CO2SYS

Last updated
CO2SYS
Original author(s) Ernie Lewis and Doug Wallace
Initial release1998
Written inQBasic, MATLAB, Python, Microsoft Excel
Available inEnglish
Website https://cdiac.ess-dive.lbl.gov/ftp/co2sys/

https://pyco2sys.readthedocs.io/en/latest/

https://ecology.wa.gov/Research-Data/Data-resources/Models-spreadsheets/Modeling-the-environment/Models-tools-for-TMDLs

CO2SYS is a family of software programs that calculate chemical equilibria for aquatic inorganic carbon species and parameters. Their core function is to use any two of the four central inorganic carbon system parameters (pH, alkalinity, dissolved inorganic carbon, and partial pressure of carbon dioxide) to calculate various chemical properties of the system. These programs are widely used by oceanographers and limnologists to understand and predict chemical equilibria in natural waters. [1]

Contents

History

Chemical equilibria in marine and freshwater systems were calculated according to various conventions for most of the 20th century, which led to discrepancies among laboratories' calculations and limited scientific reproducibility. [2] CO2SYS was first published by Ernie Lewis and Doug Wallace in 1998 as a DOS-interface program written in QBasic. [1] Subsequent developments have included several MATLAB implementations, [1] [3] two Microsoft Excel templates, [1] [4] [5] a Python package "PyCO2SYS", [6] and an R package inspired by CO2SYS, "seacarb". [1] [7] Development of the various CO2SYS programs continues as of 2021 with the addition of more chemical equilibrium parameters and compatibility with a wider range of environments, e.g. anoxic waters. [8]

Chemical Overview

The aquatic inorganic carbon system is composed of the various ionic, dissolved, solid, and/or gaseous forms of carbon dioxide in water. These species include dissolved carbon dioxide, carbonic acid, bicarbonate anion, carbonate anion, calcium carbonate, magnesium carbonate, and others. The relative amounts of each species in a body of water depends on physical variables including temperature and salinity, as well as chemical variables like pH and gas partial pressure. Variables like alkalinity and dissolved (or total) inorganic carbon further define a mass and charge balance that constrains the total state of the system. [9] [10]

Given any two of the four central inorganic carbon system parameters (pH, alkalinity, dissolved inorganic carbon, partial pressure of carbon dioxide) the remainder may be derived by solving a system of equations that adhere to the principles of chemical thermodynamics. [10]

Related Research Articles

<span class="mw-page-title-main">Bicarbonate</span> Polyatomic anion

In inorganic chemistry, bicarbonate is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula HCO
3
.

<span class="mw-page-title-main">Calcium carbonate</span> Chemical compound

Calcium carbonate is a chemical compound with the chemical formula CaCO3. It is a common substance found in rocks as the minerals calcite and aragonite, most notably in chalk and limestone, eggshells, gastropod shells, shellfish skeletons and pearls. Materials containing much calcium carbonate or resembling it are described as calcareous. Calcium carbonate is the active ingredient in agricultural lime and is produced when calcium ions in hard water react with carbonate ions to form limescale. It has medical use as a calcium supplement or as an antacid, but excessive consumption can be hazardous and cause hypercalcemia and digestive issues.

Carbonic acid is a chemical compound with the chemical formula H2CO3. The molecule rapidly converts to water and carbon dioxide in the presence of water. However, in the absence of water, it is quite stable at room temperature. The interconversion of carbon dioxide and carbonic acid is related to the breathing cycle of animals and the acidification of natural waters.

<span class="mw-page-title-main">Sodium carbonate</span> Chemical compound

Sodium carbonate is the inorganic compound with the formula Na2CO3 and its various hydrates. All forms are white, odourless, water-soluble salts that yield alkaline solutions in water. Historically, it was extracted from the ashes of plants grown in sodium-rich soils, and because the ashes of these sodium-rich plants were noticeably different from ashes of wood, sodium carbonate became known as "soda ash". It is produced in large quantities from sodium chloride and limestone by the Solvay process, as well as by carbonating sodium hydroxide which is made using the Chlor-alkali process.

A hydrogen ion is created when a hydrogen atom loses an electron. A positively charged hydrogen ion (or proton) can readily combine with other particles and therefore is only seen isolated when it is in a gaseous state or a nearly particle-free space. Due to its extremely high charge density of approximately 2×1010 times that of a sodium ion, the bare hydrogen ion cannot exist freely in solution as it readily hydrates, i.e., bonds quickly. The hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions.

<span class="mw-page-title-main">Alkalinity</span> Capacity of water to resist changes in pH that would make the water more acidic

Alkalinity (from Arabic: القلوية, romanized: al-qaly, lit. 'ashes of the saltwort') is the capacity of water to resist acidification. It should not be confused with basicity, which is an absolute measurement on the pH scale. Alkalinity is the strength of a buffer solution composed of weak acids and their conjugate bases. It is measured by titrating the solution with an acid such as HCl until its pH changes abruptly, or it reaches a known endpoint where that happens. Alkalinity is expressed in units of concentration, such as meq/L (milliequivalents per liter), μeq/kg (microequivalents per kilogram), or mg/L CaCO3 (milligrams per liter of calcium carbonate). Each of these measurements corresponds to an amount of acid added as a titrant.

<span class="mw-page-title-main">Solubility pump</span> Physico-chemical process which transports carbon

In oceanic biogeochemistry, the solubility pump is a physico-chemical process that transports carbon as dissolved inorganic carbon (DIC) from the ocean's surface to its interior.

<span class="mw-page-title-main">Dissolved inorganic carbon</span> Sum of inorganic carbon species in a solution

Dissolved inorganic carbon (DIC) is the sum of the aqueous species of inorganic carbon in a solution. Carbon compounds can be distinguished as either organic or inorganic, and as dissolved or particulate, depending on their composition. Organic carbon forms the backbone of key component of organic compounds such as – proteins, lipids, carbohydrates, and nucleic acids.

<span class="mw-page-title-main">Total organic carbon</span> Concentration of organic carbon in a sample

Total organic carbon (TOC) is an analytical parameter representing the concentration of organic carbon in a sample. TOC determinations are made in a variety of application areas. For example, TOC may be used as a non-specific indicator of water quality, or TOC of source rock may be used as one factor in evaluating a petroleum play. For marine surface sediments average TOC content is 0.5% in the deep ocean, and 2% along the eastern margins.

The Global Ocean Data Analysis Project (GLODAP) is a synthesis project bringing together oceanographic data, featuring two major releases as of 2018. The central goal of GLODAP is to generate a global climatology of the World Ocean's carbon cycle for use in studies of both its natural and anthropogenically forced states. GLODAP is funded by the National Oceanic and Atmospheric Administration, the U.S. Department of Energy, and the National Science Foundation.

<span class="mw-page-title-main">Acid neutralizing capacity</span> Measure for the overall buffering capacity against acidification of a solution

Acid-neutralizing capacity or ANC in short is a measure for the overall buffering capacity against acidification of a solution, e.g. surface water or soil water.

pCO<sub>2</sub> Partial pressure of carbon dioxide, often used in reference to blood

pCO2, pCO2, or is the partial pressure of carbon dioxide (CO2), often used in reference to blood but also used in meteorology, climate science, oceanography, and limnology to describe the fractional pressure of CO2 as a function of its concentration in gas or dissolved phases. The units of pCO2 are mmHg, atm, torr, Pa, or any other standard unit of atmospheric pressure. The pCO2 of Earth's atmosphere has risen from approximately 280 ppm (parts-per-million) to a mean 2019 value of 409.8 ppm as a result of anthropogenic release of carbon dioxide from fossil fuel burning. This is the highest atmospheric concentration to have existed on Earth for at least the last 800,000 years.

Marine chemistry, also known as ocean chemistry or chemical oceanography, is influenced by plate tectonics and seafloor spreading, turbidity currents, sediments, pH levels, atmospheric constituents, metamorphic activity, and ecology. The field of chemical oceanography studies the chemistry of marine environments including the influences of different variables. Marine life has adapted to the chemistries unique to Earth's oceans, and marine ecosystems are sensitive to changes in ocean chemistry.

<span class="mw-page-title-main">Bjerrum plot</span> Graph of polyprotic acid concentration compared to pH

A Bjerrum plot (named after Niels Bjerrum), sometimes also known as a Sillén diagram (after Lars Gunnar Sillén), or a Hägg diagram (after Gunnar Hägg) is a graph of the concentrations of the different species of a polyprotic acid in a solution, as a function of pH, when the solution is at equilibrium. Due to the many orders of magnitude spanned by the concentrations, they are commonly plotted on a logarithmic scale. Sometimes the ratios of the concentrations are plotted rather than the actual concentrations. Occasionally H+ and OH are also plotted.

The Revelle factor (buffer factor) is the ratio of instantaneous change in carbon dioxide (CO2) to the change in total dissolved inorganic carbon (DIC), and is a measure of the resistance to atmospheric CO2 being absorbed by the ocean surface layer. The buffer factor is used to examine the distribution of CO2 between the atmosphere and the ocean, and measures the amount of CO2 that can be dissolved in the mixed surface layer. It is named after the oceanographer Roger Revelle. The Revelle factor describes the ocean's ability to uptake atmospheric CO2, and is typically referenced in global carbon budget analysis and anthropogenic climate change studies.

<span class="mw-page-title-main">Oceanic carbon cycle</span> Ocean/atmosphere carbon exchange process

The oceanic carbon cycle is composed of processes that exchange carbon between various pools within the ocean as well as between the atmosphere, Earth interior, and the seafloor. The carbon cycle is a result of many interacting forces across multiple time and space scales that circulates carbon around the planet, ensuring that carbon is available globally. The Oceanic carbon cycle is a central process to the global carbon cycle and contains both inorganic carbon and organic carbon. Part of the marine carbon cycle transforms carbon between non-living and living matter.

Aqion is a hydrochemistry software tool. It bridges the gap between scientific software and the calculation/handling of "simple" water-related tasks in daily routine practice. The software aqion is free for private users, education and companies.

<span class="mw-page-title-main">Freshwater acidification</span>

Freshwater acidification occurs when acidic inputs enter a body of fresh water through the weathering of rocks, invasion of acidifying gas, or by the reduction of acid anions, like sulfate and nitrate within a lake. Freshwater acidification is primarily caused by sulfur oxides (SOx) and nitrogen oxides (NOx) entering the water from atmospheric depositions and soil leaching. Carbonic acid and dissolved carbon dioxide can also enter freshwaters, in a similar manner associated with runoff, through carbon dioxide-rich soils. Runoff that contains these compounds may incorporate acidifying hydrogen ions and inorganic aluminum, which can be toxic to marine organisms. Acid rain is also a contributor to freshwater acidification. It is created when SOx and NOx react with water, oxygen, and other oxidants within the clouds.

<span class="mw-page-title-main">Total inorganic carbon</span> Sum of the inorganic carbon species

Total inorganic carbon is the sum of the inorganic carbon species.

<span class="mw-page-title-main">Particulate inorganic carbon</span>

Particulate inorganic carbon (PIC) can be contrasted with dissolved inorganic carbon (DIC), the other form of inorganic carbon found in the ocean. These distinctions are important in chemical oceanography. Particulate inorganic carbon is sometimes called suspended inorganic carbon. In operational terms, it is defined as the inorganic carbon in particulate form that is too large to pass through the filter used to separate dissolved inorganic carbon.

References

  1. 1 2 3 4 5 Orr, J. C.; Epitalon, J.-M.; Gattuso, J.-P. (2015-03-09). "Comparison of ten packages that compute ocean carbonate chemistry" (PDF). Biogeosciences. 12 (5): 1483–1510. Bibcode:2015BGeo...12.1483O. doi: 10.5194/bg-12-1483-2015 . ISSN   1726-4189.
  2. Lewis and Wallace (1998). "Program Developed for CO2 System Calculations". ORNL/CDIAC-105. Archived from the original on 2021-01-11.
  3. Van Heuven, S.; Pierrot, D.; Rae, J.W.B.; Lewis, E.; Wallace, D.W.R. (2011), MATLAB Program Developed for CO2 System Calculations. ORNL/CDIAC-105b., Oak Ridge National Laboratory Environmental Sciences Division, Carbon Dioxide Information Analysis Center (CDIAC), doi:10.3334/cdiac/otg.co2sys_matlab_v1.1 , retrieved 2021-01-09
  4. Pierrot, D., Lewis, E., and Wallace, D. W. R.: MS Excel Program Developed for CO2 System Calculations, Tech. rep., Carbon Dioxide Inf. Anal. Cent., Oak Ridge Natl. Lab., US DOE, Oak Ridge, Tenn., 2006.
  5. Pelletier, G., Lewis, E., and Wallace, D.: CO2SY S.XLS: A calcu- lator for the CO2 system in seawater for Microsoft Excel/VBA, Wash. State Dept. of Ecology/Brookhaven Nat. Lab., Olympia, WA/Upton, NY, USA, 2007.
  6. Humphreys, Matthew P.; Sandborn, Daniel; Gregor, Luke; Pierrot, Denis; van Heuven, Steven M. A. C.; Lewis, Ernie R.; Wallace, Douglas W. R. (2021-05-13), "PyCO2SYS: marine carbonate system calculations in Python", Zenodo, Bibcode:2021zndo...4757055H, doi:10.5281/zenodo.4757055 , retrieved 2021-06-14
  7. Gattuso, J.-P., Epitalon, J.-M. and Lavigne, H. : seacarb: seawa- ter carbonate chemistry with R. R package version 3.0.6, The Comprehensive R Archive Network, http://CRAN.R-project.org/ package=seacarb, 2015.
  8. Xu, Yuan-Yuan; Pierrot, Denis; Cai, Wei-Jun (2017). "Ocean carbonate system computation for anoxic waters using an updated CO2SYS program". Marine Chemistry. 195: 90–93. Bibcode:2017MarCh.195...90X. doi: 10.1016/j.marchem.2017.07.002 .
  9. Zeebe, Richard E. (15 October 2001). CO2 in seawater: equilibrium, kinetics, isotopes. Wolf-Gladrow, Dieter A. Amsterdam. ISBN   978-0-08-052922-6. OCLC   246683387.{{cite book}}: CS1 maint: location missing publisher (link)
  10. 1 2 Stumm, Werner. (2012). Aquatic Chemistry : Chemical Equilibria and Rates in Natural Waters. Morgan, James J. (3rd ed.). Hoboken: Wiley. ISBN   978-1-118-59148-2. OCLC   830169758.