The electronic structures of boron nitride nanotubes (BNNTs) doped by organic molecules are investigated with density functional theory. Electrophilic molecule introduces acceptor states in the wide gap of BNNT close to the valence band edge, which makes the doped system a $p$-type semiconductor. However, with typical nucleophilic organic molecules encapsulation, only deep occupied molecular states but no shallow donor states are observed. There is a significant electron transfer from BNNT to electrophilic molecule, while the charge transfer between nucleophilic molecule and BNNT is neglectable. When both electrophilic and nucleophilic molecules are encapsulated in the same BNNT, large charge transfer between the two kinds of molecules occurs. The resulted small energy gap can strongly modify the transport and optical properties of the system.
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