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12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy Based on McMurry’s Organic Chemistry, 7th edition 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 Physical methods now permit structures to be determined directly. We will examine: mass spectrometry (MS) infrared (IR) spectroscopy nuclear magnetic resonance spectroscopy (NMR) ultraviolet-visible spectroscopy (VIS) 2 Why this Chapter? Finding structures of new molecules synthesized is critical To get a good idea of the range of structural techniques available and how they should be used 3 12.1 Mass Spectrometry of Small Molecules:Magnetic-Sector Instruments Measures molecular weight Sample vaporized and subjected to bombardment by electrons that remove an electron Creates a cation radical Bonds in cation radicals begin to break (fragment) Charge to mass ratio is measured 4 The Mass Spectrum Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (roughly 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+) 5 12.2 Interpreting Mass Spectra Molecular weight from the mass of the molecular ion Double-focusing instruments provide high-resolution “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 Instruments include computation of formulas for each peak 6 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 7 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 8 Mass Spectral Fragmentation of Hexane Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29 9 12.3 Mass Spectrometry of Some Common Functional Groups Alcohols: Alcohols undergo -cleavage (at the bond next to the C-OH) as well as loss of H-OH to give C=C 10 Mass Spectral Cleavage of Amines Amines undergo -cleavage, generating radicals 11 Fragmentation of Carbonyl Compounds 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 12 12.4 Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments Most biochemical analyses by MS use: - electrospray ionization (ESI) - Matrix-assisted laser desorption ionization (MALDI) • Linked to a time-of-flight mass analyzer (See figure 12.9) 13 12.5 Spectroscopy and the Electromagnetic Spectrum Radiant energy is proportional to its frequency (cycles/s = Hz) as a wave (Amplitude is its height) Different types are classified by frequency or wavelength ranges 14 Absorption Spectra Organic compound exposed to electromagnetic radiation, can absorb energy of only certain wavelengths (unit of energy) Transmits energy of other wavelengths. 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 12-12) 15 12.6 Infrared Spectroscopy IR region lower 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 Specific IR absorbed by organic molecule related to its structure 16 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 vibrations and rotations 17 12.7 Interpreting Infrared Spectra Most functional groups absorb at about the same energy and intensity independent of the molecule they are in Characteristic higher energy 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) See samples in Figure 12-14 18 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 19 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 modes Light objects connected to heavy objects vibrate fastest: C-H, N-H, O-H For two heavy atoms, stronger bond requires more energy: C C, C N > C=C, C=O, C=N > C-C, C-O, C-N, C-halogen 20 12.8 Infrared Spectra of Some Common Functional Groups Alkanes, Alkenes, Alkynes C-H, C-C, C=C, C C have characteristic peaks absence helps rule out C=C or C C 21 IR: Aromatic Compounds Weak C–H stretch at 3030 cm1 Weak absorptions 1660 - 2000 cm1 range Medium-intensity absorptions 1450 to 1600 cm1 See spectrum of phenylacetylene, Figure 12.15 22 IR: Alcohols and Amines O–H 3400 to 3650 cm1 Usually broad and intense N–H 3300 to 3500 cm1 Sharper and less intense than an O–H 23 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 24 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 C=O in Esters 1735 cm1 in saturated esters 1715 cm1 in esters next to aromatic ring or a double bond 25