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Alchemical transformation of methane (CH4) to ammonia (NH3) (see also Figure 2). The ammonia end state is shown (nitrogen, blue; hydrogen, gray; dummy atom, pink). (a) The “proper” geometry, where the dummy atom is positioned as it would be in methane. (b) One alternative position the dummy atom can adopt if attached only through nonredundant bonded terms, i.e., one bond and two angles.
