Example of how to create linked 3D animations/structures

First, edit the file viblist.js to contain the info needed for your molecule. You will need (i) its IR spectrum in JCamp (.jdx) format, (ii) its 3D molecule structure file (.mol or .pdb), (iii) the list of animated vibrations saved as individual (.xyz) files.

Then run this page again, loading the new viblist.js file for your molecule.


Select a vibrational mode from the list (from the ones contained in the file viblist.js):

Then enter the width of the peak

Click on 'Submit' to link that hot-spot with the chosen vibration .xyz file.

When you have finished all the hot-spots, click on 'Finish' to output the finished linking file (peaklinks.js). You can view the file using the program IRviewer.html (Note: you will have to edit this file to ensure it loads the correct new files that you've just created).

Example table showing the peak positions for ethylbenzoate
Atoms mode type Region (cm-1)
O-H stretch free 3600-3650
    H-bonded 3200-3500
       
N-H stretch sym 3100-3500
    asym  
       
C-H stretch alkynes 3300
    aromatics 3050-3150
    alkenes 3000-3100
    alkanes 2850-3000
    aldehydes 2700-2900
       
C=N   nitriles 2240-2260
       
C=C   alkynes 2100-2250
       
X=C=Y   allenes 1950-2270
       
C=O   anhydride 1760 & 1810
    acid chloride 1800
    ester 1730-1750
    aldehyde 1720-1740
    ketone 1705-1725
    carboxylic acid 1700-1725
    amide 1640-1670
       
C=N   imine 1640-1690
       
C=C   alkene 1600-1680
    aromatic 1475 & 1600
       
O-H      
       
N-H bend   1550-1640
       
C-H bend -CH2- 1465
    -CH3 1375 & 1450
       
C-N   amines 1000-1350
       
C-O   alcohols 1000-1300
       
C-H out-of-plane bend alkenes 650-1000
    aromatics 690-900