If most of the space in an atom is empty, why don’t we see everything transparent?

An atom is not mostly empty. It is what one is usually taught when one begins to study modern atomic theory, but it is totally incorrect.

An atom is not like a tiny solar system. In one you have a fuzzy quantum cloud of nucleons — protons and neutrons —, representing the region where they are most likely to be found, surrounded by a fuzzy quantum cloud of electrons, representing the region where they are most likely to be found. Those regions have different layers; in the first layer of the nucleonic quantum cloud there can only be two protons and two neutrons and in the first layer of the electronic quantum cloud only two electrons, to give an example in each of the clouds. But even outside these clouds you can find nucleons and electrons, albeit in a lesser probability. A very low probability does not represent a null probability. I could even mention that they are always over a region called the quantum vacuum,

But this still hasn’t answered the question.

To answer it, we first have to understand what transparency is.

A material has energy bands — ie, electron orbitals so close together that they form an energy continuum, the energy band — and those energy bands are organized in a certain way. An energy gap appears between these bands. If an electromagnetic wave has an energy corresponding to that gap or more, it is absorbed by the atoms/ions/molecules of the material and that absorption excites said atoms/ions/molecules. Also, the material will not be transparent to that electromagnetic wave. On the other hand, it will be for electromagnetic waves with energies lower than that gap.

Therefore, any material is transparent to certain electromagnetic waves and non-transparent to others.

To give examples:

  • the energy gap of glass (silicon dioxide) at a temperature of about302K ≈ _ 29∘C302 K≈29∘Cit’s about9 eV 9 eV[WikipediaEN. bandgap _“]. That means that an electromagnetic wave with an energy equal to9 eV 9 eVor more will be absorbed by the glass atoms (silicon dioxide) and that absorption will excite them. An electromagnetic wave with an energy exactly equal to9 eV 9 eVIt has a wavelength of about138nm , _ 138 nm,which corresponds to ultraviolet radiation. Above this radiation we have X-rays and gamma rays. Therefore, glass (silicon dioxide) is not transparent to ultraviolet radiation, X-rays, or gamma rays. On the other hand, it is for visible light, for infrared, for microwaves and for radio waves.
  • the energy gap of liquid water at a temperature of about300K ≈ _ 27∘C300 K≈27∘Cit’s about9.0 ± 0.2eV _ _ _ _ _ 9,0±0,two eV[Thomas Bischoff, Igor Reshetnyak, and Alfredo Pasquarello Phys. Rev. Research 3, 023182. ” Band gaps of liquid water and hexagonal ice through advanced electronic-structure calculations” (2021)]. That means that an electromagnetic wave with an energy approximately equal to9 eV 9 eVor more will be absorbed by the water molecules and that absorption will excite them. An electromagnetic wave with an energy exactly equal to9 eV 9 eVIt has a wavelength of about138nm, _ 138 nm,which corresponds to ultraviolet radiation. Above this radiation we have X-rays and gamma rays. Therefore, liquid water is not transparent to ultraviolet radiation, X-rays, or gamma rays. On the other hand, it is for visible light, for infrared, for microwaves and for radio waves.
  • the energy gap of gallium phosphide at a temperature of about302K ≈ _ 29∘C302 K≈29∘Cit’s about2.26eV _ _ _ two,26 eV[WikipediaEN. bandgap _“]. That means that an electromagnetic wave with an energy equal to2.26eV _ _ _ two,26 eVor more will be absorbed by the gallium phosphide atoms and that absorption will excite them. An electromagnetic wave with an energy exactly equal to2.26eV _ _ _ two,26 eVIt has a wavelength of about549nm , _ 549 nm,which corresponds to visible light. Above this radiation we have ultraviolet radiation, X-rays and gamma rays. Therefore, gallium phosphide is not transparent to visible light, ultraviolet radiation, X-rays, or gamma rays. On the other hand, it is for infrared, for microwaves and for radio waves.