Jmol-Application/C4/Simulated-NMR-Spectrum-using-Jmol/English
Visual Cue | Narration |
Slide Number 1
Title Slide |
Welcome to this tutorial on Simulated NMR Spectrum using Jmol. |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to,
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Slide Number 3
Learning Objectives |
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Slide Number 4
System Requirement |
Here I am using,
Ubuntu Linux OS version 20.04 Jmol version 14.32.80 Java version 11.0.16 and Working internet connection. |
Slide Number 5
Pre-requisites |
To follow this tutorial learner should be familiar with,
Nuclear Magnetic Resonance spectroscopy analysis for organic molecules and basics of Jmol interface For the prerequisite Jmol tutorials please visit this website. |
Slide Number 6
Code Files |
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Slide Number 7
About JSpecview https://jspecview.sourceforge.net jcamp-dx.org |
JSpecView is a graphical viewer for spectral data in the JCAMP-DX format.
Here is the link for more information on JspecView. |
Slide Number 8
About JSpecview |
JSpecView has been integrated into the Jmol distribution.
The Simulated proton NMR and carbon 13 NMR tools have been added in Jmol in the Tools menu. |
Cursor on Jmol interface.
Open the File menu and click on Get Mol option. |
Here I have opened the Jmol interface.
Open the File menu and click on Get Mol option. |
In the dialog-box type aniline.
Click on the OK button. |
A dialog box opens, type aniline in the text field.
Click on the OK button. |
Cursor on model of aniline. | A model of aniline loads in the panel. |
Cursor on model of aniline. | Let us get the simulated proton and carbon 13 NMR for this molecule. |
Click on the Tools menu in the main menu bar.
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Open the Tools menu in the main menu bar.
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Cursor on JSpecView window. | Wait for a few seconds.
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Cursor on the left-panel. | You will see the 3D model of the molecule in the left panel. |
Cursor on the right-panel. | The simulated spectrum is seen on the right panel. |
Cursor on the X-axis | In the simulated spectrum, the X-axis is the energy axis.
The energy axis is called delta (δ ) axis. The units are given in parts per million (ppm).
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Cursor on Y axis | The Y-axis shows the intensity of the signal. |
Cursor on the spectrum. | The spectrum for aniline shows 3 sets of signals.
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Hover the mouse over the peaks. | Hover the mouse over the peaks.
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Click on any signal on the spectrum. | Click on any signal on the spectrum.
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Click on any hydrogen atom in the model. | Click on any hydrogen atom in the model.
This feature allows us to analyze the spectrum easily and assign the peaks. |
Left-click and drag the mouse on the peaks from left to right. | Left-click and drag the mouse on the peaks from left to right to expand the peaks. |
Left-click and drag the mouse on the peaks from left to right. | We can repeat this process a couple of times until we see the splitting clearly.
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Click on the red tick. | The center of the peak is indicated as a red tick mark on the top of the graph.
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Cursor on the peaks. | In this spectrum we see a triplet around delta 7.24.
A triplet at around 7.03. A doublet at 6.77 |
Cursor on the peaks. | Let us analyze the peaks. |
Click on the peak at delta 7.24.
Cursor on meta hydrogens. Cursor on ortho and para hydrogens. |
I will start from the left side of the spectrum and click on the peak at delta 7.24
The hydrogens on meta carbon are highlighted.
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Click on set of signals at delta 7.03.
Cursor on para hydrogens. Cursor on meta and para hydrogens. |
Next click on the next set of signals at delta 7.03.
This hydrogen interacts with two neighboring hydrogens, hence this peak is a triplet. |
Click on the peak at 6.77.
Cursor on ortho hydrogens. Cursor on meta hydrogen. |
Now click on the peak at 6.77.
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Click on the peak at delta 7.24.
Point to Nitrogen in the structure. |
The protons on meta carbon atoms appear downfield when compared to ortho and para carbons.
The meta protons are deshielded. This is due to the resonance effect. |
Slide Number 9
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The lone pair on the nitrogen is involved in the conjugation.
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Cursor on peaks at delta 7.03 and 6.77. | Back to the JSpecView window,
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Right-click on the spectrum to open the context-menu.
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Right-click on the spectrum to open the context-menu.
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Cursor on Integration window.
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A window Integration for 1H NMR Simulated opens. Leave all the settings as such.
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Cursor on the integration of peaks.
Cursor on the intensity ratio values. |
Notice that on the spectrum the integration of the peaks is displayed.
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Cursor on the table in the integration window.
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The table of values will also be displayed in the integration window.
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Cursor on the black arrows on the far-right. | At the far right end of the spectral window you will see two black arrows.
One upward and one downward. |
Click on the black arrows. | Click on these arrows to increase and decrease the peak heights. |
Click on the small circle between the two arrows | Click on the small circle between the two arrows. This will display the original spectrum. |
Left-click and drag the mouse on the peaks from left to right. | Let us again expand the peaks to show the splitting of the peaks clearly. |
Click on Options on the top menu. | We can change the display scheme of the spectrum according to our preference.
Click on Options on the top menu. Here you will find checkboxes to hide or display, Toolbar, side panel and Status bar.
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Select Preferences option.
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Select Preferences option.
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Under the Element section, select Plot.
Click on Ok at the bottom of the dialog box.
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As an example, I will change the color of the plot to pink.
Under the Element section, select Plot.
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Cursor on the spectrum. | We can add more spectra to the panel.
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Cursor on the spectrum. | For example, I would like to compare it with the proton NMR spectrum of benzene. |
Click on the File menu, from the options select, Add H1 Simulation…. | Click on the File menu, from the options I will select, Add H1 Simulation…. |
Type benzene in the Open URL dialog-box.
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Open URL dialog-box opens.
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Cursor on 1H NMR of benzene. | Proton NMR spectrum of benzene is added in the right panel. |
Cursor on the panel. | Now we can see both the spectra stacked and easy to compare. |
Left-click for expanding the peaks. |
As expected, in the benzene spectrum, we can see only one peak at delta 7.37.
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Right-click on the spectrum and choose Integration from the context menu. | Right-click on the benzene spectrum and choose Integration from the context menu.
A window Integration for 1H NMR Simulated opens.
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Cursor on the integration of the peak. | The integration of the peak corresponds to 6 protons. |
Cursor on the spectra panel. | When we compare the peaks in both the spectra:
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Click on black square, click to combine button at the top-right corner of the spectrum. | The two spectra can be merged by clicking on the click to combine button.
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Cursor on the spectrum. | The two spectra are now combined into one.
This feature can be used to compare the spectra of two or more molecules. |
Click the click to split button at the top-right corner. | Click the click to split, black square button at the top-right corner.
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Click on the spectrum to activate.
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If you want to close any spectrum, first click on the spectrum to activate it.
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On the JSpecView window, Click on File menu and Choose Exit option. | Let us Exit the JSpecview window, Click on File menu and Choose Exit option. |
On the Jmol interface, Open the Tools menu and scroll down to Spectra, then from the sub-menu click on Simulated 13C NMR option. | Jmol also has a feature to display Carbon 13 NMR spectrum.
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Cursor on JSpecView window. | The JSpecView window opens with the Carbon 13 spectrum for aniline.
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Cursor on the right panel. | On the right panel, Carbon 13 spectrum of aniline is displayed.
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Click on any peak on the spectrum. | Click on any peak on the spectrum.
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Cursor on the spectrum. | The spectrum can be saved in various file formats |
Click on the File menu. Select Save as option.
Click on the Original option. Choose location as Documents folder and type file name as Aniline-CNMR. In Files of type choose, JCAMP-DX files.
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To save the spectrum, click on the File menu. Select Save as option.
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Click on File menu and select Export option, select PDF option.
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Spectra can also be exported as pdf and other image file formats.
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Only Narration | Let us summarize, |
Slide Number 10
Summary |
In this tutorial, we have,
spectra for organic molecules using JspecView.
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Slide Number 11
Summary |
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Slide Number 12
Assignment |
As an assignment,
spectra for molecules of your choice.
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Slide Number 13
About Spoken Tutorial Project |
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Slide Number 14
Spoken tutorial workshops |
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Slide Number 15
Answers for THIS Spoken Tutorial Do you have questions in THIS Spoken Tutorial? Please visit this site Choose the minute and second where you have the question. Explain your question briefly The spoken tutorial project will ensure answer. You will have to register on this website to ask questions. |
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Slide Number 16
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Spoken Tutorial project is funded by Ministry of Education (MoE), Govt. of India |
The script for this tutorial is contributed by Snehalatha Kaliappan.
Thank you for joining. |