User:Graysonchadwick/sandbox

Stable vs radioactive isotopes
All isotopes of a chemical element contain the same number of protons with with varying numbers of neutrons. The element hydrogen has three naturally occurring isotopes, $1$H, $2$H and $3$H, which are sometimes referred to as protium (H), deuterium (D) and tritium (T), respectively. Both $1$H and $2$H are stable indefinitely, while $3$H is unstable and undergoes beta decay to form $3$He. While there are some important applications of $3$H in geochemistry (such as its use as an ocean circulation tracer) these will not be discussed further here.

Isotope notation
The study of stable isotope biogeochemistry involves the description of the relative abundances of various isotopes in a certain chemical pool, as well as the way in which physicochemical processes change the fraction of those isotopes in one pool vs. another. Various type of notation have been developed to describe the abundance and change in the abundance of isotopes in these processes, and these are summarized below. In most cases only the relative amounts of an isotope are of interest, the absolute concentration of any one isotope is of little importance.

Isotope ratio and fractional abundance
The most fundamental description of hydrogen isotopes in a system is the relative abundance of deuterium and protium. This value can be reported as the isotope ratio $2$R or the fractional abundance $2$F defined as: $$^2R = \frac{^2H}{^1H}$$ and $$^2F = \frac{^2H}{^1H+^2H}$$ where $2$H and $1$H are the amounts of deuterium and protium, respectively. Fractional abundance is equivalent to mole fraction, and yields atom percent when multiplied by 100. In some instances atom percent excess is used, which reports the atom percent of a sample minus the atom percent of a standard.

Delta notation
Isotope ratios for a given substance are often reported compared to a standard with known isotopic composition, and measurements of relative masses are always made in conjuncture with measuring a standard (for more information see METHODS). In the case of hydrogen the Vienna Standard Mean Ocean Water standard is used which has a isotope ratio of 155.76 ±0.1 ppm. The delta value as compared to this standard is defined as: $$\delta^2H_{VSMOW} = \frac{^2R_{sample}}{^2R_{VSMOW}}-1$$ These delta values are often quite small, and are usually reported as per mil values (‰) which come from multiplying the above equation by a factor of 1000.

Measures of fractionation
The study of hydrogen isotope biogeochemistry relies on the fact that various physicochemical processes will preferentially enrich or deplete deuterium relative to protium (see kinetic isotope effect, etc.). There are various measures that have been developed to described the fractionation in an isotope between two pools, often the product and reactant of a physiochemical process. α notation describes the difference between two hydrogen pools A and B with the following equation: $$\alpha_{A/B} = \frac{\delta^2H^{A}}{\delta^2H^{B}}$$ Where δ$2$H$A$ is the delta value of pool A relative to VSMOW. As many delta values do not vary greatly from one another the α value is often very close to unity. A related measure called epsilon (ε) is often used which is given simply by: $$\epsilon_{A/B} = \alpha_{A/B}-1$$ These values are often very close to zero, and are reported as per mill values by multiplying α-1 by 1000. One final measure is Δ, pronounced "cap delta", which is simply: $$\Delta_{A/B} = \delta^2H^{A}-\delta^2H^{B}$$

Conservation of mass in mixing calculations
As discussed above, deuterium and protium are stable isotopes which never undergo radioactive decay. Therefore, the D/H ratio of a pool containing hydrogen will remain constant as long as no hydrogen is added or removed from the system, a property known as conservation of mass. When two pools of hydrogen A and B mix with molar amounts of hydrogen m$A$ and m$B$, each with their own starting fractional abundance of deuterium (F$A$ and F$B$), then the fractional abundance of the resulting mixture is given by the following exact equation: $$m_\Sigma F_\Sigma = m_AF_A+m_BF_B$$ The terms with Σ represent the values for the combined pools. It is often common to find the following approximation used for calculations regarding the mixing of two pools with a known isotopic composition: $$m_\Sigma \delta_\Sigma = m_A \delta_A+m_B \delta_B$$ This approximation is convenient and applicable with little error in most applications having to deal with pools of hydrogen from natural processes. The maximum difference between the calculated delta value with the approximate and exact equations is given by the following equation: $$\delta_{error} = (R_{std})[(\delta_A-\delta_B)/2]^2$$ This error is quite small for nearly all mixing of naturally occurring isotope values, even for hydrogen which can have quite large natural variations in delta values. The estimation should be avoided however when unnaturally large isotope delta values are encountered, which is particularly common in isotopic labeling experiments.

Naturally occurring isotope variation
Natural processes result in broad variations in the D/H ratio found in different pools of hydrogen. Kinetic isotope effects (LINK TO ALEX) and physical changes such as precipitation and evaporation lead to these observed variations. Ocean water varies slightly, between 0 to -10 per mil, while atmospheric water can be found to vary between approximately -200 to +100 per mil. Biomolecules synthesized by organisms will retain some of the D/H signature of the water which they were grown on, plus a large fractionation factor which can be as great as several hundred per mil (LINK TO BIOMOLECULES). Large D/H differences amounting to thousands of per mil can be found between Earth and other planetary bodies such as Mars, likely due to variations in isotope fractionation during planet formation and the physical loss of hydrogen to space. Detailed information on the extent of these natural variations can be found here (LINK TO JIUEN).

List of well known fractionation effects
A number of common processes fractionate hydrogen isotopes to produce the isotope variations found in nature. Common physical processes include precipitation and evaporation (elaborated on here (LINK TO ALEX"S DISCUSSION)). Chemical reactions also have the potential to heavily influence the partitioning of heavy and light isotopes between pools.  The rate of a chemical reaction depends in part on the energies of the chemical bonds being formed and broken in the reaction.  Since different isotopes have different masses, the bond energies are different between different isotopologues of a chemical species.  This will result in a difference in the rate of a reaction for the different isotopologues, resulting in a fractionation of the different isotopes between the reactant and product in a chemical reaction.  This is known as the kenetic isotope effect, and is described in detail here (LINK TO ALEX).  A classic example of such an isotope effect is the D/H ratio difference in the equilibrium between H$2$O and H$2$ which can have an alpha value of as much as 3-4.

Isotope ratio as tracer for fingerprint
In many areas of study the origin of a chemical or group of chemicals is of central importance. Questions such as the source of environmental pollutants, the origin of hormones in an athlete's body, or the authenticity of foods and flavorings are all examples where chemical compounds need to be identified and sourced. Hydrogen isotopes have found uses in these an many other diverse areas of study. Since many processes can affect the D/H ratio of a given chemical compound this ratio can be a diagnostic signature for compounds produced in a specific location or via a certain process. Once the D/H ratios of a number of sources are known the measurement of this ratio for a sample of unknown origin can often be used to link it back to a certain source or production method (SEE APPLICATIONS).

Environmental chemistry
An important goal of environmental chemistry is tracing the source and degradation of pollutants. Various methods have been employed for fingerprinting pools of environmental pollutants such as the bulk chemical composition of a spill, isotope ratios of the bulk chemical mixture , or isotope ratios of individual constituent compounds. Stable isotopes of carbon and hydrogen can be used as complimentary fingerprinting techniques for natural gas. Recently, the D/H ratio of hydrocarbons from the Deepwater Horizon oil spill was used to verify that their origin was likely from the Macondo well. Hydrogen isotope ratios have also been used as a measure of the relative amount of biodegradation that has occurred in oil reservoirs in China, and studies on pure cultures of n-alkane degrading organisms have shown a chain-length dependence on the amount of hydrogen isotope fractionation during degradation. Additional studies have also shown hydrogen isotope effects in the degradation of Methyl tert-butyl ether and Toluene that have been suggested to be useful in the evaluation of the level of degradation of these polluting compounds in the environment. In both cases the residual unreacted compounds became enriched in deuterium to a few tens of per mil, with variations exhibited between different organisms and degree of reaction completeness. These observations of heavy residual compounds have been applied to field observations of biodegradation reactions such as the removal of benzene and ethylbenzene, which imparted a D/H fractionation of 27 and 50 per mil, respectively. Additionally analysis of o-xylene in a polluted cite showed high residual D/H ratios after biodegradation, consistent with activation of C-H bonds being a rate limiting step in this process

Source attribution and forensics
Stable isotope ratios have found uses in various instances where the authenticity or origin of a chemical compound is called into question. Such situations include assessing the authenticity of food, wine and natural flavors; drug screening in sports (see doping); pharmaceuticals; illicit drugs; and even helping identify human remains. In these cases it is often not sufficient to detect or quantify a certain compound, since the question is the origin of the compound. The strength of hydrogen isotope analysis in answering these questions is that in many cases the D/H ratio of a natural product is related to the natural water D/H values in the area where the product was formed (ref to Sang's section on hydrologic cycle). Since D/H ratios vary significantly between different geographic areas, this can serve as a powerful tool in locating the original source of many different substance. {In the case of synthetic/natural, might be due to different pathways as well as different geographic source waters}

Food and flavor authentication
Foods, flavorings and scents are often sold with the guarantee that chemical additives come from natural sources. This claim becomes difficult to evaluate when the chemical compound has a known structure and is readily synthesized in the lab. Authentication of claims regarding the origins of these chemicals has made good use of various stable isotopes, including those of hydrogen. Combined carbon and hydrogen isotope analysis has been used to test the authenticity of (E)-methyl cinnamate, γ-decalactone and δ-decalactone. Hydrogen and nitrogen isotope ratios have been used for the authentication of alkylpyrazines used as "natural" coffee flavorings.

Doping
The isotope ratio of carbon in the steroids of athletes has been used to determine whether these steroids originated from the body of the athlete or an exogenous source. This test has been used in a number of high-profile anti-doping cases and has various benefits over simply characterizing the concentration of various compounds. Attempts are being made to create similar tests based on stable hydrogen isotopes which could be used to compliment the existing testing methods. One concern with this method was that the natural steroids produced by the human body may vary significantly based on the deuterium content of drinking water, leading to false detection of doping based on hydrogen isotope differences. This concern has been addressed in a recent study which concluded that the effect of D/H ratio of drinking water did not pose an insurmountable source of error for this anti-doping testing strategy.

Illicit Drugs
The sources and production mechanisms of illegal drugs has been another area that has seen successful application of hydrogen isotope characterization. Usually, as with other applications of stable isotope techniques, results are best when combination of multiple stable isotopes are compared with one another. δ$2$H, δ$13$C and δ$15$N have been used together to analyze tablets of MDA and MDMA and has successfully identified differences which could be used to differentiate between different sources or production mechanisms. The same combination of stable isotopes with the addition of δ$18$O was applied to heroin and associated packaging and could successfully distinguish between different samples. Analysis using deuterium NMR was also able to shed light on the origin and processing of both cocaine and heroin. In the case of heroin this site-specific natural isotopic fraction measured by deuterium NMR (SNIF-NMR) method could be used for determining the geographic origin of the molecule by analyzing so-called natural sites (which were present in the morphine from which heroin is made), as well as gaining information on the synthesis process by analyzing the artificial sites (added during drug processing).

Provenance of human remains
The geographical variation in D/H ratio in human drinking water is recorded in hair. Studies have shown a very strong relation between an individuals' hair and drinking water D/H ratios. Since tap water D/H ratio has a strong dependence on geography, a persons hair D/H ratio can be used to determine regions in which they were most likely living during hair growth. This idea has been used in criminal investigations to try and constrain the movements of a person prior to their death, in much the same way D/H ratios have been used to track animal migrations (LINK TO SUJUNGS SECTION). By analyzing sections of hair of varying ages it is possible to determine in what D/H regions a person was living at a specific time prior to their death.