QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface

2019 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour Ahmed
Keyword(s):  
Interaction Energy ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Covalent Bonds ◽  
Binding Mechanisms

The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results confirm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces.

QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface

2019 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour Ahmed
Keyword(s):  
Interaction Energy ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Covalent Bonds ◽  
Binding Mechanisms

The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results confirm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces.

scholarly journals Infrared Spectroscopic Characterization of Phosphate Binding at the Goethite-Water Interface

2018 ◽  
Author(s):  
Ashour Ahmed ◽  
Stella Gypser ◽  
Peter Leinweber ◽  
Dirk Freese ◽  
Oliver Kühn
Keyword(s):  
Ir Spectra ◽  
Interaction Energy ◽  
Phosphate Adsorption ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Binding Mechanism ◽  
Phosphate Binding ◽  
Covalent Bonds ◽  
Surface Plane

<div><div><div><p>The interaction between phosphates and soil mineral surfaces, such as Fe- and Al-(oxyhydr)oxides, plays a crucial role in the P immobilization and thus its availability for plants. The reactions of phosphates with Fe-hydroxides and especially goethite have been studied extensively. But a molecular-level picture about the phosphate binding mechanism at the goethite-water interface is still lacking. Therefore, in the current contribution we have explored the molecular binding mechanism for the adsorbed phosphate at the goethite–water interface by performing sorption kinetics experiments for orthophosphate and characterizing the adsorbed species by FT-IR spectroscopy. In parallel, periodic DFT calculations have been performed to explore the interaction mechanism as well as to calculate the IR spectra for monodentate (M) and bidentate (B) orthophosphate complexes at two different goethite surface planes (010 and 100) in the presence of water. In general, our interaction energy results give evidence that the mono-protonated B phosphate complex is more favored to be formed at the goethite–water interface although the M motif could exist as a minor fraction. Moreover, it was found that water plays an important role in controlling the phosphate adsorption process at the goethite surfaces. The interfacial water molecules form H-bonds (HBs) with the phosphate as well as with the goethite surface atoms. Further, some water molecules form covalent bonds with goethite Fe atoms while others dissociate at the surface to protons and hydroxyl groups. The present theoretical assignment of IR spectra introduces a benchmark for characterizing experimental IR data for the adsorbed KH2PO4 species at the goethite–water interface. In particular, IR spectra of the mono-protonated (2O+1Fe) B complex at the 010 goethite surface plane and the M complex at the 100 goethite surface plane were found to be consistent with the experimental data. In order to explore the role of different abundancies of surface planes and binding motifs, IR spectra obtained from weighted averages have been analyzed. Results confirmed the above conclusions drawn from interaction energy calculations.</p></div></div></div>

scholarly journals Infrared Spectroscopic Characterization of Phosphate Binding at the Goethite-Water InterfaceUntitled Item

2018 ◽  
Author(s):  
Ashour Ahmed ◽  
Stella Gypser ◽  
Peter Leinweber ◽  
Dirk Freese ◽  
Oliver Kühn
Keyword(s):  
Ir Spectra ◽  
Interaction Energy ◽  
Phosphate Adsorption ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Binding Mechanism ◽  
Phosphate Binding ◽  
Covalent Bonds ◽  
Surface Plane

<div><div><div><p>The interaction between phosphates and soil mineral surfaces, such as Fe- and Al-(oxyhydr)oxides, plays a crucial role in the P immobilization and thus its availability for plants. The reactions of phosphates with Fe-hydroxides and especially goethite have been studied extensively. But a molecular-level picture about the phosphate binding mechanism at the goethite-water interface is still lacking. Therefore, in the current contribution we have explored the molecular binding mechanism for the adsorbed phosphate at the goethite–water interface by performing sorption kinetics experiments for orthophosphate and characterizing the adsorbed species by FT-IR spectroscopy. In parallel, periodic DFT calculations have been performed to explore the interaction mechanism as well as to calculate the IR spectra for monodentate (M) and bidentate (B) orthophosphate complexes at two different goethite surface planes (010 and 100) in the presence of water. In general, our interaction energy results give evidence that the mono-protonated B phosphate complex is more favored to be formed at the goethite–water interface although the M motif could exist as a minor fraction. Moreover, it was found that water plays an important role in controlling the phosphate adsorption process at the goethite surfaces. The interfacial water molecules form H-bonds (HBs) with the phosphate as well as with the goethite surface atoms. Further, some water molecules form covalent bonds with goethite Fe atoms while others dissociate at the surface to protons and hydroxyl groups. The present theoretical assignment of IR spectra introduces a benchmark for characterizing experimental IR data for the adsorbed KH2PO4 species at the goethite–water interface. In particular, IR spectra of the mono-protonated (2O+1Fe) B complex at the 010 goethite surface plane and the M complex at the 100 goethite surface plane were found to be consistent with the experimental data. In order to explore the role of different abundancies of surface planes and binding motifs, IR spectra obtained from weighted averages have been analyzed. Results confirmed the above conclusions drawn from interaction energy calculations.</p></div></div></div>

scholarly journals Infrared Spectroscopic Characterization of Phosphate Binding at the Goethite-Water Interface

2018 ◽  
Author(s):  
Ashour Ahmed ◽  
Stella Gypser ◽  
Peter Leinweber ◽  
Dirk Freese ◽  
Oliver Kühn
Keyword(s):  
Ir Spectra ◽  
Interaction Energy ◽  
Phosphate Adsorption ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Binding Mechanism ◽  
Phosphate Binding ◽  
Covalent Bonds ◽  
Surface Plane

<div><div><div><p>The interaction between phosphates and soil mineral surfaces, such as Fe- and Al-(oxyhydr)oxides, plays a crucial role in the P immobilization and thus its availability for plants. The reactions of phosphates with Fe-hydroxides and especially goethite have been studied extensively. But a molecular-level picture about the phosphate binding mechanism at the goethite-water interface is still lacking. Therefore, in the current contribution we have explored the molecular binding mechanism for the adsorbed phosphate at the goethite–water interface by performing sorption kinetics experiments for orthophosphate and characterizing the adsorbed species by FT-IR spectroscopy. In parallel, periodic DFT calculations have been performed to explore the interaction mechanism as well as to calculate the IR spectra for monodentate (M) and bidentate (B) orthophosphate complexes at two different goethite surface planes (010 and 100) in the presence of water. In general, our interaction energy results give evidence that the mono-protonated B phosphate complex is more favored to be formed at the goethite–water interface although the M motif could exist as a minor fraction. Moreover, it was found that water plays an important role in controlling the phosphate adsorption process at the goethite surfaces. The interfacial water molecules form H-bonds (HBs) with the phosphate as well as with the goethite surface atoms. Further, some water molecules form covalent bonds with goethite Fe atoms while others dissociate at the surface to protons and hydroxyl groups. The present theoretical assignment of IR spectra introduces a benchmark for characterizing experimental IR data for the adsorbed KH2PO4 species at the goethite–water interface. In particular, IR spectra of the mono-protonated (2O+1Fe) B complex at the 010 goethite surface plane and the M complex at the 100 goethite surface plane were found to be consistent with the experimental data. In order to explore the role of different abundancies of surface planes and binding motifs, IR spectra obtained from weighted averages have been analyzed. Results confirmed the above conclusions drawn from interaction energy calculations.</p></div></div></div>

QM/MM simulations of organic phosphorus adsorption at the diaspore–water interface

2019 ◽  
Vol 21 (44) ◽  
pp. 24316-24325 ◽  
Author(s):  
Prasanth B. Ganta ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Surface Water ◽  
Molecular Mechanisms ◽  
Organic Phosphorus ◽  
Md Simulations ◽  
Available Phosphorus ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Binding Process

The available phosphorus for plants is mainly affected by the strong binding of phosphates to soil mineral surfaces. Here, we have investigated the molecular mechanisms for this binding process at the surface–water interface by QM/MM MD simulations.

scholarly journals Molecular Dynamics Simulation of Distribution and Diffusion Behaviour of Oil–Water Interfaces

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1905 ◽  
Author(s):  
Chengbin Zhang ◽  
Hanhui Dai ◽  
Pengfei Lu ◽  
Liangyu Wu ◽  
Bo Zhou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Interface Roughness ◽  
Dynamics Simulation ◽  
Water Phase ◽  
Water Molecules ◽  
Water Interface ◽  
Oil Water ◽  
And Diffusion ◽  
Diffusion Behaviors

The distribution and diffusion behaviors of microscopic particles at fluorobenzene–water and pentanol–water interfaces are investigated using molecular dynamics simulation. The influences of Na+/Cl− ions and the steric effects of organic molecules are examined. The concentration distributions of different species, the orientations of oil molecules at the interface, and oil–water interface morphology as well as the diffusion behaviors of water molecules are explored and analyzed. The results indicate that a few fluorobenzene molecules move into the water phase influenced by Na+/Cl− ions, while the pentanol molecules at the interface prefer orientating their hydrophilic groups toward the water phase due to their large size. The water molecules more easily burst into the pentanol phase with larger molecular spaces. As the concentration of ions in the water phase increases, more water molecules enter into the pentanol molecules, leading to larger interface roughness and interface thickness. In addition, a lower diffusion coefficient for water molecules at the fluorobenzene–water interface are observed when introducing Na+/Cl− ions in the water phase, while for the pentanol–water system, the mobility of interfacial water molecules are enhanced with less ions and inhibited with more ions.

scholarly journals Tuning ice nucleation with counterions on polyelectrolyte brush surfaces

2016 ◽  
Vol 2 (6) ◽  
pp. e1600345 ◽  
Author(s):  
Zhiyuan He ◽  
Wen Jun Xie ◽  
Zhenqi Liu ◽  
Guangming Liu ◽  
Zuowei Wang ◽  
...  
Keyword(s):  
Atmospheric Aerosols ◽  
Simulation Analysis ◽  
Specific Effect ◽  
Ice Nucleation ◽  
Dynamics Simulation ◽  
Cloud Formation ◽  
Water Molecules ◽  
Water Interface ◽  
Polyelectrolyte Brush ◽  
Wide Range

Heterogeneous ice nucleation (HIN) on ionic surfaces is ubiquitous in a wide range of atmospheric aerosols and at biological interfaces. Despite its great importance in cirrus cloud formation and cryopreservation of cells, organs, and tissues, it remains unclear whether the ion-specific effect on ice nucleation exists. Benefiting from the fact that ions at the polyelectrolyte brush (PB)/water interface can be reversibly exchanged, we report the effect of ions on HIN on the PB surface, and we discover that the distinct efficiency of ions in tuning HIN follows the Hofmeister series. Moreover, a large HIN temperature window of up to 7.8°C is demonstrated. By establishing a correlation between the fraction of ice-like water molecules and the kinetics of structural transformation from liquid- to ice-like water molecules at the PB/water interface with different counterions, we show that our molecular dynamics simulation analysis is consistent with the experimental observation of the ion-specific effect on HIN.

Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy

2018 ◽  
Author(s):  
Daniel R. Moberg ◽  
Shelby C. Straight ◽  
Francesco Paesani
Keyword(s):  
Temperature Dependence ◽  
Low Frequency ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Sum Frequency Generation ◽  
Water Molecules ◽  
Water Interface ◽  
Sum Frequency ◽  
Air Water Interface ◽  
Frequency Generation

<div> <div> <div> <p>The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The total vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular auto-correlation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating 0, 1, or 2 hydrogen bonds to neighboring water molecules. This analysis suggests that the low frequency shoulder of the free OH peak which appears at ∼3600 cm−1 is primarily due to intermolecular couplings between both singly and doubly hydrogen-bonded molecules. </p> </div> </div> </div>

Unveiling the Structural Insights into the Selective Inhibition of Protein Kinase D1

2019 ◽  
Vol 25 (10) ◽  
pp. 1059-1074 ◽  
Author(s):  
Raju Dash ◽  
Md. Arifuzzaman ◽  
Sarmistha Mitra ◽  
Md. Abdul Hannan ◽  
Nurul Absar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Protein Kinase ◽  
Binding Site ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Selective Inhibitors ◽  
Conserved Residues ◽  
Protein Kinase D1 ◽  
Binding Mechanisms

Background: Although protein kinase D1 (PKD1) has been proved to be an efficient target for anticancer drug development, lack of structural details and substrate binding mechanisms are the main obstacles for the development of selective inhibitors with therapeutic benefits. Objective: The present study described the in silico dynamics behaviors of PKD1 in binding with selective and non-selective inhibitors and revealed the critical binding site residues for the selective kinase inhibition. Methods: Here, the three dimensional model of PKD1 was initially constructed by homology modeling along with binding site characterization to explore the non-conserved residues. Subsequently, two known inhibitors were docked to the catalytic site and the detailed ligand binding mechanisms and post binding dyanmics were investigated by molecular dynamics simulation and binding free energy calculations. Results: According to the binding site analysis, PKD1 serves several non-conserved residues in the G-loop, hinge and catalytic subunits. Among them, the residues including Leu662, His663, and Asp665 from hinge region made polar interactions with selective PKD1 inhibitor in docking simulation, which were further validated by the molecular dynamics simulation. Both inhibitors strongly influenced the structural dynamics of PKD1 and their computed binding free energies were in accordance with experimental bioactivity data. Conclusion: The identified non-conserved residues likely to play critical role on molecular reorganization and inhibitor selectivity. Taken together, this study explained the molecular basis of PKD1 specific inhibition, which may help to design new selective inhibitors for better therapies to overcome cancer and PKD1 dysregulated disorders.

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