We suggest a method for probing global properties of clump populations in Giant Molecular Clouds (GMCs) in the case where these act as X-ray reflection nebulae (XRNe), based on the study of the clumpings overall effect on the reflected X-ray signal, in particular on the Fe K-alpha lines shoulder. We consider the particular case of Sgr B2, one of the brightest and most massive XRN in our Galaxy. We parametrise the gas distribution inside the cloud using a simple clumping model, with the slope of the clump mass function (alpha), the minimum clump mass (m_{min}), the fraction of the clouds mass contained in clumps (f_{DGMF}), and the mass-size relation of individual clumps as free parameters, and investigate how these affect the reflected X-ray spectrum. In the case of very dense clumps, similar to those presently observed in Sgr B2, these occupy a small volume of the cloud and present a small projected area to the incoming X-ray radiation. We find that these contribute negligibly to the scattered X-rays. Clump populations with volume filling factors of > 10^{-3}, do leave observational signatures, that are sensitive to the clump model parameters, in the reflected spectrum and polarisation. Future high-resolution X-ray observations could therefore complement the traditional optical and radio observations of these GMCs, and prove to be a powerful probe in the study of their internal structure. Finally, clumps in GMCs should be visible both as bright spots and regions of heavy absorption in high resolution X-ray observations. We therefore further study the time-evolution of the X-ray morphology, under illumination by a transient source, as a probe of the 3d distribution and column density of individual clumps by future X-ray observatories.
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