The molecular clouds Lupus 1, 3 and 4 were mapped with the Mopra telescope at 3 and 12 mm. Emission lines from high density molecular tracers were detected, i.e. NH$_3$ (1,1), NH$_3$ (2,2), N$_2$H$^+$ (1-0), HC$_3$N (3-2), HC$_3$N (10-9), CS (2-1), CH$_3$OH (2$_0-1_0$)A$^+$ and CH$_3$OH (2$_{-1}-1_{-1}$)E. Velocity gradients of more than 1 km s$^{-1}$ are present in Lupus 1 and 3 and multiple gas components are present in these clouds along some lines of sight. Lupus 1 is the cloud richest in high density cores, 8 cores were detected in it, 5 cores were detected in Lupus 3 and only 2 in Lupus 4. The intensity of the three species HC$_3$N, NH$_3$ and N$_2$H$^+$ changes significantly in the various cores: cores that are brighter in HC$_3$N are fainter or undetected in NH$_3$ and N$_2$H$^+$ and vice versa. We found that the column density ratios HC$_3$N/N$_2$H$^+$ and HC$_3$N/NH$_3$ change by one order of magnitude between the cores, indicating that also the chemical abundance of these species is different. The time dependent chemical code that we used to model our cores shows that the HC$_3$N/N$_2$H$^+$ and HC$_3$N/NH$_3$ ratios decrease with time therefore the observed column density of these species can be used as an indicator of the chemical evolution of dense cores. On this base we classified 5 out of 8 cores in Lupus 1 and 1 out of 5 cores in Lupus 3 as very young protostars or prestellar cores. Comparing the millimetre cores population with the population of the more evolved young stellar objects identified in the Spitzer surveys, we conclude that in Lupus 3 the bulk of the star formation activity has already passed and only a moderate number of stars are still forming. On the contrary, in Lupus 1 star formation is on-going and several dense cores are still in the pre--/proto--stellar phase. Lupus 4 is at an intermediate stage, with a smaller number of individual objects.
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