The inner couple hundred pcs of our Galaxy is characterized by significant amount of synchrotron-emitting gas, which appears to co-exist with a large reservoir of molecular gas. Many of the best studied sources in this region exhibit a mixture of 6.4 keV Fe K alpha emission, molecular line emission and nonthermal radio continuum radiation. The spatial correlation between fluorescent Fe K- alpha line emission at 6.4 keV and molecular line emission from Galactic center molecular clouds has been explained as reflected X-rays from a past outburst of Sgr A*. Here we present multi-wavelength study of a representative Galactic center cloud Sgr C using Chandra, VLA and FCRAO. We note a correlation between the nonthermal radio filaments in Sgr C and the X-ray features, suggesting that the two are related. This correlation, when combined with the distribution of molecular gas suggests against the irradiation of Sgr C by Sgr A*. Instead, we account for this distribution in terms of the impact of the relativistic particles from local (nonthermal filaments) and extended sources with diffuse neutral gas producing both a nonthermal bremsstrahlung X-ray continuum emission, as well as diffuse 6.4 keV line emission. The production rate of Fe K alpha photons associated with the injection of electrons into a cloud as a function of column density is calculated. The required energy density of low-energy cosmic rays associated with the synchrotron emitting radio filaments or extended features is estimated to be in the range between 20 and 103 eV cm-3 for Sgr C, Sgr B1, Sgr B2, and ``the 45 and -30 km s-1'' clouds. We also generalize this idea to explain the cosmic-ray heating of molecular gas, the interstellar cosmic ray ionization, the pervasive production of diffuse K alpha line and TeV emission from the Galactic center molecular clouds. In particular, we suggest that Inverse Compton scattering of the sub-millimeter radiation from dust by relativistic electrons may contribute substantially to the large-scale diffuse TeV emission observed towards the central regions of the Galaxy.