Snehalathak at 12:20, 6 February 2023

2023-02-06T12:20:19Z

Snehalathak at 12:18, 6 February 2023

2023-02-06T12:18:24Z

Snehalathak at 12:11, 6 February 2023

2023-02-06T12:11:17Z

Madhurig at 08:41, 6 February 2023

2023-02-06T08:41:06Z

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Snehalathak at 06:20, 6 February 2023

2023-02-06T06:20:55Z

Snehalathak: Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' ||Welcome to this tutorial on '''Simulated NMR Spectrum using Jmol'''. |- || '''..."

2023-02-06T06:16:39Z

Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' ||Welcome to this tutorial on '''Simulated NMR Spectrum using Jmol'''. |- || '''..."

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{|border=1
||'''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/ 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 the 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 '''0-12 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 can 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.

||Next 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'''

[[Image:image1.png.png|top]]
||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 checkboxes 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 '''also 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 1H 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.
|-
|}

@@ Line 224: / Line 224: @@
 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
+||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.
@@ Line 329: / Line 329: @@
-This corresponds to 2 meta protons. 1 para proton and 2 ortho protons.
+This corresponds to 2 meta protons, 1 para proton and 2 ortho protons.
 |-

← Older revision		Revision as of 12:11, 6 February 2023
Line 197:		Line 197:


−	Now ~~can~~ we see the splitting of the peaks clearly.	+	Now we see the splitting of the peaks clearly.

	\|-		\|-

@@ 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''',
 ||'''Jmol ''' has a feature to display '''Carbon 13''' NMR spectrum.