3-D structural modeling of humic acids through experimental characterization, computer assisted structure elucidation and atomistic simulations. 1. Chelsea soil humic acid

Inoculating functional bacteria improved the humification process by regulating microbial networks and key genera in straw composting by adding different nitrogen sources

The aim of this study was to compare the effect of functional inoculant and different nitrogen sources on the relationship among lignocellulose, precursors, and humus as well as their interactions with bacterial genera in straw composting. Results showed that inoculation improved the heating process and retained more nitrate compared to control. Inoculation increased the degradation of lignocellulosic components by 26.9%-81.6% and the formation of humus by 15.7%-23.0%. Bioinformatics analysis showed that inoculation enriched key genera Chryseolinea in complex nitrogen source (pig manure) compost and Pusillimas, Luteimonas, and Flavobacteria in single nitrogen source (urea) compost, which were related to humus formation. Network analysis found that inoculation and urea addition improved the microbial synergistic effect and inoculation combined with pig manure had more complex modularity and interactions. Combining the functional bacterial inoculant with urea helped to enhance the degradation of lignocellulose and humification process during straw composting especially with single nitrogen source.

Understanding the Effect of pH on the Solubility and Aggregation Extent of Humic Acid in Solution by Combining Simulation and the Experiment

Molecular dynamics (MD) simulations were performed to investigate the dynamics of humic acid (HA) in an aqueous solution and the influence of pH, temperature, and HA concentration. The HA model employed in MD simulations was chosen and validated using experimental chemical composition data and Fourier transform infrared (FTIR) spectra. The simulations showed that the HA molecule has a strong propensity to adopt a compact conformation in water independent of pH, while the aggregation of HA was found to be pH-dependent. At high pH, the ionized HAs assembled into a thread-like structure, maximizing contact with water. At low pH, the neutral HAs formed a droplet-like aggregate, minimizing contact with the solvent. The simulation results are consistent with experimental data from dynamic light scattering (DLS) measurements and transmission electron microscopy (TEM) imaging. This work provides new insight into the folding and aggregation of HA as a function of pH and a molecular-level understanding of the relationship between the acidity and the structure, solubility, and aggregation of HA, with direct implications for HA-based remediation strategies of contaminated sites.

Nitrate shifted microenvironment: Driven aromatic-ring cleavage microbes and aromatic compounds precursor biodegradation during sludge composting

The aim of this study was to clarify the aromatic cleavage pathways and microbes involved in the adverse effect of nitrate on aromatic compounds humic substances during sludge composting. Results showed that the functional microbes involved in aromatic compounds humic substances precursors (catechol, tyrosine, tryptophan and phenylalanine) cleavage pathways significantly enriched after nitrate addition. Linear regression analysis showed that aromatic-ring cleavage functional microbes exhibited significant negative correlation with aromatic humic substances (p < 0.05). Furthermore, network analysis indicated that most of microbial communities prefer cooperative with aromatic-ring cleavage functional microbes. Structural equation model further revealed that composting microenvironment drove aromatic-ring cleavage functional microbes activities, resulting in the biodegradation of complex aromatic compounds. This study parsed the effect of a negative factor on aromatic compounds humic substances from an opposing perspective. Properly controlling nitrate concentration and aromatic-ring cleavage functional microbes involved in precursors cleavage was suggested to the practice of composting.

Activation of biochar through exoenzymes prompted by earthworms for vermibiochar production: A viable resource recovery option for heavy metal contaminated soils and water

The industrial revolution and indiscriminate usage of a wide spectrum of agrochemicals account for the dumping of heavy metals in the environment. In-situ/ex-situ physical, chemical, and bioremediation strategies with pros and cons have been adopted for recovering metal contaminated soils and water. Therefore, there is an urgent requirement for a cost-effective and environment-friendly technique to combat metal pollution. Biochar combined with earthworms and vermifiltration is a suitable emerging technique for the remediation of metal-polluted soils and water. The chemical substances (e.g., sodium hydroxide, zinc chloride, potassium hydroxide, and phosphoric acid) have been used to activate biochar, which also faces several shortcomings. Studies reveal that extracellular enzymes have been used to activate biochar which is produced by earthworms and microbes that can alter the surface of the biochar. The present review focuses on the global scenario of metal pollution and its remediation through biochar activation using earthworms. The earthworms and biochar can produce "vermibiochar" which is capable of reducing the metal ions from contaminated water and soils. The vermifiltration can be a suitable technology for metal removal from wastewater/effluent. Thus, the biochar has a trick of producing entirely new options at a time when vermifiltration and other technologies are least expected. Further attention to the biochar-assisted vermifiltration of different sources of wastewater is required to be explored for the large-scale utilization of the process.

NMR of Natural Products as Potential Drugs

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.

Exploring the structure and dynamics of proteins in soil organic matter

Alongside inorganic materials, water, and air, soil organic matter (SOM) is one of the major components of soil and has tremendous influence on the environment given its vital role in the carbon cycle. Many soil dwelling organisms like plants, fungi and bacteria excrete proteins, whose interaction with SOM is poorly understood on an atomistic level. In this study, molecular dynamics simulations were used to investigate selected proteins in soil models of different complexity from simple co-solvent molecules to Leonardite humic acids (LHA). We analyzed the proteins in terms of their structural stability, the nature and strength of the interactions with their surroundings, as well as their aggregation behavior. Upon insertion of proteins in complex SOM models, their structural stability decreased, although no unfolding or disruption of secondary structure was observed. The interactions of proteins and SOM were primarily governed by electrostatic forces, often in form of hydrogen bonds. However, also weaker van der Waals forces made a significant contribution to the total interaction energies. Moreover, we showed that even though the molecular structure and size of SOM molecules varied, the functional groups of SOM ordered around the protein in a similar pattern. Finally, the number of aggregates formed by proteins and SOM molecules was shown to be primarily proportional to the size of the latter. Strikingly, for varying protein net charges no changes in the formation of aggregates with the strongly negatively charged LHA were observed.

Metallothionein dependent-detoxification of heavy metals in the agricultural field soil of industrial area: Earthworm as field experimental model system

Earthworms are known to reclaim soil contamination and maintain soil health. In the present study, the concentration of DTPA extractable heavy metals, Cd, Cu, Cr, Pb, and Zn in vermicasts and tissues of the earthworms (anecic: Lampito mauritii; epigeic: Drawida sulcata) collected from the soils of four different industrial sites, Site-I (Sago industry), Site-II (Chemplast industry), Site-III (Dairy industry) and Site-IV (Dye industry) have been studied. The heavy metals in industrial soils recorded were 0.01-326.42 mg kg^-1 with higher Cu, Cr, and Zn contents while the vermicasts showed lower heavy metal loads with improved physicochemical properties and elevated humic substances. The higher humic substances dramatically decreased the heavy metals in the soil. The bioaccumulation factors of heavy metals (mg kg^-1) are in the order: Zn (54.50) > Cu (17.43) > Cr (4.54) > Pb (2.24) > Cd (2.12). The greatest amount of metallothionein protein (nmol g^-1) was recorded in earthworms from Site-IV (386.76) followed by Site-III (322.14), Site-II (245.82), and Site-I (232.21). Drawida sulcata can produce a considerable amount of metallothionein protein than Lampito mauritii as the metallothionein production is dependent upon the presence of pollutants. The molecular docking analysis indicates a binding score of 980 for Cd, Cr and Cu, and 372 for Zn. Pb may bind with a non-metallothionein protein of earthworms and bio-accumulated in the internal chloragogenous tissues. Metallothionein neutralizes the metal toxicity and controls the ingestion of essential elements.

Molecular modelling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid

Soil organic matter (SOM) is abundant in the environment and plays an important role in several biogeochemical processes, including microbial activity, soil aggregation, plant growth and carbon storage. One of its key functions is the retention and release of various chemical compounds, primarily governed by the sorption process, which strongly affects the environmental fate of nutrients and pollutants. Sorption largely depends on the composition of SOM, as well as its structure, dynamics and the thermodynamic conditions. Although several approaches are available, experimental characterization of sorption mechanisms is not easy. Computational models for predicting sorption coefficients often require a wealth of experimental data for training and are only applicable to compounds and conditions related to the training dataset. Here, we use molecular dynamics (MD) simulations to study the sorption of a range of small organic compounds. As a model SOM system we use the standard Leonardite humic acid (LHA) sample, which physicochemical properties have recently been characterized computationally in detail. This model allowed us to estimate sorption propensities of the systems at two different hydration levels (water activities close to 0 and 1), showing a remarkable correlation with experimental data. Importantly, this molecular modelling approach based on perturbation free-energy calculations is rigorously derived from statistical thermodynamics and requires no experimental sorption data for training. It is therefore in principle applicable to any SOM model or thermodynamic condition. Moreover, the power of MD simulations to provide high-resolution insight into atomistic and molecular interactions was employed to explore how sorbate molecules associate with the LHA matrix and which contacts they form. The heteroatoms of both sorbate and sorbent play an important role and water molecules are identified as further key players in facilitating the sorption process.

HIGHLIGHTS

Modelling of the sorption processes in soil organic matter at atomistic level.Rigorous, physics-based approach applicable to a range of SOM systems and conditions.Remarkable level of matching with experimental data with additional insight into the molecular mechanism.Interactions between the sorbate and local environment strongly affects the sorption process.

Development of a quantitative structure-activity relationship model for mechanistic interpretation and quantum yield prediction of singlet oxygen generation from dissolved organic matter

Singlet oxygen (¹O₂) is capable of degrading organic contaminants and inducing cell damage and inactivation of viruses. It is mainly generated through the interaction of dissolved oxygen with excited triplet states of dissolved organic matter (DOM) in natural waters. The present study aims at revealing the underlying mechanism of ¹O₂ generation and providing a potential tool for predicting the quantum yield of ¹O₂ (Φ_1O2) generation from DOM by constructing a quantitative structure-activity relationship (QSAR) model. The determined Φ_1O2 values for the selected DOM-analogs range from (0.54 ± 0.23) × 10^-2 to (62.03 ± 2.97) × 10^-2. A QSAR model was constructed and was proved to have satisfactory goodness-of-fit and robustness. The QSAR model was successfully used to predict the Φ_1O2 of Suwannee River fulvic acid. Mechanistic interpretation of the descriptors in the model showed that hydrophobicity, molecular complexity and the presence of carbonyl groups in DOM play crucial roles in the generation of ¹O₂ from DOM. The presence of other heteroatoms besides O, such as N and S, also affects the generation of ¹O₂. The results of this study provide valuable insights into the generation of ¹O₂ from DOM in sunlit natural waters.

Characterization of coal-based fulvic acid and the construction of a fulvic acid molecular model

Fulvic acid (FA) is composed of many molecular units with similar characteristic structures. The characterization and molecular model construction of coal-based FA is the key for the scientific basis and applied science of FA.

Humic substances developed during organic waste composting: Formation mechanisms, structural properties, and agronomic functions

Aerobic composting is a typical biochemical process of stabilization and harmlessness of organic wastes during which organic matter degrades, and then aggregates, to produce humic substances (HSs). HSs are a core product of-and a crucial indicator of-the maturation of compost that can be used in soil amendments. The formation of HSs is affected by the characteristics of the raw materials involved, the presence of compost additives, microbial activity, temperature, pH, the C/N ratio, moisture content, oxygen content and particle size, all of which can interact with each other. The formation of HSs is therefore complex. Moreover, it is difficult to identify definitive structures of humic acids (HAs) and fulvic acids (FAs), which are the two major components of HSs. However, HSs represent the same functional groups and structural arrangements, which helps to predict their structures. Functional groups represented by phenol and carboxylic acid groups of HAs and FAs can provide various agronomic functions, such as plant growth enhancement, water and nutrient retention, and disease suppression capacity. Overall, HSs can act as a soil amendment, fertilizer, and plant growth regulator. These functions of HSs enhance the reuse potential of organic waste compost products; however, this requires scientific control of various composting parameters and appropriate application of final products.

Molecular characteristics, proton dissociation properties, and metal binding properties of soil organic matter: A theoretical study

Soil organic matter (SOM) is a key soil sorbent with a large number of reactive binding sites that may complex with metals, controlling their fate, transport, and bioavailability in soil. However, due to the complex and heterogeneous nature of SOM, it is not easy to probe its physical and chemical properties at the molecular level. In this study, an a priori method was developed to predict the molecular properties of SOM, which incorporated computational molecular modeling, SPARC Performs Automated Reasoning in Chemistry's (SPARC's) chemical reactivity models, and linear free energy relationships (LFERs). Specifically, the method uses SOM models simulated by molecular dynamics modeling based on the experimental elemental composition and functional group information of SOM. For the molecular characteristics, the molecular H/C and O/C ratios, molecular weight, aromatic index, and double bond equivalence of the SOM molecules were calculated. For the proton binding constants, the SPARC was used to calculate the microscopic pK_a values of every binding sites of individual molecules of the SOM model. Based on the pK_a values, the metal binding constants for individual monodentate binding sites were calculated using the Irving-Rossotti LFERs for different heavy metals. The results agreed reasonably with the default values used in the Windermere Humic Aqueous Model (WHAM) (VI) for the investigated metals. The theoretical SOM models, to some extent, represented the average properties of the investigated SOM. Overall, this study gives new quantitative and molecular insight into the structure and chemical properties of SOM. Detailed deprotonation and metal-SOM complexation information was gained for individual SOM binding sites. Such feasible and straightforward predictive scheme is useful to assess the risk of heavy metals in various aquatic and terrestrial environment involving heterogeneous natural organic matter.

Protaetia brevitarsis larvae can efficiently convert herbaceous and ligneous plant residues to humic acids

Utilization of the organic residues produced after crop harvesting is currently an important issue across the world. The edible insect Protaetia brevitarsis larvae can feed various organic matters. In this paper, we investigated the potential to utilize the insect to convert herbaceous and ligneous plant residues. We feed the insect larvae with maize straw and sawdust and analyzed the produced insect manure. P. brevitarsis larval was found to be able to digest both herbaceous and ligneous straw and insect manure extract shown no phytotoxicity. The mass fractions of humic acids (HAs) in the insect manure derived from maize straw and sawdust digestion were 24.37% and 14.46%, respectively. The ¹³C cross-polarization magic-angle spinning nuclear magnetic resonance (CP-MAS NMR) spectra data indicated that the HAs in the insect manure were similar to those found in the soil. These data suggested that P. brevitarsis larvae can be used to convert agricultural residues and produce organic fertilizers.

Characterization and 2D structural model of corn straw and poplar leaf biochars

The integrated experimental methods were used to analyze the physicochemical properties and structural characteristics and to build the 2D structural model of two kinds of biochars. Corn straw and poplar leaf biochars were gained by pyrolysing the raw materials slowly in a furnace at 300, 500, and 700 °C under oxygen-deficient conditions. Scanning electron microscope was applied to observe the surface morphology of the biochars. High temperatures destroyed the pore structures of the biochars, forming a particle mixture of varying sizes. The ash content, yield, pH, and surface area were also observed to describe the biochars' properties. The yield decreases as the pyrolysis temperature increases. The biochars are neutral to alkaline. The biggest surface area is 251.11 m²/g for 700 °C corn straw biochar. Elemental analysis, infrared microspectroscopy, solid-state C-13 NMR spectroscopy, and pyrolysis gas chromatography-mass spectrometry (Py-GC-MS) were also used to study the structural characteristics and build the 2D structural models of biochars. The C content in the corn straw and poplar leaf biochars increases with the increase of the pyrolysis temperature. A higher pyrolysis temperature makes the aryl carbon increase, and C=O, OH, and aliphatic hydrocarbon content decrease in the IR spectra. Solid-state C-13 NMR spectra show that a higher pyrolysis temperature makes the alkyl carbon and alkoxy carbon decrease and the aryl carbon increase. The results of IR microspectra and solid-state C-13 NMR spectra reveal that some noticeable differences exist in these two kinds of biochars and in the same type of biochar but under different pyrolysis temperatures. The conceptual elemental compositions of 500 °C corn straw and poplar leaf biochars are C₆₁H₃₃NO₁₃ and C₅₉H₄₁N₃O₁₂, respectively. Significant differences exist in the SEM images, physicochemical properties, and structural characteristics of corn straw and poplar leaf biochars.

Adsorption of Bovine Serum Albumin on Poly(vinylidene fluoride) Surfaces in the Presence of Ions: A Molecular Dynamics Simulation

Adsorption of bovine serum albumin (BSA) on poly(vinylidene fluoride) (PVDF) surfaces in an aqueous environment was investigated in the presence and absence of excess ions using molecular dynamics simulations. The adsorption process involved diffusion of protein to the surface and dehydration of surface-protein interactions, followed by adsorption and denaturation. Although adsorption of BSA on PVDF surface was observed in the absence of excess ions, denaturation of BSA was not observed during the simulation (1 μs). Basic and acidic amino acids of BSA were found to be directly interacting with PVDF surface. Simulation in a 0.1 M NaCl solution showed delayed adsorption of BSA on PVDF surfaces in the presence of excess ions, with BSA not observed in close proximity to PVDF surface within 700 ns. Adsorption of Cl^- on PVDF surface increased its negative charge, which repelled negatively charged BSA, thereby delaying the adsorption process. These results will be helpful for understanding membrane fouling phenomena in polymeric membranes, and fundamental advancements in these areas will lead to a new generation of membrane materials with improved antifouling properties and reduced energy demands.

Molecular Dynamics Simulations of the Standard Leonardite Humic Acid: Microscopic Analysis of the Structure and Dynamics

Humic substances (HS) are abundant in the environment and play an important role in a number of biogeochemical processes including microbial activity, soil aggregation, plant growth, the retention and release of nutrients, the environmental fate of pollutants, and carbon storage. They are flexible, relatively small molecules forming supramolecular structures through weak interactions. Despite the great importance of understanding their behavior at the atomic level, computational modeling, a premier high-resolution technique providing great level of detail, has been surprisingly little-employed to study humic substances. Here, we use the recently developed Vienna Soil Organic-Matter Modeler to create representative models of a real HS sample, the standard Leonardite humic acid. Molecular dynamics simulations were used to probe the structure and dynamics of the system at a range of hydration levels. The studied systems were characterized in terms of their physicochemical properties, including density, dielectric properties, hydrogen bonding, etc. Moreover, the strength of sorption was estimated for three small organic compounds: benzaldehyde, propan-2-ol, and acetone. Strikingly, the HS models were validated against experimental data showing a remarkable agreement with calculated properties. Finally, we make the equilibrated models of the standard Leonardite humic acid, together with corresponding force-field parameters, available at the Vienna Soil Organic-Matter Modeler.

Elucidating triplet-sensitized photolysis mechanisms of sulfadiazine and metal ions effects by quantum chemical calculations

Sulfadiazine (SDZ) mainly proceeds triplet-sensitized photolysis with dissolved organic matter (DOM) in the aquatic environment. However, the mechanisms underlying the triplet-sensitized photolysis of SDZ with DOM have not been fully worked out. In this study, we investigated the mechanisms of triplet-sensitized photolysis of SDZ(0) (neutral form) and SDZ(-) (anionic form) with four DOM analogues, i.e., fluorenone (FL), thioxanthone (TX), 2-acetonaphthone (2-AN), and 4-benzoylbenzoic acid (CBBP), and three metal ions (i.e., Mg(2+), Ca(2+), and Zn(2+)) effects using quantum chemical calculations. Results indicated that the triplet-sensitized photolysis mechanism of SDZ(0) with FL, TX, and 2-AN was hydrogen transfer, and with CBBP was electron transfer along with proton transfer (for complex SDZ(0)-CBBP2) and hydrogen transfer (for complex SDZ(0)-CBBP1). The triplet-sensitized photolysis mechanisms of SDZ(-) with FL, TX, and CBBP was electron transfer along with proton transfer, and with 2-AN was hydrogen transfer. The triplet-sensitized photolysis product of both SDZ(0) and SDZ(-) was a sulfur dioxide extrusion product (4-(2-iminopyrimidine-1(2H)-yl)aniline), but the formation routs of the products for SDZ(0) and SDZ(-) were different. In addition, effects of the metal ions on the triplet-sensitized photolysis of SDZ(0) and SDZ(-) were different. The metal ions promoted the triplet-sensitized photolysis of SDZ(0), but inhibited the triplet-sensitized photolysis of SDZ(-).

Molecular models of natural organic matter and its colloidal aggregation in aqueous solutions: Challenges and opportunities for computer simulations

Natural organic matter (NOM) is ubiquitous in soil and groundwater, and its aqueous complexation with various inorganic and organic species can strongly affect the speciation, solubility, and toxicity of many elements in the environment. Despite significant geochemical, environmental, and industrial interest, the molecular-scale mechanisms of the physical and chemical processes involving NOM are not yet fully understood. Recent molecular dynamics (MD) simulations using relatively simple models of NOM fragments are used here to illustrate the challenges and opportunities for the application of computational molecular modeling techniques to the structural, dynamic, and energetic characterization of metal–NOM complexation and colloidal aggregation in aqueous solutions. The predictions from large-scale MD simulations are in good qualitative agreement with available experimental observations, but also point out the need for simulations at much larger time- and length-scales with more complex NOM models in order to fully capture the diversity of molecular processes involving NOM.

Prediction of soil sorption coefficients using model molecular structures for organic matter and the quantum mechanical COSMO-SAC model

The soil sorption coefficient, K(OC), is an important property affecting the environmental fate of organic molecules. Difficulties associated with measuring K(OC) have led to many attempts to predict this property, but most rely on empirical descriptors for the soil phase determined from correlations with measured K(OC) data, and are thereby limited by the data quality and diversity. A new method is presented to predict K(OC) for nonionic organic compounds that requires only molecular structures. No calibration is performed. Using model humic acid (HA) and fulvic acid (FA) molecular structures from the literature, the soil organic matter is modeled as an organic solvent composed of HA or FA molecules. K(OC) is predicted as an organic solvent-water partition coefficient using the quantum mechanics-based model COSMO-SAC. The log K(OC) values for a set of 440 diverse, environmentally relevant chemicals are predicted with a root-mean-square error of 0.84-1.08, depending on which model HA or FA is used.

Metal cation complexation with natural organic matter in aqueous solutions: molecular dynamics simulations and potentials of mean force

Natural organic matter (NOM, or humic substance) has a known tendency to form colloidal aggregates in aqueous environments, with the composition and concentration of cationic species in solution, pH, temperature, and the composition of the NOM itself playing important roles. Strong interaction of carboxylic groups of NOM with dissolved metal cations is thought to be the leading chemical interaction in NOM supramolecular aggregation. Computational molecular dynamics (MD) study of the interactions of Na(+), Mg(2+), and Ca(2+) with the carboxylic groups of a model NOM fragment and acetate anions in aqueous solutions provides new quantitative insight into the structure, energetics, and dynamics of the interactions of carboxylic groups with metal cations, their association, and the effects of cations on the colloidal aggregation of NOM molecules. Potentials of mean force and the equilibrium constants describing overall ion association and the distribution of metal cations between contact ion pairs and solvent-separated ions pairs were computed from free MD simulations and restrained umbrella sampling calculations. The results provide insight into the local structural environments of metal-carboxylate association and the dynamics of exchange among these sites. All three cations prefer contact ion pair to solvent-separated ion pair coordination, and Na(+) and Ca(2+) show a strong preference for bidentate contact ion pair formation. The average residence time of a Ca(2+) ion in a contact ion pair with the carboxylic groups is of the order of 0.5 ns, whereas the corresponding residence time of a Na(+) ion is only between 0.02 and 0.05 ns. The average residence times of a Ca(2+) ion in a bidentate coordinated contact ion pair vs a monodentate coordinated contact ion pair are about 0.5 and 0.08 ns, respectively. On the 10 ns time scale of our simulations, aggregation of the NOM molecules occurs in the presence of Ca(2+) but not Na(+) or Mg(2+). These results agree with previous experimental observations and are explained by both Ca(2+) ion bridging between NOM molecules and decreased repulsion between the NOM molecules due to the reduced net charge of the NOM-metal complexes. Simulations on a larger scale are needed to further explore the relative importance of the different aggregation mechanisms and the stability of NOM aggregates.

Quantum chemical investigation and experimental verification on the aquatic photochemistry of the sunscreen 2-phenylbenzimidazole-5-sulfonic acid

For ecological risk assessment of the large and ever-increasing number of chemical pollutants, it is of importance to develop computational methods to screen or predict their environmental photodegradation behavior. This study developed a computational method based on the density functional theory (DFT) to predict and evaluate the photodegradation behavior and effects of water constituents, taking a sunscreen and personal care product 2-phenylbenzimidazole-5-sulfonic acid (PBSA) as a model compound. Energy and electron transfer reactions of excited state PBSA (PBSA*) with (3)O(2) and water constituents were evaluated. The computational results indicated that PBSA* could photogenerate (1)O(2) and O(2)(-)·, triplet excited state humic/fulvic acid analogs could not photosensitize the degradation, and the anions (Cl(-), Br(-), and HCO(3)(-)) could not quench PBSA* or its radical cation chemically. Experiments employing simulated sunlight confirmed that PBSA photodegraded via the direct and self-sensitization mechanism involving O(2)(-)·. The photodegradation was pH-dependent. The direct and self-sensitized photodegradation was inhibited by fulvic acid. The main photodegradation products were identified, and the pathways were clarified. These results indicate that the DFT-based computational method can be employed to assess the environmental photochemical fate of organic pollutants.

Binding of ciprofloxacin by humic substances: a molecular dynamics study

A comprehensive assessment of the potential impacts of antimicrobials released into the environment requires an understanding of their sequestration by natural particles. Of particular interest are the strong interactions of antimicrobials with natural organic matter (NOM), which are believed to reduce their bioavailability, retard their abiotic and biotic degradation, and facilitate their persistence in soils and aquatic sediments. Molecular dynamics (MD) relaxation studies of a widely used fluoroquinolone antibiotic, ciprofloxacin (Cipro), interacting with a model humic substance (HS) in a hydrated environment, were performed to elucidate the mechanisms of these interactions. Specifically, a zwitterionic Cipro molecule, the predominant species at circumneutral pH, was reacted either with protonated HS or deprotonated HS bearing Ca, Mg, or Fe(II) cations. The HS underwent conformational changes through rearrangements of its hydrophobic and hydrophilic regions and disruption of its intramolecular H-bonds to facilitate favorable intermolecular H-bonding interactions with Cipro. Complexation of the metal cations with HS carboxylates appeared to impede binding of the positively charged amino group of Cipro with these negatively charged HS complexation sites. On the other hand, an outer-sphere complex between Cipro and the HS-bound cation led to ternary Cipro-metal-HS complexes in the case of Mg-HS and Fe(II)-HS, but no such bridging interaction occurred with Ca-HS. The results suggested that the ionic potential (valence/ionic radius) of the divalent cation may be a determining factor in the formation of the ternary complex, with high ionic potential favoring the bridging interaction. Environ. Toxicol. Chem. 2010;29:90-98. (c) 2009 SETAC.

Distribution of proton dissociation constants for model humic and fulvic acid molecules

The intrinsic proton binding constants of 10 model humic acid and six model fulvic acid molecules are calculated using SPARC Performs Automated Reasoning in Chemistry (SPARC). The accuracy of the SPARC calculations is examined using estimated microscopic binding constants of various small organic acids. An equimolar mixture of the appropriate hypothetical molecules is used as a representation of soil and aqueous humic acid and fulvic acid. The probability distributions of the mixture microscopic proton binding constants and the intrinsic proton binding constants in the metal speciation models WHAM V and WHAM VI (Windermere humic aqueous models) are compared. The idea is to assess the predictive value of the molecular mixture models as representations of heterogeneous natural organic matter. For aqueous humic and fulvic acids, the results are comparable to the WHAM distribution. For soil humic acid, the WHAM probability distribution is less acidic for the carboxylic sites but similar to that of the phenolic sites. Computations made using the WHAM molecular distributions and WHAM VI are comparable to titration data for Suwannee River fulvic acid. These results suggest that mixture molecular models can be used to investigate and predict the binding of metal cations to humic and fulvic acids.

Advanced TMAH and TMAAc thermochemolysis–pyrolysis techniques for molecular characterization of size-separated fractions from aquatic dissolved organic matter

The structural similarities and differences between the original DOM and the eight size fractions separated were studied in detail with the pyrolysis technique in combination with gas chromatography and mass spectrometry (Py-GC-MS) using two alkylating reagents: TMAH (tetramethylammonium hydroxide), to find both esterified and free carboxylic acids; and TMAAc (tetramethylammonium acetate), to specify only free carboxylic acids. A statistical analysis of the original multidimensional TMAH and TMAAc pyrograms disclosed that the overall structural compositions of the five most important size fractions, accounting for 84% of the original DOM, greatly resembled each other. The remaining three minor size fractions were not classified as homogeneous associations, but they also contained the same total, covalently bound and free carboxylic acid species as the other size fractions and the original DOM mixture, thus representing some kind of intermediate forms. This fundamental outcome strongly supports the opinion that the native dissolved humic-like macromolecules resemble supramolecular associations of smaller molecular size moieties with similar structural functionalities. The concentrations of free aliphatic and aromatic dicarboxylic acids in the DOM solution were so low that their effects on the potential formation of multiply charged ions in electrospray ionization-MS (ESI-MS) studies are likely insignificant.

Thermal analytical investigation of biopolymers and humic- and carbonaceous-based soil and sediment organic matter

Improved understanding of the physical, chemical, and thermodynamic properties of soil and sediment organic matter (SOM) is crucial in elucidating sorption mechanisms of hydrophobic organic compounds (HOCs) in soils and sediments. In this study, several thermoanalytical techniques, including thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), temperature-modulated differential scanning calorimetry (TMDSC), and thermal mechanical analysis (TMA) were applied to 13 different organic materials (three woods, two humic acids, three kerogens, and five black carbons) representing a spectrum of diagenetic and/or thermal histories. Second-order thermal transition temperatures (T(t)) were identified in most materials, where the highest observed T(t) values (typically characterized as glass transition temperatures (T(g were shown to closely relate to chemical characteristics of the organic samples as influenced by diagenetic or thermal alteration. Results further suggest a positive correlation between glass transition temperature and a defined diagenetic/thermal index, where humic-based SOM (e.g., humic and fulvic acids) possess lowertransition temperatures than more "mature" carbonaceous-based SOM (i.e., kerogens and black carbons). The observed higher thermal transition temperature of aliphatic-rich Green River shale kerogen (approximately 120 degrees C) relative to that of aromatic-rich humic acids suggests that a sole correlation of aromaticity to thermal transition temperature may be inappropriate.

Quantum chemical modeling of humic acid/air equilibrium partitioning of organic vapors

Classical approaches for predicting soil organic matter partition coefficients of organic compounds require a calibration with experimental partition data and, for good accuracy, experimental compound descriptors. In this study we evaluate the quantum chemical model COSMO-RS in its COSMOtherm implementation for the prediction of about 200 experimental Leonardite humic acid/air partition coefficients without calibration or experimental compound descriptors, but simply based on molecular structures. For this purpose a Leonardite Humic Acid model monomer limited to 31 carbon atoms was derived from 13C NMR analysis, elemental analysis, and acidic function analysis provided in the literature. Altogether the COSMOtherm calculations showed a good performance and we conclude that it may become a very promising tool for the prediction of sorption in soil organic matter for compounds for which the molecular structure is the only reliable information available. COSMOtherm can be expected to be very robust with respectto new and complex compound structures because its calculations are based on a fundamental assessment of the underlying intermolecular forces. In contrast, other empirical models that are also based on the molecular structure of the sorbate have an application domain that is limited by their calibration data set that is often unknown to the user.

NMR spectroscopy study of freshwater humic material in light of supramolecular assembly

The structural similarity-dissimilarity of several humic-type derivatives, separated from a strongly colored freshwater sample by different sorbing solid techniques, tangential-flow ultrafiltration (UF), and large-scale preparative high-performance size-exclusion chromatography (HPSEC), were in detail studied with one-dimensional liquid 1H and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy, especially in light of the native humic-type dissolved organic matter (DOM-HM). The results support the applicability of functional cross-linked poly(vinylpyrrolidone) (PVP) or diethylaminoethyl-cellulose (DEAE) sorbents in concentrating representative integrated wholes of aquatic humic-type material along with a conventional nonionic XAD-8/DAX-8 (polymethyl methacrylates) technique. Apart from the fact that the acidification of the original humic water before a separation procedure seems not to be so destructive to the original structural composition of the DOM-HM as expected, the refinement of aquatic humic solutes, independent of the selected sorbing solid technique, will cause structural changes in the separated humic complexes in comparison with the situation predominating in the original starting material. Tangential-flow ultrafiltration (UF) proved an overpowering reliability to concentrate the aquatic DOM-HM. Most fundamental is the combined outcome of different HPSEC experiments and determined structural functionalities which indicate that almost all original DOM-HM solutes are aggregated mixtures consisting of structurally similar associations possessing various molecular size ranges, which can be separated from their integrated whole as nearly homogeneous and uniform species. This finding permits a reasonable starting point to go on working with more advanced multidimensional NMR techniques in resolving the uncertainty about supramolecular assembly of dissolved humic material. The tested conformity between the obtained molecular NMR descriptors and the corresponding previously collected FT-IR parameters was acceptable thus speaking for the fact that the less sensitive FT-IR spectroscopy can also provide valuable information on the structural and functional properties of heterogeneous humic-type mixtures.

Advanced thermal characterization of fractionated natural organic matter

This work focuses on an experimental investigation of the thermodynamic properties of natural organic matter (NOM), and whether fractions of NOM possess the same thermodynamic characteristics as the whole NOM from which they are derived. Advanced thermal characterization techniques were employed to quantify thermal expansion coefficients (alpha), constant-pressure specific heat capacities (C(p)), and thermal transition temperatures (T(t)) of several aquatic- and terrestrial-derived NOM. For the first time, glass transition behavior is reported for a series of NOM fractions derived from the same whole aquatic or terrestrial source, including humic acid-, fulvic acid-, and carbohydrate-based NOM, and a terrestrial humin. Thermal mechanical analysis (TMA), standard differential scanning calorimetry (DSC), and temperature-modulated differential scanning calorimetry (TMDSC) measurements revealed T(t) ranging from -87 degrees C for a terrestrial carbohydrate fraction to 62 degrees C for the humin fraction. The NOM generally followed a trend of increasing T(t) from carbohydrate to fulvic acid to humic acid to humin, and greater T(t) associated with terrestrial fractions relative to aquatic fractions, similar to that expected for macromolecules possessing greater rigidity and larger molecular weight. Many of the NOM samples also possessed evidence of multiple transitions, similar to beta and alpha transitions of synthetic macromolecules. The presence of multiple transitions in fractionated NOM, however, is not necessarily reflected in whole NOM, suggesting other potential influences in the thermal behavior of the whole NOM relative to fractionated NOM. Temperature-scanning X-ray diffraction studies of each NOM fraction confirmed the amorphous character of each sample through T(t).

Metal binding by humic acids isolated from water hyacinth plants (Eichhornia crassipes [Mart.] Solm-Laubach: Pontedericeae) in the Nile Delta, Egypt

Humic acids (HAs) are animal and plant decay products that confer water retention, metal and organic solute binding functions and texture/workability in soils. HAs assist plant nutrition with minimal run-off pollution. Recent isolation of HAs from several live plants prompted us to investigate the HA content of the water hyacinth (Eichhornia crassipes [Mart.] Solm-Laubach: Pontedericeae), a delicately flowered plant from Amazonian South America that has invaded temperate lakes, rivers and waterways with devastating economic effects. Hyacinth thrives in nutrient-rich and polluted waters. It has a high affinity for metals and is used for phytoremediation. In this work, HAs isolated from the leaves, stems and roots of live water hyacinth plants from the Nile Delta, Egypt were identified by chemical and spectral analysis and by comparison with authentic soil and plant derived HAs. Similar carbohydrate and amino acid distributions and tight metal binding capacities of the HAs and their respective plant components suggest that the presence of HAs in plants is related to their metal binding properties.