The transparent window, on to which the sample is deposited, is usually cooled using a compressed
helium or similar refrigerant. Experiments must be performed under a high vacuum to prevent contaminants from unwanted gases freezing to the cold window. Lower temperatures are preferred, due to the improved rigidity and "glassiness" of the matrix material. Noble gases such as
argon are used not just because of their unreactivity but also because of their broad optical
transparency in the solid state. Mono-atomic gases have relatively simple
face-centered cubic (fcc) crystal structure, which can make interpretations of the site occupancy and
crystal-field splitting of the guest easier. In some cases a
reactive material, for example,
methane,
hydrogen or
ammonia, may be used as the host material so that the reaction of the host with the guest species may be studied. Using the matrix isolation technique, short-lived, highly-reactive species such as
radical ions and reaction intermediates may be observed and identified by
spectroscopic means. For example, the solid noble gas
krypton can be used to form an inert matrix within which a reactive
F3− ion can sit in chemical isolation. The reactive species can either be generated outside (before deposition) the apparatus and then be condensed, inside the matrix (after deposition) by irradiating or heating a precursor, or by bringing together two reactants on the growing matrix surface. For the deposition of two species it can be crucial to control the contact time and temperature. In
twin jet deposition the two species have a much shorter contact time (and lower temperature) than in
merged jet. With
concentric jet the contact time is adjustable. ==Spectroscopy==