1. 11.3 Spectroscopic Identification of Organic compounds
IHD
IR Spectroscopy
Mass Spectroscopy
NMR

2. Chapter 11.3-21.1:Spectroscopic identification of organic compounds
11.3: Analytical techniques can be used to determine the structure of a compound, analyze the composition of a substance, or determine the purity of a compound. Spectroscopic techniques are used in the structural identification of organic and inorganic compounds.
20.1: Although spectroscopic characterization techniques form the backbone of structural identification of compounds, typically no one techniques results in a full structural identification of a molecule

3. Analytical techniques
Qualitative analysis: detection of presence but not quantity of substance in mixture
Quantitative analysis: measurement of the quantity of a particular substance in a mixture
Structural analysis: description of how atoms are arranged in molecular structures

4. Index of Hydrogen Deficiency
Learning outcomes
Understand how the number of double bonds/rings can be worked out from molecular formula

5. Index of Hydrogen Deficiency
Alkanes have maximum number of hydrogen atoms
For every two hydrogen atoms fewer than in alkane with same number of carbon atoms, there is one double bond or ring present. (double bond equivalent)
The number of double bond equivalents sometimes called degree of unsaturation or the Index of hydrogen deficiency.

6. How the index of hydrogen deficiency works.
1 A double bond and ring each counts as one IHD.
2 A triple bond counts as two IHD
Hydrocarbons (CxHy):
IHD=1/2[2C+2-H]
(where x = number of carbon, Y= number of hydrogen)
Example C4H8
½(8+2-8)= 1

7. Compounds Containing Elements Other than C and H
O and S atoms do not affect the IHD.
Halogens (F, Cl, Br, I) are treated like H atoms (CH2Cl2 has the same IHD as CH4).
For each N, add one to the number of C and one to the number H (CH5N is treated as C2H6. CH4N2O is treated as C3H6 by adding 2 to # of C and 2 to # of H).

8. Calculate IHD for C3H5N will be treated as C4 H6
IHD = 1/2(4x (6) = 4/2=2
Possible structures

9. Calculate IHD for C6H9Cl will be treated like C6H10 IHD=1/2[2C+2-H]

10. Practice problems IHD = 3 IHD = 2 IHD = 5 CH3CHCHCH2CHCH2 IHD = 1
CH3C≡CCOCH3

11. Learning outcomes Understanding
Mass spectrometry (MS), proton nuclear magnetic resonance spectroscopy (1H NMR) and infrared spectroscopy (IR) are techniques that can be used to help identify compounds and to determine their structure.

12. Learning outcome Understanding
Mass spectrometer is a technique that can help in identifying structure of organic compounds
Application and skills
Deduction of information about the structural features of a compound from percentage composition data, MS, 1H NMR or IR.

14. Mass spectrometer
Picture Source

15. Using a mass spectrum to find relative formula mass
The formation of molecular ions
When the vaporized organic sample passes into the ionization chamber of a mass spectrometer, it is bombarded by a stream of electrons. These electrons have a high enough energy to knock an electron off an organic molecule to form a positive ion. This ion is called the molecular ion.

16. The molecular ion is often given the symbol M+ or M•- the dot in this second version represents the fact that somewhere in the ion there will be a single unpaired electron. That's one half of what was originally a pair of electrons - the other half is the electron which was removed in the ionization process.
The molecular ions tend to be unstable and some of them break into smaller fragments. These fragments produce the familiar stick diagram. Fragmentation is irrelevant at this stage.

17. Using the molecular ion to find the relative formula mass
In the mass spectrum, the heaviest ion (the one with the greatest m/z value) is likely to be the molecular ion.
For example, in the mass spectrum of pentane, the heaviest ion has an m/z value of 72.

18. Analyzing mass spectrometer data C3H8

19. MS data of N,N-diethylmethylamine

20. Infrared spectroscopy

21. Learning outcome Understanding
Infrared spectroscopy is a technique that can help in identifying structure of organic compounds
Application and skills
Deduction of information about the structural features of a compound from percentage composition data, MS, 1H NMR or IR.

22. WHAT IS AN INFRA-RED SPECTRUM?
If a range of infra-red frequencies shine at an organic sample, some of the frequencies get absorbed by the compound. A detector attached to the other end of spectrum measured frequencies absorbed or transmitted.
How much of a particular frequency gets through the compound is measured as percentage transmittance.

23. What an infra-red spectrum looks like
A graph is produced showing how the percentage transmittance varies with the frequency of the infra-red radiation.

24. Analyzing IR spectrum
IR spectra are not particularly easy to analyse, nor do they give definitive information about structure. There are however, two different stages in an analysis.
1 Identification of absorptions
2 Fingerprinting
The first stage involves looking for characteristic absorptions and attempting to ascribe them to specific structural features. The second stage is usually carried out after a series of analyses leads to a possible conclusion.

25. INFRA RED SPECTRA - USES
IDENTIFICATION OF PARTICULAR BONDS
IN A MOLECULE
The presence of bonds such as O-H and C=O within a molecule can be confirmed because they have characteristic peaks in identifiable parts of the spectrum.
IDENTIFICATION OF COMPOUNDS BY DIRECT COMPARISON OF SPECTRA
The only way to completely identify a compound using IR is to compare its spectrum with a known sample. The part of the spectrum known as the ‘Fingerprint Region’ is unique to each compound.

26. INFRA RED SPECTRA - INTERPRETATION
Infra-red spectra are complex due to the many vibrations in each molecule.
Total characterisation of a substance based only on its IR spectrum is almost impossible unless one has computerised data handling facilities for comparison of the obtained spectrum with one in memory.
However, the technique is useful when used in conjunction with other methods such as nuclear magnetic resonance (nmr) spectroscopy and mass spectroscopy.
Peak position depends on bond strength
masses of the atoms joined by the bond
strong bonds and light atoms absorb at lower wavenumbers
weak bonds and heavy atoms absorb at high wavenumbers

27. INFRA RED SPECTRA - INTERPRETATION
Vertical axis Absorbance the stronger the absorbance the larger the peak
Horizontal axis Frequency wavenumber (waves per centimetre) / cm-1
Wavelength microns (m); 1 micron = 1000 nanometres

28. FINGERPRINT REGION
• organic molecules have a lot of C-C and C-H bonds within their structure
• spectra obtained will have peaks in the 1400 cm-1 to 800 cm-1 range
• this is referred to as the “fingerprint” region
• the pattern obtained is characteristic of a particular compound the frequency
of any absorption is also affected by adjoining atoms or groups.

29. IR SPECTRUM OF A CARBONYL COMPOUND
• carbonyl compounds show a sharp, strong absorption between 1700 and 1760 cm-1
• this is due to the presence of the C=O bond

30. IR SPECTRUM OF AN ALCOHOL
• alcohols show a broad absorption between 3200 and 3600 cm-1
• this is due to the presence of the O-H bond

31. IR SPECTRUM OF A CARBOXYLIC ACID
• carboxylic acids show a broad absorption between 3200 and 3600 cm-1
• this is due to the presence of the O-H bond
• they also show a strong absorption around 1700 cm-1
• this is due to the presence of the C=O bond

32. IR SPECTRUM OF AN ESTER
• esters show a strong absorption between 1750 cm-1 and 1730 cm-1
• this is due to the presence of the C=O bond

33. ALCOHOL ALDEHYDE CARBOXYLIC ACID WHAT IS IT!
One can tell the difference between alcohols, aldehydes and carboxylic acids by comparison of their spectra.
ALCOHOL
O-H STRETCH
ALDEHYDE
C=O STRETCH
O-H STRETCH
C=O STRETCH
AND
CARBOXYLIC ACID

34. CHARACTERISTIC FREQUENCIES
N-H
CN
C-Cl
O-H
C=O
C-O
C-H
Aromatic C-C
C=C
C-C alkanes

35. CHARACTERISTIC ABSORPTION FREQUENCIES
Bond Class of compound Range / cm-1 Intensity
C-H Alkane strong
C-C Alkane weak
C=C Alkene variable
C=O Ketone strong
Aldehyde strong
Carboxylic acid strong
Ester strong
Amide strong
C-O Alcohol, ester, acid, ether strong
O-H Alcohol (monomer) variable, sharp
Alcohol (H-bonded) strong, broad
Carboxylic acid (H-bonded) variable, broad
N-H Amine, Amide (approx) medium
CN Nitrile medium
C-X Chloride strong
Bromide strong
Iodide (approx) strong

36. Practice
New Data booklet
Table 26

38. Answer

39. Nuclear Magnetic Resonance
H-NMR
Nuclear Magnetic Resonance

40. Learning outcome Understanding
NMR spectroscopy is a technique that can help in identifying structure of organic compounds
Application and skills
Deduction of information about the structural features of a compound from percentage composition data, MS, 1H NMR or IR.

41. WHAT IS AN INFRA-RED SPECTRUM?
If a range of infra-red frequencies shine at an organic sample, some of the frequencies get absorbed by the compound. A detector attached to the other end of spectrum measured frequencies absorbed or transmitted.
How much of a particular frequency gets through the compound is measured as percentage transmittance.

42. NMR
Nuclear magnetic resonance relies on the magnetic field produced by a spinning nucleus containing an odd number of nucleons (protons or neutrons). In the presence of an external magnetic field the nucleus can exhibit more than one spin state and can move between these states by the absorption of electromagnetic radiation of a specific frequency (energy).
The energy absorbed can be detected and from this information about the location (environment) of the nucleus can be deduced.

45. NMR is probably the most useful tool in the organic chemists arsenal for structural determination.
As organisms are mainly water (containing H atoms with an odd number of nucleons), NMR has developed into an invaluable medical diagnostics tool, called an MRI (magnetic resonance instrument) scan.

46. Nuclear magnetic resonance
This tells us the number of hydrogen atoms in different environments within the molecule. As hydrogen is present in (almost) all organic compounds this technique is very useful. The pattern produced by the hydrogen atoms is often split into finer structure, that also gives information about the number of hydrogen adjacent to the absorbing atoms.

47. Nuclear energy levels
Nuclei with odd numbers of nucleons (protons and neutrons) can have different energy levels. To help us differentiate these energy levels we say that they have 'spin'.
A hydrogen nucleus can have two different 'spin' states. These are designated as spin = +1/2 and spin = -1/2.
For a hydrogen nucleus to change spin states it must absorb energy (promotion) or lose energy (relaxation).
Animation

48. Low resolution NMR
A low resolution spectrum looks much simpler because it can't distinguish between the individual peaks in the various groups of peaks
The numbers against the peaks represent the relative areas under each peak. That information is extremely important in interpreting the spectra

49. Interpreting L R NMR spectrum
Three peaks in the spectrum corresponds to different chemical environments of H atoms
Different sizes of peak give valuable information
Are underneath a peak is proportional to number of hydrogen atoms in that environment.
Area underneath peaks can be worked out by integration trace. The vertical heights of the steps in Integration trace are proportional to the number of hydrogen atoms in each envirnoment.

50. Interpreting L R NMR spectrum
Chemical Shift: The Horizontal scale on NMR, is given by the symbol δ has a unit parts per million ppm.
The Chemical Shift gives information about the environment of protons( Hydrogen atoms). The protons in different chemical environment give different chemical shift
Detail about chemical shift will be covered in HL syllabus.

51. NMR Spectrum of Pentan-3-one
Symmetrical molecule
Two peaks show two different chemical environment
Heights of peaks as ratio of 2;3 in integration trace, show four H atom in one environment and 6 in other.

52. Identify number of different chemical environments and ratio of H atoms in each environment2 3 3

53. NMR HL

54. Chemical Shift ( HL only)
The horizontal scale on a nuclear magnetic resonance spectrum is called chemical shift.
The symbol for chemical shift is δ.
It is measured as parts per million
The Chemical Shift gives information about the environment of protons( Hydrogen atoms). The protons in different chemical environment give different chemical shift
Chemical shift are measured relative to TMS
Chemical shift for TMS is Zero

55. Tetramethylsilane is the standard
All Hs are the same = 1 signal Si
Has lower EN than Carbon
Si absorbs in a different part of the spectrum than C when bonded to H
Si(CH3)4
Has low boiling point
Is chemically inert (non-reactive)
Is soluble in most organic solvents

56. Chemical Shift values relative to TMS
Values are given in data book let page 26, table 27

57. Using Chemical Shift

58. High-resolution 1H NMR Can show the difference in the spins of nuclei
Right: Hi-res 1H NMR
Below: 1H NMR

59. What a low resolution NMR spectrum tells you
High Resolution
Remember:
The number of peaks tells you the number of different environments the hydrogen atoms are in.
The ratio of the areas under the peaks tells you the ratio of the numbers of hydrogen atoms in each of these environments.
The chemical shifts give you important information about the sort of environment the hydrogen atoms are in.
In a high resolution spectrum, the low resolution spectrum are split into clusters of peaks.
1 peak a singlet
2 peaks in the cluster a doublet
3 peaks in the cluster a triplet
4 peaks in the cluster a quartet
The amount of splitting of the peaks gives you important extra information.

60. Interpreting a high resolution spectrum
The n+1 rule
The amount of splitting tells you about the number of hydrogens attached to the carbon atom or atoms next door to the one you are currently interested in.
The number of sub-peaks in a cluster is one more than the number of hydrogens attached to the next door carbon(s).
Singlet next door to carbon with no hydrogens attached
doublet next door to a CH group
triplet next door to a CH2 group
quartet next door to a CH3 group

61. Multiplicity (Splitting)
NEIGHBOR hydrogens = number of peaks -1

62. Multiplicity (Splitting)
3 peaks (triplet)
2 neighbor H’s
(probably CH2)
3 peaks (triplet)
2 neighbor H’s
(CH2)
6 peaks (hextet)
5 H’s
(CH3 & CH2)

64. Practice Example
11.6 page 540

65. X-Ray crystallographyHL

66. Learning outcomes Understanding
The structural technique of single crystal X-ray crystallography can be used to identify the bond lengths and bond angles of crystalline compounds.

67. Introduction
X-ray crystallography is the oldest and most precise method.
Crystallography in which a beam of X-rays strikes a single crystal, producing scattered beams.
When they land on a piece of film or other detector, these beams make a diffraction pattern of spots; the strengths and angles of these beams are recorded as the crystal is gradually rotated.
Each spot is called a reflection, since it corresponds to the reflection of the X-rays from one set of evenly spaced planes within the crystal.

69. Computational analysis
The data is analysised by computer and combined with other data to refine a model of the arrangement of atoms within the crystal. The final, refined model of the atomic arrangement - now called a crystal structure - is usually stored in a public database.

70. Information obtained
Single-crystal X-ray Diffraction is a non-destructive analytical technique which provides detailed information about the internal lattice of crystalline substances, including unit cell dimensions, bond-lengths, bond-angles, and details of site-ordering.
Directly related is single-crystal refinement, where the data generated from the X-ray analysis is interpreted and refined to obtain the crystal structure.
Crystallography is the most unambiguous method for determining structures of small molecules and macromolecules.