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The Medium Resolution Spectrometer on board JWST/MIRI will give access to mid-IR spectra while retaining spatial information. With the unparalleled sensitivity of JWST and the MIRI detectors, the MRS has the potential to revolutionise our understanding of giant exoplanet atmospheres. Molecular mapping is a promising detection and characterisation technique used to study the spectra of directly imaged exoplanets. We aim to examine the feasibility and application of this technique to MRS observations. We used the instrument simulator MIRISIM to create mock observations of resolved star and exoplanet systems. As an input for the simulator, we used stellar and planet parameters from literature, with the planet spectrum being modelled with the radiative transfer code petitRADTRANS. After processing the raw data with the JWST pipeline, we high pass filter the data to account for the stellar point spread function, and used a forward modelling approach to detect the companions and constrain the chemical composition of their atmospheres through their molecular signatures. We identified limiting factors in spectroscopic characterisation of directly imaged exoplanets with the MRS and simulated observations of two representative systems, HR8799 and GJ504. In both systems, we could detect the presence of multiple molecules that were present in the input model of their atmospheres. We used two different approaches with single molecule forward models, used in literature, that are sensitive to detecting mainly H$_2$O, CO, CH$_4$, and NH$_3$, and a log-likelihood ratio test that uses full atmosphere forward models and is sensitive to a larger number of less dominant molecular species. We show that the MIRI MRS can be used to characterise widely separated giant exoplanets in the mid-IR using molecular mapping., 18 pages, 10 figures. Accepted for publication in Astronomy & Astrophysics

Clouds are ubiquitous in exoplanet atmospheres and represent a challenge for the model interpretation of their spectra. Complex cloud models are too numerically costly for generating a large number of spectra, while more efficient models may be too strongly simplified. We aim to constrain the atmospheric properties of the directly imaged planet HR 8799e with a free retrieval approach. We use our radiative transfer code petitRADTRANS for generating spectra, which we couple to the PyMultiNest tool. We added the effect of multiple scattering which is important for treating clouds. Two cloud model parameterizations are tested: the first incorporates the mixing and settling of condensates, the second simply parameterizes the functional form of the opacity. In mock retrievals, using an inadequate cloud model may result in atmospheres that are more isothermal and less cloudy than the input. Applying our framework on observations of HR 8799e made with the GPI, SPHERE and GRAVITY, we find a cloudy atmosphere governed by disequilibrium chemistry, confirming previous analyses. We retrieve that ${\rm C/O}=0.60_{-0.08}^{+0.07}$. Other models have not yet produced a well constrained C/O value for this planet. The retrieved C/O values of both cloud models are consistent, while leading to different atmospheric structures: cloudy, or more isothermal and less cloudy. Fitting the observations with the self-consistent Exo-REM model leads to comparable results, while not constraining C/O. With data from the most sensitive instruments, retrieval analyses of directly imaged planets are possible. The inferred C/O ratio of HR 8799e is independent of the cloud model and thus appears to be a robust. This C/O is consistent with stellar, which could indicate that the HR 8799e formed outside the CO$_2$ or CO iceline. As it is the innermost planet of the system, this constraint could apply to all HR 8799 planets., Comment: Accepted for publication in A&A, 28 pages, 13 figures, updated author list