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

2021 ◽  
Author(s):  
Prasanth B. Ganta ◽  
Mohsen Morshedizad ◽  
Oliver Kühn ◽  
Peter Leinweber ◽  
Ashour A. Ahmed
Keyword(s):  
Ab Initio Molecular Dynamics ◽  
Phosphorus Species ◽  
Binding Motifs ◽  
Freundlich Model ◽  
Soil P ◽  
Op Amp ◽  
Proton Transfers ◽  
Mineral Binding ◽  
Dynamics Simulations ◽  
Phosphate Groups

Knowledge of the interaction between inorganic and organic phosphates with soil minerals is vital for improving the soil P fertility. To achieve an in-depth understanding we combined adsorption experiments and hybrid ab initio molecular dynamics simulations to analyze the adsorption of common phosphates, i.e. orthophosphate (OP), glycerolphosphate (GP) and inositolhexaphosphate (IHP), onto the 100 surface plane of goethite. Experimental adsorption data per mol P-molecule basis fitted to the Freundlich model show the adsorption strength increases in the order GP < OP < IHP, and IHP adsorption being saturated faster followed by GP and OP. Modeling results show that OP and GP form stable monodentate (M) and binuclear bidentate (B) motifs with B being more stable than M, whereas IHP forms stable M and 3M motifs. Interfacial water plays an important role through hydrogen bonds and proton transfers with OP/GP/IHP and goethite. It also controls the binding motifs of phosphates with goethite. Combining both experimental and modeling results, we propose that the B motif dominates for OP, whereas GP forms M and IHP forms a combination of M and 3M motifs. The joint approach plausibly explains why IHP is the predominant organically bound P form in soil. This study could be considered as a preliminary step for further studies for understanding the mechanisms of how microbes and plants overcome the strong IHP–mineral binding to implement the phosphate groups into their metabolism.

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

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 323
Author(s):  
Prasanth B. Ganta ◽  
Mohsen Morshedizad ◽  
Oliver Kühn ◽  
Peter Leinweber ◽  
Ashour A. Ahmed
Keyword(s):  
Ab Initio Molecular Dynamics ◽  
Phosphorus Species ◽  
Binding Motifs ◽  
Freundlich Model ◽  
Soil P ◽  
Proton Transfers ◽  
Adsorption Data ◽  
Mineral Binding ◽  
Dynamics Simulations ◽  
Phosphate Groups

Knowledge of the interaction between inorganic and organic phosphates with soil minerals is vital for improving soil P-fertility. To achieve an in-depth understanding, we combined adsorption experiments and hybrid ab initio molecular dynamics simulations to analyze the adsorption of common phosphates, i.e., orthophosphate (OP), glycerolphosphate (GP) and inositolhexaphosphate (IHP), onto the 100 surface plane of goethite. Experimental adsorption data per mol P-molecule basis fitted to the Freundlich model show the adsorption strength increases in the order GP < OP < IHP, and IHP adsorption being saturated faster followed by GP and OP. Modeling results show that OP and GP form stable monodentate (M) and binuclear bidentate (B) motifs, with B being more stable than M, whereas IHP forms stable M and 3M motifs. Interfacial water plays an important role through hydrogen bonds and proton transfers with OP/GP/IHP and goethite. It also controls the binding motifs of phosphates with goethite. Combining both experimental and modeling results, we propose that the B motif dominates for OP, whereas GP forms M and IHP forms a combination of M and 3M motifs. The joint approach plausibly explains why IHP is the predominant organically bound P form in soil. This study could be considered as a preliminary step for further studies for understanding the mechanisms of how microbes and plants overcome strong IHP–mineral binding to implement the phosphate groups into their metabolism.

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

2020 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Soil Mineral ◽  
P Efficiency ◽  
Proton Transfers ◽  
Dynamics Simulations ◽  
Near Future ◽  
Level Analysis ◽  
Phosphate Groups

Today's fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future and hence, 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] & 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 \textbf{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.

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

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 160
Author(s):  
Prasanth B. Ganta ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Soil Mineral ◽  
P Efficiency ◽  
Proton Transfers ◽  
Dynamics Simulations ◽  
Near Future ◽  
Level Analysis ◽  
Phosphate Groups

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.

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

2020 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Soil Mineral ◽  
P Efficiency ◽  
Proton Transfers ◽  
Dynamics Simulations ◽  
Near Future ◽  
Level Analysis ◽  
Phosphate Groups

Today's fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future and hence, 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] & 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 \textbf{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.

scholarly journals Proton Transport Mechanism and Pathways in the Superprotonic Phase of M3H(AO4)2 Solid Acids from Ab Initio Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Boris Merinov ◽  
Sergey Morozov
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Proton Transport ◽  
Transport Mechanism ◽  
Solid Acids ◽  
Ab Initio Molecular Dynamics ◽  
Theoretical Studies ◽  
Dynamics Simulations ◽  
Experimental And Theoretical Studies ◽  
Superprotonic Phase

The proton transport mechanism in superprotonic phases of solid acids is a subject of experimental and theoretical studies for a number of years. Despite this, details of the mechanism still...

scholarly journals Predicting Immunogenicity Risk in Biopharmaceuticals

Symmetry ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 388
Author(s):  
Nikolet Doneva ◽  
Irini Doytchinova ◽  
Ivan Dimitrov
Keyword(s):  
Machine Learning Algorithms ◽  
Computational Tools ◽  
Binding Motifs ◽  
B Cell Epitopes ◽  
Crucial Step ◽  
Histocompatibility Complex ◽  
Alignment Algorithms ◽  
Experimental Approaches ◽  
Dynamics Simulations ◽  
Allergenicity Prediction

The assessment of immunogenicity of biopharmaceuticals is a crucial step in the process of their development. Immunogenicity is related to the activation of adaptive immunity. The complexity of the immune system manifests through numerous different mechanisms, which allows the use of different approaches for predicting the immunogenicity of biopharmaceuticals. The direct experimental approaches are sometimes expensive and time consuming, or their results need to be confirmed. In this case, computational methods for immunogenicity prediction appear as an appropriate complement in the process of drug design. In this review, we analyze the use of various In silico methods and approaches for immunogenicity prediction of biomolecules: sequence alignment algorithms, predicting subcellular localization, searching for major histocompatibility complex (MHC) binding motifs, predicting T and B cell epitopes based on machine learning algorithms, molecular docking, and molecular dynamics simulations. Computational tools for antigenicity and allergenicity prediction also are considered.

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