 | The instructor will transfer all data to the chemistry server. You can also store data
on a floppy disk or zip disk. At any rate, the first thing that you need to do is locate
the NUTS program (normally, you can find it under the START key. A box should
appear and you should click "ok". Go to the file menu and select open. You can
open files from disks or from the server as follows: |
- Disk: go to the "a" drive for floppies and the "f" drive for zip
disks. Find the file you want to access, highlight it, and click on the open
button.
- Server: go to the network neighborhood and open the APOLLO server. To open
the APOLLO server in Smyth 243 you must go through the start menu to
programs to chemistry to nuts. Once in the NUTS program click ok and the program will
open. Go to file open, once there you must type h: to open the APOLLO
server. Then you can just pick the folder you need and obtain your spectra. To obtain data
from the chemistry library computers you go to start to programs to NUTS.
Then follow the same procedure except when you are supposed to type h: you type g:
Open it and you should see a number of folders that contain individual files. Several
folders should appear on this server labeled including the one for your class.
Your raw data (FID) will be transferred into the appropriate folder and
will have the following associated string:
OCM _ _ _ _ _._ _ _ _
The space following the "M" will contain letters that
designate the nucleus of interest (H or C). The next four spaces will specify the
student(s) involved. The last four spaces will contain numbers corresponding to the date
of acquisition of the raw data. For example:
OCMHBTSD.0615
This is an organic chemistry file (OCM), proton (H) NMR FID, that was
run by a pair of students, Barry Trost and Samuel Danishefsky (BTSD), that was acquired on
June 15th (0615).
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| Double click on the file you wish to open. At this point, you will be asked if you want
to auto detect import the file. Choose "yes". You should see your raw
data as a FID. |
|
| Fourier transform your FID by typing FT.
|
|
| Type QP to automatically phase the spectrum. NOTE: If this procedure does not
work then you’ll have to perform a manual phase. |
Manual phase: Type ZP. Enter the ZOOM subroutine by
double clicking the left mouse button. Highlight (using the right mouse
button) one peak at the far right end (upfield) of the spectrum and type 1. Next,
highlight one peak at the far left end (downfield) of the spectrum and type 2. Exit
the ZOOM subroutine by hitting ENTER. Now, enter the Phase-Expand subroutine by
typing PE. Hold the right mouse button down and move it in either direction
until the peak looks phased. Next, hold the left mouse button down and move it in
either direction until the peak looks phased. Exit this subroutine by hitting ENTER.
|
| AN IMPORTANT NOTE: If you are working up data for 13C NMR,
it is important to weigh the FID and introduce some line broadening prior to Fourier
transformation of the data. This process improves the signal to noise ratio and eases the
phasing process. From the Process menu, choose "conditions". Click in the
small box labeled LB and enter the value "2.5". Click "ok"
and then type EM. You can continue with the normal processing by typing FT
followed by QP. Reference your spectrum, to reference your carbon NMR you must pick
the triplet peak that can be found on the spectra. If you zoom in on them you can see that
they are three individual peaks of the same height. Make sure you are out of zoom mode and
put your cursor on the middle peak. Click and hold the left mouse button and type v, a box
should come up, in that box you will see a group called point. Choose the bottom one and
type 78. This will reference your carbon NMR to 78. |
|
| To expand a spectrum, double click the left mouse button to enter the ZOOM
subroutine. The cursor will change appearance (will now look like cross-hairs) with a ZO
near its base. Click and hold the left mouse button and drag across the spectrum to
highlight the region of interest. Click the right mouse button to expand and click
a second time to return to full scale. You can exit this subroutine by hitting ENTER. |
|
| In order to properly reference your TMS peak, you need to enter the ZOOM subroutine (as
directed in step 5) and choose a spectral window that ONLY shows the TMS peak. The TMS
peak will (for the must part) be the peak that is located farthest to the right. Once the
window has been set, type SZ, followed by ENTER and your spectrum will be
referenced to TMS (0 ppm). |
|
| In order to integrate your spectrum, choose "Integrate display" from
the Process menu (or alternatively type ID (this gets you into the integration
subroutine). Go to the Edit menu and choose "Clear broken integrals".
Click the left mouse button one time to get a red cursor line. Position the
cursor with the mouse to the left of the peak you wish to integrate. Click the left
mouse button a second time and move the cursor to the right of the peak. Click the left
mouse button a third time and the integral should appear on your spectrum. Repeat
this three step process for all peak regions of interest. If you make a mistake, clear
the integrals and start over. |
|
| To normalize the integral values, place the cursor on the integral line (of interest),
hold down the left mouse button, and type v. A box will appear on the
screen. You will want to enter the appropriate value into the "current relative
value" box followed by ENTER in order to set the integral to that value
and to normalize all other integrals relative to that value. You can now exit the
integration routine by going to the File menu and choosing "exit ID". |
|
| To obtain a list of the chemical shift of every peak in your spectrum (this process is
called peak picking), enter the ZOOM subroutine and type PP. To set the threshold
level to a different value, hold down the left mouse button and move the horizontal
line to the top of the smallest (reasonable) peak and type M (while still holding
down the left mouse button). If you want to view the peak list, type CB. |
|
| To print your spectrum (or any of the close up regions), select the
File menu and choose Print.
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