1. Analytical Techniques
Qualitative analysis: the detection of the presence but not the quantity of a substance in a mixture; for example, forbidden substances in an athlete’s blood
Quantitative analysis: the measurement of the quantity of a particular substance in a mixture; for example, the alcohol levels in a driver’s breath
Structural analysis: a description of how the atoms are arranged in molecular structures; for example, the determination of the structure of a naturally occurring or artificial product.

2. Tools We Will Study
Infrared spectroscopy is used to identify the bonds in a molecule.
Mass spectrometry is used to determine relative atomic and molecular masses. The fragmentation pattern can be used as a fingerprint technique to identify unknown substances or for evidence for the arrangements of atoms in a molecule.
Nuclear magnetic resonance spectroscopy is used to show the chemical environment of certain isotopes (hydrogen, carbon, phosphorus, and fluorine) in a molecule and so gives vital structural information.

3. Advanced Mass Spectrometry

4. Mass spectrometry
Used to determine relative atomic and molecular masses. The fragmentation pattern can be used as a fingerprint technique to identify unknown substances or for evidence for the arrangements of atoms in a molecule.

5. The Mass Spectrometer
Relative atomic masses (among other things we will discuss when we get to organic chemistry) can be determined using this instrument.

6. Determining the molecular mass of a compound
Can also use to determine relative molecular mass of a compound (Mr)
If empirical formula is known, can be used to determine molecular formula.

7. Fragmentation Patterns
Ionization process involves an e- from an electron gun hitting the incident species and removing an electron:
X(g) + e- → X+(g) + 2e-
This collision can be so energetic that it causes the molecule to break up into different fragments.
The largest mass peak corresponds to a parent ion passing through the instrument unscathed, but other ions produced as a result of this break up are also detected.
The fragmentation pattern can provide useful evidence for the structure of the compound.

8. Fragmentation Patterns
A chemist pieces together the fragments to form a picture of the complete molecule, just as the archaeologist finds clues about the past from pieces of artifacts discovered on the ground.

9. Example: ethanol relative abundance mass/charge 31 45 15 29 46 100 3030 60
mass/charge

10. Example: ethanol

11. Example: ethanol
Note: This fragmentation will yield either CH3+ and CH2OH or CH3 and CH2OH+, yielding peaks at both 15 and 31

12. Example: ethanol CH2OH+ relative abundance C2H5O+ CH3+ C2H5+ C2H5OH+
100 31
CH2OH+
relative abundance
C2H5O+ 45
CH3+ 15
C2H5+ 29 46
C2H5OH+ 30 60
mass/charge

13. So… The highest mass fragment represents the Mr of the compound.
Fragments provide clues about structure because certain numbers correspond to particular groups.

14. Fragments you will be expected to recognize:Mr
loss of… 15
CH3+ 17
OH+ 29
C2H5+ or CHO+ 31
CH3O+ 45
COOH+

15. Let’s Practice Together
Fragments
Molecular Formula

16. Step 1: Molecular Formula
First let’s calculate the molecular formula to be able to figure out fragment pieces

17. Step 2: Identify Fragments
There are many different ways we can arrange the C, H, and O in this compound.
We need to start trying to identify the fragments from their relative masses.

18. Answer

19. Index of Hydrogen Deficiency and Intro To IR

20. Hydrocarbons - Review
A hydrocarbon is a compound which contains only hydrogen and carbon
Hydrocarbons can be classified as saturated or unsaturated
Saturated hydrocarbons have only single bonds between the carbons; we can think of them as being “saturated” with as many hydrogen atoms as possible can bond to the carbons
Unsaturated hydrocarbons contain one or more multiple bonds between the carbons; since carbon can only make four bonds when it contains a multiple bond it can bond with fewer hydrogen atoms

21. Definition
The degree of unsaturation or index of hydrogen deficiency (IHD) is a measure of how many molecules of H2 would be needed in theory to convert the molecule to the corresponding saturated, non-cyclic molecule.
If a compound has a hydrogen deficiency of 1, that means one molecule of hydrogen could be added to the molecule if multiple bonds (or rings!) are broken

22. IHD from molecular formula
Given CcHhNnOoXx, where X is a halogen atom, we can use
IHD= (0.5)(2c + 2 – h – x + n)
For C4H8O2
IHD= (0.5)( )=1

23. Info From Different EM Regions (You need to know the underlined)
Radio waves can be absorbed by certain nuclei, causing them to reverse their spin. They are used in NMR and can give information about the environment of certain atoms.
Microwaves cause molecules to increase their rotational energy. This can give information about bond lengths. It is not necessary to know the details at this level.
Infrared radiation is absorbed by certain bonds causing them to stretch or bend. This gives information about the bonds in a molecule.

24. Info From Different EM Regions (You need to know the underlined!)
Visible light and ultraviolet light can produce electronic transitions and give information about the electronic energy levels within the atom or molecule.
X rays are produced when electrons make transitions between inner energy levels. They have wavelengths of the same order of magnitude as the inter-atomic distances in crystals and produce diffraction patterns which provide direct evidence of molecular and crystal structure.

25. Infrared (IR) Spectroscopy

26. Chemical Bonds As Springs
Bond Frequency:
A chemical bond can be thought of as a spring.
Each bond vibrates and bends at a natural frequency which depends on the bond strength and the masses of the atoms.

27. Bond Vibrations
Simple diatomic molecules such as HCl, HBr, and HI, can only vibrate when the bond stretches
In more complex molecules, different types of vibration can occur, such as bending, so that a complex range of frequencies is present
Diatomic
More Complex

28. Using IR to Excite Molecules
Energy needed to excite the bonds in a molecule to make them vibrate with greater amplitude occurs in the IR region.
IR radiation can cause a bond to stretch or bend.
The stronger the bond, the more energy will be required to excite the stretching vibration. This is seen in organic compounds where stretches for triple bonds such as C ≡ C and C ≡ N occur at higher frequencies than stretches for double bonds (C=C, C=N, C=O), which are in turn at higher frequencies than single bonds (C-C, C-N, C-H, O-H, or N-H).
The heavier an atom, the lower the frequencies for vibrations that involve that atom

29. Energy Absorbed The presence of separate areas of
partial positive and negative charge in a
molecule allows the electric field component of the electromagnetic wave to excite the vibrational energy of the molecule
So…A bond will only interact with the electromagnetic infrared radiation if it is polar.
The change in the vibrational energy produces a corresponding change in the dipole moment of the molecule.
The intensity of the absorption depends on the polarity of the bond.
Symmetrical non-polar bonds in N≡N and O=O do not absorb radiation, as they cannot interact with an electric field.

30. Polar Molecules
All stretches show up on the IR because there is always a dipole moment

31. Non-Polar Linear Molecules
Any stretches that retain the symmetry do not show up

32. Asymmetrical stretching Symmetrical stretching
Vibrations of H2O, SO2 & CO2
Molecule
Asymmetrical stretching
Symmetrical stretching
Symmetrical bending
H2O
SO2
CO2 - - - O O O + H H + + H H + + H H +
IR active
IR active
IR active + + + S S S - O O - - O O - - O O -
IR active
IR active
IR active - + - - + - - + - O C O O C O O C O
IR active
IR inactive
IR active

33. Double-beam IR spectrometer
One beam passes through sample
Second beam passes through reference
Purpose of reference: to eliminate absorptions caused by CO2 and H2O vapor in air, or absorptions from the bonds in the solvent used.
Baseline = 100% transmittance

34. Matching wavenumbers with bonds
“fingerprint region”
lots of overlap, so not very useful
very strong
broad and strong
broad and strong
Usually sharper than OH

35. IR spectrum of ethanol, CH3CH2OH

36. IR spectrum of ethyl ethanoate, CH3COOCH2CH3
“fingerprint region”

37. Reference Numbers

38. Propanone
The baseline at the top corresponds to 100% transmittance and the key features are the troughs which occur at the natural frequencies of the bonds present in the molecule.
The absorption at just below 1800 cm–1 shows the presence of the C= O bond and the absorption near 3000 cm–1 is due to the presence of the C– H bond. The more polar C= O bond produces the more intense absorption.

39. Ethanol
The presence of the C–H bond can again been seen near 3000 cm–1 in the spectrum of ethanol.
The broad peak at just below 3400 cm–1 shows the presence of hydrogen bonding which is due to the hydroxyl (OH) group.

40. Introduction to NMR

41. Nuclear Magnetic Resonance (NMR) Spectroscopy
Used to show the chemical environment of certain isotopes (hydrogen, carbon, phosphorous and fluorine) in a molecule and so gives vital structural information.

42. Odd Nuclei
The nuclei of atoms with an odd number of nucleons such as 1H, 13C, 19F, and 31P, spin and behave like tiny bar magnets.
If placed in an external magnetic field, some of these nuclei will line up with an applied field and, if they have sufficient energy, some will line up against it.
This arrangement leads to two nuclear energy levels; the energy needed for the nuclei to reverse their spin and change their orientation in a magnetic field can be provided by radio waves.

44. In practice, a sample is placed in an electromagnet
In practice, a sample is placed in an electromagnet. The field strength is varied until the radio waves have the exact frequency needed to make the nuclei flip over and spin in the opposite direction.
This is called resonance and can be detected electronically and recorded in the form of a spectrum
Resonance is when the radio waves have the exact frequency needed to make the nuclei flip over and spin in the opposite direction

46. The Chemical Shift
As electrons shield the nucleus from the full effects of the external magnetic field, differences in electron distribution produce different energy separations between the two spin energy levels.
Nuclei in different chemical environments produce different signals in the spectrum.
Proton or 1H NMR is particularly useful.
Hydrogen nuclei are in all organic molecules.
Act as spies and give information about their position in a molecule.

47. The TMS Standard
If we are to measure shift, we need a standard, or point of reference from which to measure.
Tetramethylsilane (TMS) is the perfect standard.
All 12 H’s are in identical chemical environments, so one signal is recorded.

48. The TMS Standard
Because Si is less electronegative than C, TMS absorbs radio waves in a different region from that absorbed by H attached only to C.
This ensures that the signal does not overlap with any signals under investigation

49. The TMS Standard TMS is also inert.
TMS is soluble in most organic solvents.
TMS can be easily removed from the sample because it has a low boiling point.
The position of the NMR signal relative to this standard is called the chemical shift of the proton. Hydrogen nuclei in particular environments have characteristic chemical shifts.
A more complete list is given in the IB data booklet.

50. The Chemical shift
Chemical shift δ is usually expressed in parts per million (ppm) by frequency, because it is calculated from:
δ =( νsample - νref ) /νref 
where νsample is the absolute resonance frequency of the sample and νref is the absolute resonance frequency of a standard reference compound, measured in the same applied magnetic field B0. Since the numerator is usually expressed in hertz, and the denominator in megahertz, δ is expressed in ppm.
The detected frequencies (in Hz) are usually referenced against TMS, which by the definition above have a chemical shift of zero if chosen as the reference.

53. Ethanal What do each of the peaks represent?
Let’s see if we can interpret the 1H NMR spectrum for ethanal
What do each of the peaks represent?
What do the relative heights mean?

54. Wait? Why are these spiky?
MORE ON THAT IN THE HL LEVEL TOMORROW!!!