Aims. We present new IRAM Plateau de Bure Interferometer observations of Arp 220 in HCN, HCO$^{+}$, HN$^{13}$C J=1-0, C$_{2}$H N=1-0, SiO J = 2-1, HNCO J$_{k,k}$ = 5$_{0,4}$ - 4$_{0,4}$, CH$_{3}$CN(6-5), CS J=2-1 and 5-4 and $^{13}$CO J=1-0 and 2-1 and of NGC 6240 in HCN, HCO$^{+}$ J = 1-0 and C$_{2}$H N = 1-0. In addition, we present Atacama Large Millimeter/submillmeter Array science verification observations of Arp 220 in CS J = 4-3 and CH$_{3}$CN(10-9). Various lines are used to analyse the physical conditions of the molecular gas including the [$^{12}$CO]/[$^{13}$CO] and [$^{12}$CO]/[C$^{18}$O] abundance ratios. These observations will be made available to the public. Methods. We create brightness temperature line ratio maps to present the different physical conditions across Arp 220 and NGC 6240. In addition, we use the radiative transfer code RADEX and a Monte Carlo Markov Chain likelihood code to model the $^{12}$CO, $^{13}$CO and C$^{18}$O lines of Arp 220 at ~2 (~700 pc) scales, where the $^{12}$CO and C$^{18}$O measurements were obtained from literature. Results. Line ratios of optically thick lines such as $^{12}$CO show smoothly varying ratios while the line ratios of optically thin lines such as $^{13}$CO show a east-west gradient across Arp 220. The HCN/HCO$^{+}$ line ratio differs between Arp 220 and NGC 6240, where Arp 220 has line ratios above 2 and NGC 6240 below 1. The radiative transfer analysis solution is consistent with a warm (~40 K), moderately dense (~10$^{3.4}$ cm$^{-3}$) molecular gas component averaged over the two nuclei. We find [$^{12}$CO]/[$^{13}$CO] and [$^{12}$CO]/[C$^{18}$O] abundance ratios of ~90 for both. The abundance enhancement of C$^{18}$O can be explained by stellar nucleosynthesis enrichment of the interstellar medium.
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