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The masses of these ions are equal with the sum of masses of abundant isotopes of the various atoms making up the molecule. Molecule ionisation energy ranges from 8 to 12 eV; for electrons, the commonly used one is 70 eV, providing maximum ionisation efficiency. After crossing the source volume, electrons are trapped on a cathode hatch , and impact-generated ions are expelled from the source by means of a plate 4 with a certain same-sign potential.

Next, such electrons are accelerated at the source-analyser interface by a V 0 potential difference. The excess energy is collected as internal energy by the molecular ion from 12 to 70 eV. The molecular ion breaks into ion fragments, with sufficient internal energy to further break themselves, and the process continues. All respective ions have a very short life span milliseconds only , which requires their removal from the source as soon as possible, for analysis purposes. Positive ions attracted to electrode E 1 enter through a slit in the area between E 1 and E 2 , where an 8 kV accelerating magnetic field operates 1 , 23 ].

Solid, liquid or gaseous organic compounds can be analysed; however, inside the ionisation chamber, samples need to be in the gas phase. The sample amount weighs microliters or micrograms and may be reduced to picograms when coupled with gas chromatography. Very volatile liquids are first vaporised and then introduced into the ionisation chamber. Gases are introduced with an accuracy valve [ 24 — 28 ]. A reactant gas is introduced into the ionisation chamber, whose molecules become ionised on collision with a beam of electrons accelerated by a V potential difference. Plasma formed is driven to the centre of the source by electrostatic lenses.

Positive chemical ionisation occurs when methane or isobutane as a reactant gas is used. For instance, ionised species may be generated where methane is used, such as. Therefore, molecular weight is easily determined, and its fragments provide information on the molecular structure. Negative chemical ionisation occurs by bombarding the reaction gas, nitrogen, butane, or isobutene, with high-energy eV primary electrons, resulting in low-energy electrons, easy to capture by sample molecules.

Capture may be non-dissociative or dissociative:. For compounds with an affinity for electrons, negative chemical ionisation is about three orders of magnitude more sensitive than positive chemical ionisation [ 30 — 32 ]. As highly dependent on experimental conditions source temperature, pressure in the ionisation chamber, reactant gas purity , mass spectra resulting from chemical ionisation are less reproducible than those obtained by electron impact [ 1 , 24 ].

Field desorption ionisation is used for high molecular mass compounds and unstable or little volatile polar compounds such as carboxylic acids and sugars [ 1 ]. The method uses a solid aromatic matrix, e. By means of a microscope, a 3—ns-pulse UV laser irradiation is focused on a small matrix spot, 0. An electronic and thermal excitation of molecules in the sample matrix occurs, able to yield protons causing ionisation. The matrix serves as an energy vector between the laser beam and the molecules of the analysed compound. Ion and neutral molecule desorption occurs after laser irradiation, as a supersonic expansion jet.

Desorbed ions are transferred to the analyser under vacuum by means of an interface. MALDI is the most used analytical method in modern biochemistry and polymer science [ 1 , 41 — 43 ]. Therefore, values on the horizontal axis are a direct reflection of m [ 1 ]. Data acquisition and processing are performed by a computer, in line with the diagram below:. Other peaks correspond to ion fragments. In relation to it, percent intensity is assigned to each signal, which represents the relative percent abundance of each ion fragment [ 1 , 44 , 45 ].

The existence of the molecular ion in the spectrum allows accurate determination of molecular mass. In certain compounds, the molecular ion is not present because it is very unstable and molecular mass cannot be determined [ 1 , 44 , 45 ]. Electron pair cations, resulting from fragmentation of the molecular ion, are usually more stable than the molecular ion and have hence greater abundance. The nitrogen rule. Molecular mass of organic compounds are even, except for those containing an odd number of nitrogen atoms. When a compound is nitrogen-free, but an odd mass corresponds to the last peak, this is definitely not the molecular peak.

The rule may be extended to fragmentation ions as well. The nitrogen rule may be explained by the fact that elements contained in organic compounds have either even valence and atomic mass O, C, S or odd valence and atomic mass H halogen and by the fact that make the compounds containing only C, H, O, S and halogen show an even molecular mass only. Illogical peaks. The difference between the predicted molecular mass and the immediately following fragment mass must correspond to the elimination of a hydrogen atom mass 1 or one CH 3 group mass There are no fragments of masses between 3—14 and 21—25 mass units mu.

A smaller difference between those limits indicates that either the sample is impure or that greater mass peak is not the molecular peak [ 1 , 44 , 45 ]. An isotope is an element that has the same number of electrons in the electronic layer but a different number of neutrons in the nucleus. Therefore, isotopes have the same chemical properties and only differ in their mass. All elements have several natural-state isotopes [ 46 — 49 ]. One may note that the lightest isotope also has the greatest abundance [ 1 , 50 — 52 ].

Abundances are calculated by assigning the values to the prominent isotope [ 1 , 3 ]. Assuming for simplicity reasons that mass 79 and 81 isotopes have the same relative abundance, the likelihood of a mixed dibromo- 79 Br— 81 Br is two times higher than that of homogeneous dibromo- 79 Br— 79 Br or 81 Br— 81 Br. A similar calculation is possible for chlorinated compounds as well. Fluorine and iodine are isotopically pure. In halogenated compounds, carbon, hydrogen and oxygen isotopes are a minority.

The 13 C isotopic contribution is 68 times higher than that of 2 H deuterium and 27 times higher than that of 17 O [ 1 , 3 ]. High-resolution mass spectrometry is widely used to determine molecular formulas of certain unknown compounds. Spectrometers have a software that compares exact masses with those of various possible formulas [ 1 , 3 ]. The molecular formula may often be obtained by high-resolution spectrometer measurements, because atomic weights are not integers. Molecular mass observed for the CO molecular ion is the sum of exact masses of the most abundant carbon and oxygen isotope, which sum differs from the CO molecular mass based on atomic masses averaging the masses of all natural isotopes of an element e.

Exact masses of certain isotopes [ 1 , 3 ]. There are tables including formulas corresponding to molecules or fragments with their exact masses, obtained by addition of exact masses of the most abundant isotopes of each element. The mass of the molecular ion is the sum of the most abundant isotope 12 C, 1 H, 16 O, etc. The impact of a very energetic electron with a molecule turns the latter into a cation radical, with loss of an electron.

A range of rearrangements or fragmentations follow, which depend on the molecule nature and structure [ 1 , 3 ]:. Straight-chain or branched hydrocarbon fragmentation occurs, resulting in formation of more stable carbocations; their stability increases in the order:. In ionisation chambers, about one molecule in 10, is ionised. This requires 8—12 eV, i. This energy is known as ionisation potential IP M. Depending on electron impact conditions, molecular ions have internal energy, E int , ranging from 0 to 10 eV. At one point, the balance of all fragments from ions of different internal energies is the mass spectrum achieved by electron impact at 70 eV.

Considering that the energy of the reverse reaction is close to 0, the E a activation energy is. Mass spectrum is the balance of a series of competing and consecutive reactions [ 54 — 56 ]. The following types of ions are produced during electronic ionisation: molecular ions, fragmentation ions, multiple charge ions, metastable ions, rearrangement ions and pair ions [ 1 , 3 , 57 , 58 ]:.

Most processes are very rapid, occurring within a few nano- or microseconds. In homolytic cleavage, each electron moves independently. One fragment is an even-electron cation and another free radical with an unpaired electron [ 1 , 3 , 54 ]:. In heterolytic cleavage, an electron pair moves together to the charged atom. Once again, fragments are an even-electron cation and a radical. The charge is placed on the alkyl group:. Further fragmentation of such a cation generally results in another even-electron cation and a fragment or even-electron molecule:.

Fragmentation of a certain bond is related to bond strength, to the possibility of low-energy transition and to the stability of arising fragments. Given the greatly reduced pressure of a spectrometer, the likelihood of collisions is low, and therefore unimolecular breakdowns occur [ 57 — 59 ]. The following general rules have been established to predict prominent peaks in electronic impact mass spectra:. The relative height of molecular ion peaks is greater for straight-chain ions and smaller than that of branched-chain ones.

Generally, the relative height of the molecular ion peak decreases with increase of the molecular mass in a homologous series. Fatty ethers may be an exception. Due to an increased stability of tertiary carbocations as compared to secondary and primary ones, likelihood of cleavage increases as the carbon atom is more substituted. The longest chain may be eliminated as a radical, because such a radical may be stabilised by stabilisation of the lone pair ion:. Double bonds and cyclic structures, particularly aromatic ones, stabilise the molecular ion and increase its likelihood.

Double bonds favour allylic cleavage, resulting in formation of resonance-stabilised allylic cations:. Heteroatom-containing compounds cleave at the C—C bond next to the heteroatom, passing the charge over to the heteroatom-containing fragment:. In the case of difficult-to-volatilise compounds or compounds whose molecular peak cannot be determined, a derivative which can be prepared that is more volatile, has a predictable cleavage pattern, a simplified fragmentation pattern and a better stability of the molecular ion.

A low-volatility polar group of compounds such as carbohydrates, dicarboxylic acids and peptides become volatile and able to render characteristic peaks by acylation of the —OH or —NH 2 groups or methylation of the —COOH groups. Trimethylsilylating of the same groups allows passage of corresponding compounds through the chromatographic column GC. Reducing ketones to hydrocarbons allows elucidation of their carbonate skeletons. Reducing polypeptides to more volatile poly-amino alcohols also allows prediction of the fragmentation pattern [ 1 , 28 ].

Mass spectrometry is particularly important to organic chemistry because it allows acquisition of information about the composition and particularly about the structure of molecular compounds. Mass spectra provide data for structural assessments, fragmentation being performed by semi-empirical rules serving to the study of unknown compounds. The identified molecular ion must correspond to spectrum ions produced by loss of fragments. A multiplet in the molecular ion area indicates the presence of a specific isotopic structure heteroatom, such as silica, sulphur, chlorine and bromine.

Proportionality of the intensity of the signal with the analyte amount allows the use of mass spectrometry in quantitative assays. For this purpose internal standard methods are used. As standard a compound similar to the analyte is employed provided that the ionisation produces easily to monitor ions different from those of the analyte. As analyte similar chemical compound, such as a deuterated isotope or analogue whose ionisation produces easily to monitor ions, different from those of the analyte can be employed [ 1 , 3 , 63 ].

Hydrocarbon mass spectra are easy to interpret because hydrocarbons have C—C and H—H bonds only. Taking into account molecule dissociation enthalpies, one finds that C—C bonds are the easiest to break:. For instance,. Ethene neutral molecules may also form:. Ions 43 and 57 are among the most stable of the spectrum with the highest peaks , consistent with their standard formation enthalpy.

Unlike higher mass ions, they do not undergo secondary fragmentation [ 3 ]:. Their identification depends on the molecular ion peak. Branched alkane spectra are largely similar to those of straight-chain alkanes, but fragment abundance does not decrease evenly.

Mass Spectrometry - A Textbook: About Book and Website

Fragmentation preferentially occurs at branching points [ 64 ]. So you can distinguish the n -alkanes from branched alkanes [ 1 , 3 ]. Cyclohexane undergoes complex fragmentation requiring much energy on cycle break. The molecular ion peak is visible in alkenes. It is difficult to locate the double bond in acyclic alkenes since it easily migrates from one fragment to the other.

Location of the double bond in cyclic alkenes results from the tendency to allylic cleavage without double-bond migration. Limonene shows a unique, retro-Diels-Alder cleavage pattern:. Similar to saturated hydrocarbons, acyclic alkenes are characterised by a number of peaks separated by 14 unit intervals. These compounds render easy-to-interpret spectra.

Bromine and chlorine compounds are mainly distinguishable by appearance of molecular peak of their natural isotopes. Based on dissociation energies of their molecule bonds, fragmentation patterns of molecular ions can be predicted:. Characteristic fragmentation of brominated and iodised compounds consists of cleavage of the C—Br and C—I bonds at low dissociation energy.

Two patterns of fragmentation are then possible:. Low-molecular-mass monochlorinated alkanes show a detectable molecular peak. Although the chlorine atom does occur in fragmentation of the molecular ion, its intervention is much smaller than in oxygen-, nitrogen- or sulphur-containing compounds.

Understanding Mass Spectra

HCl elimination occurs probably at 1,3 position, resulting in formation of a weak peak on average M— Conduct of brominated compounds is similar to that of chlorinated ones [ 65 ]:. Halogenated aromatic compounds have a prominent peak M—X when X is directly related to the cycle. When possible, the tropylium ion is easily formed [ 1 , 3 , 60 ]. Alcohols easily losing one water molecule, their molecular ion, are almost non-existent. Water loss may occur under the influence of heat even before fragmentation. Therefore, in this case, the spectrum resembles that of an alkene.

Generally, the break occurs in the bond next to the oxygen atom. Secondary and tertiary alcohols cleave with formation of ions:. Analysis of branched alcohols is more difficult [ 3 ]:. In over C 6 -chain primary alcohols, the break of C—C bonds results in spectra similar to those of alkenes. Cycloalkanes undergo complex fragmentation. Benzyl alcohol and substitution counterparts form a prominent parent peak.

Fragmentation of alkylphenols is similar to that of alkylbenzenes, which further cleave in the same way as un-alkylated phenols [ 61 , 62 ]:. Cleavage of the simple C—O bond, sometimes observed in simple ethers, gives rise to branched ions:. The molecular peak is predominant in alkyl aryl ethers. Generally, the aldehyde molecular peak may be identified. This resonance-stabilised ion arises in cyclic transition state. Based on pentanal as reference, there are four fragmentation patterns:. Spectra of straight-chain aldehydes show other characteristic peaks as well, e.

The hydrocarbon-fragmentation-like pattern becomes more prominent with an increase in the chain [ 3 ]. Ketone molecular ion peak is generally sufficiently prominent. The base peak commonly results by loss of the most important alkyl group. The molecular ion of cyclic ketones is predominant. Similar to aliphatic ketones, the first fragmentation occurs at the bond adjacent to the carbonyl group [ 53 ]:.

Part 1: Mass Spectrometry - Basics and Principle

The same ion results in cyclopentanone as well, on elimination of an ethyl radical instead of a propyl radical, the same as in cyclohexanone [ 53 ]. The molecular ion peak is predominant in aromatic ketones. In straight-chain monocarboxylic acids , although weak, the molecular peak can generally be observed. Dicarboxylic acids are termed into esters to increase their volatility. Trimethylsilyl esters 2 are very suitable. Aromatic acids display easily noticeable molecular peaks. One instance of ortho - effect is that of o -methylbenzoic o -toluic acid [ 1 , 3 , 53 ]:. Esters of aliphatic acids, even soaps, usually display one noticeable molecular peak.

The characteristic peak occurs due to common McLafferty rearrangement, with cleavage of a bond not directly adjacent to the carbonyl group. The McLafferty rearrangement of the alcohol part does not occur unless there is a competition with rearrangement of the acid part or the arising ion is stabilised, e.

Esters of aromatic acids display a predominant molecular peak. Alkyl benzoates eliminate alcohol by ortho-effect , similarly to aromatic acids. The molecular ion peak of aliphatic amines is odd, generally weak, unnoticeable even in long chain or strongly branched amines. Mass spectra reveal the presence of iminium ions due to nitrogen, which is a very good stabiliser of adjacent ions.

Tertiary amines lose an alkyl radical, resulting in formation of a resonance-stabilised iminium radical. Amino acids may undergo fragmentation in two C—C bonds next to nitrogen, favouring the one arising from loss of the carboxyl group. Unlike acyclic amines, cyclic amines have intense molecular peaks. Monomolecular aromatic amines with odd number of nitrogen atoms display an intense molecular ion [ 76 ]:. In aliphatic amides , the molecular ion of a monoamide is generally identifiable. Dominant fragmentation patterns depend on chain length as well as on the number and length of nitrogen-bound alkyl groups [ 76 ].

The base peak of primary amides with straight chain longer than that of propionamide results from McLafferty rearrangement [ 1 , 3 , 54 , 77 ]:. The molecular ion loses NH 2 , resulting in a resonance-stabilised benzoyl cation which then undergoes fragmentation, leading to the phenyl cation [ 1 , 3 , 77 ]:. Except for acetonitrile and propionitrile, molecular peaks of aliphatic nitriles are weak. Aliphatic nitro-derivatives have odd weak or absent molecular peaks. As the nitro group produces sharp polarisation of the C—N bond, the latter is broken, giving rise to hydrocarbon characteristic fragments:.

Aromatic nitro-derivatives have a prominent molecular peak. Mercaptan and thio-ether compounds render more intense molecular ion peaks than corresponding oxygen compounds. Mercaptan fragmentation is similar to that of alcohols. Fragmentations occur similarly to ethers. Cyclic sulphides fragment differently from cyclic ethers.

Mass Spectrometry – A Textbook: Book & Website

Molecular ions of saturated heterocyclic compounds show a strong tendency to transannular rearrangement, often rendering the base peak. Whether alkylated or not, heteroaromatic compounds render an intense molecular peak. The charge of the molecular ion is mainly localised on the heteroatom and not on the aromatic ring. Five-atom aromatic heterocycles display similar fragmentation patterns.

The first step consists in the cleavage of the carbon—heteroatom bond:. The pentatomic poly-heterocycles such as oxazoles, imidazoles, pyrazoles, etc. In the case of an N heteroatom, elimination of HCN is preferred. Pyrazines undergo similar fragmentations because all substituents are in ortho to nitrogen atoms [ 1 , 3 ]. As amino acids are zwitterionic compounds, often non-volatile, their methyl esters are studied instead. The spectra produced by electron impact ionisation display weak or non-existent molecular peaks, because of amino acid capacity to easily lose their carboxyl group and of their esters to easily lose their carboalkoxyl group on electronic impact [ 76 , 77 ]:.

The [M—R] ester group ion may undergo McLafferty rearrangement:. Triglyceride molecular ions convert to characteristic ions [M—O 2 CR] formed by stabilising the positive charge of the neighbouring oxygen:. Cholestane is a typical representative of steroids [ 80 ]. The intense peak molecular ion undergoes four fragmentation patterns:. Fragmentation of the C 13 —C 18 bond, favoured by C 13 being tertiary, resulting in formation of the intermediary ion which is able to fragment in various ways. Polyhydroxylated steroids such as cholesterol have spectra with weak or non-existent molecular peaks.

Dehydrations occur on heating.


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Chemical ionisation cannot be used, and the protonated molecular ion dehydrates quickly. Spectra obtained by field desorption FD mass spectrometry does not show dehydrations, and the molecular peak is present [ 1 , 3 , 81 ]. Identification of the molecular ion is the first stage for mass spectrum interpretation because the molecular ion is the source of information on molecular composition.

If the electron impact ionisation-rendered spectrum does not allow identification of the molecular ion, other ionisation methods might be used. Prominent peaks in a mass spectrum are generally those resulting from primary fragmentations. Secondary fragmentations may be used as aids for spectrum analysis.

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  7. Completely revised from the first edition, an updated and unified approach to mass spectral interpretation emphasizes the application of basic principles from undergraduate organic, analytical, and physical chemistry courses. A detailed overview of theory and instrumentation, this useful guide contains step-by-step descriptions of interpretative strategies and convenient lists and tables detailing the information needed to solve unknowns. Other features include real-world case studies and examples, skill-building problems with clearly explained answers, and easy-to-follow explanations of the important mathematical derivations.

    About the Author R. He received his PhD in organic chemistry from the University of Wisconsin-Madison, and has numerous publications dealing with the application of mass spectrometry to forensic science.

    Scope of “Mass Spectrometry – A Textbook”

    Permissions Request permission to reuse content from this site. Introduction 1 1. Overview 1 1. Sample Introduction 3 1. Ionization Source 4 1. Electron Ionization Source 5 1. Chemical Ionization 8 1. Other Ionization Methods 9 1. Electrospray Ionization 9 1. Desorption Ionization 12 1.

    Time-of-Flight TOF 13 1. Magnetic Sector 15 1. Transmission Quadrupole 17 1. Other Types of Mass Analysis 24 1. Spectral Skewing 26 1. Ion Detection 30 1. Electron Multiplier 32 1. Photomultiplier Detector 33 1. Data System 33 1. Instrument Tuning and Calibration 33 1. The Mass Spectrum 37 1. Production of the Mass Spectrum 37 1. Terminology: Ions vs.

    Peaks 41 1. Library Searches 41 1. Natural Isotopic Abundances 56 2. Atomic and Molecular Mass 59 2. Calculated Exact Masses and Mass Defects 60 2. One or More Atoms of a Single Element 64 2. Chlorine and Bromine 64 2. Ion Designation and Nomenclature 70 2. Probability Considerations with Multiple Numbers of Atoms 71 2. Silicon 82 2. Complex Isotope Clusters 83 2. Sulfur Dioxide 83 2. Diazepam 86 2. A Brief Review of Orbitals and Bonding 99 3.

    Even- and Odd-Electron Species 3. Site of Initial Ionization 3.