Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite

Abstract

Today’s fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future, and therefore effective P use is crucial to avoid food shortage. A substantial amount of P from fertilizers gets adsorbed onto soil minerals to become unavailable to plants. Understanding P interaction with these minerals would help efforts that improve P efficiency. To this end, we performed a molecular level analysis of the interaction of common organic P compounds (glycerolphosphate (GP) and inositol hexaphosphate (IHP)) with the abundant soil mineral (goethite) in presence of water. Molecular dynamics simulations are performed for goethite–IHP/GP–water complexes using the multiscale quantum mechanics/molecular mechanics method. Results show that GP forms monodentate (M) and bidentate mononuclear (B) motifs with B being more stable than M. IHP interacts through multiple phosphate groups with the 3M motif being most stable. The order of goethite–IHP/GP interaction energies is GP M < GP B < IHP M < IHP 3M. Water is important in these interactions as multiple proton transfers occur and hydrogen bonds are formed between goethite–IHP/GP complexes and water. We also present theoretically calculated infrared spectra which match reasonably well with frequencies reported in literature.

Deciphering competitive interactions: Phosphate and organic matter binding on goethite through experimental and theoretical insights

“…Consequently, the current study will revolve around discussing the processes of P binding and the impact of OM, without delving into the intricacies of bond formation and dissociation. These aspects, extensively discussed in our previous studies, entailed a comprehensive understanding of the P-binding mechanism to soil constituents at the quantum mechanics level (Ahmed et al, 2023(Ahmed et al, , 2020(Ahmed et al, , 2019(Ahmed et al, , 2018bGanta et al, 2021Ganta et al, , 2020aGanta et al, , 2020bGanta et al, , 2019Shaheen et al, 2022). Those studies aimed to elucidate the effects of various key factors on the P-binding process and its strength.…”

“…For example, phosphates like OP and GP with single phosphate groups form stable monodentate (M) and bidentate (B) binding motifs. On the other hand, phosphates containing multiple phosphate groups like IHP can bind to mineral surfaces through more than one phosphate group, forming various stable motifs like M, 2 M, and 3 M. The interaction energies of phosphates and water with goethite and diaspore surfaces increase in the order water < GP < OP < IHP (Ganta et al, 2021(Ganta et al, , 2020a, indicating that phosphates could displace water molecules at these surfaces, with IHP potentially replacing OP and GP. Additionally, water plays a critical role in controlling phosphate binding through hydrogen bond formation, dissociation at the surface, proton transfer processes, and covalent/coordination bond formation with the surface.…”

“…The initial configurations of the P-goethite, OM-goethite, and 1P:1OM-goethite complexes are designed so that the phosphates (OP/GP/IHP) and OM (CIT and HIS) molecules, as well as 1P-1OM complexes, are nearby and bound to the goethite surface except for the cases of 1P-1OM complexes in the bulk solution. This design is based on insights from previous simulation studies (Ahmed et al, 2018b(Ahmed et al, , 2019(Ahmed et al, , 2020Ganta et al, 2020aGanta et al, , 2021. To account for the influence of water on the P-goethite, OM-goethite, and 1P:1OM-goethite complexes, each modeled complex is solvated by water with a density of ≈ 1 g cm −3 .…”

Machine learning and computational chemistry to improve biochar fertilizers: a review

“…These components include mineral surfaces, free metal ions, and soil organic matter, as illustrated in Fig. 2 (Ahmed et al 2019;Ganta et al 2019Ganta et al , 2020aGanta et al 2021;Shaheen et al 2022). Their calculations involved larger simulation boxes, incorporating phosphate-mineral-water molecular models with explicit solvation at a water density of 1 g.cm -3 .…”

The Binding of Phosphorus Species at Goethite: A Joint Experimental and Theoretical Study

“…This goethite surface plane is modeled by repetition of the goethite unit cell (lattice constants : a = 9.95, b = 3.01, c = 4.62 Å) as 1a × 8b × 5c which consists of 640 atoms (160 Fe, 160 H, and 320 O atoms). The binding motifs formed between these phosphates and the goethite surface are modeled based on previous literature studies [9][10][11]41,[48][49][50]. The initial motifs of OP and GP with the goethite surface include monodentate (M, 1Fe+1O one covalent bond between phosphate non-protonated O atom and a surface Fe atom) and bidentate (B, 2Fe+2O i.e.…”