A method of performing an entangling operation between two trapped ions in a quantum computer includes selecting a gate duration value of a pulse to be applied to a first ion and a second ion in a chain of trapped ions, determining one or more tones of the pulse, each tone comprising an amplitude value and a detuning frequency value, based on the selected gate duration value and frequencies of the motional modes of the chain of trapped ions, generating the pulse having the one or more tones, each tone comprising the determined amplitude and the determined detuning frequency values, and applying the generated pulse to the first and second ions for the gate duration value. Each of the trapped ions has two frequency-separated states defining a qubit, and motional modes of the chain of trapped ions each have a distinct frequency.