The following is a description of the use the automation features of the AM-400 with and without the use of the sample changer.
One can program the complete operation of the spectrometer for acquiring data on one, or several sample(s), with one or more experiments each, and processing and plotting of the result(s). It is possible to change samples, activate the lock system and autoshim the field for each sample.
1 to 60 samples can be loaded. The blue spinners must be used and the sample inserted as usual. Push the -> or <- buttons to advance to sample position 55. It is best to place the samples starting at the first empty position (usually position 1).
It is best the prepare samples to have the same volume and same type tube for the shimming to finish quickly. If samples with different solvents are to be run, they should be grouped according to solvent. Again, this should speed up the shimming.
Depending on shimming time, 6 or more proton samples can be run per hour. This includes plots with integration and a peak printout. The carbon POWGATE experiments are set up to run for about 25 minutes. The BB and DEPT90, -135 take about an hour. If you want to shorten the number of scans, think how long this will take compared to running the default number of scans.
First, use `EXE NOBAR=D1' to set up the sample changer for use without Bar Code reader. Push the reset button on the sample changer front panel.
It might be preferable to lock and shim the first sample manually; the automatic shimming can take much time if the shims are far from optimal. If you manually place the first sample in the magnet, place the standard sample in an empty sample changer position. It will be put in the magnet after the last sample is run.
NOBAR has selected DU=D1 for Job 1 and DU=D2 for Jobs 2 and 3.
Press the F1 key (or in Job 1 type SET).
"ENTER A 4-CHARACTER CODE TO IDENTIFY YOUR DATA SET"
The first question requests a 4-character Code. Use your NMR Code.
"PROBE ID?"
The Probe ID is 1 for the QNP, 2 for the BB probe. To change it, type C (NOT <cr>!!) or press `ESC'. Select the probe with the arrow keys or the +, - buttons. Type <sp> (space bar).
"DO YOU WANT EASY SET UP DIALOGUE?"
If answer `Y', the simple menus will be presented. No parameters (e.g. NS) can be changed.
"SAMPLE NUMBER"
The numbers can range from 101-160 (60 samples), 201-260 etc. to 901-960. The first digit (1-9) allows for a user to keep older data which would otherwise be overwritten. If e.g. J123 has used 101 and wants to keep the FID's, J123 201 can be used.
The Experiment Number (0-9) is incremented if more than one experiment is to be performed on this sample, e.g. 1D Protons followed by Carbon BB, DEPT90 and 135. Answer `0' to the Number question.
"ENTER SAMPLE NAME"
1 to 8 letters can be specified. The name will be plotted as part of the parameters.
"EXPERIMENT"
If you answered `N' to the easy setup question, a more elaborate dialogue will follow. If you answered `Y', the choice of the currently available experiments will be displayed.
"SOLVENT"
This routine contains a bug; the current solvent may or may not be properly displayed. To be safe, press `ESC' and pick the solvent.
"PLOT TITLE"
Enter the title as you would for the `TI' command.
"SET UP ANOTHER EXPERIMENT?"
Experiments can be combined. A proton experiment could be followed by a phosphorus experiment etc. Answer `N' if no other experiments are desired.
"SET UP ANOTHER SAMPLE?"
Enter `N' to quit adding samples. For additional samples, answer e.g. `*5 `for 5 samples total, do NOT answer `Y'. If you mistakenly answered `Y', go through the dialogue and answer `*n', where n is the number of samples remaining.
"ENTER SAMPLE NUMBER: 102":
The sample number is incremented by one for each sample. Press `<cr>'
"ENTER SAMPLE NAME"
As above.
"ENTER PLOT TITLE"
The number, name and title question will be repeated until the number of samples specified is reached. Start acquisition as described below.
The following dialogue will be activated in addition of the one described for the "easy" setup:
"CHANGE ANY PARAMETERS?"
Unless you can interpret the meaning of the top blue status line, this question should be answered `Y'. Select the Probe, Nucleus, Experiment(s), and Processing (using `C' or `ESC', point, <sp> etc.).
"SET UP SOLVENT PARAMETERS?"
This question should always be answered `N'. If by mistake `Y' was answered, enter <cr> to all numbers.
Next, several processing and plotting parameters are prompted for. There is no way to bypass this if you start it.
"CHANGE ANY OTHER PARAMETERS?"
Any acquisition or processing parameter can be changed. D1, NS, PEN etc. can be modified. EXPT will give you an estimate of the time required. Once all parameters are set, type `EX' to get back to the menu.
Additional experiments can now be set up for this or other samples. Answer `Y' to "set up an other experiment" if you want to combine experiments.
"SET UP ANOTHER SAMPLE?"
From here on, the dialogue proceeds as in the "easy" setup mode.
Press the F2 function key or type `RUN'.
"START DATA ACQUISITION?"
`Y' to start.
"SAMPLE NUMBER"
Enter the number (e.g. 101) of the first sample in the series.
"EXPERIMENT NUMBER"
Normally the first experiment would be specified. Enter `0'(NOT 1!).
"4-CHARACTER CODE"
Confirm the previously selected code with <cr>. If the sample is in the magnet it must be locked and spinning (and shimmed). If not, the standard sample is ejected and your sample(s) will now be put in the magnet.
"START DATA EVALUATION AND PLOTTING?"
This question appears as soon as the first sample is locked. Answer `Y' to initiate the processing. As soon as the first acquisition is completed, the processing and plotting starts.
All acquisitions are done in Job 2, all processing is done in Job 3.
By typing `SET' again, the parameters for a sample can be changed by repeating the setup dialogue if that sample's run has not yet been started. One or more samples can be changed this way. It is also possible to add more samples while a run is in progress. This can be done at any time.
For 1D experiments the FID is stored on D2 (see at the very beginning) in the following format:
CODE#F.### CODE is your NMR code. #F is for experiment 0-9, FID. .### is the sample number, 101-160....901-960 etc. For SER files (includes BB, DEPT90, -135) the file name is CODE####.SER where # ### is | | | / \ \_________ 0-9 / \ 101-160 | Spectra are stored (if part of the setup) as CODE#0S.### or CODE####.SMX
The combined BB, DEPT 90, -135 uses 2 x NS for the BB spectrum to get reasonable S/N for quaternary carbons. All three spectra are automatically plotted on the same page.
Notes to Software Features:
For a better understanding about automation it is suggested that you read the description of the following commands (DISNMR Manual): AZF, APK, SREF, ABS, PC, ISEN, CLFP, CPXI
Select QNP or BB Probe:
Bruker NMR Software PROB ENGL Menu-Vs:850101
TABLE OF PROBEHEAD IDs
----------------------
1 - 5 MM QNP (1H/13C/31P) [01
2 - 5 mm BB [02
<- this is invisible on
the screen, it is used
by the program.
The list is too long to include here. Note that at present (March 3, 1988), only protons and carbon are set up.
This Menu lists the "Experiment" (I don't like this nomenclature).
Experiment means: Acquisition .AU program and
Processing .AU program.
For Protons, the (invisible on the screen) PRO is used. It consists of X00.AU for the acquisition and PR1D.AU for processing.
Bruker NMR Software STAN ENGL Menu-Vs:88615
STANDARD EXPERIMENT TABLE MOD 6/15/88, RN
-------------------------
@1 ` & ` MEANS IT IS SET UP AND WORKING. 2/23/88, RN
@1 &PRO - @7 Standard proton [PRO
@1 &PCA - @7 Standard proton followed by C13 [PCA
@1 &CAR - @7 Standard C13 [CAR
@1 &DE4 - @7 CARBON BB, DEPT 90 + DEPT 135 [DE4
@1 &PHS - @7 P31 DECOUPLED, NO NOE [PHS
@1 &PDC - @7 1H, 13C BB, DEPT-90, -135 [PDC
PCS - Proton, then C13 with
S/N check. 100 to 10k scans [PCS
BSH - SAMPLE SERVICE [BSH
ABN - " " [ABN
@3 Candidates for inclusion:
COS - Standard Cosy45 [COS
PCO - Standard proton followed by cosy45 [PCO
CHC - 2D-XH-Correlation [CHC
COP - DQ Cosy phase sensitive [COP
HSN - Proton acquisition with S/N break up [HSN
CCN - CONOESY
@3 Not considered unless requested:
JRE - 2D-J-resolved [JRE
DE1 - STANDARD DEPT ALL POSITIVE [DE1
DE2 - STANDARD DEPT CH ONLY [DE2
DE3 - STANDARD DEPT CH,CH3+, CH2- [DE3
DS1 - Dept CH only half page [DS1
CDE - C13-Dept-CH only [CDE
The solvent list is shown below. We had to make some assumptions as to which peak to lock on for solvents with more than one peak. If you find that our choice is not optimal, please let us know and we will work on it. The reference shift might need to be slightly adjusted for a given solvent. If you find that the automatic referencing is consistently off we can adjust it as well.
Bruker NMR Software SOLV ENGL Menu-Vs:880303/RN
TABLE OF SOLVENTS @7 Reference used (ppm):
----------------- @7 H 13C
THF - tetrahydrofurane-d4 @7 3.60 67.4 [18
Tol - toluene-d8 @7 2.09 20.4 [19
CD3CN - acetonitrile-d3 @7 1.93 1.3 [03
DMSO - dimethylsulfoxide-d6 @7 2.49 39.5 [12
D2O - deuteriumoxide @7 4.65 xx x [06
C6D6 - benzene-d6 @7 7.15 128.0 [04
CDCL3 - chloroform-d @7 7.25 77.0 [05
Acetone - acetone-d6 @7 2.04 29.8 [02
MeOH - methanol-d4 @7 3.3 49.0 [15
CD2Cl2 - methylenechloride-d2 @7 5.33 53.8 [16
Pyr - pyridine-d5 @7 7.55 29 [17
DMF - dimethylformamide-d6 @7 2.91 162.7 [11
EtOH - ethanol-d6 @7 1.1 56.8 [14
@3 TFA trifluoroacetic acid-d {20 |These are not set
@3 Dioxane dioxane-d8 {|up but can be added
Below is a list of the experiments presently set up; the ones we will work on next and the ones we consider not to be useful. Note that before we work on the next series, we need some feedback on the present choice of parameters etc. It takes a substantial amount of work to implement even the slightest change.
Bruker NMR Software XNUC ENGL Menu-Vs:880531 UCB Berkeley
EXPERIMENT TABLE
----------------
@7 Ready to use: Approx. Time: Name:
0 - @7 1D Protons Shim Z1 Z2 Z3. 16 scans X00 [X00
1 - 1D DECOUPLED S/N CHECK CARBON 1 HR X23 [X23
2 - @7 1D Decoupled (POWGATE) Shim Z1-2 25 min. X02 [X02
3 - @7 1D Decoupled (POWGATE) No Shim 25 min. X03 [X03
5 - @7 1D Inverse Gated Decoupling, No NOE 10 min. X05 [X05
10 - @7 CARBON BB, DEPT90 and 135, SHIM Z1-3 1 Hr Z56 [Z56
10A - @7 CARBON BB, DEPT90 & 135, NO SHIM 1 Hr Z57 [Z57
@5 To Follow:
23 - 1D Decoupled (POWGATE) S/N check To 12 Hr X23 [X23
1 - Proton experiment, shim on Z1 Z2 X01 [X01
11 - T1 measurements homonuclear Z11 [Z11
13 - 2D X,H correlation Z13 [Z13
17 - 2D COSY 45 Z17 [Z17
18 - 2D COSY DQ phase sensitive Z18 [Z18
30 - CONOESY
22 - 1D Protons with S/N check X22 [X22
@5 Not Considered:
7 - Dept tertiary only OH??!! APRIL 1 1989 [X07
8 - Dept, all positive [X08
9 - Dept, primary+tertiary pos.,secondary neg. [X09
15 - 2D relayed coherence transfer [Z15
20 - 2D NOESY phase sensitive [Z20
21 - 2D J-resolved homonuclear [Z21
The following processing routines are set up:
Bruker NMR Software XNUC ENGL Menu-Vs:880226
PROCESSING EXPERIMENT TABLE
---------------------------
@7 Working:
1 - @7 1D processing. Plot w. Integ. PP PRD1 [PR1D
6 - @7 BB, DEPT90 -135 Proc. Plot BB, DEPT PRD6 [PR6
@4 To Follow:
2 - 2D processing [PR2D
3 - 2D processing with SYM [PR2S
4 - DEPT PROCESSING WITH PK SMALL PLOT [PR4D
5 - DEPT PROCESSING PLOT STANDARD PK [PR5D
Note that the proton processing requires the printer to be active for peak print out!
The BB and DEPT Processing includes peak labeling on the plot.
On D1, there will be the journal and parameter files. Data files will be on D2 or D3. For example, the Code "CLON" was used to run five samples:
On D1:
CLONJOUR.NAL [ 8K] 13.DEC.93 $SS
CLON0X .101 [ 1K] 13.DEC.93 $SS
CLON0X .102 [ 1K] 13.DEC.93 $SS
CLON0X .104 [ 1K] 13.DEC.93 $SS
CLON0X .105 [ 1K] 13.DEC.93 $SS
CLON0X .103 [ 1K] 13.DEC.93 $SS
On D3:
CLON0F .102 [ 32K] 13.DEC.93 $SS
CLON0F .103 [ 64K] 13.DEC.93 $SS
CLON0F .101 [ 32K] 13.DEC.93 $SS
CLON0F .105 [ 64K] 13.DEC.93 $SS
CLON0F .104 [ 64K] 13.DEC.93 $SS
Since the field drifts, the filed entries in the PREFILE.999 need to be updated. The Pascal program PREFSET is used. After locking on CDCl3, run PREFSET (from the terminal connected to the 2nd region or from the console) and enter the FIELD value on the SCM.
The PC near the AM-400 can be used to set up a run. From the `NMR' group, run BARF12. An A/B switch on the serial port is used to connect the PC in parallel with the Bruker keyboard. (Please disconnect this after you are done.) BARF is written in Pascal, and has not been updated for some time. Some error messages regarding the Bruker not responding are not important. The `Start a Run Later' feature is not working. It was meant to interface to ResLog; but this was not completely implemented.