Galaxies in Hickson Compact Groups (HCGs) are believed to experience morphological transformations from blue, star-forming galaxies to red, early-type galaxies. Galaxies with a high ratio between the luminosities of the warm H2 to the 7.7mu PAH emission (Molecular Hydrogen Emission Galaxies, MOHEGs) are predominantly in an intermediate phase, the green valley. Their enhanced H2 emission suggests that the molecular gas is affected in the transition. We study the properties of the molecular gas traced by CO in galaxies in HCGs with measured warm H2 emission in order to look for evidence of the perturbations affecting the warm H2 in the kinematics, morphology and mass of the molecular gas. We analyzed the molecular gas mass derived from CO(1-0), MH2, and its kinematics, and then compared it to the mass of the warm molecular gas, the stellar mass and star formation rate (SFR). Our results are the following. (i) The mass ratio between the CO-derived and the warm H2 molecular gas is in the same range as for field galaxies. (ii) Some galaxies, mostly MOHEGs, have very broad CO linewidths of up to 1000 kms. The line shapes are irregular and show various components. (iii) The mapped objects show asymmetric distributions of the cold molecular gas. (iv) The star formation efficiency (= SFR/MH2) of galaxies in HCGs is similar to isolated galaxies. No significant difference between MOHEGs and non-MOHEGs or between early-types and spirals has been found. (v) The molecular gas masses, MH2, and MH2/LK are lower in MOHEGs (predominantly early-types) than in non-MOHEGs (predominantly spirals). This trend remains when comparing MOHEGs and non-MOHEGs of the same morphological type. The differences in the molecular gas properties of MOHEGs support the view that they are suffering perturbations of the molecular gas, as well as a decrease in the molecular gas content and associated SFR.
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