How to use JNMRPen©

Drawing with JNMRPen

Adding Items

Branching Items

Fusing,Joining Rings

Editing atoms and bonds

Undoing commands

Moving a drawing

Limitations

References

Introduction -- JNMRPen© is a Java® applet for predicting ¹³C NMR shifts for organic molecules. A user simply draws a chemical structure and clicks the NMR Shifts button or menu selection to compute the shifts.

Drawing with JNMRPen© -- Drawing chemical structures with JNMRPen© is easy. Select a menu item then click the screen to execute the command. JNMRPen works like ChemPen©, the Windows® based chemical structure drawing program from ChemPen Software. Buttons at the bottom of the window also perform several functions.

Adding items - To add an atom, a chain, a ring or a benzene click Add | item and click the screen to place the item.

Branching items - Atoms, benzenes, rings and certain functional groups can be branched from existing atoms. To branch an item select Branch | item and click near the target atom to form the branch. Branches from isolated atoms or atoms with three or more attached bonds occur along an angle that is a multiple of 45^o. Branches from atoms attached to one bond occur at 120^o relative to the existing bond. A branch from an atom at a two atom apex is directed along a vector formed by a sum of two vectors derived from the existing bonds.

Fusing, Joining Rings - To fuse a ring to a bond or to join a ring to an atom select Fuse|item or Join|item and click near the target bond or atom.

Editing atoms or bonds -- Click an atom or bond to start its editor. The atom editor can be used to change the type of atom, its charge or the number of implicit Hs. An atom can also be moved in 2 unit increments. The bond editor can toggle a bond among single, double and triple and between aromatic and non-aromatic. Shift toggles a double bond between left and right of its axis center.

Undo - reverses the most recent drawing command.

Moving a drawing - The Left, Right, Up and Down buttons move the drawing by 16 unit increments

Limitations -

JNMRPen uses no database limiting its accuracy.

JNMRPen is limited to molecules containing F,Cl,Br,I,O,N,S,P,Si

JNMRPen does not handle organometallics.

NMRPen does not suffer the above limitations.

References

F.W. Wehrli, T. Wirthlin, Interpretation of Carbon-13 NMR Spectra, Heyden & Son, Ltd., London, 1980
J. B. Stothers, Carbon-13 Nuclear Magnetic Resonance Spectroscopy, Academic Press, N.Y, 1972
G. C. Levy, G. L. Nelson, Carbon 13 Nuclear Magnetic Resonance for Organic Chemists, Wiley - Interscience, New York, 1972
E. Breitmaier, W. Voelter, C-13 Nuclear Magnetic Resonance Spectroscopy, V.5 in Monographs in Modern Chemistry, Verlag Chemie, Weinheim, 1974
D.M. Grant, E.G. Paul, J. Am. Chem. Soc., 86,2984(1964)
L. P. Lindeman, J. Q. Adams, Anal. Chem. 43,1245(1971)
D. E. Derman, M. Jautelat, J.D. Roberts, J. Org. Chem., 36, 2757(1971)
H. Kalenowski, S. Berger, S. Braun, Carbon-13 NMR Spectroscopy, J.Wiley & Sons, Ltd. New York, 1988
Olah, G.A., Kakajuna, T., Surya Prakash, G. K, Angew. Chem, 92, 837(1980)