Professional Documents
Culture Documents
Exercises - Werkcollege 2014: NMR Spectroscopy Bijvoet Center For Biomolecular Research
Exercises - Werkcollege 2014: NMR Spectroscopy Bijvoet Center For Biomolecular Research
2014
http://nmr.chem.uu.nl/Education/structuralanalysis_notes.php
Hans Wienk
Deni Mance
Rolf Boelens
NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Notes.
Chapter 1. Introduction
1. NMR deals with nuclear magnetism, arising from the magnetic moment of the nucleus
of some types of atoms. The everyday form of (macroscopic) magnetism as manifested
by permanent magnets and magnetizable materials, has a different source. Find out
which.
2. a) Draw the energy diagrams and indicate the and spin states for the following
nuclei:
3
H γ 3H = 2.8535 · 108 (T·s)−1 (I = 1/2)
113
Cd γ 113Cd = 5.9340 · 107 (T·s)−1 (I = 1/2)
b) At what frequency do these nuclear spins resonate given a 1.5 Tesla (T) magnetic
field?
c) What are the corresponding angular frequencies (“hoeksnelheid”) of the precession
motion?
3. A proton at 11.7 T resonates at 500 MHz. To what value must the magnetic field be
raised in order to obtain resonance at 600 MHz?
4. Prove that the energy of a randomly oriented magnetic moment in the static B0 field is
only dependent on the z-component of the magnetic moment (see Reader Eqns. 2.6 and
2.7).
5. Consider the compound chloroform (CHCl3) where all carbon-atoms are of the 13C-
isotope. The difference in the Larmor frequency of the 13C spin and 1H spin is 675
MHz. What is field strength of the B0 field? What is the proton Larmor frequency? Use
Table 2.1 of the Reader.
7. The equation of motion (Reader Eqn. 2.11) is crucial to describe NMR phenomena.
Derive Reader Eqn. 2.12 from Eqn. 2.11 and verify that Eqn. 2.13 is a correct solution.
EXERCISES – QUESTIONS 94
Chapter 3. An ensemble of Nuclear Spins
8. a) Consider an ensemble of 1H nuclear spins. What is the ratio of the populations of the
upper and lower states at 25 °C and a magnetic field of 2.35 T?
b) What is the population difference between the two spin states per 1·106 spins?
c) What is the population difference for 13C, under the same conditions, per 1·106 spins?
10. Sketch in a vector diagram (rotating frame, on resonance) the effect on the
magnetization of a certain proton for the following cases. For questions 10a−10e we
start with equilibrium (+Mz) magnetization.
a) Apply a 90° x-pulse.
b) Apply a 90° y-pulse .
c) Apply a 180° y-pulse
d) Apply a 90° −x-pulse
e) Apply a 270° x-pulse. What is the difference compared with d)? What if the pulse is
slightly miscalibrated (e.g. if it is slightly too short)?
f ) Start with +Mx magnetization. Apply a 90° x-pulse.
g) Start with +Mx. Apply a 90° y-pulse.
h) Start with +My. Apply a 90° x-pulse.
i) Start with +My. Apply a 90° y-pulse.
11. You want to excite equilibrium magnetization. Unfortunately your excitation pulse is
miscalibrated and is only an 80° x-pulse instead of a 90° x-pulse. Which percentage of
the equilibrium magnetization will be in the transverse plane?
12. Use the equation-of-motion (Reader Eqn. 2.11) to calculate the effect of a y-pulse. The
magnetic moment for a single spin can be replaced by the net magnetization vector M
combining all spins of the ensemble.
13. Consider exercise 9 again. Suppose you use a B1-pulse with a frequency of 400 MHz.
To examine the effect of this pulse, we need to use a rotating frame with a rotation
frequency of 400 MHz.
a) Sketch in a vector diagram the net-magnetization vector in equilibrium in this
rotating frame.
b) Sketch in a vector diagram the magnetization vector of an individual spin in this
rotating frame. What is the precession frequency of the spin in this rotating field?
EXERCISES – QUESTIONS 95
c) What is then the effective B0 field in this rotating field? Use Hz as the unit for
magnetic field strength.
d) What is the total effective field Beff in this rotating field? Assume a B1 strength of 25
kHz.
e) Predict the result of a 10 s B1-pulse.
15. Verify that Reader Eqns. 4.2 and 4.3 are valid solutions of Eqn. 4.1.
17. Sketch roughly the Fourier transforms of the following FIDs (on the left the My part of
the FID, on the right the Mx detection).
a) My Mx
b)
EXERCISES – QUESTIONS 96
c)
d)
20. You want to record a spectrum for a compound which has several signals in the range of
–12 kHz to +5 kHz. To what value must the dwell-time be set?
21. If the magnetic field varied by ± 10 nT between the edges of the sample, what level of
error would this introduce in the resonance frequency of 1H nuclei at a magnetic field
EXERCISES – QUESTIONS 97
strength of 11.7 T (500 MHz)? Compare this error to the typical line width of a 1H
signal of 1 Hz.
23. The chemical shift of two equivalent methylene protons is 3.157 ppm. Their NMR
signal is split in two lines due to the scalar coupling (J-coupling) to the attached 13C
nuclear spin. The value of the scalar coupling constant is 132.15 Hz. The magnetic field
strength is 0.5 T.
a) Calculate the chemical shift difference between the two methylene signals.
b) Calculate the frequency difference between each methylene signal and the reference
signal of TMS at 0 ppm.
c) What is the chemical shift difference when the field is ten times stronger?
The distances between the - and -protons are known. Calculate the remaining
distances and suggest assignments for the two unassigned protons.
25. Estimate the molecular weight where the NOE vanishes on a 500 MHz spectrometer
(see Reader p.47).
26. Derive Reader Eqn. 9.1 from Eqn. 4.2 and prove that at = ln(2) · T1 no signal will be
observed in a inversion-recovery experiment (assume t = ).
27. Assume Mz magnetization. What happens in the following sequence, where the delay is
a certain fixed waiting time: 90x — delay — 180x — delay? Give a vectorial
EXERCISES – QUESTIONS 98
representation of the evolution of the magnetization for two spins of unequal frequency
(relaxation can be neglected). Use the rotating frame to draw the vector diagrams.
Assume that the frequency with which this frame rotates (the zero-frequency or the
carrier-frequency) is the average of the frequencies of the two spins.
Repeat this for the sequence: 90x — delay — 180y — delay. What is the difference?
28. You measure the T2 of the 15N-spins in two 15N-labeled proteins under the exact same
conditions. The average T2 of protein A is 120 ms, while the average T2 of protein B is
60 ms. Give an explanation for this difference.
30. Figure 1 shows the NMR spectrum of the amino acid tryptophan (W) acquired in D2O
(i.e. the side chain and backbone NH protons are not visible).
EXERCISES – QUESTIONS 99
31. Figure 2 shows the NMR spectrum of the nucleotide adenosine-monophosphate (AMP,
see Reader Fig. 12.7 and 12.8) acquired in H2O.
32. The three methyl-protons in ethanal are equivalent and are 2.55, 2.78 en 2.88 Å from
the aldehyde proton. The NOE signal intensity V = constant · 1/r6.
a) Calculate the NOE intensity for the distances between each methyl proton and the
aldehyde proton assuming a constant of 1·10–50.
b) How many cross-peaks will be visible in the 2D NOESY spectrum?
c) Calculate the intensity of this / one of these cross-peaks.
d) Calculate the distance corresponding to this / these cross-peaks.
34. How many signals and what multiplicity do you expect in the 1H-spectrum for the
following compounds (take only coupling over 1–3 bonds into account):
a) methanol
b) 1-bromo-2,2-dimethyl-propane
c) 2-chloro-1-methoxy-propane
36. Two proton spectra are shown together with the formulas of the corresponding
compounds (Figure 4). Determine the structure.
37. Figure 5 shows the 1H-NMR spectrum of the amino acid proline (P) acquired in D2O
(i.e. HN and HO protons are not visible).
39. Assume this segment has an β-sheet conformation. Add the characteristic peaks you
would expect in the NOESY spectrum in Figure 6B. Use Figure 12.4 in the Reader.
40. Now the segment is located in an α-helix. Add the expected peaks in Figure 6C (use
Reader Figure 12.4).
42. We perform an exchange experiment, replacing H2O with D2O. Indicate for Figures
6B–C (Questions 39 and 40) the peaks that are still visible in this solvent (directly after
the exchange of solvent).
For Figure 6B, assume that the HN of the Tyrosine is in a H-bond with an opposite β-
strand, and the β-strand is the outer strand of a β -sheet.
For Figure 6C, first assume that the segment is located in the middle of a long α-helix.
What would be different if the helix starts with the tyrosine (Y) of the segment?
Chapter 1. Introduction
1. The type of magnetism of permanent magnets and magnetizable materials is called
ferromagnetism and is caused by a very strong interaction between the magnetic
moments of the electron spin. The magnetic moment of the electron spin is roughly 650
times as large as that of a proton.
b) The resonance frequency can be calculated using Reader Eqn. 2.10a 0 B0 .
2
Thus, the resonance frequency of 3H equals 2.8535·108 (T·s)−1 × 1.5 T / 2 =
0.68122·108 s−1 = 0.68122·102 MHz = 68.1 MHz. Likewise, the resonance frequency of
113
Cd is 5.9340·107 × 1.5 / 2 = 1.4166·107 s−1 = 14.2 MHz.
Clinical MRI scanners typically operate at 1.5 T. The protons in your brain will then
resonate at 63.8657 MHz.
c) The precession has the same frequency as the resonance frequency. The
corresponding angular frequencies are obtained by multiplying by 2 giving 4.28·108
s−1 (3H) and 8.90·107 s−1 (113Cd) (NOTE: the unit has to be s−1 and not Hz).
3. Reader Eqn. 2.10a shows that the resonance frequency depends linearly (“recht-
evenredig”) on the strength of the magnetic field. Thus, the field should be raised to
11.7 / 500 × 600 = 14.04 T.
4. Reader Eqn. 2.6 denotes the dot-product (“in-produkt”) of the magnetic moment and the
static magnetic field (two vectors), resulting in the scalar energy: E B . The
orientation of the magnetic field is normally taken to be parallel with the z-axis, thus
B 0,0,B0 . The magnetic moment will have non-zero x,y,z-projections. Thus:
5. Use Reader Eqn. 2.10a: the resonance frequency (= Larmor frequency) of the 13C spins
13C 1H
is 13C the H spins 1H
B0 . For 1
B0 . The difference in the Larmor frequency
2 2
B 13C
is thus: 1H 13C 1H B0 13C B0 1H 13C 0 B0 2 1H .
2 2 2
1H 13C
Thus, the field strengthis 2× 675·106 Hz / (2.6752·108 - 6.7266·107 (T·s)−1 ) =
4.2411500·109 Hz / 2.00254·108 (T·s)−1 = 21.18 T. The Larmor frequency of the
1H
protons is 1H B0 = 2.6752·108 (T·s)−1 × 21.18 T / 2MHz.
2
6. The resonance frequency can be calculated using Reader Eqn. 2.10a 0 Bz . Thus,
2
the resonance frequency of 1H equals 2.6752·108 (T·s)−1 × 45·10-6 T / 2 = 1916.0 Hz =
1.92 kHz. The corresponding wavelength can be calculated using c (c =
2,99792458·108 m/s), resulting in a wavelength of 156470 m = 1.56·102 km.
7. Reader Eqn. 2.11 denotes the cross-product (“uit-produkt”) of the magnetic moment
of the matrix shown
and the magnetic field. The cross-product equals the determinant
on the right-hand side of Reader Eqn. 2.11. The determinant is calculated by expansion
by minors (“ontwikkeling naar de eerste rij”):
ex ey ez
d By Bz Bx Bz Bx By
B x By B z e x ey ez
dt y z x z x y
x y z
e x B y z B z y e y B x z B z x e z B x y B y x
e x B0 y e y B0 x
Note that ex is the unit vector (1,0,0). Similarly, ey=(0,1,0) and ez=(0,0,1). That means
that the ex term shows the change of d/dt in the x-direction, etc.
d x d
x (0)cos(Bz t) y (0)sin(Bz t)
dt dt
x (0)Bz sin(Bz t) y (0)Bz cos(Bz t)
Bz x (0)sin(Bz t) y (0)cos(Bz t) Bz y
d y d
x (0)sin(Bz t) y (0)cos(Bz t)
dt dt
x (0)Bz cos(Bz t) y (0)Bz sin(Bz t)
Bz x (0)cos(Bz t) y (0)sin(Bz t) Bz x
d z d
z (0) 0
dt dt
Here you have to use the chain-rule (“ketting-regel”): d/dt (f(g(t)) = d/dg f × d/dt g.
Note that you have to assume that the answer is correct to establish the correctness of
the answer!
3
e0.01611310 0.99998389
b)
Thus, for an ensemble of 1·106 spins there are 1·106 × 0.500004 = 500004 spins in the
-state and 1000000–500004 = 499996 spins in the -state. The population difference
for a real sample, expressed as a fraction of 106 spins, is thus 8.06 spins.
c) For 13C spins, this is 2.02 spins.
b) The frequency of the B1-pulse should match the energy-difference between the two
energy-levels, which means that it should be identical to the Larmor-frequency (see
Reader Eqns. 2.9 and 2.10). Thus, the frequency should be 500 MHz.
c) The magnetization vector precesses around the B1-field with 1 B1 (see Reader
2
Eqn. 3.2). The rotation frequency is: 2.6752·108 (T·s)−1 × 0.60·10-3 T / 2 = 25546 Hz.
A 90°-pulse corresponds to a quarter of a rotation. Thus, the length should be ¼ ×
1/25546 = 9.79 s.
d) To describe the effect of the 90°-pulse, the rotating frame must have the same
frequency as the B1-pulse, 500 MHz.
10. a) + My
b) –Mx
d) –My
e) –My
The magnetization vector now travels in the opposite direction to end up at the same
point. If the pulse is slightly too short, a 90° –x-pulse will rotate the magnetization
vector to some point above the xy-plane, whereas a 270° x-pulse will rotate the vector to
some point under the xy-plane. Note that because of the three times longer pulse, this
‘mismatch’ will be thrice as large, i.e. the effects of miscalibration are more pronounced
for longer pulses.
f) +Mx
g) +Mz
h) –Mz
i) +My
12. Again we use the equation of motion, Reader Eqn. 2.11. In the rotating frame B =
(0,B1,0):
ex ey ez
By Bz B Bz Bx By
Bx By B z e x ey x ez
My Mz Mx Mz Mx My
Mx My Mz
B1 0 0 0 0 B1
e x ey ez
My Mz Mx Mz Mx My
e x B1 M z e z B1 M x
e x B1 M z e z B1 M x
dM x
B1 M z
dt
e x B1 M z e z B1 M x
dM
dM y
Thus, dt , or: 0
dt
e x B1 M z e z B1 M x
dM z
B1 M x
dt
The solution of the differential equation is analogous to Reader Eqn. 2.13 (just swap the
x,y,z indices):
M z (t ) M 0 cos(B1t )
Which simplifies to: M x (t ) M 0 sin(B1t ) when starting from equilibrium
M y (t ) 0
magnetization. Thus we see a simple rotation around the y-axis going from +z to –x.
b) The magnetic moment of an individual spin will make an angle with z-axis and
precesses around the B0-field with 500 MHz in the laboratory frame. When
transforming into the rotating frame, the new precession frequency is = –RF
(Reader Eqn. 5.2), where is the lab-frame Larmor frequency and RF the rotation
frequency of the rotating frame. The spin thus precesses with 500 – 400 = 100 MHz.
c) As the spin still precesses in this rotating field, it must still feel a B0-field. This field
is now much smaller as the precession frequency is also smaller. When we express the
strength of the B0-field in MHz, the strength is 500 MHz in the lab-frame and 100 MHz
in the rotating frame.
d) The total effective field is the vector-sum of the reduced B0 and B1. So the strength is:
2
Beff B0,reduced B12 100 10 25 10
6 2 3 2
100 MHz. The angle of this effective
field with the z-axis is:
B 25 10 3
arctan 1 arctan 6
arctan0.25 103 0 .
B
0,reduced
100 10
e) Since the frequency of the B1-pulse (400 MHz) is much lower than the resonance
frequency of the spins (500 MHz), the spins are not affected by the pulse. So the
orientation of the net-magnetization vector will not change.
b) In the laboratory frame: the magnetization vector starts some where in the xy-plane
and precesses around the z-axis. Simultaneously, the length of the vector becomes
smaller due to T2-relaxtion. In the rotating frame, the magnetization starts at the +y-axis
and simply shrinks to eventually vanish.
15.
d
t
dM z
dt
dt
M eq M z (0) M eq e T1
t t
d d d
M eq M z (0)e T1 M eq e T1
dt dt dt
t t
1 T1 1 T1
0 M z (0) e M eq e
T1 T1
t
M z (t ) M eq
1
M z (0) M eq e T1
T1 T1
and
dt dt
t
1 T2
M x ( 0) e
T2
t
1 M (t )
M x (0)e T2 x
T2 T2
1
16. The line width (l.w. or ½) is related to the T2 via: l.w. . a) 0.318 Hz; b) 31.8
T2
Hz; c) 31.8 kHz; d) chloroform = a, dissolved protein = b, solid protein = c. The T2
becomes shorter as the tumbling time of a molecule becomes longer (= slower
tumbling). Chloroform is a very small molecule so tumbles very rapidly, resulting in
very slow T2 relaxation = large T2 values. A solid protein does not tumble at all,
resulting in very fast T2 relaxation = small T2 values.
e)
17. Realize that in the observed FID the present frequency is jRF (Reader Eqn.
5.2). ≠ so when j≠rfIn a), transverse magnetization starts at +y, then turns to
+x, so turns faster than the rotating frame. Therefore in the spectrum the frequency will
have a positive value. Also, when in and FID intensity goes to zero, T2 relaxation occurs
and line-widths are not zero (Reader Eqn. 5.6). In the FID shown in b) the visible
wavelength is longer, so the visible frequency is smaller than in a). The direction of
rotation is the same as for a), so frequency is positive. The signal decays with similar
speed as in a), so the T2 and line width is the same. In c) the frequency and sign of the
FID are the same as in b), but the signal decays to zero faster. That means that T2 is
shorter and the signal gets broadened. In d), the magnetization starts at +y and then
turns to –x. This means that is rotates slower than the rotating frame and gives a
negative frequency.
c) d)
18. At 40°C you can record twice as many scans within a the same time as at 20°C. In 2
hours, you thus record 2 × 2/3 = 4/3 as much scans at 40oC as in 3 hours at 20°C. The
4
signal-to-noise is thus better at 40°C.
3
Chapter 6. Spectrometer
hardware
19. a) In the context of NMR resolution is used to refer to the resolving power of the NMR
spectrum, i.e. the degree to which peaks with small differences in resonance frequency
can be distinguished.
b) According to Reader Eqn. 6.1 one can: raise the number of spins (higher
concentration), raise the field, increase the number of scans, lengthen the relaxation
time (higher temperature, lower viscosity medium) or lower the temperature of the
detection circuit (not of the sample).
c) The “sino” of a 13C experiment will be much lower due to the lower number of spins
and the lower gyro-magnetic ratio. In most cases there will be slightly more favorable
T2 for the 13C spins than the 1H spin. Disregarding this last effect, the relative “sino” is:
5 5
21. The relative error in the resonance frequency will be equal to the relative error in the
magnetic field, which is 10 nT / 11.7 T ≈ 1·10-9. This creates an absolute error of 5·108
Hz × 1·10-9 = 0.4–0.5 Hz, roughly half of the natural line width. So even this small
variation in B0 his is unacceptable and must be improved by shimming.
22. The precession-frequency in the rotating frame () is given by: = – RF (Reader
Eqn. 5.2), where is the frequency of the signal of interest and RF the rotation
frequency of the rotating frame. In this case it is easy to calculate the frequencies with
respect to an reference signal at 0 ppm. Thus, we need to translate ppm to Hz: at 500
MHz, 1 ppm corresponds to 1 millionth of 500 MHz is 500 Hz.
Thus, the frequency of signal at 2 ppm is 2 × 500 = 1000 Hz (with respect to a signal
at 0 ppm), the frequency of the signal at 7 ppm is 7 × 500 = 3500 Hz (with respect to a
signal at 0 ppm) and the frequency RF of the rotating frame is 4.7 × 500 = 2350 Hz.
Thus, the frequency difference for the signal at 2 ppm is 1000 – 2350 = -1350 Hz (a
counter clockwise rotation) and for the signal at 7 ppm is 3500 – 2350 = +1150 Hz (a
clockwise rotation).
2 ppm = –1350 Hz
y'
23. a) The frequency difference between the components of the doublet is determined by
the scalar coupling constant and is not influenced by the magnetic field strength. The
frequency difference is thus 132.15 Hz. At 0.5 T, the resonance frequency of 1H equals
2.6752·108 (T·s)−1 × 0.5 T / 2 = 21.28856519 MHz, 1 ppm is thus 21.28856519 Hz,
and 132.15 Hz = 6.207557852 ppm (dus 2 × 3.103778926).
b) The reference signal of TMS is at 0 ppm. The difference to the center of the
methylene doublet is thus 3.157 ppm. At 0.5 T, the resonance frequency of 1H equals
2.6752·108 (T·s)−1 × 0.5 T / 2 = 21.28856519 MHz. 3.157 ppm thus equals 3.157·10-6
× 21.3 MHz = 3.157 x 21.3 Hz = 67.2080003 Hz. The two lines are thus at 67.2080003
+/- 132.15/2 Hz from 0 ppm, which makes the shortest frequency distance equal to 1.13
Hz.
c) Ten times smaller, i.e. 0.6207557 ppm. Therefore the signals appear much closer to
each other in the spectrum (3.46737785 and 2.84662215). So, the J-coupling constant is
The distance between the 2 and 5 proton is 2 × 2.45 = 4.9 Å. The distance between
the 2 and 6 proton is 2 × cos(30) × 2.45 = 4.24 Å. So the first distance, must be to the
2-proton, and the second is to the 6 proton. (Use the molecular structure on Reader
p.122 to prove these relations).
25. The NOE vanishes for · c = 1.118 (p.47). Thus, c = 1.118 / (500 × 2 × × 106) =
3.75·10-10 s. This corresponds to a molecular weight of c × 2.4·1012 = 854 Dalton
(Reader Eqn. 4.6).
M z M eq M z (0) M eq e T1
t
M eq M eq M eq e T1
t
M eq 2M eq e T1
t
M eq 1 2e T1
and
ln 2T1
ln 1
M z ln(2)T1 M eq 1 2e T1 M eq 1 2e ln 2 M eq 1 2e 2 M eq 1 2 12 0 .
(Using the rule that –ln(x) = ln (x-1) = ln(1/x)).
27. +My - precession creates an –x component – 180x pulse rotates the +y component to –y
but the leaves the x-component unaffected: effectively the vector is reflected in the xz-
plane – precession rotates the vector along the same angle as in the first part and in the
same direction, thus leaving the vector aligned the –y-axis. This sequence is called a
spin-echo (note that the last three Figures show projections on the x’y’-plane).
28. The T2 relaxation time depends on the rotational correlation time which is a measure for
the tumbling time of the molecule. Large molecules have long tumbling times (tumble
very slowly) and have very short T2’s (see Reader Figure p.21). Thus protein B must be
larger than protein A.
31. a) COSY: cross peaks between H1’×H2’; H2’×H3’; H3’×H4’; H4’×H5’; H4’×H5’’;
H5’×H5’’.
b) TOCSY: cross peaks between all sugar protons. No cross peak between H2 and H8
c) NOESY: cross peaks between all sugar protons. Possibly also H1’×H2; H1’×H8;
H2’×H8; H3’×H8, H4’×H8; H5’/H5”×H8, etc. Signal intensities between sugar and
base depend on the base orientation.
32. a) V = C × r-6. Substituting the values results in signal volumes of 3.64·107, 2.17·107
and 1.75·107, respectively.
b) Only one, since the methyl protons are dynamically averaged to equivalence.
c) It will be the sum of the volumes above, so 7.56·107.
d) The corresponding single distance is 2.25 Å, shorter than the three actual distances!
When calculating protein structures from NOESY cross-peak volumes this effect must
be taken into account to prevent distorted structures.
34. a) CH3OH
–CH3 doublet (1:1); –OH: quartet(1:3:3:1)
b) (CH3)3–C–CH2Br
–CH3 singlet; –CH2 singlet
c) CH3−CHCl−CH2−O−CH3
–CH3 doublet; –CH quartet of triplets (1:2:1) in case JCH3-CH >> JCH2-CH or a triplet of
quartets in case JCH3-CH << JCH2-CH. If the two J’s are equal, then a sextet results with
relative intensities 1:5:10:10:5:1; –CH2 doublet; –OCH3 singlet.
35. The triplet at 9.7 ppm –COH; the quartet of doublets at 2.4 ppm –CH2, the triplet at 1.1
ppm –CH3.
37.
38. see Figure below. The peaks around 7 ppm are the aromatic ,-protons of Y.
39. add dN(i,i+1) strong peak and dNN(i,i+1) weak peak. Note that the dNN(i,i+1) contacts
should be symmetrical with respect to the diagonal.
42. If the β-strand is on the outside of a β-sheet, the amide proton of every second residue is
exposed to the solvent. E.g. if Y’s HN is in a H-bond, the amide protons of V,L,S will
be unprotected and will exchange rapidly disappear from the spectrum. If the segment is
in the middle of a long helix, all peaks remain visible because the amide protons are
protected by hydrogen bonds (at least initially, they will be exchanged only very
slowly). If the helix starts at Y, the amide protons Y,V,G will be unprotected and will
exchange rapidly and disappear from the spectrum.
Magnetic Resonance Imaging (MRI) is eigenlijk NMR, maar dan gebruikt om afbeeldingen te
maken van objecten. Het principe van MRI onderzoeken we in deze opgave.
Stel je een NMR-buis voor die gevuld is met watten en twee glazen bolletjes (Figuur 1A).
Beide bolletjes zijn gevuld met water en ze bevinden zich allebei in het gevoelige gedeelte
van de detectiespoel. Het water in de bolletjes geeft een signaal in het 1H-spectrum; de watten
niet.
Figuur 1
Nu wordt in de z-richting een extra magneetveld aangelegd waarvan de sterkte variëert met de
z-coördinaat (de hoogte in de NMR-buis). Dit wordt ook wel een veldgradiënt G(z) genoemd.
Voor deze gradiënt geldt: G(z) = G·z waarbij G gelijk is aan de gradiëntsterkte in mT/cm. De
spins in bolletje A ervaren dus een andere sterkte van het magneetveld dan de spins in bolletje
B (voor A is dat B0 + G·zA en voor B is dat B0 + G·zB).
Je voert dit experiment uit. Neem aan dat B0 gelijk is aan 14.1 T en G = 0.0282 mT/cm. In het
NMR spectrum zie je twee signalen (beide zonder opsplitsing en met gelijke intensiteit).
a) Leg uit waarom je twee signalen ziet.
b) Welk bolletje (A of B) geeft een signaal bij hogere frequentie? Leg uit.
Je meet het verschil in chemical shift tussen de twee signalen: = 1.274 ppm.
c) Bereken het hoogteverschil (z) tussen bolletje A en B.
Stel nu dat we een derde bolletje water toevoegen precies tussen A en B in.
d) Schets het NMR spectrum.
Je stopt vervolgens een normale NMR-buis gevuld met water in de spectrometer. De buis is
gevuld tot de de hoogte van bolletje A (Figuur 1B). Je zet de gradiënt weer aan en neemt het
spectrum op.
e) Schets het NMR spectrum en leg uit waarom het er zo uitziet.
Tenslotte stop je een stuk weefsel in een NMR-buis. In het midden tussen de plek van bolletje
A en B bevindt zich een stuk bot, ter hoogte van bolletje B bevindt zich een holte gevuld met
2. T1 en waterondrukking
a) Laat met een vectordiagram zien wat de uitkomst van het experiment is als =0 en beide
pulsen langs de +x-as gegeven worden. Je begint met evenwichtsmagnetisatie.
b) Hoe verhoudt de intensiteit van het meet-signaal zich tot de intensiteit van de
evenwichtsmagnetisatie als =0?
De algemene formule voor het herstel van de evenwichtsmagnetisatie door T1-relaxatie is:
M z ( ) M eq M z (0) M eq e .
T1
c) Hoe lang is ten opzichte van T1 als je met deze sequentie geen signaal-intensiteit ziet?
Deze puls-sequentie kan ook gebruikt worden om het signaal van water te onderdrukken
wanneer je een spectrum van een eiwit in oplossing wilt opnemen. De T1 van een water-
proton is ca. 4s; de T1 van een eiwit-proton ca. 1s.
d) Waarom kan de T1 van een proton-spin in verschillende moleculen zo verschillend zijn?
e) Schets de relatieve intensiteit van het signaal voor een water-proton en voor een eiwit-
proton als functie van de wachttijd .
f) Wat is de optimale waarde van om het water-signaal te onderdrukken? En hoeveel
procent van de maximale signaalintensiteit verlies je in dit geval voor het eiwit-proton?
3. Reacties in 2D
Stel je voor dat je een lichtgevoelige stof onderzoekt. De stof kan met behulp van laserlicht
van verschillende golflengten in verschillende vormen worden gebracht. Een bepaald proton
kan onder invloed van deze lichtpulsen in drie verschillende chemische omgevingen verkeren:
A 220nm
B 450nm
C
Neem nu aan dat in de situatie van b) de conversie voor de reactie van A naar B 65% is en die
voor de reactie van B naar C 90% is.
c) Wat zijn dan de relatieve intensiteiten van de pieken in het spectrum bij b)?
…T A G S L E V Y…
1 2 3 4 567 8
De volgende figuren laten COSY en TOCSY spectra van het peptide zien. De spectra tonen in
F2 alleen het gebied tussen 6.4 en 10.4 ppm.
a) Ken zoveel mogelijk signalen toe; geef in het TOCSY spectrum voor alle pieken aan wat
de toekenning is (één-lettercode bij de diagonaal-piek en , etc. bij de kruis-pieken.
Stel nu dat het segment een turn bevat (zie het NOESY spectrum).
c) Welke residuen maken deel uit van de turn? BONUS-punt: Welk type turn is dit?
1. (12p)
a) Omdat de magneetveldsterkte bij de twee bolletjes verschillend is, heeft het water ook
verschillende Larmor-frequenties. Daarom krijg je twee signalen in het spectrum. (2p)
b) Bolletje A zit bij een postieve z-coordinaat terwijl bolletje B zich bij een z-coordinaat ≈ 0
bevindt. De magneetveldsterkte Beff = B0 + G·z is dus bij A hoger dan bij B en dus is de
Larmorfrequentie van A hoger. (2p)
c) ppm Hz: = B/2 <=> = 2.6752·108 /2 = 6.00·108 Hz = 600 MHz (1p). 1
ppm is dus 600 Hz. Het frequentieverschil tussen de twee pieken is daarom 600*1.274 =
764.8 Hz (1p). Nu moeten we deze frequentie relateren aan een magneetveldsterkte, dus weer:
= B/2 <=> B = 2*764.83/2.6752·108 = 17.96 T (1p). (Dit kan je ook in
één keer berekenen door bovenstaande formules te combineren tot: B = B0*1.274·10–6).
Dit is het verschil in magneetveldsterkte tussen bolletje A en B. Dit moeten we relateren aan
de z-coordinaat. Daarvoor moet je de gradient-sterkte G gebruiken: 0.0282 mT/ cm => 1 mT
= 35.46 cm <=> 1 T = 35.46·10–3 cm. Dus 17.96 T komt overeen met 17.96*35.46·10–3 cm
= 0.637 cm (1p). (4p totaal)
d) Er is nu een derde signaal precies tussen de twee andere signalen (2p).
e) Omdat er nu op iedere z-coordinaat water is, krijg je als het ware een superpositie van alle
signalen voor ieder denkbeeldig bolletje voor iedere waarde van z. De optelsom is een brede
lijn (1p). De breedte van het signaal komt overeen met de hoogteverschil tussen de onderkant
en de bovenkant (1p). (2p totaal)
f) Bij het bot zul je geen signaal zien omdat er geen water in zit, bij het spierweefsel is er wel
signaal, maar niet zo intens als bij de holte. Het spectrum is als het ware een afbeelding van
de waterdichtheid van het object langs de z-as en kan daarmee gebruikt worden om de bouw
van het weefsel aan te duiden.
2. (12 p)
a) De 220nm flits creëert een fractie toestand B (onvolledige omzetting), dus tijdens t1 heb je
evolutie van het proton met A en B. De 450nm flits zet vervolgens alle B volledig om in C,
terwijl er niets verder met A gebeurt. Daarom heb je tijdens t2 dus evolutie met C en A.
Schematisch:
B B B
65.0 6.5 (rel. int. 6.5%)
C C B,C
58.5 (rel. int. 58.5%)
(stap 1 = 2p en stap 2 = 2p) (4p totaal)
4. (12p)
a) toekenning alle residuen op diagonaal (3p); toekenning alle kruis-pieken (3p) (6p totaal)
b) op juiste plaats en ook intensiteit in verhouding: dNN en dNN(i,i+2) aan beide zijden van de
diagonaal (2p); dN, dN(i,i+3) en dN(i,i+4) (2p) (4p totaal)
c) juiste residuen turn (2p) BONUS: +1 voor herkennen turn
Totaal 4*12= 48p. tel je score op, tel er 6 bij op en deel door 5.4 je cijfer.
Vector properties
Figure A.1
(A.1).
The number of the components basically determines the dimension of a vector: 2-dimensional
(2 components) vs. 3-dimensional (3 components). The components are related to the
coordinate system in use. Figure A.2 shows vectors described in Cartesian coordinates.
Figure A.2
One can describe vector algebra in both graphically (using arrows) and with components.
The magnitude of the vector is the same as the length of the arrow shown in Figure A.2:
(A.2).
APPENDICES 135
A vector whose magnitude is unity (= 1) is called a unit vector (“eenheidsvector”). The unit
vector of vector v shown in Figure A.2 can be obtained by dividing the vector by its own
magnitude.
(A.3).
The unit vector of the axes in a coordinate system (unit coordinate vectors) can be expressed
as
(A.4),
where i, j & k (or ex, ey, ez) are the unit vectors of the X, Y & Z axes, respectively.
Vector algebra
(A.5).
If two vectors are equal to each other, all the corresponding components are equal to each
other:
(A.6).
Vectors of the same type can be added to yield the resultant vector. Adding two
vectors is equivalent to adding their components (Figure A.3):
Figure A.3
APPENDICES 136
(A.7).
As shown in Figure A.3, vectors a and b were connected tip-to-tail, forming two sides of a
triangle. The third side of the triangle is the resultant vector (c) drawn from the tail of the first
vector to the tip of the second vector. The sequence of addition is not important
(commutative):
(A.8).
Addition of more than two vectors can be performed similarly, two at a time:
(A.9).
As shown in Eqn. A.9, vector addition is associative. One can move the vectors freely to
connect tip-to-tail. The sequence of addition is not important.
(A.10).
APPENDICES 137
Figure A.4
Figure A.4 shows two equivalent graphical methods to find c. As shown in Eqn. A.10, vector
subtraction is a special case of vector addition.
Figure A.5
(A.11)
where d = a scalar multiplier. The vector lengthens when d > 1 while it shortens if d < 1. If d
is negative, the direction of the vector reverses. The vector operation shown in Eqn. A.11 is
commutative:
(A.12).
APPENDICES 138
(A.13).
Finally, let's revisit Figure A.2. As shown in Figure A.6, a vector can be expressed as
the sum of the component vectors:
Figure A.6
(A.14),
where i, j & k are the unit coordinate vectors of the X, Y & Z axes, respectively.
Vector multiplication
There are two different kinds of vector multiplication: the scalar product
(“inprodukt”) and the vector product (“uitprodukt”). First, the scalar product is defined:
(A.15).
The result of the scalar product is a scalar. It tells us something about the influence of
one vector on another vector. The scalar product is also called the dot product following the
product symbol used. It is commutative:
(A.16)
APPENDICES 139
and distributive:
(A.17).
(A.18)
As shown in Eqn. A.18, the square of the magnitude of a vector is the same to the scalar
product of the vector with itself. Let's apply this to the triangle formed by the three vectors
shown in Figure A.7:
Figure A.7
(A.19).
(A.20).
(A.21),
APPENDICES 140
where is the angle between the two vectors. So the scalar product can also tell us something
about the angle between the vectors. Eqn. A.21 is an alternative definition of the scalar
product, and from Eqn. A.21:
(A.22).
Another important vector multiplication is the vector product. It is also called as the
cross product following the symbol used and is defined as:
(A.23).
It is understandable why it is called the vector product since the result of this multiplication is
another vector. From Eqn. A.23:
(A.24)
and
(A.25).
(A.26).
APPENDICES 141
(A.27).
One very interesting thing here is the fact that the resulting vector from the cross product is
always perpendicular to the two vectors involved in the cross product:
(A.28).
The right-hand rule: the direction of the resulting vector is the direction a right-handed
screw advances when it is rotated from the direction of the first vector to the direction of the
second vector through the smallest angle between them.
From this right-hand rule the unit vectors are described as follows (see Figure A.6):
(A.29).
APPENDICES 142
Matrix properties
(A.30).
As shown in Eqn. A.30, a m x n (dimension) matrix has m rows and n columns. The elements
of the matrix are denoted by aij where i = the row number, and j = the column number. 3 x 3
and 3 x 1 matrices are the most commonly used types. A matrix with m = n is called a square
matrix. In a diagonal matrix which is also a square matrix, all elements except the diagonal
ones (i = j) are zero.
(A.31).
When a matrix is multiplied by a scalar, all the elements of the matrix are multiplied by the
scalar value:
(A.32).
Matrix multiplication
One of the most useful properties of the matrix is the matrix multiplication. Imagine a
system of linear equations:
APPENDICES 143
(A.33),
where a's & c's = scalars, and x, y & z = the unknowns. Eqn. A.33 can be rewritten as:
(A.34).
Eqn. A.34 is expressed in matrix multiplication form. The general form of matrix
multiplication is
(A.35)
or
(A.36).
Note that the number of columns in the left vector (n in Eqn. A.35) must be the same to the
number of rows in the right matrix. The dimension of the resulting vector is m (rows of the
left matrix) x p (columns of the right matrix) as shown in Eqn. A.35.
However, it is distributive:
c(a+b) = ca + cb (A.38)
APPENDICES 144
(A.40).
Matrix determinant
(A.41).
(A.42).
APPENDICES 145
Goniometry:
The tangens of an angle is defined as the ratio between opposite and adjacent sides of a
rectangled triangle en is therefore:
Thus:
Rotations:
Figure A.8
APPENDICES 146
Appendix B: 1H and 13C chemical shifts of common functional groups
APPENDICES 147
Appendix C: Random coil 1H chemical shifts for the common amino
acids
NH H H NH H H
S 8.38 4.50 3.88 For X in GGXA, pH 7, 35ºC (Bundi and Wüthrich 1979) .
APPENDICES 148
Random Coil Chemical shifts (in ppm) for the 20 common amino acids in acidic 8 M urea (from Wright, Dyson
et. al., Journal of Biomolecular NMR, 18: 43–48, 2000).
APPENDICES 149
APPENDICES 150
Appendix D: Nuclear Overhauser Effect
The population change of the -state, d/dt(n), after a disturbance from equilibrium
can be expressed using the W0, W1a, W1b and W2 rates. The rate equation is:
d
n (W1B W1B W2 )(n n eq
) W2 (n n
eq
)
dt (D.1).
W1 A (nA neqA ) W1B (n A n Aeq )
Thus, the -state looses magnetization (first term), but also gains some magnetization from
the -, the - and the -states.
Similar expression can be found for the time dependence of the other three states.
Now we look at the net population differences of spin A and B, nA and nB, resp. These are
d d d d d
nA n n n n
dt dt dt dt dt
(D.3a,b).
d d d d d
nB n n n n
dt dt dt dt dt
If we now introduce in Eqns. D.3 the results from Eqn. D.1 (and the expressions for the other
spin states) we can derive the dependency of the population from the transition rates:
d
n A (W0 2W1 A W2 )(n A n Aeq ) (W2 W0 )(n B n Beq )
dt
(D.4a,b).
d
n B (W0 2W1B W2 )(n B n B ) (W2 W0 )(n A n A )
eq eq
dt
It can be derived that the first terms of Eqns. D.4a and D.4b describe the T1 relaxation of spins
A and B, respectively:
1
A (W0 2W1 A W2 )
T1 A
(D.5a,b).
1
B (W0 2W1B W2 )
T1B
The second term of Eqn. D.4 results in transfer of magnetization from A to B. We define the
cross-relaxation between A and B as
= W2 – W0 (D.6).
APPENDICES 151
With this definition, from Eqn. D.4 we arrive at the Solomon-Bloembergen equations:
d
n A A (n A n Aeq ) (n B n Beq )
dt
(D.7a,b).
d
n B B (n B n Beq ) (n A n Aeq )
dt
Now let us return to the steady-state NOE experiment of Chapter 8. Spin B was
selectively saturated (nB = 0). After some time the two-spin system will reach a steady state
with
d
nA 0 (D.8).
dt
Eqn. D.7a then becomes
d
n A 0 A (n A n Aeq ) (n B n Beq ) (D.9),
dt
(n A n Aeq ) n B B
eq
(D.10).
n Aeq A n Aeq A A
Here we exploited the fact that the macroscopic magnetization MA is proportional to the
population nA, and that the populations are themselves proportional to the gyro-magnetic ratio
(Eqns. 2.8 and 3.1).
For identical nuclei A = B, and A = , and Eqn. D.10 reduces to the simple form
(D.11).
APPENDICES 152
Appendix E: 2D NOESY experiment
In mathematical terms the 2D NOE experiment can be described as follows. During the
evolution period the transversal magnetization of nucleus B can be written as
iB t
M B M Beq e 1 M
eq
B
cos( B t1 ) i sin( B t1 ) (E.1).
According to the Solomon equation (Eqn. D.7) we have for MA a dependency from MB
d
M A a ( M A M Aeq ) AB ( M B M Beq ) (E.3).
dt
For short mixing times m T1 A1 we can neglect spin-lattice relaxation and Eqn. E.3
becomes approximately
d
M A AB ( M B M Beq ) (E.4).
dt
M A AB M Beq 1 cos( B t1 )
d
Using Eqn. E.2: (E.5).
dt
M A
AB M Beq 1 cos( B t1 ) (E.6),
m
i t
During the detection period this evolves with e A 2 and after Fourier transformation
we will have a cross-peak at (B,A) in the 2D spectrum (F1, F2), correlating the protons A
and B in the 2D NOESY spectrum. The intensity of this cross-peak is
I ( B , A ) ~ AB m (E.8).
c
Since for biomolecules we have AB ~ 6
(E.9)
rAB
APPENDICES 153
Appendix F: Amino acid COSY, TOCSY and NOESY cross-peaks.
APPENDICES 154
APPENDICES 155
APPENDICES 156
APPENDICES 157
APPENDICES 158
APPENDICES 159
APPENDICES 160
APPENDICES 161
APPENDICES 162
APPENDICES 163
Appendix G: Typical chemical shift values found in nucleic acid
APPENDICES 164
Appendix H: Typical short proton–proton distances for B-DNA
All distances are given in Å. Sequential distances (to its 3' neighbor) below the diagonal,
intraresidual distances above the diagonal.
APPENDICES 165