TopSpin NMR Training Courses Manual.ppt

Topspin manual

1. Dr. Sandra van Meurs
Bruker BioSpin Ltd, UK
[email protected]
TopSpin
TopSpin Training Course, 22
nd
November 2006

2. Overview
•Introduction to TopSpin
•Acquiring data through IconNMR
•Processing data
•Plotting/storing data
•Interpretation –a worked example
•Questions

3. What is the same?
•Before looking at the new features it is worth mentioning what
has not changedin TopSpin:
-Parameters and Data format: you can still process
TopSpin data with XWINNMR (not from AVII hardware)
-Most text commandsare either the same or aliased to the
equivalent TopSpin command (i.e. you still type efp, …)
-IconNMRhas a few new features, but broadly remains the
same –automation users will not need re-training, and
most will never notice any difference!
-XWINPLOTis essentially the same, so if you are already
using it in xwinnmr you are ready for TopSpin Plot Editor!

4. What is New?
•Integrated data browser
•Command line history (and concatenation)
•Configurable interface
•Full support for handling multiple datasets
•New interactive tools for Phasing, Integration, Peak Picking,…
•Interactive guides (acquisition, processing, relaxation,…)
•Acquisition status bar and tools
•Extendable via AU programs, Python programs, etc.
(including access to user interface)
• …and much much more!

5. Acquiring Data
•Sample preparation is key
•Selecting the right experiment:
-What information do you need?
-Which experiment(s) will give you this information?

6. IconNMR

7. Manipulating your experiment

8. Main types of experiment
ProtonCarbon HMQC/
HSQC
COSY HMBC NOE
1H 13C 1H-13C
correlation
1H-1H
correlation
Long range
1H-13C
correlation
Through
space 1H-1H
correlation
1 -5 mg5 –25
mg
5 –10 mg1 –5 mg5 -10 mg 1 –5 mg
1 –5 min10 –30
min
10 –20
min
5 –10 min10 –30 min2 min –6
hours*
OH
HH
H
H
H
H
H
OH
CH
2
H
2C
CH
3
C
OH
HH
H
H
H
H
H
C
C
C
OH
HH
H
H
H
H
H
C
C
C
OH
HH
H
H
H
H
H
C
C
H
H

9. 7.57.06.56.05.55.04.54.03.53.02.52.01.51.00.50.0 ppm
3.153.002.081.031.00 Example of a PROTON spectrum
3H
t
J = 7.1 Hz
3H
dd
J =1.7, 6.9 Hz
2H
q
J =7.1 Hz
1H
dq
J =1.7, 15.5 Hz
1H
dq
J = 6.9, 15.5 Hz
Me OMe
O
1
2
3
5
6
4
2 3 15 6

10. Example of CARBON spectraC13DEPT45
170160150140130120110100 90 80 70 60 50 40 30 20 10 0ppm
170160150140130120110100 90 80 70 60 50 40 30 20 10 0ppm
170160150140130120110100 90 80 70 60 50 40 30 20 10 0ppm
170160150140130120110100 90 80 70 60 50 40 30 20 10 0ppm
C13CPD
C13DEPT135
C13DEPT90
C13DEPTQ
4 5
1/6
2/3 2/3
Me OMe
O
1
2
3
5
6
4

11. ppm
1.01.52.02.53.03.54.04.55.05.56.06.57.07.5 ppm
1.0
1.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
5.5
6.0
6.5
7.0
7.5 Example of a COSY spectrum
Me OMe
O
1
2
3
5
6
4
2 3 15 6

12. ppm
1.01.52.02.53.03.54.04.55.05.56.06.57.07.5 ppm
140
120
100
80
60
40
20
0 Example of an HSQC spectrum
Me OMe
O
1
2
3
5
6
4
2 3 15 6

13. Example of an HMBC experimentppm
1.01.52.02.53.03.54.04.55.05.56.06.57.07.5 ppm
200
180
160
140
120
100
80
60
40
20
0
Me OMe
O
1
2
3
5
6
4
2 3 15 6

14. An introduction to processing
•Most spectra run through IconNMR will be processed
(and perhaps printed) already
•You could simply open the processed spectrum and look at
the data
•You could reprocess -fundamentally:
-multiplier, Fourier transform and phase
(more on this later)
•Then you can integrate, peak pick, calibrate etc.

15. Data Display Buttons
Vertical
position
Hz or ppm
Horizontal
position
Vertical scaleHorizontal scale
grid
•Buttons seen will depend upon data-type (1D or 2D),
and any customisation!
Measure
distance
Retain
scale
Last
expansion
Y-scale
All
File handling, print,
copy/paste, last 1D/2D/3D
datasets
See later…

16. Processing 1D data
•Processing guide (automatic/manual)
-Processing -> Data Processing Guide
•Command line automatic: “xaup” –this will probably
also print a spectrum
•Command line manual: em, ft, apk/apks
•Button: if you have one set up….
…of course you could set one up…

17. Processing 2D data
•Processing guide (automatic/manual)
-Processing -> Data Processing Guide
•Command line automatic: “xaup” –this will probably
also print a spectrum
•Command line manual: xfb, abs1, abs2
•Button: if you have one set up….
… of course you could set one up …

18. Other Buttons –interactive menus
phase
correction
calibratio
n
baseline correction
peak picking
integration
multiple display
zoom overview

19. Output
•Printer icon
•File -> Print
•Ctrl P
“screen dump”

20. Worked example0.60.70.80.91.01.11.21.31.41.51.61.71.81.92.02.12.22.32.42.5 ppm
6.233.192.031.071.031.001.001.00
1
H spectrum
DMSOO
CH
3
CH
3
CH
3
H
H
H
H
H
H
H
1
2
3
4
5
6
7
A B
C

21. ppm
0.81.01.21.41.61.82.02.22.4 ppm
10
15
20
25
30
35
40 HSQC
CH
CH
3
CH
2O
CH
3
CH
3
CH
3
H
H
H
H
H
H
H
1
2
3
4
5
6
7
A B
C

22. HSQC expansionppm
1.81.92.02.12.22.32.4 ppm
41.5
42.0
42.5
43.0
43.5
44.0
CH
CH
3
CH
2
1O
CH
3
CH
3
CH
3
H
H
H
H
H
H
H
1
2
3
4
5
6
7
A B
C

23. COSYppm
1.21.41.61.82.02.22.4 ppm
1.2
1.4
1.6
1.8
2.0
2.2
2.4
1
2
3 5 4
6
7O
CH
3
CH
3
CH
3
H
H
H
H
H
H
H
1
2
3
4
5
6
7
A B
C

24. HMBCppm
0.81.01.21.41.61.82.02.22.4 ppm
10
15
20
25
30
35
40
45
50
55
1
2
3
5 4
6
7
CH
CH
3
CH
2
C
CO
CH
3
CH
3
CH
3
H
H
H
H
H
H
H
1
2
3
4
5
6
7
A B
C

25. 2D NOESYppm
0.70.80.91.01.11.21.31.41.51.61.71.81.92.02.12.22.32.4 ppm
0.8
1.0
1.2
1.4
1.6
1.8
2.0
2.2
2.4
1
2
3 5 4
6
7
C

26. 2D NOESY expansionppm
1.51.61.71.81.92.02.12.22.32.4 ppm
0.75
0.80
0.85
0.90
0.95
1.00
1
2
3 5 6
C
A
BO
CH
3
CH
3
CH
3
H
H
H
H
H
H
H
1
2
3
4
5
6
7
A B
C

27. 1D selective NOESY 0.70.80.91.01.11.21.31.41.51.61.71.81.92.02.12.22.3 ppm
1
23
5
4
6
7
CB
AO
CH
3
CH
3
CH
3
H
H
H
H
H
H
H
1
2
3
4
5
6
7
A B
C

28. Interpretation summary
•Techniques

13
C NMR
DEPT variations

1
H NMR
COSY
HSQC/HMQC
HMBC
NOESY (1D and 2D)
•Key Uses
Chemical environment, carbon count
Multiplicity determination
Chemical environment, quantification
Spin-spin coupled nuclei
Directly bonded
1
H and
13
C

1
H and
13
C correlation across multiple bonds
Interactions through space

29. Summary
•Think about data you need … don’t waste instrument time by
submitting every sample for all experiments
•Remember sometimes you can obtain C13 chemical shifts
from combination of 2D spectra when sample is limited
•Use processing guides !!
•Remember you can create a button for tasks you often repeat
•“Save” is implicit in TopSpin –any processing changes you
make will be remembered for next time
•“Prnt” gives you quick and dirty screen dump
•Plot Editor gives you pretty spectra for hard/electronic copy
• ………….any questions??