Lab of Molecular Electrochemistry

J. Heyrovský Institute of Physical Chemistry of the CAS, v.v.i.
Department of Molecular Electrochemistry and Catalysis

PHREEQC is one of the most favourite geochemical modelling software which is, however, generally still not known among chemists. PhreePlot is a charting & plotting extension of PHREEQC for creating commonly needed types of diagrams.

JH-CEBOCALE

The program package contains several database files, which differ in number of included species and related parameters. The newly presented database JH-CEBOCALE.dat is a composition of existing files llnl.dat, sit.dat, minteq.v4.dat, thermoddem.dat and PSINA.dat plus many other equilibrium data added either directly from literature (i.e. they are experimental-based), or as results of qualified predictions (mainly empirical). The main distinctions from the already existing databases are:

• constrained equilibrium concept based definitions of many species, especially organic and bioorganic building blocks. Their formulation was made with respect to the molecular structure and expected reactivity sites identification (valid for aqueous solutions). The concept was used for redox couples with no reliable thermodynamic connections to the parent element as well, e.g. [Ru(CN)₆]³⁻/[Ru(CN)₆]⁴⁻.

• use of any available data (experimental, calculated or predicted on basis of qualified estimations) for better description of complex systems where huge number of species are employed. The data integrity was in this case preffered to critical selection in terms of unified experimental, evaluation and statistical methology. Therefore, the ambition of collecting as many elements, their valence states and individual species equilibrium data as possible was at least at zeroth level fulfilled.

The mentioned unique features of JH-CEBOCALE.dat are, however, connected with few risks, namely:

• problem with (re)definition of some species. It arises from the non-uniform denotation of the identical species in the literature. Typical examples of this category are couples as HNbO₃/Nb(OH)₅, AlO₂⁻/[Al(OH)₄]⁻ etc.

• difficulties related to standard state definition. They can result in either incorrect values of equilibrium constants or even in mismatch among particular species involved in the equilibrium. Such troubles sometimes occur in case of e.g. Rh(III), Ru(III), Pd(II), Ir(III), Os(III), Pt(II), Pt(IV), Au(III) complexes because the typical aquo ions (on whose basis the complex formation equilibria with other ligands are likely to be formulated) either do not exist at all or they are ill-defined.

• lack of internal data consistency from the point of view of additional properties. Each source database contains for each entry an unique set of tabulated data that enables advanced calculations, e.g. speciation temperature dependence, density of the solution etc.

• due to inconsistency of temperature dependence data it is highly recommended not to perform calculations on systems far away from 25 °C.

The experimental (at the moment very incomplete) kinetic version JH-CEBOCALE-k.dat enables modelling of systems where the rate laws and appropriate rate constants are known from the literature, with respect to PHREEQC limitation to aqueous solutions mainly of inorganic species. The RATES definition block is included in the database, the KINETICS block is available in the file JH-CEBOCALE-k_1.1_kinetics.phr. It can be used either whole as it is (e.g. Test.phr) or - better (not all of the reactions are tabulated for the same temperature) - by copying the desired reaction number with the input parameters to the user defined input file. Because the database contains intentionally disconnections between individual oxidation states of each element, it is also possible to use it only for equilibrium calculations in cases where redox processes are known not to proceed.

To get inspiration, for what PHREEQC calculations could be useful not in geology, geochemistry or hydrogeology but in chemistry, following tutorial with some application examples was prepared.

Tutorial examples

Example	Input file	Output file	Graph file	Extratext file
Titration curve
Reaction stoichiometry
Systematic error
Original model
New model
Distribution diagrams and diagrams of prevealing existence Distribution diagram Diagram of the prevealing existence (solid phase included) Diagram of the prevealing existence (solid phase not included)
Pourbaix diagrams Pourbaix-like diagram (solid phase included) Pourbaix-like diagram (solid phase not included)
(Non)redox systems (constricted equilibrium) Method 1 Method 2 Method 3
Reaction kinetics
Exchange equilibria

Running PHREEQC on mobile devices

Nowadays, the trend of penetrating scientific calculations to mobile devices is still more apparent. Contrary to e.g. quantum chemical calculations, the hardware requirements of PHREEQC modelling are not huge. However, except from Intel based tablets with Windows, vast majority of today used mobile phones and tablets is running on wide spread ARM processor architectures which do not support native x86 applications. We offer several alternative ways to run PHREEQC on ARM devices including the native binaries (fastest, most recommended).

Native PHREEQC installers / binaries for Android

IMPORTANT: Although we provide here our specific PHREEQC packages, they are strongly based on the Notepad++ distribution except the main executable, our database, example files and few remarks. Please note that the effort of our team is to bring PHREEQC also to platforms other than x86 and x64, however, we are not authors of PHREEQC and did no scientific work concerning the code itself. For this, we gratefully acknowledge D.L. Parkhurst and C.A.J. Appelo.