1. Introduction to Organic spectroscopy
The rest of topic 11

2. Spectroscopic techniques
1. Mass spectrometry:
- A technique capable of identifying the presence of various mass segments of organic molecules.
2. Infrared (IR) spectroscopy:
An analytic technique which can identify the presence of certain characteristic functional groups based on their absorption of electromagnetic radiation in the infrared band.
3. Nuclear magnetic resonance (NMR) spectroscopy:
- An analytic technique which utilizes intense magnetic fields and high power radio frequency pulses to excite the nuclei of the atoms being studies.

3. Mass spectrometry
This technique only allows for the detection of ions.
Intense beta radiation is used to “fragment” the organic molecules into various positively charged pieces.
It is not possible to control how the molecule fragments.
The fragments can be detected and reported by the detector of the instrument giving mass information about the molecule.
Works for organic molecules too!

4. Remember this

5. Actually, it looks more like this

6. Fragmentation patters
The output of a mass spec. shows the mass of the fragments created in the ionization phase.
This technique does not tell you what the molecule is, it tells you the masses of the pieces it can be fragmented into.
Common fragments are listed on page 27 of the IB data booklet.
Of course, there are many other fragments not listed.

7. Reading a mass spectrum

8. Analysis of the spectrum
Always identify the parent ion peak. This is the peak with the greatest mass. This is the mass of the complete molecule with only a single electron missing.
The other peaks should correspond to masses of “fragments” of the parent molecule.
The trick is to remember each fragmentation usually results in two ions which may both be detected.
Masses should correspond to those on the period table.
(This is not true if you have a specific isotope in your sample) should not be an issue for this course
Technique is often used when you think you know the substance you have. You are checking to confirm the fragments.

9. Assess the fragmentation pattern

10. Lets Try working with C2h4O2

11. Tips on fragmentation patterns
To support your proposed structure you must be able to identify how the molecule is fragmenting. If you can’t do this then it hurts your case for the proposed structure.
Sometimes there are fragments which are hard to identify/justify. Real samples can be contaminated or contain isotopes of carbon, oxygen, and halogens which can complicate this analytical approach.
If you are trying to prove you have a certain molecule, the parent peak should match the molar mass for that molecule.
Often, highly reactive functional groups (carboxylic acids) will show a peak at molecular mass +1. This is the random addition of fragmented hydrogen to the carbonyl oxygen. It is usually low in intensity.
If significant fragments do not match with the mass spectrum then your structure is likely not correct.
Usually only make +1 ions making the m/z ratio issues less confusing.

12. Additional practice
Page contains additional examples involving mass spectrometry.

13. The degree of unsaturation
Often referred to as the “index of hydrogen deficiency” (IHD)
This value indicates how many molecules of hydrogen (H2) would be required to convert the molecule to being saturated.
Knowing the degree of unsaturation can assist a chemist is assessing if the proposed structure is possible.
IB claims you will not need to be concerned with ring structures.
Molecules in testing should remain relatively simple.

14. Degree of unsaturation
Here is the approach which works for any organic compound. In simple molecules a visual assessment is often a more efficient approach.
unsaturation-index-of-hydrogen-deficiency/

15. Infrared (IR) spectroscopy
All chemical bonds are understood to be vibrating continually like small springs. The two atoms in a bond move back and forth due to the thermal energy they have. (all particles are in constant motion)
Chemists have come to realize the vibrations of these bonds are very specific and consistent. This has allowed for the analytical technique of infrared spectroscopy to be developed.
Relies on the use of electromagnetic radiation from the IR band.
When a sample is exposed to a specific wavelength/frequency of IR radiation, bonds where are sensitive to that frequency absorb the radiation and begin to vibrate more.
By knowing exactly what frequencies were emitted, a detector can determine which radiation was absorbed by analyzing which frequencies do not reach the detector.
This allows chemists to deduce which types of bonds are present in the molecule.

16. Basic concept of IR spectroscopy

17. What does an IR spectrum look like?

18. They can also look like this

19. IR Data
Page 25 of the IB data booklet lists the bond types you need to be concerned with. There are more comprehensive lists online and in IR databases.
To support the presence of a particular bond/functional group, there must be absorption on the IR spectrum very near the prescribed wavenumber.
Electronegativity plays a role in how the bonds behave. As a result, slight shifts in the accepted values may occur when highly electronegative atoms/functional groups are present.
IB testing should use relatively simple molecules to avoid exceptional situations.
Usually you are looking for expected peaks and not trying to identify all peaks.

20. Lets assign the IR peaks of ethanol

21. Try this one !

22. Tips on IR spectra
When assigning peaks, assign those which are more obvious first.
If attempting to determine between multiple molecules, look for evidence of a feature which will be easily identified in the spectrum.
Remember, bonds are effected by other bonds around them. The values listed for a particular bond are there to guide you. They can be outside of the limits stated but there needs to be a cause. (influence from highly electronegative atoms/groups)
If you have additional information from other analytical techniques don’t forget to use that information in assisting you. One spectrum can’t tell you everything!!
Use the IB data booklet to assist you with the regions of absorption.

23. Nuclear magnetic resonance imaging (NMR)
This technique is different in that it relies on the nucleus of the atom for information.
There are many different types of NMR.
We will only be studying proton NMR also know as 1H NMR.
When we look at a proton NMR it only gives information about the hydrogen atoms.
Each hydrogen in a different chemical environment will show up on a proton NMR.
Can be done with very small sample sizes.
This technique is based on complicated nuclear physics/chemistry, which means it is a bit tricky when it comes to reading the spectrum.

24. NMR basic operation
Radio frequency radiation is absorbed by the nuclei in the sample and causes them to spin against the magnetic field. (known as “exciting” the nulcei.
As the nuclei relax, they release the absorbed energy in the form of RF radiation.
The instrument can “hear” the emitted single and converts it into a visual output signal.
The processing of the signal is complex and requires extensive programming and mathematical analysis.
We only need to be able to read the output spectrum

25. What using an NMR looks like

26. What you need to know to read an NMR spectrum
Chemical shift: The position of the signal on the x-axis of the spectrum. It gives information about the number of chemical environments and the nature of the chemical environment. (Useful table in IB data booklet)
Integration: The area under the curve gives information about the number of hydrogen atoms at a specific chemical shift.
Splitting: Also known as the “multiplicity”, tells you how many hydrogen neighbors the hydrogen you are measuring has.

27. What are chemical environments?
Since all atoms have electrons and protons, they are influenced by the presence of electrons and protons of other atoms due attraction and repulsion of the subatomic particles. This is true even if they are not bonded directly to each other!
Lets look at ethanoic acid 
“A” is chemically different than “B”
All “B” atoms are chemically equivalent as
the carbon-carbon bond is free to rotate.
This molecule will only give two signals on an NMR spectrum.
(1 for each different “H” environment)

28. Ethanoic acid NMR spectrum

29. NMR of Ethanol (3 different H atoms)

30. Shift corresponds to electronegativity
The x-axis measures the chemical shift in ppm. The shift is actually giving information about how exposed the nucleus of the hydrogen atom is.
Low shifts correspond to hydrogen atoms which are shielded well by electrons. (meaning they are bonded to low electronegative atoms.)
High shifts correspond to hydrogen atoms which are lacking electron cover. They are said to be “deshielded”. (meaning they lack electrons and must therefore be bonded to highly electronegative atoms.)
So, the x-axis tells you the number of chemical environments and the nature of those environments. (very useful for organic chemists!!)
Don’t forget we are measuring the radio frequency emissions from the nucleus. The electrons are not what is being measured here. (they actually block the signal we want to receive)

31. Chemical Environment determines shift

32. Integration of the spectrum
This tells you how many hydrogen atoms are in the chemical environment indicated by the chemical shift.
This is usually calculated by the instrument and plotted on the spectrum when using modern equipment.
It is possible for the integration to be given graphically and you need to measure it with a ruler to determine the number of hydrogen atoms represented by the peak(s)
You should have a ruler, I doubt they will require you to measure the integration.
The important this is to know the integration tells you the number of hydrogen in a given environment.

33. Notice the integration curves

34. Splitting (multiplicity)
The signal from each hydrogen is influenced by other hydrogens near it. It causes the signal of a hydrogen to split into multiple peaks.
The splitting is still based on the chemical environment the hydrogens are in.
The multiplicity (number of peaks) is not the same as the number of hydrogens. (integration tells number of H in a given environment)
The multiplicity tells you how many direct neighbors the hydrogens in that chemical environment have. (still extremely useful)
The n + 1 rule applies when reading splitting.
The number of neighbors is always one less than the multiplicity.
A singlet indicates a proton with no neighbors.

35. Splitting analysis

36. Determining number of “H” neighbors

37. Tips on reading NMR
Don’t try to read everything in the spectrum. Look for specific distinguishing features which support your chemical structure. You don’t always need all of the information which can be derived from any given spectrum. (this does require some experience to be selective)
Make sure you understand what each aspect of the spectrum tells you. It is very common for people to confuse what something means.
ie. Splitting: Tells how many direct H neighbors there are. (can get tricky!)
Integration: Gives number of H’s in a given chem. environment.
chemical shift: Gives chemical environment info.

38. Putting it all together
Organic chemists use all three techniques (Mass spec., IR spec., and NMR)
This allows them to determine everything they need to know about the molecules they build and work with.
Each characterization technique gives critical information about a particular aspect of the molecule.
When all three techniques are used, it gives strong evidence about the actual structure and composition of the molecule.
Once you know how to read each spectrum you can answer almost any question about a molecule by using the appropriate technique/combination of techniques. (logical thinking and problem solving skills are the key)

39. Make sure you know this!!
IB wants to make sure you understand the principles which allow each of these techniques to function.
Mass spectrometry: uses an electron beam to fragment the molecules into ions so they can be accelerated and detected by the detector.
Infrared spectrometry: Uses the IR portion of the electromagnetic spectrum to determine the types of bonds present in a molecule.
Nuclear magnetic resonance: Uses radio frequency (RF) radiation to excite the nuclei of atoms and detects their RF emission when they relax.