Difference between revisions of "Jmol-Application/C4/Simulated-NMR-Spectrum-using-Jmol/English"

Latest revision as of 17:50, 6 February 2023

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, Predict the proton and carbon 13 NMR spectra for organic molecules using JSpecView. Change the display parameters of the plot. Integrate the peaks in the proton NMR spectrum.
Slide Number 3 Learning Objectives	Stack two or more spectra Combine two spectra Save the spectrum in jdx format. Export the spectrum in various image file formats.
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 https://spoken-tutorial.org	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	The input files required for this tutorial are available in the Code files link. Please download and extract the files. Make a copy of all the files and then use them for practising
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. I will begin the demonstration with a simple aromatic amine, aniline. 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. Scroll down and select Spectra from the sub-menu select Simulated 1H NMR option.	Open the Tools menu in the main menu bar. Scroll down and select Spectra, from the sub-menu select Simulated 1H Spectrum option.
Cursor on JSpecView window.	Wait for a few seconds. The simulated proton NMR for aniline molecule opens in a JSpecView window.
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). Most often the signal area for organic compounds ranges from 0 to 12 ppm.
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. These correspond to the 3 sets of protons on the molecule.
Hover the mouse over the peaks.	Hover the mouse over the peaks. The value of the chemical shift is displayed on the spectrum.
Click on any signal on the spectrum.	Click on any signal on the spectrum. The corresponding protons are highlighted on the 3D model in the left panel.
Click on any hydrogen atom in the model.	Click on any hydrogen atom in the model. The corresponding peak is highlighted in the spectrum. 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. Now we see the splitting of the peaks clearly.
Click on the red tick.	The center of the peak is indicated as a red tick mark on the top of the graph. Click on the red tick, the delta value of this peak is displayed.
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. This peak corresponds to hydrogens on meta carbon atoms. This hydrogen interacts with two neighboring hydrogens, hence this peak is a triplet.
Click on set of signals at delta 7.03. Cursor on para hydrogens. Cursor on meta and para hydrogens.	Now click on the next set of signals at delta 7.03. The hydrogen on the para carbon is highlighted. 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. The hydrogens on the ortho carbons are highlighted. This hydrogen interacts with only one neighboring hydrogen. Hence it is a doublet.
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 Resonance structures of Aniline	The lone pair on the nitrogen is involved in the conjugation. The electron density is less at meta position and more at ortho and para positions. Please refer to the additional reading material for more information.
Cursor on peaks at delta 7.03 and 6.77.	Back to the JSpecView window, The ortho and para hydrogen atoms are shielded when compared to meta. Hence they appear upfield.
Right-click on the spectrum to open the context-menu. Click on Integration from the options in the context menu.	Right-click on the spectrum to open the context-menu. Here we see several options. I will select Integration.
Cursor on Integration window. Click on Apply.	A window Integration for 1H NMR Simulated opens. Leave all the settings as such. Click on Apply.
Cursor on the integration of peaks. Cursor on the intensity ratio values.	Notice that on the spectrum the integration of the peaks is displayed. The ratio of intensity corresponds to 2:1:2. This corresponds to 2 meta protons, 1 para proton and 2 ortho protons.
Cursor on the table in the integration window. Close the Integration window.	The table of values will also be displayed in the integration window. Close the Integration window.
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 check boxes to hide or display, Toolbar, side panel and Status bar. I will leave them all checked.
Select Preferences option. Cursor on Preferences dialog box. Click on the Display scheme tab in the Preferences dialog box. Drag the window to resize it.	Select Preferences option. Preferences dialog box opens, click on the Display scheme tab. I will resize the Preferences window to see the options clearly. Various parameters can be changed for the elements listed here.
Under the Element section, select Plot. Select pink from the Color Scheme. Click on Ok at the bottom of the dialog box. Cursor on the pink color peaks.	As an example, I will change the color of the plot to pink. Under the Element section, select Plot. Select pink from the Color Scheme. Click on OK at the bottom of the dialog box. Note the pink color peaks in the plot.
Cursor on the spectrum.	We can add more spectra to the panel. We can compare the spectrum of aniline with the spectrum of any other compound.
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. Click on the Ok button.	Open URL dialog-box opens. Type benzene in the search field. Click on the OK button.
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. Expand the peaks by left-clicking and dragging on the area covering the peaks.
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. Click on the Apply button and close the window.
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: The chemical shifts in aniline have shifted upfield. This is because the protons in aniline experience more shielding.
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. You can locate this button as a black square at the top-right corner of the spectrum.
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. This will split the spectrum to the stacking mode.
Click on the spectrum to activate. Click on the x button on the top-right corner.	If you want to close any spectrum, first click on the spectrum to activate it. Then click on the cross button on the top-right corner.
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 has a feature to display Carbon 13 NMR spectrum. Open the Tools menu and scroll down to Spectra. Then from the sub-menu click on Simulated 13C specturm option.
Cursor on JSpecView window.	The JSpecView window opens with the Carbon 13 spectrum for aniline. Let us expand the peaks to show the splitting peaks clearly.
Cursor on the right panel.	On the right panel, Carbon 13 spectrum of aniline is displayed. 4 peaks corresponding to 4 sets of carbon atoms are seen.
Click on any peak on the spectrum.	Click on any peak on the spectrum. The corresponding carbons on the 3D model of aniline are highlighted. Click on the carbons on the 3D model. The corresponding peaks are highlighted. The carbon attached to nitrogen and meta carbon are deshielded. Their peaks appear downfield. The ortho-para carbons are shielded and hence appear upfield.
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. Click on Save button.	To save the spectrum, click on the File menu. Select Save as option. There are options in the sub-menu to save as original, jdx, cml and xml file formats. I will choose the Original option. A save dialog box opens. Select a convenient location to save the file. I will choose the location as Documents folder and type the file name as Aniline-CNMR. The file will be saved as .jdx file format. In Files of type choose, JCAMP-DX Files. Click on Save button. This file can be opened in JSpecView and further edits can be made.
Click on File menu and select Export option, select PDF option. In the Print Layout dialog box, click on Create PDF option. In the save dialog-box, choose location as Documents folder and file name as Aniline-CNMR-1. Select Files of Type as PDF. Click on Save button.	Spectra can also be exported as pdf and other image file formats. Click on File menu and select Export As option. Here you will find many file options. I will select the PDF option. Print Layout dialog box opens. Here you can change the settings if desired. I will leave them as such and click on Create PDF button. A Save dialog box opens. Select a suitable destination and name for the file. I will choose the location as Documents folder and file name as Aniline-CNMR-1. Select Files of Type as PDF Files. Click on Save button. Title for Printing dialog box opens. I will type the title as Simulated Aniline 13C NMR. Click on the OK button.
Only Narration	Let us summarize,
Slide Number 10 Summary	In this tutorial, we have, Predicted the proton and carbon 13 NMR spectra for organic molecules using JspecView. Changed the display parameters of the plot. Integrated the peaks in the proton NMR spectrum.
Slide Number 11 Summary	Stacked two or more spectra on the panel. Combined two spectra. Saved the spectrum in jdx format. Exported the spectrum in PDF format.
Slide Number 12 Assignment	As an assignment, Simulate the proton and carbon 13 NMR spectra for molecules of your choice. Explore more features of the JSpecView interface.
Slide Number 13 About Spoken Tutorial Project	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
Slide Number 14 Spoken tutorial workshops	We conduct workshops using spoken tutorials and give certificates. For more details, please contact us.
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.	Please post your timed queries in this forum.
Slide Number 16 Acknowledgement	Spoken Tutorial project is funded by Ministry of Education (MoE), Govt. of India
	The script for this tutorial is contributed by Snehalatha Kaliappan. This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Madhurig, Snehalathak

@@ Line 528: / Line 528: @@
 |-
-|| On the Jmol interface, Open the '''Tools '''menu and scroll down to '''Spectra''', then from the sub-menu click on '''Simulated 13C NMR '''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 ''' has a feature to display '''Carbon 13''' NMR spectrum.

Difference between revisions of "Jmol-Application/C4/Simulated-NMR-Spectrum-using-Jmol/English"

Latest revision as of 17:50, 6 February 2023

Contributors and Content Editors

Navigation menu

Personal tools

Namespaces

Variants

Views

Actions

Search

Navigation

Tools