We propose a laser-free method for creation of a phonon two-mode squeezed state and a beam-splitter transformation, using time-varying electric fields and non-linear couplings between the normal modes in a linear ion crystal. Such non-linear Coulomb-mediated interactions between the collective vibrational modes arise under specific trap-frequency conditions in an ion trap. We study the quantum metrological capability for parameter estimation of the two quantum states and show that a Heisenberg limit of precision can be achieved when the initial state with n phonons evolves under the action of the beam-splitter transformation. Furthermore, we show that the phonon non-linearity and the spin-dependent force can be used for creation of a three-qubit Fredkin gate.