# Structure Determination by NMR

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1 Structure Determination by NMR * Introduction to NMR * 2D NMR, resonance assignments J Correlated Based Experiments * COSY - Correlated Spectroscopy * NOESY - Nuclear Overhauser Effect Spectroscopy * HETCOR - Heteronuclear Correlated Spectroscopy/HMQC * COLOC/HMBC * J-Resolved Dr. M.A.Versaini, 2D NMR Spectroscopy 1

2 Structure Determination by NMR Biological molecules such as proteins and nucleic acids can be large and complex. They can easily exceed 2000 atoms. Knowing their structure is critical in understanding the relationship between structure and function. X-ray crystallography is an excellent method to determine detailed 3D structures of even some of the largest biological molecules. However, it has some significant difficulties. Getting crystals and is the structure biologically relevant. NMR can be used to determine 3D structure and dynamics in solution! It s limitation is molecular size. However, this is changing. Dr. M.A.Versaini, 2D NMR Spectroscopy 2

3 TATA Box Binding Protein Bound to DNA Duplex 2071 atoms 2175 bonds Dr. M.A.Versaini, 2D NMR Spectroscopy 3

4 NMR Structure Determination What is NMR? How does NMR work? How is a three dimensional structure elucidated? Dr. M.A.Versaini, 2D NMR Spectroscopy 4

5 Nuclear Magnetic Resonance Nuclear spin m = g I h m - magnetic moment g - gyromagnetic ratio I - spin quantum number h - Planck s constant m I is a property of the nucleus Mass # Atomic # I Odd Even or odd 1/2, 3/2, 5/2, Even Even 0 Even Odd 1, 2, 3 As an exercise determine I for each of the following 12 C, 13 C, 1 H, 2 H, 15 N. Dr. M.A.Versaini, 2D NMR Spectroscopy 5

6 Apply an external magnetic field (i.e., put your sample in the magnet) z w w = g B o = n/2p B o m m w w - resonance frequency in radians per second, also called Larmor frequency n - resonance frequency in cycles per second, Hz g - gyromagnetic ratio B o - external magnetic field (the magnet) Spin 1/2 nuclei will have two orientations in a magnetic field +1/2 and -1/2. Dr. M.A.Versaini, 2D NMR Spectroscopy 6

7 Net magnetic moment z w m +1/2 B o m -1/2 w Dr. M.A.Versaini, 2D NMR Spectroscopy 7

8 Ensemble of Nuclear Spins B o B o = 0 B o > 0 Randomly oriented Highly oriented N S Each nucleus behaves like a bar magnet. Dr. M.A.Versaini, 2D NMR Spectroscopy 8

9 The net magnetization vector w z w x one nucleus many nuclei z w z M o - net magnetization vector allows us to look at system as a whole y y x x Dr. M.A.Versaini, 2D NMR Spectroscopy 9

10 Allowed Energy States for a Spin 1/2 System E DE = g h B o = h n -1/2 DE +1/2 antiparallel parallel B o = 0 B o > 0 Therefore, the nuclei will absorb light with energy DE resulting in a change of the spin states. Dr. M.A.Versaini, 2D NMR Spectroscopy 10

11 Energy of Interaction DE = g h B o = h n The frequency, n, corresponds to light in the radiofrequency range when B o is in the Teslas. This means that the nuclei should be able to absorb light with frequencies in the range of 10 s to 100 s of megaherz. Note: FM radio frequency range is from ~88MHz to 108MHz. 77 Se, g = 5.12x10 7 rad sec -1 T -1 n = g B o /2p Dr. M.A.Versaini, 2D NMR Spectroscopy 11

12 Nuclear Spin Dynamics z M o z M o z y y M o y x x x RF on RF off RF off Effect of a 90 o x pulse Dr. M.A.Versaini, 2D NMR Spectroscopy 12

13 Nuclear Spin Evolution z z z M o y y y x x M o w x RF receivers pick up the signals I x Time y Dr. M.A.Versaini, 2D NMR Spectroscopy 13

14 Free Induction Decay The signals decay away due to interactions with the surroundings. A free induction decay, FID, is the result. Fourier transformation, FT, of this time domain signal produces a frequency domain signal. FT Time Frequency Dr. M.A.Versaini, 2D NMR Spectroscopy 14

15 Spin Relaxation There are two primary causes of spin relaxation: Spin - lattice relaxation, T 1, longitudinal relaxation. lattice Spin - spin relaxation, T 2, transverse relaxation. Dr. M.A.Versaini, 2D NMR Spectroscopy 15

16 Nuclear Overhauser Effect Caused by dipolar coupling between nuclei. The local field at one nucleus is affected by the presence of another nucleus. The result is a mutual modulation of resonance frequencies. N S N S Dr. M.A.Versaini, 2D NMR Spectroscopy 16

17 Nuclear Overhauser Effect The intensity of the interaction is a function of the distance between the nuclei according to the following equation. I = A (1/r 6 ) I - intensity A - scaling constant r - internuclear distance 1 H r 1,2 1 H 1 2 r 1,3 r 2,3 1 H 3 Arrows denote cross relaxation pathways r 1,2 - distance between protons 1 and 2 r 2,3 - distance between protons 2 and 3 The NOE provides a link between an experimentally measurable quantity, I, and internuclear distance. NOE is only observed up to ~5Å. Dr. M.A.Versaini, 2D NMR Spectroscopy 17

18 Scalar J Coupling Electrons have a magnetic moment and are spin 1/2 particles. J coupling is facilitated by the electrons in the bonds separating the two nuclei. This through-bond interaction results in splitting of the nuclei into 2I + 1states. Thus, for a spin 1/2 nucleus the NMR lines are split into 2(1/2) + 1 = 2 states. 1 H 1 H 12 C 12 C Multiplet = 2nI + 1 n - number of identical adjacent nuclei I - spin quantum number Dr. M.A.Versaini, 2D NMR Spectroscopy 18

19 Scalar J Coupling The magnitude of the J coupling is dictated by the torsion angle between the two coupling nuclei according to the Karplus equation. J = A + Bcos(q) + C cos 2 (q) A = 1.9, B = -1.4, C = 6.4 H H q H 12 Karplus Relation C C H 3 J A, B and C on the substituent electronegativity Dr. M.A.Versaini, 2D NMR Spectroscopy 19 q

20 Torsion Angles Coupling constants can be measured from NMR data. Therefore, from this experimental data we can use the Karplus relation to determine the torsion angles, q. Coupling constants can be measured between most spin 1/2 nuclei of biological importance, 1 H, 13 C, 15 N, 31 P The most significant limitation is usually sensitivity, S/N. Dr. M.A.Versaini, 2D NMR Spectroscopy 20

21 Chemical Shift, d The chemical shift is the most basic of measurements in NMR. The Larmor frequency of a nucleus is a direct result of the nucleus, applied magnetic field and the local environment. If a nucleus is shielded from the applied field there is a net reduction if the magnetic field experienced by the nucleus which results in a lower Larmor frequency. d is defined in parts per million, ppm. d = (w - w o )/w o * 10 6 Dr. M.A.Versaini, 2D NMR Spectroscopy 21

22 Biomolecular NMR Experiments J Correlated Based Experiments COSY - Correlated Spectroscopy 2QF-COSY - Double Quantum Filtered Spectroscopy HETCOR - Heteronuclear Correlated Spectroscopy E.COSY - Exclusive COSY HOHAHA - Homonuclear Hartmann Hahn (TOCSY) Nuclear Overhauser Based Experiments NOESY - Nuclear Overhauser Effect Spectroscopy ROESY - Rotating Frame Overhauser Effect Spectroscopy Three Dimensional Experiments Use a Combination NOESY - TOCSY NOESY - NOESY Dr. M.A.Versaini, 2D NMR Spectroscopy 22

23 Summary There are three primary NMR tools used to obtain structural information Nuclear Overhauser effect - internuclear distances J Coupling - torsion angles Chemical shift - local nuclear environment (Chemical exchange can also be monitored by NMR.) Dr. M.A.Versaini, 2D NMR Spectroscopy 23

24 Homonuclear 2D correlation techniques Through Bond: n J HH (scalar coupling) COSY : COrrelated SpectroscopY Directly coupled neighbors Relay-COSY : RELAY-COrrelated SpectroscopY Directly coupled neighbors and protons coupled to the coupled neighbors (relay transfer) TOCSY : TOtal Correlation SpectroscopY Directly coupled neighbors and protons coupled to the coupled neighbors (More efficient than Relay) Through Space: Distance NOESY : NOE SpectroscopY ROESY : ROE SpectroscopY NOE in Rotating frame Dr. M.A.Versaini, 2D NMR Spectroscopy 24

25 C 4 H 8 O CH 3 CH 2 CH 2 OH Dr. M.A.Versaini, 2D NMR Spectroscopy 25

26 C 4 H 8 O: COSY CH 3 CH 2 CH 2 OH CH 2 OH CH 2 CH 3 Dr. M.A.Versaini, 2D NMR Spectroscopy 26

27 1 H NMR of glucose derivative Dr. M.A.Versaini, 2D NMR Spectroscopy 27

28 a/b 5 2D-COSY of glucose derivative 5 4 AcO AcO H AcO H O 6 a/b OCH H H OAc H

29 C 5 H 8 O 2 I= 5 8/2 +1 = 2 CH 2 - O O-C=O CH 2 - O 29

30 C 5 H 8 O 2 CH 2 - O d c b a b CH a CH 2 c CH 2 d CH 2 O C=O 2 5 Dr. M.A.Versaini, 2D NMR Spectroscopy 30

31 C 8 H 16 O : I = 8 16/2 + 1 = 1 3H CH 2 CO CH 2 4H 2H 2H 2H 3H Ketone C=O 31

32 5 Me-1 C 8 H 16 O Me1 CH 2 2 CH 2 3 CH 2 4 CH 2 5 C=O 5 CH 2 7 Me-8 3 CH 2 7/5 Me8 Dr. M.A.Versaini, 2D NMR Spectroscopy 32

33 C 11 H 20 O 4 X 2 2H CH 2 CH 3 2H 3H 3H O CH 2 CH 3 O-C O-C=O 33

34 C 11 H 20 O 4 O CH 2 CH 3 CH 2 CH 3 O = C O CH 2 CH 3 CH 3 CH 2 C CH 2 CH 3 O = C O CH 2 CH 3 Only missing quaternary carbon Dr. M.A.Versaini, 2D NMR Spectroscopy 34

35 COSY-45 H2 Br H 1 Br Br H 3 J 1,2 => negative J 1,3 J 2,3 => positive Dr. M.A.Versaini, 2D NMR Spectroscopy 35

36 COSY-45 If we consider cross peak 2/1 Passive couplings involving passive nuclei 3 - (J 1,3 and J 2,3 ) have same Sign (positive slant) If we consider cross peak 3/1 Passive couplings involving passive nuclei 2 - (J 1,2 and J 2,3 ) have different Sign (negative slant) Dr. M.A.Versaini, 2D NMR Spectroscopy 36

37 Phase sensitive COSY Dr. M.A.Versaini, 2D NMR Spectroscopy 37

38 COSY-90: disaccharide H3 H2 H1 H5a H5b H4/2 H3? H1 H2 Dr. M.A.Versaini, 2D NMR Spectroscopy 38

39 COSY45: H2 and H4 overlap at ~ 4.7 ppm. Cross-peak in COSY-45 allow to assign H3 and H5a/b unambiguously as H4 is coupled to a geminal pair => different sign in J 2/ /5a/5b? 5a 5b Dr. M.A.Versaini, 2D NMR Spectroscopy 39

40 H3 H4 H2 H6a/b H5 Dr. M.A.Versaini, 2D NMR Spectroscopy 40

41 H5 H3 H3 H4 H2 H6a H5 H2 H6b H4 Deshielded multiplet H1 H6a/b H5 H6a H6b H4 Dr. M.A.Versaini, 2D NMR Spectroscopy 41

42 1 H 13 C Assignment H HMQC & & & Dr. M.A.Versaini, 2D NMR Spectroscopy 42

43 Dr. M.A.Versaini, 2D NMR Spectroscopy 43

44 HMBC Spectra Dr. M.A.Versaini, 2D NMR Spectroscopy 44

45 J-Resolved Spectrum Dr. M.A.Versaini, 2D NMR Spectroscopy 45

46 How we solve the structure of an unknown compound with the help of 2D-NMR Spectrum????? Dr. M.A.Versaini, 2D NMR Spectroscopy 46

47 Dr. M.A.Versaini, 2D NMR Spectroscopy 47

48 CHOH CHOH CH 2 OH = m/z : 91 - CH OH - CH - OH - CH 2 - OH - CH 2 - OH Dr. M.A.Versaini, 2D NMR Spectroscopy 48

49 CHOH CHOH CH 2 OH = m/z : 91 Broad band DEPT Spectrum Dr. M.A.Versaini, 2D NMR Spectroscopy 49

50 [ CHOH CHOH CH 2 OH = m/z : 91] X 2 = 182 HO HO H H CH 2 OH H H OH OH CH 2 OH 6 D-Mannitol Dr. M.A.Versaini, 2D NMR Spectroscopy 50

51 COSY_45 Dr. M.A.Versaini, 2D NMR Spectroscopy 51

52 COSY_45 Dr. M.A.Versaini, 2D NMR Spectroscopy 52

53 HSQC Dr. M.A.Versaini, 2D NMR Spectroscopy 53

54 HMBC Dr. M.A.Versaini, 2D NMR Spectroscopy 54

55 J-resolved Dr. M.A.Versaini, 2D NMR Spectroscopy 55

56 J-resolved Dr. M.A.Versaini, 2D NMR Spectroscopy 56

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