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It goes back in history, Vcc applies to transistors, Volts collector common, Vdd applies to fets, Volts drain ?. Vee, Volts emitter ?. It's been lost with the passage of time!
Programming Pulse voltage. Back when the 2708 EPROM was king, the programming was done with 25V pulses applied to the Vpp pin. The timing requirements on this voltage were rather stringent (and the algorithm complicated), so the next parts, starting with 2716, used a FIXED 25V voltage and the programming pulse was just a TTL signal applied to the PGM pin.
However, the name of the Vpp pin lives on, even though it is now used to only supply a DC voltage. You will find it even on FLASH devices. Applying 12V to this pin (again, DC, not pulses) speeds up the programming of the FLASH (but it is not necessary).
In some microcontrollers, such as FLASH-based PICs, the Vpp is required only to put the part into programming mode, not to actually program the internal FLASH memory. For that there is an internal charge pump. But the name Vpp is still used.
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