scholarly journals Estimation of WHAM7 constants for GaIII, InIII, SbIII and BiIII from linear free energy relationships, and speciation calculations for natural waters

2020 ◽  
Vol 17 (2) ◽  
pp. 140 ◽  
Author(s):  
Edward Tipping ◽  
Montserrat Filella
Keyword(s):  
Organic Matter ◽  
Metal Binding ◽  
Metal Ion ◽  
Natural Waters ◽  
Chemical Speciation ◽  
Equilibrium Constants ◽  
Model Parameters ◽  
Binding Model ◽  
Critical Elements ◽  
Linear Free Energy

Environmental contextNatural organic matter exerts a powerful control on chemical conditions in waters and soils, affecting pH and influencing the biological availability, transport and retention of metals. Modelling can help to predict these effects, but for many metals, model parameters are missing. We report parameters for four technology-critical elements in a chemical speciation model, and consider the chemistries of the elements in natural waters. AbstractWe compiled the equilibrium constants for the interactions of the technology-critical elements (TCEs) GaIII, InIII, SbIII and BiIII with ammonia, fluoride, hydroxyl and ligands with oxygen atoms. We then combined them with predictive equations to estimate parameters for Humic Ion-Binding Model VII, which permits the calculation of metal binding by natural organic matter (fulvic acid, FA, and humic acid, HA). Derived values of the Model VII parameter quantifying the interaction of metal ions with carboxyl-type groups (log KMA) were among the highest estimated so far, as were the values for the parameter (ΔLK2) that quantifies the tendency of the metal ion to interact with softer ligand atoms (N and S). The Windermere Humic Aqueous Model, version 7 (WHAM7), which incorporates Model VII, was then used to estimate the chemical speciation of each TCE element.

scholarly journals Humic Ion-Binding Model VII: a revised parameterisation of cation-binding by humic substances

2011 ◽  
Vol 8 (3) ◽  
pp. 225 ◽  
Author(s):  
E. Tipping ◽  
S. Lofts ◽  
J. E. Sonke
Keyword(s):  
Organic Matter ◽  
Metal Binding ◽  
Environmental Chemistry ◽  
Equilibrium Constants ◽  
Laboratory Data ◽  
Cation Binding ◽  
Model Parameters ◽  
Ion Binding ◽  
Binding Model ◽  
Mean Values

Environmental contextNatural organic matter exerts a powerful control on chemical conditions in waters and soils, affecting pH and influencing the biological availability, transport and retention of metals. To quantify the reactions, we collated a wealth of laboratory data covering 40 metals and acid–base reactions, and used them to parameterise the latest in a series of Humic Ion-Binding Models. Model VII is now available to interpret field data, and contribute to the prediction of environmental chemistry. AbstractHumic Ion-Binding Model VII aims to predict the competitive reactions of protons and metals with natural organic matter in soils and waters, based on laboratory results with isolated humic and fulvic acids (HA and FA). Model VII is simpler in its postulated multidentate metal binding sites than the previous Model VI. Three model parameters were eliminated by using a formal relationship between monodentate binding to strong- and weak-acid oxygen-containing ligands, and removing factors that provide ranges of ligand binding strengths. Thus Model VII uses a single adjustable parameter, the equilibrium constant for monodentate binding to strong-acid (carboxylate) groups (KMA), for each metallic cation. Proton-binding parameters, and mean values of log KMA were derived by fitting 248 published datasets (28 for protons, 220 for cationic metals). Default values of log KMA for FA were obtained by combining the fitted values for FA, results for HA, and the relationship for different metals between log KMA and equilibrium constants for simple oxygen-containing ligands. The equivalent approach was used for HA. The parameterised model improves on Model VI by incorporating more metals (40), providing better descriptions of metal binding at higher pH, and through more internally consistent parameter values.

Metal ion binding by humic substances as emergent functions of labile supramolecular assemblies

2020 ◽  
Vol 17 (3) ◽  
pp. 252 ◽  
Author(s):  
Elena A. Vialykh ◽  
Dennis R. Salahub ◽  
Gopal Achari
Keyword(s):  
Molecular Weight ◽  
Organic Matter ◽  
Humic Substances ◽  
Metal Binding ◽  
Metal Ion ◽  
Computational Modelling ◽  
Intermolecular Forces ◽  
Metal Complexation ◽  
Emergent Properties ◽  
Metal Availability

Environmental contextThe fundamental basis for the high flexibility of humic substances is still unclear, though it is crucial for the understanding of metal bioavailability and toxicity in soil and aqueous environments. We show at the molecular level how characteristics of organic matter affect metal binding depending on the environmental conditions. Such understanding will help in the modulation of metal availability in soil and water in changing environmental situations. AbstractIn this work, we explore the hypothesis that humic substances (HS) can be perceived as labile supramolecular assemblages, the functioning of which is mainly determined by chemical composition and characteristics, the size of molecular units and weak intermolecular forces, rather than the exact primary structure of molecular moieties and their spatial configuration. To test the hypothesis, 72 computational models of three different organic mixtures were composed. The formation of inner and outer sphere metal–ligand complexes, metal binding sites, complex configurations, binding energies and aggregation/dissolution as emergent properties of HS were determined under various conditions. The results of computational modelling revealed that: (i) the highest Cu2+ binding (55.6%) was by the SRFA-22 organic model, which represents low-molecular-weight fulvic acids. In contrast, the highest amount of inner-sphere Mg–organic matter complex (63.4%) was formed in SRHA-6, which has higher-molecular-weight constituents. Therefore, a correlation between the type of cation, the system aromaticity and the extent of metal complexation is proposed. (ii) Increase of metal ion concentration and decrease of water content resulted in an increase in the number of hydrogen bonds and more compact and stable aggregates with lower hydrophilic and higher hydrophobic surface areas in SRFA-22. However, in SRHA-6, the results varied owing to the competition between metal binding, H-bonding and non-polar interactions in the structural arrangement of the aggregates. In general, the aggregation process, driven by metal complexation and water removal, resulted in the formation of more stable conformers, with lower potential energy, with the only exception of SRHA-6–Cu.

scholarly journals Chemical speciation of organic matter in natural waters. Interaction of nucleotide 5’ mono-, di- and triphosphates with major components of seawater

2004 ◽  
Vol 16 (1-2) ◽  
pp. 1-8 ◽  
Author(s):  
Francesco Crea ◽  
Concetta De Stefano ◽  
Antonio Gianguzza ◽  
Daniela Piazzese ◽  
Silvio Sammartano
Keyword(s):  
Organic Matter ◽  
Natural Waters ◽  
Chemical Speciation

Chemical Speciation of Hg(II) with Environmental Inorganic Ligands

2004 ◽  
Vol 57 (10) ◽  
pp. 993 ◽  
Author(s):  
Kipton J. Powell ◽  
Paul L. Brown ◽  
Robert H. Byrne ◽  
Tamas Gajda ◽  
Glenn Hefter ◽  
...  
Keyword(s):  
Organic Matter ◽  
Complex Formation ◽  
Numerical Modelling ◽  
Thermodynamic Data ◽  
Natural Waters ◽  
Chemical Speciation ◽  
Interaction Coefficients ◽  
Low Concentrations ◽  
The Common ◽  
Inorganic Ligands

Abstract Complex formation between Hg(ii) and the common environmental ligands Cl−, OH−, CO32−, SO42−, and PO43− can have profound effects on Hg(ii) speciation in natural waters with low concentrations of organic matter. Hg(ii) is labile, so its distribution among these inorganic ligands can be estimated by numerical modelling if reliable values for the relevant stability constants are available. A summary of critically reviewed constants and related thermodynamic data is presented. Recommended values of log10βp,q,r° and the associated reaction enthalpies, ΔrHm°, valid at Im = 0 mol kg−1 and 25°C, along with the equations and specific ion interaction coefficients required to calculate log10βp,q,r values at higher ionic strengths and other temperatures are also presented. Under typical environmental conditions Hg(ii) speciation is dominated by the reactions Hg2+ + 2Cl− ↔ HgCl2(aq) (log10β2° = 14.00 ± 0.07), Hg2+ + Cl− + H2O ↔ Hg(OH)Cl(aq) + H+ (log10β° = 4.27 ± 0.35), and Hg2+ + 2H2O ↔ Hg(OH)2(aq) + 2H+ (log10*β2° = −5.98 ± 0.06).

scholarly journals Trace metal speciation predictions in natural aquatic systems: incorporation of dissolved organic matter (DOM) spectroscopic quality

2012 ◽  
Vol 9 (4) ◽  
pp. 356 ◽  
Author(s):  
Kristin K. Mueller ◽  
Stephen Lofts ◽  
Claude Fortin ◽  
Peter G. C. Campbell
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Trace Metal ◽  
Metal Binding ◽  
Natural Waters ◽  
Metal Speciation ◽  
Chemical Species ◽  
Metal Species ◽  
Fluorescence Measurements ◽  
Shield Lakes

Environmental contextTo assess the risk posed by environmental contaminants such as metals, one needs to be able to identify the key chemical species that prevail in natural waters. One of the recognised stumbling blocks is the need to quantify the influence of heterogeneous dissolved organic matter (DOM). Here we explore the possibility of using the optical signature of DOM to determine its quality, to alleviate the need to make assumptions about its metal-binding properties and to improve the prediction of trace metal species distributions in natural waters. AbstractTo calculate metal speciation in natural waters, modellers must choose the proportion of dissolved organic matter (DOM) that is actively involved in metal complexation, defined here as the percentage of active fulvic acid (FA); to be able to estimate this proportion spectroscopically would be very useful. In the present study, we determine the free Cd2+, Cu2+, Ni2+ and Zn2+ concentrations in eight Canadian Shield lakes and compare these measured concentrations to those predicted by the Windermere Humic Aqueous Model (WHAM VI). For seven of the eight lakes, the measured proportions of Cd2+ and Zn2+ fall within the range of values predicted by WHAM; the measured proportion of Cu2+ falls within this range for only half of the lakes sampled, whereas for Ni, WHAM systematically overestimated the proportion of Ni2+. With the aim of ascribing the differences between measured and modelled metal speciation to variations in DOM quality, the percentage of active FA needed to fit modelled and measured free metal concentrations was compared with the lake-to-lake variation in the spectroscopic quality of the DOM, as determined by absorbance and fluorescence measurements. Relationships between the percentage of active FA and DOM quality were apparent for Cd, Cu, Ni and Zn, suggesting the possibility of estimating the percentage of active FA spectroscopically and then using this information to refine model predictions. The relationships for Ni differed markedly from those observed for the other metals, suggesting that the DOM binding sites active in Cd, Cu and Zn complexation are different from those involved in Ni complexation. To our knowledge, this is the first time that such a distinction has been resolved in natural water samples.

scholarly journals Chemical Speciation and Bioavailability of Iron in Natural Waters - Linkage of Forest, River and Sea in View of Dynamics of Iron and Organic Matter

2016 ◽  
Vol 39 (6) ◽  
pp. 197-210 ◽  
Author(s):  
Masafumi NATSUIKE ◽  
Tetsuro KIKUCHI ◽  
Ying Ping LEE ◽  
Hiroaki ITO ◽  
Manabu FUJII ◽  
...  
Keyword(s):  
Organic Matter ◽  
Natural Waters ◽  
Chemical Speciation

scholarly journals Assessing WHAM/Model VII against field measurements of free metal ion concentrations: model performance and the role of uncertainty in parameters and inputs

2011 ◽  
Vol 8 (5) ◽  
pp. 501 ◽  
Author(s):  
Stephen Lofts ◽  
Edward Tipping
Keyword(s):  
Metal Ion ◽  
Chemical Speciation ◽  
Model Performance ◽  
Model Parameters ◽  
Analytical Technique ◽  
Ion Concentrations ◽  
Model Predictions ◽  
Free Ion ◽  
Free Metal ◽  
Free Metal Ion

Environmental contextThe chemical speciation of metals in waters is of great importance in determining their transport, fate and effects in the environment. Modelling chemical speciation is valuable for making predictions about these effects. Here a model of metal speciation is tested against field data, and recommendations are made as to how both model and measurements might be improved in future. AbstractA key question in the evaluation of chemical speciation models is: how well do model predictions compare against speciation measurements? To address this issue, the performance of WHAM/Model VII in predicting free metal ion concentrations in field samples has been evaluated. A statistical sampling method considering uncertainties in input measurements, model parameters and the binding activity of dissolved organic matter was used to generate distributions of predicted free ion concentrations. Model performance varied with the metal considered and the analytical technique used to measure the free ion. Generally, the best agreement between observation and prediction was seen for aluminium, cobalt, nickel, zinc and cadmium. Important differences in agreement between model and observations were seen, depending upon the analytical technique. In particular, concentrations of free ion determined with voltammetric techniques were largely over-predicted by the model. Uncertainties in model predictions varied among metals. Only for aluminium could discrepancies between observation and model could be explained by uncertainties in input measurements and model parameters. For the other metals, the ranges of model predictions were mostly too small to explain the discrepancies between model and observation. Incorporating the effects of uncertainty into speciation model predictions allows for more rigorous assessment of model performance.

Chemical speciation of environmentally significant heavy metals with inorganic ligands. Part 1: The Hg2+– Cl–, OH–, CO32–, SO42–, and PO43– aqueous systems (IUPAC Technical Report)

2005 ◽  
Vol 77 (4) ◽  
pp. 739-800 ◽  
Author(s):  
Kipton J. Powell ◽  
Paul L. Brown ◽  
Robert H. Byrne ◽  
Tamás Gajda ◽  
Glenn Hefter ◽  
...  
Keyword(s):  
Natural Waters ◽  
Chemical Speciation ◽  
Equilibrium Constants ◽  
Critical Evaluation ◽  
Interaction Theory ◽  
Interaction Coefficients ◽  
Weighted Linear Regression ◽  
Technical Report ◽  
The Common ◽  
Inorganic Ligands

This document presents a critical evaluation of the equilibrium constants and reaction enthalpies for the complex formation reactions between aqueous Hg(II) and the common environmental inorganic ligands Cl–, OH–, CO32–, SO42–, and PO43–. The analysis used data from the IUPAC Stability Constants database, SC-Database, focusing particularly on values for 25 °C and perchlorate media. Specific ion interaction theory (SIT) was applied to reliable data available for the ionic strength range Ic < 3.0 mol dm–3. Recommended values of log10βp,q,r° and the associated reaction enthalpies, ∆rHm°, valid at Im = 0 mol kg–1 and 25 °C, were obtained by weighted linear regression using the SIT equations. Also reported are the equations and specific ion interaction coefficients required to calculate log10βp,q,r° values at higher ionic strengths and other temperatures. A similar analysis is reported for the reactions of H+ with CO32– and PO43–. Diagrams are presented to show the calculated distribution of Hg(II) amongst these inorganic ligands in model natural waters. Under typical environmental conditions, Hg(II) speciation is dominated by the formation of HgCl2(aq), Hg(OH)Cl(aq), and Hg(OH)2(aq).

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

scholarly journals Photochemical effects on the interaction of enzymes and dissolved organic matter in natural waters

2003 ◽  
Vol 48 (5) ◽  
pp. 1818-1824 ◽  
Author(s):  
Norman M. Scully ◽  
Lars J. Tranvik ◽  
William J. Cooper
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Natural Waters
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