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Chemical Speciation Modeling

(20.09.2019)


Background:
Chemical speciation describes the distribution of an element amongst chemical species in a system. Such information is cruciual for understanding environmental fate and transport, bioavailabiliy and toxicity. Speciation analysis is meant to provide such information. However, because trace element concentrations are sometimes very low, speciation and sample matrix are complex, analytical technques are unfortunately not always effective for determining overall speciation. In these cases, it may be useful to identify the various classes of species of an element in order to determine their summed concentration in each class. Such fractionation can be based on different class properties, such as their solubility, affinity, size or molecular mass, to name only few. In certain situations, the fractions can be analyzed further for individual species based on subsequent analyses and calculations.

In cases, where analytical techniques cannot obtain the full species distribution, the determination of the chemical speciation relies on the use of analytical methods in conjunction with chemical speciation models.

Chemical Equilibrium Modeling
Equilibrium models can be used when the reactions considered are fast or the system has sufficient time to reach equilibrium. Under such conditions the system can be described by using thermodynamic equilibrium modeling. The components of the model are selected such that all species can be formed by the components, and no component can be formed by a combination of other components.

Essential components of creating the model are the formulation of objectives, the documentation of the scientific basis for the analysis and the experts judgements and assujmptions made. The following steps are necessary for creating a valuable model:

Choice of scenario
Based on the current level of understanding of the system, a sequence of future events is postulated.

Formulation of conceptual models
The processes envisaged in the scenario descriptions are described by appropriate scientific theories, models and data by making also some physical and chemical approximations.

Construction of the mathematical model
The conceptual models are translated into a suitable numerical form for calculating the relevant system properties under the given assumptions and postulated events.

Calculations
Effective calculation requires well tested computer code that provides numerical stability also for coupled processes such as reactions and mass-transport.


Uncertainty of the modelng
Unfortunately speciation modeling involves significant uncertainty. In general the uncertainty can be differentiated into four distinct types:
decision rule uncertainty, model uncertainty, parameter uncertainty, and parameter variability.

Models are by choice and necessity incomplete. Therefore, modeling  may  be performed at different levels of sophistication and necessary  elements are approximations, estimates and expert judgement, based on the perception of the problem at hand. The challenge is to find a model that represents the physico-chemical phenomena sufficiently well, to determine the numerical data required and to estimate the consequences of the inherent uncertainties in the models.


Thermodynamic data

A crucial part of any equilibrium modeling calculation is the selection of equilibrium constants that quantify the strength of interactions between metals and ligands. Precise thermodynamic data are necessary because they provide the  scientific understanding of the processes taking place. Uncertainty studies have reviealed that uncertainty for thermodynamic values is much greater around the very dilute range (trace element speciation) and the more concentrated range, where data for the thermodynamic constants are comparatively sparse. Minimal uncertainty is predicted in conditions where one species is dominant over all others, but when many species are close in stability, uncertainty increases substantially. However, the uncertainty in the global models often by far outweighs the uncertainty in the thermodynamic input data. Anyhow, as far as possible, uncertainty analysis should be included in moddeling evaluation especially when complex species distribution is important.


Several databases exist that report experimental results for speciation constants. Most aqueous speciation programs come supplied with a standard thermodynamic database. Unfortunately, many of these databases have been shown to contain significant errors.
 
Thermochemical Database Project (TDB) at the Nuclear Engery Agency (NEA) of OECD

EPA - Data Systems and Software at U.S. Environmental Protection Agency

Chemistry WebBook - NIST Standard Reference Database Number 69, last update 2018 
(thermochemical, thermophysical, and ion energetics data compiled by NIST under the Standard Reference Data Program)


GEMS Default Thermodynamic Data Base (PSI/Nagra update 12/07)

IUPAC Stability Constants Database by Academic Software (no longer commercially available)

JESS Database is the world's largest single source of thermodynamic information relating to electrolytes, reactions in aqueous media, and hydrocarbon phase equilibria. The full contents of certain databases are available to inspect online

Thermochimie - a thermodynamic database initially created and developed by Andra (French National Radioactive Waste Management Agency), for more than twenty years (1995). In October 2014, Radioactive Waste Management Limited (NDA, UK) joined the project and the "ThermoChimie consortium" was formed. In March 2018, Ondraf/Niras (National Agency for Radioactive Waste Management, Belgium) also joined the "ThermoChimie consortium".

ThermoML - an XML-based IUPAC standard for storage and exchange of experimental thermophysical and thermochemical property data

Thermodynamic database MALT2 from the Japan Society of Calorimetry and Thermal Analysis


Thermodynamic Data and Property Calculation Sites on the Web
Meta list at UIC Thermodynamics Research Laboratory - University of Illinois at Chicago

THEREDA - the THErmodynamic REference DAtabase project from a German consortium

A recent review compared the quality and consistency of data provided by these databases:

Wolfgang Hummel, Montserrat Filella, Darren Rowland, Where to find equilibrium constants ?, Sci. Total Environ., 692 (2019) 49-59. DOI: 10.1016/j.scitotenv.2019.07.161




Chemical Speciation Modeling Software

Multicomponent thermodynamic equilibrium speciation modeling has been incorporated into publicly available and commercial modelling software.

Programs based on the Law of mass Action

EQ3/6 - licencing procedure from LLNL - US$ 500 for non-US academic institutions.
Information  is available about some useful tools for performing pH-, Eh-, or concentration scans with EQ3/6 and download them. There is also a collection of tips and remarks available

PHREEQC home page at U.S.G.S. informs about code development, GUIs, and couplings to other software. The most recent version is 3.0 and includes an interfcae for MS Windows. There is a form-based user-interface, WEB-PHREEQ for remote calculations (Department of Geosciences, North Dakota State University). There is also a separate graphical interface to PHREEQC, PHREEQCI from U.S.G.S.

MINTEQA2 from the U.S. EPA, current version is 4.03 of May 2006.
New: Visual Minteq from KTH Stockholm, current version is 3.1 of December 2013.
and MINTEQA2 for Windows from Allison Geoscience Consultants, Inc.

CHEPROO - CHEmical PRocesses Object-Oriented is a tool to be coupled with transport codes, it is maintained by UPC in Barcelona

CHEAQS Next by Wilko Verweij (NL) is a computer program for calculating CHemical Equilibria in AQuatic Systems., which is a follow-up of CHEAQS Pro

CHESS allows to simulate the equilibrium state of complex solutions including minerals, colloids, organics and gases. It comes with Java-based GUI (JCHESS) and graphing tool (JPLOT). Maintained in the past by Jan van der Lee, at present not accessible. Cost: 2900 Euro (Console Mode Version of CHESS is available for free for Linux users).

Geochemist's Workbench® from the University of Illinois at Urbana-Champaign. Cost: 700 USD for the essential package and 1300 USD per year for the standard package (including reaction paths).

HSC Chemistry® from Outotec Research Oy / Finland. basic licence starting at 1500 Euro.

JESS by Peter M May (Murdoch University, Australia) and Kevin Murray (Insight Modelling Services, Garsfontein East, South Africa)

MINEQL+ Version 5.0 32-bit Win 7,8,10 -GUI interface to MINEQL-successor from W.Schecher (ERS - Environmental Research Software, Hallowell, ME). Cost: 635 USD.

WATEQ4F provided free of charge by U.S.G.S.



Programs based on the Minimization of Gibbs Free Energy

CHEMSAGE© from GTT Aachen / Germany. Cost: 2495 USD.

FACT Facility for the Analysis of Chemical Thermodynamics, by the Centre for Research in Computational Thermochemistry (CRCT) at the University Montréal, closely cooperating with GTT

GEMS-PSI by D.Kulik at PSI / Switzerland (latest version is 3.5 from May 2019)




Related reviews

Darren Rowland, Peter M. May, Progress in Aqueous Solution Modelling: Better Data and Better Interfaces, J. Solution Chem., 48 (2019) 1066–1078. DOI: 10.1007/s10953-019-00871-5

Tamas Kiss, Eva A. Enyedy, Tamas Jakusch, Orsolya Domotor, Speciation of Metal Complexes of Medicinal Interest: Relationship between Solution Equilibria and Pharmaceutical Properties, Curr. Med. Chem., 26/4 (2019) 580-606. DOI: 10.2174/0929867325666180307113435

Peter M.May, Darren Rowland, JESS, a Joint Expert Speciation System – VI: thermodynamically-consistent standard Gibbs energies of reaction for aqueous solutions, New J. Chem., 42/10 (2018) 7617-7629. DOI:  10.1039/C7NJ03597G

Tamas Kiss, Eva A. Enyedy, Tamas Jakusch, Development of the application of speciation in chemistry, Coord. Chem. Rev., 352 (2017) 401-423. DOI: 10.1016/j.ccr.2016.12.016

Agnieszka Jeske, Use of innovative and advanced computer simulation of chemical speciation of heavy metals in soils amd other environmental samples. Soil Sci. Annu., 65/2 (2014) 65-71. DOI: 10.2478/ssa-2014-0010

Jeane M. Van Briesen, Mitchell Small, Chris Weber, Jessica Wilson, Modelling Chemical Speciation: Thermodynamics, Kinetics and Uncertainty, in : Grady Hanrahan Ed.), Modelling of Pollutants in Complex Environmental Systems, ILM Publications (2010) 133-149.

Peter M.May, Darren Rowland, Thermodynamic Modeling of Aqueous Electrolyte Systems: Current Status, J.Chem. Eng. Data, 62 (2017) 2481−2495. DOI:10.1021/acs.jced.6b01055

D.G. Lumsdon, L.J. Evans, Predicting chemical speciation and computer simulation, in: A.M. Ure, C.M. Davidson (eds.), Chemical speciation in the environment, Blackwell Science, London, 2002, 89-130. DOI: 10.1002/9789470988312.ch5



Related EVISA Resources

Components database: Chemical Speciation Modelling Software
Link database: All about modelling chemical speciation


 Related EVISA Resources: Brief summaries

About Speciation

   Speciation as a discipline in Analytical Chemistry – Definitions   
   Why should elemental speciation be done ?
   Why is elemental speciation analysis not done routinely ?
   Speciation analysis as a tool to enhance the quality of life
   Speciation and Toxicity

Research fields related to elemental speciation

   Chemical speciation analysis for the life sciences
   Chemical speciation analysis for nutrition and food science
   Trace element speciation analysis for environmental sciences
   Speciation analysis for the study of metallodrugs and their biomolecular interactions

Speciation Analysis - Striving for Quality

   Problems to be solved in the field of speciation analysis
   Error sources in speciation analysis - Overview
   Sample preservation for speciation analysis - General recommendations
   Species transformation during speciation analysis
   Certified Reference Materials for Chemical Speciation Analysis
   Standard methods for elemental speciation analysis



Further chapters on techniques and methodology for speciation analysis:

Chapter 1: Tools for elemental speciation
Chapter 2: ICP-MS - A versatile detection system for speciation analysis
Chapter 3: LC-ICP-MS - The most often used hyphenated system for speciation analysis
Chapter 4: GC-ICP-MS- A very sensitive hyphenated system for speciation analysis
Chapter 5: CE-ICP-MS for speciation analysis
Chapter 6: ESI-MS: The tool for the identification of species
Chapter 7: Speciation Analysis - Striving for Quality
Chapter 8: Atomic Fluorescence Spectrometry as a Detection System for Speciation Analysis
Chapter 9: Gas chromatography for the separation of elemental species
Chapter 10: Plasma source detection techniques for gas chromatography
Chapter 11: Fractionation as a first step towards speciation analysis
Chapter 12: Flow-injection inductively coupled plasma mass spectrometry for speciation analysis
Chapter 13: Gel electrophoresis combined with laser ablation inductively coupled plasma mass spectrometry for speciation analysis
Chapter 14: Non-chromatographic separation techniques for speciation analysis



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last time modified: September 20, 2019









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