(E)Gasboard

A microcosm or closed incubation is a sealed bottle with known liquid and gas headspace volumes. Because gases partition between both phases, the headspace gas percentage alone does not give the total amount in the bottle.

Here, GC peak areas or measured gas percentages are converted to gas amounts using calibration, pressure, temperature, bottle volumes and gas solubility. pH can be included for CO₂ and H₂S speciation. NaCl-equivalent concentration is optional.

What this tool does

From GC peak area to bottle amount

Example: convert a CO peak area into headspace %, then calculate the amount present in the headspace, liquid and complete bottle.

From a target concentration to a gas dose

Example: calculate how much O₂ to add to reach 150 µM dissolved O₂ at the entered bottle conditions.

Excel batch analysis

One row per bottle and time point; gas columns contain GC peak areas. Supported gas headers are recognized automatically, and blank gas cells are ignored.

Example measurement input

experiment_id	sample_id	time_h	pressure_bar_abs	temperature_C	bottle_volume_mL	liquid_volume_mL	salinity_g_L_NaCl	pH	CO	CO2	CH4	O2	H2S	N2O	NO	N2	C2H6
WK3_example	1_CO	3.6333	1.58325	23	120	39.56	0	7.27	829.056	274.38	2.40
WK3_example	1_CO	16.1667	1.54525	23	120	39.06	0	7.27	408.20	455.30	7.50

Recognized gas columns: CO, CO2, CH4, O2, H2S, N2O, NO, N2 and C2H6.

Example calibration input

gas_id	calibration_id	gas_percent	peak_area
CO	CO_0.935_rep1	0.93541	100.6
CO	CO_4.516_rep1	4.51637	530.0

Measurement template Calibration template Example measurements Example calibration

Measurements

Calibration

Excel output Include plots in Excel output

Single calculation

Gas Gas in headspace (%) Absolute pressure (bar) Temperature (°C) Bottle volume (mL) Liquid volume (mL) NaCl-equivalent (g/L) pH, optional

Gas dosing

Calculate the amount of gas required to reach a target dissolved concentration after gas-liquid equilibration. NaCl-equivalent concentration is optional.

Gas Target dissolved concentration (µM) Target refers to Bottle volume (mL) Liquid volume (mL) Temperature (°C) NaCl-equivalent (g/L) Initial gas in headspace (%) Initial pressure (bar abs) Dosing gas (%) Dosing pressure (bar abs) pH, optional

Calculations

This page describes how a GC response or measured headspace gas percentage is converted into a gas amount for the complete bottle. The same equations are used for single calculations, batch analysis and gas dosing.

Res ipsa loquitur.

GC peak area→gas %→ partial pressure→headspace amount →dissolved amount→total bottle amount

Parameters and units

Parameter	Symbol	Meaning
GC peak area	A	Instrument response measured for a standard or sample
Gas concentration	x	Percentage of the headspace made up by the selected gas
Gas fraction	y_i	Gas concentration expressed as a fraction from 0 to 1
Absolute pressure	P_abs	Total pressure in the bottle
Partial pressure	p_i	Pressure contributed by the selected gas
Bottle volume	V_bottle	Total internal bottle volume
Liquid volume	V_liquid	Volume occupied by liquid
Headspace volume	V_headspace	Gas-filled bottle volume
Temperature	T	Bottle temperature when pressure and gas composition apply
Compressibility factor	Z	Fixed at 1 in v0.1
Gas constant	R	8.314462618 J mol^-1 K^-1
Henry solubility	H_s^cp	Dissolved concentration per gas partial pressure
Gas amount	n	Amount of gas; results are reported in mmol

Internal calculation units are Pa, m³, K and mol.

1. GC peak area to gas concentration

For a multipoint calibration, every calibration observation is retained, including replicates. A straight line is fitted:

A = m x + b

The sample gas concentration is then:

x_{sample} = \frac{A_{sample} - b}{m}

The calibration summary reports slope, intercept, R², number of observations and calibration range. Samples outside that range are still calculated but are flagged as extrapolations.

For a multipoint calibration, the normal model includes an intercept. If that unconstrained fit would give a negative intercept - and therefore a physically impossible negative predicted peak area at 0% gas - the intercept is constrained to 0 and the slope is refitted by least squares through the origin.

With only one non-zero standard, a proportional calibration through zero is used because slope and intercept cannot both be estimated.

2. Gas concentration to partial pressure

y_{i} = \frac{x_{i}}{100}

P_{abs} [Pa] = P_{abs} [bar] \times 10^{5}

p_{i} = y_{i} P_{abs}

Pressure is absolute pressure. Water vapour is neglected in v0.1, so the entered pressure is treated as the pressure of the modelled dry gas mixture. Because partial pressure changes with gas fraction and bottle pressure, it is reported per gas and time point in Results rather than as a static metadata value.

3. Headspace amount

V_{headspace} = V_{bottle} - V_{liquid}

T [K] = T [°C] + 273.15

n_{headspace} = \frac{p_{i} V_{headspace}}{Z R T}

v0.1 uses Z = 1 and is intended for normal incubation pressures.

4. Temperature-dependent Henry solubility

The Henry convention used here is:

H_{s}^{cp} = \frac{c}{p}

with units mol m^-3 Pa^-1.

Reference values are stored at 298.15 K and corrected to the bottle temperature using Sander (2023):

H_{s}^{cp} (T) = H_{s}^{cp,*} \exp [B (\frac{1}{T} - \frac{1}{298.15})]

Stored temperature-range metadata are used for warnings where a supporting range is available. For entries without such a range, the two-parameter correction should be regarded as a local temperature approximation.

Gas solubility constants used

Gas	H_s^cp,* at 298.15 K	B (K)	Stored temperature range
CO	9.70 × 10^-6	1300	278-323 K
CO₂	3.40 × 10^-4	2300	-
CH₄	1.40 × 10^-5	1600	275-328 K
NO	1.90 × 10^-5	1600	-
N₂O	2.40 × 10^-4	2600	-
H₂S	1.00 × 10^-3	2100	-
C₂H₆	1.90 × 10^-5	2400	275-328 K
N₂	6.40 × 10^-6	1300	278.15-323.15 K
O₂	1.30 × 10^-5	1500	274-328 K

All Henry solubility values, temperature coefficients and stored ranges are selected from Sander (2023).

5. Optional salting-out correction

NaCl-equivalent concentration is optional. If it is blank or 0, the pure-water Henry solubility is used. When a value is supplied, the Weisenberger-Schumpe salting-out correction is applied where a gas-specific parameter is available:

\log_{10} (\frac{c_{water}}{c_{salt}}) = K_{s} c_{NaCl}

This is an NaCl-equivalent approximation, not a full mixed-electrolyte model. CO has no parameter in this model, so CO is left uncorrected and flagged.

6. Dissolved amount

c_{dissolved} = H_{s}^{cp} (T) p_{i}

n_{dissolved} = c_{dissolved} V_{liquid}

This is the molecular dissolved gas amount. For CO₂ and H₂S, pH-dependent pools are calculated separately.

7. Optional pH-dependent speciation

CO₂ / carbonate

CO₂* ⇌ H⁺ + HCO₃⁻

HCO₃⁻ ⇌ H⁺ + CO₃²⁻

At 25 °C, the implemented values are:

pK_a1 = 6.352
pK_a2 = 10.329

Both are recalculated for the sample temperature.

H₂S / sulfide

H₂S ⇌ H⁺ + HS⁻

HS⁻ ⇌ H⁺ + S²⁻

At 25 °C, the implemented values are:

pK_a1 ≈ 6.980
pK_a2 = 14.00

H₂S, HS⁻ and S²⁻ are included. Around neutral pH the S²⁻ fraction is normally extremely small.

8. Total bottle amount

n_{total} = n_{headspace} + n_{molecular,dissolved}

This definition is the same for every gas. Estimated DIC and estimated dissolved total sulfide are separate outputs.

CO₂: physical CO₂ and estimated DIC

CO₂ has two useful outputs and they are deliberately kept separate.

Physical CO₂

n_{CO₂,physical} = n_{CO₂,headspace} + n_{CO₂*,dissolved}

This is the same physical total reported as total bottle amount.

Estimated dissolved inorganic carbon

DIC = CO₂* + HCO₃⁻ + CO₃²⁻

Estimated DIC is only added when pH is available. It does not replace the physical CO₂ result.

Detailed carbonate species remain in Extended_data.

Gas dosing

The target dissolved concentration is converted back to the required gas partial pressure. For CO₂ and H₂S, the target can mean molecular dissolved gas or the estimated total dissolved pool. pH is required for DIC or dissolved total sulfide targets.

If the target is already reached, gas to add is reported as 0.

Current assumptions and scope

Each measurement is treated as the measured state of the bottle at that time point.
Dissolved amounts are equilibrium estimates from Henry's law.
Absolute pressure is used.
Water vapour is neglected in v0.1. A correction is planned for a later version.
v0.1 uses Z = 1.
Salting out is optional and uses NaCl-equivalent concentration.
Full mixed-electrolyte corrections are not included.
Volatile fatty acids are not included.
Formal uncertainty propagation is not included.

References

Henry solubility and temperature dependence
Sander, R. (2023). Compilation of Henry's law constants (version 5.0.0) for water as solvent. Atmospheric Chemistry and Physics, 23, 10901-12440. doi:10.5194/acp-23-10901-2023

Optional salting-out correction
Weisenberger, S. & Schumpe, A. (1996). Estimation of gas solubilities in salt solutions at temperatures from 273 K to 363 K. AIChE Journal, 42, 298-300. doi:10.1002/aic.690420130

Carbonate and sulfide speciation are documented here by the equations and pKa values implemented in the calculation.

Metrics & citation

(E)Gasboard is an open tool for gas calculations in closed incubations.

It runs in the browser and includes GC calibration, gas-liquid partitioning, Henry-law calculations, optional salting-out correction, CO₂/H₂S speciation, batch analysis, plots and Excel output.

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Software output

Open research software with documented calculations and a public web interface.

Citation

(E)Gasboard, Reinier A. Egas, 2026, v0.1. DOI pending.

Requests, suggestions or ideas for improvements are very welcome - please reach out.

(E)Gasboard

What this tool does

Excel batch analysis

Example measurement input

Example calibration input

Results

Calibration curve

Gas amount

Calculated data

Single calculation

Gas dosing

Calculations

Parameters and units

1. GC peak area to gas concentration

2. Gas concentration to partial pressure

3. Headspace amount

4. Temperature-dependent Henry solubility

Gas solubility constants used

5. Optional salting-out correction

6. Dissolved amount

7. Optional pH-dependent speciation

CO₂ / carbonate

H₂S / sulfide

8. Total bottle amount

CO₂: physical CO₂ and estimated DIC

Physical CO₂

Estimated dissolved inorganic carbon

Gas dosing

Current assumptions and scope

References

Metrics & citation

Software output

Citation