Department of Chemistry NMR Facility
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Mestrec23 1-D NMR Instructions1. VIRTUES OF THE SOFTWARE---The most useful feature of this software is its ease of use and exporting images to other documents(i.e. pdf, word-processing and spread sheets). When you have the spectra displayed as you want just copy it by typing Crtl-c or Edit-->Copy from the main menu (you can also use the copy icon on the tool bar). In MS Word go to Edit-->Paste Special then OK. You can use the paste icon on the tool bar for the same process (Crtl-v works also). If your PC allows you to redirect your printer to output in pdf format then you can send NMR spectra to others without NMR processing software. Since one can zoom in and out using the zoom tool in a pdf document one does not need specialized software.2. VICES OF THE SOFTWARE---One should realize that each program has its own unique way of accomplishing certain tasks. Here are a few things you MUST keep in mind when using this program to minimize frustrations:
3. OBTAINING A COPY OF THE SOFTWARE---(download Mestrec23 software)This program is shareware (for non profits) and can be freely distributed. Also: At the NMR PC you can make use the CD burner and copy the folder named "NMR Installation Programs". Now you can extract the 1D and 2D processor to your CD.SELECTING SPECTRA--- The most common problem you may encounter is applying an action to spectrum, which is not the intended spectrum. When displaying multiple spectra, as in an expansion or a stacked plot, you can select and manipulate spectra independently by clicking on the baseline of the spectra you want to manipulate. You can also press the Tab key to toggle between spectra. You must also pay close attention when selecting a spectra with the mouse because the x axis is also independently selectable. The program indicates the currently selected spectrum with a symbol. The default symbol is @ but others are available in the Edit-->Spectrum Properties-->Display Properties->Show Icon on Active Spectrum. APPLY TO ALL SPECTRA--In many of the options look for “ Apply to all spectra”. This option is always available on the bottom tool bar and useful when working with stacked plots EXPANSIONS---When displaying an expansion the program moves the original axis to the middle of the screen. You must move it back below the original spectrum. TOOLBAR---When using the toolbar you must replace a tool after its intended use on the selected spectra, otherwise you will reply the tool. An easier route to replacing a tool is to press the ESC key. KNOWN BUGS---If one is working on an expansion and tries to pick peaks and integrate peaks in the expansion the program will crash. One should separate these tasks into two different spectra (i.e. integrate the original spectra and peak pick in the expansion or vice versa) 4. OPENING FILES: ON THE PC FROM THE BRUKER 300---Double click on the 1D NMR Processor icon on the desktop. To open files click on the Folder icon on the tool bar or go to File-->Open. Click on the black triangle in the “Look In” text field and choose the drive called Bruker 300 (the H drive). Find the folder with your login ID and open the NMR folder. Find the experiment you are interested in open the file named fid. You should see an fid on the screen.
If the data is archived to a CD then simply find it like any other file using File-->Open then navigating the directory structure to find the FID of interest.
5. PROCESSING---One can apply a window function or line broadening before transforming by using the corresponding icons on the toolbar. If the file was generated through Icon-NMR a window function and line broadening have already been applied. Once you see the fid click on the FT icon (on the toolbar) and click OK. You can manually phase (6th icon from right) or auto phase (5th icon from the right). To manually phase display the entire spectrum (increase intensity of peaks to see the baseline, directions below) and click the manual phase icon. In the phasing window adjust the zero and first order phases with the dials. You can move the pivot point with the slider bar to the largest intensity peak. Remember the zero order phase will have the most change close to the pivot point and the first order phase will have the most effect on peaks far from the pivot point. If the baseline is distorted you may want to explore baseline correcting at some point (7th icon for the right).
6. REFERENCING---This task is recommended since the referencing in Icon-NMR may not be exact. Click on the reference icon (4th from the right) and move the cursor over the peak to reference. To adjust the value click on the peak when the chemical shift is displayed. You have the option to select a value or enter a custom value.
7. CONTROLLING THE DISPLAYING---Remember the tool being used works on the selected spectrum and must be returned to the tool bar via pressing the ESC key or clicking on the tool's icon.
8. MANIPULATING THE SPECTRA---Display the region or select the spectra you want to manipulate then use the following procedures:ZOOMING IN/OUT---Use the magnifying glass to zoom in on the region of interest. Use the “Full” icon to return to the full spectrum. INTENSITY---Use the + and – icons to increase or decrease the intensity of the peaks. EXPANSIONS---Click on the expansion icon (10th icon from the left). Read the caveats section about the initial display of this action. The original spectra will be active so one must select the expansion spectra by clicking on it. Now you can process regions within the expansion just as with the original spectra. The expansion can be moved vertically with the mouse. To move it horizontally press and hold Shift then use the mouse. PEAK PICKING---One very powerful feature of this program lies in its ability to select peaks independently. If you want your peaks displayed on the screen (and printed on the spectra) you must go the main menu and choose: Tools-->Peak Peaking-->Options-->Show Peak Picking on the Screen. Select your spectra and click on the peak picking icon (3rd from the right). Click and drag a box around the top of the peaks of interest. If Show Peak Picking on the Screen was selected then you should see the value displayed on the screen along with a table of values (you can print a list of peaks, generate a spread sheet file, delete entries, etc.). You should explore the Tools-->Peak Peaking menu items for the full range of possibilities. One can change the axis to Hz (on the bottom tool bar) for measuring coupling constants (easier way discussed next). MEASURING COUPLING CONSTANTS---You can use this convenient utility to directly measure coupling constants in Hz on the screen. On the main menu go to Tools-->Measure Coupling Constants. The first click establishes the peaks from which you will be measuring (the anchor peak). Placing the cursor on the next peak in the multiplet will display the coupling constant. If you click on the peak you will notice an entry displayed in the Coupling Constants table. Checking the box to the left of the entry in the table will display a coupling tree for the peaks being compared and the coupling constant in Hz. INTEGRATION---This routine works much like Peak Picking. Click on the integration icon (2nd from the right) and “box-in” the peak. The height of the box does not matter but the width of the box should encompass the full base of the peak. To reference all integrals to one particular integral replace the integral tool by pressing the ESC key or click on the icon. Next, right click on the "known" integral and enter its desired value. One should explore the Tools-->Integration menu for many options associated with how integrals are displayed. LINE WIDTHS AND SIGNAL-TO-NOISE---The information icon (1st from the right) is used to display useful information about a particular peak. Click on the icon then click on the peak you want to know more about. Replace the tool when finished. ADDING TEXT---Text is added by simply clicking on the text icon (7th icon from left). The text can be repositioned and edited by double clicking on it.
9. PRINTING---One can use Print Preview to see the output prior to printing. One can also resize the margins in this window but any text is not moved along with the spectra. You can change the line thickness (1 to 3 should suffice) under File-->Print Out Options.10. STACKED PLOTS---This procedure opens and process all the fid exactly the same. This is not to say all the fids must have been collected using the same parameters (i.e. SW, O1, temperature etc.)
OPENING AND PROCESSING THE FILES---Go to File-->Open or click on the folder icon. Chose the Open Several fid’s button at the bottom of the window. Find the first fid to open and click on Add File. Go to the other fids and add them to the list. When all the fids are added click on Open. Once the fids are opened transform with the FT icon and choose “Apply to all spectra”. REFERENCING AND DISPLAYING---One should reference each spectra individually by selecting it and using the reference icon. To display one axis across the bottom go to Edit-->Spectrum Properties-->Scale Properties-->Show Only the Scale of the Currently Active Fid. Before printing make sure the bottom spectrum is active. To display the same region of each spectrum go to View-->Set Limits and enter the desired limits. Each spectra can be scaled individually by selecting it and using the + and – icons.
LAYOUT MENU---This menu has some specialized options for stacked plots and can be used to make a traditional white washed plot.