We discuss the design and optimisation of two types of junctions between surface-electrode radiofrequency ion-trap arrays that enable the integration of experiments with sympathetically cooled molecular ions on a monolithic chip device. A detailed description of a multi-objective optimisation procedure applicable to an arbitrary planar junction is presented, and the results for a cross junction between four quadrupoles as well as a quadrupole-to-octupole junction are discussed. Based on these optimised functional elements, we propose a multi-functional ion-trap chip for experiments with translationally cold molecular ions at temperatures in the millikelvin range. This study opens the door to extending complex chip-based trapping techniques to Coulomb-crystallised molecular ions with potential applications in mass spectrometry, spectroscopy, controlled chemistry and quantum technology.
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