Every atom is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Only the most common variety of hydrogen has no neutrons. More than 99.94% of an atom's mass is in the nucleus. The protons have a positive electric charge, the electrons have a negative electric charge, and the neutrons have no electric charge. If the number of protons and electrons are equal, then the atom is electrically neutral. If an atom has more or fewer electrons than protons, then it has an overall negative or positive charge, respectively – such atoms are called ions.
The electrons of an atom are attracted to the protons in an atomic nucleus by the electromagnetic force. The protons and neutrons in the nucleus are attracted to each other by the nuclear force. This force is usually stronger than the electromagnetic force that repels the positively charged protons from one another. Under certain circumstances, the repelling electromagnetic force becomes stronger than the nuclear force. In this case, the nucleus splits and leaves behind different elements. This is a form of nuclear decay.
In 1897, J. J. Thomson discovered that cathode rays are not electromagnetic waves but made of particles that are 1,800 times lighter than hydrogen (the lightest atom). Thomson concluded that these particles came from the atoms within the cathode — they were subatomic particles. He called these new particles corpuscles but they were later renamed electrons. Thomson also showed that electrons were identical to particles given off by photoelectric and radioactive materials. It was quickly recognized that electrons are the particles that carry electric currents in metal wires. Thomson concluded that these electrons emerged from the very atoms of the cathode in his instruments, which meant that atoms are not indivisible as the name atomos suggests.
J. J. Thomson thought that the negatively-charged electrons were distributed throughout the atom in a sea of positive charge that was distributed across the whole volume of the atom. This model is sometimes known as the plum pudding model.
Ernest Rutherford and his colleagues Hans Geiger and Ernest Marsden came to have doubts about the Thomson model after they encountered difficulties when they tried to build an instrument to measure the charge-to-mass ratio of alpha particles (these are positively-charged particles emitted by certain radioactive substances such as radium). The alpha particles were being scattered by the air in the detection chamber, which made the measurements unreliable. Thomson had encountered a similar problem in his work on cathode rays, which he solved by creating a near-perfect vacuum in his instruments. Rutherford didn't think he'd run into this same problem because alpha particles are much heavier than electrons. According to Thomson's model of the atom, the positive charge in the atom is not concentrated enough to produce an electric field strong enough to deflect an alpha particle, and the electrons are so lightweight they should be pushed aside effortlessly by the much heavier alpha particles. Yet there was scattering, so Rutherford and his colleagues decided to investigate this scattering carefully.
Between 1908 and 1913, Rutheford and his colleagues performed a series of experiments in which they bombarded thin foils of metal with alpha particles. They spotted alpha particles being deflected by angles greater than 90°. To explain this, Rutherford proposed that the positive charge of the atom is not distributed throughout the atom's volume as Thomson believed, but is concentrated in a tiny nucleus at the center. Only such an intense concentration of charge could produce an electric field strong enough to deflect the alpha particles as observed.
The development of the mass spectrometer allowed the mass of atoms to be measured with increased accuracy. The device uses a magnet to bend the trajectory of a beam of ions, and the amount of deflection is determined by the ratio of an atom's mass to its charge. The chemist Francis William Aston used this instrument to show that isotopes had different masses. The atomic mass of these isotopes varied by integer amounts, called the whole number rule. The explanation for these different isotopes awaited the discovery of the neutron, an uncharged particle with a mass similar to the proton, by the physicist James Chadwick in 1932. Isotopes were then explained as elements with the same number of protons, but different numbers of neutrons within the nucleus.
In 1913 the physicist Niels Bohr proposed a model in which the electrons of an atom were assumed to orbit the nucleus but could only do so in a finite set of orbits, and could jump between these orbits only in discrete changes of energy corresponding to absorption or radiation of a photon. This quantization was used to explain why the electrons' orbits are stable (given that normally, charges in acceleration, including circular motion, lose kinetic energy which is emitted as electromagnetic radiation, see synchrotron radiation) and why elements absorb and emit electromagnetic radiation in discrete spectra.
Later in the same year Henry Moseley provided additional experimental evidence in favor of Niels Bohr's theory. These results refined Ernest Rutherford's and Antonius van den Broek's model, which proposed that the atom contains in its nucleus a number of positive nuclear charges that is equal to its (atomic) number in the periodic table. Until these experiments, atomic number was not known to be a physical and experimental quantity. That it is equal to the atomic nuclear charge remains the accepted atomic model today.
Chemical bonds between atoms were explained by Gilbert Newton Lewis in 1916, as the interactions between their constituent electrons. As the chemical properties of the elements were known to largely repeat themselves according to the periodic law, in 1919 the American chemist Irving Langmuir suggested that this could be explained if the electrons in an atom were connected or clustered in some manner. Groups of electrons were thought to occupy a set of electron shells about the nucleus.
The Bohr model of the atom was the first complete physical model of the atom. It described the overall structure of the atom, how atoms bond to each other, and predicted the spectral lines of hydrogen. Bohr's model was not perfect and was soon superseded by the more accurate Schrödinger model, but it was sufficient to evaporate any remaining doubts that matter is composed of atoms. For chemists, the idea of the atom had been a useful heuristic tool, but physicists had doubts as to whether matter really is made up of atoms as nobody had yet developed a complete physical model of the atom.
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