1. © 2016 Cengage Learning. All Rights Reserved. John E. McMurry www.cengage.com/chemistry/mcmurry Chapter 12 Structure Determination: Mass Spectrometry and Infrared Spectroscopy

2. © 2016 Cengage Learning. All Rights Reserved. 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. © 2016 Cengage Learning. All Rights Reserved. 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. © 2016 Cengage Learning. All Rights Reserved. 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

5. © 2016 Cengage Learning. All Rights Reserved. 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

6. © 2016 Cengage Learning. All Rights Reserved. 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

7. © 2016 Cengage Learning. All Rights Reserved. Figure 12.1 - The electron-ionization, magnetic-sector mass spectrometer

8. © 2016 Cengage Learning. All Rights Reserved. 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

9. © 2016 Cengage Learning. All Rights Reserved. Figure 12.2 - The Quadrupole Mass Analyzer

10. © 2016 Cengage Learning. All Rights Reserved. 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+)

11. © 2016 Cengage Learning. All Rights Reserved. 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

12. © 2016 Cengage Learning. All Rights Reserved. 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

13. © 2016 Cengage Learning. All Rights Reserved. Mass Spectral Fragmentation of Hexane  Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29

14. © 2016 Cengage Learning. All Rights Reserved. Worked Example  The male sex hormone testosterone contains only C, H, and O and has a mass of 288.2089 amu, as determined by high-resolution mass spectrometry  Determine the possible molecular formula of testosterone

15. © 2016 Cengage Learning. All Rights Reserved. Worked Example  Solution:  Assume that hydrogen contributes 0.2089 to the mass of 288.2089  Dividing 0.2089 by 0.00783 ( 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 20-30 hydrogens and whose mass is 288

16. © 2016 Cengage Learning. All Rights Reserved. Worked Example  The possible formula for testosterone is C 19 H 28 O 2

17. © 2016 Cengage Learning. All Rights Reserved. Mass Spectrometry of Some Common Functional Groups  Alcohols  Fragment through alpha cleavage and dehydration

18. © 2016 Cengage Learning. All Rights Reserved. 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

19. © 2016 Cengage Learning. All Rights Reserved. Mass Spectrometry of Some Common Functional Groups  Halides  Elements comprising two common isotopes possess a distinctive appearance as a mass spectra

20. © 2016 Cengage Learning. All Rights Reserved. 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

21. © 2016 Cengage Learning. All Rights Reserved. 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

22. © 2016 Cengage Learning. All Rights Reserved. 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

23. © 2016 Cengage Learning. All Rights Reserved. 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

24. © 2016 Cengage Learning. All Rights Reserved. Figure 12.15 - MALDI–TOF Mass Spectrum of Chicken Egg-White Lysozyme

25. © 2016 Cengage Learning. All Rights Reserved. Spectroscopy and the Electromagnetic Spectrum  Waves are classified by frequency or wavelength ranges

26. © 2016 Cengage Learning. All Rights Reserved. Spectroscopy and the Electromagnetic Spectrum  Electromagnetic radiation seems to have dual behavior  Possesses the properties of a photon  Behaves as an energy wave

27. © 2016 Cengage Learning. All Rights Reserved. Spectroscopy and the Electromagnetic Spectrum  Speed of the wave  The unit of electromagnetic energy is called quanta

28. © 2016 Cengage Learning. All Rights Reserved. Spectroscopy and the Electromagnetic Spectrum  Considering the plank equation and multiplying ɛ by Avogadro’s number N A :

29. © 2016 Cengage Learning. All Rights Reserved. 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

30. © 2016 Cengage Learning. All Rights Reserved. Worked Example  Calculate the energy in kJ/mol for a gamma ray with λ = 5.0×10 -11 m  Solution:

31. © 2016 Cengage Learning. All Rights Reserved. Infrared Spectroscopy  IR region has lower energy than visible light (below red - produces heating as with a heat lamp)  Wavenumber:

32. © 2016 Cengage Learning. All Rights Reserved. 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

33. © 2016 Cengage Learning. All Rights Reserved. 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 - 1500cm -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

34. © 2016 Cengage Learning. All Rights Reserved. Table 12.1 - Characteristic IR Absorptions of Some Functional Groups

35. © 2016 Cengage Learning. All Rights Reserved. Figure 12.20 - IR Spectra of Hexane, 1-Hexene, and 1-Hexyne

36. © 2016 Cengage Learning. All Rights Reserved. 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

37. © 2016 Cengage Learning. All Rights Reserved. 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 -

38. © 2016 Cengage Learning. All Rights Reserved. Worked Example  Using IR spectroscopy, distinguish between the following isomers:  CH 3 CH 2 OH and CH 3 OCH 3  Solution:  CH 3 CH 2 OH is a strong hydroxyl bond at 3400– 3640 cm -1  CH 3 OCH 3 does not possess a band in the region 3400–3640 cm -1

39. © 2016 Cengage Learning. All Rights Reserved. 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 1300 cm -1

40. © 2016 Cengage Learning. All Rights Reserved. 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

41. © 2016 Cengage Learning. All Rights Reserved. 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

42. © 2016 Cengage Learning. All Rights Reserved. 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

43. © 2016 Cengage Learning. All Rights Reserved. Aromatic Compounds  Alcohols  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

44. © 2016 Cengage Learning. All Rights Reserved. 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

45. © 2016 Cengage Learning. All Rights Reserved. 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

46. © 2016 Cengage Learning. All Rights Reserved. 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 membered ketones absorb at 1780cm -1

47. © 2016 Cengage Learning. All Rights Reserved. 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

48. © 2016 Cengage Learning. All Rights Reserved. Worked Example  Identify the possible location of IR absorptions in the compound below

49. © 2016 Cengage Learning. All Rights Reserved. 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

50. © 2016 Cengage Learning. All Rights Reserved. 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