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Temperature is proportional to the average kinetic energy of particles in a medium. When impinged by infrared radiation, what happens on the microscopic level that translates that EM wave into the thermal motions of particles?

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Many people have the misconception that only infrared radiation creates heat. Actually electromagnetic radiation over all frequencies carries energy. The shorter the wavelength, the higher the energy.

Different elements and compounds (or molecules and atoms) have different resonant frequencies and so electromagnetic radiation of the same frequency tends to excite those particular materials, leading to heating - the absorption of the energy.

It just so happens that the everyday materials we are in contact with (water in your skin for example) is resonant with infrared frequencies, and so absorbs the infrared.

Why does the black pavement tend to be hotter than the white concrete on a sunny day? Because black tends to absorb a wider band of wavelengths and thus more energy.

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    $\begingroup$ This doesn't explain exactly what happens at a molecular level. $\endgroup$ – Abhigyan Chattopadhyay Feb 19 '18 at 3:35
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The answer is of course that the material involved has to have some channel through which it interacts with that electromagnetic wave - at its most basic, the material needs to be able to absorb the radiation.

You specifically ask about infrared radiation. The photons of infrared radiation (radiation is emitted and absorbed in quanta called photons) have energies of $\sim 0.1$ eV. It turns out that this energy is similar to the differences in energy between different excited states (vibrational and rotational) of molecules. So molecular material is very effective at absorbing infrared radiation, especially at photon energies that coincide with energy differences between these molecular energy levels. Excited molecules may also emit infrared radiation as well.

This energy can then be "shared out" amongst molecules, increasing their translational speeds by collisions between the molecules, which also excites or de-excites molecules between different energy levels.

When these processes come into equilibrium such that the molecules have a particular distribution of speeds and a particular distribution of occupation of their energy levels then this is what we characterise as a temperature.

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