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Composition & Solution Chemistry

Note

The chemistry model on this page covers what a biology lab needs: dissolution into ions, molar concentration, and pH. It is not a complete physical chemistry treatment. pH here is a direct estimate from net H⁺/OH⁻ concentration. It is correct for strong electrolytes but not for weak acids, weak bases, or buffers. Acid/Base Chemistry describes activity coefficients, ionic strength, and equilibrium effects. pH(::Stock) uses that model when a stock contains a reagent with registered weak acid or base chemistry, and the formula below otherwise.

A Stock is measured in Reagents, the physical things that are weighed out. A Composition expresses the same stock as molar quantities of Species values, accounting for what each reagent dissolves into. composition(s::Stock) derives it, and the derivation is one-directional. The examples use the saline from Stocks:

julia> saline = 1u"mL" * rgt"water" + 5u"g" * rgt"sodium_chloride";

julia> r = composition(saline);

julia> sort(string.(keys(r.amounts)))
3-element Vector{String}:
 "Cl⁻"
 "Na⁺"
 "water"

composition sums the contribution of every reagent, dissociating or not. water does not dissociate, so it contributes its own identity, the default dissolution.

Reading a Composition

mass and molar_amount read a Composition's quantity of a given Species:

julia> mass(r, spc"Na+")
1.9669627005070887 g

julia> molar_amount(r, spc"Na+")
0.08555817487991287 mol

Atoms

atoms gives the amount of each element in a stock, from the elemental formulas of the species in its composition. The reagents here are defined with a formula and with a dissolution (see Reagents & Species):

julia> @reagent formulawater "water with a formula" Liquid "H2O" 1.0u"g/mL" missing
water with a formula

julia> @reagent formulasalt "salt with a formula" Solid (spc"Na+" + spc"Cl-") 2.16u"g/mL" missing
salt with a formula

julia> s = 18.015u"mL" * formulawater + 0.1u"mol" * formulasalt;

julia> atoms(s, :H)
2.0 mol

julia> atoms(s, :Cl)
0.1 mol

julia> atoms(s, :Fe)
0 mol

Multiplying an amount by Unitful.Na gives a number of atoms. Only reagents contribute, and a reagent contributes only if it has a registered formula. When a stock holds a reagent whose formula is not registered, or whose amount cannot be computed, atoms returns what it can count and warns that the result is a lower bound. A reagent declared opaque contributes nothing and does not warn.

total_concentration

The molar concentration of a Species across the whole stock:

julia> total_concentration(saline, spc"Na+")
0.08555817487991287 mol mL⁻¹

pH and net_hydrogen_ion_concentration

pH is derived from net_hydrogen_ion_concentration, which nets the canonical H⁺ and OH⁻ Species values (see Reagents & Species) against each other. saline is a neutral salt, so the result is neutral:

julia> pH(saline)
7.0

CHESS registers hydrochloric acid with the dissolution H⁺ + Cl⁻:

julia> acid = 0.1u"g" * rgt"HCl" + 100u"mL" * rgt"water";

julia> net_hydrogen_ion_concentration(acid)
2.7428822206374456e-5 mol mL⁻¹

julia> pH(acid)
1.5617928406001496

Because pH subtracts OH⁻ from H⁺, a base is registered with its dissolution (for example Na⁺ + OH⁻ for NaOH) and not a negative H⁺ count. Dissolution coefficients must be non-negative, and mixing an acid and a base nets out through the subtraction.