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Interactive 1H spectrum

Interactive 1H spectrum

1H spectrum of codeine viewed with Chime plugin

Note that Chime now works with Microsoft Internet Explorer 6.0, but this requires the latest Chime version 2.6 Service Pack 4.  See details.

The spectrum below was exported from NUTS in JCAMP format, which can be displayed by the Chime plugin.  With the cursor in the spectrum window, press the left mouse button and drag to define a region to be expanded.  Repeating this action will revert to display of the entire spectrum.

Clicking on a peak will highlight the corresponding H in the structure shown to the right.  See details on how this is done.

The structure can be rotated, etc. – see below.

Chime plug-in is required to display interactive structure

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The 3 NOEs listed below allow stereospecific assignment of the CH2s in codeine.  Click on the buttons to highlight the corresponding Hs, along with the interatom distance.  The numbering scheme is shown below.

H-5H-18′      

H-16H-17      H-18H-13       Reset     

Manipulating the spectrum:

Clicking the left mouse button within the spectrum window will display the coordinates of the mouse at the top right corner, so you can read off chemical shifts.  (This does not appear to work properly in the latest version of Chime.)

Right clicking in the spectrum window displays this menu:

 

Manipulating the structure:

Rotatation:  Place the mouse cursor anywhere within the black frame.  Press and hold the left mouse button and move the mouse to rotate the structure.

X & Y Translation:  Hold down Control (Macintosh: Command), then press and hold the Right mouse button, then move the mouse.

 Zoom:  Hold down Shift, then press and hold the Left mouse button, then move the mouse. Up/down movements zoom up and down.

Z Rotation: .Hold down Shift (Macintosh: Shift plus Command), then press and hold the Right mouse button, then move the mouse. Right/left movements rotate around Z.

Interatom distance measurement:  Toggle on display of distances by right clicking in the Chime frame.  Choose Select, then Mouse Click Action, then Distance (menus illustrated below).  Click on the first atom, then the second atom.  The distance is displayed in the gray status bar at the bottom of the Window.

 

 

How’d they do that?

Displaying the spectrum is simple, requiring the following html code.  No script or modification of the JCAMP file is needed.  Note that omission of jcamp_revplot="true" will result in the spectrum being displayed backwards (TMS on the left).

(Thanks to Dr. Reinhold Stoermann, University of Bremen, for pointing out the need for the correct MIME type, without which this won’t work on Netscape or Opera.)

<embed SRC="1h.jdx"  

type="chemical/x-jcamp-dx"

width="75%"  

height="50%"  

jcamp_revplot="true"  

pluginspage="http://www.mdli.com/chemscape/chime/">

The file 1h.jdx is the spectrum, exported from NUTS in JCAMP format.  

The structure is a pdb file (text file containing atomic coordinates), and is displayed using the following html code:

<embed SRC="codeine.pdb"

type="chemical/x-pdb"

width="300"< /font> height="300" display3D="sticks" color3D="cpk"

options3D="specular" script="zoom 125; rotate z 168; rotate y -28; rotate x -177"

frank="false" name ="codeine" pluginspage="http://www.mdli.com/chemscape/chime/" align="right">

<noembed>Chime plug-in is required to display interactive structure</noembed></p>

 

Correlating the spectrum and structure, so that clicking on the spectrum highlights the corresponding atom, is done by inserting the assignment information into the JCAMP file, which can be done with any text editor.  The lines which do this are:

##$ASSIGNMENT TYPE= CHIME ##$CHIME TARGET= codeine ##PEAK ASSIGNMENT= (XYWA) (5.71, -1, 0.1, <select *; spacefill off; select atomno=31; spacefill 110>) (5.3, -1, 0.1, <select *; spacefill off; select atomno=30; spacefill 110>) (4.89, -1, 0.1, <select *; spacefill off; select atomno=16; spacefill 110>) (6.66, -1, 0.1, <select *; spacefill off; select atomno=27; spacefill 110>) (4.18, -1, 0.1, <select *; spacefill off; select atomno=32; spacefill 110>) (3.35, -1, 0.1, <select *; spacefill off; select atomno=21; spacefill 110>) (6.57, -1, 0.1, <select *; spacefill off; select atomno=26; spacefill 110>) (3.84, -1, 0.1, <select *; spacefill off; select atomno=41 or atomno=42 or atomno=43; spacefill 110>) (2.58, -1, 0.1, <select *; spacefill off; select atomno=36; spacefill 110>) (2.40, -1, 0.1, <select *; spacefill off; select atomno=37; spacefill 110>) (2.44, -1, 0.1, <select *; spacefill off; select atomno=38 or atomno=39 or atomno=40; spacefill 110>) (2.67, -1, 0.1, <select *; spacefill off; select atomno=22; spacefill 110>) (2.9, -1, 0.1, <select *; spacefill off; select atomno=33; spacefill 110>) (2.06, -1, 0.1, <select *; spacefill off; select atomno=34; spacefill 110>) (1.88, -1, 0.1, <select *; spacefill off; select atomno=35; spacefill 110>) (3.04, -1, 0.1, <select *; spacefill off; select atomno=29; spacefill 110>) (5, -1, 5, <select *; spacefill off>)

The "chime target" refers to the label assigned to the codeine structure, specified in the html code above as  name ="codeine".  The atomno’s are the atom numbers as listed in the .pdb file.


Last updated: 02/02/2006