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This thesis comprises several independent research studies on transition metal complexes as trapped ions in isolation. Electrospray Ionization (ESI) serves to transfer ions from solution into the gas phase for mass spectrometric investigations. Subsequently, a variety of experimental and theoretical methods provide fundamental insights into molecular properties of the isolated complexes: InfraRed (Multiple) Photon Dissociation (IR-(M)PD) spectroscopy provides information on binding motifs and molecular structures at cryo temperatures as well as at room temperature. Collision Induced Dissociation (CID) serves to elucidate molecular fragmentation pathways as well as relative stabilities of the complexes at room temperature. Quantum chemical calculations via Density Functional Theory (DFT) substantiate the experimental results and deepen the fundamental insights into the molecular properties of the complexes. Magnetic couplings between metal centers in oligonuclear complexes are investigated by Broken Symmetry DFT modelling and X Ray Magnetic Circular Dichroism (XMCD) spectroscopy.