1. John E. McMurry www.cengage.com/chemistry/mcmurry Paul D. Adams University of Arkansas Chapter 12 Structure Determination: Mass Spectrometry and Infrared Spectroscopy

2.  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 (UV-VIS) Determining the Structure of an Organic Compound

3.  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 Why this Chapter?

4.  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 12.1 Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments

5.  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 + ) The Mass Spectrum

6.  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: C 5 H 12 and C 4 H 8 O but:  C 5 H 12 72.0939 amu exact mass C 4 H 8 O 72.0575 amu exact mass  Result from fractional mass differences of atoms 16 O = 15.99491, 12 C = 12.0000, 1 H = 1.00783  Instruments include computation of formulas for each peak 12.2 Interpreting Mass Spectra

7.  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 Other Mass Spectral Features

8.  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 Interpreting Mass-Spectral Fragmentation Patterns

9.  Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29 Mass Spectral Fragmentation of Hexane

10. Alcohols:  Alcohols undergo  -cleavage (at the bond next to the C- OH) as well as loss of H-OH to give C=C 12.3 Mass Spectrometry of Some Common Functional Groups

11.  Amines undergo  -cleavage, generating radicals Mass Spectral Cleavage of Amines

12.  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 Fragmentation of Carbonyl Compounds

13.  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) Fragmentation of Carbonyl Compounds

14.  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 12.5 Spectroscopy and the Electromagnetic Spectrum

15.  An 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) Absorption Spectra

16.  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 an organic molecule is related to its structure 12.6 Infrared Spectroscopy

17.  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 Infrared Energy Modes

18.  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)  Let’s examine Figure 12-14 12.7 Interpreting Infrared Spectra

19. Figure 12.14

20.  4000-2500 cm -1 N-H, C-H, O-H (stretching)  3300-3600 N-H, O-H  3000 C-H  2500-2000 cm -1 C  C 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 Regions of the Infrared Spectrum

21.  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 Differences in Infrared Absorptions

22. Alkanes, Alkenes, Alkynes  C-H, C-C, C=C, C  C have characteristic peaks  absence helps rule out C=C or C  C 12.8 Infrared Spectra of Some Common Functional Groups

23.  Weak C–H stretch at 3030 cm  1  Weak absorptions 1660 - 2000 cm  1 range  Medium-intensity absorptions 1450 to 1600 cm  1  See spectrum of phenylacetylene, Figure 12.15 IR: Aromatic Compounds

24.  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: Alcohols and Amines

25.  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 IR: Carbonyl Compounds

26.  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 C=O in Ketones

27. Let’s Work a Problem Propose structures for a compound that fits the following data: It is an alcohol with M + = 88 and fragments at m/z = 73, m/z = 70, and m/z = 59

28. Answer Answer: We must first decide on the the formula of an alcohol that could undergo this type of fragmentation via mass spectrometry. We know that an alcohol possesses an O atom (MW=16), so that leads us to the formula C 5 H 12 O for an alcohol with M + = 88, with a structure of: One fragmentation peak at 70 is due to the loss of water, and alpha cleavage can result in m/z of 73 and 59.