A method of performing a computation using a quantum computer includes generating a first laser pulse and a second laser pulse to cause entanglement interaction between a first trapped ion and a second trapped ion of a plurality of trapped ions that are aligned in a first direction, each of the plurality of trapped ions having two frequency- separated states defining a qubit, and applying the generated first laser pulse to the first trapped ion and the generated second laser pulse to the second trapped ion. Generating the first laser pulse and the second laser pulse includes stabilizing the entanglement interaction between the first and second trapped ions against fluctuations in frequencies of collective motional modes of the plurality of trapped ions in a second direction that is perpendicular to the first direction.