See, it's funny because...well...if you don't know the phrase, check out this video.
Hydrogen bonds form between two molecules that have high electronegativity differences between hydrogen and another nonmetal (typically F, N, or O). Hydrogen and the highly electronegative element can get very close to each other due to hydrogen's small atomic radius, so the molecules attract very strongly.
That makes this joke especially ironic because James Bond almost never got emotionally close to any of his co-stars...except Teresa Draco, of course.
The joke has also been made about ionic and covalent bonds...because it's an easy joke to make...
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