Determining the Structure of an Organic Compound

Transcription

1 Chapter 12- Structure Determination: Mass Spectrometry and Infrared Spectroscopy Ashley Piekarski, Ph.D. Determining the Structure of an Organic Compound The analysis of the outcome of a reac=on requires that we know the full structure of the products as well as the reactants In the 19 th and early 20 th centuries, structures were determined by synthesis and chemical degrada=on 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) 1

2 Why this Chapter? Finding structures of new molecules synthesized is cri=cal To get a good idea of the range of structural techniques available and how they should be used 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 ca=on radicals begin to break (fragment) Charge to mass ra=o is measured htp:// watch?v=jwao0o0_qm 2

3 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 ca=on is parent peak or molecular ion (M + ) 12.2 Interpreting Mass Spectra Molecular weight from the mass of the molecular ion Double-focusing instruments provide high-resolu=on exact mass atomic mass units distinguishing specific atoms Example MW 72 is ambiguous: C 5 H 12 and C 4 H 8 O but: C 5 H amu exact mass C 4 H 8 O amu exact mass Result from fractional mass differences of atoms 16 O = , 12 C = , 1 H = Instruments include computa=on of formulas for each peak 3

4 Other Mass Spectral Features If parent ion not present due to electron bombardment causing breakdown, soder methods such as chemical ioniza=on are used Peaks above the molecular weight appear as a result of naturally occurring heavier isotopes in the sample (M+1) from 13 C that is randomly present Interpreting Mass-Spectral Fragmentation Patterns The way molecular ions break down can produce characteris=c fragments that help in iden=fica=on Serves as a fingerprint for comparison with known materials in analysis (used in forensics) Positive charge goes to fragments that best can stabilize it 4

5 Mass Spectral Fragmentation of Hexane Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, Mass Spectrometry of Some Common Functional Groups Alcohols: Alcohols undergo α-cleavage (at the bond next to the C-OH) as well as loss of H-OH to give C=C 5

6 Mass Spectral Cleavage of Amines Amines undergo α-cleavage, genera=ng radicals 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 α cleavage 6

7 12.4 Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments Most biochemical analyses by MS use: - electrospray ioniza=on (ESI) - Matrix-assisted laser desorp=on ioniza=on (MALDI) 12.5 Spectroscopy and the Electromagnetic Spectrum Radiant energy is propor=onal to its frequency (cycles/s = Hz) as a wave (Amplitude is its height) Different types are classified by frequency or wavelength ranges 7

8 Absorption Spectra Organic compound exposed to electromagne=c radia=on, 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 transmited produces an absorp6on spectrum Energy absorbed is distributed internally in a dis=nct and reproducible way (See Figure 12-12) 12.6 Infrared Spectroscopy IR region lower energy than visible light (below red produces hea=ng as with a heat lamp) 2.5 x 10-6 m to 2.5 x 10-5 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 propor=onal to frequency Specific IR absorbed by organic molecule related to its structure htp:// 8

9 Infrared Energy Modes IR energy absorp=on corresponds to specific modes, corresponding to combina=ons of atomic movements, such as bending and stretching of bonds between groups of atoms called normal modes Energy is characteris=c of the atoms in the group and their bonding Corresponds to vibra=ons and rota=ons 12.7 Interpreting Infrared Spectra Most func=onal groups absorb at about the same energy and intensity independent of the molecule they are in Characteris=c higher energy IR absorp=ons in Table 12.1 can be used to confirm the existence of the presence of a func=onal group in a molecule IR spectrum has lower energy region characteris=c of molecule as a whole ( fingerprint region) See samples in Figure

10 Regions of the Infrared Spectrum cm -1 N-H, C-H, O-H (stretching) N-H, O-H 3000 C-H cm -1 C-C and C-N triple bonds(stretching) cm -1 double bonds (stretching) C=O C=C cm -1 Below 1500 cm -1 fingerprint region 19 Differences in Infrared Absorptions Molecules vibrate and rotate in normal modes, which are combina=ons of mo=ons (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: CC triple bond, CN triple bond > C=C, C=O, C=N > C-C, C-O, C- N, C-halogen 10

11 12.8 Infrared Spectra of Some Common Functional Groups IR: Aromatic Compounds Weak C H stretch at 3030 cm -1 Weak absorp=ons cm -1 range Medium-intensity absorp=ons 1450 to 1600 cm -1 11

12 IR: Alcohols and Amines O H 3400 to 3650 cm -1 Usually broad and intense N H 3300 to 3500 cm -1 Sharper and less intense than an O H IR: Carbonyl Compounds Strong, sharp C=O peak 1670 to 1780 cm -1 Exact absorp=on characteris=c of type of carbonyl compound 1730 cm -1 in saturated aldehydes 1705 cm -1 in aldehydes next to double bond or aromatic ring 12

13 C=O in Ketones 13