Detection by mass spectrometry
A mass spectrum of an organic compound will usually contain a small peak of one mass unit greater than the apparent molecular ion peak (M) of the whole molecule. This is known as the M+1 peak and comes from the few molecules that contain a 13C atom in place of a 12C. A molecule containing one carbon atom will be expected to have an M+1 peak of approximately 1.1% of the size of the M peak, as 1.1% of the molecules will have a 13C rather than a 12C. Similarly, a molecule containing two carbon atoms will be expected to have an M+1 peak of approximately 2.2% of the size of the M peak, as there is double the previous likelihood that any molecule will contain a 13C atom.
In the above, the mathematics and chemistry have been simplified, however it can be used effectively to give the number of carbon atoms for small- to medium-sized organic molecules. In the following formula the result should be rounded to the nearest integer:
where C = number of C atoms, X = amplitude of the M ion peak, and Y = amplitude of the M +1 ion peak.
13C-enriched compounds are used in the research of metabolic processes by means of mass spectrometry. Such compounds are safe because they are non-radioactive. In addition, 13C is used to quantify proteins (quantitative proteomics). One important application is in stable isotope labeling by amino acids in cell culture (SILAC). 13C-enriched compounds are used in medical diagnostic tests such as the urea breath test. Analysis in these tests is usually of the ratio of 13C to 12C by isotope ratio mass spectrometry.
The ratio of 13C to 12C is slightly higher in plants employing C4 carbon fixation than in plants employing C3 carbon fixation. Because the different isotope ratios for the two kinds of plants propagate through the food chain, it is possible to determine if the principal diet of a human or other animal consists primarily of C3 plants or C4 plants by measuring the isotopic signature of their collagen and other tissues.
Uses in science
Due to differential uptake in plants as well as marine carbonates of 13C, it is possible to use these isotopic signatures in earth science. Biological processes preferentially take up the lower mass isotope through kinetic fractionation. In aqueous geochemistry, by analyzing the δ13C value of carbonaceous material found in surface and ground waters, the source of the water can be identified. This is because atmospheric, carbonate, and plant derived δ13C values all differ. In biology, the ratio of carbon-13 and carbon-12 isotopes in plant tissues is different depending on the type of plant photosynthesis and this can be used, for example, to determine which types of plants were consumed by animals. Greater carbon-13 concentrations indicate stomatal limitations, which can provide information on plant behaviour during drought. [2] Tree ring analysis of carbon isotopes can be used to retrospectively understand forest photosynthesis and how it is impacted by drought. [3]
In geology, the 13C/12C ratio is used to identify the layer in sedimentary rock created at the time of the Permian extinction 252 Mya when the ratio changed abruptly by 1%. More information about usage of 13C/12C ratio in science can be found in the article about isotopic signatures.
Carbon-13 has a non-zero spin quantum number of ½, and hence allows the structure of carbon-containing substances to be investigated using carbon-13 nuclear magnetic resonance.
The carbon-13 urea breath test is a safe and highly accurate diagnostic tool to detect the presence of Helicobacter pylori infection in the stomach. [4] The urea breath test utilizing carbon-13 is preferred to carbon-14 for certain vulnerable populations due to its non-radioactive nature. [4]
In chemistry, a chemical formula is a way of presenting information about the chemical proportions of atoms that constitute a particular chemical compound or molecule, using chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, commas and plus (+) and minus (−) signs. These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a chemical name since it does not contain any words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulae can fully specify the structure of only the simplest of molecules and chemical substances, and are generally more limited in power than chemical names and structural formulae.
Deuterium is one of two stable isotopes of hydrogen. The nucleus of a deuterium atom, called a deuteron, contains one proton and one neutron, whereas the far more common protium has no neutrons in the nucleus. Deuterium has a natural abundance in Earth's oceans of about one atom of deuterium among every 6,420 atoms of hydrogen. Thus deuterium accounts for approximately 0.0156% by number of all the naturally occurring hydrogen in the oceans, while protium accounts for more than 99.98%. The abundance of deuterium changes slightly from one kind of natural water to another.
Neon is a chemical element with the symbol Ne and atomic number 10. It is a noble gas. Neon is a colorless, odorless, inert monatomic gas under standard conditions, with about two-thirds the density of air. It was discovered in 1898 as one of the three residual rare inert elements remaining in dry air, after nitrogen, oxygen, argon and carbon dioxide were removed. Neon was the second of these three rare gases to be discovered and was immediately recognized as a new element from its bright red emission spectrum. The name neon is derived from the Greek word, νέον, neuter singular form of νέος, meaning 'new'. Neon is chemically inert, and no uncharged neon compounds are known. The compounds of neon currently known include ionic molecules, molecules held together by van der Waals forces and clathrates.
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms. Study of structure determines their structural formula. Study of properties includes physical and chemical properties, and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes the chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical study.
Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as well as with other compounds. Oxygen is Earth's most abundant element, and after hydrogen and helium, it is the third-most abundant element in the universe. At standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula O
2. Diatomic oxygen gas currently constitutes 20.95% of the Earth's atmosphere, though this has changed considerably over long periods of time. Oxygen makes up almost half of the Earth's crust in the form of oxides.
Urea, also called carbamide, is an organic compound with chemical formula CO(NH2)2. This amide has two amino groups joined by a carbonyl functional group. It is thus the simplest amide of carbamic acid.
The urea breath test is a rapid diagnostic procedure used to identify infections by Helicobacter pylori, a spiral bacterium implicated in gastritis, gastric ulcer, and peptic ulcer disease. It is based upon the ability of H. pylori to convert urea to ammonia and carbon dioxide. Urea breath tests are recommended in leading society guidelines as a preferred non-invasive choice for detecting H. pylori before and after treatment.
Isotope separation is the process of concentrating specific isotopes of a chemical element by removing other isotopes. The use of the nuclides produced is varied. The largest variety is used in research. By tonnage, separating natural uranium into enriched uranium and depleted uranium is the largest application. In the following text, mainly the uranium enrichment is considered. This process is crucial in the manufacture of uranium fuel for nuclear power plants, and is also required for the creation of uranium-based nuclear weapons. Plutonium-based weapons use plutonium produced in a nuclear reactor, which must be operated in such a way as to produce plutonium already of suitable isotopic mix or grade. While different chemical elements can be purified through chemical processes, isotopes of the same element have nearly identical chemical properties, which makes this type of separation impractical, except for separation of deuterium.
Carbon-14, C-14, 14
C or radiocarbon, is a radioactive isotope of carbon with an atomic nucleus containing 6 protons and 8 neutrons. Its presence in organic materials is the basis of the radiocarbon dating method pioneered by Willard Libby and colleagues (1949) to date archaeological, geological and hydrogeological samples. Carbon-14 was discovered on February 27, 1940, by Martin Kamen and Sam Ruben at the University of California Radiation Laboratory in Berkeley, California. Its existence had been suggested by Franz Kurie in 1934.
Ureases, functionally, belong to the superfamily of amidohydrolases and phosphotriesterases. Ureases are found in numerous bacteria, fungi, algae, plants, and some invertebrates, as well as in soils, as a soil enzyme. They are nickel-containing metalloenzymes of high molecular weight.
A radioactive tracer, radiotracer, or radioactive label is a chemical compound in which one or more atoms have been replaced by a radionuclide so by virtue of its radioactive decay it can be used to explore the mechanism of chemical reactions by tracing the path that the radioisotope follows from reactants to products. Radiolabeling or radiotracing is thus the radioactive form of isotopic labeling. In biological contexts, use of radioisotope tracers are sometimes called radioisotope feeding experiments.
Isotopic labeling is a technique used to track the passage of an isotope through a reaction, metabolic pathway, or cell. The reactant is 'labeled' by replacing specific atoms by their isotope. The reactant is then allowed to undergo the reaction. The position of the isotopes in the products is measured to determine the sequence the isotopic atom followed in the reaction or the cell's metabolic pathway. The nuclides used in isotopic labeling may be stable nuclides or radionuclides. In the latter case, the labeling is called radiolabeling.
Rapid urease test, also known as the CLO test, is a rapid diagnostic test for diagnosis of Helicobacter pylori. The basis of the test is the ability of H. pylori to secrete the urease enzyme, which catalyzes the conversion of urea to ammonia and carbon dioxide.
Monoisotopic mass (Mmi) is one of several types of molecular masses used in mass spectrometry. The theoretical monoisotopic mass of a molecule is computed by taking the sum of the accurate masses of the most abundant naturally occurring stable isotope of each atom in the molecule. For small molecules made up of low atomic number elements the monoisotopic mass is observable as an isotopically pure peak in a mass spectrum. This differs from the nominal molecular mass, which is the sum of the mass number of the primary isotope of each atom in the molecule and is an integer. It also is different from the molar mass, which is a type of average mass. For some atoms like carbon, oxygen, hydrogen, nitrogen, and sulfur, the Mmi of these elements is exactly the same as the mass of its natural isotope, which is the lightest one. However, this does not hold true for all atoms. Iron's most common isotope has a mass number of 56, while the stable isotopes of iron vary in mass number from 54 to 58. Monoisotopic mass is typically expressed in daltons (Da), also called unified atomic mass units (u).
This glossary of chemistry terms is a list of terms and definitions relevant to chemistry, including chemical laws, diagrams and formulae, laboratory tools, glassware, and equipment. Chemistry is a physical science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions; it features an extensive vocabulary and a significant amount of jargon.
Mass spectral interpretation is the method employed to identify the chemical formula, characteristic fragment patterns and possible fragment ions from the mass spectra. Mass spectra is a plot of relative abundance against mass-to-charge ratio. It is commonly used for the identification of organic compounds from electron ionization mass spectrometry. Organic chemists obtain mass spectra of chemical compounds as part of structure elucidation and the analysis is part of many organic chemistry curricula.
The atomic mass (ma or m) is the mass of an atom. Although the SI unit of mass is the kilogram (symbol: kg), atomic mass is often expressed in the non-SI unit dalton (symbol: Da) – equivalently, unified atomic mass unit (u). 1 Da is defined as 1⁄12 of the mass of a free carbon-12 atom at rest in its ground state. The protons and neutrons of the nucleus account for nearly all of the total mass of atoms, with the electrons and nuclear binding energy making minor contributions. Thus, the numeric value of the atomic mass when expressed in daltons has nearly the same value as the mass number. Conversion between mass in kilograms and mass in daltons can be done using the atomic mass constant .
Breath gas analysis is a method for gaining information on the clinical state of an individual by monitoring volatile organic compounds (VOCs) present in the exhaled breath. Exhaled breath is naturally produced by the human body through expiration and therefore can be collected in non-invasively and in an unlimited way. VOCs in exhaled breath can represent biomarkers for certain pathologies. Breath gas concentration can then be related to blood concentrations via mathematical modeling as for example in blood alcohol testing. There are various techniques that can be employed to collect and analyze exhaled breath. Research on exhaled breath started many years ago, there is currently limited clinical application of it for disease diagnosis. However, this might change in the near future as currently large implementation studies are starting globally.
Exalenz Bioscience Ltd. is a biotechnology company that develops and manufactures non-invasive diagnostic medical devices for gastrointestinal and liver conditions. The company's technology uses a continuous flow of a patient's breath to diagnose illness. Exalenz is headquartered in Modi’in, Israel and is publicly traded on the Tel Aviv Stock Exchange as EXEN. U.S. headquarters are in Jersey City, New Jersey.
Position-specific isotope analysis, also called site-specific isotope analysis, is a branch of isotope analysis aimed at determining the isotopic composition of a particular atom position in a molecule. Isotopes are elemental variants with different numbers of neutrons in their nuclei, thereby having different atomic masses. Isotopes are found in varying natural abundances depending on the element; their abundances in specific compounds can vary from random distributions due to environmental conditions that act on the mass variations differently. These differences in abundances are called "fractionations," which are characterized via stable isotope analysis.