Molecular clouds within 300 pc of the galactic center (GC) are known to exhibit different physical properties and chemistry than those in the outer Galaxy. High kinetic temperatures (>100K) well above the dust temperatures are found in these molecular clouds. This rules out gas-dust collisions as the main heating mechanism for the molecular clouds in the GC, so alternative mechanisms which only act directly on the gas are required. Several heating mechanisms have been proposed (UV radiation, enhanced flux of Cosmic Rays, supersonic "turbulence" and ambipolar diffusion) but the lack of a detailed knowledge of the properties of these clouds has prevented from drawing any definite conclusions. We propose to make a detail investigation of the physical conditions, namely the energetics, kinematics, ionization structure and chemical composition of an unbiased sample of 30 molecular clouds in the GC region by observing selected lines from key molecules (OH, CO, H2, CH, HeH+) and neutral and ionized atoms (CII, OI, NII, SiI, SiII, SI, SIII and NeII). These data will provide, for the first time, the abundance of those species which will allow us to understand the energy balance (cooling and heating) of molecular clouds in the GC. Our understanding of the properties of molecular clouds in the center of the Galaxy is extremely important, with this information for a nearby prototype, we have a unique comparison with more distant galaxies for which our angular resolution and sensitivity are inadequate.