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Isotopologues are molecules that differ only in their isotopic composition. Simply, the isotopologue of a chemical species has at least one atom with a different number of neutrons than the parent.

An example is water, where some of its hydrogen-related isotopologues are: "light water" (HOH or H2O), "semi-heavy water" with the deuterium isotope in equal proportion to protium (HDO or 1H2HO), "heavy water" with two deuterium isotopes of hydrogen per molecule (D2O or 2H2O), and "super-heavy water" or tritiated water (T2O or 3H2O), where the hydrogen atoms are replaced with tritium isotopes. Oxygen-related isotopologues of water include the commonly available form of heavy-oxygen water (H218O) and the more difficult to separate version with the 17O isotope. Both elements may be replaced by isotopes, for example in the doubly labeled water isotopologue D218O.

Isotopologues differ from isotopomers in that the atom(s) of different isotope may be placed anywhere in a molecule, while isotopomers specify where the atom of different isotope is located within a molecule. Logically, it follows that two isotopomers of a compound may be the same isotopologue, but two isotopologues must necessarily be two isotopomers. In the example of mono-deuterated ethanol, CH3-CH2-O-D and CH2D-CH2-O-H are two distinct isotopomers of the same isotopologue with molecular formula C2H5DO. Isotopomerism is analogous to constitutional isomerism (relative positions of atoms in a molecule). Some molecules like water and carbon dioxide only have one isotopomer per isotopologue, as the positions of the non-central atoms are indistinguishable.

Isotopologues may be singly, doubly, or multiply substituted.

Singly-Substituted Isotopologues
Singly-substituted sotopologues may be used for nuclear magnetic resonance experiments, where deuterated solvents such as deuterated chloroform (CDCl3) do not interfere with the solutes' 1H signals, and in investigations of the kinetic isotope effect.

Doubly-Substituted Isotopologues
Measurement of the abundance of doubly substituted isotopologues of gases such as CO2, methane , nitrogen and oxygen have been used in the field of stable isotope geochemistryto trace equilibrium and kinetic processes in the environment.

Currently measured doubly-substituted isotopologues include:


 * 13C18O16O (see also clumped isotopes) [1]
 * 13CH3D [2]
 * 12CH2D2 [2]
 * 18O18O and 17O18O[4]
 * 15N15N ,[3]
 * 14N15N18O and 15N14N18O

Analytical Requirements
Because of the relative rarity of the heavy isotopes of C, H, and O, IRMS of doubly-substituted species requires larger volumes of sample gas and longer analysis times than traditional stable isotope measurements, thereby requiring extremely stable instrumentation. In addition, the doubly-substituted isotopologues are often subject to isobaric interferences, as in the methane system where 13CH5+ and 12CH3D+ ions interfere with measurement of the 12CH2D2+ and 13CH3D+ species at mass 18. A measurement of such species requires either very high mass resolving power to separate one isobar from another [3], or modeling of the contributions of the interfering species to the abundance of the species of interest. Tunable Infrared Laser Direct Absorption Spectroscopy has also emerged as a method to measure doubly substituted species free from isobaric interferences, and has been applied to the methane isotopologue 13CH3D [5].

Equilibrium Fractionation
When a light isotope is replaced with a heavy isotope (e.g., 13C for 12C), the bond between the two atoms will vibrate more slowly, thereby lowering the zero-point energy of the bond and acting to stabilize the molecule. An isotopologue with a doubly-substituted bond is therefore slightly more thermodynamically stable, which will tend to produce a higher abundance of the doubly-substituted (or “clumped”) species than predicted by the statistical abundance of each heavy isotope (known as a stochastic distribution of isotopes). This effect increases in magnitude with decreasing temperature, so the abundance of the clumped species is related to the temperature at which the gas was formed or equilibrated. By measuring the abundance of the clumped species in standard gases formed in equilibrium at known temperatures, the thermometer can be calibrated and applied to samples with unknown abundances [1] [2].

Kinetic Fractionation
The abundances of multiply substituted isotopologues can also be affected by kinetic processes. As for singly substituted isotopologues, departures from thermodynamic equilibrium in a doubly-substituted species can implicate the presence of a particular reaction taking place. Photochemistry occurring in the atmosphere has been shown to alter the abundance of 18O2[4] from equilibrium, as has photosynthesis. Measurements of 13CH3D and 12CH2D2 can identify microbial processing of methane, and have been used to demonstrate the significance of quantum tunneling in the formation of methane, as well as mixing and equilibration of multiple methane reservoirs [2]. Variations in the relative abundances of the two N2O isotopologues 14N15N18O and 15N14N18O can distinguish whether N2O has been produced by bacterial denitrification or by bacterial nitrification [7].