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The natural compounds of boron have many applications, primarily as a dietary supplement. The research is based on the discovery that the diester chlorogenoborate complex can be detected and quantified from green coffee beans. The study reports that such a diester molecule can also be synthesized in a stable form via the direct reaction of boric acid and chlorogenic acid in a mixture of acetonitrile–water (1:1, v/v) and left to evaporate over a period of 48 h at room temperature, resulting in a spirocyclic form (diester complex). The diester complex, with its molecular structure and digestibility attributes, has potential application as a prebiotic in gut health and oral health, and as a micronutrient essential for microbiota in humans and animals.