Jupiter’s clouds are formed at different altitudes in the planet’s atmosphere. Except for the top of the Great Red Spot, the white clouds are the highest, with cloud-top temperatures of about 120 kelvins (K; −240 °F, or −150 °C). These white clouds consist of frozen ammonia crystals and are thus analogous to the water-ice cirrus clouds in Earth’s atmosphere. The tawny clouds that are widely distributed over the planet occur at lower levels. They appear to form at a temperature of about 200 K (−100 °F, −70 °C), which suggests that they probably consist of condensed ammonium hydrosulfide and that their colour may be caused by other ammonia-sulfur compounds such as ammonium polysulfides. Sulfur compounds are invoked as the likely colouring agents because sulfur is relatively abundant in the cosmos and hydrogen sulfide is notably absent from Jupiter’s atmosphere above the clouds.

Jupiter is composed primarily of hydrogen and helium. Under equilibrium conditions—allowing all the elements present to react with one another at an average temperature for the visible part of the Jovian atmosphere—the abundant chemically active elements are all expected to combine with hydrogen. Thus it was surmised that methane, ammonia, water, and hydrogen sulfide would be present. Except for hydrogen sulfide, all these compounds have been found by spectroscopic observations from Earth. The apparent absence of hydrogen sulfide can be understood if it combines with ammonia to produce the postulated ammonium hydrosulfide clouds. Indeed, hydrogen sulfide was detected at lower levels in the atmosphere by the Galileo probe. The absence of detectable hydrogen sulfide above the clouds, however, suggests that the chemistry that forms coloured sulfur compounds (if indeed there are any) must be driven by local lightning discharges rather than by ultraviolet radiation from the Sun. In fact, the causes of the colours on Jupiter remain undetermined, although investigators have developed several viable hypotheses.

Sulfur compounds have also been proposed to explain the dark brown coloration of the ammonia clouds detected at still lower levels, where the measured temperature is 260 K (8 °F, −13 °C). These clouds are seen through what are apparently holes in the otherwise ubiquitous tawny clouds. They appear bright in pictures of Jupiter that are made from its thermal radiation detected at a wavelength of five micrometres, consistent with their higher temperatures.

The colour of the Great Red Spot has been attributed to the presence of complex organic molecules, red phosphorus, or yet another sulfur compound. Laboratory experiments support these ideas, but there are counterarguments in each case. Dark regions occur near the heads of white plume clouds near the planet’s equator, where temperatures as high as 300 K (80 °F, 27 °C) have been measured. Despite their blue-gray appearance, these so-called hot spots have a reddish tint. They appear to be cloud-free regions—hence the ability to “see” into them to great depths and measure high temperatures—that exhibit a blue colour (from Rayleigh scattering of sunlight) overlain with a thin haze of reddish material. That these so-called hot spots occur only near the equator, the elliptical dark brown clouds only near latitude 18° N, and the most prominent red colour on the planet only in the Great Red Spot implies a localization of cloud chemistry that is puzzling in such a dynamically active atmosphere.

At still lower depths in the atmosphere, astronomers expect to find water-ice clouds and water-droplet clouds, both consisting of dilute solutions of ammonium hydroxide. Nevertheless, when the probe from the Galileo spacecraft entered Jupiter’s atmosphere on December 7, 1995, it failed to find these water clouds, even though it survived to a pressure level of 22 bars—nearly 22 times sea-level pressure on Earth—where the temperature was more than 400 K (260 °F, 130 °C). In fact, the probe also did not sense the upper cloud layers of ammonia and ammonium hydrosulfide. Unfortunately for studies of Jovian cloud physics, the probe had entered the atmosphere over a hot spot, where clouds were absent, presumably caused by a large-scale meteorological phenomenon related to the downdrafts observed in some storms on Earth.

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Proportions of constituents

Prior to the deployment of the Galileo probe, astronomers had relied upon studies of the planet’s spectrum to provide information about the composition, temperature, and pressure of the atmosphere. In the particular version of this technique known as absorption spectroscopy, light or thermal radiation from the planet is spread out in wavelengths (colours, in visible light, as in a rainbow) by the dispersing element in a spectrograph. The resulting spectrum contains discrete intervals, or lines, at which energy has been absorbed by the constituents of the planet’s atmosphere. By measuring the exact wavelengths at which this absorption takes place and comparing the results with spectra of gases obtained in the laboratory, astronomers can identify the gases in Jupiter’s atmosphere.

The presence of methane and ammonia in Jupiter’s atmosphere was deduced in this way in the 1930s, while hydrogen was detected for the first time in 1960. (Although 500 times more abundant than methane, molecular hydrogen has much weaker absorption lines because it interacts only very weakly with electromagnetic waves.) Subsequent studies led to a growing list of new constituents, including the discovery of the arsenic compound arsine in 1990. The table includes a list of Jupiter’s atmospheric constituents and their abundances as determined by Earth-based, spacecraft, and atmospheric probe observations.

If the condition of chemical equilibrium held rigorously in Jupiter’s atmosphere, one would not expect to find molecules such as carbon monoxide or phosphine in the abundances measured. Neither would one expect the traces of acetylene, ethane, and other hydrocarbons that have been detected in the stratosphere. Evidently, there are sources of energy other than the molecular kinetic energy corresponding to local temperatures. Solar ultraviolet radiation is responsible for the breakdown of methane, and subsequent reactions of its fragments produce acetylene and ethane. In the convective region of the atmosphere, lightning discharges (observed by the Voyager and Galileo spacecraft) contribute to these processes. Still deeper, at temperatures around 1,200 K (1,700 °F, 930 °C), carbon monoxide is made by a reaction between methane and water vapour. Vertical mixing must be sufficiently strong to bring this gas up to a region where it can be detected from outside the atmosphere. Some carbon monoxide, carbon dioxide, and water in the atmosphere come from icy particles bombarding the planet from space.

Galileo’s probe carried a mass spectrometer that detected the constituent atoms and molecules in the atmosphere by first charging them and then spreading them out with a magnetic field according to their masses. This technique had the advantage that it could measure noble gases like helium and neon that do not interact with visible and infrared light. As the probe descended through the atmosphere on its parachute, its spectrometer also studied variations in abundance with altitude. This experiment finally detected the previously missing hydrogen sulfide, which was found to be present even lower in the atmosphere than anticipated. Evidently this cloud-forming gas, like ammonia and water vapour, was depleted in the upper part of the hot spot by the aforementioned downdraft. It was not possible to measure oxygen, because this element is bound up in water, and the probe did not descend into the hot spot deeply enough to reach the atmospheric region where this condensable vapour is well-mixed.

The elemental abundances in Jupiter’s atmosphere can be compared with the composition of the Sun (see the right two columns of the table). If, like the Sun, the planet had formed by simple condensation from the primordial solar nebula that is thought to have given birth to the solar system, their elemental abundances should be the same. A surprising result from the Galileo probe was that all the globally mixed elements that it could measure in the Jovian atmosphere showed the same approximately threefold enrichment of their values in the Sun, relative to hydrogen. This has important implications for the formation of the planet (see below Origin of the Jovian system). Spectroscopy from Earth reveals a large spread in the values of other elements (phosphorus, germanium, and arsenic) not measured by the probe. The abundances of the gases from which these elemental abundances are derived depend on dynamical phenomena in Jupiter’s atmosphere—principally chemical reactions and vertical mixing. The significance of the helium and neon depletions is discussed in the section The interior, below.

Another difference with solar values is indicated by the presence of deuterium on Jupiter. This heavy isotope of hydrogen has disappeared from the Sun as a result of nuclear reactions in the solar interior. Because no such reactions occur on Jupiter, the ratio of deuterium to hydrogen there should be identical to the ratio of those isotopes in the cloud of interstellar gas and dust that collapsed to form the solar system 4.6 billion years ago. Since deuterium was made in the big bang that is postulated to have begun the expansion of the universe, a still more accurate measurement of the deuterium/hydrogen ratio on Jupiter would allow the calibration of expansion models.