Nano-Boron Enhances Boron Accumulation and Alters the Tomato Leaf Metabolome: Molecular Modeling of Leaf-Surface and Boron Transporter–Metabolite Interactions

Abstract Boron (B) deficiency severely limits tomato (Solanum lycopersicum L.) productivity and fruit quality, particularly in alkaline or low-organic-matter soils, while conventional foliar boron fertilizers suffer from low uptake efficiency and environmental losses. In this study, we developed and characterized a novel nanoboron (NB) formulation and evaluated its efficacy compared with boric acid using physicochemical characterization, molecular simulations, greenhouse studies, metabolomics, and field validation. Physicochemical analyses confirmed stable nanoscale particles (∼58 nm hydrodynamic diameter, PDI 0.266, zeta potential −15.7 mV) with favorable colloidal stability. Molecular dynamics simulations demonstrated stable interfacial association of the nanoformulation with the leaf surface model without disruptive penetration. The foliar application in tomato cv. Shivam resulted in significantly higher boron accumulation in NB-treated leaves (1550–2080 ppm over 4–14 days) compared with boric acid and untreated controls. Untargeted metabolomics revealed distinct metabolic reprogramming, with significant modulation of stress-associated metabolites and volatile compounds following NB treatment. Molecular docking suggested potential interactions of differentially regulated metabolites with boron transporters (BOR1, NIP5;1) and antioxidant-related proteins, indicating possible links to boron homeostasis and redox regulation. Field-level validation demonstrated that NB significantly improved reproductive and yield parameters, including flower number, fruit set, fruit weight, and total yield (∼21 t ha–1), compared with conventional boric acid treatments. Collectively, these findings demonstrate that the NB formulation is an effective and sustainable foliar boron delivery system with enhanced nutrient use efficiency and promising agronomic benefits for tomato cultivation.