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UNDERSTANDING MASS SPECTRA Second Edition UNDERSTANDING MASS SPECTRA: A Basic Approach SECOND EDITION R. Martin Smith A JOHN WILEY & SONS, INC., PUBLICATION Copyright#2004byJohnWiley&Sons,Inc.Allrightsreserved. PublishedbyJohnWiley&Sons,Inc.,Hoboken,NewJersey. PublishedsimultaneouslyinCanada. Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmittedinany formorbyanymeans,electronic,mechanical,photocopying,recording,scanning,orotherwise, exceptaspermittedunderSection107or108ofthe1976UnitedStatesCopyrightAct,withouteitherthe priorwrittenpermissionofthePublisher,orauthorizationthroughpaymentoftheappropriateper-copy feetotheCopyrightClearanceCenter,Inc.,222RosewoodDrive,Danvers,MA01923,978-750-8400, fax978-646-8600,oronthewebatwww.copyright.com.RequeststothePublisherforpermissionshould beaddressedtothePermissionsDepartment,JohnWiley&Sons,Inc.,111RiverStreet,Hoboken, NJ07030,(201)748-6011,fax(201)748-6008. 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LibraryofCongressCataloging-in-PublicationData: Smith,R.Martin. Understandingmassspectra:abasicapproach.–2nded./R.MartinSmith. p. cm. Includesbibliographicalreferencesandindex. ISBN0-471-42949-X(acid-freepaper) 1.MassSpectrometry. I.Title. QD96.M3S65 2005 5430.0873–dc22 2004003683 PrintedintheUnitedStatesofAmerica 10 9 8 7 6 5 4 3 2 1 CONTENTS Preface to the Second Edition xi Acknowledgments xv Abbreviations and Notations Used in This Book xvii 1 Instrumentation 1 1.1. Introduction / 1 1.1.1. Overview / 1 1.1.2. Sample Introduction / 3 1.2. Ionization Source / 4 1.2.1. Electron Ionization Source / 5 1.2.2. Chemical Ionization / 8 1.2.3. Other Ionization Methods / 9 1.2.3.1. Electrospray Ionization / 9 1.2.3.2. Desorption Ionization / 12 1.3. m/z Analysis / 13 1.3.1. Time-of-Flight (TOF) / 13 1.3.2. Magnetic Sector / 15 1.3.3. Transmission Quadrupole / 17 1.3.3.1. Selected Ion Monitoring (SIM) / 21 1.3.4. Quadrupole Ion Trap (QIT) / 22 1.3.5. Other Types of Mass Analysis / 24 1.3.5.1. Mass Spectrometry/Mass Spectrometry(MS/MS) / 24 1.3.5.2. Accurate m=z Analysis / 26 1.3.6. Spectral Skewing / 26 1.4. Ion Detection / 30 1.4.1. Electron Multiplier / 32 1.4.2. Photomultiplier Detector / 33 v vi CONTENTS 1.5. Data System / 33 1.5.1. Instrument Tuning and Calibration / 33 1.5.2. The Mass Spectrum / 37 1.5.2.1. Production of the Mass Spectrum / 37 1.5.2.2. Terminology: Ions vs. Peaks / 41 1.5.3. Library Searches / 41 1.5.4. Using the Data System to Analyze GC/MS Data / 45 1.6. Criteria for Good-Quality Spectra / 50 Additional Problems / 51 Mass Spectrometric Resources on the Internet / 52 References and Suggested Reading / 53 2 Elemental Composition from Peak Intensities 56 2.1. Natural Isotopic Abundances / 56 2.1.1. Atomic and Molecular Mass / 59 2.1.2. Calculated Exact Masses and Mass Defects / 60 2.2. Determining Elemental Composition from Isotope Peak Intensities / 64 2.2.1. One or More Atoms of a Single Element / 64 2.2.1.1. Chlorine and Bromine / 64 2.2.1.2. Ion Designation and Nomenclature / 70 2.2.1.3. Probability Considerations with Multiple Numbers of Atoms / 71 2.2.1.4. Isotope Peak Intensity Ratios for Carbon-Containing Ions—The Xþ1 Peak / 74 2.2.1.5. A, Aþ1, and Aþ2 Elements / 77 2.2.1.6. Isotope Peak Intensity Ratios for Carbon-Containing Ions—The Xþ2 Peak / 78 2.2.1.7. Overlapping Peak Clusters—Contributions from 13C Only / 80 2.2.1.8. Silicon / 82 2.2.2. Complex Isotope Clusters / 83 2.2.2.1. Sulfur Dioxide / 83 2.2.2.2. Diazepam / 86 2.3. Obtaining Elemental Compositions from Isotope Peak Intensities / 89 Examples / 91 Additional Problems / 96 References / 98 CONTENTS vii 3 Ionization, Fragmentation, and Electron Accounting 99 3.1. A Brief Review of Orbitals and Bonding / 99 3.2. Even- and Odd-Electron Species / 101 3.3. Site of Initial Ionization / 103 3.4. Types of Fragmentation / 107 3.5. The Nitrogen Rule / 109 3.6. Energy Considerations in Fragmentation Processes / 110 3.6.1. Fragmentation Rates / 110 3.6.2. Metastable Ions / 112 3.6.3. Energy Diagrams / 113 3.6.4. Stevenson’s Rule / 116 Additional Examples / 117 Problems / 119 References / 120 4 Neutral Losses and Ion Series 121 4.1. Neutral Losses / 121 4.1.1. Losses from the Molecular Ion / 121 4.1.2. Loss of Small Molecules from Aromatic Ions / 126 4.2. Low-Mass Ion Series / 131 4.2.1. n-Alkane Spectra / 132 4.2.2. Effect of Chain Branching on the Spectra of Aliphatic Hydrocarbons / 134 4.2.3. Ion Series for Nonaromatic Compounds / 136 4.2.4. Aromatic Ion Series / 142 4.2.5. Use of Ion Series: Mass Chromatograms / 145 Additional Problems / 148 References / 148 5 A Rational Approach to Mass Spectral Problem Solving 150 5.1. Guidelines for Solving Mass Spectral Problems / 150 Examples / 153 Problems / 161 Reference / 163 6 a-Cleavage and Related Fragmentations 164 6.1. Introduction / 164 6.2. Benzylic Cleavage / 166 viii CONTENTS 6.3. Cleavage Next to Aliphatic Nitrogen / 170 6.3.1. Structural Relationships: a-Cleavage in 1-Phenyl-2-aminopropanes / 171 6.3.2. Cleavage Next to Electron-Deficient Nitrogen / 176 6.3.3. a-Cleavage in Complex Nitrogenous Ring Systems / 179 6.4. Cleavages of Aliphatic Oxygenated Compounds / 180 6.4.1. a-Cleavage / 180 6.4.2. Bond Cleavage Away from the Ionization Site / 184 6.4.3. Cleavage at Carbonyl Groups / 186 6.5. Elimination Fragmentations in Oxygen and Nitrogen Compounds / 192 6.5.1. Secondary Elimination from Initial a-Cleavage Ions / 192 6.5.2. Hydride Shifts / 195 6.5.3. Elimination Fragmentations of Some Aromatic Compounds / 196 6.5.4. Water Elimination in Aliphatic Alcohols / 198 Examples / 200 Additional Problems / 202 References / 206 7 Important Mass Spectral Rearrangements / 207 7.1. Introduction / 207 7.2. g-Hydrogen Rearrangement / 208 7.2.1. McLafferty-Type Rearrangement / 208 7.2.2. g-Hydrogen Rearrangement in Alkylbenzenes / 213 7.2.3. g-Hydrogen Rearrangement Initiated by a Remote Ionization Site / 217 7.3. Cyclohexanone-Type Rearrangement / 223 7.4. Retro Diels–Alder Fragmentation / 228 7.5. Double-Hydrogen (McLaffertyþ1) Rearrangement / 234 Additional Problems / 236 References / 237 8 Rationalizing Mass Spectral Fragmentations 238 8.1. General Guidelines / 238 8.2. Loss of Small Molecules / 241 8.2.1. Loss of Small Molecules from Aromatic Ions Revisited / 241 8.2.2. g-Butyrolactone / 243 8.3. Ephedrine / 246 8.4. Ortho Effect: The Hydroxybenzoic Acids / 251 CONTENTS ix Additional Problems / 254 References / 256 9 Structure Determination in Complex Molecules Using Mass Spectrometry 257 9.1. Introduction / 257 9.2. ‘‘Designer Drugs’’ Related to MDA / 258 9.3. Cocaine and Its Metabolites / 262 9.3.1. Peak Correlations / 263 9.3.2. Proposed Fragmentations / 268 9.3.3. Application / 271 9.4. Phencyclidine and Its Analogs / 274 9.4.1. Fragmentations of Phencyclidine / 274 9.4.2. Phencyclidine Analogs / 282 9.5. A Practical Problem / 284 References / 285 10 Answers to Problems 287 Index 353 PREFACE TO THE SECOND EDITION Mass spectrometry (MS) has undergone a profound change over the past decade. Instrumentation and techniques related to the automated analysis of biomolecules andnewdrugsnowaccountforalargepercentageoftheresearchandpublications in this field. In comparison, gas chromatography/mass spectrometry (GC/MS) and electron ionization (EI) mass spectra of ‘‘small’’ molecules play a less important role than they once did. But GC/MS is far from dead, and EIMS continues to be the ionization method of choice for many laboratories that routinely analyzevola- tilizable low molecular mass compounds such as drugs, flavor and odor compo- nents, pesticides, and petroleum products. This situation seems unlikely to change in the near future. The interpretation of EI mass spectra has always been a challenging subject to learnandtoteach—especiallytoindividualswhohavenothadthebenefitofagra- duateeducationinchemistryorwhohavebeenoutofcollegeforseveralyears.The challenge is compounded by manufacturer-encouraged reliance on library search results for compound identification. Why learn anything about spectral interpreta- tionwhenthecomputercandoallthework?Theanswertothisquestionissimple, as most conscientious users quickly realize. The library search often does not provide a realistic answer or (worse) may provide an answer that looks correct but is not.Evensoftwareprogramsthatprofessto‘‘interpret’’unknownspectra can only provide probable answers. After that, you are left to your own devices. It was tempting to substantially increase the breadth and depth of the material thatwascoveredinthefirstedition.However,myexperiencehasbeenthatanency- clopedic presentation of mass spectral interpretation does not givebeginningmass spectrometrists what they need, which is a presentation that provides a few funda- mental concepts in a logical, organized manner, without distracting and unneces- sary detail. I wrote and revised this book for beginning mass spectrometrists, and I have retained the simplicity of its approach for that reason. My own understanding of mass spectral interpretation has developed, and con- tinuestodevelop,bytrialanderror.Iamadmittedlymostlyself-taught.Myknowl- edgeofmassspectralliteraturehasbeenlimitedbythenatureofmycareer,whose primaryfocuswasforensicscience,notmassspectrometry.Somewillseethatasa xi