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Besides monoatomic oxygen, what other monoatomic or chemically reactive atmospheric or environmental constituents, if any, are present at orbital altitudes that aren't present at lower altitudes, and how do they affect spacecraft materials, instruments and equipment?

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Here I found a document that details the composition of the upper atmosphere: Empirical Modelling of the Thermosphere. In 300 km height, the main constituent of air is atomic oxygen at a density of about 10^14 atoms per cubic meter. There is some percentage of nitrogen, but all other elements seem to be negligible. There might be some more aggressive gases being released from the materials of the satellite itself - which is one of the reasons every component needs to be tested before it is allowed to be used in space.

To elaborate a bit on the influence of oxygen: As a satellite travels at about 7800 m/s, each square meter of its surface cuts through 7800 m^3 of air each second. This amounts 25 µg/s or 2 g/day.

I can't give details on the influence on the material of the satellite though. But NASA reports on the effect on the shuttle surfaces that "looked frosty because they were actually being eroded and textured".

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Above 100km altitude, there are few enough atmospheric particles that they can largely travel without collision. Because of this, chemical reactions mostly cease and become mostly irrelevant; without particle collisions, no reactions take place. In this region, called the Heterosphere, different species are spread into layers based on their atomic mass. This chart shows the general layers in which each species of particle inhabits. To answer the second part of the question, the particles in this region are so far apart that they likely have very little impact on spacecraft passing through them, as there simply aren't enough particles to have a noticeable effect.

References:

http://history.nasa.gov/NP-119/ch6.htm#n71

http://www.worldlibrary.org/articles/heterosphere

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    $\begingroup$ You have not heard of polymer degradation in LEO due to atomic oxygen erosion? $\endgroup$ – My Other Head Jan 15 '16 at 12:17

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