Tandem mass spectrometryTandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides. The molecules of a given sample are ionized and the first spectrometer (designated MS1) separates these ions by their mass-to-charge ratio (often given as m/z or m/Q).
Rotational–vibrational spectroscopyRotational–vibrational spectroscopy is a branch of molecular spectroscopy concerned with infrared and Raman spectra of molecules in the gas phase. Transitions involving changes in both vibrational and rotational states can be abbreviated as rovibrational (or ro-vibrational) transitions. When such transitions emit or absorb photons (electromagnetic radiation), the frequency is proportional to the difference in energy levels and can be detected by certain kinds of spectroscopy.
Ion trapAn ion trap is a combination of electric and/or magnetic fields used to capture charged particles — known as ions — often in a system isolated from an external environment. Atomic and molecular ion traps have a number of applications in physics and chemistry such as precision mass spectrometry, improved atomic frequency standards, and quantum computing. In comparison to neutral atom traps, ion traps have deeper trapping potentials (up to several electronvolts) that do not depend on the internal electronic structure of a trapped ion.
Molecular vibrationA molecular vibration is a periodic motion of the atoms of a molecule relative to each other, such that the center of mass of the molecule remains unchanged. The typical vibrational frequencies range from less than 1013 Hz to approximately 1014 Hz, corresponding to wavenumbers of approximately 300 to 3000 cm−1 and wavelengths of approximately 30 to 3 μm. For a diatomic molecule A−B, the vibrational frequency in s−1 is given by , where k is the force constant in dyne/cm or erg/cm2 and μ is the reduced mass given by .
Mass spectrometryMass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a mass spectrum, a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio.
Quadrupole ion trapIn experimental physics, a quadrupole ion trap or paul trap is a type of ion trap that uses dynamic electric fields to trap charged particles. They are also called radio frequency (RF) traps or Paul traps in honor of Wolfgang Paul, who invented the device and shared the Nobel Prize in Physics in 1989 for this work. It is used as a component of a mass spectrometer or a trapped ion quantum computer. A charged particle, such as an atomic or molecular ion, feels a force from an electric field.
IonAn ion (ˈaɪ.ɒn,_-ən) is an atom or molecule with a net electrical charge. The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by convention. The net charge of an ion is not zero because its total number of electrons is unequal to its total number of protons. A cation is a positively charged ion with fewer electrons than protons while an anion is a negatively charged ion with more electrons than protons.
Gas chromatography–mass spectrometryGas chromatography–mass spectrometry (GC–MS) is an analytical method that combines the features of gas-chromatography and mass spectrometry to identify different substances within a test sample. Applications of GC–MS include drug detection, fire investigation, environmental analysis, explosives investigation, food and flavor analysis, and identification of unknown samples, including that of material samples obtained from planet Mars during probe missions as early as the 1970s.
Infrared spectroscopyInfrared spectroscopy (IR spectroscopy or vibrational spectroscopy) is the measurement of the interaction of infrared radiation with matter by absorption, emission, or reflection. It is used to study and identify chemical substances or functional groups in solid, liquid, or gaseous forms. It can be used to characterize new materials or identify and verify known and unknown samples. The method or technique of infrared spectroscopy is conducted with an instrument called an infrared spectrometer (or spectrophotometer) which produces an infrared spectrum.
Ion-mobility spectrometry–mass spectrometryIon mobility spectrometry–mass spectrometry (IMS-MS) is an analytical chemistry method that separates gas phase ions based on their interaction with a collision gas and their masses. In the first step, the ions are separated according to their mobility through a buffer gas on a millisecond timescale using an ion mobility spectrometer. The separated ions are then introduced into a mass analyzer in a second step where their mass-to-charge ratios can be determined on a microsecond timescale.
Ion sourceAn ion source is a device that creates atomic and molecular ions. Ion sources are used to form ions for mass spectrometers, optical emission spectrometers, particle accelerators, ion implanters and ion engines. Electron ionization Electron ionization is widely used in mass spectrometry, particularly for organic molecules. The gas phase reaction producing electron ionization is M{} + e^- -> M^{+\bullet}{} + 2e^- where M is the atom or molecule being ionized, e^- is the electron, and M^{+\bullet} is the resulting ion.
Fourier-transform ion cyclotron resonanceFourier-transform ion cyclotron resonance mass spectrometry is a type of mass analyzer (or mass spectrometer) for determining the mass-to-charge ratio (m/z) of ions based on the cyclotron frequency of the ions in a fixed magnetic field. The ions are trapped in a Penning trap (a magnetic field with electric trapping plates), where they are excited (at their resonant cyclotron frequencies) to a larger cyclotron radius by an oscillating electric field orthogonal to the magnetic field.
Rearrangement reactionIn organic chemistry, a rearrangement reaction is a broad class of organic reactions where the carbon skeleton of a molecule is rearranged to give a structural isomer of the original molecule. Often a substituent moves from one atom to another atom in the same molecule, hence these reactions are usually intramolecular. In the example below, the substituent R moves from carbon atom 1 to carbon atom 2: Intermolecular rearrangements also take place.
Conformational isomerismIn chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). 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.
Polyatomic ionA polyatomic ion (also known as a molecular ion) is a covalent bonded set of two or more atoms, or of a metal complex, that can be considered to behave as a single unit and that has a net charge that is not zero. The term molecule may or may not be used to refer to a polyatomic ion, depending on the definition used. The prefix poly- carries the meaning "many" in Greek, but even ions of two atoms are commonly described as polyatomic. In older literature, a polyatomic ion may instead be referred to as a radical (or less commonly, as a radical group).
Ion channelIon channels are pore-forming membrane proteins that allow ions to pass through the channel pore. Their functions include establishing a resting membrane potential, shaping action potentials and other electrical signals by gating the flow of ions across the cell membrane, controlling the flow of ions across secretory and epithelial cells, and regulating cell volume. Ion channels are present in the membranes of all cells. Ion channels are one of the two classes of ionophoric proteins, the other being ion transporters.
Selection ruleIn physics and chemistry, a selection rule, or transition rule, formally constrains the possible transitions of a system from one quantum state to another. Selection rules have been derived for electromagnetic transitions in molecules, in atoms, in atomic nuclei, and so on. The selection rules may differ according to the technique used to observe the transition. The selection rule also plays a role in chemical reactions, where some are formally spin-forbidden reactions, that is, reactions where the spin state changes at least once from reactants to products.
Claisen rearrangementThe Claisen rearrangement is a powerful carbon–carbon bond-forming chemical reaction discovered by Rainer Ludwig Claisen. The heating of an allyl vinyl ether will initiate a [3,3]-sigmatropic rearrangement to give a γ,δ-unsaturated carbonyl, driven by exergonically favored carbonyl CO bond formation (ΔΔHf = -327 kcal·mol−1). The Claisen rearrangement is an exothermic, concerted (bond cleavage and recombination) pericyclic reaction. Woodward–Hoffmann rules show a suprafacial, stereospecific reaction pathway.
Vibronic spectroscopyVibronic spectroscopy is a branch of molecular spectroscopy concerned with vibronic transitions: the simultaneous changes in electronic and vibrational energy levels of a molecule due to the absorption or emission of a photon of the appropriate energy. In the gas phase, vibronic transitions are accompanied by changes in rotational energy also. Vibronic spectra of diatomic molecules have been analysed in detail; emission spectra are more complicated than absorption spectra.
VibrationVibration () is a mechanical phenomenon whereby oscillations occur about an equilibrium point. The oscillations may be periodic, such as the motion of a pendulum, or random, such as the movement of a tire on a gravel road. Vibration can be desirable: for example, the motion of a tuning fork, the reed in a woodwind instrument or harmonica, a mobile phone, or the cone of a loudspeaker. In many cases, however, vibration is undesirable, wasting energy and creating unwanted sound.
