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Quick Start Guide (English)

1. Open the program#

Open NMRium with the following link:

https://www.nmrium.org/nmrium/

2. Open spectra#

To open spectra, your data must be in one of the following file types:

  • JCAMP-DX (.dx, .jdx, .jcamp)
  • zipped folder in Bruker format (raw data od processed)
  • Jeol (.jdf)
  • NMRium file (.nmrium)

Drag the file you want to open into the gray box Drag and drop here in the middle of the screen. You can open a set of spectra of a molecule by either dragging the spectra individually into the workspace or by dragging a zip folder containing all spectra. Also, you can open several spectra at once in the Bruker folder structure as a zip file.

3. Select a spectrum#

On the right side of the workspace, various areas are available in an expandable menu. Click on the head of the Spectra field. The measured nuclei (e.g. ¹H, ¹³C, etc) are displayed in the opened field. Click on a nucleus to find the experiments associated with it. To select an experiment, click the corresponding line. The experiment appears in the workspace.

Wobble curves

If your imported Bruker folder contains so-called wobble curves, it is useful to delete them from the list for further processing. You can identify them by the name wobble. Click the corresponding spectrum with the right mouse button. In the appearing menu, click delete to delete the wobble curve.

Changing the color of a spectrum

You can change the color of the spectrum by clicking the colored square in the line for the spectrum. In the appearing window, you can select a different color. For 2D experiments, the colors for the negative and positive cross-peaks are additionally selectable.

4. Delete a spectrum#

To delete a single spectrum, right-click the spectrum in the menu spectra on the right side. Click delete in the appearing menu to delete the spectrum. To delete all spectra, click on the trash icon on the left above the listed spectra.

5. Zoom a section#

To zoom a section of a spectrum, drag over it with the left mouse button. You can repeat this process as often as you like. Double-click anywhere in the spectrum to undo the last magnification step. This step can also be repeated. The intensity level of the signals can be changed using the mouse wheel. To return to the full spectrum, click on the Zoom-Out button in the menu bar on the left side of the spectrum.

6. Insert a molecular structure#

There are two possibilities to insert a molecular structure into the program:

Molfile

Drag the molfile into the workspace. The Structures field appears, showing the inserted molecular structure as well as the molecular weight and the molecular formula.

Integrated structure editor

Click on the Structures menu on the right side of the screen and then on the + sign. A window opens where you can draw your molecular structure. Then click on the Save button. In the Structures field, the drawn molecular structure appears as well as the molecular weight and the molecular formula.

7. Processing of raw data (currently only 1D)#

NMRium offers the possibility to perform a Fourier transformation (FT) on the raw data of one-dimensional NMR spectra. To process an FID, open the FID by dragging it into the Drag and drop here box (section 2).

Fourier transformation#

To prepare the FID for the Fourier transformation, click the Zero Filling icon to the left of the spectrum. Set the desired values for Size (zero filling) and Line Broadening (exponential window function) and click Apply. Then start the Fourier transformation by clicking on the FFT Filter button to the left of the spectrum.

Size and LB values

If you are not sure which values to set, you can use the following recommendations as a reference:

Size: Choose twice as many points as in the original FID.

Line Broadening (LB): Specify 0.3 Hz for ¹H spectra and 1-3 Hz for ¹³C.

Phase correction#

Click the Phase correction icon to the left of the spectrum. You can choose between manual and automatic phase correction.

Automatic phase correction

Click the Apply button, the phase will be corrected automatically.

Manual phase correction

You can perform zero-order and first-order phase correction.

For zero-order phase correction, click and hold the green PH0 button above the spectrum. By moving the mouse to the left or right, you can perform phase correction until the signal is correctly phased and release the button. By double-clicking, you can move the pivot point (red line) for the first-order phase correction.

The first order phase correction is performed analogously by pressing PH1. The focus should be on the signals that are as far away as possible from the signal under the pivot point. Clicking the Apply button completes the phase correction.

Baseline correction#

Click the Baseline correction icon to the left of the spectrum. You can choose between two possible algorithms: polynomial and AIR PLS.

  • To use the algorithm polynomial, you may define a degree and then click apply.
  • To apply the AIR PLS algorithm, you may define both maximum iteration and a tolerance range and then click apply.

8. Referencing#

Click the Peaks Picking button to the left of the spectrum. Find your solvent signal (or the reference signal). When you point at it with the crosshairs, press the shift key and the left mouse button at the same time. The value of the signal will be shown both in the spectrum and in a list on the right side of the spectrum in the Peaks field. Select one of the two displayed values (in the spectrum single click with the left mouse button, in the list double click with the left mouse button) and enter the correct reference value.

9. Peak Picking#

Click on the Peaks Picking button. You can choose between automatic peak picking and manual peak picking.

Automatic peak picking

A list appears above the spectrum in which you can specify the maximum number of peaks, the noise factor and the minimum-maximum ratio (Min Max Ratio). Then press Apply. The chemical shift of the peaks is displayed both in the spectrum and in a list on the right side of the spectrum in the Peaks field.

Manual peak picking

Locate a signal. When you see it in the crosshairs, press the shift key and simultaneously the left mouse button. The value of the signal will be shown in a list both in the spectrum and on the right side of the spectrum in the Peaks field.

10. Delete peaks#

If you want to delete a single peak, find the corresponding signal on the right side of the spectrum in the list in the Peaks field. Click the trash icon on the far right of the line, the peak will be deleted.

If you want to delete all peaks, click on the trash icon located above the signal list under the Peaks field. Confirm that you want to delete all peaks by clicking Yes in the window that opens.

11. Choosing the values to display in the "Peaks" list#

You can display various information in the Peaks list. Open the Peaks list on the right side of the spectrum. Click on the gear wheel at the top right. All measured nuclei will be displayed. You can choose to display the following values for each nucleus:

  • Peak Number
  • Peak Index
  • Chemical shift (ppm)
  • Chemical shift (Hz)
  • Width
  • Intensity

Place a checkmark next to the values that you want to have displayed for the respective nucleus. Then click on the green check mark at the top right.

12. Integration#

Click the Integral tool button on the left side of the spectrum. To integrate a signal, hold down the Shift key and move the mouse over the signal while holding down the left mouse button. Then release both the Shift and the left mouse button. Proceed in this way with each signal that you want to integrate. The integrals are displayed in a list on the right side of the spectrum in the Integrals button.

It is predefined that the relative number of all integrated H atoms is 100. To change the number, click on the sum symbol above the list. In the window that opens, you can either enter the number of H atoms manually and then click on Set or accept the number of H atoms specified by the sum formula by clicking on Set in the lower area.

13. Delete integrals#

If you want to delete a single integral, find the corresponding signal on the right side of the spectrum in the list in the Integrals field. Click the trash icon on the far right of the line, the integral will be deleted. Alternatively, you can click on the red fieldat the bottom of the spectrum that belongs to the respective integral. The corresponding integral will be deleted.

If you want to delete all integrals, click on the trash icon located above the signal list in the Integrals button. Confirm that you want to delete all integrals by clicking Yes in the appearing window.

14. Picking ranges and determination of coupling constants#

Click on the Ranges Picking button on the left side of the spectrum to specify signal assignment ranges, for example to determine coupling constants. You have the option of either manually or automatically defining the assignment ranges:

Automatic ranges picking

A list appears above the spectrum. Click on the button Auto ranges picking, the assignment ranges will be determined automatically and displayed both in the spectrum and in a list on the right side of the spectrum in the Ranges field. The corresponding coupling constants are determined automatically.

Manual ranges picking

Press the Shift key and move the mouse over the range you want to set. The marked assignment range is displayed both in the spectrum and in a list on the right side of the spectrum in the Ranges field. The corresponding coupling constants are determined automatically.

15. Delete ranges#

If you want to delete a single range, find the corresponding range on the right side of the spectrum in the list in the Ranges field. Click the trash icon on the far right of the line, the range will be deleted. If you want to delete all ranges, click on the trash icon located above the signal list in the ranges field. Confirm that you want to delete all ranges by clicking Yes in the window that opens.

16. Assignment of signals#

To assign signals, you have to define assignment ranges (section 14) and insert a molecular structure (section 6). Open the Ranges and Structures fields on the right side. Specify the correct number of relative H atoms by clicking the sum icon above the Ranges list. In the window that opens, you can either enter the number of H atoms manually and then click on Set or accept the number of H atoms specified by the sum formula by clicking on Set in the lower area.

In the list, click the box under the link icon in the line of the signal you want to assign, . A red zero appears there. Then assign the signal by clicking on the corresponding atoms in the structural formula. Proceed in the same way with all other ranges. You can also assign several, different H atoms to a range by clicking successively on all H atoms in the structural formula that belong to the respective signal. If you want to assign diastereotopic H atoms, hold the Shift key while clicking the corresponding H atom in the structure. This makes both diastereotopic H atoms visible.

17. Export of assigned spectra#

To export the assigned spectra, click on the Export button to the left side of the spectrum. A field will open where you can select in which format you want to export your spectrum. You have the following options:

  • Export as SVG
  • Export as PNG
  • Save data
  • Copy image to Clipboard

Click on Save data to save the assigned spectrum with all stored information and to be able to edit it later. An .nmrium file is created and offered for download.

info

An .nmrium file is a compressed text file containing all information of the (partially) assigned stored spectra. Depending on the number of spectra contained, saving can take longer, as can opening an .nmrium file again.