1 Chapter 13: Mass spectrometry and Infrared spectroscopy Learning Objectives: 1. Be able to predict the fragmentation patterns expected to arise in the mass spectrum of alkanes, alkyl halides, ethers, alcohols, and ketones. 2. Be able to describe what happens to a compound in a mass spectrometer 3. Be able to use the mass spectrum of a compound to find the molecular mass, and to help identify the structure of a compound. 4. Be able to describe what happens to a compound when it absorbs infrared radiation. 5. Be able to use of a chart of functional group IR absorptions, and to help identify the structure of a compound. 6. Be able to use result from elemental analysis to deduce the number of carbon, hydrogen, and nitrogen in the molecular formula.* * Supplemental material, not included in the textbook Sections: 13.1 Mass Spectrometry 13.2 The Mass Spectrum – Fragmentation 13.3 Isotope in Mass Spectrometry 13.4 Determination of Molecular Formulas: High-Resolution Mass Spectrometry 13.5 Fragmentation at Functional Groups* 13.6 Spectroscopy and the Electromagnetic Spectrum# 13.7 Infrared Spectroscopy 13.8 Characteristic Infrared Absorption bands 13.9 The Intensity of Absorption bands# 13.10 The position of Absorption bands 13.11 C-H Absorption Bands 13.12 The Shape of Absorption Bands* 13.13 Absence of Absorption Bands# 13.14 Infrared Inactive Vibrations# 13.15 Identifying Infrared Spectra Additional material: Calculation of molecular formula using information from mass spectrometry and elemental analysis * Sections that will be focused # Sections that will be skipped Recommended additional problems 32, 45, 46, 50, 51, 542 Class Note 13.1 Mass Spectrometry and 13.2 The Mass Spectrum – Fragmentation Mmoleculeelectron beamM+emolecular ion(a radical cation)Cations detected by collector:fragmentationM (M-m)(M-n)mpnfragmentation(M-n-p)M (M-m) (M-n)(M-n-p)qfragmentation(M-m-q)q A. Most of the instrument is designed to detect cations. B. Relative abundance of fragmentation pattern depends on the energy of the electron beam.3 13.3 Isotope in Mass Spectrometry A. Relative abundance of carbon on molecular ion 12C: 98.89% (0.989) 13C: 1.11% (0.011) (M) (M+1) Each carbon contributes 0.011 abundance to the abundance of M+1 peak => relative abundance of M+1 peak = (number of carbon in the analyzed molecule) x relative abundance of M x 0.011 => (number of carbon in the analyzed molecule) = relative abundance of M+1 peak ÷ (relative abundance of M x 0.011) * Not very accurate for compound with high molecular weight Example: M (150): 16.28 and (M+1) (151): 1.664 B. Relative abundance of Cl on molecular ion 35Cl: 75.77% (0.76) 37Cl: 24.23% (0.24) (M) (M+2) For compound with one Cl: M/(M+2) ≈ 3/1 relativeabundancem/z (m/e)M+(M+2)+(M-n)+Compound with one chloride(M-n+2)+n(M-n-Cl)+Cl5 C. Relative abundance of Br on molecular ion 79Br: 50.69% (0.51) 81Br: 49.31% (0.49) (M) (M+2) For compound with one Br: M/(M+2) ≈ 1/1 relativeabundancem/z (m/e)M+ (M+2)+(M-n)+Compound with one bromide(M-n+2)+n(M-n-Br)+Br6 13.4 Determination of Molecular Formulas: High-Resolution Mass Spectrometry Use Table 13.3 13.5 Fragmentation at Functional Groups* A. Alkyl halides (CH3CH2CH2Br and (CH3)2CHCl)7 B. Ethers (CH3CH2CH(CH3)OCH(CH3)2)8 C. Alcohols (CH3CH2CH2CH2CH(OH)CH3)9 D. Ketones (CH3CH2CH2COCH3)10 13.7 Infrared Spectroscopy Figure 13.12 (stretching and bending) 13.8 Characteristic Infrared Absorption bands Table 13.4 (OH, NH, and C=O) 13.10 The position of Absorption bands A. Effect of mass B. Effect of bond order11 D. Effect of resonance and inductive effect acyl halide > ester > aldehyde > ketone > amide 13.11 C-H Absorption Bands RC C H R2C CHH R2HC CH2HRHH RRRH Htranscis * NMR provides more reliable characterization.12 13.12 The Shape of Absorption Bands NH, NH2, OH, and CO2H 13.15 Identifying Infrared Spectra C=O and H-bond13 Additional material: Calculation of molecular formula using information from mass spectrometry and elemental analysis A. Example 1 From Mass Spec M+: 99 From elemental analysis: C: 60.5%; H: 9.1%; N: 14.1% B. Example 2 From Mass Spec M+: 142, relative intensity: (M+/(M+2)+ = 100/35 From elemental analysis: C: 58.9%; H: