2-Interpretation of Mass Spectra, McLafferty (1993)

INTERPRETATION OF MASS SPECTRA FOURTH EDITION Fred W. McLafferty / Frantiiek Turecek‘Table 21. Natural isotopic abundances of common elements.* 2 aos a ‘a 1% ow 7 004 18 020 2 51 30 a4 2 079 3 a4 a7 320 8 ora ‘Table 22. /sotopic contributions for carbon and hydrogen. Ifthe abundance of the peak A is 100 (after correction for isotopic contributions to it), than its Isotopic ‘contributions will be: A+) A+ +) HD AH o 1 0.00 18 15 04 ° 22 oor 8 wv 04 ° 33 oo4 20 19 ox c “4 oor 2 24 01 c 55 on 2 23 02 c 85 018 2 28 02 cs 17 025 2 33 93 G 88 034 2 39 03 e 98 oe a 45 oa re 110 ose 3 52 os. cn wat os? 30 12 09 Cy 132 080 “ 24 13 cy 43 0.94 55 6 26 cu 154 rr] 6 2 46 Cn 165 13 n0 0 2 For auch ational elomont present ade por atom: en tyn.0970, 0068455. 078 a ao oan 8 9.4: 8 44.c4 220; 96,973. ‘Typieal values or A+ 8) Cy, O62. Cy 018, Ce 87.Mase oA 3. Abundances of isotopic peaks (unit resolution) from element combinations." Ato At4 AO ATE Ewomont ofA A AST AY? ACS ea Bret, cl, Brel, Br Gl, Brch, Brch Cle Bric, 8, cr Hg, eric er a Che Po 210 25 108, om 316 204 A Ast Age wo 05 wo 0108 wo 00318 wo 2 23 wo 051 ad wo 08 4a wo 027 jo 1888 oat a4 io 15, 1. wo 02k wo 8 Ps 0, 6 re 1068 24 1088 25100. a 4 3. 100, 100 32 400 38, 100 “6 100 3 100 4 100 v7. 100 66. 77 100. 7 100 @ 100. ot 100, ro 400, 2 +00. “ 100. 82 100. 9 100. 4 100. “6 100. uo 7B 2 8. 8 2. 3 @. 2 70. 3 4“ characor fr etfrentiating laren! combinations giving sm 02 04 o1 13 2 2a oa 46 20. 6 1 ww 5 1 1 oo. 1 0 siete PI 2 0 1 cae) @ oo 3 oO 2 m8 | @ oH 4 ge so 16 4s wo 8 m0 8 3 8 6. 100 6 2 no a8 © 100 aan ee Rebutona Ne vale inleann 0.05% fr eolrms containing decimal Ngure, <0.5% for BREST TBee bomom ony "As 10.396. 7H + 1,796. A 10 18%INTERPRETATION OF MASS SPECTRA FOURTH EDITION Fred W. McLafferty Frantiek Turetek LMERSITY OF WASHINGTON UNIVERSITY SCIENCE 800K acca CalorieUniversity Science Books ‘55D Gate Five Road Sausalito, CA 94965, Fax: (415) 332-5393 Production manager: Irene Imyeld Manuscript and copy editor: Aidan Kelly Text and jacket designer: Robert Ishi Mlustrator: John Choi Compositor: Asco Trade Typesetting Lid. Printer and binder: Maple-Vail Book Manufacturing Group Copyright ©) 1993 by University Science Books Reproduction or translation of any part ofthis work beyond that permitted by Section 107 or 108 of the 1976 United States Copyright Act without the permission of the copyright owner is unlawful. Requests for permission or further information should be addressed to the Permissions Department, University Science Books Library of Congress Catalog Number: 92-82536 ISBN 0-935702-25 Printed in the United States of America woe 76S 4——————————————— Preface to the Fourth Edition Molecular mass spectrometry continues to show an exponential growth, with a substantial proportion of its applications still requiring the identification of unknown mass spectra. The first edition of this book was published more than 25 years ago, when most instruments could measure only a few unknown mass spectra per hour. The Preface to the 1980 Third Edition estimated worldwide instrument sales at nearly 1,000 mass spectrometers per year; the present rate is several times that, with more than a dozen major manufacturers. These instruments are also far more efficient, the great majority being computerized gas- chromatograph/mass-spectrometer (GC/MS) systems that can turn out up to 100 unknown mass spectra in a 10-minute GC/MS run, Although automated computer-matching procedures of such spectra are now sufficiently fast to keep Lup with this output (Chapter 10), these are still only an aid to, not a replacement for, the skilled interpreter. As a confirmation of this, the course given by the authors on “Interpretation of Mass Spectra for Teachers of Interpretation Courses” at the 1991 Conference of the American Society for Mass Spectro- metry attracted 30 attendees The most important addition to this book, in the opinion of the senior author, is its co-author. Frank Turegek, who is now at the University of Washington as an Associate Professor, has had a distinguished research career, with well over a hundred publications in many areas of mass spectrometry titical to this book. He has made especially important contributions to the mechanisms in Chapters 7-9, representing more than one-third of the book. Our extensive revisions have had the objective of correlating ion dissociation ‘mechanisms on a much broader scale, with emphasis on basic attributes such as ionization energies, proton affinities, and bond-dissociation energies. We have also attempted to show how these mechanisms are applicable to the unimolecular dissociations of ions formed by any ionization method, including the ex- citing variety of new methods for obtaining mass spectra of large molecules.ice to te Fourth Eaton Remaining unchanged, however, is the conviction that the most important part of learning how to interpret unknown mass spectra is actually to practice interpreting mass spectra. As this book has exhorted the student for more than 25 years, you should attempt to solve one or two unknowns for every hour of Iccture or self-study. Try seriously to solve the unknowns before checking the answers in Chapter 11; write down next to the spectral data your calculated elemental composition assignments, possible structures, and postulated mechanisms so that you can later compare these to the book's reasoning in Chapter IL. Try these steps also on unknowns from your own research, You should find that putting together the pieces of the MS jigsaw puzzle is fun. It certainly has been fun for us. Prefaces to the previous two editions have had quotations from the famous mass spectromettist Mao Tse-Tung. As suggested by Drs. Roy W. King and Kain Sze Kwok, William Shakespeare also deserves citation, saying in Hamlet “Witness this army, of such mass and charge”. Perhaps he anticipated the new co-author's revisions in Chapter 8 with his words in Coriolanus: “Get you home, you fragments” Fred W. MeLafferty Trnaca, New York Frantiek Tureéek SEATTLE, WASHINGTON April 1992a Contents Preface to the Fourth Edition xi Acknowledgments xiii Glossary and Abbreviations xv 1 / Introduction 1 1 12 13 14 15 18 17 18 19 Appearance of the Mass Spectrum 1 Formation of the Mass Spectrum 4 Mass Analysis of lons 7 Jon Abundance Measurement 11 Sample Introduction Systems 14 Mixture Analysis 12 Molecular Structure Information 12 Standard Interpretation Procedure 13 General References 15 2/ Elemental Composition 19 24 22 23 24 25 26 27 28 Stable Isotopes; Classitication According to Natural Abundance 19 “A + 2" Elements: Oxygen, Silicon, Sultur, Chlorine, and Bromine 20 ‘A+ 1" Elements: Carbon and Nitrogen 23 ‘A Elements: Hydrogen, Fluorine, Phosphorus, and fodine 25 Rings plus Double Bonds 27 Exercises 28 Compositions of All Peaks Where Possible 30 Deducing Elemental Compositions 33 3] The Molecular ton 35 3A 32 33 34 35 36 a7 Requirements for the Molecular lon 36 Odd-Electron Ions 36 The Nitrogen Rule 37 Relative Importance of Peaks 38 Logical Neutral Losses 39 Molecular lon Abundance versus Structure 41 Typical Mass Spectra 414 | Basic Mechanisms of lon Fragmentation 51 4,1 Unimolecular ton Decompositions 52 42 Basic Factors that Influence lon Abundance 52 43. Reaction initiation at Radical or Charge Sites 54 44 Reaction Classifications 54 45. Sigma Bond Dissociation (a) 56 46 Radical-Site Initiation (2-Cleavage) $7 47 Charge-Site Initiation (Inductive Cleavage, i) 64 48 Decompositions of Cyclic Structures 68 49 Radical-Site Aearrangements 72 410 Charge-Site Rearrangements 78 4.11 Summary of Types of Reaction Mechanisms 83 5 / Postulation of Molecular Structures 85 5.1 General Appearance of the Spectrum 85 52 Low Mass lon Series 91 53 Small Neutral Losses 97 54 Characteristic ions 99 55. Postulating Possible Structures 100 56 Assignment of he Most Probable Structure 101 ry Techniques 103 61 Soft Ionization Methods 10 62 lonization of Large Molecules 105 63. Exact Mass Measurements (High Resolution) 109, 64 Tandem Mass Spectrometry (MS/MS) 108 65 Combined Techniques 112 66 The Shift Technique 112 67 Chemical Derivatives 114 68 General References 114 Contents 7 | Theory of Unimolecular ton Decompositions 115 7.1 Energy Deposition and Rate Functions 115, 72. Thermodynamic vs. Kinetic Etfects 117 73 Quasi-Equilibrium Theory 118 7.4 Derivation of PE) Functions 120 75 Calculation of K(E) Functions 125 7.6 Thermochemical Relationships and Potential Energy Surfaces 127 77 Examples 192 78 General References 134 8 / Detai 8.1 Unimolecular lon Decompositions 135 82 Product Stability 138 83° Steric Factors 151 led Mechanisms and lon Fragmentation 135Contents a4 as a6 ar 88 39 a0 a1 a2 9 / Mass Spectra of Common Compound CI 9a 92 93 94 95 86 97 98 99 9.10 oat a2 Reaction Initiation at Radical or Charge Sites 160 Reaction Classifications 165 ‘Sigma-Bond Dissociation (o) 169 Radical-Site initiation (o-Cleavage) 171 Charge-Site initiation (inductive Cleavage, /) 173 Decompositions of Cyclic Structures 179 Hydrogen Rearrangements 191 ‘Other Rearrangements 213 General References 221 25 Hydrocarbons 226 Alcohols 240 ‘Aldehydes and Ketones 246 Esters 251 Acids, Anhydrides, and Lactones 258 Ethers 260 Thiols and Sulfides 265 Amines 270 Amides 274 Nitrite and Nitro Compounds 276 Aliphatic Halides 278 Other Types of Compounds 280 10 / Computer Identification of Unknown Mass Spectra 263 104 102 103 104 105 ‘The Database of Reference El Mass Spectra 284 Retrieval: The Probability Based Matching System 264 Interpretation: The Selt-Training Interpretive and Retrieval System 287 Application of PBM and STIRS 290 General References 291 11 J Solutions to Unknowns 293 Bibliography 321 Appendix 339 Table A.1_Nuclidic Masses and Isotopic Abundances 399 Table A.2_ Natural Abundances of Combinations of Chlorine, Bromine, Silicon, and Sulfur 340 Table A3. Ionization Energy and Proton Affinity Values 949 Table A4 Molecular lon Abundances vs. Compound Type 348 Table AS Common Neutral Fragments 348 Table AS Common Fragment lons 351 Table A7 Common Elemental Compositions of Molecular, tons 385 Index 361Contents a4 as a6 ar 88 39 a0 a1 a2 9 / Mass Spectra of Common Compound CI 9a 92 93 94 95 86 97 98 99 9.10 oat a2 Reaction Initiation at Radical or Charge Sites 160 Reaction Classifications 165 ‘Sigma-Bond Dissociation (o) 169 Radical-Site initiation (o-Cleavage) 171 Charge-Site initiation (inductive Cleavage, /) 173 Decompositions of Cyclic Structures 179 Hydrogen Rearrangements 191 ‘Other Rearrangements 213 General References 221 25 Hydrocarbons 226 Alcohols 240 ‘Aldehydes and Ketones 246 Esters 251 Acids, Anhydrides, and Lactones 258 Ethers 260 Thiols and Sulfides 265 Amines 270 Amides 274 Nitrite and Nitro Compounds 276 Aliphatic Halides 278 Other Types of Compounds 280 10 / Computer Identification of Unknown Mass Spectra 263 104 102 103 104 105 ‘The Database of Reference El Mass Spectra 284 Retrieval: The Probability Based Matching System 264 Interpretation: The Selt-Training Interpretive and Retrieval System 287 Application of PBM and STIRS 290 General References 291 11 J Solutions to Unknowns 293 Bibliography 321 Appendix 339 Table A.1_Nuclidic Masses and Isotopic Abundances 399 Table A.2_ Natural Abundances of Combinations of Chlorine, Bromine, Silicon, and Sulfur 340 Table A3. Ionization Energy and Proton Affinity Values 949 Table A4 Molecular lon Abundances vs. Compound Type 348 Table AS Common Neutral Fragments 348 Table AS Common Fragment lons 351 Table A7 Common Elemental Compositions of Molecular, tons 385 Index 361A(iull arrow) ‘ifishhook) Ci] 2, alpha cleavage amu, AE “A” element + element “A+ 2" clement (A) peak (A +1) peak base peak B cA CAD Glossary and Abbreviations Radical cation, odd-el ctron ion (for example, CH. Transfer of an electron pair. Transfer of single electron. Relative abundance of the ion within the brackets. R § C,—¥; cleavage of a bond on an atom adjacent to the atom bearing the odd electron (but not the bond to the latter atom), Atomic mass unit, dalton. Appearance energy; formerly appearance potential Monoisotopic element (hydrogen is also considered. to be an “A” element), Element with an isotope whose mass is 1 amu above that of the most abundant isotope, but which is not an “A +2" element. Element with an isotope whose mass is 2 amu above that of the most abundant isotope. Peak whose main elemental formula is composed of only the most abundant isotopes. ‘The peak one mass unit above the A peak. Peak representing the most abundant ion in the spectrum Magnetic field strength; magnetic analyzer. Collisional activation, collisional excitation. Collisionally activated dissociation; also CID, collision induced dissociation Chemical ionization,xvi eyclization, re D(A-B) dalton daughter ion DI, desorption displacement, rd distonic radical ion climination, re EM" 4D") E EA EE*, even-electron EL EIEIO ev FAB FD, FI FTMS ccs hybrid MS/MS Ick 1E Reaction in which a cyclized product (either the ion or neutral) is formed, Dissociation energy of the A—B bond. ‘An atomic mass unit (!2C = 12 daltons; 1.66 «10% g) See product ion. Direct generation of ions from a condensed phase sample, Reaction in which cyclization to form a new bond at ‘a carbon (oF other) atom results in the loss of another group attached to that carbon atom. An ion" with separated radical and charge sites. Reaction in which cyclization to form a new bond between two parts of an ion results in the loss of the actual group connecting these parts. Critical energy for the reaction M* + D"’; also called activation energy, E, Ton internal energy required so that half of M* ions will decompose to yield D™ before leaving the ion source. Electrostatic analyzer. Electron alfinity. Ton in which the outer-shell electrons are fully paired; a “closed shell” ion. Electron ionization, Electron induced excitation in organics, Electron volt = 96.487 kJ/mol (06 keal/mol Fast atom bombardment Field desoption, ionization. Fourier-transform MS. A gas chromatograph interfaced to a mass spectrometer That utilizing two types of mass spectrometers, such as double-focusing and quadrupole instruments. Ton cyclotron resonance. Tonization energy; formerly ionization potential,int isobaric isotopic peak KE) LC/MS LD im, metastable M*, molecular ion (M—1y" Me MH* MI spectra mmu, millimass units Ms. MS/MS, MS" n-electrons nonisotopic peak NR xvii Inductive initiation of a reaction through electron withdrawal by the charge site. Relative intensity of a peak. Of the same nomi compositions. 1 mass but of different elemental Peak whose elemental composition contains an isotope not of the highest natural abundance. ‘The function describing the change in the rate constant, k, with change in the internal energy, E, of the precursor ion for a particular ion-decomposition reaction A liquid chromatograph interfaced to a mass spectrometer. Laser desorption for ionization of non-volatile samples. ‘The mass of the ion in daltons divided by its charge (usually unity), a Thomson; m/e has also been used, An ion decomposing between the ion source and detector of the mass spectrometer. The ionized molecule; “the molecular ion” is the peak representing the ionized molecule that contains only the isotopes of greatest natural abundance. The ion formed by the loss of one mass unit from Ne Methyl, CH, Protonated molecules, (M + H)* Mass spectra formed by metastable ion dissociations. 0,001 atomic mass unit; a millidalton. Mass spectrometry. MS done in tandem with multiple (n) mass analyzers; mass separated ions from one analyzer are dissociated or reacted to form new ions mass separated by the next analyzer. Nonbonding electrons. A peak whose elemental composition has only isotopes of highest natural abundance. Neutralization-reionization.xvill OE", odd-electron ion Pa PA Precursor, parent Product (daughter) jon PUE) PD Q 1, rearrangement r+db re,rd,re, rH RDA relative abundance 9, sigma-electron ionization reaction, Lees Leo simple cleavage sIM sims Thomson Vv Gowen a Ton in which an outer-shell electron is unpaired; a radical ion, Pascal (1 Pa = 0.0075 torr: 1 atm = 1.013 x 10* Pa). Proton al ity The decomposing ion in any reaction, The ion formed by dissociation of a precursor ion The distribution function deseribing the probability for particular values of internal energy of an ion. Plasma desorption ionization, such as that utilizing er Quadrupole analyzer. A reaction in which the molecular connectivity of the atoms in either the ionic or neutral product is not the same as that in the precursor ion, Number of rings plus double bonds. Rearrangements involving cyclization, displacement, elimination, and hydrogen transfer, respectively. Retro-Diels-Alder reaction. ‘The abundance of an ion relative to that of the most abundant ion in the spectrum (or, if so stated, relative 10 Lions) A simple cleavage reaction visualized as taking place through initial ionization at the sigma bond cleaved in the reaction, Total abundance of all ions in the spectrum, Total abundance of all ions in the spectrum of mass 40 and above. An ion-decomposition reaction which involves cleavage of only a single bond. Selected ion monitoring, Secondary ion mass spectrometry. ‘An m/z unit Volts; specific use, accelerating voltage ‘The number of charges on an ion ( used for this definition), ” was formerlyIntroduction 1.1 Appearance of the mass spectrum Learning how to identify a simple molecule from its electron-ionization (EI) ‘mass spectrum is much easier than from other types of spectra. The mass spec trum shows the mass of the molecule and the masses of pieces from it. Thus the chemist does not have to learn anything new—the approach is similar to an arithmetic brain-teaser. Try one and see. Unknown 1.1 tery Relative In the bar-graph form of a spectrum (as in that for Unknown 1.1), the abscissa indicates the mass (actually m/z, the ratio of mass to the number of charges on the ions employed), and the ordinate indicates the relative intensity. If you need a hint, remember that the atomic weights of hydrogen and oxygen are 1 and 16, respectively. Check your answer (the solutions to the unknowns are given in Chapter 11), 1Now try another simple spectrum, Unknown 1.2. Your structure will be correct if the molecule and its pieces have masses corresponding to those of the spectrum. (Make a serious attempt to solve each unknown before looking at the solution. This isa vital part of the book's instruction.) Unknown 1.2 esty fii. Relative Unknown 1.3 contains carbon, hydrogen, and oxygen atoms. Obviously the possibilities for arranging these in a molecule of molecular weight 32 are limited. Compare any molecular-structure possibilities with the major peaks of the spectrum, Unknown 1.3 100. 7 Relatve intensity me 2 The tabular data for Unknowns 1.1, 1.2, and 1.3 include additional low- abundance peaks that can be important (“Int.” is the peak intensity relative to the most intense peak as 100). The mass spectrometer has a dynamic range much greater than the three orders of magnitude shown; that is, jon abundances1.1 Appearance of he mess spectrum 3 ‘of «0.1% can be measured reproducibly. For the mass-spectral data of the unknowns in this book, a reproducibility of + 10% relative or +0.2 absolute, whichever is the greater, will be used. With modern instruments, such reproducibility is achievable with relatively small sample sizes and fast measurement times. Unknown 1.1 Unknown 1.2 mz Int mz im 1 10°; see Section 6.1), such as Fast Atom Bombardment (FAB; see Barber et al. 1982), can be made relatively “soft” to yield stable ionized molecular species. 1.3 Mass analysis of ions ‘The ion beam from the source can be separated according to the respective masses (actually m/z, the ratio of the mass to the number of charges, for which the term “Thomson” is also used) of the ions by a variety of techniques. Magnet- ic deflection, quadrupole filter, ion trap, time-of-flight, and cyclotron resonance are the separating techniques most commonly used in commercial mass spectrometers. Excellent detailed discussions of these methods are available in the general references, ‘Magnetic sector. The single-focusing (focusing for direction) mass spectrometer in Figure 1.4 uses a large potential difference (1 to 10 kV) between the ion- acceleration electrodes (Figure 1.3). Small potentials applied to the “repeller” and “ion-focus” electrodes are adjusted to maximize the ion current out of the source exit slit. This slit acts as the entrance focal point of the ion-optics system of the mass analyzer, allowing a diverging beam of entering ions of the same mass-to-charge ratio (m/z) to be focused on the analyzer exit slit ‘The magnetic field acts as the mass analyzer. The m/z value in Thomsons of the ions which can pass through the exit slit depends on the radius (r, em) of the ion path in the magnetic field, the field strength (B, gauss), and the ion- accelerating potential (V, volts) as defined by the fundamental equation (Beynon 1960)11 itoduation Tovacuum pure | Magnet collector Analyzer tube Figure 14, Single-focusing, magnetic sector mass spectrometer. iz = 482 « 10°. ay This can be derived on the basis that the ions of elementary charge ¢ (as distin- ‘guished from 2, the number of charges on the ion) have all been given the same kinetic energy eV = }mv” (but different velocities, ) in acceleration, and that the force exerted by the magnet, Bev, must be equal to the centrifugal force, mo*/r. Note that an ion of m/z = 100 would require 1x 10°* s to leave the ion source after formation (10-V repeller, 5 mm distance), and 1 x 10° s to travel 1 m after acceleration by 5 KV, For the mass analysis of such ions, the pressure is maintained at ~10~* Pa (75 x 10-7 torr), or 10°* atm, a mean free path (air) of ~70 m. Quadrupole mass filter and ion trap. Wolfgang Paul shared the 1989 Nobel Prize in Physics for his conception of this novel instrumentation. For the qua- 10° at m/z 100), and capabilities for ion- molecule reactions and tandem mass spectrometry (MS"). 14 lon-abundance measurement The positive ions striking the collector produce a flow of neutralizing electrons proportional to the ion abundance, and this current can be measured accurately and with great sensitivity by modern electronic techniques. Amplification of the ion signal by an electron multiplier can make possible the detection of a single ion arriving at the collector. Although the efficiency of ionization and transmis- sion in the mass spectrometer may yield only one ion at the collector for ~ 10° sample molecules introduced, useful spectra can be obtained from subnanogram samples, and specific detection of subpicogram (<10-!? g) samples is possible (Figure 1.2). Thus the method can be used in a variety of research and analytical problems for which most of the usual structural tools do not have sufficient sensitivity Changing the magnetic or electric fields that effect separation causes ions of different m/z values to teach the collector. On-line computer systems produce sets of mass and abundance values directly by measuring the field and ion ‘current corresponding to each peak. These systems can record complete mass spectra several times per second, which is especially valuable for GC/MS (see below). However, the scan rate affects the accuracy of ion-abundance measurement, which is important for deducing elemental compositions from isotope ratios: check the performance of your instrument with known samples to be sure you have not sacrificed this accuracy unnecessarily. 1.5 Sample-introduction systems For conventional El and Cl, the sample must be vaporized so that the molecules will be separated from each other before ionization. Direct introduction into the ion source is preferred for the study of compounds of low volatility; samples are inserted with a probe through a vacuum lock into the ion source,where they are vaporized by heating. With this system, one can obtain spec: tra of nonpolar molecules of molecular weight ~ 1000 in nanogram amounts. Warning: it is very easy to use too much sample in the direct-introduction system; one crystal that is just large enough to see should be sufficient. The heating rate should also be controlled carefully to avoid volatilizing the sample too rapidly. More volatile samples can be introduced through a reservoir system. A large excess of sample (~0.1 mg) is vaporized into an evacuated, heated reservoir, from which the sample flows through a small orifice (molecular leak) into the ion source at a nearly constant rate. This makes spectral measurements more reproducible, which is helpful for quantitative analysis of multicomponent systems as well as for matching of unknown and reference spectra. ‘The mass spectrometer can also be directly coupled to a gas chromatograph (GC/MS; sce Section 6.5) so that the eluted components go directly to the ion source, where their complete spectra are obtained “on the fly.” By “selected ion monitoring,” measuring two or more peaks sequentially, both high specificity and high sensitivity of detection can be achieved for compounds chosen in advance (Figure 1.2), Methods for interfacing to other separating devices, such fas the high-performance liquid chromatograph (LC/MS), have also been described (see Section 6.5). ‘The analytical mass spectrometer was introduced commercially in 1941. For two decades its main application was quantitative analysis of light hydrocarbon mixtures and similar samples, often with accuracies of 1% absolute, Such analyses depend directly on lincar superposition of the spectra of the compo- rents, in the same way that Beer's law governs spectrophotometric mixture analysis. The low-pressure conditions for electron ionization cause each mixture ‘component to contribute independently to the measured spectrum of the sample, so that the spectrum’s abundances can be reflected by a series of simultane- us equations using data from reference spectra of the pure components, Thus, if you can identify correctly one component of an unknown mixture spectrum, you can then subtract out the reference spectrum of that component (“spectrum Stripping”) and attempt to interpret the residual spectrum. Note, however, t spectral superposition will not necessarily be linear for CI and other spectra obtained at pressures high enough for competitive ion-molecule reactions. To- day, most MS mixture analysis utilizes combined instrumentation such as GCIMS (Karasek and Clement 1988; Evershed 1989; Catlow and Rose 1989). 1.7 Molecular structu Information ‘The main purpose of this book is to show how molecules can be structurally characterized from the masses of their ionized fragments. The EI mass spectrum1.8 Standard interpretation procedure 13 ‘of an average compound contains ~2°° bits of data, the mass and abundance values resulting from electron bombardment of the molecule. These data depend on the molecule’s structure; the interpretation process attempts to convert the spectral information into molecular-structure predictions which are as complete and reliable as possible. The 70-eV electron energies used are well above the ~ 10 + 3 eV required for the ionization of molecules. The sample pressure in the ionization chamber is kept low enough (below 10°? Pa) that secondary collisions of the ions with molecules or electrons will be negligible. The initial result of the electron interaction with the molecule is formation of the molecular ion by ejection of another electron. Part (sometimes all) of the molecular ions decompose further to yield the fragment ions of the spectrum. For example, the principal peaks in the spectrum of methanol (Unknown 1.3) are probably formed by the unimolecular processes in Equations 1.2: (CHOW + @ + CHOH" (rvz32) + 20" CHOHY +0H,0H* (avz3n) +H (12) 0H," tmz 18) +08 (CH.OH' + CHO® (e220) +H, The dot will be used to indicate a radical, so that the symbol" signifies a radical ion, Species containing such an unpaired electron are termed “odd-clectron” (OE); similarly, an ion with only paired electrons is an “even-electron” (EF) ion, Note in Equations 1.2 that only one ion can be formed in the unimolecular decomposition of an ion, and that a radical product (neutral or ionic) must be formed from an OE*" ion, It should be reemphasized that only unimolecular reactions are important in EI fragmentations; the sample pressure in the ion source is made low enough (o avoid reactions between ions and molecules. ‘When one is interpreting the EI mass spectrum, identification of the molecular ion (M*) establishes the molecular weight and often the elemental composition of the molecule. If no M* is present, soft ionization (Section 6.1) can often supply this information. The EI fragment ions indicate the pieces of which the molecule is composed, and the interpreter attempts to deduce how these pieces fit together in the original molecular structure. Spectra/structure correlations have now been published for a wide variety of complex molecules. 1.8 Standard interpretation procedure In the game of “twenty questions” the most efficient approach usually is to classify the unknown first between major categories, e.g., "Is the person male?" Molecular structure elucidation is similar, “blind alleys” can best be minimized“ 11 troduction if certain types of data in the spectrum are used before others. As a general approach, information is acquired efficiently in the following order: (a) Molecular weight, elemental composition, rings-plus-double-bonds; (b) Substructures; (c) Connectivities of substructures; (d) Postulated possible molecules, comparing each structure against all avail able data. Reference EI mass spectra of 220,000 different compounds are collected in MeLafferty and Stauffer 1992, ‘To learn to use the variety of information that is available in the mass spec trum, you should follow the outline of this book step by step in interpreting fan unknown spectrum. This “Standard Interpretation Procedure” is set forth inside the back cover in the form of a checklist to be used when you are interpreting an unknown, This is a general, simplified approach applicable to the “average” El mass spectrum, With experience the first several steps will be fast and largely automatic. While you are learning, however, each step should be done in this order, and your postulations, assignments, and conclusions from each step should be recorded, preferably on the spectrum. If more than one ‘explanation appears possible for a particular spectral feature, be sure to note all possibilities Other sample information. It is important to incorporate all other available structural information (chemical, spectral, sample history) into the interpreta~ tion wherever appropriate. When a sample is submitted by another research worker to the mass-spectrometer laboratory for analysis, it is surprising how often other pertinent information is not transmitted. One of the strongest reasons to have the researcher interpret the mass spectra of his or her own samples is the importance of this information, for which that person will have the broadest and most thorough understanding. This is also one of the main incentives for the preparation of the book: mass spectrometry should not be just for mass spectrometrists Obtaining a useful spectrum. The interpretation procedure of this book assumes, the unknown EI spectrum to be that of a pure compound, (If several compounds are present in the sample, the resulting spectrum will represent a linear superposition of the component spectra.) Even with good sample purity, care must be taken to avoid thermal of catalytic decomposition during introduction. Anom- alous peaks can also arise from “background” due to leaks, previous samples (“memory”), or chromatographic column bleed. A background spectrum taken just before or after the sample run should be subtracted from the sample spec- ‘trum; however, note that the presence of the sample can affect the desorption rate of the background material, Unless scan times must be minimized, the spectrum should be scanned from m/z 12, of at least m/z 26, to well above the5 expected molecular weight of the sample, and even further if nonbackground peaks still are found. (Data for the spectra in this book will generally start at m/z 12, since there is little useful information below that value in mass spectra of organic molecules.) Ifa soft ionization technique is available, use it to obtain an independent measurement of the molecular weight. tis imperative that the measured m/z values be correct (+ <0.5 mass units) Common background peaks, such as those of air (Unknown 1.4), can serve as internal standards. If there is any doubt, add an internal mass standard, such as perfluoroalkanes, C,Fz,+2, and take a second scan. With computerized data systems it is usually quite convenient to check the accuracy of mass assignments. The reproducibility of peak-intensity measurements should also be checked. A multi-Cl/Br compound such as CsCl, provides a convenient standard, since its isotopic abundances are accurately predictable (Chapter 2) ‘Multiply charged ions. Most peaks in a mass spectrum appear, conveniently, at integral mass numbers (for the exact mass differences, see Section 6.3). However, multiply charged ions can appear at fractional masses; for example, in Un- known 1.3 there is a peak at m/z 15.5 of 0.2% intensity, representing the doubly charged ions of mass 31 (see Chapter 6). 1.9 General references With amazing vision, Sir J.J. Thomson (1913) wrote: “There are many problems in chemistry which could be solved much better by this than by any other method”, There is now a large and fascinating literature that is highly recommended to the more broadly interested reader. Books. Beynon 1960; Beynon et al. 1968; Beynon and Brenton 1982; Biemann 1962; Bowers 1979, 1984; Buchanan 1987; Budzikiewicz et al. 1967; Burlingame 1970, 1985; Chapman 1986; Constantin et al. 1990; Davis and Frearson 1987; Dawson 1976; Delongh 1975; Duckworth et al. 1986; Facchetti 1985; Gaskell 1986; Gross 1978; Hamming and Foster 1972; Hill 1972; Howe et al. 1981; Karasek and Clement 1988; Kiser 1965; Lehman and Bursey 1976; Levsen 1978; ‘Maccoll 1972; March 1989; Marshall 1990; McCloskey 1990; McDowell 1963; McEwen and Larsen 1990; McLafferty 1963, 1983; McLafferty and Stauffer 1989, 1991; MeLafferty and Venkataraghavan 1982; Middleditch 1979; Millard 1978; Milne 1971; Porter 1985; Rose and Johnstone 1982; Seibl 1970; Spiteller 1966; Suelter and Watson 1990; Waller 1972; Waller and Dermer 1980; Watson. 1985; White 1986; Wright and Wood 1986; Yinon 1987; Zaretskii 1976. Journals and serials. Organic Mass Spectrometry, Wiley (Chichester, England): International Journal of Mass Spectrometry and Ion Processes, Elsevier (Amster16 11 itoauetion dam); Biological Mass Spectrometry (formerly Biomedical and Environmental Mass Spectrometry), Wiley (Chichester, England), Mass Spectrometry Reviews, Wiley (New York); Rapid Communications in Mass Spectrometry, Wiley (Chi- chester, England); Journal of the American Society for Mass Spectrometry, Elsevier (New York); Mass Spectroscopy, The Mass Spectroscopy Society of Japan (Tokyo); Mass Spectrometry Bulletin, Royal Society of Chemistry (Cam- bridge, England); Burlingame et al. 1980-1992, “Biennial Reviews of Mass Spec- trometry,” in Analytical Chemistry; Specialist Periodical Reports: Mass Spectro- metry, Royal Society of Chemistry (Cambridge, England), Vols. 1-10; Chemical Abstracts Selects: Mass Spectrometry, Chemical Abstracts Service (Columbus, OW). Before continuing to Chapter 2, try Unknowns 1.6 to 1.9, again ignoring the small peaks adjacent to large ones. Wait until you are really “stuck” before turning to Chapter 11 for help. Unknown, mz Int 100 rat) q 336 2 et 3 Bos a % 100 5 a zg Unknown 1.7 men 100 var eT 100 es iHE i 4 oe bs ae 3 te i aa s toh ae i oe ts aaa 3 ae : as 22 Elemental Composition A first key piece of information for identifying an unknown compound is its molecular formula, the number of each of its constituent clements. The method of choice for this is usually mass spectrometry. Its most powerful technique for this uses exact mass measurement with a high-resolution mass spectrometer; measurement of the mass of a peak with sufficient accuracy defines its elemental composition unequivocally (Section 6.3). However, even with instrumentation of unit-mass resolution the presence of isotopes of known natural abundance ‘makes possible a useful and simple method for deducing the elemental composition of many ions. The presence of a less-abundant isotope gives the “isotopic peaks” that you were told to ignore as anomalous in solving the unknowns of ‘Chapter I. Even if you have high-resolution information on elemental compositions available to you, it is important to understand thoroughly the use of isotopic abundances, which is basie to an understanding of mass spectra and of experiments that use labeling with stable isotopes. Finally, the elemental composition is also important information for the fragment peaks of the mass spectrum: so you should attempt (o identify the elements making up each peak of the ‘mass spectrum wherever possible. 2.1 Stable isotopes: lassitication according to natural abundances A chemically pure organic compound will give a mixture of mass spectra because the elements that compose it are not isotopically pure. Recall the case of the element neon, which Sir J. J, Thomson (1913) showed gave not one peak at its chemical atomic weight of 20.2, but two peaks at masses 20.0 and 22.0, in relative abundances of 10:1. Of the common elements encountered in organic compounds (shown in Table 2.1, inside the front cover), many have more than one isotope of appreciable natural abundance. The isotopic abundances of other 920 2 etementl Composton elements are shown in Table A.1 (in the Appendix): however, this book covers the mass spectra only of compounds containing the eleven elements of Table 2.1 — miz Int. 100- * 2 The effect of isotopes on a mass spectrum is illustrated in Unknown 2.1, which contains molecular ions at m/z 36 and 38. Their characteristic isotopic ratio of 3:1 should make the element easily recognizable from the data of Table 2.1, Note that the interpretation of m/z 36 as a fragment ion (loss of two H) from m/z 38 would be totally misleading. It is highly important that you become familiar with the data of Table 2.1. Note that the isotope of lowest mass is the ‘most abundant for all these elements, quite fortunately. Note also that the isotopic abundances of the elements can be classified into three general categories: ‘A.” those elements with only one natural isotope in appreciable abundance; ‘A+ 1,” those elements that have two isotopes, the second of which is one mass unit heavier than the most abundant isotope; and “A + 2.” those elements that have an isotope that is two mass units heavier than the most abundant isotope. The “A + 2° elements are the easiest to recognize; so you should look for these first. We will use a similar classification for mass-spectral peaks: an A peak is one whose main elemental formula is composed of only the most abundant isotopes its (A + 1) peak is the peak one mass unit higher; and so forth. 22 “A42 xygen, silicon, sultur, chlorine, and bromine A second isotope makes an especially prominent appearance in the spectrum if it is more than one unit higher in mass than the most abundant isotopic species. Bromine and chlorine, and to a lesser extent silicon and sulfur, are striking common examples. The presence of these elements in an ion is often easily recognized from the “isotopic clusters” produced in the spectrum. Thus elements of Unknowns 2.2 and 2.3, like Unknown 2.1, can be recognized from the22 "A 4.2" element: oxygen, icon sul, horned bromine a characteristic isotopic ratio of the ions separated by two mass units. (For now, ignore the small peaks next to the large ones.) An initial inspection of the bar graph is often an easy way to identify such isotopic clusters. For simplification, ‘only the molecular ion data are included. Linear superposition of isotopic patterns. If there is more than one atom of these elements present in the molecule, the result is even more striking. For hydrogen bromide the isotopic molecular ions at m/z 80 and 82 (H7°Br and H®"Br) are in the relative proportions of roughly 1:1. The mass spectrum of Br shows prominent molecular ions at masses 158, 160, and 162, of relative abundances 1:2:1 due to the ions ”Br,, "?Br*'Br and *"Br”Br, and * Bra, respectively. In a similar fashion, any ion structure containing three bromine atoms will exhibit four peaks at intervals of two mass units in the ratio 1:3:3:1, and the 3:1 isotopic ratio of *°C1/?"Cl yields three peaks in the ratio 9:6:1 for ion species containing two chlorine atoms (see Figure 2.1. Unknown 2.2 mie 100 96 100. 1 oy = 38 96. z 74a i q Unknown 23, mz Int 104 4100, al 6 09 2 @ 80 al a2 2 1 Bement Compeation er, Br cl, (100) 97 100 100 x1.00 x1.00 x1.00 st] p49 32 100197 100 x097 x097 sr] yao x02 100 - 2 i100 100 97 ai“ se 100 sr | 49 64 34 92 yo Figure 2:1. Linear superposition of bromine and chlorine peak patterns, The characteristic patterns resulting from combinations of the chlorine, bromine, sulfur, and silicon isotopes are illustrated by Table 2.3 (inside front cover), arranged in increasing order of the relative abundances of (A + 2) and (A + 4). Numerical values for combinations of “A + 2° elements are given in Table A.2. These were calculated from the binomial expansion (a +b)" = a" + na"*b + n(n = 1)a"~262/2! + n(n — 1) ~ 2)a"~65/(31) + ---. Thus for the peaks containing four chlorine atoms, the intensity of the (A + 4) relative to A should be 4-3-17-0327/2 = 0614 Osygen and abundance accuracies. The (A + 2) relative abundance of oxygen is very low (0.2%), and thus high abundance accuracy is necessary to deduce the number of oxygen atoms (for example, Unknown 2.3). For the unknowns in this book, a possible relative error of + 10% or absolute error of +0.2 (on the scale that the abundance of the highest peak = 100), whichever is greater, in the value of (A + n)J/[A] will be assumed, resulting in an uncertainty of =O, in caleu- lating the number of oxygens in the highest peak. Further, there often is a substantial probability that several atoms of the “A + 1" element carbon are present, producing a small contribution to the (A + 2) peak: so it is usually necessary to calculate the number of oxygen atoms after the “A + 1” elements as well as the other “A + 2” elements have been identified Absence of “A + 2” elements. The value of “negative information” should not be overlooked. Another reason for checking first for the presence of “A + 2" elements is that one often finds them to be absent. Consider any peak A (frag-23°°A+ 1 element: carbon and nitrogen 23 ment ion as well as M™) in a mass spectrum and the peak two mass units higher [the (A + 2) peak]; if [(A + 2)VI[A] < 3%, the peak A cannot contain the most abundant isotope of the elements Si, S, Cl, or Br (if A contains more than cone ion formula, this ratio determines the proportion of ions free of these elements). Table 2.1 (inside front cover) shows that if peak A contains one **Si atom, [(A + 2)]/[A] > 3.4%, because in nature 3.4 *°Si atoms must be found with every 100 atoms of **Si. The ratio [(A + 2)]/LA] can be greater than 3.47% if ions of some other composition also contribute to the (A + 2) peak 2.3 “A +1" elements: carbon and nitrogen The three “A +1” elements in Table 2.1 are hydrogen, carbon, and nitrogen, but the ?H/'H ratio is so low that we shall consider hydrogen to be an “A” element. Each element exhibits its isotopic abundances independently; thus the carbon atom in the CH,Br molecule of Unknown 2.2 contributes 1.1% of the intensity of the m/z 94 peak (!2CH,”°Br*) to the m/z 95 peak (?°CH,”*Br’), and of the m/z 96 ()7CH,"*Br*) to the 97 (!°CH,"*Br*). Unknown 2.3, which contains no “A + 1° elements, shows [m/z 65]/[m/z 64] close to that expected for cone carbon (but actually due to °S'°0,” and 1?8°O'0*}; that gives us another reason why “A + 2” elements should be identified first. Increasing the number of carbon atoms in an ion increases the probability that one of these atoms will be a °C isotope; [(A + LA] for a Cg ion will thus exhibit ten times the probability of C,, or 10 x 1.1% = 11%. This fact provides a way to deduce the number of carbon atoms, which is obviously of key importance in interpreting the spectra of organic compounds. [At this stage, do not worry about detecting nitrogen as an “A + 1” element; the “nitrogen rule” in Section 3.3 will be helpful for this.] Table 2.2 (inside the front cover) tabulates the probability that an ion of a specified number of !?C atoms will contain one '°C atom. The factor of 1.1% per carbon atom varies slightly (~2% relative) with the organic source, such as petroleum (low value) versus a contem- porary plant source; we will ignore the small contribution of deuterium from the usual hydrogen content of the ion. [The 1.1% is equivalent to C/!2C = 1.087% with 1.5 H atoms per C atom; +0.5 H/C changes the intensity of (A + 1) by only £0.7% ofits value, (A + 2) by + 1.5% of its value,} In Unknown 24, calculate (after checking for “A + 2° elements] the maximum number of carbon atoms in the ions of m/z 43 and 58, The results indicate that m/z 43 peak is formed from the m/z 58 by the loss of what group? Note that many small peaks in Unknown 2.4 were relatively unimportant for deriving its structure, such as peaks which can be formed from abundant peaks by the loss of hydrogen or which represent doubly charged ions. In other unknowns of this book, unimportant peaks will often be omitted. For Unknown 2.5, find the elemental formula of the molecular ion; this is the largest (“base”) peak in the spectrum, indicating high stability,26 2 Elemertat Compostion Unknown 2.4 met mei eos «16 \ 3 03 a a. ie fo et 88 ®t 2 08. “33 2 sb 03 2 oat ofa * es on ote g » ox x 0 3 as “on 08 é oe SOF * a ot Bota te “ta (08 Ho = on = OF mee = 4a ugeeead = 18 =o so & os ninown 25 mit mm 02 = 08 a ” bbe & 02 eee oe 40 & on on = 20 i os & oe 2 82 eta E ol ets Bt 2°] & 08 m0 3 wy 88 me é s e 2 9a | * a Oe regen 5 2 ® » i 0 st 19. 19 68 mm « o i 2% f 02 Double C-13. The Unknown 2.5 spectrum also contains a minor, but important, peak at m/z 80 of 0.2%, intensity. Assigning this as the "*O contribution of one £80 atom in m/z 78 would mean that the latter contains no more than five carbon atoms, whereas the m/z 79 abundance indicates six. The peak at m/z 80 actually arises from C,H" ions containing two 'C atoms and four C atoms. The abundance of such (A + 2)* ions relative to the A* ion depends on the number of carbon atoms, just as ((A + 1)" J/[A"] does: these abundances are also tabulated in Table 2.2, Of course, (A + 2)* isotopic contributions can also arise from “A + 2” elements. After one has assigned the number of carbon and nitrogen atoms from24 "A" elements: hydrogen, Cuorne, phosphors, end odine 25 the (A + 1)* abundance value, the (A + 2)* value must be rechecked for the detection of oxygen; although the '*O/!%O value of 0.2% is small, the abundance accuracies assumed in this book (the greater of +0.2 absolute or + 10% relative) usually allow one to calculate the oxygen to within +1 atoms for the base peak. If infrared or NMR spectra of the unknown are available, these can provide definitive evidence for the presence of specific oxygen functionalities. For Unknown 2.6, deduce the elemental compositions of the m/z 72 and 55 peaks; do these suggest its molecular structure? —— ™ = 7 Bs 2 | ire “ts E alts i ne é e ae . aot a & 2 8s ei Bb & fs & ete be mG wo Bs mos wydrogen, fluorine, phosphorus, and Iodine After the number of each “A + 2° and “A + 1” element has been fixed (or estimated, depending on the experimental accuracy), the balance of the mass of the peak must be due to the monoisotopic “A” elements. The assignment of the total elemental composition (or of the several possible compositions) is then com- pleted by using numbers of these elements consistent with rules of bonding. Illustrating this with the previous spectra, the base peak at m/z 36 of Un- known 2.1 must contain one chlorine, based on the abundance of its A + 2. Subtracting the mass of chlorine, 35, from the mass of this peak, 36, leaves a difference of one, which of course must arise from the presence of one hydro- zen. The m/z 94 peak for Unknown 2.2 contains one bromine and one carbon;26 21 Elemental Composition 94 — 79 — 12 = 3, so the elemental composition of the base peak is CHBr. For Unknown 2.3, the m/z 64 peak was assigned the elements SO,: 32 + (2 x 16) = 64, so there are no “A” elements. For Unknown 2,4, the m/z 43 and 58 peaks contained C, and C,, respectively; thus 43 — 36 and 58 — 48 indicate the ‘number of hydrogen atoms in each. Note that only hydrogen atoms can be used to account for this difference until the value is as large as 19, the mass of fluorine. Additionally, the number of hydrogens can often be inferred from the proton NMR spectrum, and the minimum number of carbon atoms from the C-13 NMR spectrum. Try this partial spectrum representing a single fragment ion: ver 10. 1 00 1m 00 No “A +2" or “A+ I” elements are possible. All the “A” elements but phosphorus are monovalent; so this grouping must be due to a single monovalent (A) element (which?), or a pair, or a combination of these with phosphorus (thus H,P, is a conceivable assignment). The fragment ions of two further examples involve the same masses: mz int. 100.100, m 11 00 700 a0 What is the maximum number of “A + 2° elements? Of“A + 1” elements? For the data in the first column, the presence of one carbon should be an obvious possibility: did you think of N,? Compositions that satisfy the data are CF, and PF, Try these procedures with Unknowns 2.7 and 28aa Pe) i uo : 2 100 » soe 2 ao " | Unknown 28 mein 2 08 a ® 19 02 i eet 30 ] mu 10 g as 17 2 4 85 08 34 a 0s g 83 @ & 03 6 100, m2 & 18 s ‘02 7 58 mo? 1002 2.5 Rings plus double bonds Because of the valences ofthe elements involved, the total number of rings and double bonds in a molecule ofthe formula C,H,N,O, will be equal to x — Sy + 42+ 1 (Pellegrin 1983). For ions, the calculated value may end in “}” (indicating in “even-electron ion,” Section 3.2), and this fraction should be subtracted to obtain the true value, How to use this should be more obvious from inspection of the examples in Box 2.1. The valve 4 found for pyridine represents the ring and three double bonds of this molecule The 5.5 caleulated for the benzoyl ion represents the rng, the three double bonds of benzene, and the double bond of28 2 / Elemental Compostion Box 2.1. Rings plus Double Bonds (r + db) For the general formula C.HN,O, {more general case (110, where =H, F, Cl, Br =O, 8: l=N, P; and IV=C, Si, ete) Total rings plus double bonds =x ~ y+ }z+1 For an even-electron in (see Section 3.2), the true value will be followed by "! Examples: HIN: rings plus double bonds = 5-25 405+1=4 For example, pyridine’ (ode-electron) 6,H,0: rings plus double bonds =7~ 25+ 1=55 For example, C,H,CO™, benzoyl (ever-electron) the carbonyl group. Calculate the number of rings and double bonds for the ‘empirical formulas that you found for m/z 43 and 58 in Unknown 24 Ifother elements are present, these are counted as additional atoms of the element C, H, N, or O to which they correspond in valence. Thus, the number of silicon atoms should be added to the number of carbon atoms, the number of halogen atoms to the number of hydrogen atoms, and the number of phosphorus atoms to the number of nitrogen atoms. Note also that this is based on the lowest valence state of the elements and does not count double bonds formed to elements in higher valence states. Thus, the formula indicates one double bond in CH,NO; (nitromethane), no double bonds in CHjSO;CH, (dimethylsulfone), and a negative value, —0.5, in HyO*. Such a negative value should be noted, because it arises from rearrangement or chemical ionization, Values more negative than this are not possible, and so must be due to incorrect assignment of elemental composition or incorrect calculation of rings plus double bonds. 26 Exercises Extensive experience has shown that practice is necessary to develop one’s ability to calculate elemental compositions from isotopic abundances. (Perhaps this is because the chemist must become accustomed to the fact that the mass spectrum shows his/her carefully purified compound to be a mixture of isotopically different molecules.) It is important that you understand this procedure, since it is the key primary step in interpreting an unknown spectrum. To avoid confu- sion, follow the stepwise procedure below while you are learning. Table 23 illustrates this procedure with data from the M* region of the spectrum of tert-butyithiophene, CyH, 28. Note that this is not done for the m/z 140 abundance, because the ++ 10% accuracy in abundance is relative to the abundance of that peak, (i) Insert the expected experimental accuracies on the original data, in the “Intensity” column (not on the normalized data of Step ii.Table 2.3. The M" region of the spectrum of ter-butyithiophene. 2 RAT mein pees he ee a 1905 2 2 Es 100. 100, 100. 100,100, 00 254025 10 410 o8 00 88 99 88 4 j2:02 48208 «44.0203 or1s02 oa 408 04 (ii) Normalize all data (including experimental accuracies) of the peak group; ie, multiply all by the factor needed to set [A] equal to 100% (iii) Find all possible “A + 2” elements (the value for oxygen will not be accurate), and show their expected abundance contributions in separate columns (S, and O, in the example; actually, at this stage up to three ‘oxygens can be considered). (iv) Above the clement symbols place their mass values, (o guard against the ‘mass total becoming too high. Assign the possible number of carbons, showing these in similar columns. Subtraction of the *'S contribution to m/z 141 places the carbon-isotope contribution in the range 8.2 to 10.2%, leading to C, and Cy as possibilities. However, S, and C, total 140 mass units, equal to that of peak A; CS is a highly unlikely ion formula, making C, the favored assignment, The column headed A + I, S, shows that every 8.8 ions of "7C;°C%S ‘will be accompanied by 4.4% x 88 = 0.4 ions of 'C,'3C™S, predicting ‘a corresponding contribution to m/z 143. (vi) Assign the (A) elements by difference. The postulated C,S formula accounts for 96 + 32 = 128 of the 140 mass units of peak A; H,2 is the obvious choice for the remainder. o Using this procedure, can you assign compositions and values for rings plus double bonds to the fragmentary spectra shown in Unknowns 2.9 through 2.147 The peaks of Unknowns 2.9, 2.10, and 2.12-2.14 contain the molecular ion (M™); peaks in Unknown 2.11 arise by loss from Mas indicated. None of Unknown 2.9 Unknown 2.10 men mz int 10 10 rae! 120 8 332100 7% 41 88 7% 0. 14 or a] “eo me <0430 2 / Elemental Composition Unknown 2.11 Unknown 2.12 mz int me Int 09 we 22 8540. (Mm 10)" 014 820 wo 74 a 13 126 3% 00 18S —_____—_— 06 Unknown 2:13 Unknown 2.14 ment men rieeeatact 1% 00 1298. m0 7367 130100, 174100. m8 7% 65 13298 1608 m2 eee m2, 43017 re 1700 these contain nitrogen; its identification is discussed in Chapter 3. Unknown 2.10 contains a measurement of higher absolute accuracy than the stated ++0.2. 2.7 Compositions of all peaks where possible For the pieces of the molecule displayed in its mass spectrum, knowledge of the elemental composition, as well as the mass, is also very valuable in structural clucidation. Even without exact mass measurement, one can often restrict the possibilities for elemental-composition assignment for important peaks by using isotopic-abundance data, Here the chief difficulty is that the abundance mea sured at a particular mass value can actually represent contributions from more than one elemental composition. Such interferences are possible even for isotopic peaks of molecular ions. ‘Maximum number of atoms of the element. In calculating the elemental composition of a peak A above, we assumed that the only contributions to the (A + 1) and (A +2) peaks were from the less-abundant isotopes of the elements in A. However, this is not necessarily true; there could be important additional contributions to the (A + 1) and (A + 2) peaks (and, occasionally, to peak A) for which corrections must be made. For the (A + I) and (A + 2) peaks, these could227 Compeaitions of ll peaks where pose a arise from other fragment ions (or impurities, background, or ion-molecule reactions); for the (A + 1) peak these could also arise from heavy isotope contributions of “A + 2” elements, such as from the (A — 1) peak. Without such corrections, the calculations thus give the maximum number of atoms of each type in the elemental composition. Interference from other fragment ions. In Unknown 2.4 calculating the number ‘of carbon atoms of mjz 41 from the relative abundance of ions in m/z 42 gives a ridiculously high number of carbon atoms; [42*}/[41*] = 12/27 = 44%, corresponding to 40 carbon atoms in Table 22. Although this is correct for the maximum number of C atoms, itis hardly a helpful calculation; the reason for this value is that most of the m/z 42 peak arises from '?C,!H,” , another fragment ion that contains only the most abundant isotopes. This peak is part of a group of peaks, each separated from its neighbor by one mass unit, of the formulas C,Hp.7. Unknown 2.4, which is the spectrum of butane, CgHo, has several other peak groups which correspond to the fragment ions C;Ho-3. C,H... and C4Ho-o- The only (A) peaks for which the corresponding (A + 1) and (A + 2) peaks do not contain interfering fragment ions are m/z 15, 29, 43, and 58, corresponding to CH,*, C,Hs*, CsH,", and C,H" Thus the most useful isotopic-abundance calculations are generally those that use the significant peaks which are at the high-mass end of peak groups. ‘Can you deduce the elemental compositions of any other ions in Unknowns 25 and 26? Interference from “A + 2” elements of lower-mass peaks. The full mass spectrum of methyl bromide (Unknown 2.2) also contains fragment ions from the loss of H atoms: CBr*, 3% CHBr*, 2%; and CH,Br*, 4% (with CHBr*, 100%). The resulting mass spectrum is a linear superposition of these ion contributions (see Figure 2.2). Each species must give a 1:1 pair of 7°Br, *'Br peaks, and there must be a 1:1% "°C peak for each '2C peak. Starting with the m/z 91 C”Br* species, its presence demands a similar intensity at m/z 93. Similarly, the CH*Br* peak at m/z 92 demands an equal-intensity peak at m/z 94. Now, in evaluating the contribution of CH,”°Br* and CH,”°Br* at masses 93 and 94, ‘one must first subtract the contribution of the *'Br isotope of the lower-mass species; so one finds a 4% (not 7%) contribution from CH,°"Br* at m/z 95. This figure must then be subtracted from the measured intensity value to estimate the ‘amount due to the "°C contribution from m/z 94. However, it is much simpler (and here more accurate) to calculate the “A + 1” elements from the [m/z 97]/ [m/z 96] ratio, since m/z 94 and 96 must contain the same number of carbon atoms, Because the lower-mass fragment ions cannot contribute to this (A + 1) peaks, the [(A + 1)/LA] ratio of 1.1% correctly indicates the presence of one carbon atom. Again, the most useful isotopic calculations generally are those that use the significant peaks at the high-mass end of peak groups. Here a peak's significance is determined by the intensity values accuracy of the peak32 2 1 tamanial Composition o cHer 2 2 a ow [ff Fe _ | e i . 0 (MoH ea os | 08 °7'02 1.0 100 96 w 31 2z | 22 | 07 99 007 100 98 Spectrum ao] st] ae 2 L_L1z 24 007 Figure 23. Isotopic peaks inthe spec mz 130 132 138 136 trum of CHCl, (Unknown 2.14),2 Doducng elemental compositions 33 ncessary for the calculation. In Unknown 2.14 the needed m/z 137 peak has an intensity of 0.0 + 0.2%, so that [m/z 137|/[m/z 136] = <6% or 0-5 carbon atoms. If you cannot sort out the overlapping isotopic contributions, see the breakdown in Figure 2.3 Insummary, ifn “A + 2” elements are present, the (A + 1) peak Land possibly other (A + 2n + 1) peaks] will contain isotopic contributions from the (A — 1) peak [and possibly other (A —2n— 1) peaks]. In calculating the number of carbon atoms by using [(A + 1)]/[A], one should correct for such isotopic interferences. Alternatively, use [(A + 2n+ DCA + 2n)] corresponding to the ks of highest mass, since the (A ~ 1) peak cannot make an isotopic contribution to these Erroneously low values for an element. Occasionally a significant proportion of the peak A intensity will be due to the isotopic contribution of an “A+ 1” clement in the (A — 1) peak, or an “A +2” element in the (A — 2) peak. For example, the spectrum of butylbenzene shows the group of peaks: mnt er 100, 25s, 3 39 oon The ratio [m/z 93]/{[m/z 92] = 7.1%, equivalent to 6.4 carbon atoms, although 92 is mainly C,Hg”. Actually, 7.7% of m/z 92 and 0.25%, of 93 are due to 2C,8CH," and 2C,!°C,H,*, respectively; thus CCH," = 3.65% and 12C}H,” = 47.3%, and their ratio is 7.7% as expected for seven carbons. 2.8 Deducing elemental compositions [Above we derived peak intensities in the methyl bromide spectrum from knowledge of abundances of particular ion compositions; however, for an unknown spectrum we face the opposite problem. The suggestions that follow should increase your efficiency in arriving at all reasonable solutions to such a problem. 1. Highest mass peaks. Use first those peaks which should yield composition assignments of high accuracy as well as high utility. The least isotopic contamination to the (A), (A + 1}, etc., peaks should be found in the peak group (compositions differing only in numbers of hydrogens) of highest mass (especially if it contains M”). Further, for any particular peak group, the high-mass peaks should contain the least isotopic contamination,a 21 Elemental Compoctton 2. Highest intensity peaks. Within these limits, the accuracy of elemental composition calculations obviously should improve with increasing peak intensity. 4. Selection of the A peak. "The desired (A) peak of the peak group is the one of highest mass which contains only the most abundant isotopes (such as '7C, '°O, 35C i is also called the “nonisotopic” peak. As the first candidate for A, try the largest peak in the group; if the second largest is at a mass higher than (A + 2), try it instead as peak A [note in Table 2.3 the rarity of base peaks for assignments above (A + 2) peaks]. Next, if [(A — 2)]/LA] > 30% check the possible C\/Br isotopic patterns (Tables 2.3 and A.2) to see if these are isotopic peaks of the same elemental formula. For example, the largest peak of the Br, isotopic cluster is actually the (A + 4) peak. Here a useful correlation is the fact that the {M —2)* is usually much less abundant than either M" or (M— 1)*; occa~ sionally, however, (M-— 1)" is more abundant than M". Next, calculate the possible elemental compositions for this (A) peak; if an assignment cannot be found that accounts for the intensities of the higher-mass peaks within experimental crror, at least one of these must contain nonisotopic ions, and thus should be used as peak A. As an example, try the m/z 91-94 data from the butylbenzene spectrum on the previous page. Because m/z 91 cannot contain more than seven carbon atoms, no elemental composition for this (A) peak can account for the abundance of mj: 92; it thus must be used as peak A 4. Other (A) peaks. See if useful information on clemental compositions can be obtained from lower mass peaks in each group of peaks differing by one mass ‘uit. It is possible that their compositions differ by more than just the number of hydrogen atoms. Even “negative information” (Section 2.2) can be helpful 5. Consistency of composition assignments. Another reason to deduce the ele: ‘mental composition of all peaks where possible is to check these for internal consistency. The elemental composition of M* if present) gives the maximum umber of each element that can be found in any lower-mass peak. Similarly, the fragment ion compositions will usually show some mutual consistencis these to infer the more probable composition(s) if more than one agrees within experimental error. Common differences found between the compositions of ‘molecular and fragment ions are given in Table A.5 and are discussed in Section 3.5. Common structural assignments for fragment ions are given in Table A.6 {see Section 5.2). Table A.7 gives compositional assignments for molecular ions containing the eleven common elements; use this to check if you have considered all possibilities.3 The Molecular lon ‘The molecular ion, M"’, provides the most valuable information in the mass spectrum; its mass and elemental composition show the molecular boundaries into which the structural fragments indicated in the mass spectrum must be fitted. Unfortunately, for some types of compounds the molecular ion is not sufficiently stable to be found in appreciable abundance in the El spectrum, ‘An increasingly large proportion of mass-spectrometry facilities also have a “soft ionization” technique such as chemical ionization or fast-atom bombardment (CI or FAB, Chapter 6) available, Such data should be used for molecular- ‘weight assignment wherever possible. However, even with evidence from soft ionization, the unknown spectrum should still be examined as described in this chapter, since this should lead to useful structure information as well as verifica- tion of the M* assignment. By convention, mass spectrometrists calculate the molecular weight (m/z of, “the” molecular-ion peak) in terms of the mass of the most-abundant isotope of ‘each of the elements present. For benzene (CH), which has substantial m/z 79 and m/z 80 peaks, the molecular ion is considered to be at mass 78 (C = 12, H = 1). M* for the molecule Br, is considered to be 158, twice the mass of the rmost-abundant isotope, "Br, although in the mass spectrum of Br, the most- abundant ion is at m/z 160 (Section 2.2). Within these constraints, in the EI mass spectrum of a pure compound the molecular ion, ifpresent, must be found at the highest value of m/z in the spectrum. There are further tests which must be used to ascertain if this peak does not represent the molecular ion, although these tests cannot demonstrate the converse.36 11 The Moleoutar on 3.4. Requirements for the molecular ion The following are necessary, but not sufficient, requirements for the molecular jon in the mass spectrum of a pure sample, free of extraneous peaks such as those from background and ion-molecule reactions. 1. It must be the ion of highest mass in the spectrum. 2. It must be an odd-electron ion (Section 3.2). 3. It must be capable of yielding the important ions in the high-mass region ‘of the spectrum by loss of logical neutral species (Section 3.5). If the ion in question fails any of these tests, it cannot be the molecular ion; if it passes all these tests, it may or may not be the molecular ion. 3.2 Odd-electron tons For EI spectra, the sample molecule becomes ionized by losing an electron, leaving one electron unpaired, and therefore the molecular ion is a radical species. Such an ion, either molecular or fragment, with an unpaired electron is called an “odd-electron” (OE) ion, and is designated by the symbol”. It is often useful and convenient in explaining and classifying ion-decomposition reactions to distinguish between such radical ions and “even-electron” (EE) ions, those in which the outer-shell electrons are fully paired; the symbol * will be used only to refer to even-electron ions. ‘This concept can be visualized in its simplest form with structures (Equations 3.1 to 33) that include the outer-shell electrons. The ease of, aGen — a8: GB) ClCH, —+ HCHCH, or HyO=CH,” (62) or cH 63) ionization of these electrons is generally in the order n> x > 0 (Chapter 4). Usually several canonical resonance forms can be drawn to approximate the clectron distribution in the ion. Note that the symbolism*” is meant to indicate only an ion with an unpaired electron, not an electron in addition to those the formula represents; adding an electron to CH, would give the negative ion, cay Paralleling their neutral counterparts, ions containing only paired electrons (EE*) are generally more stable, and thus are more often the abundant fragment ions in EI mass spectra. For example, cleavage of a C—H bond in CH," forms23 The nrogen rule 7 the stable EE* ion CH,* and H-. Further, soft ionization methods such as chemical ionization and fast-atom bombardment tend to give EE* molecular ion species such as MH”, resulting in the much smaller degree of fragmentation found in such spectra. if you can establish the elemental composition for the proposed molecular jon, the tings-plus-double-bonds formula will show immediately i the fon is an codd- or even-clectron species. For the gencral formula C,H,N,O,, the value of x —Jy-# $2 + L will bea whole number for any odd-electron ion, and end in $ for an even-electron ion. Examples are given in Box 2.1 3.3 The nitrogen rule For most clements encountered in organic compounds, there is a fortunate correspondence between the mass of an element's most-abundant isotope and its valence; either both are even-numbered, or both are odd-numbered, with nitrogen as the major exception. This leads to the so-called “nitrogen rule,” which can be stated as follows: If a compound contains no (or an even number of nitrogen atoms, its molecular ion will be at an even mass number. An examples, the following molecules yield even-mass molecular ions: 1,0, : cH, m/2 16, CH, m/z 26, HOH, jz 32; CCF, imjz 104; C.H,OH, mlz 94; CH ,COOH, m/z 284, cholesterol, CysHagO, m/z 386; HNN, m/z 32; and aminopyridine, CsHN3, m/z 94. An odd number of nitrogen atoms causes M* to be at an odd mass number: NH, jz 17; C.HsNH,, mjz 45; and quinoline, CgHyN, m/z 129. ‘Thus if the ion of highest m/z is at an odd mass number, to be the molecular ion it must contain an odd number of nitrogen atoms. This relationship applies to all ions, not just M* thus the nitrogen rule can also be stated as follows ‘An odd-electron ion will be at an even mass number if it contains an even number38 2.1 Te Molecuarton Table 3.4. Nitrogen rule Mase values: Odd_——_Even No Na Ne Fey OF" NaN Ns oe ee of nitrogen atoms, Similarly, an even-electron ion containing an even number of, nitrogen atoms will appear at an odd mass number. You may find this confusing at first; until you get used to working with this, it will probably be easier to derive this from the first statement, remembering that M* is an odd-electron ion. In summary, see Table 3.1 Unknown 3.1. Indicate whether ions of the following formulas are odd-clectron or even-electron: C,Ha, CsH;0, CyHoN, CHyNO, CyHsCIBr, CeH,0S, CayF so. Hj, and C,H,SiO. Which of these ions will appear at even mass numbers? 3.4 Relative importance of peaks OE* ions have a special mechanistic significance, as discussed in Section 44 Because of this you should indicate all important OE" ions, making these directly on the spectrum (in the Figures of this chapter these mass numbers are circled). This is the next step in the “Standard Interpretation Procedure” inside back cover). The “importance” of a peak, after one has corrected its abundance for contributions of ions containing less-common isotopes, generally increases with: (i) increasing intensity: (i) increasing mass in the spectrum; (iii) increasing mass in the peak group (particularly the most or the second- most number of hydrogen atoms for an OE” peak). Important OE* ions are even less probable in the lower-mass end of the spectrum; thus intense even-mass peaks in this region are usually due to ions containing an odd number of nitrogen atoms, such as CH,N*, m/z 30 (Mun, 1981), Similar reasoning leads to a corollary of the nitrogen rule: A scarcity of important even-mass ions, especially at lower m/z values, indicates ‘an even-mass molecular weight. However, the reverse is not always true; the presence of abundant even-mass ions does not necessarily indicate an odd-mass M°. This rule is helpful for the mass spectrum of neopentane, molecular weight 72, which shows no molecular ion (Figure 3.1).35 Logloal nour ostos 39 Relative intensity Figure 34. Mass spectrum of neopentane 3.5 Logical neutral losses There are only a certain number of neutral fragments of low mass that are commonly lost in decompositions of molecular ions. The presence of an “important” jon separated from the highest-mass ion by an anomalous mass or elemental formula will indicate that the latter ion is not the molecular ion. Presence of ‘an abundant (as compared to its neighboring ions) ion $ mass units below the ion of highest m/z would have to represent the loss of five hydrogen atoms—a highly unlikely decomposition. Small neutral fragments lost from the molecular jon are commonly those attached by a single bond. For example, if Figure 3.1 had been obtained from an unidentified pure compound, m/z 57 might be considered as M"' of CH,CH—CHNH,, with m/z 41 and 42 as losses of NH and CH,, respectively. However, a significant (M — CH)" peak is very rare. Thus, the presence of a nonisotopic ion of m/z 43 indicates that the m/z 57 ion cannot be the molecular ion, even though it is the highest-mass nonisotopic peak in the spectrum, Such a mass difference of CH, is commonly encountered when two such homologous ions are produced by decomposition or a larger ion, here, C.H,2"" producing C,H," and CyH,"; this can also be due, however, to the ‘molecular ion of an unexpected impurity which is a homolog of the unknown compound. Mass losses of 4 to 14 and 21 to 25 that give important peaks are highly unlikely. Remember these ranges: Table A.5 presents a more complete list of them, and of neutral fragments which are commonly lost. Maximum expected relative abundances are given by Speck (1978); for example, (M — 2)*"is usually much less abundant than either M*’ or (M — 1)* (Section 2.6) If the elemental composition of the fragment lost can be deduced, this gives, aan even more powerful test. For example, the presence of a major (M — 15)" ion is common, but a major (M — NH)" ion is probably an anomalous ion; the loss of 35 is logical only if chlorine is present, Can the ion of highest mass be the molecular ion if the following are the ‘major ions of high mass in the spectrum?40 11 Tae Molecular ton Unknown 3.2, CigHsO, CoH yO, CoH 20, CyoH 3, Cal so Unknown 33. CigHyas CsoHlis, CoH gs CoHoy CoH, CoH Identifying and testing the molecular jon are important keys to Unknowns 3.4 and 3.5. Hint: In Unknown 34, use (64° ]/[63*] and [99° /[98"] to calculate the number of carbon atoms, since m/z 62 and 97 also contain an isotopic contribution from an “A + 2° element in m/z 60 and 95, respectively. on pence et ment ar 18 30 soar % 08 26 40 a 1 61100 OM & “se a or 32 ws 03 & “o7 & 70 15 e 18 = @ my 3 sr aa Ser & 4 m8 to ts 02 10 78, “59 jor Ot 3 1 * zg i * $4] |27 Typlcal mess spect a Unknown 3.5 mz In Relative intensity 8 44 xa 190 wo 28 no 82 wo 12 1528 16 08 wr 3.6 Molecular-ion abundance versus structure ‘The abundance of the molecular ion, [M*], depends mainly on its stability and the amount of energy needed to ionize the molecule (Table A.3). Particular structural features tend to show characteristic values of these properties, so that the magnitude of [M"] provides an indication of the structure of the molecule. Table A.4 gives typical [M"'] values for a number of types of compounds, listed in order of decreasing abundance 3.7 Typical mass spectra Figures 3.2 to 3.28 present spectra that also show such trends. These figures will often be referred to later in the book. The mechanistic symbols below will be explained in Chapter 4 © Important odd-electron ion Important peak formed by 2H rearrangement (C,Hay-1 10s, Section 4.10) {Important odd-clectron ion series T Important even-electron ion series Peak formed by sigma clectron ionization a Peak formed by alpha cleavage i Peak formed by inductive cleavageyy I bt cree ] Figure 34. Mass ~~ Laeger Figure 22, Mass spectrum of dodecane. a aaa t , Mass spectrum of 4-methylunde wo) spectrum of 2,24,6,6-pentamethytheptane ns. Figure 25, Mass spectrum of I-dodecene.Relative intensity Relative intenty Relate intensity Relative intensity vile. ~ both tere ea ee er eee ee 1a | # s PMA Loa ye wid be. rept | Figure 38, Mass spectrum of hexyl ether1 108 ® g z i iy a i % é i i ey e ot va Heth Ere iT BEETS LS Eh ae ae “4 Relative iteniy 8 8 Figure 3.10, Mass spectrum of 2-dodecanone. dlr ee 2 Figure 3.11. Mass spectrum of 6-dodecanone. meee wt ete | abo! | “a0 Figure 3.12, Mass spectrum of dodecanoie acid @ Figure 2:12, Mass spectrum of methyl undecanoate.10: Relative intensty md oe ow ue we | io Figure 3.14, Mass spectrum of decyl acetate. 106 ewe am | seo Figure 3.18. Mass spectrum of hexyl benzoate. Figure 2:16, Mass spectrum of dodecylamine, ee ‘Figure 3.17. Mass spectrum of dihexylamine.Relate intensity Relative intensity Relative intensity Relative intensity ARAK = arp gegre a ee ear 2) @ Cea a a eu oa nas specrom of dodanie Se we a se) « a i af. teat hd f, didi, a cae aaah a ai eG Seats ene Ne eee ae ¢ . awe | re eee ee aaa ae uae ates Figure 3.21, Mass spectrum of dodecanethiol.Ls ills ayy peel 1s a a | ell ®, vin ; lil 1 Figure 2:23, Mass spectrum of I-chlorododecane. Figure 3.24. Mass spectrum of I-bromododecane. diteRelaveltensty Relative intensity 43 3.1 The Molecular ton helen * Figure 3.28. Mass spectrum of the trimethylsilyl derivative of deeanol, ete eomonl ahaa le lal Figure 3.27. Mass spectrum of triethyl phosphate {In general, the chemical stability of the molecule parallels the stability of M*, and so is reflected in the abundance of M*; [M"'] usually increases with increased unsaturation and number of rings, as illustrated by the striking abundance of M*" in strychnine (Figure 3.28) The effect of molecular weight is less clear-cut; increasing the chain length up to C, or Cy generally decreases [M*] substantially (see Table A.4), but often [M""] increases again for longer straight chains (Sections 9.4, 9.5). Chain-branching substantially decreases M" stability and thus its abundance. If less energy is required to ionize the molecule (that is, if it has a lower ionization energy), more molecular ions of lower internal energy (‘cool ions”) can be formed, and [M*] will end to be higher. As shown in Table A.3, the ease of ionization of the outer-shell nonbonding electrons on heteroatoms increases in going down a column or to the left in a row of the periodic table. This accounts for the dramatic increase in [M'"] for mercaptans in comparison to the corresponding alcohols (Figures 38 and 3.21}; primary amines (Figure 3.16) show a smaller, though sigaificant, increase in [M*] versus the corresponding alcohols‘uyuyfais jo uuransods ssepy “@e' omn6ia Aysuony ome,50 23.) The Molecular ton ‘Try one more unknown, 36, before tackling the next important area, Mechanisms. Unknown 3.6 mint a — 1 3 “ia 2208 z & «0. 4 4305 a 6 13 » so 47 £ a4 ss 45 3 @ os 14 & 44 R09 | ; 2 2 aan! oa mb we me | 1D 18 802 % 20 s7 100, eto i998 10 1) 90. 1203 wm 3t4 Basic Mechanisms of lon Fragmentation ‘Our initial statement (Chapter 1) that “the mass spectrum shows the mass of the molecule and the masses of pieces from it” is oversimplified, in that it neglects the important second dimension of a mass spectrum: ion abundance. The abundance of a specific fragment ion relative to the abundances of the molecular ion and other fragment ions can be a very useful indication of the structure of that ‘fragment and its environment in the molecule. However, to make use of this information, we must understand the factors that control fragment-ion abundances. A preliminary, somewhat empirical, discussion of these factors will be given here. A more detailed treatment of mechanisms appears in Chapter 8, and the basic processes involved in forming mass spectra will be examined in Chap- tet 7, However, it is important to appreciate that mass spectrometry is not sensitive to all structural features, and that the complex and competitive interac tions ofits chemistry limit our present capability to interpret spectra using only these basic factors. To recognize for more complex molecules what alternative structural possibilities could give rise to the observed mass-spectral features, ‘we must study the spectra of closely related molecules. Such unimolecular ion-decomposition reactions can be viewed as another field of chemistry, but fortunately for most chemists studying this book, there are many close similarities to pyrolytic, photolytic, radiolytic, and other ener- ‘etic reactions, and there are even many general similarities to condensed-phase (solution) organic reactions, The largest points of difference are that ionic and often radical species are involved in each reaction in the mass spectrometer, and their combined effects sometimes appear unusual to the organic chemist. Chem- ists may also question the reliability of structural relationships based on te- arrangement reactions. However, many of these are based on well-established chemistry and can provide key molecular information st82 411 Basle Mechaniims of on Fragmentation 4.1 Unimolecular ion decompositions, Mass-spectral reactions are unimolecular; the sample pressure in the EI ion source is kept sufficiently low that bimolecular (“ion-molecule”) or other collision reactions are usually negligible, Energetic (70 eV) electrons interact with the gaseous sample molecules at widely varying distances, so that the molecular ions (M") are formed with a wide range of internal energies. Those that are sufficiently “cool” will not decompose before collection, and will appear as M" in the spectrum. I suliciently excited, the M* ions can decompose by a variety of energy-dependent reactions, each of which results in the formation of an ion and a neutral species; this primary product ion may have sulficient energy to decompose further. In the mass spectrum of ABCD (Equation 4.1), the abundance of BCD” will depend on the average rates of its formation and decomposition, whereas [BC*] will depend on the relative rates of several competitive and consecutive reactions. Isomerization is a possible unimolecular reaction; formation of the OF* ion AD involves rearrangement (7) of the atom-bonding relationships of ABCD" aacp asco” ——+ A’seco- = opt ect+> (4) ——+ 0. + Bc" - A+act AD™+ BC, 4.2 Basic factors that influence ion abundance The following general guidelines for predicting unimolecular ion decompositions follow basic chemical principles. Stability of the product ion. The most important general factor affecting the abundance of a product ion is its stability. Key types of ion stabilization include electron sharing involving a nonbonding orbital of a heteroatom, such as in the acetyl ion CH;—C--O ++ CH, C=O (the latter is isoelectronic with CH,—C=N), and resonance stabilization, such as in the allyl cation CH,=CH—CH, + CH;—CH—CH, and the benzyl cation C,HjCH,* (however, the phenyl cation is much less favored, because it has only five reclectrons, but six are required for aromaticity), For OE ions, isomers with separated radical and charge sites (“distonic radical ions,” Radom et al. 1984) can be more stable than their classical counterparts: CH,CH,CH,CH=O" CH,CH,CH,CH=O"H, CH,NH,” +CH,N*Hy,442 Bani factors that influence fon abundance 53 ‘Stevenson's rule (1951). Cleavage of a single bond in an odd-electron ion can lead to wo sets of ion and radical products; ABCD* can give A* + -BCD or A-+ BCD". The fragment with the higher tendency to retain the unpaired electron should have the higher ionization energy (IE, Table A.3). Thus there should be a higher probability for forming the fragment ion corresponding to the lower TE value; because this ion usually is also the more stable, it should be the more abundant of the complementary pair of ions resulting from this bond. cleavage (Audier 1969; McLafferty et al. 1970b; Harrison et al. 1971). Loss of the largest alkyl. A notable exception, in which abundance decreases oh pt tone » whoa» on ICHGCHC Hal > (arg GouH) ty of the neutral product. Although the ionic product stability is generally ‘much more important in influencing the reaction pathway, a favorable product site for the unpaired electron can provide an additional influence. Such radical stabilization can be provided by electronegative sites such as oxygen (alkoxyl radical, ‘OR) or resonance (‘CH,—CR=OH* «+ CH,—CR—OH"). The neutral product can also be a molecule; small stable ones of high ionization energy (and low proton affinity) such as Hy, CH,, H;O, C3H,, CO, NO, CH,OH, H,S, HCl, CH, =C=O, and CO, are often favored (Table A.5). Entropy/steric effects. Reactions yielding the moststable products, those with the lowest enthalpy requirements, often have stringent requirements for the position of the atoms in the transition state. This is especially true of rearrange- ‘ment reactions, in which the transition-state structure will represent only a very small fraction of the possible ion conformations. Thus for the same precursor ions of higher internal energies, the energy can favor dissociations of les restric- tive entropy requirements, such as simple bond cleavages, that have higher enthalpy barriers Unknown 4.1. Predict the most abundant product ion in the mass spectrum of54 41 Bale Mechanisms of on Fragmentatlon 4.3 Reaction Initiation at radical or charge sites, To predict preferred decomposition pathways, we will use the simplistic as- sumption that the reactions arc initiated at the favored sites for the unpaired electron and for the positive charge in the decomposing ion, Such a site is Viewed as providing the driving force for specific types of reactions which are characteristic ofthe chemical nature ofthe site. Although this gives only, at best, an approximation of the actual electronic displacements, it provides a convenient way to correlate (and for you to remember) a large numberof the reactions of diverse structural moieties. Further, the dissociations resulting from radical ‘and charge-site initiation are, respectively, homolytic and heterolytic cleavages, common classifications of organic chemistry (McMurry 1984) ‘The most favored radical and charge sites in the molecular ion are assumed to arise from loss of the molecule’s electron of lowest ionization energy (IE, Table A.3). Relative energy requirements are similar to those for the electronic transitions affecting ultraviolet spectra; favorability for ionization generally is on the order of a < x- < n-electrons. ‘Sigma (o): RH,C:cHR’ Se AH,CTCHA P(g): AC: Non bonding (7 ‘The symbol * at the end of the molecule signifies an odd-electron ion without designating the radical site, Use of either “or * within the molecule, as in CH," CH,, implies localization of the radical or the charge. 4.4 Reactlon classitications Decompositions involving only the cleavage of a single bond in the odd-electron (OE") molecular ion must produce an even-electron (EE*) fragment ion and a neutral radical species: CHsCH,"CHy ——~ HCH, + «CH «4. coy + CH? ‘The two fragments compete for the charge and the unpaired electron; the abundances of the two ionic products from this type of reaction would be equal only by coincidence (Stevenson's Rule, Section 4.2) In contrast, an OF" ion is formed from M* by cleavage of two bonds between the products. Rearrangements and reactions involving fragmentation of a ring are two ways in which abundant OB ions can be produced:444 Reaction cansitesions 55 Heo—cHOH" < H.C=CHOH" + HC=CH, (charge retention) He—eH, Hz" (charge migration) 44) 4 RS HOH™ (charge retention) hE, HOH + HC=cH;" (enarge mgraton) Again, the two fragments compete for the charge and radical. Ina simila ion, cleavage of three bonds of M*" produces an EE” ion: crore orgy = cinch + Cats ee 4S) The decompositions of even-electron ions are strongly influenced by the preference for formation of an EE* ion and EE® neutral (the “even-electron rule Cummings and Bleakney 1940, Friedman and Long 1953, Karni and Mandelbaum 1980). Production of an OE* ion from an EE* ion must be accompanied by formation of a radical neutral species, involving the energetically unfavorable separation of an electron pair (Equations 4.6) “ CHACH, + O=Cl, (charge migration) cricH bom —- core + HOCH, yarangamer charge tenon ™~ CHCH + O=CH;’ (untavored) (4.6) m gin < CHp==CH + CHz==CH, (charge retention) H0—CH, CHe=GH + CH=CH,” (urfavored) Field's rule (1972). In EE* ion decompositions forming the same EE* product, the tendency of a neutral to leave without the charge is greater for molecules of lower proton affinity (PA). In Equation 4.6, the formation of CH,” with O=CH, (PA = 7.4 eV) would be greatly favored over the formation of C;H," with S—CH, (PA = 8.9 eV) from C,H,S'=CH,. ‘The seven main types of cation fragmentations discussed in this chapter are those not in brackets in Table 4.1. Odd-clectron ion decompositions involving the cleavage of one bond are discussed in Sections 4.5 to 4.7, of two bonds in 4.8 and 49, and of three bonds in 4: 11; EE* decompositions cleaving one and two56 41 ane Mechantame ol on Fragmentation Table 4.1. Types of ion decompositions Precursor Number of Charge Charge on bonds cleaved retention _migation OE" (4) 1 EE" (2) EE" (7) OE" (Me) 2 OE" fas) OE" (a) oe" (M") 3 EE" (aaa) (EE* (a ee 1 foe" ce! eet 2 ee oer “esis ana ate alan active ea Bahavor (roertion or migration) as two sroaion. Brackets nd froduts of resctions dacussed\n Chaps 8 bonds are covered in Sections 4.7 and 4.10, respectively. Note that OE" forma tion is favored only for the cleavage of two bonds in an OB" precursor, this is Why you should mark important OE ions (Section 3.4, Summary. The ion-decomposition mechanisms discussed in the rest of this chapter are summarized inside the back cover for ready reference. 4.5 Sigma-bond dissociation (0) Akanes) RGR; Ze R- + ORy (7) If the electron lost in ionization comes from the saturated bond framework, single-bond cleavage will of course be favored; ionization of ethane increases the C—C bond length by ~30% and halves its bond dissociation energy (Bellville 1982), The more-abundant ionized fragment will be the one better able to stabi- lize the positive charge. For saturated hydrocarbons such ionization from the ‘o-bond system is the lowest energy process; this can then account for favored alkane fragmentation at carbon atoms that are more highly substituted, and which therefore should more readily carry the charge in the products. (The percentage values indicate the ion abundance relative to the base peak of the spectrum.) (CH)C—CH,CHy > (CHa AC" CH:CH; Se (CHygC" + -CHLCHs (48) 100% Also compare the abundances of the homologous C,H,y41” ions (an{6 Radice inltaton (cleavage) 87 series,” Section 5.2) in Figures 3.2 to 3.4, and in the spectrum of pristane, Figure 4,1, However, for the o-bond dissociations at the same carbon atom, such as that leading to the formation of the key m/z 113 and 183 peaks in Figure 4.1, the rule for loss of the largest alkyl radical applies, [(M ~ CgHy3)"] < [(M — C,,H,,)"]. The abundant C,H,,,;° ions such as m/z 43 and $7 formed by secondary fragmentations will be discussed in Section 5.1 46 Radical-site initiation (2-cleavage) Equations 4.9 to 4.12 summarize the homolytic dissociations (McMurry 1984) discussed in this section. Saturated sto: ae + RA (49) Yr + ch=cH, 4.10) Unsaturated R- heteroatom: a akore (ave GY Don, He wo, a1 ‘cleavage on " - Reaction initiation at the radical site arises from its strong tendency for electron pairing; the odd electron is donated t0 form a new bond to an adjacent atom. This is accompanied by cleavage of another bond to that a-atom; thus this is commonly called the “a-cleavage reaction”: an antes cH Lon, £ He Se -GHy + CH =OCH, (<> CHs—OC>Hs) (4.13) {50% (COHy" = 100%) (see Figure 39). Neutral radical species undergo analogous a-cleavages (Green 1980; Ci and Whitten 1989). A “Yishhook” hall-arrow indicates transfer of a single electron; such homolytic cleavage must move the site of the unpaired electron. A doubly barbed arrow will be used to indicate the transfer to an clectron pair; such heterolytic cleavage moves the charge site (Section 4.7; Shannon 1964). ‘The driving foree is like that underlying the high reactivity of neutral radicals in processes such as dimerization and hydrogen abstraction. The tendency for the radical site to initiate a reaction in competition with the charge site generally parallels the radical site's tendency to donate electrons: N > S, O, x, R- > Cl, Br > H, where x signifies an unsaturated site and R- an alkyl radical, (This‘(ouvsnprtusd yiouresiar-p1'01'9'2) 3M J0 wnsroeds ssepy “Ly sunbig Asus omer445 Radics ination (x-clenvegs) 59 ordering does not mean, however, that a chlorine atom cannot initiate a radical- site reaction in the absence of stronger driving forces.) The donating ability of a particular site is affected by its molecular environment; for predicting this, conventional resonance and inductive effects are generally applicable. Ionization of an aliphatic ether (Equation 4.13) should occur preferentially by loss of an neclectron of the oxygen. Donation of the unpaired electron to the adjacent C—O bond is followed by transfer of an electron from another bond of this a-carbon atom. The resulting one-electron bond then cleaves to give the alkyl radical and the resonance-stabilized oxonium ion; the greater the double- bond character of this ion, the lower will be the critical (activation) energy of the reaction, Note that only the radical site moves; the charge site remains on the oxygen. Unknown 4.2. Predict which will be the most-abundant product ion in the mass spectrum of HO—CH,—-CH,~NH a-Cleavage at the carbonyl group can be visualized similarly with formation of the stable aeylium ion as in Equation 4.14 (see Figures 3.10 and 3.11) Opts NBG Be catlgs + Coty — CHO (414) Hs 100% A reaction initiated by an olefinic double bond (or phenyl x-system) yields an ally! (or benzyl) ion (Equation 4.15}; here the radical site can be on either atom of the double bond. An allylic-type cleavage should be less favored at Cian Loony, 2 CHy+ + CH,=CH—CH, (<> GHy—CH=CH, ) ‘00. oa onan Boer cH yc ced (eo 100% (ais) a carbonyl double bond because resonance stabilization of this product requires positive charge localization on a monovalent oxygen, with the other canonical structure, an extremely unstable a-acylearbonium ion (Dommroese 1987), whereas the trivalent oxonium ion is the most-favored site (Equation 4.16): cramer to See OH + CH=CIOHI—0 ——~ bH—c1esHy=0 0.516 (CaHs0* = 100%) (4.16)60 4 Bane Mechaniams of on Fragmentation Unknown 4.3. The “loss of the largest alkyl” rule predicts that the abundant loss of H is an uncommon fragmentation pathway. Postulate a structure for Unknown 43 for which such a loss is reasonable Unknown 43 mlz mz int mz ink re 2 14 nm 18 33 587 nm 38 2 5603. 2 08 aay a 38 Bios 48 5866. 2 10 » 8 551 % 0s 04 60 7 % 10 aon 8 48 % 06 4% 08 & 19 97 100. a7 19 6 30 86 4 08 08 76 @3t 628 024 36 ss o7 S40 6 62 Relative intenaty Loss of the largest alkyl radical. This rule (Section 4.2) is generally applicable to a-cleavage reactions. Note that there are two a-bonds for the carbonyl ix for , three for an alcohol HOC— or primary amine HyNC— i an ether CO 1 predicts that the spectrum of 3-methyl-3-hexanol (Figure 4.2) should show characteristic peaks at m/z 73, 87, and 101, with abundances decreasing in the order shown in Equation 4.17. Note also that the a-cleavage loss of any alkyl group (or H) must give a peak in the corresponding ion series, such as m/z 29, 43, 57, .. for aldehydes or ketones; 31, 45, 59, ... for alcohols or ethers, and 30, 4, 58, ... for amines. (Section 5.2) | . and nine for a tertiary amine N@=C—),. This rule |45 Radical ate iitaton(-eleavoge) a Relate intensity Figure 4.2. Mass spectrum of 3-methy!-3-hexanol. cy Be IHCICHI=OH) > ICHCICHY=OH > mz 79, 100% smiz07, 50% [CH;C(CHy)=OH] smiz101, 10% (417) z 3 Ny pel Ls ha, ewe, Mas specu ft mao | ‘utylamine, ‘The overwhelming driving force provided by the nitrogen atom’s electron- donating ability makes the «-cleavage reaction dominant in the spectra of aliphatic amines. The only a-groups in fert-butylamine are methyls, and this loss yields the major peak of the spectrum (Figure 4.3) this represents 58% of all ions collected. There are two a-methyls and four a-hydrogens in diethylamine (Figure 4.4); methyl loss is still dominant, yielding 30% of the total ions, versus 6% for loss of H (the large m/z 30 peak is discussed in Section 4.10), For unbranched alkylamines (R—NH,, R = CH, (0 ,4Hz9), the m/z 30 is the most- abundant ion. The replacement of a terminal hydrogen atom in dodecane by anNHCH,CH, Relate intensity sl 1 Figure 4.4, Mass spectrum of me TST kT de Gethsinmin amine group causes the profound spectral change shown between Figures 3.2 and 3.16. ‘Test your understanding of these concepts with Unknowns 4.4 to 4.8, which are spectra of isomeric C,H, ,N alkylamines. Unknown 44048 Intensity ma a4 45 48 47 48 18 o7 05. 34 13 39 a 23 27 45 1 a5 2 48 51 ry of 22 2 22 22 36 1 a4 Fo 100 100 29 33 73 a 21 22 13 03 on 3 13 02 2 2 20 0 os 05 u 24 os. a 28 28 ta 35 oa 2 wr 04 14 Ey 60 e 12 58 a8 72 3 “a 20 13 16 a 100. 6 os 16 02 18 28 6 re 24 81 73 23 a 02 eI a2 50 18 8 03, 19 100. 100. 10. 2 90 01 39 39 o n 00 00 06 10 oa n 10 13 96 w. 2a a 10. 0 1 Es 12pee ee oo : i rn enna m, * 100 * z | z j i | ts 1 , ; c Caen cas ea mn o ) = w z z 2 2 ie Bal ds . dal 1 ta a First write down the eight possible amines of molecular weight 73. Start with the four spectra that have a base peak at m/z 58; which of your structures will show a ready loss of 15? (Thus, which have an a-methyl group?) You should havecH, CH Oty Hs Hs (CHjzCNH,, C)H4CHNH,, CHCHNHCH,, CHNHC;Hy, and CH,N(CHs)p The spectra of two of these are Figures 4.3 and 44. The other isomeric Cy amines of Unknowns 4.4 through 48 contain the remaining three a-methylamines; yet in only two is mass $8 the base (largest) peak. Why? This should be obvious from the possible molecular structures. To assign structures to Unknowns 44 through 48, try predicting the major ions in the spectra of all the isomeric C, alkylamines. The spectrum of one isomer is not included in these unknowns. Which one? 4.7 Charge-site initiation (inductive cleavage, /) Equations 4.18 to 4.21 summarize the heterolytic dissociations (McMurry 1984) discussed in this section. ee en bee aa R d ee* te oem 420) te n+ veoH (a2n Initiation of a cleavage reaction by the positive charge involves attraction of an electron pair, The tendency for the formation of R* from RY is: halo- gens > O, $> N, C; for elements of the same row of the periodic table this tendency parallels the inductive effect (I) of Y. However, stabilization of the charge is generally more important than that of the unpaired electron for determining reaction products (Section 4.2) in both the formation and the decomposition of the precursor; because these heterolytic cleavages require migration of the charge, they are generally less favored than radical-site reactions. ‘Oxygen is intermediate in its ability to influence either a or i reactions. In an aliphatic ether attraction of an electron pair initiated by the localized positive charge on the oxygen can form the alkyl ion and the alkoxyl radical; in this case the charge site is moved (Equation 4,22; see Figure 39). Note that the bond cleaved (R’—CH,—OR) is nor that cleaved by the radical-site initiation447 Charge-eintation (nducte cleavage, ) 65 cate LB cut, Le cgi + 00H, . 40% (422) — cHcH.cH—cH 8 Le MHD Cast, Cats (423) 100% 3% 30% ae (CHy.ch—cH, 61 (MHCN™ , Cato®, Cote? (CHyscH—cH, 6) (MHD. Cate". Cath” 94) % 4% 100% (R'+-CH,—OR, Equation 4.13). The reaction is also competitive for many nitroalkanes, alkyl iodides, secondary and tertiary alkyl bromides, and tertiary alkyl chlorides, but not for RCH,—Y compounds of higher CY bond strengths, such as unbranched alkanols and alkyl chlorides; for these [iM — HYy"] > [(M — ¥)"] as in Equation 4.23 (see Section 49). As is expected for an inductive effect, the influence of the charge site can affect a bond that is farther away if it has more polarizable electrons; the loss of CHCl is much larger in Equation 4.24 than in 4.23. This reaction will not cleave a multiple bond to a heteroatom, For the carbonyl group (Equation 4.25), electron-pair attraction to the charge site yields the canonical resonance structure; inductive cleavage of this then gives the alkyl ion and acyl radical. However, these products are the complements of the alkyl radical and acylium ion formed by a-cleavage (Equation 4.14), in contrast to the a- and i-reactions (Equations 4.13 and 4.22) at a saturated heteroatom, R ("5+ ) te eR eo yay Considering Equations 4.14 and 4.25, one would expect aliphatic ketones to show four major ions from cleavage of the two bonds to the carbonyl group; the favored acylium ion should be the one formed through loss of the larger alkyl group, and the favored carbonium ion should be the more stable one. Unknowns 49 and 4.10 are the spectra of 3-pentanone and 3-methyl-2- butanone; which is which?Un Relative intensity - = se Even-electron ions. As discussed in Section 4.4, the favored decomposition of an EE" ion yields another EE" ion and a molecule as the neutral product. Product molecules of low proton affinity are favored, such as those of Equations 4.26 4.28 (PA = 7.4, 6.2, and 7.2 eV, respectively; Field’s Rule, Section 4.4). Equations 4.26 and 4.27 are two-step pathways for forming the same products produced by Equations 4.22 and 4.25, respectively. However, these are energetically less favorable by 0.2-0.8 eV (20-80 kJ/mol) than their one-step counterparts. a te cHo+ R426) + Rt co (427) ron Halon, he ne mo 428) ‘The initial ions produced by chemical ionization (Cl) are mainly EE* ions such as MH" and (M — H)*: other soft ionization methods such as fast-atom bombardment can also produce such abundant BE* ions (Section 6.1). For decompositions of the MH" ion (Equation 4.28), the loss of molecules of lower proton affinity (Table A.3) is generally more favorable (Field's Rule, Section 44). The EI mass spectrum of ephedrine (Figure 4.5) shows no molecular jon; the spectrum is so dominated by the a-cleavage reaction leading to CH N*H=CHCH, (m/z 58) that there are only weak peaks indicative of the rest of the molecule. However, the CI spectrum (Figure 4.5) has abundant ions at m/z 166, MH", indicating the molecular weight, and at 148, (M+ H — H,0)*. The latter, formed by inductive cleavage (Equation 4.28), thus indicates the presence of the hydroxyl group. Despite the lower tendency for charge-site47 Charges inition (ductive. oe) o a ass HCH | OH HCH, 1 ou den, ~Gte rs om fn bag dace = etna CF 8 vole y 105 Eade, oO { Relatve intensity if Relative intensty 2 4 e om Lat the a [gsesay owas ect ie a) Figure 45, Electron ionization and chemical ionization (CH, reagent) mass spectra of ephedrine reactions of the amino group, the small peak produced in the CI spectrum at jz 135 (Equation 4.29) is very useful, since it indicates the N-methyl group. Note that the preference for loss of H;O versus H;NCH, follows Field’s Rule (PA = 7.1 and 94, respectively). Finally, because the formation of an EE* product is so highly dependent on its stability, its further dissociation into stable products often necessitates substantial rearrangement or even fragmentation remote from the charge site (Gross 1989a; Chapter 8), in iy —CHOH—CHCH,—ONPH.CH, = Gay —oHoH—CHoH, + HANH, 429lc Mechanisms fon Fragmentation In Unknown 4.11 the m/z 130 peak has the elemental composition CyH, 40. Use the above mechanisms in elucidating the structure of this molecule. (Hint: ‘The molecular ion information from Table A.4is also valuable.) Unknown 4.11 mz aaa = = 2 18 215, 300s no 3 56 09 a 2 @ 29 98 “ “10 5 % 36 je 120 52s. Th Bleep S48 ey To 7 100 84s 322 n 47 mua lene ral BOs. wi od 19021 iH 4.8 Decompositions of cyclic structures The cleavage of two bonds in a ring is necessary to produce a fragment ion (Equation 4.30), Cleavage of one bond causes no change in mass, producing O=C+ Ca zee me56 (430) only a distonic radical ion (Radom et al. 1984; Gross and MeLafferty 1971), one with a distance between its radical and charge sites. The unpaired electron in this isomeric ion is donated to form a new bond to the adjacent carbon atom,‘) @ . a | 4 wae cyclohexane. Relative intensity with concomitant cleavage of another bond to that a-carbon, Although the radical site has moved, the original cyclic nature causes this second bond cleav. age to place the unpaired electron on the charged fragment, producing an odd- electron ion, The mass spectrum of cyclohexane is shown in Figure 4.46 (sce also Figure 3.6, Note that the important OE* ion C,H,* (m/z 56) has the most hydrogens (Section 3.4) of any non-isotopic C,H,* ion. Retro-Diels-Alder (Mandelbaum 1983; Ture8ek and Hanus 1984). In cyclohex- ene the r-clectrons provide a favored site for the initial charge and radical (Equation 4.31), Donation of this unpaired electron produces a distonic radical- ion isomer by a-cleavage; a second such reaction eliminates neutral C;H,. Note that the other product is ionized 1,3-butadiene, so that this corresponds to a retro-Diels-Alder reaction, In reactions yielding an OE" product, the stabilization of the unpaired electron as well as the charge is an important driving force; note that both of these are much better stabilized in the ion product of Equation 431 than in that of 430. ‘As with other hydrocarbon fragmentation reactions, the retro-Diels-Alder reaction will be important only if no preferable fragmentations are possible. Thus the addition of a functional group can dramatically reduce the abundance of ions from this reaction. Conversely, functional groups that can promote cleavage of any of the ring allylic bonds favor the retro-Diels-Alder reaction (Tureéek and Hanus 1984). Unknowns 4.12 and 4.13 show the spectra of a- and f-ionone (Figure 4.7). Pair the structures and spectra, and justify your choice.70 41 Rae Mecano Fragmataton os * S\ BS YS ene imiz 54; R= H, 80% (C3Hy* = 100%) tl UE =9.1) P= Cols, 0.4% (431) aS, \ 5 ae : (crarge migration) Zo . * 2 RaH, (IE = 105), <5% Fla GoHs, (IE =8.4), 100% A (432) Unknown 4.12 | | | 1 Relative intensity i ilu [. j i dial te Le Ly448 Decompoutions of eee stucures n , A SS S = E i Figure 48, Mass spectrum of 4-phenyleyclohexene, Charge migration. ‘The final step of Equation 4.31 is shown as a homolytic bond cleavage, with each of the separating fragments retaining one of the electrons. However, heterolytic cleavage (i) is also possible (Equation 4.32), moving the positive charge to produce the ionized alkene (Figure 4.8). In the transition state the alkene and olefin are competing for an electron; according to “Stevenson's Rule” the product more likely to lose the electron is the one with the lowest ionization energy, (IE, Table A.3). Thus for R = H, the ionization of butadiene is favored over that of ethylene. However, for R= phenyl, the resulting styrene ion should be favored. If the JE values are similar, both ions should be present. Look for both; note that the mass sum of these complementary OE* ions is equivalent to the molecular weight Unknown 4.14, Ionization from a nonbonding electron orbital can also trigger such ring fragmentations. Predict an abundant odd-electron fragment ion in the mass spectrum of p-dioxane,Ed 41 Bane Mechaniams of on Fragmentation 49 Radical site rearrangements There are also important mass-spectral reactions which produce ions whose atoms have not retained the connectivity relationships ofthe original molecule; part of the precursor ion has reacted with another part before or during decom- Position, Sometimes such rearrangements are so extensive that they make the product jon useless (or misleading) for deducing structure; such “random” rearrangements are common where o- (and sometimes f-) ionization is necessary. Fortunately, many rearrangements occur by means of “specific” mechanisms which are now well understood, and these product ions are thus valuable for deducing structure. Hydrogen-atom rearrangements initiated at a radical site, the main subject ofthis section, are an important class of reactions exhibited by 4 wide variety of structures. AS with OE" formation from a cyclic molecular ion, the initial rearrangement product is a distonic radical ion (Hammerum 1988) 7-H rearrangement to an unsaturated group with P-cleavage. An unpaired electron can also be donated to form a new bond to an adjacent atom through space: as in Equation 4.14, the second electron of this pair is supplied by transfer from another bond to this adjacent atom, resulting in its cleavage (Equation 4.33). Flatteringly, this is usually referred to as the “McLafferty rearrangement” (McLafferty 1956, 1959; Kingston et al. 1974; Turedek et al. 1990a). For compounds containing an unsaturated functionality such as the carbonyl group, the 7-hydrogen atom is transferred by a sterically favorable six-membered-ring transition state. However, in this process the initial cleavage does not result in (charge retention) + Nae Ke eT (mv258: R= CH, 40% UE = 87eV) R= CoHs, 5% , H Lk T De R=CHy (IE =9.7), 5% R=CeHs (IE = 84), 100% (433) (charge migration) (434)449 Radical se rearrangements 3 the loss of part ofthe ion, but only in a change in the position of the radical site to form the isomeric distonic radical ion. The new radical site can now initiate ‘an a-cleavage reaction resulting in fragmentation of the carbon-carbon bond which is beta to the carbonyl group with loss of an olefin or other stable molecule to form the odd-electron ion; an OE" is formed because two bonds are cleaved to effect fragmentation in Min this rearrangement reaction (Table 4., Part ofthe driving force for the fist step (rH) is provided by the formation of the extremely strong O—H bond which makes the distonic intermediate more stable than the original ketone ion. Part of the driving force for the second step is the resonance stabilization of the radical site in the product ion, which is isoelectronic with the allyl radical (see Heinrich 1986). Note that this requires B-bond cleavage in the second reaction step, and thus necessitates 7-H transfer to produce the reactive intermediate Such hydrogen rearrangement through a six-membered-ring intermediate yields characteristic OE ions for a wide variety of unsaturated functional igroups, such as aldehydes, ketones (Figures 3.10 and 3.11), esters (Figures 3.13 to 3.15), acids (Figure 3.17), amides (Figures 3.19 and 3.20), carbonates, phos- phonates, sulfites, ketimines, oximes, hydrazones (Equation 4.35), alkenes, alkynes, and phenylalkanes (Equation 4.36; see Figure 3.7, i ww eee] J (435) S . 4 (436) (mz 91 = 100%) mz 92, 60% Unknown 4.15. What is the mass of the characteristic OE" ion (or ions) which will be formed by this six-membered-ring H rearrangement from each of, the following M*"4 46 Basle Mechaniams of on Fragmentation cHonyoHcHicarals” - CHYCH,oHCICHAI—=OH, i . | cnscnscralocnch,” . CaHsOCH.GHE" , cHycreoloct,cn,"” » ishhooks,” for each. Draw out the mechanism, complete with “ Unknowns 4.16 and 4.17. These are the spectra of 3- and 4-methyl pentanone; which is which? Unknown 4:16 ee) Relatve intensity Note that these isomers produce the same peaks by a-cleavage (m/z 43 and 85) and by i-cleavage (m/z 15 and 57), whereas the f-cleavage rearrangement makes it possible (o distinguish between the isomers by characterizing the substituents on the a-position. The tendency for rearrangement is greater for hydrogen on branched, allylic, oxygen, or other labile sites.egements 75 Unknown 4.18. Does an important odd-electron ion aid in the solution of this unknown’? Unknown 4 nt mz int inven 1% 03 19 2 5 B12 i % 39 zon, ss OS. 03-20 Boo 6 33 wa ta = 39 ee 10 58s 2 6 10 106 08 3 0 6 07 1510 09 7% 08 603 a 53 rie aoa oor 2 04 73 82 1908 27 mB BT 12. so 27 17 527 era 31 100 Reatve intensity ‘Charge migration can also occur (Equation 4.34). In the dissociation transition state, the separating products can compete for the ionic charge, paralleling the complementary OE" ion formation in ring cleavages (Section 48). The favored ion product should arise from the fragment of lower ionization energy (IE) (Stevenson's Rule). Although the spectrum of 4-methyl-2-pentanone (Un- known 4.16) shows 30% of the rearrangement product CH,—CH(OH)CH,* (m/z 58, 1E = 87 eV), a far greater amount than that of the complementary CyHe" (IE = 9.7 eV), substitution of a S-phenyl (Figure 49) reverses this, yielding 100% CgHsCH=CH," (m/z 104, JE =84 eV). The spectrum of €\H,COOC,H, shows [CJH;COOH " ] IE = 10.2 eV) > [CaHy" ]UE= 105 eV), whereas those of CsHjCOOC3H, (n- or iso-) show [CsHg"] (IE = 9.7 eV) > [CsH;COOH"]. Although the charge retention OE*” product has gained an H atom in the rearrangement, the charge migration OE* product has lost a hydrogen; thus the former usually has the most H atoms in its peak group,76 46 Bale Mechanisms ol on Fragmentation Relative intensy Ps r Figure 49, Mass spectrum of S-phenyl-2-pentanone. but the latter may have one less. Again, the sum of these complementary masses equals that of M”"; in Figure 49, 58 + 104 = 162, Hydrogen rearrangement to a saturated heteroatom with adjacent cleavage. Even ino unsaturated functionality is present, such an intramolecular H transfer can also take place to an initial radical site on a saturated heteroatom, such as Equation 4.37 ‘Again, the unpaired electron is donated to form a new bond to an adjacent {in appropriate conformations) H atom, with concomitant cleavage of another 4. ROH Cote ss Lap + HOH w On we, D (charge retention oF an > m Cabs mvz84, 11% m2 58, 100% (charge migration) (4.38)449 Radlea ae rearangemente 7 bond to that hydrogen. However, a second radical-site reaction is not favored, since stabilization of the unpaired electron in the product CH;CH,0" H, is no better than that in the intermediate -CH3(CH,),0"H,, Instead, a chargesite reaction is now possible, forming inthis case the (M — H0)* peak by cleavage cof a bond to the heteroatom. (Water loss is much more favorable for primary aleohols than for secondary, and especially more than for tertiary, alcohols because of the increasing competition with a-cleavage,) Further charge-site reactions can give secondary products by cleavage of a bond that is two or more bonds further from the heteroatom (Equation 4.38). The products formed are not greatly affected by which hydrogen is transferred inthe first step (a sixcmembered-ring intermediate is not required). Further, the resulting heteroutom-containing fragment is saturated, and so competes less well for the charge (Table A.3), making charge migration (Equations 4,38, 4.40) much more common, The charge-migration reaction favors electronegative spe- te e HNC + We wide enone (charge retention) (4.39) J Sl " (m270, 100%) (charge migration) (4.40) cies; small saturated molecules of higher ionization energy and lower proton affinity (Table A.3) such as HO, CzH, (second step of Equation 4.38), CH OH, HCL and HBr are commonly lost in this way (found in Figures 3.8, 3.20, 3.23, and 3.24, but not 3.16), For charge retention the second step instead involves a radical-site reaction that is much more favorable if it provides stabilization of the unpaired electron (Equation 4.39 versus 4.37). The “ortho-effect” reaction (Equation 441) indicative of aromatic ring position results from a combination of a labile hydrogen available for rearrangement and a stable ion product from charge migration.78 46) Bane Mechaniams of on Fragmentation DAO Wy. ye e ‘No oH oS HOR. (aay ; y A oH Unknown 4.19 involves some important points that have been covered previ- ously, Be sure you understand its solution before proceeding. The utility of the m/z 965 peak formed by metastable ion decomposition will be discussed in Section 6.4 Displacement reactions, rd. Only brief mention will be made here of one of several types of nonhydrogen rearrangements (see Section 8.10). Two atoms or groups (one usually bearing the radical site) can react intramolecularly; formation of this new bond is accompanied by cleavage of another bond to one (or both) of these groups. Cyclization (Equation 4.42) to form a divalent chloro- nium ion with displacement of an alkyl group accounts for the largest peak in the spectra of appropriate I-chloro- and -bromoalkanes (Figures 3.23, 3.24), This reaction is much less important in branched haloalkanes and for functionalities with a higher tendency for radical-site reactions. The mass spectrum of n-dodecyl mercaptan (Figure 3.21) shows the following C,H,,.,S* ions: 1, 23% (CH, SH" from a-cleavage, n = 2, 9% m = 3, 1% m= 4, 11% (five- membered ring); and n= 5, 2%, Note the similar “ion series” (Section 5.2) in dodecylamine (Figure 3.16), (4.42) 4.10 Charge-site rearrangements Even-electron acyclic ion decompositions in which the charge site retains its location and the electrons remains paired, both of which are usually desirable{410 Cherge-ite rearengements 79 sae 438 =m mae =e =e 33 5 2 no oe aOR Ba Boat Soe 2% 2 on ge 3 te £3 oat ae Ss Be a Bs of oon oe Sb oe £8 e 8 Po o8 z : ® @ & a tet ee ee ee rental compositions of the mv 112 and 129 ions are Ca and G0 iy. by bighrescuton made spaciroMoty from an energetic standpoint, involve rearrangement (Section 4.4). Because the charge site does not move, this can be located on less-electronegative functionalities, even an amine N, and more-electronegative functionalities such as Cl can leave with the neutral product (McLafferty 19806; Kingston er al. 1983). Here we will discuss only hydrogen rearrangement, for which this reuction is favored if loss of a molecule of low proton alinty is involved; a common mechanism ‘of those possible involves @ proton-bound intermediate (Y—H* —Z: Morton 1982; Bowen and Williams 1980; McAdoo 1988a). The resulting product ions ccan have their atoms scrambled to a confusing degree; thus the structural impli- cations of these product ions must be interpreted with caution. However, the80 4 Bane Mechaniams of on Fragmentation EE? ion rearrangement of hydrogen to an unsaturated group containing a heteroatom, with elimination of an unsaturated neutral, can provide valuable information. This reaction gives the second largest peak in the spectrum of diethylamine, Figure 4.4 (Equation 4.43). The transition-state size requires an ethyl or larger group on the nitrogen for this rearrangement. Thus this reaction provides a spectral distinction between (CH),CNH, (Figure 43), (CH,),CHNHCH, and CH,CH,N(CHs); (Unknowns 4.5 and 4.6). Although these three spectra also show a base peak of (M—CH,)* by a-cleavage, their ‘m/z 30 peaks are much lower than that of diethylamine (note that these are still appreciable, so that such data must be utilized with caution), Ho=cH, a oe Hy, NH=CH,. si 7 cuycndinon en, =e fn! Hes Hace Hf=cH, (4.43) Unknown 4.20. Predict the principal peaks in the mass spectrum of Nemethyl-N:isopropyl-N-butylamine Eyen-clectron ions can also undergo H rearrangements which do not involve the charge site (nor an unsaturated heteroatom), such as reaction 444, The resulting peaks should be used with caution for assigning functional group CH 4 KG wot “ ~ oe ft rae ' bronco FS onge ih, . euinamon, (4.44) locations, however; note that m/z 55 is the base peak in both 1,3- and 1,1 dichlorobutane (Figure 4.10). (Chemical ionization. Because Cl produces mainly even-electron ions, for such spectra it is especially important to recognize that rearrangement is common- place in EE” dissociations (Harrison 1983; Kingston et al, 1983; Crombie and Harrison 1988). Although the site of CI protonation in a molecule should be that of highest proton affinity, Field's Rule predicts that the neutral lost will be that of lowest PA value; thus an initially formed ion HyN*—R—OH must rearrange an H atom to lose H,O (PA = 7.7 eV) instead of NH, (PA = 9.1 eV), Figure 45 provides an example.410 Charges rearrangements at 7 ngedqe—pu os i” z @® a ie if R oor al 4, Lis i Shon i Figure 4:10. Mass spectra of 1,3- and 1,1-dichlorobutane. Rearrangement of two hydrogen atoms (the “McLafferty + 1" rearrangement) is a characteristic decomposition of esters and similar functional groups that can be rationalized (Equation 4.46) using a transfer of the second hydrogen by a mechanism analogous to reaction 4.43. An added driving force is the resonance stabilization of the EE* product ion (three bonds are cleaved in the reaction). For propyl and higher esters, a stable allylic radical can be produced; however, significant C,H, and CsHs losses occur from ethyl and isopropyl esters to produce vinyl radicals. Although this (M—C,H3,.;)° ion is often formed in relatively low abundanee, you should be able to recognize it from the unusual masses 27, 41, 55, etc, lost (Table A.5) in its formation. This rearrangement provides useful characteristic of esters (Figures 3.14 and 3.15), thioesters, amides (Figure 3.20), phosphates (Figure 3.28), and even sulfones (R,SO,, Fig- ure 3.27}; this is why you should mark important (M—C,Hz,_1)* ions of oxy- genated compounds (Step 4, Standard Interpretation Procedure). However, formation of the OE” product by single H rearrangement (Equation 4.45) is often the dominant process.a HO ® fe 1 oe (445) 446) HO" HoT Re One of the above mechanisms should help in the elucidation of Unknown 4.21 Ununown 4.21 me int mie Ine 27 38 6. 0s 2 25. sr 1s wow, 2 5a 6 oe 1% 68 3 24 15 20 53 03 mos 1% 05 a 60 7% 30 1513 2 03 rs] “903 @ 09 % 03 1603 5 30 soa o7 1720 sou 105100 wo 03 5208 1678 27 170s m 1954411 summary of ype of reaction mechanism 83 4.11 Summary of types of reaction mechanisms. The summary inside the back cover is intended to underscore the relationships of the common types of reactions which ions can undergo, using examples from this chapter. You should use this as a checklist when you are attempting to predict the spectrum of a molecule; to use it effectively, however, you will have to understand the material of the preceding sections. The following conventions have been employed. R indicates an alkyl group, but this could also contain another functionality; if species contains more than one R group, these are not necessarily identical. Y indicates a heteroatom functionality, but itis not limited (o the valence indicated (thus “YR” might actually be a chlorine atom). U indicates a saturated connecting chain of two or more atoms; © indicates a stable cyclic or unsaturated molecule. In reactions in which an alkyl group is lost, the loss of the largest is generally favored. Note also that in this summary, as well as in the rest of the book, the designation of a homolytic bond cleavage often omits the second fishhook; it should be understood that the second electron of the bond becomes the unpaired electron of the radical product.5 Postulation of Molecular Structures ‘There are several major kinds of general structural information available in the mass spectrum. These are particularly helpful if you have no information from other sources concerning the unknown molecule. The over-all appearance of the spectrum and the low mass peaks can give a general indication Of the type of compound; use the figures in Chapter 3 as examples for study. Furthermore, the neutral fragments lost in forming the high mass peaks can provide information on specific structural features. The fragmentation behavior of the indicated type of molecule is then used to postulate structures for the unknown. Be sure fo examine your unknown spectrum for each of the types of information described here, as outlined in the Standard Interpretation Proce- dure inside the back cover. 5.1 General appearance of the spectrum A brief inspection of the bar-graph spectral presentation can tell the exper- enced interpreter a substantial amount about the unknown molecule. You have already seen how the mass and relative abundance of the molecular ion indicate the size and general stability of the molecule (Section 3.6), In addition, the number of abundant ions in the spectrum and their distribution in the mass seale are indicative of the type of molecule and the functional groups present. For example, a glance at the spectrum of Unknown 5.1 should tell you that this isa highly stable molecule. Deduce its elemental composition; this should correspond to a value for rings plus double bonds which is consistent with this stability, Not only are there no weak bonds in the molecule, but apparently the main fragmentation pathways are of approximately the same low probabil What is a possible structure?386 5 Poxtlation of Molacuar Structures Unknown 5.1 mit me int me Int 8 18 ow, wr a7, ag est we 74 © 02 maT 3 (Os. 6a 49 ms OB. sR m8 2688 2 16 7 eo) wr 88 et 14 a 4 128100 6 27 Cl == m1 8 74 1008: es 09 Relative intensity 8 eddetet thet Soccer Figure 5.1. Mass spectrum of nicotine. ‘A molecule composed of stable substructures connected by relatively weak bonds should give a spectrum with a few prominent fragment ions, such as that of nicotine, Figure 5.1 In the spectrum of Unknown $.2 the m/z 43 peak is by far the most prominent in the spectrum. The bond that is cleaved in the formation of this ion would be expected to be the weakest in the molecule from its known chemical reactivity,87 Unknown 52 % ts ye 3 i g = 20 Sa an] 2716 2 on s Sw é Soe 2 i e on rain to oma mee eee Unknowns 5.3 and 5.4 are the spectra of larger molecules producing only a few prominent peaks. In evaluating the m/z 50 and 51 peaks of Unknown 5.3, don't forget that the importance of a peak decreases with decreasing mass, as well as with decreasing abundance. Unknown 5.9 mz int mz mo 15 =» ou 6 62 7 18 6 214 104 Soa 105 Oo 8 108 sos 107 aa 20) 128 Relative intensity 181 152 183 156 181 182 183 4 34 18 14 8 08.Unknown 5.4 mz In mz Int mz Ink a 8 mm 66 199100. ary) 2, wo 75 213 7% 28 wi 88. % 15 7 36 224 eon is 03 ua 02 on m4. 18508 5183 1 30 1955 6 09 m3 14 1774 eon 1440 18831 6 19 moot 48822 1002 100 ie 1 11 In unbranched alkanes, the most easily cleaved bonds (the o-bonds between secondary carbons) are nearly equivalent in bond strength. The resulting mass spectra (Figures 3.2 and 5.2) have many peaks of regularly varying abundances. Study these typical “picket fence” spectra so that you can recognize them on sight. Note the striking similarity of the spectra of Figures 3.2 and 5.2, despite their difference in molecular weight. All the “important” peaks except M"” are even-electron ions. The rates of the initial decomposition reactions of any molecular ion involving cleavages of the diflerent carbon-carbon bonds are comparable to each other, as are the secondary decompositions of the primary product ions. This accounts for the regular increase in abundances with decreased sizes of the alkyl ions. The possibility of rearranged products of greater stability becomes higher with the secondary reactions, so that the structures of the smaller ions, such as CyH,* and C,H", are largely the more-stable branched carbonium ion structures. Thus the distribution of ions is maximized in the Cy and C, region of higher alkanes. Further substitution of a carbon atom increases the probability of cleaving its bonds: compare Figures 32-34 and 4.1. After you rercad Section 4.5, try Unknowns 5.5 to 5.7, which are Cy Hy. isomers. Don’t forget that a-bond cleavages give EE* C,H3,.;* ions, not OE C,H,” ions. In these unknowns ignore such important OE” ions, which are discussed in Section 9.20 = 60g si wos Annas aseasoap Sead, 1 =} ay jo saauepungr aanau a4, "SURO red ——eaeeayeaeaaa9@@*”=m”—=”—”—” oer” ‘psu oanUnknown 5.5‘5.2 Low-mass ton series 1 Alkanes substituted with electronegative groups that do not significantly lower the ionization energy (eg, Cl, Br, NOz, CN) show very similar effects of chain branching on the C,H3,.” ion abundances (see Figures 3,233.25). 5.2 Low-mass ion series Study the mass spectra in Figures 3.2 to 3.28 and this chapter for such “picket- fence” peak series, especially at lower masses. You should find many spectra in which several groups of peaks are separated by 14 mass units; others have a slightly smaller separation (12 or 13 mass units). In Figures 3.2 to 3.28 these peaks have been marked with a bar top. Such low-mass ion series are important for providing general information (heteroatoms, rings-plus-double-bonds) on particular substructures. The individual peaks at higher masses representing primary fragmentation products are more important as indicators of specific structural features (review Section 3.4 on the relative importance of peaks) Although secondary decompositions commonly involve rearrangements (EE", Section 4,10), the low-mass C,Hz,+1” ion series so produced in Unknowns 5.5 to 57 is a reliable indicator of the presence of an alkyl chain. Unknown 5.6 actually has CH, and C,H, (but not CH.) groups attached to a tertiary bon, although [C5H,*] > [C,Ho*] > [CH,"]; it is the losses of CH," and ‘C,H: that produce the “important” peaks at m/z 211 and 169, respectively. Try to identify any low-mass ion series before postulating specific structures for higher mass peaks. At lower masses there are fewer possible ion assignments for a particular mass value (and these are usually EE"); a sizable m/z 29 peak is usually CH," or CHO*, whereas m/z 129 has literally hundreds of isobaric possibilities. Thus the information from low-mass ion series can limit the possible assignments for high-mass ions. Series separated by CH, groups. Many structural features give rise to a significant homologous series of ions starting at the low-mass end of the spectrum, such as the continuous series of alkyl ions, C,Hy_.;*, in alkane spectra. The high probability of rearrangement on forming the lowest-mass ions produces a much more complete homologous series with much less variation in ion abundances than at higher masses. Thus a quick inspection of the spectrum of Un- known 5.8, which is known to contain no oxygen, starting at the low-mass end indicates the presence of an alkyl moiety. The fact that the C,Haq4,* ions can be traced from CH, to CsH,,” (to CyH,5" at higher sensitivity) is a valuable indication of the maximum size of the alkyl moiety92 5 | Postultion of Molecular Structures Unknown 58 ere mz int meine maint 1% 32 08 02 a 34 & 10 09 mort & ‘or 10328 on 7 08 ioe 58 re @ 14 is 2 aon 08 wet 2 ‘30 nm 08 Ww 3 an os ie 08 “06 Py) ie 22 2 1s nm 61 1% 02 BB me 85 i 8s 2 18 38 it 08 5 19 03 a4 & 4 & 18 we 03 20 0 14 1% 0a @ 10. 10 = ‘08 2 8 ia ® 24 ® 75 12 03 z i g 3 1 » ill ele 7% ° 1 8 ‘2 w e ‘ Ae Vet =D wo wm) two | two | wo [As shown in Table 5.1, the C,H,y.;” alkyl series gives peaks at m/z 15, 29, 43, etc. Insertion of an oxygen atom (such as substitution of H by OH) gives the m/z 31, 45, 59, etc, CH3,+10” series which is characteristic of saturated alcohols and ethers; see Figures 3.8 and 3.9, Saturated amines yield the C,Hy_y2N* series ‘m/z 30, 44, 58, etc; now these EE* ions are at even mass numbers (Figures 3.16 to 3.18). Increasing the number of rings-plus-double-bonds by one decreases the ‘mass by two units; aliphatic aldehydes and ketones give the C,H,-10° series at m/z 29, 43, 51, ete. (Figures 3.10 and 3.11). Unfortunately, this overlaps the CyHayea series, since CO corresponds to C,H, in mass. Be sure you have tried to assign elemental compositions to these peaks; if [44* 1/[43*1 is only 2.2%, the peak cannot be part of a C,Hz_y:* seties. Conversely, if the molecularFunction” Formula a mie values iris CoHana = 40 54 68 e2 Alkeny,eycloalkyt CH ° 27 41 55 69 83 Alkenes, cycloalkanes, alkyrv= CHa” + 2 42 56 7084 Allyl Cena? 42 1820 43577185 ‘Aldehydes, ketones Coin 07 +2 29 43 57 71.85 ‘amines CHereaN" 43 30 44 58.72 06 ‘Alcohols, ethers raha i St 45 5973.87 ‘acids, estore Coen sO} + 45 5973 87 ‘Thiois,eultdes Cian +6 33° a7 61 75 89 hloroalkyt cine “8 35 49 63 7791 Aeomatic on 2t0 8 —__98,39,50-52, 69-65, 75-78" “connected a strate alphate subsructre tno tmane 4a (omey 176) a ose number corresponds to an Neonianing or OE” seis. “Forwmen Hie moles oom proton any Tofthese peaks may not be of sgnicant abundance na parkclar spectrum, ena neighboring peaks jon contains no oxygen, this cannot be the C,H,,-O* series. Table 5.1 shows @ similar overlap in the 31, 45, 59, etc. series between the C,H,,.,0* ions (alcohols, ethers) and the C,H3,-.,* ions (acids, esters), a more complete list is given in Table A.6. Tn evaluating such ion series, use the criteria of peak importance; don't forget that in a “peak group” (compositions differing only in the number of hydrogens) the peak with the most H atoms is the most important. The spectra of alkanes (Figures 3.2 to 3.4, Unknowns 5.5 to 5.7) contain both C,H,..' and CyHasy," series; obviously, the presence of the former should not’ be interpreted as indicating an alkenyl or cycloalkyl group (Table 5.1). Both of these series also appear in the spectrum of 1-dodecene (Figure 3.5; however, now the C,Hay-1° series is more important than C,Hz,+1', since the former can be followed up to much higher masses ‘Note in the dodecene spectrum (Figure 3.5) that the OE" series C,H,” is also prominent, generally larger than the C,Ha,y* seties. However, for an unknown showing important low-mass ions at even mass numbers, do not forget that these could also be due to OE" ions formed from specific cleavages, such as m/z 58 in Figures 3.10 and 3.11; look carefully to see if there is actually a series of such even-mass ions, and do not be fooled by isotope peaks (in Figures 3.10 and 3.11 the m/z 30, 44, 72, and 86 peaks are entirely due to "°C isotopic contributions). Such a series of even-mass ions can also be due to4 '5 J Portuation of Molecuiar Structures EE" ions containing a nitrogen atom, such as the m/2 30, 44, 58, 72, ete. peaks in Figures 3.16-3.18, Here, a multiplicity of f peaks in this series indicates that the rest of the spectrum must be studied carefully for other signs of the presence of nitrogen, ‘The spectra of Unknowns 5.9 and 5.10 are very similar, with m/z 224 shown to be C,gH,2"" in both, However, one is unique in containing an important ion series (note that these are best identified by starting at the low-mass end of the spectrum). What possible kinds of molecules are these? z 5 8 q i ® Ion series separated by CH and C. Compounds with a hydrogen-to-carbon ratio much less than two cannot show a significant series of ions spaced at CH, intervals (see Unknown 5.1, naphthalene, CoH). The low-mass ions of such compounds can still show characteristic series. A very important series is that shown by aromatic hydrocarbons at m/z 38. , 50-2, 63-5, and 75-8 (CyHo.sx 10 C,H,). Heterocyclic compounds containing oxygen and nitrogen atoms and5.2 Low-mass ion series Led compounds containing these elements near an aromatic ring show peaks at similar m/z values plus additional peaks at m/z 40, 53, 66, and 79 (the “high” aromatic series of Table A.6) because of replacement of CH by N, ot CH; by O. Although the aromatic series is often of relatively low abundance, the unique- rss of its mass values (Table 5.1) usually makes it quite recognizable; note its absence in Unknowns 5.9 and 5.10 compared to 5.3, 54 and 5.8, Using Figures 3.210 3.27 as unknowns, se if you can deduce which contain aromatic moieties using this series. 'As can be seen in Figures 3.23 and 3.24, the replacement of hydrogen atoms by halogen atoms, X, changes the homologous series spacings by CHX or CX, causing a marked change in the appearance of the spectrum. Additionally, the electronegative halogen atoms are much more easily lost than hydrogen atoms, so that ions separated by X and HX in mass are also found. For chlorine and bromine, these are casily identified because of the “isotope clusters.” Fluorine and iodine have only one natural isotope each—!°F and '271—but these can usually be recognized by the very unusual mass differences they cause. Recognizing ion series. Chemists quickly become able to identify carbonyl peaks in an infrared spectrum or CH, peaks in a proton NMR spectrum. Simi- larly, you will feel much more “at home” with mass spectra if you can easily recognize the possible significance of mass values. Use the C,Hayii” series 15, 29, 43, 7, ele. as your reference scale. Note that in the 1006 region, ths is only {wo mass units lower (113, 127, 141, 155, etc), because (CH); corresponds to 98 ‘mass units (Figure 5.2); the 200s region is then 211, 225, 239, 253, and so forth. ‘Also, because CH; (14) can be replaced by NH (15) or O (16), one can estimate the total number of C, N, and O atoms by dividing by 14 if the spectrum contains a significant saturated ion series. For unsaturation, such as indicated by an aromatic ion series, add twice the r + db value (for phenyl, add 8) before dividing by 14, As a handy rule of thumb, 100 mass units are approximately (CHN+Op. In Unknowns 5.11 and 5.12 notice in particular the general appearance of the spectra and their ion seriesoanown 5:31 ent ime ink me im ear @ 92 @ 08 me 88 & 58 % 2 8 45 © 09 & 08 us 43 10 as ® 20 & 08 ior s8 es 08 moors nea 2 2 98 10 “7s sos ‘Os % 30 je 08. a 8 m8 ie sis ‘to me 33 ee 2 42 Os 3 100, Os a Oe oo a 08 its 3 z 30- é 5 - — . 1 om ® 1 1 Unknown 5:12 ei 2 wo ® wD 30 a oP Bo a xB £ 2 Os Ew " a?) i ms 3 ” sos a) es) ew ms el? ® 8 (hae Fa a meee ee & 2a5.3 Smal neutral losses 97 5.3 Small neutral losses Perhaps the simplest and most specifi assignments that can be made in the spectrum are for the small neutral species lost in the formation of the frag- ‘ment ions of highest mass in the spectrum, especially those formed directly from the molecular ion. For example, important ions at masses (M — 1)*, (M — 15)°, (M— 18)°, and (M — 20)" almost always represent the losses of H, CH, H,O, and HF, respectively, from the molecular ion, Because formation of such large primary ions involves the lowest probability of a randomizing rearrangement, such “smail-neutral loss” peaks are of major significance in deducing the molecular structure. Thus an abundant peak corresponding to (M—1)* indicates a labile hydrogen atom (and the absence of other labile substituents). A list of common small, neutral fragments lost in the formation of important spectral peaks is set forth in Table A.5; their use as tests for the molecular ion was discussed in Section 3.5. As discussed in Section 3.4, these high-mass peaks are of high relative importance; even those of <1% intensity can be useful for structure determination. The specific loss of a larger neutral can also be structurally characteristic, but its identification often requires distinction from adjacent low-mass ion series. This is less a problem with low-mass odd-clectron ions, since OE" ion series are relatively rare. However, carefully examine any EE* ion representing a peak more important than any other in its ion series, especially if it is nearly the highest mass in its peak group; replacement of CH, by NH or O raises the mass and usually lowers the ionization energy. In the spectrum of hexyl formate (Figure 5.3), you should easily identify the C,H,_.,0° 1,45, 59, 73, 87, and 101. However, the tiny peak at m/2 47 is especially important, because itis at the highest mass of its peak cluster m/z 36-47, and there are negligible peaks in its ion series at m/z 33, 61, 75, and 89. Examining Table A.6, we can see that this strongly indicates the presence of a second oxygen or a sulfur atom. If you knew the molecular weight, you should have also marked 7 as an important (M — C,H,,.,)* ion of an unknown that could contain —8 Relative intensity 8 me Sm wm | We 1m Figure 6.3. Mass spectrum of hexyl formate‘oxygen. The m/z 47 peak actually arises by the double-hydrogen rearrangement oss of CoH, a characteristic dissociation of formates (Section 4.10), Ifthe “logical neutral loss” test indicates that the peak of highest mass is not the molecular ion, this illogical mass difference then represents the difference between the masses lost from the molecular ion in forming these two fragments, For example, if there is an important peak three masses below the peak of highest mass, this could represent the loss of HO from any unstable molecular ion that also easily loses CH. An important peak 13 mass units below the peak of highest mass could be due to the loss of CH, or CO from a molecular ion that also loses CH, easily, Note that if the mass difference is an odd number, and nitrogen is not present, then one of the two fragment peaks must represent an OE" ion. . 7 2 a tdeler sel» 1]Rolatve intensity ‘$4 Characteristic ions. 99 In Unknown 5.13, chemical ionization and exact mass measurements show that m/z 119 is formed by the loss of C,H, from the molecular ion; such small neutral losses are indicative of the structure. Did you identify both important ion series? 8.4 Characteristic ions Deduction of the structural information from a larger ion is more dificult, because of the larger number of theoretically possible assignments for it. Despite this, for many specific mass (and, especially, elemental composition) values, there are only a few characteristic structural groupings that commonly give rise to the corresponding peak in mass spectra, Such “characteristic ions” are sur- prisingly helpful in suggesting possible fragments of the molecule. You should already be familiar with some of these, like the m/= 30 from amines, m/z 77 from phenyl, and m/z 105 from methylbenzyl or benzoyl (Unknown 5.3). If Figure 54 were an unknown, the experienced interpreter would immediately suspect phthalate from the presence of the base peak at m/z 149. However, in a data base representing 140,000 different mass spectra (MeLafferty and Staulfer 1991), only 1530 of the 700 spectra giving @ m/z 149 base peak are phthalates, so that such leads must be carefully checked. Phthalates are ubiquitous impurities found in ‘mass spectra, since they are common components of plasticizers (tubing, cap liners, gaskets) and chromatographic column packings. Thus the next step in the interpretation of the spectrum is to note the possible structural significance of all important peaks. Where more than one possible interpretation exists, be sure to note all of them; if other evidence in the spectrum eliminates one or more of these possibilities, these remaining will be much more meaningful. Possible assignments for ions are given as part of the ion series of Table A.6, Mass Spectral Correlations (McLafferty and Venkataraghavan 1 a BB ». Oo, | y at 7 tephra yet weer Figure $4, Mass spectrum of diethyl phthalate100 5 | Posulation of Molecular Structures 1982) shows what elemental compositions and structures are possible for a peak, and what the relative probability is for cach of these postulations, The Important Peak Index of the Registry of Mass Spectral Data (McLafferty and Stauffer 1991) provides a listing of compounds which give a particular m/2 value as the ‘most important, second most important, etc. peak in their spectra, 5.5 Postulating possible structures Often the first six steps of the Standard Interpretation Procedure (facing back cover) yield a confusingly large number of structural clues, since a mass spectrum can have hundreds of peaks, of which even those of <1% abundance can be important. At this stage itis best to concentrate first on the structural fea~ tures indicated the most clearly. Review (or write down) the general type of fragmentations expected (inside back cover) for the indicated substructures or compound classes. These product ions will appear in ion series whose masses depend on the size and kind of substituents; such ion series differing by CH, groups were discussed in Section 5.2, but an ion series can also contain high mass ions from specific cleavages typical of functional groups. Now check the unknown mass spectrum for its most important peaks belonging to each of these series, and use their position in the series to limit the number of structural possibilities for each corresponding substructure or compound class. For example, in Unknown 5.13 there are strong indications that this is a chloroalkane; the alkyl moiety accounts for the peaks at m/z 29, 43, $7, 71, and 99, and the chloroatky! moiety accounts for the peaks at m/z 63/65, 77/79, 91/93 and 119) 121, Mechanistically, sigma-bond cleavage at alkane branches should be the most facile dissociation pathway; the important peaks in these series at m/z 57, 99, and 119/121 thus should represent the substituents C,H, CHC! (loss of 49), and C3Hs. Placing these on a tertiary CH can account for the m/z 148 molecular ion, making this a possible structure of the unknown. In Figure 5.3, the isolated m/z 47 peak indicated that this might be a formate ester (Section 5.2). Mechanistically, the alkyl functionality would produce an alkyl ion series; both C,Hy_40° and C,H,,-/O; products at m/z 31, 45, 59, 73, 87, 101 would be expected, as observed. Additionally, a single-hydrogen rearrangement with charge retention would produce a peak in the series m2 46, 60, 74, of which none is appreciable, and with charge migration in the series m/z 28, 42, 56, 70, 84, etc. Here the important peak at m/z 84 (CgH,,), of highest mass in this series, is then a strong indication that this is a hexyl ester; the OE* base peak at m/z 56 does not misleadingly indicate a butyl ester, since examina- tion of all peaks in this C,H,” series shows the higher mass, and thus the potentially more important, CH," peak. Charge migration is favored over charge retention (Section 4.9) because the ionization energy of formic acid, 11.3 eV, is larger than that of alkenes (9-10.5 eV)56 Assignment of the most probable structure 101 5.6 Assignment of the most probable ructure The above steps, and all other available information, should be used fist to list all structures conceivably possible. For each serious candidate structure, predict its spectrum from the appropriate dissociation mechanisms, and compare this with the unknown spectrum carefully. The elimination of all but one possibility for the molecular structure does not, of course, prove that this one is correct. Prediction of fragmentation pathways becomes increasingly difficult with increasing size of a molecule. For this, reference spectra are particularly valuable; by far the largest available printed collection is the Registry of Mass Speciral Data (McLalferty and Stauffer 1989), containing the spectra of more than 112,000 different compounds, of which over 89,000 are represented by structural images. The expanded 1992 Registry on electronic media contains 220,000 different mass spectra. Ifa reference spectrum of your proposed compound is not available, try correlating the reference spectra of similar molecules. Remember that abundance values can vary by more than an order of magnitude between 03 % 08 072. 09 7% 08 sos 22 30 7 2 wt 18 10. mm 18 18844 09 7 50 ar 37, os. Os 1813 15 1 48 12 1. Pa Relatve intensity 8 8 got Bs 8 2 a a r ee ee ee eee102 5 Powtlaton of Molcuar Structures instruments; so you must measure a reference spectra of the postulated compound under the same instrumental conditions used with the unknown in order to have high confidence in the answer. Even here, it is highly important to understand the “blind spots” of mass spectrometry (Chapters 8 and 9), such as the close similarity between the mass spectra of meta- and para-aromatic isomers, or the insensitivity to chirality, before making absolute structural assignments. Follow the “Standard Interpretation Procedure” in attempting to assign structures to Unknowns 5.14 and 5.15, Unknown 5.15 Relative intensity6 Auxiliary Techniques ‘The limitations of the structural information in the normal mass spectrum can be partly offset by special mass-spectral techniques. Although a complete description of these is beyond the scope of this book, you should have a basic familiarity with their capabilities. 6.1 Soft ionization methods Low-energy electron ejection, Lowering the energy of the bombarding electrons (eg. to 15 eV) will also lower the average (but not the minimum) internal energy of the molecular ions, Such low-energy M"’ ions can also be produced by field ionization, charge exchange, or photoionization (Section 7.4). For structure elucidation it is sometimes useful to eliminate higher-energy reactions that give secondary product ions that are much less representative of the original structure. However, lower electron energies increase the relative abundance of primary rearrangement reactions (Section 7.2). Further, lowering the electron ‘energy decreases the absolute abundance ofall ions; although the relative abundance of the molecular ion increases, it nevertheless is more difficult to detect at lower electron energies (unless it has been obscured by fragment ions from 4 higher-molecular-weight impurity). Lowering the molecule’s energy (such as with supersonic expansion, Amirav 1991) before ionization does produce M”" of even lower internal energy, increasing [M*] (Section 7.4) EE? molecular species from ion-molecule reactions, The most common method of producing a stable ion containing the sample molecule is to react it with an ionized EE” species. An early example was the use of high sample pressures under El conditions to produce MH” ions from compounds not yielding M* (McLafferty 19576), Chemical ionization (CI; see Munson and Field 1966, Harrison 1992) is very useful, in that most (although not all) molecules that do 103104 8) Ausary Technique not yield molecular ions by FI can produce Cl ions indicative of the molecular weight. CI conditions produce abundant thermal electrons, giving highly efficient electron capture for negative ion formation from electronegative molecules (Figure 1.2; Budzikiewicz 1981, 1983b; Bowie 1984, 1989; Hites 1988), Recently a wide variety of powerful methods for the ionization of large molecules (even of molecular weight > 10° have been developed; most yield such EE* molecular species (Section 6.2). Chemical ionization. For Cl the reagent gas R is introduced into the ion source (~05 torr, ~70 Pa) at a concentration in large excess (~10*:1) to that of the sample, and is ionized by electron (~-500 V) bombardment or electric discharge (Hunt 1975), The R* ions initially formed can react further with other R molecules to form reactive ion species that then attack the sample molecule M: Ree — RM ee 1) RU eR RH + ROH, or (ROH) H RH. (6.2) RH + M ——= Re MY (protonation) (63) (R-H)' # Me (R=2H) + MHT (protonation) 64) (RH) + MM ——= + (=H)" (hyde abstraction) (65) AY +M —— Ren (charge exchange) 66) ‘Among this wide variety of possible ionization reactions, the most common are: protonation (Equations 6.3 and 6.4), which is favored for sample molecules of proton affinity higher than that of the reagent; hydride abstraction (Equation 655), which is common for lower-proton-affinity molecules, such as alkanes; and charge exchange (6.6), which is favored for reagents of high ionization energy, such as helium. The internal energy of the resulting ionized M species depends oon the reagent chosen and the ion source temperature and pressure (number of thermalizing collisions). For example, Figure 6.1 (Fjeldsted et al. 1990) shows the CI spectra of lavanduyl acetate (PA = ~8.7 eV) using CH, (PA = 5.7 eV), isobutane (reagent C,H", PA of iso-C,Hg = 8.5 eV), and NH, (PA = 9.0 eV) Further dissociation is nearly complete for the highly exothermic CH,” reaction, and minor for the NH,” reaction. Such unimolecular fragmentations obey the mechanisms outlined in Chapters 4 and 8; the major m/z 137 product ion is formed by CHyCOOH loss, consistent with Field's Rule: PA(CH,COOH) = 8.2 eV, PA(C,oHyg) = ~817 eV. The m/z 154 product in the NH/CI spectrum corresponds to CH;COOH loss from (M + NH,)°. Thus CI spectra can pro- Vide structural as well as molecular weight information, Similar CI spectra can01 Bell lentestion metodo 105 q z*] em se nae ope ce i sar ie @ Ea pete pe mato by alo! Wee seo” 1 abo” abo | 21a MNT mee do” Talo” Te” be! T Tabs” "cto Figure 6.1, The Cl mass spectra of lavanduyl acetate (MW 196), using CH,, iso-C.Hyo, and NH as reagent gases, be generated at much lower pressures by using long-lived trapped ions in the ion cyclotron resonance (ICR; see Lehman and Bursey 1976, and Bowers 1979, 1984) or ion trap (IT; see Cooks er al, 1991) instruments. For definitions of PA and gas-phase acidity and basicity, see Bursey 1990.108 1 unary Techn 6.2 Ionization of large molecules For conventional direct-probe introduction, a sample must have sufficient vapor pressure and thermal stability to be vaporized in the ion source. This severely limits the application of mass spectrometry to important samples such as biological macromolecules, industrial polymers, and petroleum residues. Inten- sive recent research progress has resulted in highly useful methods, The most widely used are described briefly here; many recent references (Section 68) give extensive details Fast-atom bombardment (FAB). Introduced by Barber et al. (1982), FAB is particularly suitable for polar molecules, providing ionized molecular species for molecular weights up to ~20 kDa (Williams et al, 1987; Tower 1989), A solution of the sample in a low-volatiity matrix such as glycerol is bombarded with fast, heavy atoms (¢., Xe; ions such as Cs* give similar results) in the ion source, producing the continuous ion beam necessary for scanning instruments ‘The method is very convenient for appropriate samples, but matrix reactions produce background ions at nearly every mass value, Plasma desorption (PD) and laser desorption (LD). These pulsed ionization techniques are particularly suitable for the time-of-flight instrument, which has the additional advantage of unlimited mass range. TOF resolving power of 500-1,000 has been a disadvantage, but recent improvements are promising (Benninghoven 1989; Karas er al. 1989; Hillenkamp et al. 1991). PD, pioneered bby Macfarlane (1976), first showed that mass spectra could be obtained rou- tinely from large molecules. Fission of **#Cf produces two 100-MeV products that simultaneously ionize the thin-film samples and start the TOF clock, but produce litle ion fragmentation. Tonization of molecules as large as 50 kDa with mass measuring errors of +0.1% have been reported Pioneering laser desorption (LD) capabilities (Posthumus et al. 1978) have been greatly extended (Karas and Hillenkamp 1988) by dissolving the sumple in a solid matrix that is a highly efficient absorber of the laser radiation, so as to ionize molecules as large as 300 kDa (Hillenkamp et al. 1991). The absence of matrix effects and mass measuring errors of +0.01%,-0.1% make LD a particularly promising method for protein mixtures (Chait etal. 1990) Electrospray ionization (ESI). Pioneered by Dole (Dole et al. 1971), for ESI a solution of the sample is sprayed at atmospheric pressure through a several- Kilovolt potential difference toward the differentially pumped entrance to the mass spectrometer (Smith er al. 1992), The resulting droplets are electrostati- cally charged; as the solvent evaporates, electrostatic repulsion produces smaller and smaller droplets, until the macromolecule is expelled “saturated” with charges (Fenn et al. 1989). Thus a protein can bear a proton for every 5-17 amino acids, yielding peaks at m/z 600-2000 even for 200 kDa proteins (Feng etme al, 1991), Similarly, polynucleotides can yield negative ions of such m/z values by losing a proportionate number of protons. This drastically reduced upper limit for m/z measurement makes ESI amenable to most types of mass spectrometers. ESI mass spectra have been measured for molecules as large as $ x 10° Da (Nohmi and Fenn 1992), and structural information has been obtained from albumin (66 kDa) by tandem mass spectrometry (Loo et al. 1991). Using Fourier- transform (ICR) mass spectrometry (Section 1.3), ESI spectra of myoglobin (17 kDa) show 900,000 resolving power and <0001 Da mass-measuring errors (Beu etal. 1993), Pyrolysis. Useful structural information about complex mixtures of high molecular weight, such as bacteria, plant specimens, coal, high polymers, and sewage sludge, can be obtained from the mass spectra of their thermal decomposition products (Meuzelaar er al. 1980, 1989; Schulten 1986; Balistreri etal. 1991), To minimize secondary reactions, small samples (10™* to 10°? g) are preferable, as are reproducible pyrolysis conditions, such as rapid RF heating of 8 wire to its Curie temperature. Laser, spark, and other flash-heating methods have also been used. Of particular interest is an automated system for continuous particle beam sample intoduction with Curie-point pyrolysis in the MS vacuum chamber. This system can distinguish different strains of bacteria, reporting results every 15 s (Snyder and Harden 1990) 6.3 Exact mass measurements (high resolution) Measurement of the mass of an ion with sufficient accuracy provides an un- equivocal identification of its elemental (and isotopic) composition. This technique is often referred to as “high resolution” mass spectrometry, since double- focusing (Figure 6.2) or FT/ICR (Section 1.3) instruments are usually used. However. if interfering masses requiring high resolution are absent, sufficiently ‘accurate mass measurements (~20 ppm) can be achieved for low-mass ions with single focusing or quadrupole instruments of 1,000-2,000 resolution, Elements can be identified in this way because monoisotopic atomic weights are not exact whole numbers. When we take as standard the mass of !?C as 12.00000000 (sce Table A.t), then m for 'H = 1,007825035, for "*N 14,00307400, and for 10 = 1599491463 (the least significant figure, 10° daltons, represents 9.3 eV of energy). Every isotope has a unique, characteristic “mass defect”; so the mass of the ion, which shows the total mass defect, identifies its isotopic and elemental composition, For example, an ion with a mass of 43.0184 must be C,H,O*; it cannot be CH," (m = 43.0547), C3HgN* (m = 430421), CH,N,* (m = 43.0296), CHNO™ (m= 43.0058), or C3F* (m = 42.9984), To distinguish these compositions requires an accuracy in mea~ suring mass of 130 ppm. The usefulness of elemental composition information increases exponenti- ally with increasing mass, as does the required mass-measuring accuracy. Figure108 ‘wdd 5-7 Jo fovsno0e stuawnasur [erosouos wapoy “(661 UOT ‘Loy poreua8Sexa Ul usoys) K832u9 fed Uo! Jo Sis Om at "saIoWOsTIAds Sse TUISNO9}-9}QnOp LOsUYoY-I9IN. 9 aINBLS us e190, soshiour uaGlew eristanesnenponreensercatangonecneunanan eaoo-000§ RSSRRRRNART A ied Figure 6.3, Exact masses of possible ions of m/= 310 containing carbon, hydrogen, not ‘more than three nitrogen atoms, and not more than four oxygen atoms. 63 shows the exact mass ofa variety of possible fons of molecular weight 310; distinguishing these requires a mass-measuring accuracy of 2 ppm. 6.4 Tandem mass spectrometry (MS/MS) “Double resonance” techniques are useful in several spectroscopic methods. In ‘mass spectrometry there arc analogous MS/MS techniques for measuring the mass spectrum of a peak in a mass spectrum, Such secondary unimolecular ion reactions should be the same as those producing normal mass spectra. MS/MS has two major applications (McLafferty 1983; Busch et al. 1988), ‘One application uses the first mass spectrometer (MS-I) as a separating device for mixtures; soft ionization produces MH* or a similar molecular species for each component. After MS-I separation, energy is added to MH” to yield dissociation product ions that are then separated in MS-II; this mass spectrum is then used for structural characterization of that mixture component (McLatfferty ‘and Bryce 1967; Krueger et al. 1976; MeLafferty and Bockhoff 1978). One of the most important MS/MS applications has been to protein sequencing, with initial chemical or enzymatic degradation to a complex oligopeptide mixture, and partial LC separation, with the impure LC fractions ionized by FAB. MH* ions corresponding to each of the oligopeptides are separated in MS-I, fragmented by adding energy, and the product ions separated in MS-II to provide nearly complete sequence information (McLalferty et al. 1970; Wipf et al. 1973; Biemann and Martin 1987; Tomer 1989). The tandem double-focusing mass spectrometer (McLalferty 1980a) has proven particularly valuable for this, with FT/ICR promising for larger peptides (Beu et al. 1993). The most widely used instrument for such MS/MS mixture measurements has been the triple quadrupole (Yost and Enke 1979; Hunt et al, 1989) using low-energy (10-100 eV) collisions in the central quadrupole. Such collisional activation (CA) with a target gas is the most common method of adding energy to the separated ions, although collisions with a surface and by photons, electrons, and ions can be110 ©) Ausary Techniques used. High-energy (e.g, 10 keV) CA causes dissociation (CAD) of single-charged peptide ions of masses up to ~2.5 kDa Biemann and Martin 1987), but of multiply charged ESI ions as large as 66 kDa (Loo et al. 1991), ‘The second application involves hard-ionization (EI) mass spectra, measuring MS-II mass spectra of a molecule’s fragment ions to characterize their structures (Shannon and McLafferty 1966). For example, in the mass spectrum of the hypothetical molecule A,B,C, the presence of ions corresponding in mass to ABY and ABC’ could indicate cither of the molecules A~-B—C—B—A or A—B—B—C—A. However, the presence of AB® in the secondary mass spectrum of the ABC* fragment ion would be possible, barring rearrangements, only for the structure A—B—C_B A. In the mass spectrum of N-methyl-N- isopropyl-N-butylamine (Figure 9.18) a-cleavages give the prominent ions at m/z 86 and 114, and their further rearrangement decompositions yield other abundant ions at m/z 44 and 58, respectively (Equation 6.7). If this were the spectrum of an unknown, the compound N-methyl-N-ethyl-N-2-pentylamine would also have to be considered, since it should also give rise to these peak (Equation 6.8). However, the observation of m/z 58 in the MS-II spectrum of mm/s 144 would eliminate the latter compound from consideration; its spectrum Should show m/z 114» m/z 44, onomjene, SH. ono “eye ot ot, oe « mzii4 mz58 (CHy,CHIICH,CH, (67) iF « $a . “Ces (oHoeoHi—or, SEES Hote by oH, izes rizae Hy . = Cotte ‘ orient, SH ott coe oH, by on er si @ mizits mize cnscticnca (63) CH, 2 CH CHy oS aah, ote yg crongion HC dn Hs cH, miz86 mz58apacromeny (aren? ae Unknown 6.1. Try Unknown 4.19 again, using the metastable ion (m*) data. For the reaction m, —> m3, m* = m?/m, ‘When run under the same experimental conditions, the normal EI mass spectrum of a particular molecule, such as toluene, is independent of the sample's source, and can thus serve as a useful “fingerprint” for identification. In the same way, the high-energy CAD spectrum (McLalferty et al. 1973a,b) of a particular ion is virtually independent (+5% for peaks from higher-energy decompositions) of its source and internal energy: CHyCH—OH™ ions from (CH,),CHOH, (CH,),CHOCH(CH,),, and Sa-pregnan-20f-ol-3-one (which has a CH,CHOH- side chain) yield CAD spectra which are identical within experimental error and substantially diferent from that of CH;O—CH,* (Van de Sande and MeLafferty 1975b). The relative abundances of products formed by spontaneous metastable ion dissociation (MI spectra, Section 7.3) and of CAD products from lower-energy processes can be affected by precursor-ion internal energy; thus, for ion structure identification, the peaks found in the ion’s MI spectrum are omitted from its CAD spectrum. In a special extension of this technique, the mass-analyzed primary ions are neutralized to form a beam of dissociating neutrals, whose products are re- ionized to form an NR mass spectrum (McLafferty et al. 1980a; Wesdemiotis and MeLafferty 1987; Holmes 1989; McLatferty 1990), Such dissociation of the Unknown 6.2 100 2 401 22 14 14 n8 23 16 08112 6) Rusary Teedaquee corresponding neutrals can make possible the quantitative (3% in Zhang et al. 1991) characterization of ions that isomerize easily, such as five C,H" (Feng et al, 1989) and four CH,” isomers (Zhang et al. 1989, 1991). “Remote-site fragmentation” developed by Gross and coworkers (Jensen et al. 1985; Jensen and Gross 1987; Gross 1989) similarly reduces isomerization preceding alkyl-chain fragmentation by stabilizing the charge away from the site. For long-chain fatty acids lithiated cations or carboxylate anions are generally useful for this, Unknown 6.2. Use the secondary decompositions indicated by the metastable jon (m*) peaks to eliminate all but one isomeric possibillty (m* = m,?/m,) 6.5 Combined techniques Instrument systems combining a gas chromatograph and mass spectrometer (GC/MS, McLafferty 1957a; Goblke 1959, McFadden 1973; Odham etal, 1984; Karasek and Clement 1988; McLafferty and Michnowicz 1992) have proven to be of high value for analysis of complex mixtures, such as those from human biological fluids, plant extracts, pollutants, industrial processes, and samples for forensic study. With an on-line computer, useful mass spectra of the GC effluent can be collected several times per second. The high-performance liquid chro- ‘matograph (LC) can separate mixtures not amenable to GC separation; LC/MS is now relatively routine, with a variety of successful interfacing techniques (Catlow and Rose 1989; Arpino 1990). Of these, particle beam (“MAGIC", Winkler er al. 1988) is particularly relevant, since it makes possible the measure- ‘ment of El spectra of low-volatility molecules as large as ~ 1,000 daltons. Other very promising combination techniques use such MS detection with supercritical fluid chromatography (Smith et al. 1985; Chester and Pinkston 1990) and capillary-zone electrophoresis (Kuhr 1990). MS/MS was described above. 66 The shift technique Often the addition of a small functional group to a large molecule such as an alkaloid changes the spectrum merely by increasing the mass of the specific ion fragments which contain this functional group, but without greatly changing the relative abundances of these ions example. An obvious example is isotopic substitution; deuterium labeling of a compound increases the mass of each ion by one for each deuterium atom incorporated, but isotope effects on ion relative abundances are generally small. Replacement of a hydrogen by a group of low influence (such as methyl, methoxyl, or chlorine) at an unreactive position (for example, a ring, especially an aromatic ring) often gives ion abundances similar to those of the original spectrum. Using this to discover the nature and position of a substituent added to a molecule has been termed the “shift technique” by(66 The shift technique a Biemann (1962), who demonstrated its great utility for the indole alkaloids These stable ring structures contain functional groups that strongly influence the decomposition, minimizing the effect on the spectrum of molecular substitution, The method is less useful for molecules containing less-influential groups, such as terpenes or steroidal alcohols. ‘Unknown 6.3. The spectrum of this unknown indole alkaloid (middle) is compared to the spectra of two known structures. What functional groups does the : vers l. a Re hee - i a. = 2. Ne Y i : tel th cle pert er oe muta t| To» et ded14 61 Auatiary Techniques unknown contain? Where are they most probably located on the molecular skeleton? 6.7 Chemical derivatives Chemical conversion of a compound to an appropriate derivative can sometimes improve the resulting mass-spectral data, either by increasing the compound’s vapor pressure or by making its spectrum more easily interpretable. ‘The former has become much less important with the development of ionization methods for nonvolatile compounds (Section 6.2). Introduction of a functional group which will strongly direct the fragmentation (for example, amino, ethylene ketal) will substantially change the mass-spectral information (Anderegg. 1988). This could be used, for example, to cause fragmentation in part of a steroid molecule about which the original mass spectrum gave little information (ection 9.6} Derivatization can be used as a chemical test of specific structural features of the unknown molecule, with the mass spectrum of the subsequent product uused to measure the results. Thus the number of enolizable hydrogen atoms in a molecule can be readily calculated from the mass spectrum after exchange with deuterium; the exchange need not be complete, since itis only the mass (not the relative abundance) of the product formed with the largest number of deuterium atoms that needs to be observed. Such exchange using CI ionization can be particularly convenient, for example, with H,0/D,0 or NH,/ND3 as the ionizing reagent gases (Hunt et al. 1972; Harrison 1983, pp. 129-131). General references Beckey 1977; Budde 1979; Burlingame and Castagnoli 1985; Busch et al. 1988; Cooks 1973, 1978; DeGraeve 1986; Facchetti 1985; Gaskell 1986; Harrison 1992; Jensen 1987; Karasek 1985; Lai 1988; Lubman 1990; McCloskey 1990; McEwen and Larsen 1990; McFadden 1973; McLaflerty 1983; McNeal 1986; Merritt 1980; Meuzelaar et al. 1989; Morris 1981; Odham et al, 1984; Suelter and Watson 1990,7 Theory of Unimolecular lon Decompositions To understand thoroughly the capabilities, and especially the limitations, of, mass spectrometry for structure elucidation, one must be familiar with the basic theoretical aspects of unimolecular ion decompositions. Sections 7.1 and 7.2 are appropriate for introductory courses designed to teach fundamental interpretive skills. The nomenclature and abbreviations adopted here follow those of the GIANT tables (Lias er al, 1988), whose introduction is recommended reading, as well as the references at the end of this chapter. 7.1 Energy deposition and rate functions, P(E) and KE) Tonization of the sample molecules with 70-eV electrons produces molecular ions whose internal energy values (E) cover a broad range (0 to >20 eV), aver- aging a few eV (1 eV = 23 kcal/mol = 96.5 kJ/mo)). In the upper part of the Wahrhaftig (1962, 1986) diagram (Figure 7.1), this distribution is described by the probability function P(E). This range of energies is dramatically different from the <1 eV thermal-energy distribution usually found in condensed-phase reactions. The initially formed M"" ions range from cold to “red hot”; not sur- prisingly, these thus show a wide range of decomposition behavior. Only unimolecular reactions are possible for the gaseous ions formed by ET under the usual MS operating conditions. The nature and extent of these reactions depend only on the ion’s structure and internal energy, irrespective of the ionization method (Rosenstock et al. 1952). Without collisions, itis the energy originally deposited in the ion from the ionization process (plus the small amount of thermal energy originally in the precursor molecule) that causes the ion to decompose or isomerize. The probability of any such reaction is expressed as the rate constant k, which obviously must change with the precursor ion's internal energy, E. Hypothetical k(E) functions showing the change of logk with E are also given in Figure 7.1 (lower half), which shows that ions of 1816 11 Theory of Unimolecular lon Decomposition Pe) Map" } EQ(A8*) SAD) Increasing Internal energy —e eu’ @ internal energy Figure 71. The Wabrhafig diagram: relationship of P(E) and k(E) for unimolecular ion decompositions of ABCD . Sze text for definitions. (Walrhafig 1962, 1986) the lowest internal-energy values will not have appreciable decomposition rates, and so will appear as M* in the spectrum. A rate constant of ~ 10° s~ or greater is necessary for ion-source decomposition (lifetimes ~10* s or less). Logk = 6 on the curve (Figure 7.1, lower half) for the reaction M* + AD" thus defines the minimum M" internal energy for AD" formation, which is somewhat higher than the reaction critical energy, Eo (AD); this terminology is preferable to “activation energy.” and is defined as the difference between the zero-point energy of M"" and that of the activated complex for M* + AD* (Robinson and Holbrook 1972), At higher M" energies k(M"" > AB") becomes greater than k(M* > AD"), so that the formation of AB! is favored. (Meta- stable ion decompositions, m*, are discussed later.) Note that the minimum reaction rates producing measurable fragment ions can be much lower in trapped ion sources. ‘The actual ion abundances are determined by both the P(E) and the k(E) ‘relationships. The relative proportion of M'" ions that remain undissociated is determined by the lowest energy required for ion source dissociation and the relative proportion of M* ions formed with internal energies below this energy. These relationships are shown by the vertical dashed lines in Figure 7.1,17.2 Tharmedynamie verwua Kinetic tects Ww with the shaded areas of the P(E) curve representing the relative proportions formed. If the ionizing electron energy is lowered, this will reduce the number of M™* ions formed with higher energies more than it will reduce the number of those formed with lower (note that all arc lowered), so that the relative proportion of M* ions that do not dissociate will increase. ‘Note that the shaded areas of the P(E) curve represent the initial abundances of AD™ and AB*. Those ions formed with sufficient internal energy will decompose further; the abundances of the resulting product ions (and of the undissociated AD” and AB*) will depend in turn on the P(E) and k(E) functions of AD* and AB* 7.2 Thermodynamic versus kinetic effects ‘The hypothetical system of Figure 7.1, in which [AB*] > [AD"*} illustrates another important aspect of unimolecular decompositions: the reaction of lowest critical energy does not necessarily produce the most-abundant ion. Sim- ilatly, the temperature of a condensed-phase synthesis reaction is raised to opti- ‘mize the yield of the desired product through “kinetic control.” In Figure 7.1 the reaction ABCD" AD™ has the more favorable enthalpy, but ABCD*’ + ‘AB* has the more favorable entropy. The transition states depicted in Figure 7.2 for these reactions rationalize this behavior. In the rearrangement forming AD* two new bonds are formed, offsetting the energy required to cleave A—B ‘and C—D. The critical energy for AB* formation is higher, since this requires BC cleavage. However, the sterie requirements for AD" formation are much more strict than those for AB” formation; in the terminology often used for such transition states, these are, respectively, “tight” and “loose” activated complexes. For higher-energy ABCD" ions, the B—C bond dissociation can take place ‘whenever sufficient energy accumulates in this bond. However, for AD" formation, the energy requirements must be met at the same time that A and D are Amon Bec! “Want compen aBo—0" ™ aa acetic 9 ee “co “oose complex” Figure 7.2118 71 Theory of Unimolecular on Decompoutons within bonding distance, which is true for only a small proportion of all possible conformations of ABCD” ‘These offsetting enthalpy and entropy effects in general lead to a substantial number of competing primary reactions as well as the consecutive secondary and further reactions; thus the mass spectrum of a larger molecule can have hhundreds of peaks. The competitive nature of these reactions can mean that relatively small changes in molecular structure result in large differences in peak abundances, For this reason, in interpreting an unknown spectrum itis helpful to study the spectra of closely related compounds. 7.8 Quast-equilibrium theory ‘The famous quasi-equilibrium theory (QET), originally formulated by Rosenstock Wallenstein, Wahrhaftig, and Eyring (1952), provides a physical description of rmass-spectral behavior which is now generally accepted. Ionization of the molecule, which takes place in approximately 10""* s, initially yields the excited molecular ion without change in bond length (a Franck-Condon process). Ex- cept for the smallest molecules. transitions between all the possible energy states of this ion are sufficiently rapid that a “quasi-equilibrium” among these energy states is established before ion decomposition takes place. Thus the probabilities of the various possible decompositions of an ion depend only on its structure and internal energy, and not on the method used for the initial ionization, or on the structure of the precursor for, or formation mechanism of, the ion undergoing decomposition. Thus an ion’s decomposition depends only on its internal energy and its k(E) functions. When we show mechanistically the molecular ion with a localized charge and radical site, itis not necessary that the ionization actually removes an electron at that site; this is just an attempt to depict the ground electronic state before decomposition. Few exceptions have been found to the QET. These “non-ergodic” dissociations generally involve small molecules (ewer, more widely separated states), excited electronic states that are similarly “isolated,” and very fast decompositions (< 10!" s). The largest ionic system for which non-ergodic dissociation has been established is CHC(—O°F)CH, + [CH,C(—O")CH,}* > [(M — CH,)*] > [(M ~CH,)'] (Turecek and McLafferty 1986; Turetek et al. 1990) The thermochemical appearance energy, AE(AD' ), is the minimum energy necessary to produce AD" from the ground-state neutral molecule. The critical energy, E,(AD*") is the minimum internal energy of M"’ required for the decomposition to yield AD", and thus AE(AD") = [E(M) + E(AD" ). (These and other relationships to be discussed later are shown in Figure 73.) Molecu- lar ions containing internal energy <£, cannot decompose, regardless of the amount of time allowed for decomposition. However, the probability that M' ions of internal energy > £, will produce AD" in the ion source depends on the78 Quashequloram theory 119 Rearrangement ' — ee x AD" + BC} —— t zD%on) 8 8 | tascoy eae.) 1e(a0) = = san{asco) Const Reaction coordinate —~ Figure 72. Thermochemical energy relationships for unimolecular ion decompositions in the mass spectrometer. rate constant, k; In[M*Jo/[M"] = kt. We shall define E,(AD™’) (Figure 7.1) as the internal energy of precursor ions which have an equal probability of leaving the ion source as M” or AD": similarly, EAB") is the AB* energy producing equal amounts of AB* and AD”. Thus, to produce AD* within 10° sin the ion source requires an energy excess above the corresponding thermochemical appearance energy. This causes the measured appearance energy to be higher than the thermochemical value by approximately E, — E,, which is known as the “kinetic shift" although this is often <001 eV, it can be as large as 2 eV (Lifshitz 1982; Huang and Dunbar 1990). Note that the magnitude of the kinetic shift depends on the slope of the log k(E) curve in the vicinity of E, For fragment ions other than the one of lowest appearance energy, such as AB* in Figure 7.1, an additional kinetie factor, the "competitive shift.” also120 7 Theory of Unimolecular on Decompositions increases the measured appearance energy with reference to E,(AB*). Most M* ions whose energy corresponds to that required for k = 10° S-* for M*' AB* will decompose instead to produce AD", sinov & for this reactlon is much larger. The internal energy of M” must be E,(AB") as shown in Figure 7.1 to yield equal rates of formation for AB* and AD" MI spectra. (In spectroscopy, a “metastable” state is a thermodynamically un- se state that has not yer dissociated for kinetic reasons; in contrast, in MS a ‘metastable ion"is one that does dissociate, but whose dissociation is delayed for kinetic reasons) The decompositions of metastable ions in a field-free drift re- jon are reactions of rate-constant values just below the minimum required for jon-source decomposition. The reactions yielding MI spectra thus represent narrow range of k values, ~10* 10% mol s~* (much lower values for ICR and ion-trap instruments). In Figure 7.1, AD” ions in the MI spectrum of M“ designated as m* (M" + AD"), thus arise with highest probability from M~ ions of energies between £,(AD~) and F,(AD™), and their abundance is represented by the area of the corresponding narrow window in the P(E) curve. Tight complex reactions, which cause a larger kinetic shift, will thus tend to give more abundant metastable ion decompositions. In the same manner the metastable ions m*(M' > AB') must arise from M" of energies corresponding to k be- ‘tween 10° and 10°, but the probability of such ions decomposing instcad in the ion source by M"-+AD" is much higher (see Figure 7.1), so that Im*(M* + AB')] will be only a small fraction of the abundance indicated by the relative area of the corresponding window in the P(E) curve of M* Thus for MS/MS studics the utility of MI spectra is severely limited by the discrimination against high-energy dissociation products and the variability of ion abundances with precursor internal-energy distribution 7.4 Derivation of P(E) functions. Most methods for approximating P(E) of a molecular ion involve measurement of the energy transferred in producing M" from M, to which must be added the internal energy of M before ionization. Because ionization involves a vertical transition, the energy necessary to produce M depends on the electronic energy level in the neutral molecule of the electron which is expelled. Thus the effect of a structural feature on the energy of a molecular electronic state can be reflected in the internal energy of M*” produced by ionization from this state. The representation of the P(E) function of M~, such as in Figure 7.1, results from plotting E for each state against the relative transition probability (Franck- Condon factor) for the state, convoluted with the internal energy of the neutral molecule (eg., at 298° K, 0.07 eV for CHCl and 0,12 eV for CHyp; Weitzel et174 Derivation of P(E) fnctions 12 Figure 74. Photoelectron spectrum of N; (left, vertical energy scale, corresponding clectronie/vibrational energy levels of N; and N,"' and molecular orbitals of N (Bahr 1973, with permission), al, 1991). The photoclectron spectrum (Turner et al. 1970; Ghosh 1983; Mor- rison 1986; Song 1991), which represents such transition probabilities for photoionization, provides a useful approximation of P(E) from electron ionization (Meisels et al, 1972). Penning ionization, transferring energy from the 19.8-¢V 2'S He atoms, is more favorable for the outer molecular orbitals (Fujisawa etal 1986). As a simple example (Figure 7.4), the photoelectron spectrum of N, is shown with a vertical energy scale (as in Figure 7.3) correlated with the energy differences between the ground electronic state of neutral N, and the three lowest N," electronic states, The ionization energy (IF), the amount of energy required to remove an electron from the highest N; electronic level, 2pe,, should define the low-energy limit of the P(E) curve. Although this corresponds to the largest peak (30,), at even-lower energies two “hot bands” are discernible. These correspond to electron loss from vibrationally excited levels of the neutral's ground electronic state, whereas the small peak just above the IE value corresponds to forming the ion’s ground electronic state in its first excited vibrational state. This ionic vibrational spacing is 0.272 eV, a small decrease from the 0.291 eV of the ‘ground N, state hot bands, so that the 2 po, state is nearly nonbonding. For the next band, electron loss from the strongly bonding 2p, level, the spacing is much lower (0.229 eV}, showing the expected bond weakening resulting from122 11 Theory of Unimolecular on Dacompouions CHaCHaCety) Aas as NH, CaHCHaC eC i ' ‘ ' 1 v ' 1 ' 1 1 Pred t Hl ' 10 . Sp NH CH eHyS # Gyhg He veakte) Gglig OCH, Cry” —P GHD + ty 6 Figure 75, Approximate P(E) and &(E) functions for the reactions CgH sCH,CH,— CH" > CgHsCH, | and p-NH,C,H,CH,CH,CJH," + NH,C,H,CH,* ++ Cally CH", and &(E) for CHsOCH," > C HOH’. Note that the energy scale is modified from that of Figure 7.1 to show the eflect of adding the p-NH substituent,‘74 Dorlvatin of P(E) turetions 123 ionization, The many vibrational peaks are also consistent with the high bonding character, with the more-intense second peak resulting from its more favorable vertical transition. Loss of the nominally antibonding 2sa, electron shows & slightly increased (0.297 eV) vibrational spacing, consistent with bond strength- ening with ionization at higher energies. The 20, and Is electronic orbitals require 38 and 410 eV, respectively, for electron removal. A larger number of molecular bonds increases the density of photoelectron peaks. The resulting P(E) curves for 1,2-diphenylethane and its p-amino derivative are shown in Figure 7.5 (MeLalferty et al. 1970b). The low-energy peak of the former corresponds to x-electron ionization, whereas addition of the amino cs possible ionization at lower energy duc to n— x delocalization. inge in IE caused by substitution in a molecule such as ABCD in Figure 7.3 is due to the larger stabilization energy conferred by the substituent ‘on ABCD" than on ABCD (neutral). The IE values of a variety of substituted aromatic compounds show a good correlation with @* constants for para substituents (Table A.3), and those of homologous series can be related empirically (Holmes and Lossing 1991), For such larger molecules, their initial internal cncrey must be added to that resulting from ionization (hot bands of lower IE result only from vibrational excitation in the electronic state from which ionization occurs). Lowering the sample temperature before ionization can thus increase [M*"] and affect product abundances (Maccoll 1986; Bowen and Maccoll 1989; Brauers and von Bunau 1990). The most dramatic effects have been achieved with supersonic ‘expansion of the sample beam (Amirav 1991), finding M™ peaks with El from @ large proportion of molecules that do not show these in their normal mass spectra ‘The initial P(E) function for a product ion A* formed from M" (see Figure 7.6) will be determined by: (1) P(E) of M*"; (2) k(E) for the reaction forming A* from M*; (3) (E) for other reactions competitive with A’ formation (M*"-+ B*, M~ C*} and (4) partitioning of the excess energy in M*" between the A* ion and the neutral product N°. Figure 7.7 shows the P(E) of CHO" formed from 2-hexanone and from 2-undecanone. The much-lower average energy of the latter P(E) is due mainly to the partitioning of the excess energy of M’, which is divided in proportion to the number of vibrational degrees of freedom in the ion and neutral products. This is seen in the so-called “degrees-of-freedom” effect (Bente et al, 1975), which relates the metastable ion abundance, [m*], for the further decomposition of a particular fragment ion to the size of the molecular ion from which itis formed. In general, for a homologous series of molecular ions. a linear relation is found for logi[m*/[AB* ]) versus the reciprocal of the number of vibrational degrees of freedom in the molecular ion yielding AB*. More precise methods are available to study the dissociation of ions formed with specific amounts of internal energy. Charge exchange can be specific, ¢8, IB(Ar) = 15.75973 + 0.00001; if E(M) = 10.0 eV, neutralization of Ar* (ground124 7 | Tory of Unimolecular on Decompositions Pew 7 feria eye ° Ton Intern Energy —> Figure 7.6. Rekationship of P(F) and k(E for molecular and product jons in mass- spectral relations; see text for definitions. I is assumed for the process M*"-+ A” + N° that Fo(rev) = 0, and that the excess internal energy of M* is divided equally between AA” and N° (MeAdoo et al. 1974; Bente er al. 1975) state) by M should yield M"" with 5.76 eV of extra internal energy. Photoelectron photoionization coincidence (PEPICO) spectroscopy ionizes M with a known energy photon, measuring the cnergy of the emitted photoelectron and the re sulting product ions in coincidence (Dannacher 1984),7.5 Caevlation of KE) tnetlone 125 WoOoNS ws » PEI { ! WSs2 Pema Log ise" \" Pteero See Elev) Ev) Figure 7.7, Data and results of calculations for 2-hexanone and 2-undecanone: {@) photoelectron spectrum of the molecule (experimental data}: (b) calculated functions for P(Ehy. and P(E)y. .cyx,o::(e) calculated K(E) functions for @) M'" + CH,O"; Gi) M7 CHO" fill) M7" + C,H"; (4) calculated value of P(E\e,yor functions. The vertical line at 1.2 eV represents the “metastable window" for CH,O* -+C,H,0* 7.5 Calculation of &(E) functions Some of the accessible energy states of an ion can correspond to activated complexes capable of undergoing decompositions; the minimum energy at which such an energy state can be populated corresponds to E, for the minimum energy reaction. The rate constant for a particular reaction will be a function of the energy-state population ofits activated complex relative to the population of all other energy states of the decomposing ion. This is described by the Rice-Ramsperger-Kassel-Marcus (RRKM) theory (Robinson and Holbrook 19725 eye 12 PHEW) nz ay126 where fis Planck's constant, Z isthe partition funetion for the adiabatic degrees of freedom, # refers to the activated complex, * refers to the active molecule (which here is an ionic species), P'(E — E,) is the number of states in the energy range E — E,, and p(X) is the density of states. Adiabatic, in contrast to active, degrees of freedom cannot contribute their energy freely to the dissociating bond. In the active molecule the nonfixed internal energy, F, is randomly dis- Uributed over all degrees of freedom. In the activated complex one degree of freedom has been transformed into the translational coordinate requiring E,, 50 that only E — B, is available for distribution. The partition function includes the symmetry factor, which is the number of identical pathways by which the reaction takes place. ‘The RRKM form of the theory is preferred because it uses an exact enumera- tion of states. However, some discussions of mass-spectral reactions continue to use the approximate form of the theory, (Ey ra) where v is the frequency factor, F is the internal energy of the reacting ion, and n is the number of vibrational degrees of freedom. (The magnitude of v is qualitatively related to the “looseness” of the activated complex.) The predictions of this theory are poorer, especially for lower-energy ion decompositions. The probability that energy sulicient to cause reaction, F, will reside in the ‘activated complex depends on the number of activated-complex energy states available for energy residence versus the number of energy states elsewhere in the ion to which the internal energy could be distributed. If the excess internal energy, F — E,, is small, k increases rapidly with increasing E (see Figure 7.1), since an incremental increase in E will increase P* proportionately much more than p*. The rate of increase of k with F should decrease as E — E, becomes larger, approaching a constant value as E, becomes very small compared to E. ‘The maximum reaction rate is limited by the time required to separate the two atoms of the dissociating bond (~ 10? sec), which depends on its vibrational frequency. Equation 7.1 predicts further that a change in structure can affect the K(E) funetion by effects on (1) E,. (2) P*/p*, and (3) Z¢/Z* (1) £,, Ifa structural change-increases the critical energy, the excess energy, E~ E,, of the activated complex must decrease, so that the number of states found between E, and E should also decrease. Thus k will exhibit a lower value, since the probability of accumulating the energy E, in the reaction coordinate will be decreased. The energy states are quantized, so that at E = E, only the ground state of the activated complex is available; the equation demands that Ofor E < E,. The minimum rate, ME) azta ale (73)7.8 Thermochemical relationships and potential energy suraces 127 will also be reduced by an increase in E, because of the increase in p*(E,). Note that an increase in E, will increase both E, and the kinctic shift, E, — E,, since the slope of k(E) will decrease. Q) Pp*. A modification of the molecular ion structure which adds or sub- tracts states, or changes the energy values of states, will changc P#/p*, and will thus also change the k(E) function, If, while other parameters are constant, the number of vibrational degrees of freedom (n) in the reactant ion is increased, *(E) will increase. This will lower gigs and will thus usually increase the kinetic shift, which is the amount of excess internal energy necessary to reach k = 10°, A major factor that determines P¥jp* is the nature (energy levels and degeneracies) of the vibrational degrees of freedom, all of which are assumed to be active. [tis also possible that the number of active internal rotational states, the so-called “free rotors,” can change in going from the active molecule to the activated complex. A reaction is said to have a “loose complex” if the number of internal rotational states have increased at the expense of vibrational states; for example, stretching of a C—C bond in the activated complex would allow increased rotation of the attached groups while decreasing the vibrational frequency of the bond. A reaction is said to have a “tight complex” if rotational degrees of freedom are frozen out in the (ransition state, Rearrangements are a common example of this, since the juxta- position of atoms demanded by the transition state effectively stops rotation about their adjacent bonds. A change in the number of free rotors can have an important effect on the rate constant, since the density of rotational states is much larger than that of vibrational states. This predicts that reactions with tight complexes will have a much slower inerease of k with increase in E (lower slope of k(E) in Figure 7.1) and will exhibit a much larger kinetic shift. G) Z1/Z*. The partition function includes the symmetry factor, which takes account of the fact that the total rate will be proportional to the number of identical reaction pathways. Z'/Z* also reflects the moments of inertia of the activated complex relative to the active molecule; such values usually fall between I and 10. 7.8 Thermochemical relationships and potential energy surfaces A substantial collection of ionic thermochemical data has been tabulated (Lias et al. 1988) and such data can be estimated for other species (Lossing and Holmes 1984; Holmes 1986). Equations 7.4 and 7.5 repeat the simple cleavage and rearrangement reactions of Figures 7.1-7.3. The thermochemical relation~ ships for these reactions are shown in Figure 7.3 using values for the ABCD ——= ABCD" 8° + -00 a) asco” ——~ ap" + B: 3)128 11 Theory a Uninolecule fon Decompostor corresponding reactions of 2-hexanone*. Let AH,(ABCD) signify the heat of formation of ABCD from the constituent elements, and D(B—C) be the dissociation energy of the B—C bond, AH,(AB*) + AH,(-CD) is the thermochemical threshold for Equation 7.4. AE(AB") is the thermochemical appearance energy of AB, so that AE(AB') — IE(ABCD) = £,(ABCD'’ + AB"). The activated complex may be of higher energy than the sum of the energies of the products in their ground states; this excess energy is a reflection of the critical energy for the reverse reaction, E,(rev). Significant values of E,(rev) are more common for rearrangement reactions. If E,(rev) is negligible, E, for reaction 7.4 is equal to the bond-dissociation energy of the ion and is predicted directly (Figure 7.3) from Equations 7.67.8. E)(AB) = AHVIABY) + AH)(-CD) ~ anABCO™) (76) = AHAB.) + IE(AB+) + AM(-CD) — AM(ABCD) ~ IE(ABCD) an = IE(AB-) + DiAB—co) ~ IE (ABCD) (78) Note that Equation 7.8 uses bond-dissociation energies of neutral species (Table A3), to which the organic chemist’s intuition and knowledge of mechanistic principles should be directly applicable. For two competing reactions of the same molecular ion (and thus the same E(M) values), Equation 7.8 predicts that ‘AE, is determined by ALE of the respective radicals (Stevenson's Rule) and AD of the respective bonds. Further, a structural change usually affects 1E(AB-) ‘much more than D(AB—CD) or TE(ABCD), which is why product ion stability is usually the most influential factor determining product ion abundance (Section 82) Potential-energy diagrams (Figures 7.8-7.10) ean provide a more graphic way to present the thermochemical relationships for these reactions. In this representation the reaction is viewed as a classicat motion of the system along the reaction coordinate over a potential-energy curve or surface, The term “classical” simply means that the system cannot penetrate the potential-energy surface. The reaction coordinate in Figure 7.8 represents the changing length of the BC bond, while other coordinates, such as bond-angle changes due to re- hybridization, are neglected. Three regions are important: (1) the region near the equilibrium geometry of ABCD" on the bottom of the potential-energy well; (2) the region around the highest-energy point on the surface, which often corresponds to the transition state; and (3) the region on the right-hand side of the diagrams which corresponds to equilibrium configurations of the products AB‘ + CD: separated to a distance at which their mutual interaction is negligible. The energy scale is chosen to reflect the relative thermochemical stabilities (AH, of the reactants and products. The shapes of the potential-enerey curvesEnergy 18 Thermochemical 129 AB's CO" ABT+"CD. Coordinate 18 73 Figure 78. Potential energy diagram for a simple cleavage reaction proceeding (a) without and (b) with reverse activation energy. Figure 78, Diagrams for reactions with (a) charge retention and (b) charge migration, are mostly unknown, and are drawn arbitrarily only to indicate that the motion along the reaction coordinate is continuous, The simple cleavage reaction in Figure 7.8(a) is characterized by a continu- ously increasing potential-energy curve which reaches its maximum in the products region. The transition state, ifit can even be located, occurs at large separation of the products, and its energy is the thermochemical threshold of the reaction; Equations 7.6 to 7.8 are applicable, Figure 7.8(b) describes a simple cleavage decomposition having a well-developed transition state whose energy lies above the thermochemical threshold. Thus the decomposition exhibits @ reverse activation energy, with D(AB—CD*) for the B—C bond greater than the thermochemical value and dependent on the reaction path. Figure 79 illustrates simple cleavage reactions proceeding by charge retention and charge migration, The products AB* + “CD and AB: and CD" differ130 11 Theory a Unimolecular lon Decompoalons Energy Coordinate(s) Figure 7.10, Potential-encrey surfaces resulting in (a) higher or (bj lower similaity for the mass spectra of isomers only in the location of the electron, and thus correspond to two different clec= tronic states of the supersystem (AB + CD)". In 7.9(a) the charge is localized largely in the AB part of the ABCD” ion and remains there as the fragments separate (charge retention). For example, x-cleavage in C,H—CH,OH™ produces mainly CH;OH™, 1£(CH,OH-) = 76 eV, with much less (16%) CH", JE(C,H.¢) = 8.1 eV. Thus the ground electronic state of M*’ correlates with the products’ ground state. Although [as shown in Figure 7.9(b)} ionization in (CH,),CH—CH,OH also occurs from the oxygen lone-pair orbital, the ionization energy of the alkyl radical (CH),CH is substantially lower (7.4 eV). Now, the ground state of M~ correlates with CH,OH” + (CH,),CH: [AB + -CD in Figure 7.9(b)] repre-78 Thermochemical relationships and potetileneray surtces 131 senting the first excited state of the products, whereas the products’ ground state, CH,OH + (CH,),CH", correlates with an excited state of M*. During sociation the system first follows the ground-state potential curve, but at the intersection a large fraction of M* crosses to the other curve to produce ener getically favorable products. Charge distribution in competing OE" fragmenta tions depends on the energy gap given by the IE difference (Stevenson's rule) and the efficiency of curve hopping for charge migration reactions. For ALE > 0.3 eV, the energetically favored produets predominate (Harrison et al. 1971, “Random rearrangements, Elects leading to closcly similar spectra for isomers (Section 49) can also be visualized with energy surfaces (Figure 7.10). These effects can be complex, containing several local minima and transition states (such as ion-neutral complexes), and leading to product ions that are either EE* (as shown) or OE" (eg, ABCD" = DABC* > DA~ + B=C). The true reaction coordinates in such a case are multidimensional, since they contain the Iengths of the bonds being broken and formed as well as the changes in the bond Tengths and dihedral angles in the rest of the ion. In these conventional two- dimensional diagrams (Figure 7.10), the true coordinates are projected into a common “coordinate” which now depicts different events along the reaction path and serves merely as a graphical means of arraying the structures. If isomerization of an ion is rate-determining (Williams 1977), the tendency for a reversible rearrangement is dependent on the height of the barrier separating the isomeric precursor ions relative to the barrier height for dissociation: the isomerization itself may be endo- or exothermic. Figure 7.10(a) shows a rearrangement in which the barrier between ABCD" and ACBD" is lower than the minimum energy needed for decomposition to AC! + BD. fons ABCD* and ACBD” can interconvert before decomposition, which can cause loss of the information carried by the original ABCD" structure. A similar energy diagram has been used to explain the close similarity of the El and CAD mass spectra of I- and 2-butene*’ ions (Feng et al. 1989). Note, however, that a low isomerization barrier does not necessarily Iead to structural ambiguity. For example, classical hydrogen rearrangements through a distonic radical ion, ABCD’ —+-DABC’, that then dissociate to give an OE" ion BC’ can have a reverse activation-energy barrier competitive with dissociation; an example is CD,CH,CH,CO,H* = CD,CH,CH,CO,HD* = CHD,CH,CH,CO;D* = CHDCH,CH,C(OD),* > CHD=CH, + CH:—= C(OD),* (Smith and MeLalferty 1971), causing H/D scrambling. However, the neutral molecular counterpart of the distonic radical-ion intermediate is an unstable diradical, -CHyCHCH,C(OH),’, and thus is not a reasonable alternative for structural assignment of an unknown molecule, A “random” rearrangement, such as that of I-butene, forms a non-distonic isomer, which must involve ‘8 multiple-step pathway or an intermediate ion-neutral complex132 7 Theory of Unimolecular lon Decompositions Figure 7.10(b) shows a rearrangement in which the isomeric ions are separated by a higher energy barrier, whose height determines the fraction of ACBD" that can escape reverse isomerization and decompose directly to AC* + “BD. To produce AC" from ABCD” instead of ACBD* requires eross- ing this higher barrier through a tight activated complex, so that the isomers will form AC* at different rates. Other ABCD" dissociations such as AB* formation can now be important; the more competitive these are with the isomerization, the more diferent the mass spectra ofthe isomers willbe. 7.7 Examples The applicability of Equation 7.1, and especially the usefulness of the concept of the “looseness” or “tightness” of the activated complex, arc illustrated by a few ‘model calculations that have been carried out for larger molecules (Equations 7.9 t0 7.11), The best agreement between the experimental data and the caleu- ed k(E) functions (Figure 7.5) was obtained by assuming that the activated complex undergoes an increase of one or two free rotors over the ion for Equa tion 79, a reduction of one free rotor in Equation 7.10, and an increase of three (© four free rotors in Equation 7.11, In Equation 7.9 the importance of product- ion stability (sce Chapter 4) suggests that the activated complex resembles the products more than the precursor. In such a model the central C—C bond will be substantially dissociated, thus lowering the barrier to rotation about this bond, and inercasing the number of free rotors in the activated complex. CgHsCHyCH:CsHe” ——= CH; {= 13, Ep=1.8eV) 9) PHHANCHACH:CHiCHY —e p-HaNCrM? (Eoe07, Epettevy — (7:10) — ott (= 23, E=7eV) ay ©) — Op-ed 4G) — env osm om Quite a different situation is indicated for the decomposition of p-amino-1,2- diphenylethane. The presence of the p-amino group should lower the ionization energy of the benzyl radical, lowering E,, and thus lower the kinetic shift. This is not observed, however, suggesting a substantial reduction in the “looseness” of the activated complex. The presence of the amino group will increase the elec-tron density in the N—-C bond of the molecular ion; however, in the activated complex, the partial formation of the resonance stabilized p-aminobenzyl ion should also reduce the free rotation about the Claryl)—CH, bond, offsetting the increased rotation about the central C—C bond. This indicates that the configuration of the activated complex for Equation 7.10 is substantially “tighter” than that for the active molecule, in direct contrast to the situation in Equation 19. ‘The critical energy for Equation 7.11 is even higher than that for Equa- tion 7.9 because of the lowered value of 1B, and there is an even greater increase in the value of the combined kinetic and competitive shifts. The significant abundance of this product ion in the 70 eV spectrum indicates that k(EF) for Equation 7.11 must rise much more rapidly than that for Equation 7.10. The transition-state for Equation 7.11 must involve an even greater increase in free rotors than for Equation 7.9, based on the fact that the partial charge on the amino group and the adjacent aromatic ring must now decrease in the transi tion state, lowering the double-bond character of the adjacent bonds. The alternative formation of C;H,* from an excited electronic state would constitute an ‘unusual exception to the quasi-equilibrium theory. ni’ Gono = nO) Gin Se reepoee (7.14) Small changes in structure can have a large eflect on the mass spectrum if these make possible new reactions of higher-rate constants over an appreciable range of precursor-ion internal energies. Thus the dramatic differences between the spectra of dodecane and I-aminododecane (Figures 3.2 and 3.16) are due pri- ‘marily to the high rate constant for the new reaction forming the CH—NH* ion. Increasing the critical energy of a reaction decreases the slope of the K(E)134 17 1 Theory of Unimolecular curve, so that a higher-energy reaction must have a sufficiently looser activated complex in order to be competitive Structural effects on the P(E) function of the molecular ion can also affect the mass spectrum, particularly inthe abundances of the molecular and metastable ions, Addition of « m-amino group 10 1.2-diphenylethane lowers the critical energy for benzylic cleavage by only 0.2 eV, but lowers the ionization energy by L1 eV; this produces a doubling of the molecular-ion abundance. Adding a p-nitto group to 1,2-diphenylethane make no appreciable change in either the TE value of the molecule or the AE-value of the benzyl ion (10.5 + 0.2 eV). However, the nitro group greatly increases the population of the P(E) curve of M* around 10.5 eV, presumably through ionization at the nitro group, resulting in a several-fold inercase in the ion abundance arising from the metastable decomposition M*’ + C,H,*; in Figure 7.5 note the low population of C(H.CHCH,C,H," ions in the energy region required for this metastable decomposition, 7.8 General references. Bowers 1979, 1984; Futrell 1986, Ghosh 1983; Holmes 1986; Levsen 1978; Lossing and Holmes 1984; Mark 1985; Morrison 1986; Robinson and Holbrook 1972; Turner 1970.8 Detailed Mechanisms of lon Fragmentation Interpreting a mass spectrum has the same basic requirements as explaining the products of any chemical reaction, demanding a sufficient understanding of the relevant chemistry. For example, the addition of a double bond to a complex molecule such as clivonine (Figure 8.1) should make only relatively minor changes to its infrared and nuclear magnetic resonance spectra, However, a new double bond could profoundly change the chemistry, as it does the mass spe ‘trum (McLafferty, Loh, and Stauffer 1990), There are now many excellent reviews of mechanisms of unimolecular ion reactions; these are listed at the end of the chapter. A thorough discussion is not possible here; in this chapter, as in ‘Chapter 4, the main emphasis will be on mechanisms that are especially useful for interpretation of EI (70 eV), Cl, and other cationic mass spectra. 8.1 Unimolecular ion decompositions To review and reemphasize the positive ion reactions important for deducing, structure, the mass spectrum shows competing and consecutive unimolecular reactions (Figure 8.2). Primary dissociation products such as ABC* and CD* represent pieces of the original molecule, and thus provide direct evidence of molecular structure. Examples are given in Equations 8.1 and 82 (for 2- hexanone™’ see also Figure 73 and Section 7.5). Values in eV over arrows represent the overall endothermic enthalpy change from the initial precursor; the activation energy in exeess of this endothermicity (reverse E,) will be substantially higher for rearrangement (r#) than for simple cleavage reactions. Values sneath a species represent its heat of formation (AH,) and, in parentheses, the ionization energy (IE) of the corresponding neutral. Even if isomerization is competitive with primary dissociation, a structurally indicative ion can be formed by dissociation of the isomer (Figure 7.10). Such a “specific rearrangement” can involve direct isomerization to a distonic radical ion (a 135136 (6918 ‘39 suontenbg 205) suunseaddy pu suruoNy yo mioods sew 19 2M “8 nba OT oat ome Saaeiiie: aan eiaatine @ a Ayan omnes ‘Ayana aane;oy181 Unimolecular on decompositions 137 dissociation Ae sect #0 — wiato* tp ——— tec ee te | —— 8+ 007 —+ cro t tearanement 7 Sao" + ec —+ at BS AD + BC" - Bc Figure 82. Common unimolecular ion reactions. distance between its radical and charge sites; Radom et al. 1984), eg. CH(CH,)CH,CH,C(—O" H)CH, from 2-hexanone*’ (Equation 8.2; the O6-cV bactier is due to a reverse activation energy of 0.9 eV); this ion is not available by direct ionization of a stable compound. However, hydrogen migration can also iead to an ionic isomer of another molecule (e.24 CsHio" Equation 8.1), so that this rearrangement increases the uncertainty of identification; the uncertainty will usually be greater for a lower isomerization barrier [Figures 7.10(a) vs. 7.10(b)]. tons undergoing such “rando rearrangements characteristically require higher cnergies for direct dissociation (1.7 eV for CsH,CH CH,” vs. 0.7 eV for C,HoCOCH,"), so that several isomerization steps (or isomeric equilibration) can be competitive with dissociation. In consecutive dissociations, the further reactions of an EE product ion such as C,H,” + CyHy" (Equation 8.1) or CsHoCO* + C,Hy* (Equation 82) will tend toward more isomerization; the secondary an A (60%) AF 180 yg gS NOM 28 HUE) = 8710.0) 25 cy) + chy 15 Bars) 11165) -08 i 7 = Sa Cds + + Ser Gala! + He 12 9.88.1) " 11.166) 0 xX . J coo S Abe cay + 3 as 99%.7) 96 @)138 1 etates Machaniams ol on Fragmentation 14 city. + O=CCH, (100%) 2+ co + BH iS%) re os 8a ctr 11388) 9 24 . a 34 . om) 22. carer tom) + omdor, 21+ cay: eam + ca 8.8(8.0) 02 ‘ 9.3(8.1) 05 6869) 07 caycor an) + cry —22e ct + 00 g 5,715.9) 15, ‘ 8.68.0) 14 oo | |r “| : + Pigg oe ccot + coro) 4-H 9907) my suey 25 (8.2) products will thus have less structural integrity, and their significance for struc tural assignment will be much more species-dependent. However, such products are still useful in low-mass “ion series” to indicate the heteroatoms and rings plus-double-bonds of particular substructures. Basie factors affecting ion abundance. To be abundant in a mass spectrum, a fragment ion must be produced competitively from one or more precursors and must be relatively stable to further fragmentation. The most competitive fragmentation pathways of the molecular ion are those of the lowest free-energy change, and thus of the most favorable changes in enthalpy and entropy. The enthalpy factor is reflected in the strong tendency to form the most-stable products, especially the most-stable ionic product. Qualifying this, the loss of the largest alkyl group is favored, and the entropy factor places steric restrictions on product formation. 8.2 Product stability For competitive reactions (Figure 82), the relative stability of both products is of primary importance in increasing their formation, as well as reducing the further dissociation of the product ion. For simple bond-cleavage reactions the reverse activation energy is usually small, so that the driving force is the enthalpy change of the reaction, relative to the values for other such competing pathways, The relative enthalpy change is determined by the heats of formation, and thus the stabilities of the resulting ionic and neutral product pair. As shown in Figure 73 and Equations 7.678, this is equivalent to the dissociation energy182 Produetetabiy 139 {D, Table A.3) of the bond(s) cleaved in the neutral counterpart of the reactant plus the ionization energy (IE) of this reaction’s product that is ionized; the fact that IE values depend much more on structure than D values do (Table A.3) is the reason why product-ion stability is of key importance for determining fragmentation pathways. Note, however, that this applies to the comparison of reactions in which only one bond is dissociated. When two bonds are cleaved, ‘wo are usually formed, so that the overall bond dissociation energy can be substantially lower (Figure 7.3). Thus OE" ions can be as abundant products as EE! ions whose corresponding neutrals have IE values 1 to 3 eV lower (Equations 8.1 and 8.2) Th interpreting mass spectra, for cach important primary product ion remember to check the abundance of its complementary produet ion: m/2(CD* ‘m/x(ABCD™) — mjz(AB*). The competitiveness of these products will depend mainly on the product-stability effects, since the steric effects will usually be equivalent. Product-ion stability. Whustrating this primary criterion, the IE(R) values for H-, CHy, CsH¢, is0-CyH,", and tert-C,Hy: (Table 8.1) span a range of 69 eV, whereas the dissociation energies of their bonds to alkyl groups R', D(R—R’), show a range of only 0.9 eV. The heat of formation (AH,) values also illustrate the importance of structural stabilization of cations versus neutrals, with ionic AH, values spanning a range of 86 eV, whereas the AH, values of the corresponding neutral radicals show a range of only 1.7 This much-larger effect of structure on IE and AH, values of ions than on. those of neutrals can also be seen for other functionalities of Table A.3. For the ionization energy, note that the substitution of a heteroatom into an alkyl radical can (Table 8.1) increase (CH,CH,: -> CHO*, 8.1 + 8.6 eV) as well as decrease (CH,CH;--» HOCH,;, 8.1 > 76 eV) the TE value (singlet CH,O* is Table 8.1. Energetics of simple radicals, eV Alkyl racicals FR Di IER) AMF) Hany # 43 136 22 158 cH 37 98 15 "4 Cite 36 a1 13 os fot, 35 74 u 85 ten 34 87 os. 12 ‘Substituted radicals, AME) Hyon, i oH, ony cH, 1300 oa 1318) 94 ° 03 (78) 13 02188) 38140 17 betaied Mechaniams of on Fragmentation unstable, and its triplet is ~3.5 eV less stable than CH,OH*), Sometimes heteroatom addition affects the neutral more than the corresponding ion: ‘AH,(Ph:) — AH,(PhO-) = 26 eV, but AH,{Ph') ~ AH,(PRO*) = 23 eV, re- Aecting better stabilization by monovalent oxygen of the unpaired electron in PhO: than of the charge in PhO* (Ph = pheny}) For simple dissociation reactions involving a single bond cleavage, the most-favored common products (Table A.3, Radicals) are thus immonium {R,C=N'R',) and imminium (RC=N° R’) ions for nitrogen-containing compounds, oxonium (R;CO'R') and acylium (RC—O") ions for oxygen- containing compounds, and allyl, benzyl, and tropylium ions for hydrocarbons. Structural effects on IE values are generally as expected from the principles of physical-organie chemistry. An example is the classic study of Harrison, Kebarle, and Lossing (1961) showing an excellent correlation of the IF values of substituted benzyl radicals YCgH,CH," with Hammett/Brown 0” values (also see Lias 1988, p. 19, and Tureéek et al. 1990a); the substitution of p-NO, by p-NH, decreases the IE value by 2.5 eV. The effect on the IE values of the corresponding molecules YCsH,CH;CH,C,H, is two-thirds of this, but also correlates with o’ values (Section 7.7; for an extensive discussion see MeLafferty et al. 1970). In general, structural effects are somewhat more important for EE than for OE" ions (Table A.3), for example, AH(C3H,") is 26 eV higher than AH,(C;H,OH™), while AH,(CjH,") is 3.3 eV higher than 4H,(CHsCHOH'). (For the corresponding neutrals the AAH, values are 1.6 and 1.9 eV, respectively). Loss of the largest alkyl group. his rule is the major exception to the importance of product-ion stability. For unsubstituted alkyl groups bonded to the same, or equivalent, carbon atom(s), the product-ion abundances produced by their losses will reflect the size of the alkyl group. Note that (Equa- tion 8.2) C,H,COCH,” yields 2% C,HyCO™ vs, 100% CHCO", even though formation of the latter Fequires 0.4 eV more energy. Thus an important loss of H, such as from (CH,),0” or PhCOH™, usually indicates absence of alkyl groups larger than methyl, Alkynes and alkyl cyanides and fluorides (whose - and m-electrons are much less involved in ionization than in product ion-stabilization: Sections 86, 9.10, 9.11) often provide an exception. These show a higher preference for H: loss than most compounds do, with [(M — H)]" > [M*}; for example, for MesCHCN™, [(M — H)*] = 50% and [(M — Me)" ] = 25%, but H loss occurs almost exclusively from the methyl group. Also, alkyl losses from silicon atoms do not always obey this rule (Prefferkorn et al. 1983) Zahorszky (1982) has made extensive quantitative studies on the competitive loss of alkyl radicals from M*", The abundance ratio of the resulting product{8.2 Product atabiity 141 ions (plus any of their further decomposition products) is usually inversely proportional to their masses (loss of ethyl or larger radicals). The a-cleavage of ethyl propyl butyl earbinol at 13 eV (to eliminate secondary decompositions) pro. duces peaks at 129, 115, and 101 with relative abundances of 787% 85%, and 100%, respectively; predicted abundances are 101/129 = 78% and 115/101 88%, (At electron energies near their appearance thresholds this does not hold; eg. the loss of C.Hy: from C,HgCOCH, ' , Equation 8.2, requires more energy than the loss of CH). This may be another manifestation of the “degrees-of- freedom” effec, in which the abundance of the same metastable ion product {rom homologous precursors is found to be inversely related to the number of vibrational degroes of freedom of the decomposing fon (McAdoo er al. 1974; Bente et al. 1975; Section 7.4). Ifthe ion contains more energy than that required for dissociation, the statistical distribution ofthis excess favors the largest alkyl group. Charge competition in OE* decompositions: Stevenson's Rule. In a singly charged ion, cleavage of a specific bond yields two products, only one of which can be charged. Stevenson's Rule and its modified formulations (Audier 1969; Harrison et al. 1971; Tureéek and HanuS 1984) state that ionization-enerey values govern charge retention vs. charge migration in OE"* decompositions, During dissociation the separating fragments compete for the charge, with the winner being ionized. If in M* one bond is cleaved (Equations 8.3-8.4), two incipient radical species compete for the charge, whereas with two bonds CoHyCHz0CH; b= CH” or ——= OCHS! Boev a6ev 25% 1% (83) GaHty!CHZOCHy — ——= Gay" or cH,==00H," B1ev 69ev a% 100% x=GyHstCOCH, Le x-Gytst or 2» cHACOt n- 80 70ev 10% 100% 84) s- 73 30% 100% 1 67 100% 35% cleaved (Equation 8.5) two incipient molecules compete. Of the two products in ditect charge competition, the fragment of lowest ionization energy (IF, Table

2-Interpretation of Mass Spectra, McLafferty (1993)

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