JSpecView and JMol viewers.

Convener: Prof. S. W. Homans (Tel: 33125, Email: s.w.homans@leeds.ac.uk)
Demonstrator: Neil Syme

 

Introduction

This exercise will give you the opportunity to use the select peaks in an NMR spectrum and see the corresponding atoms highlighted. This webpage uses the JSpecView Java applet to display NMR spectra and select peaks. JSpecView was written by Prof Robert John Lancashire, (Department of Chemistry, University of the West Indies, Mona, Kingston, Jamaica). It is linked to the JMol Java applet which displays the molecules.

1. Using JSpecView

In the JSpecView spectrum applet (on the left below):

  • Click on an NMR peak to highlight it in pink. The atoms producing this peak will then be highlighted in yellow on the JMol applet (on the right below).
  • Click the "Remove all highlights" button to remove the highlights.
  • The "Show annotated regions" button will highlight those peaks which have been linked to the molecule display.
  • Click the "CNMR (Carbon-13 NMR) spectrum" radio-button to dsiplay Carbon NMR.
  • Click the "HNMR (Hydrogen-1 NMR) spectrum" radio-button to dsiplay Hydrogen (Proton) NMR, which this practical is mainly based on.

 

Select NMR type:       HNMR (Hydrogen-1 NMR) spectrum         CNMR (Carbon-13 NMR) spectrum

Select a peak to see the atoms highlighted on the molecule.
Toggle Grid     Reverse Plot


OR select an atom see a peak highlighted on the NMR spectrum.

2. Using JMol

With the mouse pointer over the JMol molecule viewer (shown on the right above):

  • Keeping the mouse pointer still over any atom will display its atom number (eg. H#9).
  • Hold the left-mouse button down while moving the mouse. This will enable you to rotate the molecule.
  • Turning the mouse scroll-wheel will zoom in or out on the molecule. (You may need to click once with the left mouse-button to set the JMol window to monitor the mouse scroll-wheel.)
  • Clicking the right mouse button will display a pop-up menu of options to configure the display, but you don't need to change these at present, but can play with it later.

Using JSpecView and JMol

Now we will use these JSpecView and JMol applets to answer the following questions about this NMR spectrum. Don't hesitate to ask Prof. Homans or a demonstrator if necessary.

Question 31: In Hexane, how may atoms correspond to the Hydrogen-1 NMR (HNMR) peak at 0.9 PPM ?
(Note PPM is the horizontal scale of the JSpecView applet).

  4 Hydrogen atoms
  6 Hydrogen atoms
  6 Carbon atoms
  8 Hydrogen atoms
  14 Hydrogen atoms

 

Question 32: In the Hydrogen-1 NMR (HNMR) spectrum of Hexane, why is the peak at 0.9 PPM taller than the peak at 1.3 PPM ?

Because:
  the number of corresponding atoms is indicated by the frequency of the peak, not the height
  the 0.9 PPM peak corresponds to more atoms (than the 1.3 PPM peak) so should be taller
  the many small peaks beside the 1.3 PPM peak indicate that this spectrum has many errors
  the 1.3 PPM peak has a greater area under it
  it is an optical illusion, the 1.3 PPM peak actually is taller than the 0.9 PPM peak

 

Question 33: On the Hydrogen-1 NMR of Hexane, there are small peaks at 0.0 PPM and at 7.3 PPM. What do you think the small peak at 0.0 PPM is due to ?

  electrical interference from power supply
  an error in the analysis of the data
  Deuterium (2H) atoms
  movement of the NMR machine while acquiring the spectrum
  a calibration peak

 

Question 34: How many peaks are visible in this Carbon-13 NMR (CNMR) spectrum of Hexane ?

  1 peak
  2 peaks
  3 peaks
  4 peaks
  5 peaks

 

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Now click the "Post my answers & Goto next page" button below. Thankyou.

(There may be a few seconds delay before the next page appears).