1. Chapter 12 Structure Determination: Mass Spectrometry and Infrared Spectroscopy

2. Learning Objectives
Mass spectrometry of small molecules: Magnetic-sector instruments
Interpreting mass spectra
Mass spectrometry of some common functional groups
Mass spectrometry in biological chemistry: Time-of-flight (TOF) instruments
Spectroscopy and the electromagnetic spectrum
Infrared spectroscopy
Interpreting infrared spectroscopy
Infrared spectra of some common functional groups

3. 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
Spectroscopic methods shown below now permit structures to be determined directly.
mass spectrometry (MS)
infrared (IR) spectroscopy
nuclear magnetic resonance spectroscopy (NMR)
ultraviolet-visible spectroscopy (VIS)
We will examine:

4. Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments
Mass spectrometry (MS) determines molecular weight by measuring the mass of a molecule
Components of a mass spectrometer:
Ionization source - Electrical charge assigned to sample molecules
Mass analyzer - Ions are separated based on their mass-to-charge ratio
Detector - Separated ions are observed and counted
Mass spectrometry of small molecules: Magnetic- sector instruments

5. Figure 12.1 - The electron-ionization, magnetic-sector mass spectrometer
Mass spectrometry of small molecules: Magnetic- sector instruments

6. Electron-Ionization, Magnetic-Sector Mass Spectrometer
Small amount of sample undergoes vaporization at the ionization source to form cation radicals
Amount of energy transferred causes fragmentation of most cation radicals into positive and neutral pieces
Molecular ions and resulting fragments pass through a strong magnetic field in a curved pipe that segregates them according to their mass-to-charge ratio
Positive fragments are sorted into a detector and are recorded as peaks at the various m/z ratios. Mass of the ion is the m/z value
Mass spectrometry of small molecules: Magnetic- sector instruments

7. Quadrupole Mass Analyzer
Comprises four iron rods arranged parallel to the direction of the ion beam
Specific oscillating electrostatic field is created in the space between the four rods
Only the corresponding m/z value is able to pass through and reach the detector
Other values are deflected and crash into the rods or the walls of the instrument
Mass spectrometry of small molecules: Magnetic- sector instruments

8. Representing the Mass Spectrum
Plot mass of ions (m/z) on (x-axis) versus the intensity of the signal (roughly corresponding to the number of ions) on (y-axis)
Tallest peak is base peak (Intensity of 100%)
Peak that corresponds to the unfragmented radical cation is parent peak or molecular ion (M+)
MS of Propane (CH3CH2CH3, MF = C3H8, Mass = 44)
Propane

9. 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: C5H12 and C4H8O but:
C5H12 has exact mass of amu, and C4H8O has exact mass of amu.
Result from fractional mass differences of atoms 16O = , 12C = , 1H =
Instruments include computation of formulas for each peak
If parent ion not present due to electron bombardment (70 eV EI) causing breakdown, “softer” methods such as 13 eV EI and 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
C-13 abundance is 1.1%

10. Other Mass Spectral Features
The way molecular ions break down can produce characteristic fragments of a compound that help in identification
Serves as a “fingerprint” for comparison with known materials
Positive charge goes to fragments that best can be stabilized
Interpreting mass spectra

11. Mass Spectral Fragmentation of Hexane
Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29
Interpreting mass spectra

12. Mass Spectrometry of Some Common Functional Groups
Alcohols
Fragment through alpha cleavage and dehydration
Mass spectrometry of some common functional groups

13. Mass Spectrometry of Some Common Functional Groups
Amines
Nitrogen rule of mass spectrometry
A compound with an odd number of nitrogen atoms has an odd-numbered molecular weight
Amines undergo -cleavage, generating alkyl radicals and a resonance-stabilized, nitrogen-containing cation
Mass spectrometry of some common functional groups

14. Mass Spectrometry of Some Common Functional Groups
Halides: Elements comprising two common isotopes possess a distinctive appearance as a mass spectra
Mass spectrometry of some common functional groups

15. 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
Mass spectrometry of some common functional groups

16. Worked Example
List the masses of the parent ion and of several fragments that can be found in the mass spectrum of the following molecule
Mass spectrometry of some common functional groups

17. Worked Example Solution: The molecule is 2-Methyl-2-pentanol
It produces fragments resulting from dehydration and alpha cleavage
Peaks may appear at M+=102(molecular ion), 87, 84, 59
Mass spectrometry of some common functional groups

19. Mass Spectroscopy in Biological Chemistry: Time-of-Flight (TOF) Instruments
Most biochemical analyses by MS use soft ionization methods that charge molecules with minimal fragmentation
Electrospray ionization (ESI)
High voltage is passed through the solution sample
Sample molecule gain one or more protons from the volatile solvent, which evaporates quickly
Matrix-assisted laser desorption ionization (MALDI)
Sample is absorbed onto a suitable matrix compound
Upon brief exposure to laser light, energy is transferred from the matrix compound to the sample molecule
Mass spectrometry in biological chemistry: Time-of-Flight (TOF) instruments

20. Figure 12.15 - MALDI–TOF Mass Spectrum of Chicken Egg-White Lysozyme
Mass spectrometry in biological chemistry: Time-of-Flight (TOF) instruments

21. Spectroscopy and the Electromagnetic Spectrum
Radiant energy is proportional to its frequency (Hz) as a wave
Electromagnetic spectrum is divided into different energy regions by frequency or wavelength ranges
Spectroscopy and the electromagnetic spectrum

22. Background: IR Spectroscopy
Key concept: Functional groups within a molecule absorb IR light if they have polar bonds (polarizability) or dipole moments.
Terminology
Wavelength: distance between peaks/troughs of wave
Frequency: number of wave cycles that pass a fixed point in 1 second
Wavenumber: number of cycles of the wave per cm
IR spectroscopy can be used to identify the functional groups
(NH2, OH, CHO, COOH, C=C etc.) present in our compounds
based on the location of peaks in the IR spectrum.
Higher the wavenumber higher the frequency.

23. Absorption Spectrum
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
In infrared radiation, absorbed energy causes bonds to stretch and bend more vigorously
In ultraviolet radiation, absorbed energy causes electrons to jump to a higher-energy orbital
Spectroscopy and the electromagnetic spectrum

24. Infrared Spectroscopy
IR region has lower energy than visible light (below red - produces heating as with a heat lamp)
Wavenumber:
Infrared spectroscopy

25. Infrared Energy Modes
Molecules possess a certain amount of energy that causes them to vibrate
Molecule absorbs energy upon electromagnetic radiation only if the radiation frequency and the vibration frequency match
Infrared spectroscopy

26. Interpreting Infrared Spectra
IR spectrum interpretation is difficult as the arrangement of organic molecules is complex
Disadvantage - Generally used only in pure samples of fairly small molecules
Advantage - Provides a unique identification of compounds
Fingerprint region cm-1 to 400 cm-1 (approx)
Complete interpretation of the IR spectrum is not necessary to gain useful structural information
IR absorption bands are similar among compounds
Interpreting Infrared Spectra

27. 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 presence or absence 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

28. Regions of the Infrared Spectrum
cm-1 N-H, C-H, O-H (stretching)
N-H, O-H
3000 C-H
cm-1 CºC and C º N (stretching)
cm-1 double bonds (stretching)
C=O
C=C cm-1
Below 1500 cm-1 “fingerprint” region

29. Table 12.1 - Characteristic IR Absorptions of Some Functional Groups
Interpreting Infrared Spectra

30. Figure 12.20 - IR Spectra of Hexane, 1-Hexene, and 1-Hexyne
Interpreting Infrared Spectra

31. Regions of the Infrared Spectrum
Region from 4000 to 2500 cm-1 can be divided into areas characterized by:
Single-bond stretching motions
Triple-bond stretching motions
Absorption by double bonds
Fingerprint portion of the IR spectrum
Interpreting Infrared Spectra

32. Worked Example
Using IR spectroscopy, distinguish between the following isomers:
CH3CH2OH and CH3OCH3
Solution:
CH3CH2OH is a strong hydroxyl bond at 3400–3640 cm-1
CH3OCH3 does not possess a band in the region 3400–3640 cm-1
Interpreting Infrared Spectra

33. Infrared Spectra of Some Common Functional Groups
Alkanes
No functional groups
C–H and C–C bonds are responsible for absorption
C–H bond absorption ranges from 2850 to 2960 cm-1
C–C bonds show bands between 800 to cm-1
Infrared Spectra of Some Common Functional Groups

34. Infrared Spectra of Some Common Functional Groups
Alkenes
Vinylic =C–H bonds are responsible for absorption from 3020 to 3011cm-1
Alkene C=C bonds are responsible for absorption close to 1650cm-1
Alkenes possess =C–H out-of-plane bending absorptions in the 700 to 1000 cm-1 range
Infrared Spectra of Some Common Functional Groups

35. Infrared Spectra of Some Common Functional Groups
Alkynes
C≡C stretching absorption exhibited at 2100 to 2260 cm-1
Similar bonds in 3-hexyne show no absorption
Terminal alkynes such as 1-hexyne possess ≡C–H stretching absorption at 3300 cm-1
Infrared Spectra of Some Common Functional Groups

36. Aromatic Compounds Weak C–H stretch at 3030 cm1
Weak absorptions at 1660 to 2000 cm1 range
Medium-intensity absorptions at 1450 to 1600 cm1
Infrared Spectra of Some Common Functional Groups

37. Aromatic Compounds Alcohols Amines O–H 3400 to 3650 cm1
Usually broad and intense
Amines
N–H 3300 to 3500 cm1
Sharper and less intense than an O–H
Infrared Spectra of Some Common Functional Groups

38. Carbonyl Compounds
Strong, sharp C=O peak in the range of 1670 to 1780 cm1
Exact absorption is characteristic of type of carbonyl compound
Principles of resonance, inductive electronic effects, and hydrogen bonding provides a better understanding of IR radiation frequencies
Infrared Spectra of Some Common Functional Groups

39. Carbonyl Compounds Aldehydes 1730 cm1 in saturated aldehydes
1705 cm1 in aldehydes next to double bond or aromatic ring
Low absorbance frequency is due to the resonance delocalization of electron density from the C=C into the carbonyl
Infrared Spectra of Some Common Functional Groups

40. Ketones
Saturated open-chain ketones and six-membered cyclic ketones absorb at 1715cm-1
Five-membered ketones absorb at 1750cm-1
Stiffening of C=O bond due to ring strain
Four members absorb at 1780cm-1
Infrared Spectra of Some Common Functional Groups

41. Carbonyl Compounds Esters Saturated esters absorb at 1735 cm-1
Esters possess two strong absorbances within the range of 1300 to 1000 cm-1
Esters adjacent to an aromatic ring or a double bond absorb at 1715 cm-1
Infrared Spectra of Some Common Functional Groups

42. Worked Example
Identify the possible location of IR absorptions in the compound below
Infrared Spectra of Some Common Functional Groups

43. Worked Example Solution:
The compound possesses nitrile and ketone groups as well as a carbon–carbon double bond
Nitrile absorption occurs at 2210–2260 cm-1
Ketone exhibits an absorption bond at 1690 cm-1
Double bond absorption occurs at 1640–1680 cm-1
Infrared Spectra of Some Common Functional Groups

44. Summary
Mass spectrometry determines the molecular weight and formula of a molecule
Infrared (IR) spectroscopy identifies functional groups in a molecule
Electromagnetic radiation is used in infrared spectroscopy
Organic molecules absorb a certain frequency from electromagnetic radiation