12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy Based on McMurry’s Organic Chemistry, 6 th 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 19 th and early 20 th 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)

12.1 Mass Spectrometry (MS) 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 (see Figure 12-1)

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 + )

MS Examples: Methane and Propane Methane produces a parent peak (m/z = 16) and fragments of 15 and 14 (See Figure 12-2 a) The MS of propane is more complex (Figure 12-2 b) since the molecule can break down in several ways

12.2 Interpreting Mass Spectra Molecular weight from the mass of the molecular ion Double-focusing instruments provide high-resolution “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 computation of formulas for each peak

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 13 C that is randomly present

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

12.5 Spectroscopy of 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

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 12-11)

12.6 Infrared Spectroscopy of Organic Molecules IR region lower energy than visible light (below red – produces heating as with a heat lamp) 2.5  10  6 m to 2.5  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 proportional to frequency Specific IR absorbed by organic molecule related to its structure

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

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 12-13

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 (stretching) cm -1 double bonds (stretching) –C=O –C=C cm -1 Below 1500 cm -1 “fingerprint” region

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

12.8 Infrared Spectra of Hydrocarbons C-H, C-C, C=C, C  C have characteristic peaks –absence helps rule out C=C or C  C

12.9 Infrared Spectra of Some Common Functional Groups Spectroscopic behavior of functional group is discussed in later chapters Brief summaries presented here

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: Aromatic Compounds Weak C–H stretch at 3030 cm  1 Weak absorptions cm  1 range Medium-intensity absorptions 1450 to 1600 cm  1 See spectrum of phenylacetylene, Figure 12.15

IR: Carbonyl Compounds Strong, sharp C=O peak 1670 to 1780 cm  1 Exact absorption characteristic of type of carbonyl compound –1730 cm  1 in saturated aldehydes –1705 cm  1 in aldehydes next to double bond or aromatic ring

C=O in Ketones 1715 cm  1 in six-membered ring and acyclic ketones 1750 cm  1 in 5-membered ring ketones 1690 cm  1 in ketones next to a double bond or an aromatic ring

C=O in Esters 1735 cm  1 in saturated esters 1715 cm  1 in esters next to aromatic ring or a double bond