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Data on the toxicity of 6-methyl-2-oxoperhydropyrimidin-4-yl urea to aquatic organisms are not available for all trophic levels. Thus in accordance with Regulation (EC) No 1907/2006, Annex XI, 1.5. the assessment of the aquatic toxicity of the substance is partly based on information on the structurally related substance N,N''-(isobutylidene)diurea (CAS No 6104-30-9).

6-methyl-2-oxoperhydropyrimidin-4-yl urea (CAS No 1129-42-6) and N,N''-(isobutylidene)diurea (CAS No 6104-30-9) show extensive structural similarities. These similarities comprise the molecular structure of both substances as well as their molecular masses (N,N''-(isobutylidene)diurea: 174 g/mol, 6-methyl-2-oxoperhydropyrimidin-4-yl urea: 172 g/mol). The potential of both analogue substances to bioaccumulate is low according to their log Kow values (N,N''-(isobutylidene)diurea: -0.9; 6-methyl-2-oxoperhydropyrimidin-4-yl urea: -1.34).  Both substances are characterized by a low adsorption potential (log Koc N,N''-(isobutylidene)diurea: 1.4, log Koc 6-methyl-2-oxoperhydropyrimidin-4-yl urea: 0.098) and by a low vapor pressure (VP N,N''-(isobutylidene)diurea: 4.7 E-12 Pa, VP 6-methyl-2-oxoperhydropyrimidin-4-yl urea: ≤ 0.35 Pa). Thus a similar toxicity of the analogue substances can be expected.

Data on the short term toxicity of 6-methyl-2-oxoperhydropyrimidin-4-yl urea (CAS No 1129-42-6) is only available for aquatic invertebrates. In a screening study testing the effect of the substance on Daphnia magna an EC50 > 100 mg/L was determined.
For the structural analogue substance N,N''-(isobutylidene)diurea CAS No 6104-30-9 data are available for all three trophic levels (algae, aquatic invertebrates and fish). Effects of the substance on the tested organisms were not observed in the presented tests. In a study following OECD guideline 203 on fish a LC50 >1000 mg/L was observed after a study period of 96 hours. Comparable effect concentrations were determined for aquatic invertebrates and algae. In a guideline study following Directive 84/449/EEC, C.2 conducted with Daphnia magna as test organisms an EC50 of 500 mg/L was determined. Whereas in a test in accordance to DIN 38412, part 9 on algae an EC50 >500 mg/L was reported.

Experimental data on the long-term toxicity of 6-methyl-2-oxoperhydropyrimidin-4-yl urea are not available. However, based on the results of short-term toxicity tests for the structurally related substance N,N''-(isobutylidene)diurea CAS No 6104-30-9 and on the physico-chemical properties of 6-methyl-2-oxoperhydropyrimidin-4-yl urea (e.g. low log Pow) chronic effects of the substance on aquatic organisms are not expected. As the substance is readily biodegradable it is not likely that aquatic organisms are exposed to the test substance since it will be ultimately degraded in sewage treatment plants.

Data on the inhibition of nitrification in activated sludge microorganisms is available for 6-methyl-2-oxoperhydropyrimidin-4-yl urea. In a study following DIN EN ISO 9509:1995 an EC50 >100 mg/L was determined after 4 hours incubation time.