Mantras do not work that way; but certain bījāśara-s work on chakras. Each bījāśara works on a particular chakra. For example, laṁ works on mūlādhāra, vaṁ on svādhiṣṭhāna, etc. When we recite these bījāśara-s, if we give more emphasis on ṁ, we can feel subtle vibrations on the respective chakras. Pañcapūjā of a japa is based on this principle. Typically, pañcapūjā is a shorter form of antaryāga in navāvaraṇa pūjā.
Any mantra will produce heat in the body, provided it is properly initiated and repeated. There is no question of a particular mantra affecting a particular chakra. When mantras produce heat in the body, kundalini is also awakened automatically. This also produces heat in the body.