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

2. Learning Objectives (12.1)
Mass spectrometry of small molecules: Magnetic-sector instruments
(12.2)
Interpreting mass spectra
(12.3)
Mass spectrometry of some common functional groups
(12.4)
Mass spectrometry in biological chemistry: Time-of-flight (TOF) instruments

3. Learning Objectives (12.5)
Spectroscopy and the electromagnetic spectrum
(12.6)
Infrared spectroscopy
(12.7)
Interpreting infrared spectroscopy
(12.8)
Infrared spectra of some common functional groups

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. 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
Mass spectrometry of small molecules: Magnetic- sector instruments

6. Electron-Ionization, Magnetic-Sector Mass Spectrometer
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. Figure 12.1 - The electron-ionization, magnetic-sector mass spectrometer
Mass spectrometry of small molecules: Magnetic- sector instruments

8. 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

9. Figure 12.2 - The Quadrupole Mass Analyzer
Mass spectrometry of small molecules: Magnetic- sector instruments

10. Representing 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 (Intensity of 100%)
Peak that corresponds to the unfragmented radical cation is parent peak or molecular ion (M+)
Mass spectrometry of small molecules: Magnetic- sector instruments

11. Interpreting Mass Spectra
Provides the molecular weight from the mass of the molecular ion
Double-focusing mass spectrometers have a high accuracy rate
In compounds that do not exhibit molecular ions, soft ionization methods are used
Interpreting mass spectra

12. Other Mass Spectral Features
Mass spectrum provides the molecular fingerprint of a compound
The way molecular ions break down, can produce characteristic fragments that help in identification
Interprets molecular fragmentation pattern, assisting in the derivation of structural information
Interpreting mass spectra

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

14. Worked Example
The male sex hormone testosterone contains only C, H, and O and has a mass of amu, as determined by high-resolution mass spectrometry
Determine the possible molecular formula of testosterone
Interpreting mass spectra

15. Worked Example Solution:
Assume that hydrogen contributes to the mass of
Dividing by ( difference between the atomic weight of one H atom and 1) gives 26.67
Approximate number of H in testosterone
Determine the maximum number of carbons by dividing 288 by 12
List reasonable molecular formulas containing C,H, and O that contain hydrogens and whose mass is 288
Interpreting mass spectra

16. Worked Example The possible formula for testosterone is C19H28O2
Interpreting mass spectra

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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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

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

25. Spectroscopy and the Electromagnetic Spectrum
Waves are classified by frequency or wavelength ranges
Spectroscopy and the electromagnetic spectrum

26. Spectroscopy and the Electromagnetic Spectrum
Electromagnetic radiation seems to have dual behavior
Possesses the properties of a photon
Behaves as an energy wave
Spectroscopy and the electromagnetic spectrum

27. Spectroscopy and the Electromagnetic Spectrum
Speed of the wave
The unit of electromagnetic energy is called quanta
Spectroscopy and the electromagnetic spectrum

28. Spectroscopy and the Electromagnetic Spectrum
Considering the plank equation and multiplying ɛ by Avogadro’s number NA:
Spectroscopy and the electromagnetic spectrum

29. 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

30. Worked Example
Calculate the energy in kJ/mol for a gamma ray with λ = 5.0×10-11m
Solution:
Spectroscopy and the electromagnetic spectrum

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

32. 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

33. 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

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

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

36. 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

37. Harmonic Oscillator System comprising two atoms connected by a bond
In a vibrating bond, the vibrating energy is in a constant state of change from kinetic to potential energy and vice versa
Equation for natural frequency of vibration for a bond -
Interpreting Infrared Spectra

38. 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

39. 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

40. 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

41. 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

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

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

49. 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

50. 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