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They perceived the idea of the atom or what they called "atomos" which was both indestructible and indivisible. They used this idea to justify the different properties of various materials. The different shapes, arrangements and orientations influenced properties of materials.
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He proposed that: All matter consists of atoms which are indestructible and indivisible, that all atoms of an element have the same mass and properties, compounds are formed by a combination of two or more elements and in a chemical reaction atoms are rearranged.
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Dalton used his experiment with a cathode ray tube to interpret the deflection of rays by electrically charged plates and magnets as evidence of “bodies much smaller than atoms” (electrons) .
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Through his discovery of the electron, J.J Thomson proposed a new model of the atom, The Plum Pudding Model. This model, proposed that electrons of negative charge were distributed throughout a positive base, much like a plum pudding.
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Through his alpha foil experiment Rutherford was able to disprove J.J Thomson' model. The experiment consisted of firing alpha particles at an extremely thin piece of a good foil and tracing their path. Although, most went straight through the goil foil, very, very few rebounded. This led him to prove that there was a dense but tiny nucleus which held the positive charge.
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Shortly after the discovery of the Nucleus, Bohr expands on he movement of the electrons. His theory was that electrons travelled in fixed orbits and energy levels around the nucleus. If an atom gave of or absorbed energy it would jump to a different orbit suggesting that they could jump between energy levels.
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After a series of experiments they kept seeing that the atomic number (number of protons) was less than the atomic mass. This was unusual as electrons hardly weighed anything and hey were significant differences in these two numbers. Rutherford suggested the idea of a neutron, a particle with mass but no charge. This was later proven by a series of experiments.