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.
In stereochemistry, stereoisomerism, or spatial isomerism, is a form of isomerism in which molecules have the same molecular formula and sequence of bonded atoms (constitution), but differ in the three-dimensional orientations of their atoms in space. This contrasts with structural isomers, which share the same molecular formula, but the bond connections or their order differs. By definition, molecules that are stereoisomers of each other represent the same structural isomer.
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, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds. While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers. Conformations that correspond to local maxima on the energy surface are the transition states between the local-minimum conformational isomers. Rotations about single bonds involve overcoming a rotational energy barrier to interconvert one conformer to another. If the energy barrier is low, there is free rotation and a sample of the compound exists as a rapidly equilibrating mixture of multiple conformers; if the energy barrier is high enough then there is restricted rotation, a molecule may exist for a relatively long time period as a stable rotational isomer or rotamer. When the time scale for interconversion is long enough for isolation of individual rotamers, the isomers are termed atropisomers. The ring-flip of substituted cyclohexanes constitutes another common form of conformational isomerism.
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.
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique based on re-orientation of atomic nuclei with non-zero nuclear spins in an external magnetic field. This re-orientation occurs with absorption of electromagnetic radiation in the radio frequency region from roughly 4 to 900 MHz, which depends on the isotopic nature of the nucleus and increased proportionally to the strength of the external magnetic field. Notably, the resonance frequency of each NMR-active nucleus depends on its chemical environment. As a result, NMR spectra provide information about individual functional groups present in the sample, as well as about connections between nearby nuclei in the same molecule. As the NMR spectra are unique or highly characteristic to individual compounds and functional groups, NMR spectroscopy is one of the most important methods to identify molecular structures, particularly of organic compounds.
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.
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.
Equilibrium isotope fractionation is the partial separation of isotopes between two or more substances in chemical equilibrium. Equilibrium fractionation is strongest at low temperatures, and forms the basis of the most widely used isotopic paleothermometers : D/H and 18O/16O records from ice cores, and 18O/16O records from calcium carbonate. It is thus important for the construction of geologic temperature records. Isotopic fractionations attributed to equilibrium processes have been observed in many elements, from hydrogen (D/H) to uranium (238U/235U). In general, the light elements are most susceptible to fractionation, and their isotopes tend to be separated to a greater degree than heavier elements.
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.
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.
