Geiger: from 1910 paper on scattering of alpha particles from gold foil. This paper is at the ChemTeam site.
Hans Geiger and Ernest Marsden: 1913 paper comparing backscatter of alpha particles to the predictions of Rutherford's nuclear model of the atom. This paper is at the ChemTeam site.
Otto Hahn and Fritz Strassmann: 1939 paper reporting a result they barely believe themselves: barium, lanthanum, and cerium obtained from the bombardment of uranium by neutrons, then a more definite announcement of uranium fission. These papers are at the ChemTeam site. View biographical information on Hahn and Strassmann.
Lise Meitner and Otto Frisch: 1939 paper invokes fission of uranium to explain neutron bombardment results. This paper is at the ChemTeam site. Link to a biographical sketch of Meitner.
Ernest Rutherford: 1900 paper introduces concept of radioactive half-life and measures half-life of "thorium emanation" (now known as 220Rn). This paper is at the ChemTeam site. View page images of original.
Ernest Rutherford and T. Royds: 1909 paper identifying the α particle with doubly-charged helium. The paper is worth reading for the careful marshalling of one last conclusive piece of evidence about the nature of the particles Rutherford and his co-workers had been studying for a decade.
Ernest Rutherford: abstract of a 1911 paper proposing the nuclear model of the atom to explain results of scattering experiments. This paper is at the ChemTeam site.
Ernest Rutherford: 1911 paper proposing the nuclear model of the atom to explain results of scattering experiments. This paper is on Google Books.
Ernest Rutherford: 1919 paper describing the bombardment of nitrogen by alpha particles. Rutherford concludes the nitrogen atoms are disintegrated in the process. So atoms are not indestructable after all, and the alchemists' dreams of transmutation are realized.
Ernest Rutherford: 1920 lecture describing the state of knowledge of nuclear structure at a time after the discovery of isotopy and atomic number but before the neutron; the standard picture included electrons in the nucleus. View page images of original.
M. L. Oliphant, P. Harteck, and Ernest Rutherford: 1934 note from the Rutherford lab describes fusion ('transmutation') of deuterium. These papers (preliminary note and more detailed paper) are at the ChemTeam site.
Frederick Soddy: 1913 paper which gives the rules for chemical transformations accompanying α and β decay; its discussion of "non-separable" elements all but defines (but does not name) isotopy, including a speculation that they are not limited to radioactive elements. See a biographical sketch of Soddy.
Frederick Soddy: 1913 paper which introduces the term "isotopes" for atoms which have the same nuclear charge but different mass.
Frederick Soddy: from 1913 review article; discusses isotopes and the displacement law
Silvanus Thompson: Thompson thought of performing the same sorts of experiments as Becquerel at about the same time; comparison of this paper with Becquerel's highlights the luck and genius of Becquerel. This article also illustrates the confusion immediately following the discovery of X-rays and radioactivity: the former were not believed to be electromagnetic and the latter was! See biographical information on Thompson.
Friedrich Wöhler: synthesis of urea from inorganic materials, conventionally regarded as fatal to the idea that organic compounds could only be produced through a "vital force." This paper is at the ChemTeam site. View page images of original (in German). See biographical information on Wöhler.
Dmitrii Mendeleev, (1871): table from Annalen, suppl. VIII, 133 (1871).
Dmitrii Mendeleev, (1871): excerpt on periodic law and predicted elements Annalen, suppl. VIII, 133 (1871). Link to page images (in German).
Dmitrii Mendeleev: excerpt from 1871 paper on periodicity of the elements focuses on the properties of the predicted element eka-boron, now known as scandium. This paper is on Rod Beavon's chemistry site.
Henry Moseley (excerpts, 1913 & 1914): X-ray spectra of the elements reveal integers characteristic of each element, namely the atomic number. This paper was transcribed by John Park. See his essay on Moseley and his work.
Francis Bacon (1620): Before caloric and the kinetic theory, Bacon reviewed a wide range of observations about heat and related phenomena to illustrate his inductive scientific method, and suggested that heat is related to motion. There is even a mention of triboluminescent candy (in Table II, number 11). (Link to a biographical sketch of Bacon or to page images of the entire book.)
John Dalton, excerpts from A New System of Chemistry (1808). Describes how heat (caloric) was believed to combine with matter, especially gases. (See also Lavoisier excerpt in this section.) Heat capacity of gases proposed to vary inversely with atomic weight (like law of Dulong & Petit).
Cato Guldberg and Peter Waage: "Studier over Affiniteten", describing law of mass action to the Norwegian Academy of Sciences and Letters in 1864. This paper is at the ChemTeam site, as is this picture. View page images of original (in Norwegian). See biographical information on Guldberg or Waage.
Josiah Willard Gibbs: voluminous two-part article from the 1870s on equilibrium in heterogeneous systems. View page images of part 1 and part 2. The general criteria in terms of energy and entropy are given early on, here.
Walter Nernst: 1914 paper distinguishes between energy and what we call free energy with the assistance of his "new heat law" (third law of thermodynamics). View page images of the original (in German).
Comptes Rendus hebdomadaires des séances de l'Académie des sciences , volumes 1-261 (1835-1965)--most of them, at least. This resource is available as page images at the Bibliothèque national de France. Entire volumes are posted, so this resource spans the range of sciences.
Justus Liebig: Familiar Letters on Chemistry (1843). This monograph on chemistry and some of its applications to agriculture and industry in the middle 19th century is available at Google Books.
Philosophical Transactions of the Royal Society, volumes 50-67 (1757-77). This resource is available as page images at the Internet Library of Early Journals, Bodelian Library, Oxford University. Entire volumes are posted, so this resource spans the range of natural philosophy.
Louis-Jacques Thénard: 1819 paper announces discovery of hydrogen peroxide and describes some of its properties (including some painful tests: don't try this at home)