I can make 3D models based on MM2 energy minimization using Chem3D. It will easily provide low-energy conformations (though it sometimes finds a local minimum rather than the absolute minimum). Is that sufficient? -- Ed (Edgar181) 13:15, 11 February 2011 (UTC)[reply]
Hi Edgar. Isn't there any chance to get at a professional program for free? For example scistore offers the download of "MOPAC 2009 for ChemBio3D 12.0" free of charge for academics. Commercial pricing is $5,000. I have, at the moment, no computer at my private disposal, and I admit that I don't know that program.
The question is whether one accepts the MM2 structures as an interim solution. At least on the long run they should be replaced to meet the quality requirements of an encyclopedia. One has to consider that many of the existing 3-d structures on commons are of poor quality and sometimes gruesome. In the above series the phenyl-benzyl compound #4 has to reflect the pi-pi interaction, otherwise it is worthless. -131.173.17.182 (talk) 20:49, 11 February 2011 (UTC)[reply]
I don't know of any way of getting a professional program for free. MM2 minimization in Chem3D gives a structure in which pi-stacking is evident. -- Ed (Edgar181) 21:35, 11 February 2011 (UTC)[reply]
Interesting, (at the first glance) that structure doesn't look bad! So I request you to do also the rest. My intention is to illustrate the sterical diversity of the side chain on the basis of this series of MAT ligands. To be able to compare the structures and to make the SAR comprehensible it is important to have the structures accurately aligned (at the aryl system). Optimum would be to have differnt views: front, top, side view. -131.173.17.182 (talk) 22:51, 11 February 2011 (UTC)[reply]
Is there experimental evidence that the aromatic rings are pi-stacked in the bioactive conformation? Instead of starting from computational-chemistry minimization, would be more appropriate (for this application) to start from a ligand-bound NMR/X-ray/docked-into-known-receptor-structure or something. Could use that exact (frozen) core with minimized sidechain variations, or else with nonfrozen core so that perhaps sidechain effects might alter that. At least for wikipedia articles, I'm not comfortable implying SAR based on "visual inspection of our own minimized structures". DMacks (talk) 23:11, 11 February 2011 (UTC)[reply]
I think it would be difficult to work out exactly what views/alignments you want. If I create .pdb files for energy minimized structures for you, would it be possible for you to use a free program such as Accelrys Discovery Studio to create the images in the orientations that you want? -- Ed (Edgar181) 15:00, 14 February 2011 (UTC)[reply]
Ed. My own possibilities are very limited. Start with the tropanes. Align the phenyl plane with the x-axis to get the (raw) top view. Flip it to the front view (90°), set the 1,2-bond of the phenyl vertical to get the reference orientation. Flip it (90°) to that side that offers the best sight onto the most important structural features (e.g. side chain), do it ad libitum. For ibo, the preferred azepene conformation is chair. Set the "3,4"-bond of the indole horizontal. In the case of three views I would prefer a van-der-Waals-like rendering.
DMacks. There is a paper that examines congeners in which a linker connects both phenyls at their ends and rigidifies such conformations, and concomitantly display significant biological affinity. To come up to your critical annotation I canceled two structures, I regard the tropanes to be sufficiently rigid, and I additionally will comment on it.
Leyo. Corina demo is easy to handle, on the other hand it fails too often.
I'm sorry, but I can't quite understand your directions. I'd like to help, but I suspect that your request is more complicated that what can be handled through a venue such as this. -- Ed (Edgar181) 15:51, 18 February 2011 (UTC)[reply]
Lots of MOS problems...the explicit atom-labels obscure the key connectivity changes we need to see clearly. Also weird to have the alkyl substituents wedged on the alkenes in the reactant/reaction. IMDA is really powerful, would be great to have the "other" diastereomeric details included as well (the two methine C where the rings are fused), but I can't remember which is the kinetic result for the 3E-1,3,9-decatriene → decalin type of reaction. DMacks (talk) 02:33, 4 August 2010 (UTC)[reply]
(for the updated one)...much clearer! Still geometric problem: neither the methyl on the diene nor the methyene leading to the carboxylic acid (on the simple alkene) should be wedged. It's very serious...can't tell if the alkene is cis or trans, and therefore can't tell if the wedged H on the product is correct stereochemistry. I wonder if a "2x2" layout (reactant and mechanistic-intermediate in top row, then down-ish arrow leading to the two products in a second row) would make the image more useful?--would allow it to be displayed larger without demanding as much horizontal/side-scrolling width. DMacks (talk) 05:55, 9 August 2010 (UTC)[reply]
(for "and again") Now it's almost certainly outright wrong. You are not retaining the geometric relationship in the dienophile going into the product. Consider File:Bothexoendo.png, you are not retaining the correct a/b/c/d cis vs trans nature. DMacks (talk) 17:06, 9 August 2010 (UTC)[reply]
We're talking about Scheme 1 of DOI:10.1016/S0040-4039(03)00288-0 right? The diagrams and text descriptions clearly identify the dienophile part (the simple alkene not diene) as having trans geometry, which makes sense in light of standard Diels–Alder chemistry, not cis as you drew. Also, their EWG (the carbonyl carbon) is immediately attached to that alkene carbon, there is no C extra C between them. DMacks (talk) 16:04, 10 August 2010 (UTC)[reply]
I think I've finally got it fixed. I ended up having to add the implicit H atoms to convince myself that the stereochemistry was right, and I ended up keeping both transition states. I don't know where my brain has been these past few days... Thanks for sticking with me. --shoy (reactions) 01:26, 11 August 2010 (UTC)[reply]
