(Redirected from Fragmentation (chemistry)) In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. Since a given nominal mass may correspond to several molecular formulas, lists of such possibilities are especially useful when evaluating the spectrum of an unknown compound. Consequently, the radical cation character of the molecular ion (m/z = 170) is delocalized over all the covalent bonds. Of the three cleavage reactions described here, the alpha-cleavage is generally favored for nitrogen, oxygen and sulfur compounds. When an organic sample that is vaporized is passed in an ionization chamber of a mass spectrometer, it will be bombarded with electrons. It also mentions the M+2 peak for isotopes of chlorine and bromine. or an even # N atoms, odd-electron ions To use this calculator Click Here. The three essential functions of a mass spectrometer, and the associated components, are: In the case of methylene chloride, the molecular ion consists of three peaks at m/z=84, 86 & 88 Da, and their diminishing intensities may be calculated from the natural abundances given above. Mass spectrometry (MS) is a powerful analytical technique widely used by chemists, biologists, medical researchers, and environmental and forensic scientists, among others. The fragmentations leading to the chief fragment ions will be displayed by clicking on the appropriate spectrum. . This distinction is illustrated nicely by the follwing two examples. A mass spectrum will usually be presented as a vertical bar graph, in which each bar represents an ion having a specific mass-to-charge ratio (m/z) and the length of the bar indicates the relative abundance of the ion. Because the strong nuclear forces that bind the components of an atomic nucleus together vary, the actual mass of a given isotope deviates from its nominal integer by a small but characteristic amount (remember E = mc2). More Spectroscopy Tools: A nice collection of applications for interpreting NMR, IR and mass spectra. Understanding Chemistry . This organic chemistry video tutorial provides a basic introduction into mass spectrometry. The following mass spectrum of cocaine demonstrates how a forensic laboratory might determine the nature of an unknown street drug. Residual energy from the collision may cause the molecular ion to fragment into neutral pieces (colored green) and smaller fragment ions (colored pink and orange). Department of Chemistry Chernoff Hall Room 102 Queen’s University 90 Bader Lane Kingston, Ontario, Canada K7L 3N6 Office: 613-533-6539 Lab: 613-533-6000 ext.74253 Fax: 613-533-6669. Most stable organic compounds have an even number of total electrons, reflecting the fact that electrons occupy atomic and molecular orbitals in pairs. The following diagram displays the mass spectra of three simple gaseous compounds, carbon dioxide, propane and cyclopropane. The nature of the fragments often provides a clue to the molecular structure, but if the molecular ion has a lifetime of less than a few microseconds it will not survive long enough to be observed. By clicking on each spectrum in turn, a partial fragmentation analysis and peak assignment will be displayed. Organic Chemistry: IR and Mass Spectrometry Teach Yourself Chemistry Visually in 24 Hours - by Dr. Wayne Huang and his team. Unless otherwise noted, LibreTexts content is licensed by CC BY-NC-SA 3.0. Mass Spectrometry and its Applications to Organic Chemistry, von J. H. Beynon Elsevier Publishing Co., Amsterdam‐London‐New York‐Princeton 1960. The fragments of a molecule cause a unique pattern in the mass spectrum. The four most important types of spectrometry that organic chemists routinely use are: Mass Spectrometry (MS) Nuclear Magnetic Resonance Spectrometry (NMR) Infrared Spectrometry (IR) Ultraviolet-Visible Spectrometry (UV-Vis) In one common procedure, ionization is effected by a high energy beam of electrons, and ion separation is achieved by accelerating and focusing the ions in a beam, which is then bent by an external magnetic field. Hours. In the analytical technique of mass spectrometry, atoms or molecules are ionized using a high-energy electron beam and then separated based on their mass-to-charge ratios (m/z). Among simple organic compounds, the most stable molecular ions are those from aromatic rings, other conjugated pi-electron systems and cycloalkanes. The small m/z=39 ion in propane and the absence of a m/z=29 ion in cyclopropane are particularly significant in distinguishing these hydrocarbons. Most organic mass spectrometry is still carried out on instruments designed on Dempster's model. • Mass Spectrum: On x- axis of mass spectrum is the mass to … Monday to Friday 9:00 a.m. to 5:00 p.m. The precise isotopic composition of chlorine and bromine is: The presence of chlorine or bromine in a molecule or ion is easily detected by noticing the intensity ratios of ions differing by 2 Da. . Diethylmethylamine, on the other hand, has one nitrogen and its molecular mass (m/z = 87) is an odd number. Mass spectrometry therefore not only provides a specific molecular mass value, but it may also establish the molecular formula of an unknown compound. Simply enter an appropriate subscript number to the right of each symbol, leaving those elements not present blank, and press the "Calculate" button. The center and right hand spectra show that chlorine is also composed of two isotopes, the more abundant having a mass of 35 Da, and the minor isotope a mass 37 Da. Protein digestion is a key challenge in mass spectrometry (MS)-based structural proteomics. Also, the structure of most fragment ions is seldom known with certainty. The heart of the spectrometer is the ion source. . Environmental pollutants, pesticide residues on food, and controlled substance identification are but a few examples of this application. odd-number mass, odd-electron ions By localizing the reactive moiety, certain fragmentation processes will be favored. The LibreTexts libraries are Powered by MindTouch® and are supported by the Department of Education Open Textbook Pilot Project, the UC Davis Office of the Provost, the UC Davis Library, the California State University Affordable Learning Solutions Program, and Merlot. Mass spectrometry is without a doubt an indispensable tool for the chemistry disciplines like organic and organometallic chemistry. A less common fragmentation, in which an even-electron neutral fragment is lost, produces an odd-electron radical cation fragment ion. This leaves behind a molecular ion (colored red in the following diagram). The first two fragmentation paths lead to even-electron ions, and the elimination (path #3) gives an odd-electron ion. The impact of the electrons on the molecule (M) causes the ejection of an electron from the molecule to form a positively charged ion … Some of these ions fragment into smaller cations and neutral fragments. It also shows the effect of isotopes such as Carbon-13 on the mass spectrum. The positive charge commonly resides on the smaller fragment, so we see a homologous series of hexyl (m/z = 85), pentyl (m/z = 71), butyl (m/z = 57), propyl (m/z = 43), ethyl (m/z = 29) and methyl (m/z = 15) cations. Advanced Mass Spectrometry: Applications in Organic and Analytical Chemistry discusses the concepts that are essential in the effective utilization of mass spectrometry. Plausible assignments may be seen by clicking on the spectrum, and it should be noted that all are even-electron ions. The presence of a functional group, particularly one having a heteroatom Y with non-bonding valence electrons (Y = N, O, S, X etc. Fundamentally, mass spectrometry involves ionization of a sample through bombarding it with high-energy electrons. The most intense ion is assigned an abundance of 100, and it is referred to as the base peak. Watch the recordings here on Youtube! In order to measure the characteristics of individual molecules, a mass spectrometer converts them to ions so that they can be moved about and manipulated by external electric and magnetic fields. The series includes High School Chemistry, AP Chemistry, General Chemistry, Organic Chemistry and Biochemistry. This article is cited by 76 publications. The unit mass resolution is readily apparent in these spectra (note the separation of ions having m/z=39, 40, 41 and 42 in the cyclopropane spectrum). Based on the measured m / z and their peak intensities, the formula and chemical structure can be determined manually [ 30] and/or by comparison with a reference database of spectra. Bond cleavage generates a radical and a cation, and both fragments often share these roles, albeit unequally. Its structure is uncertain, but two possibilities are shown in the diagram. Since a molecule of carbon dioxide is composed of only three atoms, its mass spectrum is very simple. High resolution measurements are of greatest value, as they allow verifying synthetic work and/or identification of unknown natural occurring compounds. The mass spectrometric analysis of organic compounds gives information on the molecular mass, chemical formula, chemical structure, or quantity of the analyte. Mass Spectrometry. on N or O), fragmentation pathways may sometimes be explained by assuming the missing electron is partially localized on that atom. even-number mass, even-electron ions When non-bonded electron pairs are present in a molecule (e.g. The three essential functions of a mass spectrometer, and the associated components, are: Because ions are very reactive and short-lived, their formation and manipulation must be conducted in a vacuum. It should be noted that the presence of halogen atoms in a molecule or fragment ion does not change the odd-even mass rules given above. 1. be able to use data from a mass spectrometer to: determine the relative molecular mass of an organic compound from the molecular ion peak; suggest possible structures of a simple organic compound from the m/z of the molecular ion and fragmentation… OCR Chemistry A. Module 4: Core organic chemistry Mass Spectrometry is a process by which the atomic mass of atoms or molecules is determined. Although it is not truly a type of spectroscopy, mass spectrometry is nevertheless another instrumental method that chemists use to analyze compounds. Modern mass spectrometers easily distinguish (resolve) ions differing by only a single atomic mass unit, and thus provide completely accurate values for the molecular mass of a compound. A few examples of these rearrangement mechanisms may be seen by clicking the following button. The masses of molecular and fragment ions also reflect the electron count, depending on the number of nitrogen atoms in the species. A clever and informative site from the University of Erlangen-Nuremberg, Institute of Organic Chemistry : Spectroscopy Tools: A useful site providing information for NMR, IR and mass spectroscopy. Mass spectrometry is a technique by which the molecular mass of a compound may be determined. The result of a Mass Spectrometry is a graph plotting mass per … Two other common elements having useful isotope signatures are carbon, 13C is 1.1% natural abundance, and sulfur, 33S and 34S are 0.76% and 4.22% natural abundance respectively. Created at the University of Potsdam. The Queen’s Mass Spectrometry Facility currently consists of four mass spectrometers. After all, it is easier to remove (ionize) a non-bonding electron than one that is part of a covalent bond. Missed the LibreFest? Atmospheric pressure is around 760 torr (mm of mercury). Further examples of functional group influence on fragmentation are provided by a selection of compounds that may be examined by clicking the left button below. analytical method to find the molecular mass of a compound and indirectly helped to prove the identity of isotopes Most of the fragment ions have odd-numbered masses, and therefore are even-electron cations. This influence is thought to occur because of a "localization" of the radical cation component of the molecular ion on the heteroatom. Although using hydrogen–deuterium exchange kinetics with MS (HDX-MS) to interrogate the high-order structure of proteins is now established, it can be challenging for β-barrel proteins, which are important in … Fragmentation of Br2 to a bromine cation then gives rise to equal sized ion peaks at 79 and 81 Da. The third strongest ion in the spectrum has m/z=39 (C3H3). Mass spectrometry is an analytical technique to measure the mass-to-charge ratio of ions that can be used to identify unknown compounds, determine the isotopic composition of elements in a compound, and quantify the amount of a compound in a sample. The molecular ion in a mass spectrum is always a radical cation, but the fragment ions may either be even-electron cations or odd-electron radical cations, depending on the neutral fragment lost. The mass spectrum of dodecane on the right illustrates the behavior of an unbranched alkane. . The pressure under which ions may be handled is roughly 10-5 to 10-8 torr (less than a billionth of an atmosphere). A perpendicular magnetic field deflects the ion beam in an arc whose radius is inversely proportional to the mass of each ion. Spectroscopy is the study of interaction between matter and electromagnetic radiation. When these electrons collide with a molecule in the sample, they can dislodge an electron, creating either a cation radical or a cation and a neutral radical. Mass spectrometry is a very useful method for the determination of the structure of organic compounds although the technique has not yet been widely employed in this field. The mass spectra of elements . However, accurate measurements show that this is not strictly true. Alcohols, ethers and highly branched alkanes generally show the greatest tendency toward fragmentation. The molecular ion is the strongest ion in the spectra of CO2 and C3H6, and it is moderately strong in propane. The complexity of fragmentation patterns has led to mass spectra being used as "fingerprints" for identifying compounds. ), can dramatically alter the fragmentation pattern of a compound. When a single electron is removed from a molecule to give an ion, the total electron count becomes an odd number, and we refer to such ions as radical cations. By designing mass spectrometers that can determine m/z values accurately to four decimal places, it is possible to distinguish different formulas having the same nominal mass. The role of mass spectrometry in organic chemistry It is well known that mass spectrometry (MS is a very versatile physical method which is appli,2 to many branches of chemistry. The ions are sorted and separated according to their mass and charge. Atomic mass is given in terms of the unified atomic mass unit (symbol: μ) or dalton (symbol: Da). Spectroscopic techniques are widely used for the structure elucidation of … To make use of a calculator that predicts the isotope clusters for different combinations of chlorine, bromine and other elements Click Here. Extremely small samples of an unknown substance (a microgram or less) are sufficient for such analysis. A majority of the fragment ions have even-numbered masses (ions at m/z = 30, 42, 56 & 58 are not labeled), and are even-electron nitrogen cations. Composition tables are available for this purpose, and a particularly useful program for calculating all possible combinations of H, C, N & O that give a specific nominal mass has been written by Jef Rozenski. Both distributions are observed, but the larger ethyl cation (m/z=29) is the most abundant, possibly because its size affords greater charge dispersal. It can be used to find relative isotopic abundance, atomic and molecular mass, and the structure of a compound. Cleavage of a carbon-carbon bond gives methyl and ethyl fragments, one of which is a carbocation and the other a radical. The five peaks in this spectrum demonstrate clearly that natural bromine consists of a nearly 50:50 mixture of isotopes having atomic masses of 79 and 81 Da respectively. This six lecture course builds on the introductory material presented in the second year Organic Spectroscopy course, with emphasis on applications of modern NMR and mass spectrometry techniques in organic and biological chemistry. • m/z : The mass spectrometer detects mass to charge ratio m divided by z of the molecular ion. The ions are then detected electronically and the resulting information is stored and analyzed in a computer. How the mass spectrum of an element can be used to find its relative atomic mass. This ion is referred to as molecular ion- or parent ion. Structural characterization and regiochemical differentiation of α-cyanoethylindole isomers in the gas phase. For example, the small m/z=99 Da peak in the spectrum of 4-methyl-3-pentene-2-one (above) is due to the presence of a single 13C atom in the molecular ion. Here molecules of the sample (black dots) are bombarded by electrons (light blue lines) issuing from a heated filament. Cations formed by the electron bombardment (red dots) are pushed away by a charged repellor plate (anions are attracted to it), and accelerated toward other electrodes, having slits through which the ions pass as a beam. Gianluca Giorgi, Fabio Ponticelli. . Journal of Synthetic Organic Chemistry, Japan Vol. A similar bond cleavage in cyclopropane does not give two fragments, so the molecular ion is stronger than in propane, and is in fact responsible for the the base peak. So m/1. As a rule, odd-electron ions may fragment either to odd or even-electron ions, but even-electron ions fragment only to other even-electron ions. The … How the mass spectrometer works . This is called an EI (electron-impact) source. Repeated clicks will cycle the display. Tables of precise mass values for any molecule or ion are available in libraries; however, the mass calculator provided below serves the same purpose. The mass spectra of organic compounds. University of ArizonaIowa State University University of Leeds. This is manifested most dramatically for compounds containing bromine and chlorine, as illustrated by the following examples. The molecular ion of propane also has m/z=44, but it is not the most abundant ion in the spectrum. Without a molecular ion peak as a reference, the difficulty of interpreting a mass spectrum increases markedly. We also acknowledge previous National Science Foundation support under grant numbers 1246120, 1525057, and 1413739. The most intense ion is assigned an abundance of 100, and it is referred to as the base peak. Advanced Organic Spectroscopy, held in Michaelmas Term. The highest-mass ion in a spectrum is normally considered to be the molecular ion, and lower-mass ions are fragments from the molecular ion, assuming the sample is a single pure compound. A commonly used instrument design is diagrammed in Fir,ure l. The molecules, of mass M, are ionized by an electron beam in the source. Two main lines of development can be discerned: (i) organic chemical analysis. Each of the three tasks listed above may be accomplished in different ways. Mass spectrometry (MS) is an analytical techniques that is used to measures the mass-to-charge ratio of ions.The results are typically 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. The molecules of these compounds are similar in size, CO2 and C3H8 both have a nominal mass of 44 Da, and C3H6 has a mass of 42 Da. The numbers displayed in the M+1 and M+2 boxes are relative to M being set at 100%. Although less important in this respect, 15N and 18O also make small contributions to higher mass satellites of molecular ions incorporating these elements. Thus, relative to 12C at 12.0000, the isotopic mass of 16O is 15.9949 Da (not 16) and 14N is 14.0031 Da (not 14). In assigning mass values to atoms and molecules, we have assumed integral values for isotopic masses. Even though extensive fragmentation has occurred, many of the more abundant ions (identified by magenta numbers) can be rationalized by the three mechanisms shown above. (ii) gas phase chemistry of organic ions. An explanation of how a mass spectrum is produced. A small sample is ionized, usually to cations by loss of an electron. Fortunately, most organic compounds give mass spectra that include a molecular ion, and those that do not often respond successfully to the use of milder ionization conditions. 1. This video discusses the mass spectrum of ketones, alcohols, alkanes, and alkyl halides with bromine and chlorine. In most alkane spectra the propyl and butyl ions are the most abundant. It explains how to match the correct molecular fragments with the corresponding m/z peaks in the mass spectrum. Since a mass spectrometer separates and detects ions of slightly different masses, it easily distinguishes different isotopes of a given element. These are summarized in the following diagram, where the green shaded box at the top displays examples of such "localized" molecular ions. Ions with no nitrogen Note the use of different curved arrows to show single electron shifts compared with electron pair shifts. Non-volatile solids and liquids may be introduced directly. The m/z = 42 ion might be any or all of the following: C3H6, C2H2O or C2H4N. Fragment ions themselves may fragment further. A mass spectrometer operating in this fashion is outlined in the following diagram. The results are presented as a mass spectrum, which shows the relative abundances of the ions on the y-axis and their m/z ratios on the x-axis. The dalton is classified as a "non-SI unit whose values in SI units must be obtained experimentally". For more information contact us at email@example.com or check out our status page at https://status.libretexts.org. Mechanisms for some of these rearrangements have been identified by following the course of isotopically labeled molecular ions. These are accompanied by a set of corresponding alkenyl carbocations (e.g. Due to these electrons that have high energy, the electron from the organic molecule will be knocked out and a positive ion will be formed. MASS SPECTROMETRY MENU . Loss of a chlorine atom gives two isotopic fragment ions at m/z=49 & 51 Da, clearly incorporating a single chlorine atom. This application was developed at Colby College. molecular ion peak gives molecular mass- the peak at the highest m/z value on the right hand side. The fragmentation of molecular ions into an assortment of fragment ions is a mixed blessing. The Nature of Mass Spectra A mass spectrum will usually be presented as a vertical bar graph, in which each bar represents an ion having a specific mass-to-charge ratio (m/z) and the length of the bar indicates the relative abundance of the ion. A small sample of the compound is vaporised in a mass spectrometer under high vacuum and then subjected to bombardment by a beam of high-energy electrons. Finally, it discusses the mclafferty rearrangement which occurs following the electron ionization of ketones.My Website: https://www.video-tutor.netPatreon Donations: https://www.patreon.com/MathScienceTutorAmazon Store: https://www.amazon.com/shop/theorganicchemistrytutorHere are some other useful videos:H NMR Spectroscopy:https://www.youtube.com/watch?v=MhiiIKpm5Xw\u0026t=159sIR Spectroscopy:https://www.youtube.com/watch?v=_Xi5ZVbbftIOrganic Chemistry 1 Final Exam Review:https://www.youtube.com/watch?v=YQIlAfjR2f4Organic Chemistry 2 Final Exam Review:https://www.youtube.com/watch?v=T5NaUdVfAOc Since there are no heteroatoms in this molecule, there are no non-bonding valence shell electrons. Lighter ions are deflected more than heavier ions. With MS, we are looking at the mass of a molecule, or of different fragments of that molecule. both properties accurately. The … It is defined as one twelfth of the rest mass of an unbound atom of carbon-12 in its nuclear and electronic ground state, and has a value of 1.660538782(83)x10-27 kg. m/z = 55, 41 &27) formed by loss of 2 H. All of the significant fragment ions in this spectrum are even-electron ions. It discusses the difference between the base peak and the parent peak. Odd-electron fragment ions are often formed by characteristic rearrangements in which stable neutral fragments are lost. The table on the right illustrates this important feature, and a double-focusing high-resolution mass spectrometer easily distinguishes ions having these compositions. Since molecules of bromine have only two atoms, the spectrum on the left will come as a surprise if a single atomic mass of 80 Da is assumed for Br. The charge distributions shown above are common, but for each cleavage process the charge may sometimes be carried by the other (neutral) species, and both fragment ions are observed. Loss of a hydrogen atom, either before or after ring opening, produces the stable allyl cation (m/z=41). In recent years there has been a gradual change towards using the dalton in preference to the unified atomic mass unit. The molecular ion is also the base peak, and the only fragment ions are CO (m/z=28) and O (m/z=16). Even though these compounds are very similar in size, it is a simple matter to identify them from their individual mass spectra. The calculator on the right may be used to calculate the isotope contributions to ion abundances 1 and 2 Da greater than the molecular ion (M). even-number mass. The formation of fragmentation patterns . The weak even -electron ions at m/z=15 and 29 are due to methyl and ethyl cations (no nitrogen atoms). Indeed, in the previously displayed spectra of 4-methyl-3-pentene-2-one and N,N-diethylmethylamine the major fragment ions come from alpha-cleavages. Most of the ions formed in a mass spectrometer have a single charge, so the m/z value is equivalent to mass itself. . Topic 7A: Mass spectrometry. Have questions or comments? The separated ions are then measured, and the results displayed on a chart. Useful tables of common fragment ions and neutral species may be viewed by clicking the right button. Even with simple compounds like these, it should be noted that it is rarely possible to explain the origin of all the fragment ions in a spectrum. The Mass Spectrometer In order to measure the characteristics of individual molecules, a mass spectrometer converts them to ions so that they can be moved about and manipulated by external electric and magnetic fields. The title particularly covers the fundamentals of the modern techniques, along with the technological concerns of mass spectrometry. The simplest and most common fragmentations are bond cleavages producing a neutral radical (odd number of electrons) and a cation having an even number of electrons. Legal. A few such mechanisms are shown above. 24 (1966) No. A precise assignment could be made from a high-resolution m/z value (next section). It also helps distinguish between molecules of similar masses based on their structure, since it improves the amount of fragmentation that occurs, and hence, extends the fragmentation pattern. [ "article:topic-category", "authorname:wreusch", "showtoc:no" ], information contact us at firstname.lastname@example.org, status page at https://status.libretexts.org. Fluorine and iodine, by contrast, are monoisotopic, having masses of 19 Da and 127 Da respectively. Mass Spectrometry Location. When a high energy electron collides with a molecule it often ionizes it by knocking away one of the molecular electrons (either bonding or non-bonding). Gases and volatile liquid samples are allowed to leak into the ion source from a reservoir (as shown). Fragmentation of C-C bonds occurs because they are usually weaker than C-H bonds, and this produces a mixture of alkyl radicals and alkyl carbocations. The combination of crystallography and mass spectrometry (ESI‐MS) of isolated crystals and the solutions taken from the reaction as a function time reveal seven intermediate steps leading to 2 , but six steps for 5 which a different sequence takes place.