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Structural Analysis 3

Structural Analysis 3. Gordon Watson Chemistry Department, Kelso High School. Adv Higher Unit 3 Topic 4. Introduction. This topic continues to explore methods used in the Structural Analysis of organic molecules including NMR Spectroscopy and X-Ray Crystallography. +. +.

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Structural Analysis 3

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  1. StructuralAnalysis 3 Gordon Watson Chemistry Department, Kelso High School Adv Higher Unit 3 Topic 4 Unit 3.4 Structural Analysis

  2. Introduction This topic continues to explore methods used in the Structural Analysis of organic molecules including NMR Spectroscopy and X-Ray Crystallography. Unit 3.4 Structural Analysis

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

  4. + + + + + Orientation The distribution of nuclear spins is random in the absence of an external magnetic field. Unit 3.4 Structural Analysis

  5. + + + + + Magnetic Field, Ho Magnetic Field When a field is applied they line up parallel to the applied field, either spin aligned or spin opposed. Unit 3.4 Structural Analysis

  6. + + + + + Magnetic Field, Ho Energy Levels Energy levels between the spin aligned and spin opposed states are slightly different. There is a slight excess of nuclear magnetic moments spin aligned parallel to the applied field, (lower energy). Unit 3.4 Structural Analysis

  7. + DE ' DE + increasing field strength Magnetic Field Strength The splitting of the energy levels is proportional to the strength of the magnetic field. Low energy - radio waves Unit 3.4 Structural Analysis

  8. DE Radio Frequency in Radio Frequency out APPLIED FIELD Proton Resonance Unit 3.4 Structural Analysis

  9. NMR Spectrometer The basic arrangement of an NMR spectrometer is shown above. Unit 3.4 Structural Analysis

  10. 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 104 gauss):1H absorbs radiation having a frequency of 200 MHz (200 x 106 s-1) 13C absorbs radiation having a frequency of 50.4 MHz (50.4 x 106 s-1) The frequency of absorbed electromagnetic radiation for a particular nucleus (such as 1H) depends on its molecularenvironment. This is what makes NMR spectroscopy such a useful tool. Unit 3.4 Structural Analysis

  11. H H H H H H H butanone Molecular Environment Unit 3.4 Structural Analysis

  12. C H 3 H C Si C H 3 3 C H 3 Reference Molecule Tetramethylsilane, TMS, is used as a reference molecule. 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. TMS is given a value of 0. The values for hydrogen atoms in other molecules will be shifted, due to the deshielding effect of other atoms in the molecule. The values for equivalent hydrogen atoms can be slightly different due to the coupling effect of adjacent hydrogen atoms. Unit 3.4 Structural Analysis

  13. 3H O 3H H 2H H H H H H H H d 3 2 1 0 C H 3 H C Si C H 3 3 C H 3 NMR Spectrum These hydrogens have beenshiftedleast, and their signal has beensplit into 3 by the couplingeffect of the2 adjacent hydrogens. Thesehydrogenshave beenshiftedmore, but their signal has not beensplit due to the absence of adjacent hydrogens. Thesehydrogenshave beenshiftedmost, and their signal has beensplit into 4 due to the presence of 3 adjacent hydrogens. Unit 3.4 Structural Analysis

  14. More Vocabularly It is often convienient to describe the relative positions of the resonances in an NMR spectrum.  For example, a peak at a chemical shift, d, 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. Unit 3.4 Structural Analysis

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

  16. H C X Deshielding X = electronegative atom Anything that pulls electrons away from the hydrogen atom will reduce the shielding effect of the sigma electrons. Unit 3.4 Structural Analysis

  17. H3C-Br H3C-F H3C-Cl H3C-I TMS Electronegativity CH3Fd 4.3 ppm least shielded H big shift CH3OCH3d 3.2 ppm CH3N(CH3)2d 2.2 ppm CH3CH3d 0.9 ppm CH3Si(CH3)3d 0.0 ppm most shielded H no shift The more electronegative the group, the greater the shift. Unit 3.4 Structural Analysis

  18. H3C-Cl H3C-C-Cl TMS Quantity & Distance • CHCl3d 7.3 ppm • CH2Cl2 d 5.3 ppm • CH3Cld 3.1 ppm The larger the number of electronegative groups present, the greater the shift. The closer to the electronegative group, the greater the shift. Unit 3.4 Structural Analysis

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

  20. 3H 5H 7 TMS 2 d H H H C C H H H H H H H Pi Bonds Integration of the peaks will supply you with the number of hydrogens. Spectrum of methylbenzene (toluene). CH3CH3 d 7.3 ppm d 5.3 ppm d 0.9 ppm Unit 3.4 Structural Analysis

  21. Integration 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. Unit 3.4 Structural Analysis

  22. H-NMR Chemical Shifts 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. Unit 3.4 Structural Analysis

  23. 3H O 3H H 2H H H H H H H H d 3 2 1 0 Splitting - Coupling Protons have themselves small magnetic fields. These can increase, or decrease, slightly the magnetic field experienced by adjacent hydrogens. This is called coupling. Any effect on Hydrogens on the same carbon is already part of the d value measured by the NMR spectrometer, while Hydrogens 3 bonds away, —C—C—H, are too far to feel an effect. Unit 3.4 Structural Analysis

  24. HA C HA HX C C or Coupling - 1 hydrogen An isolated H atom would produce a single peak If a single hydrogen is present on the adjacent carbon then two possibilities exist. The field of the hydrogen can align with or against the magnetic field - two slightly different shifts - a doublet. Unit 3.4 Structural Analysis

  25. HA HX C C or or or HX Coupling - 2 hydrogens If two hydrogens are present on the adjacent carbon then four possibilities exist. These two combinations would have same effect. Three slightly different shifts - a triplet. Unit 3.4 Structural Analysis

  26. A Pattern Emerges 0 adjacent hydrogens - a singlet produced 1 adjacent hydrogen - a doublet produced 2 adjacent hydrogens - a triplet produced 3 adjacent hydrogens - a quadruplet produced 4 adjacent hydrogens - a quintuplet produced Unit 3.4 Structural Analysis

  27. Information in NMR Spectrum • number of signals - number ofdifferent typesof hydrogens. • their intensity (as measured by relative areas under peak ….called integration,gives integral values) - number of each type of hydrogen. • their shift, d - proximity to electronegative groups/ pi electrons etc. • splitting pattern (coupling) - how many hydrogens on adjacent carbons. Unit 3.4 Structural Analysis

  28. 3H O 3H H 2H H H H H H H H d 3 2 1 0 Spectrum Explained Unit 3.4 Structural Analysis

  29. Spectrum 1 Unit 3.4 Structural Analysis

  30. Spectrum 2 Unit 3.4 Structural Analysis

  31. Spectrum 3 Unit 3.4 Structural Analysis

  32. Spectrum 4 Unit 3.4 Structural Analysis

  33. Spectrum 5 Unit 3.4 Structural Analysis

  34. Spectrum 6 Unit 3.4 Structural Analysis

  35. Spectrum 7a A more ‘realistic’ problem: Elemental analysis has shown that the empirical formula of a compound is C11H14O2 178 amu Mass Spectrum shows the molecular ion to be: Molecular Formula C11H14O2 C=O aromatic The IR Spectrum shows the presence of a carbonyl group, no hydroxyl group, no aldehyde hydrogens, and a busy fingerprint region idicative ofaromatic : Phenyl group (C6H5) , ester group COO, leaving C4H9. Unit 3.4 Structural Analysis

  36. Spectrum 7b 3H at d0.9 must be CH3 next to CH2 (triplet) 2H at d2.1 must be CH2 next to CH3 (quadruplet) 2H at d2.8 must be CH2 next to CH2 (triplet) 2H at d4.4 must be CH2 next to CH2 (triplet) 5H at d7.2 must be aromatic H’s at d0.9 and d2.1 must be —CH2CH3 - low shift suggests attached to C=O rather than —O—. H’s at d2.8 and d4.4 must be —CH2CH2 - highest shift (d4.4) probably attached to —O— while lower shift (d2.8) is attached to phenyl group. Unit 3.4 Structural Analysis

  37. Spectrum 7b 3H at d0.9 must be CH3 next to CH2 (triplet) 2H at d2.1 must be CH2 next to CH3 (quadruplet) 2H at d2.8 must be CH2 next to CH2 (triplet) 2H at d4.4 must be CH2 next to CH2 (triplet) 5H at d7.2 must be aromatic H’s at d0.9 and d2.1 must be —CH2CH3 - low shift suggests attached to C=O rather than —O—. H’s at d2.8 and d4.4 must be —CH2CH2 - highest shift (d4.4) probably attached to —O— while lower shift (d2.8) is attached to phenyl group. Unit 3.4 Structural Analysis

  38. X-Rays Unit 3.4 Structural Analysis

  39. x-ray sensitive photographic film beam of x-rays x-rays scattered by crystal crystal x-ray source X-Ray Crystallography Unit 3.4 Structural Analysis

  40. Scattering The layers of atoms in the molecules make the crystal act like a diffraction grating causing the x-rays to scatter. Unit 3.4 Structural Analysis

  41. Diffraction Pattern The diffraction pattern of spots that is obtained is then used to create an electron density map. Unit 3.4 Structural Analysis

  42. Electron Density Map Electron density map of trichlorophenol compared with the structural formula Unit 3.4 Structural Analysis

  43. StructuralAnalysis 3 End of Topic 4 Unit 3.4 Structural Analysis

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