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12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy Determining the Structure of an Organic Compound • The analysis of the outcome of a reaction requires that we know the full structure of the products as well as the reactants • In the 19th and early 20th centuries, structures were determined by synthesis and chemical degradation that related compounds to each other 2 Determining the Structure of an Organic Compound • Physical methods now permit structures to be determined directly. We will examine: – mass spectrometry (MS)—this chapter – infrared (IR) spectroscopy—this chapter – nuclear magnetic resonance spectroscopy (NMR)—Chapter 13 – ultraviolet-visible spectroscopy (VIS)— Chapter 14 3 12.1 Mass Spectrometry (MS) • Sample vaporized and bombarded by energetic electrons that remove an electron, creating a cation-radical • Bonds in cation radicals begin to break (fragment) 4 Mass Spectrometer 5 The Mass Spectrum • Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (corresponding to the number of ions) (y-axis) • Tallest peak is base peak (100%) – Other peaks listed as the % of that peak • Peak that corresponds to the unfragmented radical cation is parent peak or molecular ion (M+) 6 MS Examples: Methane and Propane • Methane produces a parent peak (m/z = 16) and fragments of 15 and 14 (See Figure 12-2 a) 7 MS Examples: Methane and Propane • The Mass Spectrum of propane is more complex (Figure 12-2 b) since the molecule can break down in several ways 8 9 12.2 Interpreting Mass Spectra • Molecular weight from the mass of the molecular ion • Double-focusing instruments provide highresolution “exact mass” – 0.0001 atomic mass units – distinguishing specific atoms • Example MW “72” is ambiguous: C5H12 and C4H8O but: – C5H12 72.0939 amu exact mass C4H8O 72.0575 amu exact mass – Result from fractional mass differences of atoms 16O = 15.99491, 12C = 12.0000, 1H = 1.00783 10 Other Mass Spectral Features • If parent ion not present due to electron bombardment causing breakdown, “softer” methods such as chemical ionization are used • Peaks above the molecular weight appear as a result of naturally occurring heavier isotopes in the sample – (M+1) from 13C that is randomly present 11 12.3 Interpreting Mass-Spectral Fragmentation Patterns • The way molecular ions break down can produce characteristic fragments that help in identification – Serves as a “fingerprint” for comparison with known materials in analysis (used in forensics) – Positive charge goes to fragments that best can stabilize it 12 2,2-Dimethylpropane: MM = 72 (C5H12) 13 Mass Spectral Fragmentation of Hexane • Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29 14 Hexane 15 Practice Problem 12.2: methylcyclohexane or ethylcyclopentane? 16 Mass Spectral Cleavage Reactions of Alcohols • Alcohols undergo -cleavage (at the bond next to the C-OH) as well as loss of H-OH to give C=C 17 Mass Spectral Cleavage of Amines • Amines undergo -cleavage, generating radicals 18 Fragmentation of Ketones and Aldehydes • A C-H that is three atoms away leads to an internal transfer of a proton to the C=O, called the McLafferty rearrangement • Carbonyl compounds can also undergo cleavage 19 Fragmentation of Ketones and Aldehydes 20 12.5 The Electromagnetic Spectrum 21 Wavelength and Frequency 22 Absorption Spectra • Organic compounds exposed to electromagnetic radiation can absorb photons of specific energies (wavelengths or frequencies) • Changing wavelengths to determine which are absorbed and which are transmitted produces an absorption spectrum • Energy absorbed is distributed internally in a distinct and reproducible way (See Figure 12-11) 23 Infrared Absorption Spectrum of Ethanol 24 12.6 Infrared Spectroscopy of Organic Molecules • IR region is lower in photon energy than visible light (below red – produces heating as with a heat lamp) • 2.5 106 m to 2.5 105 m region used by organic chemists for structural analysis • IR energy in a spectrum is usually measured as wavenumber (cm-1), the inverse of wavelength and proportional to frequency: • Wavenumber (cm-1) = 1/l(cm) • Specific IR absorbed by organic molecule is related to its structure 25 IR region and vicinity 26 Infrared Energy Modes • IR energy absorption corresponds to specific modes, corresponding to combinations of atomic movements, such as bending and stretching of bonds between groups of atoms called “normal modes” • Energy is characteristic of the atoms in the group and their bonding • Corresponds to molecular vibrations 27 Infrared Energy Modes 28 12.7 Interpreting Infrared Spectra • Most functional groups absorb at about the same energy and intensity independent of the molecule they are in • Characteristic IR absorptions in Table 12.1 can be used to confirm the existence of the presence of a functional group in a molecule • IR spectrum has lower energy region characteristic of molecule as a whole (“fingerprint” region) 29 30 31 32 Regions of the Infrared Spectrum • 4000-2500 cm-1 N-H, C-H, O-H (stretching) – 3300-3600 N-H, O-H – 3000 C-H • 2500-2000 cm-1 CC and C N (stretching) • 2000-1500 cm-1 double bonds (stretching) – C=O 1680-1750 – C=C 1640-1680 cm-1 • Below 1500 cm-1 “fingerprint” region 33 Regions of the Infrared Spectrum 34 Differences in Infrared Absorptions • Molecules vibrate and rotate in normal modes, which are combinations of motions (relates to force constants) • Bond stretching dominates higher energy (frequency) modes 35 Differences in Infrared Absorptions • Light objects connected to heavy objects vibrate fastest (at higher frequencies): CH, N-H, O-H • For two heavy atoms, stronger bond requires more energy (higher frequency): C C, C N > C=C, C=O, C=N > C-C, CO, C-N, C-halogen 36 12.8 Infrared Spectra of Hydrocarbons • C-H, C-C, C=C, C C have characteristic peaks 37 Hexane 38 Alkenes 39 1-Hexene 40 Alkynes 41 12.9 Infrared Spectra of Some Common Functional Groups • Spectroscopic behavior of functional groups is discussed in later chapters • Brief summaries presented here 42 IR: Alcohols 43 Amines 44 IR: Aromatic Compounds • Weak C–H stretch at 3030 cm1 • Weak absorptions 1660 - 2000 cm1 range • Medium-intensity absorptions 1450 to 1600 cm1 45 Phenylacetylene 46 IR: Carbonyl Compounds • Strong, sharp C=O peak 1670 to 1780 cm1 • Exact absorption characteristic of type of carbonyl compound – 1730 cm1 in saturated aldehydes – 1705 cm1 in aldehydes next to double bond or aromatic ring 47 Practice problem 12.7: 48 Phenylacetaldehyde 49 C=O in Ketones • 1715 cm1 in six-membered ring and acyclic ketones • 1750 cm1 in 5-membered ring ketones • 1690 cm1 in ketones next to a double bond or an aromatic ring 50 C=O in Esters • 1735 cm1 in saturated esters • 1715 cm1 in esters next to aromatic ring or a double bond 51 Chromatography: Purifying Organic Compounds • Chromatography : a process that separates compounds using adsorption and elution – Mixture is dissolved in a solvent (mobile phase) and placed into a glass column of adsorbent material (stationary phase) – Solvent or mixtures of solvents passed through – Compounds adsorb to different extents and desorb differently in response to appropriate solvent (elution) – Purified sample in solvent is collected from end of column – Can be done in liquid or gas mobile phase 52 Principles of Liquid Chromatography • Stationary phase is alumina (Al2O3) or silica gel (hydrated SiO2) • Solvents of increasing polarity are used to elute more and more strongly adsorbed species • Polar species adsorb most strongly to stationary phase – For examples, alcohols adsorb more strongly than alkenes 53 High-Pressure (or High-Performance) Liquid Chromatography (HPLC) • More efficient and complete separation than ordinary LC • Coated silica microspheres (10-25 µm diameter) in stationary phase • High-pressure pumps force solvent through tightly packed HPLC column • Detector monitors eluting material • Figure 12.17: HPLC analysis of a mixture of 14 pesticides, using acetonitrile/water as the mobile phase 54 HPLC of Pesticide Mixture 55 Prob. 12.39: Cyclohexane or Cyclohexene? 56 Problem 12.48: Unknown hydrocarbon 57 Problem 12.49: Unknown hydrocarbon2 58 Some Useful Websites: • Interpretation of IR spectra (CSU Stanislaus): http://wwwchem.csustan.edu/Tutorials/INFRARED.HTM • IR Spectroscopy Tutorial (CU Boulder): http://orgchem.colorado.edu/hndbksupport/irtutor/tutorial. html • NIST Chemistry WebBook: http://webbook.nist.gov/chemistry/ • SDBS Data Base: http://www.aist.go.jp/RIODB/SDBS/menu-e.html 59