Use of molecular electron spins as qubits for quantum computing will depend on the ability to produce molecules with weak but measurable interactions between the qubits.H ere we demonstrate use of pulsed EPR spectroscopy to measure the interaction between two inequivalent spins in ahybrid rotaxane molecule.Molecular electron spins are potential qubits for quantum information processing (QIP).[1] Much recent work has been dedicated to showing that the phase memory times of S = 1/2 molecules can be controlled, and extended to the point where multiple spin manipulations will be possible.[2] One of the key next steps is to study the interactions between such spins. Recently,A rdavan et al. have shown using double electronelectron resonance (DEER) spectroscopy that the interaction between electron spins in {Cr 7 Ni}r ings can be controlled to fall within the range needed for two qubit gates.[3] These studies were performed on dimers of {Cr 7 Ni}rings [4] where the S = 1/2 spins in each half are identical.Systems containing different spins also have great potential for QIP as there is then the possibility of manipulating each spin separately.T his underpins the g-engineering idea proposed by Takui and co-workers for organic radicals [5] and work employing heterometallic lanthanide dimers.[6] Large differences in g-values could also be used as am eans to implement entangling two qubit gates.[7] Quantifying weak interactions between very different spins is challenging.I n cases where the interaction can easily be measured, for example by magnetometry or continuous-wave (CW) electron paramagnetic resonance (EPR) spectroscopy, [8] the interaction will be too large to permit implementation of both one-and two-qubit gates in the same molecule.[3] CW EPR spectroscopy can still be au seful tool to investigate dipolar interactions;byobserving the line broadening of aN triplet in at wo-qubit structure,Z hou et al. showed the existence of ad ipolar interaction that they could estimate in conjunction with spin density calculations.[9] On the other hand, DEER spectroscopy, [10] while ap owerful tool to measure weak interactions by directly manipulating two weakly interacting spins with specific microwave pulses,i s limited as the bandwidth of the microwave source must encompass the resonant frequency of both electron spins.Here we report at wo-qubit assembly comprising an organic radical within the thread of ah ybrid [2]rotaxane containing a{Cr 7 Ni}ring:this is aheterospin system where the constituent spins possess vastly different g-values.T oquantify the weak interaction between the spins we use "Relaxation Induced Dipolar Modulation" (RIDME) spectroscopy, [11] which has been developed in structural biology to measure distances between dissimilar spins. [12] To make the [2]rotaxane an organic thread was synthesized containing as econdary amine and terminating in an aldehyde (see the Supporting Information for details).