2. KHS ChemistryUnit 3.4 Structural Analysis1 Structural Analysis 3 Adv Higher Unit 3 Topic 4 Gordon Watson Chemistry Department, Kelso High School

3. KHS ChemistryUnit 3.4 Structural Analysis2 Introduction Structural AnalysisNMR Spectroscopy X-Ray Crystallography This topic continues to explore methods used in the Structural Analysis of organic molecules including NMR Spectroscopy and X-Ray Crystallography.

4. KHS ChemistryUnit 3.4 Structural Analysis3 Nuclear Spin nuclear spin Nuclei with an odd mass or odd atomic number, eg 1 H, have “nuclear spin” (in a similar fashion to the spin of electrons). ++ magnetic field Since a nucleus is a charged particle in motion, it will develop a magnetic field. The magnetic field generated by a nucleus of spin + 1 / 2 is opposite in direction from that generated by a nucleus of spin – 1 / 2.

5. KHS ChemistryUnit 3.4 Structural Analysis4 Orientation + + + + + The distribution of nuclear spins is random in the absence of an external magnetic field.

6. KHS ChemistryUnit 3.4 Structural Analysis5 Magnetic Field line up parallel spin alignedspin opposed When a field is applied they line up parallel to the applied field, either spin aligned or spin opposed. + + + + + Magnetic Field, H o

7. KHS ChemistryUnit 3.4 Structural Analysis6 Energy Levels Energy levels spin alignedspin opposed Energy levels between the spin aligned and spin opposed states are slightly different. + + + + + Magnetic Field, H o slight excess spin aligned lower energy There is a slight excess of nuclear magnetic moments spin aligned parallel to the applied field, (lower energy).

8. KHS ChemistryUnit 3.4 Structural Analysis7 Magnetic Field Strength EEEE  E ' increasing field strength + + strength radio waves The splitting of the energy levels is proportional to the strength of the magnetic field. Low energy - radio waves

9. KHS ChemistryUnit 3.4 Structural Analysis8 Proton Resonance APPLIED FIELD EE Radio Frequency in Radio Frequency out

10. KHS ChemistryUnit 3.4 Structural Analysis9 NMR Spectrometer NMR spectrometer The basic arrangement of an NMR spectrometer is shown above.

11. KHS ChemistryUnit 3.4 Structural Analysis10 Relationships The frequency of absorbed electromagnetic radiation is different for different elements, and for different isotopes of the same element. For a field strength of 4.7 T (4.7 x 10 4 gauss): 1 H absorbs radiation having a frequency of 200 MHz (200 x 10 6 s -1 ) 13 C 13 C absorbs radiation having a frequency of 50.4 MHz (50.4 x 10 6 s -1 ) The frequency of absorbed electromagnetic radiation for a particular nucleus (such as 1 H) depends on its molecular environment. This is what makes NMR spectroscopy such a useful tool.

12. KHS ChemistryUnit 3.4 Structural Analysis11 Molecular Environment H H H HH H H butanone

13. KHS ChemistryUnit 3.4 Structural Analysis12 Reference Molecule TMS is given a value of 0. CH 3 CH 3 CH 3 CH 3 Si Tetramethylsilane Tetramethylsilane, TMS, is used as a reference molecule. identical environment shieldingno coupling effect on each other All the hydrogens are in an identical environment and, more importantly, are far enough apart (with a Si shielding them) to have no coupling effect on each other. shifted deshielding The values for hydrogen atoms in other molecules will be shifted, due to the deshielding effect of other atoms in the molecule. coupling adjacent The values for equivalent hydrogen atoms can be slightly different due to the coupling effect of adjacent hydrogen atoms.

14. KHS ChemistryUnit 3.4 Structural Analysis13 NMR Spectrum shifted split coupling2 adjacent hydrogens These hydrogens have been shifted least, and their signal has been split into 3 by the coupling effect of the 2 adjacent hydrogens. O H H H H H H H H 3H 2H 3H  0321 CH 3 CH 3 CH 3 CH 3 Si hydrogensshifted split adjacent hydrogens These hydrogens have been shifted more, but their signal has not been split due to the absence of adjacent hydrogens. hydrogensshifted split adjacent hydrogens These hydrogens have been shifted most, and their signal has been split into 4 due to the presence of 3 adjacent hydrogens.

15. KHS ChemistryUnit 3.4 Structural Analysis14 More Vocabularly resonances It is often convienient to describe the relative positions of the resonances in an NMR spectrum. downfielddeshielded upfieldshielded For example, a peak at a chemical shift, , of 10 ppm is said to be downfield or deshielded with respect to a peak at 5 ppm, or if you prefer, the peak at 5 ppm is upfield or shielded with respect to the peak at 10 ppm.

16. KHS ChemistryUnit 3.4 Structural Analysis15 Shielding reduces shield Since this reduces the field experienced at the nucleus, the electrons are said to shield the proton applied magnetic field induced magnetic field sigma orbital opposes The electrons around the proton create a magnetic field that opposes the applied field.

17. KHS ChemistryUnit 3.4 Structural Analysis16 Deshielding HCX X = electronegative atom pulls electrons reduce the shielding Anything that pulls electrons away from the hydrogen atom will reduce the shielding effect of the sigma electrons.

18. KHS ChemistryUnit 3.4 Structural Analysis17 Electronegativity CH 3 F  4.3 ppmleast shielded H big shift CH 3 OCH 3  3.2 ppm CH 3 N(CH 3 ) 2  2.2 ppm CH 3 CH 3  0.9 ppm CH 3 Si(CH 3 ) 3  0.0 ppmmost shielded Hno shift TMS H 3 C-IH 3 C-FH 3 C-Cl H 3 C-Br The more electronegative the group, the greater the shift.

19. KHS ChemistryUnit 3.4 Structural Analysis18 Quantity & Distance CHCl 3  7.3 ppm CH 2 Cl 2  5.3 ppm CH 3 Cl  3.1 ppm The larger the number of electronegative groups present, the greater the shift. TMSH 3 C-ClH 3 C-C-Cl The closer to the electronegative group, the greater the shift.

20. KHS ChemistryUnit 3.4 Structural Analysis19 More Deshielding downup The magnetic field goes down through the centre of the ring and up through the hydrogen atoms on the outside. applied magnetic field induced magnetic field Pi electrons Pi electrons (in muliple bonds) are perpendicular to sigma electrons.

21. KHS ChemistryUnit 3.4 Structural Analysis20 Pi Bonds Spectrum of methylbenzene (toluene). TMS 3H 5H   2 Integration number Integration of the peaks will supply you with the number of hydrogens. HH HH HH C CHHHH CH3CH3CH3CH3CH3CH3CH3CH3  7.3 ppm  5.3 ppm  0.9 ppm

22. KHS ChemistryUnit 3.4 Structural Analysis21 Integration relative heights Most of the time you can expect to be told the number of H atoms at each position. Alternatively, the relative heights of the integrations, (along with molecular formula), can be used.

23. KHS ChemistryUnit 3.4 Structural Analysis22 H-NMR Chemical Shifts type In ‘Theory’ Shifts can be used to identify which type of molecule the hydrogens are in. In reality, IR spectroscopy will have identified the type of molecule. NMR is mainly used to help identify the position of the hydrogens.

24. KHS ChemistryUnit 3.4 Structural Analysis23 Splitting - Coupling O H H H H H H H H 3H 2H 3H  0321 adjacent coupling Protons have themselves small magnetic fields. These can increase, or decrease, slightly the magnetic field experienced by adjacent hydrogens. This is called coupling. same carbon Any effect on Hydrogens on the same carbon is already part of the  value measured by the NMR spectrometer, while Hydrogens 3 bonds away, —C—C—H, are too far to feel an effect.

25. KHS ChemistryUnit 3.4 Structural Analysis24 Coupling - 1 hydrogen An isolated H atom would produce a single peak C HAHA single hydrogen two possibilities If a single hydrogen is present on the adjacent carbon then two possibilities exist. C HAHA C HXHX or align withagainst doublet The field of the hydrogen can align with or against the magnetic field - two slightly different shifts - a doublet.

26. KHS ChemistryUnit 3.4 Structural Analysis25 Coupling - 2 hydrogens two hydrogens four possibilities If two hydrogens are present on the adjacent carbon then four possibilities exist. triplet Three slightly different shifts - a triplet. C HAHA C HXHX HXHX or These two combinations would have same effect.

27. KHS ChemistryUnit 3.4 Structural Analysis26 A Pattern Emerges 0 adjacent hydrogens singlet 0 adjacent hydrogens - a singlet produced 1 adjacent hydrogen doublet 1 adjacent hydrogen - a doublet produced 2 adjacent hydrogens triplet 2 adjacent hydrogens - a triplet produced 3 adjacent hydrogens quadruplet 3 adjacent hydrogens - a quadruplet produced 4 adjacent hydrogens quintuplet 4 adjacent hydrogens - a quintuplet produced

28. KHS ChemistryUnit 3.4 Structural Analysis27 Information in NMR Spectrum ¶ number of signals - different types ¶ number of signals - number of different types of hydrogens. · their intensity number · their intensity (as measured by relative areas under peak ….called integration,gives integral values) - number of each type of hydrogen. their shift,  proximity to electronegative  their shift,  - proximity to electronegative groups/ pi electrons etc. splitting patterncoupling ¹ splitting pattern (coupling) - how many hydrogens on adjacent carbons.

29. KHS ChemistryUnit 3.4 Structural Analysis28 Spectrum Explained O H H H H H H H H 3H 2H 3H  0321

30. KHS ChemistryUnit 3.4 Structural Analysis29 Spectrum 1

31. KHS ChemistryUnit 3.4 Structural Analysis30 Spectrum 2

32. KHS ChemistryUnit 3.4 Structural Analysis31 Spectrum 3

33. KHS ChemistryUnit 3.4 Structural Analysis32 Spectrum 4

34. KHS ChemistryUnit 3.4 Structural Analysis33 Spectrum 5

35. KHS ChemistryUnit 3.4 Structural Analysis34 Spectrum 6

36. KHS ChemistryUnit 3.4 Structural Analysis35 Spectrum 7a A more ‘realistic’ problem: C 11 H 14 O 2 Elemental analysis has shown that the empirical formula of a compound is 178 amu molecular ion Mass Spectrum shows the molecular ion to be: C=O aromatic carbonyl group, aromatic The IR Spectrum shows the presence of a carbonyl group, no hydroxyl group, no aldehyde hydrogens, and a busy fingerprint region idicative of aromatic : Molecular FormulaC 11 H 14 O 2 Phenyl group (C 6 H 5 ), ester group COO, leaving C 4 H 9.

37. KHS ChemistryUnit 3.4 Structural Analysis36 Spectrum 7b triplet 3H at  0.9 must be CH 3 next to CH 2 (triplet) quadruplet 2H at  2.1 must be CH 2 next to CH 3 (quadruplet) triplet 2H at  2.8 must be CH 2 next to CH 2 (triplet) triplet 2H at  4.4 must be CH 2 next to CH 2 (triplet) H’s at  0.9 and  2.1 must be —CH 2 CH 3 - low shift suggests attached to C=O rather than —O—. aromatic 5H at  7.2 must be aromatic H’s at  2.8 and  4.4 must be —CH 2 CH 2 - highest shift (  4.4) probably attached to —O— while lower shift (  2.8) is attached to phenyl group.

38. KHS ChemistryUnit 3.4 Structural Analysis37 Spectrum 7b triplet 3H at  0.9 must be CH 3 next to CH 2 (triplet) quadruplet 2H at  2.1 must be CH 2 next to CH 3 (quadruplet) triplet 2H at  2.8 must be CH 2 next to CH 2 (triplet) triplet 2H at  4.4 must be CH 2 next to CH 2 (triplet) H’s at  0.9 and  2.1 must be —CH 2 CH 3 - low shift suggests attached to C=O rather than —O—. aromatic 5H at  7.2 must be aromatic H’s at  2.8 and  4.4 must be —CH 2 CH 2 - highest shift (  4.4) probably attached to —O— while lower shift (  2.8) is attached to phenyl group.

39. KHS ChemistryUnit 3.4 Structural Analysis38 X-Rays

40. KHS ChemistryUnit 3.4 Structural Analysis39 X-Ray Crystallography x-rays scattered by crystal x-ray source beam of x-rays crystal x-ray sensitive photographic film

41. KHS ChemistryUnit 3.4 Structural Analysis40 Scattering The layers of atoms in the molecules make the crystal diffraction gratingscatter act like a diffraction grating causing the x-rays to scatter.

42. KHS ChemistryUnit 3.4 Structural Analysis41 Diffraction Pattern diffraction pattern The diffraction pattern of spots that is obtained electron density map is then used to create an electron density map.

43. KHS ChemistryUnit 3.4 Structural Analysis42 Electron Density Map Electron density map Electron density map of trichlorophenol compared with the structural formula

44. KHS ChemistryUnit 3.4 Structural Analysis43 End of Topic 4 Structural Analysis 3