NMR

Question 1

In 1D FT NMR

What is D1?

Answer 1

Relaxation delay

Question 2

In 1D FT NMR

What is T1?

Answer 2

Spin-lattice relaxation time

Question 3

In 1D FT NMR

What is T2?

Answer 3

Spin-spin relaxation time

Question 4

In 1D FT NMR

What is AQ?

Answer 4

Acquisition time

Question 5

In 1D FT NMR

What is PW?

Answer 5

Size of the flip angle

Question 6

In 1D FT NMR

What is TR?

Answer 6

Repetition time

Question 7

In 1D FT NMR

What does TR equal to?

Answer 7

D1+AQ

Question 8

If a quantitative spectra is to be acquired with a 90 deg flip angle WHAT should be set 5-7 times larger than WHAT

Answer 8

TR more than T1

of the slowest relaxing spin

Question 9

What does reducing the flip angle lead to?

2 points

Answer 9

1. Reduction in TR
2. Reduced sensitivity

Question 10

What is Earnst angle?

Answer 10

Optimal flip anfle for TR/T1 ratio

Question 11

Why is using a smaller value of PW benifitial to shorter relaxation time?

Answer 11

Not all the magnetisation is tipped into the xy plane, therefore it takes shorter time for the spins to relax back to equilibrium

Question 12

What happens to integrals if TR is too short

Answer 12

Wrong integral values

As not all the nuclei have relaxed back

Question 13

For spin-spin relaxation

Why is there no point to aquire the signal after 3T2

Answer 13

Noise dominates the signal

Question 14

What will happen to the resolution of NMR lines if T2 is too long?

Answer 14

Decreases, as noise domitates the signal, so fine structure of the lines is lost

Question 15

For applying weighted functions prior to FT

What does Lorentz to Gauss converstion do?

To peaks and S/N

2 points

Answer 15

1. Narrower signals
2. Better S/N than regular FID, worse than exponential curve

Question 16

For applying weighted functions prior to FT

What does exponential curve do?

To peaks and S/N

2 points

Answer 16

1. Exponential line broadening
2. Better S/N than regular FID and Gaussian

Question 17

EXSY

What does the exchange regime depend on?

2 points

Answer 17

1. rate of chemical exchange
2. chemical shift separation in Hz ,between the two peaks

Question 18

EXSY

What is rate of chemical exchange affected by?

Answer 18

Temperature

Question 19

EXSY

What is the chemical shift separation in Hz ,between the two peaks affected by?

Answer 19

Spectrometer frequency

Question 20

Coalescence temperature

Answer 20

Temperature when the 2 signals merge into 1 peak of rotamers

Question 21

Why does COSY/HSQC make it easy to determine rotamers?

Answer 21

Cross peaks are only observed between the same isomer

Question 22

EXSY

Why does NOESY show peaks even for different rotamers?

Answer 22

Due to mixing time, the configuration of the molecule changes

Question 23

EXSY

In 2D NOESY what do the positive peaks show when negative x-peaks indicate chemical exchange?

Answer 23

Proximity in space

Question 24

What is the basis of EXSY experiments in ligand-proteins

Answer 24

The basis of these experiments is the fact that the NH chemical shift is different in the free protein and in the complex, but only for amino acids that are part of the binding site or are in its vicinity

Question 25

What is NOE and what does it stand for?

Answer 25

The nuclear Overhauser effect (NOE) is the transfer of nuclear spin polarization from one population of spin-active nuclei (e.g. 1H, 13C, 15N etc.) to another via cross-relaxation

Question 26

Describe the properties of a small molecule ## Footnote 5 points

Answer 26

1. < 100 D 2. Short rotation correlation times 3. Long relaxation times (T1, T2) 4. Fast translational diffusion 5. Weak positive NOE

Question 27

Desribe the properties of biomacromolecule ## Footnote 5 points

Answer 27

1. > 5 kD 2. Long rotational correlation times, slow tumbling 3. Short relaxation times (T2) 4. Slow translational diffusion 5. Strong negative NOE

Question 28

How is binding of a ligand is detected? ## Footnote 2 points

Answer 28

* A small molecule behaving like a large molecule * Transfer of magnetisation from a macromolecule to a ligand

Question 29

What is the purpose of the T2 filter?

Answer 29

Keep the spins in the transverse plane where they relax

Question 30

Desctibe the process of obtaining a T2 relaxation edited spectra ## Footnote 3 points

Answer 30

1. Apply T2 filter to small molecules only, all signals will be preserved 2. Then apply the filter to protein + small molecules, some signals will be lost 3. Subtract 2 from 1, the binder becomes visible

Question 31

Advantages of selective excitation ## Footnote 2 points

Answer 31

1. Fast acquisition for 1D/2D spectra, as only area of interest is sampled 2. High digital resolution, allows to extract coupling constants

Question 32

Disadvantages of selective excitation ## Footnote 4 points

Answer 32

1. Automation is problematic 2. If too many signals need inspecting, it may be more efficient to acquire 2D spectra 3. If signals are not separated, selective excitation is more complex 4. Selective 1D or nonselective 2D 1H NMR experiments become problematic when significant signal overlap is present