straightforward due to the natural ability of quantum computers to simulate unitary time evolution, circuit depth limitations restrict the maximum time that can be simulated and hence the extraction of frequency-domain properties. Computing properties directly in the frequency domain is therefore desirable, but the circuits require large depth when the typical hardware gate set consisting of single- and two-qubit gates is used. Here, we report the experimental quantum computation of the response properties of diatomic molecules directly in the frequency domain using a three-qubit iToffoli gate, enabling a reduction in circuit depth by a factor of two. We show that the molecular properties obtained with the iToffoli gate exhibit comparable or better agreement with theory than those obtained with the native CZ gates. Our work is among the first demonstrations of the practical usage of a native multi-qubit gate in quantum simulation, with diverse potential applications to the simulation of quantum many-body systems on near-term digital quantum computers.