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[Display omitted] • Structures of isolated kilodalton ligand-protected gold nanoclusters are studied. • By means of gas-phase InfraRed Multiple Photon Dissociation spectroscopy compared to quantum chemistry calculations. • Nanocluster complexes consist of ten or eleven gold atoms that are bound to glutathione or phosphine ligands. • Theoretical calculations are able to reproduce well the experimental IR spectra, although the size of such species makes difficult a precise assignment among the many possible molecular arrangements. This paper reports an attempt to structurally characterize isolated ligand-protected gold nanoclusters by means of gas-phase InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy compared to quantum chemistry Density Functional Theory (DFT) calculations. The mass-selected kilodalton nanocluster complexes consist of ten or eleven gold atoms that are bound to glutathione or phosphine ligands and are produced by ElectroSpray Ionization (ESI) in the form of multiply charged anions or cations. This study allows us to build some methodology benchmarks for species that are large for IRMPD experiments and that are used for biochemistry applications. These gas-phase results on isolated ions are compared to condensed phase data from Fourier-Transform InfraRed (FTIR) spectroscopy and to theoretical IR spectra that are calculated with two different functional/basis sets, namely B3LYP/6-31G* and M06L/LanL2DZ, at the scaled static harmonic level. Although theoretical calculations are able to reproduce well the experimental IR spectra, the size of such species and the presence of many possible interactions between ligands make difficult a precise assignment among the many possible molecular arrangements. [ABSTRACT FROM AUTHOR]