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An uracil-azo derivative of quinoline, 1,3-dimethyl-5-(8′-quinolinyl-azo)-6-aminouracil (H2L, 1), was synthesized and then converted into its atropisomers, 1,3-dimethyl-8-(8′-quinolinyl)azaxanthine (α-atropisomer (2) and β-atropisomer (3)). It is indeed a notable accomplishment that the atropisomers were synthesized selectively under dissimilar reaction conditions. Additionally, an axially elongated 5-coordinated distorted square pyramidal copper(II)-complex, [CuII(HL)(H2O)2]NO3 (4), was synthesized from H2L, where it acts as a tridentate ligand. Single crystals of compounds 2–4 were analyzed for their stereochemical characterization. The compounds (2 and 3) belong to the same space group P21 with Z = 2. Based on a torsional angle about N3–N2–C1–C9, which is 48.7(2)° for the α-atropisomer (2) and −48.7(2)° for the β-atropisomer (3), respectively, they are revealed to be atropisomers. According to TD-DFT analysis, the α-atropisomer (2) is 0.05 kcal mol−1 more energetically stable than the β-atropisomer (3). The 5-coordinated Cu1 centre adopts a distorted square pyramidal geometry (space group P21/n, Z = 4), wherein the coordination sites were occupied by three-N and two O-donor atoms from the HL− moiety and the two H2O molecules, respectively. The polycrystalline sample of 4 was subjected to direct current (dc) variable-temperature magnetic susceptibility studies over the temperature range of 1.8–300 K. The magnetic study suggests that copper(II) ions in the crystal lattice have a weak antiferromagnetic interaction, demonstrating the complex to be a mononuclear species. According to the EPR study, the distorted square-pyramidal copper(II) complex may have a dx2−y2 orbital as a ground state. All the compounds have shown significant efficacy against the bacterial plant pathogen, Ralstonia solanacearum Smith. and the fungal plant pathogen, Rhizoctonia solani Kuhn., which cause bacterial wilting of solanaceous crops and sheath blight of rice, respectively. Besides, the atropisomers have demonstrated effectiveness against another bacterial plant pathogen, Xanthomonas oryzaepv. oryzae. that causes bacterial blight of rice. The atropisomers thus differ with respect to biological efficacy towards both bacterial and fungal diseases. [ABSTRACT FROM AUTHOR]