<h1>Indole Molecule Files</h1>

Basic Instructions For Chime Viewing:
The use of chime is relatively simple, so I think for now I'm going to be lazy and let you play with it. Holding down the left mouse button while moving the mouse rotates the molecule. The right mouse button typically gives you a variety of options such as 2-D rendering and a variety of views such as ball and stick, line etc...try changing the view with each of these, as they start in line form, the bruceolines are especially interesting to look at w/ Van der Waals radii on, you get a real idea of just how linear a molecule they are.

If you don't have the chime viewer yet, check out MDLI's chime download site:
MDL Information Systems Chime Support Site

I've decided to start dividing up the mol files and the best system I've run across for classification of indole alkaloids based on structure is that of Atta-ur-Rahman and Anwer Basha in "Biosynthesis of Indole Alkaloids" (1983). It's really nice because it covers basically all the indole alkaloids without creating a large "other" category and also makes enough sense to work with easily...always a good sign of a well thought out classification system. I'll try to differentiate these classes without stealing their reasoning too much. Basically the classes are derived from the structure of the non-tryptophan unit of the structure:

Class I indole alkaloids are derivatives which arise from the alpha or beta condensation products of tryptamine with an unrearranged secologanin skeleton. These include the commonly known Corynanthe alkaloids as well as Strychnos and Yohimbe groups.
Class II indole alkaloids are similar to class I, in being derived generally from the condensation of tryptamine with the secologanin skeleton. However, in this class, the secologanin skeleton is cleaved between C-3 and C-4 and a new bond is formed between C-2,6 and C-4. These include the Aspidosperma and Hunteria type alkaloids.
Class III indole alkaloids are actually a "mongrel mix" of iboga type alkaloids which are similar to class II alkaloids in the cleavage of the secologanin skeleton at the C-2 position, but with new bond formation between C-2,6 and C-5. It also includes all alkaloids which are derivatives of the condensation of tryptamine with a C-10 skeleton which comes from large rearrangements of the original secologanin skeleton.
Class IV indole alkaloids include non-tryptophan indole alkaloids (carbazoles), non-isoprenoid tryptophan alkaloids (includes most indole alkaloids from TiHKAL...) and the fungal indole alkaloids (includes the rest of the indole alkaloids from TiHKAL). This class represents most of my study efforts. Class V indole alkaloids are the bis-indole alkaloids. These are dimeric indole alkaloids, with the possibility of each of the indole moeities belonging to a separate class.
Trimeric and tetrameric indole alkaloids are simply a further extension of the bisindoles.

The links to the simple indole derivatives (indole, convalutamydines etc. are in the class IV page...I'm not really sure they belong there, if anyone knows the answer to this pleas email me...I think that they are generally not even considered true indole alkaloids in some cases...