A closely integrated theoretical and experimental effort to understand chemical bonding using X-ray spectroscopic probes is presented. Theoretical techniques to simulate XAS (X-ray absorption spectroscopy), XES (X-ray emission spectroscopy), RIXS (resonant inelastic X-ray scattering) and XPS (X-ray photoelectron spectroscopy) spectra have been developed and implemented within a density functional theory (DFT) framework. In combination with new experimental techniques, such as high-resolution XAS on liquid water under ambient conditions and XES on complicated surface adsorbates, new insight into e.g. hydrogen-bonded systems is obtained. For the (3×2) overlayer structure of glycine/Cu(110), earlier work has been extended to include adsorbate-adsorbate interactions. Structures are optimized for large cluster models and for periodic boundary conditions. It is found that specific features in the spectra arise from hydrogen-bonding interactions, which thus have important effects at the molecular-orbital level. XAS on liquid water shows a pronounced pre-edge feature with significant intensity, while the spectrum of ice shows only little intensity in this region. Theoretical spectrum calculations, based on instantaneous structures obtained from molecular-dynamics (MD) simulations, show that the pre-edge feature in the liquid is caused by water molecules with unsaturated hydrogen bonding. Some aspects of the theoretical simulations will be briefly discussed.