Advances in understanding the phosphate binding to soil constituents: A Computational Chemistry perspective.

Phosphorus (P) is an indispensable element to all forms of life and its efficient use in fertilizers is one of the conditions for food security. The efficiency of P fertilizers is affected by P mobilization and P fixation, both depending on the P binding strength to soil constituents. This review provides an overview of the P binding to soil constituents, especially to P-fixing mineral surfaces and its investigation using state-of-the-art Computational Chemistry (CC). A particular focus will be on goethite (α-FeOOH), which is highly significant in the context of P fixation in soils, given its prevalence, high susceptibility to P, and wide distribution across both oxic and anoxic environments. First, a brief overview will be given on experimental efforts related to the P adsorption at mineral surfaces and the factors affecting this process. Here, we will discuss the process of P adsorption, with a focus on important factors that influence this process, such as pH, surface crystallinity and morphology, competing anions, and electrolyte solutions. We will also explore the various techniques used to study this process and investigate the resulting binding motifs. Next, a brief introduction into common CC methods, techniques, and applications is presented, highlighting the advantages and limitations of each approach. Then, a comprehensive discussion of a wide range of the most relevant computational studies related to the phosphate binding issue will be provided. This will be followed by the main part of this review which is focusing on a possible strategy to cope with the soil heterogeneity by breaking down the complexity of P behavior in soil into well-defined models that can be discussed in terms of particular key factors. Hence, different molecular model systems and molecular simulations are introduced to reveal the P binding to soil organic matter (SOM), metal ions, and mineral surfaces. Simulation results provided an in-depth understanding of the P binding problem and explained at a molecular level the effects of surface plane, binding motif, kind and valency of metal ions, SOM composition, water, pH, and redox potential on the P binding in soil. On this basis, an overall molecular picture of P binding in soil can be then obtained by combining results for the different models. Eventually, challenges and further modifications of the existing molecular modeling approaches are discussed, such as steps necessary to bridge the molecular with the mesoscale.

Stepwise redox changes alter the speciation and mobilization of phosphorus in hydromorphic soils.

Sustainable engineering and management of hydromorphic arable soils need deep knowledge about the redox-mediated interactions between nutrients and soil colloids. Consequently, we examined the redox-mediated interactions of P with metal oxides and organic carbon (OC) in toe-, mid-, and upper-slope arable soils under dynamic redox changes using geochemical (biogeochemical microcosm), spectroscopic (XANES), and molecular (quantum chemical calculations (QCC)) approaches. We controlled the redox potential (EH) in two directions i.e., 1) slowly oxidizing direction (SOD; EH increased from -286 to +564 mV); and 2) slowly reducing direction (SRD; EH decreased from +564 to -148 mV). In the SOD of all soils, P, Fe2+ and OC mobilized at EH ≤ 200 mV, due to the pH decrease from 7.2 to 4.1 and dissolution of Fe-oxyhydroxides/carbonates, as indicated by the decrease of Fe-P and Ca-P determined by P-K-edge-XANES. At EH > 200 mV, P immobilized due to the strong P binding with Fe3+ as suggested by QCC. In the SRD of mid-slope-soil, P immobilized with decreasing EH, due to pH increase and P retention by aromatic carbon and/or precipitation by carbonates, as supported by increase of organic-P and Ca-P. These findings help for management of P in arable soils.

Coarse-grained molecular dynamics simulations of nanoplastics interacting with a hydrophobic environment in aqueous solution.

Nanoplastics (NPs) are emerging threats for marine and terrestrial ecosystems, but little is known about their fate in the environment at the molecular scale. In this work, coarse-grained molecular dynamics simulations were performed to investigate nature and strength of the interaction between NPs and hydrophobic environments. Specifically, NPs were simulated with different hydrophobic and hydrophilic polymers while carbon nanotubes (CNTs) were used to mimic surface and confinement effects of hydrophobic building blocks occurring in a soil environment. The hydrophobicity of CNTs was modified by introducing different hydrophobic and hydrophilic functional groups at their inner surfaces. The results show that hydrophobic polymers have a strong affinity to adsorb at the outer surface and to be captured inside the CNT. The accumulation within the CNT is even increased in presence of hydrophobic functional groups. This contribution is a first step towards a mechanistic understanding of a variety of processes connected to interaction of nanoscale material with environmental systems. Regarding the fate of NPs in soil, the results point to the critical role of the hydrophobicity of NPs and soil organic matter (SOM) as well as of the chemical nature of functionalized SOM cavities/voids in controlling the accumulation of NPs in soil. Moreover, the results can be related to water treatment technologies as it is shown that the hydrophobicity of CNTs and functionalization of their surfaces may play a crucial role in enhancing the adsorption capacity of CNTs with respect to organic compounds and thus their removal efficiency from wastewater.

Molecular level picture of the interplay between pH and phosphate binding at the goethite-water interface.

The soil pH plays a substantial role in controlling phosphorus (P) adsorption and mobilization. These processes are strongly affected by the phosphate interaction strength with P-fixing soil minerals such as goethite. The target of the current contribution is to draw a molecular level picture of the interplay between pH and phosphate binding at the goethite-water interface via a joint experimental-theoretical approach. Periodic density functional theory (DFT) calculations were carried out to provide a molecular level understanding of the pH dependence of P adsorption. To validate the modeling approach, adsorption experiments of phosphate at goethite were performed in the pH range of 4-12. There was agreement between experiments and simulations in the description of the adsorption behavior by two pH-dependent successive stages. The adsorption increases along the pH change from 4 to 8. A further increase of pH leads to a decrease of adsorption. By comparing with literature data it is concluded that the first stage will be observed only if there is no significant change of the surface charge at low pH. Moreover, the molecular modeling results point to the abundance of the monodentate (M) binding motif at both extremely low and high pH ranges. Otherwise, the bidentate (B) one is predominant along the intermediate pH range. These observations could resolve the existing debate about the assignment of phosphate-goethite binding motifs. Furthermore, the results point to a decrease of pH upon phosphate sorption due to an induced acidification of soil solution. The present joint experimental-theoretical approach provides a better understanding and description of the existing phosphate sorption experiments and highlights new findings at the atomistic/molecular scale.

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

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.

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

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. The related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphates onto Fe-oxide surfaces. But a molecular-level understanding of 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) monodentates 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 the 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 the 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.

Influence of metal ions on glyphosate detection by FMOC-Cl.

Glyphosate (GLP, N-(phosphonomethyl)glycine) is the most important broadband herbicide in the world, but discussions are controversial regarding its environmental behaviour and distribution. Residue analyses in a variety of environmental samples are commonly conducted by HPLC-MS where GLP needs to be derivatised with 9-fluoromethoxycarnonyl chloride (FMOC-Cl). Since this derivatisation reaction was suspected to be inhibited by metal ions in the sample matrix, the present study provides a comprehensive experimental study of the effect of metal ions (Al3+, Ca2+, Cd2+, Co2+, Cu2+, Fe2+, Fe3+, Mg2+, Mn2+, Zn2+) on derivatisation and GLP recovery. Results show that some metals (Cd2+, Co2+, Cu2+, Mn2+ and Zn2+) decreased the GLP recovery down to 19 to 59%. Complementary, quantum chemical modelling of 1:1 GLP-metal complexes as well as their reactivity with respect to FMOC-Cl was performed. Here, a decrease in reactivity of FMOC-Cl towards GLP-metal complexes is observed; i.e. the reaction is non-spontaneous in contrast to the free GLP case. The present results are in accord with previous studies and provide an explanation that full GLP recovery in different matrices was never reached. Remedy strategies to compensate for the inhibition effect are explored such as pH adjustment to acidic or alkaline conditions or addition of ethylenediaminetetraacetic acid (EDTA). In general, our results question the use of internal isotopic labelled standards (ILS) since this presupposes the presence of the analyte and the ILS in the same (free) form.

Infrared spectroscopic characterization of phosphate binding at the goethite-water interface.

The interaction between phosphates and soil mineral surfaces, such as Fe- and Al-(oxyhydr)oxides, plays a crucial role in the immobilization of P 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 of the phosphate binding mechanisms at the goethite-water interface is still lacking. Therefore, in the current contribution we have explored the molecular binding mechanisms 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 mechanisms and to assign 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 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. Furthermore, some water molecules form covalent bonds with goethite's 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, the 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 abundances of surface planes and binding motifs, IR spectra obtained from weighted averages have been analyzed. The results confirmed the conclusions drawn from interaction energy calculations.

Acceleration of a ground-state reaction by selective femtosecond-infrared-laser-pulse excitation.

Infrared (IR) excitation of vibrations that participate in the reaction coordinate of an otherwise thermally driven chemical reaction are believed to lead to its acceleration. Attempts at the practical realization of this concept have been hampered so far by competing processes leading to sample heating. Here we demonstrate, using femtosecond IR-pump IR-probe experiments, the acceleration of urethane and polyurethane formation due to vibrational excitation of the reactants for 1:1 mixtures of phenylisocyanate and cyclohexanol, and toluene-2,4-diisocyanate and 2,2,2-trichloroethane-1,1-diol, respectively. We measured reaction rate changes upon selective vibrational excitation with negligible heating of the sample and observed an increase of the reaction rate up to 24%. The observation is rationalized using reactant and transition-state structures obtained from quantum chemical calculations. We subsequently used IR-driven reaction acceleration to write a polyurethane square on sample windows using a femtosecond IR pulse.

Molecular level investigation of the role of peptide interactions in the glyphosate analytics.

The detection of the herbicide glyphosate (GLP) in environmental samples is most often conducted after derivatizing the target molecule with the chromophore 9-fluorenylmethyloxycarbonyl chloride (FMOC-Cl). However, this method is sensitive to all primary and secondary amines, which can occur in the sample matrix as well. In order to quantify the interference of primary and secondary amines on GLP detection, we have used well-defined peptides such as pentaglycine (PG) and albumin as well as mixtures of peptides such as peptone. These peptides have been added to the derivatization solution of GLP at different constant concentration levels and UV extinction coefficients have been determined. Data analysis supported by quantum chemical modeling of the GLP-peptide, FMOC-GLP, and FMOC-peptide complexation reactions facilitated the identification of two interfering impacts of peptide on GLP derivatization: (i) increase of the signal due to reaction with FMOC-Cl leading to an overestimation of GLP concentration and (ii) decrease of GLP recovery due to complex formation and therefore inhibition of GLP derivatization, which leads to an underestimation. Specifically, our results indicated that the GLP-peptide- and peptide-FMOC-interactions are mainly affected by type of interfering peptides as well as concentration of each peptide and GLP in the environmental samples.

Exploring the nature of the clopidogrel-bromocresol green interaction via spectrophotometric measurements and quantum chemical calculations.

Clopidogrel is an oral, thienopyridine class antiplatelet agent used to inhibit blood clots in coronary arteries, peripheral vascular and cerebrovascular diseases. A spectrophotometric method was developed for clopidogrel bisulfate (CLOP·H2SO4) determination using bromocresol green (BCG) as an ion-pairing agent. To explore the binding nature of CLOP·H2SO4 with BCG at a molecular level, quantum chemical calculations have been performed. DFT based full geometry optimization has been carried out for BCG and clopidogrel in basic (CLOP) and protonated (CLOP+) forms as well as for BCG ion-pairs with CLOP and CLOP·H2SO4. The DFT calculations referred to the stability of the BCG-CLOP+ ion-pair and its spontaneous formation reaction from BCG and CLOP·H2SO4 compared to the BCG-CLOP-ion-pair. Furthermore, the UV-visible spectra and their corresponding excited states and electronic transitions for BCG, BCG-CLOP+ ion-pair, and BCG-CLOP ion-pair have been investigated. These spectra provided a molecular level understanding of the nature of the different intra-molecular and intermolecular electronic transitions in the BCG ion-pairs with CLOP+. Moreover, the quantitative analysis based on extracting a yellow-formed ion-pair into chloroform from aqueous medium was carried out. The ion-pair exhibits an absorption maximum at 413 nm. The optimum conditions of the reactions were studied experimentally and optimized. The calibration graph shows that CLOP·H2SO4 can be determined up to 100.0 µg mL-1 with detection limit (LOD) of 0.57 µg mL-1 and quantification limit (LOQ) of 1.86 µg mL-1. The low relative standard deviation values, 0.16-1.16, indicate good precision. The results were compared to other published data and were treated statistically using F and t-tests.

Unravelling the nature of glyphosate binding to goethite surfaces by ab initio molecular dynamics simulations.

Investigation of the interaction between glyphosate (GLP) and soil minerals is essential for understanding GLP's fate in the environment. Whereas GLP-goethite binding has been discussed extensively, the impact of water as well as of different goethite surface planes has not been studied yet. In this contribution, periodic density functional theory-based molecular dynamics simulations are applied to explore possible binding mechanisms for GLP with three goethite surface planes (010, 001, and 100) in the presence of water. The investigation included several binding motifs of monodentate (M) and bidentate (B) type. It was found that the binding stability increases in the order M@001 < M@010 < (2O + 2Fe) B@100 < M@100 < (1O + 2Fe) B@001 < (2O + 1Fe) B@010. This behavior has been traced to the presence of intramolecular H-bonds (HBs) in GLP as well as intermolecular HBs between GLP and water, GLP and goethite, and water and goethite. These interactions are accompanied by proton transfer from GLP to water and to goethite, and from water to goethite as well as water dissociation at the goethite surface. Further, it was observed that the OH- species can replace the adsorbed GLP at the goethite surface, which could explain the well-known drastic drop in GLP adsorption at high pH. The present results highlight the role of water in the GLP-goethite interaction and provide a molecular level perspective on available experimental data.

Towards a molecular level understanding of the sulfanilamide-soil organic matter-interaction.

Sorption experiments of sulfanilamide (SAA) on well-characterized samples of soil size-fractions were combined with the modeling of SAA-soil-interaction via quantum chemical calculations. Freundlich unit capacities were determined in batch experiments and it was found that they increase with the soil organic matter (SOM) content according to the order fine silt > medium silt > clay > whole soil > coarse silt > sand. The calculated binding energies for mass-spectrometrically quantified sorption sites followed the order ionic species > peptides > carbohydrates > phenols and lignin monomers > lignin dimers > heterocyclic compounds > fatty acids > sterols > aromatic compounds > lipids, alkanes, and alkenes. SAA forms H-bonds through its polar centers with the polar SOM sorption sites. In contrast dispersion and π-π-interactions predominate the interaction of the SAA aromatic ring with the non-polar moieties of SOM. Moreover, the dipole moment, partial atomic charges, and molecular volume of the SOM sorption sites are the main physical properties controlling the SAA-SOM-interaction. Further, reasonable estimates of the Freundlich unit capacities from the calculated binding energies have been established. Consequently, we suggest using this approach in forthcoming studies to disclose the interactions of a wide range of organic pollutants with SOM.

Regioselective synthesis and ab initio calculations of fused heterocycles thermally and under microwave irradiation.

Pyrazolo[1,5-a]pyrimidine, triazolo[1,5-a]pyrimidine, and pyrimido[1,2-a]benzimidazole, pyrido[1,2-a]benzimidazole ring systems incorporating phenylsulfonyl moiety were synthesized via the reaction of 3-(N,N-dimethylamino)-1-(thiophen-2-yl)-2-(phenylsulfonyl)prop-2-en-1-one derivatives with the appropriate aminoazoles as 1,3-binucleophiles and 1H-benzimidazol-2-ylacetonitrile using conventional methods as well as microwave irradiation. The regioselectivity of the cyclocondensation reactions was confirmed both experimentally by alternative synthesis of reaction products and theoretically using ab initio quantum chemical calculations namely the Density Functional Theory (DFT). The theoretical work was carried out using the Becke, three parameter, Lee-Yang-Parr hybrid functional (B3LYP) combined with the 6-311++G(d,p) basis set. It was found that the final cyclocondensation reaction product depends mainly on the initial addition to the activated double bond by the nitrogen atom of the 1,3-binucleophiles that has the higher electron density.

Interaction of polar and nonpolar organic pollutants with soil organic matter: sorption experiments and molecular dynamics simulation.

The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question "How organic pollutants interact with SOM?" is still lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model and carried out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), simulating the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and theoretical investigations explored four major points regarding sorption of SAA and HCB on soil, yielding the following results. 1--The interaction depends on the SOM chemical composition more than the SOM content. 2--The interaction causes a site-specific adsorption on the soil surfaces. 3--Sorption hysteresis occurs, which can be explained by inclusion of these pollutants inside soil voids. 4--The hydrophobic HCB is adsorbed on soil stronger than the hydrophilic SAA. Moreover, the theoretical results showed that HCB forms stable complexes with all SOM models in the aqueous solution, while most of SAA-SOM complexes are accompanied by dissociation into SAA and the free SOM models. The SOM-cavity modeling had a significant effect on binding of organic pollutants to SOM. Both HCB and SAA bind to the SOM models in the order of models with a small cavity>a large cavity>no cavity. Although HCB binds to all SOM models stronger than SAA, the latter is more affected by the presence of the cavity. Finally, HCB and SAA bind to the hydrophobic functional group (naphthalene) stronger than to the hydrophilic one (carboxylic acid) for all SOM models containing a cavity. For models without a cavity, SAA binds to carboxylic acid stronger than to naphthalene.

Hydrogen bond coupling in sodium dihydrogen triacetate.

The coupling of hydrogen bonds is central to structures and functions of biological systems. Hydrogen bond coupling in sodium dihydrogen triacetate (SDHTA) is investigated as a model for the hydrogen bonded systems of the type O-H…O. The two-dimensional potential energy surface is derived from the full-dimensional one by selecting the relevant vibrational modes of the hydrogen bonds. The potential energy surfaces in terms of normal modes describing the anharmonic motion in the vicinity of the equilibrium geometry of SDHTA are calculated for the different species, namely, HH, HD, DH, and DD isotopomers. The ground state wave functions and their relation to the hydrogen bond structural parameters are discussed. It has been found that the hydrogen bonds in SDHTA are uncoupled, that is elongation of the deuterated hydrogen bond does not affect the non-deuterated one.

How soil organic matter composition controls hexachlorobenzene-soil-interactions: adsorption isotherms and quantum chemical modeling.

Hazardous persistent organic pollutants (POPs) interact in soil with the soil organic matter (SOM) but this interaction is insufficiently understood at the molecular level. We investigated the adsorption of hexachlorobenzene (HCB) on soil samples with systematically modified SOM. These samples included the original soil, the soil modified by adding a hot water extract (HWE) fraction (soil+3 HWE and soil+6 HWE), and the pyrolyzed soil. The SOM contents increased in the order pyrolyzed soil

Controlled experimental soil organic matter modification for study of organic pollutant interactions in soil.

Interactions of organic pollutants with soil organic matter can be studied by adsorption of the pollutants on well-characterized soil samples with constant mineralogy but different organic matter compositions. Therefore, the objectives of the current study are establishing a set of different, well-characterized soil samples by systematic modifications of their organic matter content and molecular composition and prove these modifications by advanced complementary analytical techniques. Modifications were done by off-line pyrolysis and removal/addition of hot-water extracted organic fraction (HWE) from/to the original soil sample. Both pyrolysis-field ionization mass spectrometry (Py-FIMS) and synchrotron-based C- and N- X-ray absorption near-edge structure spectroscopy (XANES) were applied to investigate the composition of the soil organic matter. These complementary analytical methods in addition to elemental analysis agreed in showing the following order of organic matter contents: pyrolyzed soil