Beyond Yield: Molecular Crop Quality as a Missing Dimension of Green Chemistry in Sustainable Agriculture

Green chemistry provides a conceptual and technological framework for redesigning agricultural inputs and analytical workflows toward safer, more efficient, and more sustainable crop production. In this review, molecular crop quality is proposed as a chemical and metabolomic endpoint of green chemistry in sustainable agriculture. Rather than evaluating agricultural interventions proposed as compatible with green chemistry only through yield, input reduction, or environmental performance, this review focuses on their capacity to reshape crop composition, including micronutrient density, primary metabolites, specialized metabolites, bioactive compounds, antioxidant potential, and bioaccessibility. Particular attention is given to nano-enabled biofortification, biogenic nanomaterials, plant-derived biostimulants, microbial consortia, and biodegradable carrier systems as tools that may modulate nutrient uptake, redox signaling, transcriptional regulation, and selected biosynthetic pathways. Representative changes in phenolics and flavonoids, carotenoids, glucosinolates, and capsaicinoids are discussed as examples of how agricultural interventions evaluated within a green chemistry framework can influence functional and nutritional traits at the molecular level. The review also considers green extraction and analytical platforms, including ultrasound-assisted extraction, microwave-assisted extraction, supercritical-fluid extraction, LC-MS, ICP-MS, NMR, and antioxidant assays, as essential tools for reliable assessment of molecular crop quality. Finally, safety-related challenges are critically examined, including nanoparticle characterization, dose-dependent phytotoxicity, environmental fate, bioaccessibility, and regulatory uncertainty. By integrating green chemistry, plant metabolism, nano-enabled biofortification, biostimulation, and analytical chemistry, this review outlines a framework for assessing crop quality beyond yield and highlights the need for standardized, mechanistically informed, and safety-oriented approaches to future agricultural innovation.