QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface
The fate of phosphorus (P) in the eco-system is strongly affected by the interaction of phosphates with soil components and especially reactive soil mineral surfaces. As a consequence, P immobilization occurs which eventually leads to P inefficiency and thus unavailability to plants with strong impl...
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| Format: | Article |
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Frontiers Media S.A.
2020-06-01
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| Series: | Frontiers in Forests and Global Change |
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| Online Access: | https://www.frontiersin.org/article/10.3389/ffgc.2020.00071/full |
| _version_ | 1818187735176839168 |
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| author | Prasanth B. Ganta Oliver Kühn Oliver Kühn Ashour A. Ahmed Ashour A. Ahmed |
| author_facet | Prasanth B. Ganta Oliver Kühn Oliver Kühn Ashour A. Ahmed Ashour A. Ahmed |
| author_sort | Prasanth B. Ganta |
| collection | DOAJ |
| description | The fate of phosphorus (P) in the eco-system is strongly affected by the interaction of phosphates with soil components and especially reactive soil mineral surfaces. As a consequence, P immobilization occurs which eventually leads to P inefficiency and thus unavailability to plants with strong implications on the global food system. A molecular level understanding of the mechanisms of the P binding to soil mineral surfaces could be a key for the development of novel strategies for more efficient P application. Much experimental work has been done to understand P binding to several reactive and abundant minerals especially goethite (α-FeOOH). Complementary, atomistic modeling of the P-mineral molecular systems using molecular dynamics (MD) simulations is emerging as a new tool in environmental science, which provides more detailed information regarding the mechanisms, nature, and strength of these binding processes. The present study characterizes the binding of the most abundant organic phosphates in forest soils, inositol hexaphosphate (IHP), and glycerolphosphate (GP), to the 100 diaspore (α-AlOOH) surface plane. Here, different molecular models have been introduced to simulate typical situations for the P-binding at the diaspore/water interface. For all models, quantum mechanics/molecular mechanics (QM/MM) based MD simulations have been performed to explore the diaspore–IHP/GP–water interactions. The results provide evidence for the formation of monodentate (M) and bidentate (B) motifs for GP and M and as well as two monodentate (2M) motifs for IHP with the surface. The calculated interaction energies suggest that GP and IHP prefer to form the B and 2M motif, respectively. Moreover, IHP exhibited stronger binding than GP with diaspore and water. Further, the role of water in controlling binding strengths via promoting of specific binding motifs, formation of H-bonds, adsorption and dissociation at the surface, as well as proton transfer processes is demonstrated. Finally, the P-binding at the 100 diaspore surface plane is weaker than that at the 010 plane, studied previously (Ganta et al., 2019), highlighting the influential role of the coordination number of Al atoms at the top surface of diaspore. |
| first_indexed | 2024-12-11T23:15:45Z |
| format | Article |
| id | doaj.art-fa4b40c49cfc4311bbd7391feefc5ccb |
| institution | Directory Open Access Journal |
| issn | 2624-893X |
| language | English |
| last_indexed | 2024-12-11T23:15:45Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Forests and Global Change |
| spelling | doaj.art-fa4b40c49cfc4311bbd7391feefc5ccb2022-12-22T00:46:33ZengFrontiers Media S.A.Frontiers in Forests and Global Change2624-893X2020-06-01310.3389/ffgc.2020.00071519744QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore SurfacePrasanth B. Ganta0Oliver Kühn1Oliver Kühn2Ashour A. Ahmed3Ashour A. Ahmed4Institute of Physics, University of Rostock, Rostock, GermanyInstitute of Physics, University of Rostock, Rostock, GermanyDepartment of Life, Light, and Matter (LLM), University of Rostock, Rostock, GermanyInstitute of Physics, University of Rostock, Rostock, GermanyDepartment of Life, Light, and Matter (LLM), University of Rostock, Rostock, GermanyThe fate of phosphorus (P) in the eco-system is strongly affected by the interaction of phosphates with soil components and especially reactive soil mineral surfaces. As a consequence, P immobilization occurs which eventually leads to P inefficiency and thus unavailability to plants with strong implications on the global food system. A molecular level understanding of the mechanisms of the P binding to soil mineral surfaces could be a key for the development of novel strategies for more efficient P application. Much experimental work has been done to understand P binding to several reactive and abundant minerals especially goethite (α-FeOOH). Complementary, atomistic modeling of the P-mineral molecular systems using molecular dynamics (MD) simulations is emerging as a new tool in environmental science, which provides more detailed information regarding the mechanisms, nature, and strength of these binding processes. The present study characterizes the binding of the most abundant organic phosphates in forest soils, inositol hexaphosphate (IHP), and glycerolphosphate (GP), to the 100 diaspore (α-AlOOH) surface plane. Here, different molecular models have been introduced to simulate typical situations for the P-binding at the diaspore/water interface. For all models, quantum mechanics/molecular mechanics (QM/MM) based MD simulations have been performed to explore the diaspore–IHP/GP–water interactions. The results provide evidence for the formation of monodentate (M) and bidentate (B) motifs for GP and M and as well as two monodentate (2M) motifs for IHP with the surface. The calculated interaction energies suggest that GP and IHP prefer to form the B and 2M motif, respectively. Moreover, IHP exhibited stronger binding than GP with diaspore and water. Further, the role of water in controlling binding strengths via promoting of specific binding motifs, formation of H-bonds, adsorption and dissociation at the surface, as well as proton transfer processes is demonstrated. Finally, the P-binding at the 100 diaspore surface plane is weaker than that at the 010 plane, studied previously (Ganta et al., 2019), highlighting the influential role of the coordination number of Al atoms at the top surface of diaspore.https://www.frontiersin.org/article/10.3389/ffgc.2020.00071/fullP-efficiencyP-adsorptioninositolhexaphosphate (IHP)glycerolphosphate (GP)diaspore (AlOOH)QM/MM simulations |
| spellingShingle | Prasanth B. Ganta Oliver Kühn Oliver Kühn Ashour A. Ahmed Ashour A. Ahmed QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface Frontiers in Forests and Global Change P-efficiency P-adsorption inositolhexaphosphate (IHP) glycerolphosphate (GP) diaspore (AlOOH) QM/MM simulations |
| title | QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface |
| title_full | QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface |
| title_fullStr | QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface |
| title_full_unstemmed | QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface |
| title_short | QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface |
| title_sort | qm mm molecular dynamics investigation of the binding of organic phosphates to the 100 diaspore surface |
| topic | P-efficiency P-adsorption inositolhexaphosphate (IHP) glycerolphosphate (GP) diaspore (AlOOH) QM/MM simulations |
| url | https://www.frontiersin.org/article/10.3389/ffgc.2020.00071/full |
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