Multiline observations of C18O and SiO isotopomers toward 33 molecular peaks in the Galactic center region, taken at the SEST, JCMT and HHT telescopes, are presented. The C18O presumably traces the total H2 column ensity, while the SiO traces gas affected by shocks and high temperature chemistry. The J =2->1 line of SiO is seen only in few regions of the Galactic disk. This line is easily detected in all Galactic center sources observed. A comparison of the strength of the rare isotopomers ^29SiO and 30SiO to the strength of he main isotopomer 28SiO implies that the J = 2 -> 1 transition of 28SiO, is optically thick. The isotope ratio of 29Si/30Si of 1.6 in the Galactic center clouds s consistent with the terrestrial value. Large Velocity Gradient models show that the dense component (nH_2 >= 104%) in typical molecular cores in the Galactic center is cool (Tkin ~ 25 K), contrary to what is usually found in Giant Molecular Clouds in the disk, where the densest cores are the hottest. High kinetic temperatures, > 100 K, known to exist from NH3 studies, are only present at lower gas densities of a few 103% , where SiO is highly subthermally excited. Assuming that C18O traces all of the molecular gas, it is found that in all cases but one, SiO emission is compatible with arising in gas at higher density that is (presently) relatively cool. The relative abundance of SiO is typically 10-9, but differs significantly between individual sources. It shows a dependence on the position of the source within the Galactic center region. High abundances are found for the locations bar potential models predict for preferred collision regions. These results can be used to relate the amount of gas that has encountered shocks within the last ~ 106 years to the large scale kinematics in the inner ~ 500 pc of the Galaxy.