In organic chemistry, the Cahn–Ingold–Prelog (CIP) sequence rules are a standard process to completely and unequivocally name a stereoisomer of a molecule. The purpose of the CIP system is to assign an R or S descriptor to each stereocenter and an E or Z descriptor to each double bond so that the configuration of the entire molecule can be specified uniquely by including the descriptors in its systematic name. A molecule may contain any number of stereocenters and any number of double bonds, and each usually gives rise to two possible isomers. A molecule with an integer n describing the number of stereocenters will usually have 2n stereoisomers, and 2n−1 diastereomers each having an associated pair of enantiomers. The CIP sequence rules contribute to the precise naming of every stereoisomer of every organic molecule with all atoms of ligancy of fewer than 4.
Monosaccharides, also called simple sugars, are the simplest forms of sugar and the most basic units (monomers) from which all carbohydrates are built. Chemically, monosaccharides are polyhydroxy aldehydes with the formula H-[CHOH]
n-CHO or polyhydroxy ketones with the formula H-[CHOH]
m-CO-[CHOH]
n-H with three or more carbon atoms.
In chemistry, a structural isomer of a compound is another compound whose molecule has the same number of atoms of each element, but with logically distinct bonds between them. The term metamer was formerly used for the same concept.
Carbon-13 (13C) is a natural, stable isotope of carbon with a nucleus containing six protons and seven neutrons. As one of the environmental isotopes, it makes up about 1.1% of all natural carbon on Earth.
In physical organic chemistry, a kinetic isotope effect (KIE) is the change in the reaction rate of a chemical reaction when one of the atoms in the reactants is replaced by one of its isotopes. Formally, it is the ratio of rate constants for the reactions involving the light (kL) and the heavy (kH) isotopically substituted reactants (isotopologues): KIE = kL/kH.
In chemistry, a molecule or ion is called chiral if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes. This geometric property is called chirality. The terms are derived from Ancient Greek χείρ (cheir) 'hand'; which is the canonical example of an object with this property.
Isotopic labeling is a technique used to track the passage of an isotope through chemical reaction, metabolic pathway, or a biological cell. The reactant is 'labeled' by replacing one or more specific atoms with their isotopes. The reactant is then allowed to undergo the reaction. The position of the isotopes in the products is measured to determine what 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.
In chemistry, isotopologues are molecules that differ only in their isotopic composition. They have the same chemical formula and bonding arrangement of atoms, but at least one atom has a different number of neutrons than the parent.
Kinetic fractionation is an isotopic fractionation process that separates stable isotopes from each other by their mass during unidirectional processes. Biological processes are generally unidirectional and are very good examples of "kinetic" isotope reactions. All organisms preferentially use lighter isotopes, because "energy costs" are lower, resulting in a significant fractionation between the substrate (heavier) and the biologically mediated product (lighter). For example, photosynthesis preferentially takes up the light isotope of carbon 12C during assimilation of atmospheric CO2. This kinetic isotope fractionation explains why plant material (and thus fossil fuels, which are derived from plants) is typically depleted in 13C by 25 per mil (2.5%) relative to most inorganic carbon on Earth.
A cyclic compound is a term for a compound in the field of chemistry in which one or more series of atoms in the compound is connected to form a ring. Rings may vary in size from three to many atoms, and include examples where all the atoms are carbon, none of the atoms are carbon, or where both carbon and non-carbon atoms are present. Depending on the ring size, the bond order of the individual links between ring atoms, and their arrangements within the rings, carbocyclic and heterocyclic compounds may be aromatic or non-aromatic; in the latter case, they may vary from being fully saturated to having varying numbers of multiple bonds between the ring atoms. Because of the tremendous diversity allowed, in combination, by the valences of common atoms and their ability to form rings, the number of possible cyclic structures, even of small size numbers in the many billions.
Metabolic flux analysis (MFA) is an experimental fluxomics technique used to examine production and consumption rates of metabolites in a biological system. At an intracellular level, it allows for the quantification of metabolic fluxes, thereby elucidating the central metabolism of the cell. Various methods of MFA, including isotopically stationary metabolic flux analysis, isotopically non-stationary metabolic flux analysis, and thermodynamics-based metabolic flux analysis, can be coupled with stoichiometric models of metabolism and mass spectrometry methods with isotopic mass resolution to elucidate the transfer of moieties containing isotopic tracers from one metabolite into another and derive information about the metabolic network. Metabolic flux analysis (MFA) has many applications such as determining the limits on the ability of a biological system to produce a biochemical such as ethanol, predicting the response to gene knockout, and guiding the identification of bottleneck enzymes in metabolic networks for metabolic engineering efforts.
The mass recorded by a mass spectrometer can refer to different physical quantities depending on the characteristics of the instrument and the manner in which the mass spectrum is displayed.
In chemistry, isomers are molecules or polyatomic ions with identical molecular formula – that is, the same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism refers to the existence or possibility of isomers.
Nuclear magnetic resonance decoupling is a special method used in nuclear magnetic resonance (NMR) spectroscopy where a sample to be analyzed is irradiated at a certain frequency or frequency range to eliminate or partially the effect of coupling between certain nuclei. NMR coupling refers to the effect of nuclei on each other in atoms within a couple of bonds distance of each other in molecules. This effect causes NMR signals in a spectrum to be split into multiple peaks. Decoupling fully or partially eliminates splitting of the signal between the nuclei irradiated and other nuclei such as the nuclei being analyzed in a certain spectrum. NMR spectroscopy and sometimes decoupling can help determine structures of chemical compounds.
Isotopic analysis by nuclear magnetic resonance allows the user to quantify with great precision the differences of isotopic contents on each site of a molecule and thus to measure the specific natural isotope fractionation for each site of this molecule. The SNIF-NMR analytical method was developed to detect the (over) sugaring of wine and enrichment of grape musts, and is mainly used to check the authenticity of foodstuffs and to control the naturality of some aromatic molecules. The SNIF-NMR method has been adopted by the International Organisation of Vine and Wine (OIV) and the European Union as an official method for wine analysis. It is also an official method adopted by the Association Of Analytical Chemists (AOAC) for analysis of fruit juices, maple syrup, vanillin, and by the European Committee for Standardization (CEN) for vinegar.
Clumped isotopes are heavy isotopes that are bonded to other heavy isotopes. The relative abundance of clumped isotopes (and multiply-substituted isotopologues) in molecules such as methane, nitrous oxide, and carbonate is an area of active investigation. The carbonate clumped-isotope thermometer, or "13C–18O order/disorder carbonate thermometer", is a new approach for paleoclimate reconstruction, based on the temperature dependence of the clumping of 13C and 18O into bonds within the carbonate mineral lattice. This approach has the advantage that the 18O ratio in water is not necessary (different from the δ18O approach), but for precise paleotemperature estimation, it also needs very large and uncontaminated samples, long analytical runs, and extensive replication. Commonly used sample sources for paleoclimatological work include corals, otoliths, gastropods, tufa, bivalves, and foraminifera. Results are usually expressed as Δ47 (said as "cap 47"), which is the deviation of the ratio of isotopologues of CO2 with a molecular weight of 47 to those with a weight of 44 from the ratio expected if they were randomly distributed.
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.
Methane clumped isotopes are methane molecules that contain two or more rare isotopes. Methane (CH4) contains two elements, carbon and hydrogen, each of which has two stable isotopes. For carbon, 98.9% are in the form of carbon-12 (12C) and 1.1% are carbon-13 (13C); while for hydrogen, 99.99% are in the form of protium (1H) and 0.01% are deuterium (2H or D). Carbon-13 (13C) and deuterium (2H or D) are rare isotopes in methane molecules. The abundance of the clumped isotopes provides information independent from the traditional carbon or hydrogen isotope composition of methane molecules.
NAIL-MS is a technique based on mass spectrometry used for the investigation of nucleic acids and its modifications. It enables a variety of experiment designs to study the underlying mechanism of RNA biology in vivo. For example, the dynamic behaviour of nucleic acids in living cells, especially of RNA modifications, can be followed in more detail.
The stable isotope composition of amino acids refers to the abundance of heavy and light non-radioactive isotopes of carbon, nitrogen, and other elements within these molecules. Amino acids are the building blocks of proteins. They are synthesized from alpha-keto acid precursors that are in turn intermediates of several different pathways in central metabolism. Carbon skeletons from these diverse sources are further modified before transamination, the addition of an amino group that completes amino acid biosynthesis. Bonds to heavy isotopes are stronger than bonds to light isotopes, making reactions involving heavier isotopes proceed slightly slower in most cases. This phenomenon, known as a kinetic isotope effect, gives rise to isotopic differences between reactants and products that can be detected using isotope ratio mass spectrometry. Amino acids are synthesized via a variety of pathways with reactions containing different, unknown isotope effects. Because of this, the 13C content of amino acid carbon skeletons varies considerably between the amino acids. There is also an isotope effect associated with transamination, which is apparent from the abundance of 15N in some amino acids.
