1. Structural Analysis AH Chemistry Unit 3(d)

2. Overview Elemental microanalysis Mass spectroscopy Infra-red spectroscopy NMR spectroscopy X-ray crystallography

3. Elemental mircoanalysis Sometimes called “combustion analysis”. Is used to determine the masses of C, H, O, S and N in a sample of an organic compound in order to find the empirical formula. The masses of other elements in the compound have to be determined by other methods.

4. Empirical formula practice 1. A sample of an organic compound with a mass of 1.224g was completely burned in oxygen and found to produce 2.340g of CO 2 and 1.433g of water only. Calculate the empirical formula of the organic compound.

5. Empirical formula practise 2. Oxalic acid is found in rhubarb and contains only the elements carbon, hydrogen and oxygen. When 1.540g of oxalic acid was burned in oxygen, 1.504g of CO 2 and 0.310g of water were formed. (a) Calculate the empirical formula for oxalic acid. (b) If the molecular mass of oxalic acid is 90.0, what is its molecular formula?

6. Empirical formula practice 3. An organometallic compound known as ferrocene contains only the elements Fe, C and H. When 1.672g of ferrocene was combusted in oxygen, 3.962g of CO 2 and 0.810g of water were formed. Calculate the empirical formula of ferrocene.

7. Mass spectroscopy

8. What is it used for? To determine the accurate molecular mass and structural features of an organic compound.

10. How does it work? 1.The sample is vaporised and then ionised by being bombarded with electrons. 2.Fragmentation can occur when the energy available is greater than the molecular ionisation energy. 3.The parent ion and ion fragments are accelerated by an electric field and then deflected by a magnetic field. 4.The strength of the magnetic field is varied to enable the ions of all the different mass/charge ratios to be detected in turn. A mass spectrum is obtained.

11. Mass spectra: boron

12. Mass spectra: zirconium Zirconium has five isotopes as follows: –zirconium-90 (51.5%) –zirconium-91 (11.2%) –zirconium-92 (17.1%) –zirconium-94 (17.4%) –zirconium-96 (2.8%) Sketch a diagram of the mass spectrum you would expect to be produced.

13. Mass spectra: zirconium

14. Mass spectra: chlorine Chlorine has two isotopes: chlorine-35 and chlorine-37 in a relative abundance of 3 atoms to 1 atom. Sketch a diagram of the mass spectra you would expect to be produced.

16. Mass spectra: chlorine Why?

17. Mass spectra: pentane

18. Mass spectra: pentan-3-one

20. Infra-red spectroscopy

21. What is it used for? To identify specific functional groups in organic compounds.

22. How does it work? Infra-red radiation is made up of a continuous range of frequencies. By shining these at an organic compound, some are absorbed and some are not. Those absorbed cause parts of the molecule to vibrate. The wavelengths which are absorbed depend on the type of chemical bond and the groups or atoms at the ends of these bonds.

23. A detector measures the intensity of the transmitted radiation at different wavelengths. A spectrum is produced. Infra-red spectra are expressed in terms of wavenumber. The unit of measurement of wavenumber which is the reciprocal of wavelength, is cm -1.

25. Types of bond vibration Bond bending Bond stretching

26. Energy of the bond vibration depends on bond length, mass of atoms etc... Therefore different bonds vibrate in different ways, with different energies. By shining radiation with exactly the right frequency on the bond, you can kick it into a higher energy state. CO

27. Bond bending The same principle applies, but the frequencies of the absorbed radiation differ from that of bond stretching. O H H

29. Fingerprint region

30. This is the complicated region due to a wide variety of bond bending vibrations in the molecule. Different molecules have unique fingerprint regions.

31. Similar in this area. Indicates –OH group and that the compound is an alcohol. Different in this area. By comparing to known spectra, you can identify which alcohol you have.

32. Some useful pointers C-C bonds have vibrations which occur over a range of wavelengths in the finger print region – difficult to pick out. C-O bonds are also very difficult to detect in this region. Other useful detectable bonds usually occur outside the fingerprint region. Ignore the trough just below 3000 cm -1 – this is the C-H bond.

33. Thoughts on this molecule?

34. NMR spectroscopy

35. What is it used for? To gain information about the chemical environment of hydrogen atoms in organic molecules.

36. Hydrogen nuclei spin on their own axis, either clockwise or anti-clockwise. They behave like tiny magnets.

37. Absorption of radiation in the radio frequency region causes the low energy nuclei to flip to the high energy orientation. The radiation emitted when the nuclei relax back to the low energy orientation is detected and plotted as a spectrum of lines. strong magnetic field (low energy) Energy (high energy)

38. The lines on the spectrum are positioned relative to a standard substance, typically tetramethylsilane (TMS): Si CH 3 H3CH3C The line (peak) produced by the 12 H atoms in TMS is set at zero. The position of other H atoms away from this peak is known as the chemical shift (  ). 10 5 0 Chemical shift 

39. There are 3 pieces of information given in a spectrum: 1. The number of different hydrogen environments CH 4 1 hydrogen environment CH 3 1 hydrogen environment CH 3 CH 2 CH 3 2 hydrogen environments CH 3 CH 2 OH3 hydrogen environments Each hydrogen environment produces a peak at a different chemical shift. A chart of environments and chemical shifts is shown on page 15 of the data booklet.

40. 2. The number of hydrogen atoms in each environment. The area under the peaks of each environment gives the ratio of the number of hydrogen atoms present. CH 3 CH 2 CH 3 2 hydrogen environments Ratio - 3:1 332

41. 3. The number of hydrogen atoms on adjacent carbon atoms. n+1 rule (where n = H atoms): 0 Number of adjacent H atoms Shape of line singlet 1 2 doublet triplet quartet 3

42. Spectrum A: 1 2 3 ab c bca

43. Spectrum B: CCC HHH OH HHH H a bcd 1 22 3 abcd

46. X-Ray Crystallography

47. What is it used for? To determine the precise 3D structure of an organic compound.

48. A single crystal of an organic compound is exposed to X-rays of a single wavelength. Inter-atomic distances in the compound are similar to the wavelength of X-rays. The crystal acts as a diffraction grating. The X-rays are scattered by electrons in the crystal, producing a diffraction pattern. From this, an electron density map can be produced.