Novel series of ring junction N-substituted  pyrimidine derivatives viz. 7-(Sub-phenyl)-6-(sub-benzoyl)-5-methyl-2,4,7-tetrahydro-3,4,8-triazainden-1-ones III(1-16)have been synthesized by Cyclocondensation of 6-Methyl-5-(sub-benzoyl)-4-(sub-phenyl)-3,4-dihydro-1-H-pyrimid-2-one/thiones with amino acid such as glycine by using microwave assisted method in presence of POCl₃ + PPA mixture acts both as a catalyst and as a solvent which makes the process eco-friendly, economic and easy. The structures of the synthesized compounds have been conformed on the basis of IR,H¹-NMR,UV and Elemental analysis. Some of them have been screened for their antimicrobial activitity against fungal pathogens like Aspergillus oryzae and Fusarium oxysporum and bacterial pathogens like E-coli (Gram –ve) and Staphylococci (Gram +ve) . Also cytotoxicity and  phytotic(antifungal) effects  of some newly synthesized compounds on crop plants Vigna radiata (Green gram) and Gossypium herbaceum L. (Cotton)  have been checked.