The NMR PChem Lab

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The NMR PChem Lab
This userguide is to help you Get your NMR data
from the Unix world into Windows Work up the
spectra and understand where to look for the
relevant numerical data. Get the quantitative
results into a Word document. Carry out the
computations and error analysis.
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Transfer your Raw Data
This will put it onto the Local PC in a Drive
location you specify. It only needs to be done
once Best practice is to make a folder for
yourself, then back this up to floppy or USB
stick, so your data is secure The raw data from
the spectrometer (in folders) is in a format
particular to the NMR machine. You will not be
able to open it directly. You can import this
data into the NUTS format, and save the converted
form. Even this converted data will only be
openable by the NUTS application.
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Next, Process the raw FID data to make it
interpretable
The NMR data Processing program is a Windows
application called NUTS. Its icon is on the
desktop, and looks like an acorn. Double click
the icon
Pull down FileRunMacro
In NUTS, a macro is in place to translate the raw
data into NUTS format, and process it from a time
into a frequency (ppm) scale.
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Open the Macro, and give it some information
This Macro will ask you for a file name. Remember
where you put the raw data? Navigate to the file,
and drill down until you find the entry
Proton.fid. Open it! Then open the file called
fid.
There are many macros in the folder. Guess which
one we will be using! Select and click the open
button.
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The Spectrum should convert and open as a
frequency display
The NUTS screen has a spectrum displayed. This
might be a good time to Save the converted
file! (put with your other folders)
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Use the slider Bar to increase the Vertical scale
of the display
We may see that the phase (level baseline going
into, out from all peaks) is not totally correct.
This can influence the numerical result we are
aiming toward
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Touching up the Phase
3. Use Enter key to leave the ZO subroutine.
Now click back onto the screen, put the red
cross-hair on any peak near the right side of the
display. While holding the mouse there, type P
Step 1. Use the Zoom in tool from the View
pulldown.
2. Let up on the mouse, and move the cross-hairs
into the rectangle. Then click once with the
right mouse button
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Now type PH and enter the phase fixing
subroutine
1. Hold down the LMB, and drag mouse back and
forth to level the baseline in the right-hand
part of the data
2. Hold down the RMB, and drag mouse back and
forth to level the baseline in the leftt-hand
part of the data. Then push Enter to leave the
phase subroutine.
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Now we have a Respectable Data Set. Lets look
at the data from a Chemists point of View.
There are lots of peaks, collected into
multiplets with fine structure. The chemical
shift regions are tied to the electronic
environment of each kind of hydrogen atom. We
can also see that there are some of the clusters
that are large and others that are consistently
small. This is because there are now two forms
of the compound present. The ratio is not 11.
Each kind of hydrogen has a major and a minor
representation in the mixture
CH3s, CH2?, CH2? and acetone solvent all
overlapped.
CH2?
CH?
m,M
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Only part of the Spectrum shows peaks from the
Major and Minor forms separated enough to
quantify them clearly.
Lets ZOom in.
The ?, and ? region expanded.
After the phase is fixed, type at the gtprompt BF
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Now we use the Integration tool to evaluate the
areas in the key regions
A level trace appears, rising up as it measures
area under a peak. Note a new slider bar, can
rescale the integration trace.
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Staying in the Integration Subroutine, lets make
it quantitatively useful!
The resets on the trace sets the baseline back to
zero and eliminates having to draw lines with a
pencil and measure with a ruler. The quantity
that has to be measured is the rise between the
two level lines.
Double click LMB here, to lay down the green
line, then move cursor past peaks and click the
stop point. A sectioned out integration appears.
Repeat the process for the other clusters.
Dont hit the Enter key until you want to leave
the integration subroutine.
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Lets get the computer to do some work for us!
In the dialog box, set the value for this peak,
e.g., as 1.00. Units are arbitrary scale factors
and all the peaks will be uniformly corrected.
Drag the cursor (red line) into one of the
isolated peak regions. (dont click) Type V
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Now we have some numbers
Lets save the processed data to disk, then copy
the annotated picture to a WORD doc, that you can
take home and work on
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Working up the Data
Make a spreadsheet, and insert into adjacent
columns the area for comparable Major(trans) and
Minor(cis) forms
Solvent Area t Area c Kt/c
acetone 1.00 0.26 3.85
(trial1) 2.28 0.56 4.07
(mean)
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Propagation of the Indeterminate Error
The numbers you extracted here are really the
NMRs estimate of the molarity (in a relative
sense, ) of each kind of hydrogen. (The
quantities are all contained in the same volume
of solution). Depending on the spectrum, the
peaks are whole number integer multiples of 1
H. For example the data here gives an integration
of 1.0 for the alpha H and 2.28 for the two delta
Hs. So the second value is really 1.14 (2.28/2)
per H. The Keq we need here is a calculated
quantity Kt/c
As we see above, t is available, but our
several measurements show some scatter in the
quantity. We must compute the way that this error
is transmitted into the calculated result. Error
is transmitted into calculated values resulting
from multiplication or division of measureables
according to the following equation The s values
are standard errors of the quantities.
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Lets do an example
t values per H 1.00, 1.14, 1.16, 0.98 c
values per H 0.26, 0.28, 0.25, 0.30 For t, mean
is 1.07, s 0.93 For c, mean is 0.27,
s0.022 Kt/c 3.96
And sK 0.47 K3.96 ? 0.47
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Points for discussion in your lab Report
Although we know (from the literature) that the
dominant form in all the solvents is the trans,
some questions remain What are the chemical
differences among the solvents? (polarity,
acid/base, hydrogen bonding) What are the
chemical differences between the cis and trans
forms of acetyl proline? Does question 1 have any
thing to to with question 2? Can we make any
sense of the positions in the NMR spectrum of the
related cis,trans partner H atoms?