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 * JResolved 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. Xray 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 throughbond 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 2QFCOSY  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 RelayCOSY : RELAYCOrrelated 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 2DCOSY 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 OC=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 Me1 C 8 H 16 O Me1 CH 2 2 CH 2 3 CH 2 4 CH 2 5 C=O 5 CH 2 7 Me8 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 OC OC=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 COSY45 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 COSY45 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 COSY90: 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. Crosspeak in COSY45 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 JResolved Spectrum Dr. M.A.Versaini, 2D NMR Spectroscopy 45
46 How we solve the structure of an unknown compound with the help of 2DNMR 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 DMannitol 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 Jresolved Dr. M.A.Versaini, 2D NMR Spectroscopy 55
56 Jresolved Dr. M.A.Versaini, 2D NMR Spectroscopy 56
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