The Spice must flow ...


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Ziggy
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The Spice must flow ...

Post by Ziggy »

As a chemist, I thought it would be fun project to translate the image of the Spice molecule from DE into a molecular modelling package. Turned out to be a lot of work and have corrected some errors in the original e.g. removing the erroneous extra copper atom in the porphyrin moiety. Then I performed a simple semi-empirical geometry optimisation on the structure, since a full quantum calculation would literally take months on a desktop machine. Nevertheless, thought you guys might like to see. Of course the claim in the DE is that this is merely a monomer unit but easy to imagine this structure repeated in a chain. Have shown a few different views in tube, ball & spoke and space-fill format, with the latter being the most veridical.

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Not an obsessive Dune fan at all … :roll:
georgiedenbro
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Re: The Spice must flow ...

Post by georgiedenbro »

Wish I could understand what any of that means. Nice images, though :)
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Serkanner
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Re: The Spice must flow ...

Post by Serkanner »

georgiedenbro wrote:Wish I could understand what any of that means. Nice images, though :)
So do I .. :lol:

Very cool images indeed.
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and wrote a Dune Novel."
Ziggy
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Re: The Spice must flow ...

Post by Ziggy »

:lol: Yeah right, sorry. Was fully engaged in nerd mode when I made that post. In short, what the software does is attempt to compute the 'shape' of how the molecule is likely to be arranged in RL. Bases this on which configuration has the minimum energy. Since chemical bonds can rotate, bend and stretch, with large molecules like erm … melange, the calculation is very complex and time consuming so I've used a simpler, faster but less accurate method to do so. Given it's just for fun I don't think there's any need to run this one on a cluster!

Similar principle as protein folding which some of you may have been involved with through Folding@Home.

Now if anyone is in the mood to try cooking this up, please do report back with any symptoms such as hearing the voices of relatives in your head, seeing next weeks' winning lottery numbers and so on.
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SadisticCynic
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Re: The Spice must flow ...

Post by SadisticCynic »

Very cool. :clap:

What was the original image like? A structural formula?
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Ziggy
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Joined: 15 Dec 2009 07:34
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Re: The Spice must flow ...

Post by Ziggy »

Yes indeed, the original structural formula comes from the melange entry in the DE ...

Image
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Naib
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Re: The Spice must flow ...

Post by Naib »

Great work. :clap:

As a biochemist I did this years ago with a couple of sets of plastic organic chemistry model sets. I had it for years and then my 4 year old niece saw it and took it apart.

I should get a couple of new sets and do it again.
Ziggy
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Re: The Spice must flow ...

Post by Ziggy »

Have loads of Molymod and you are tempting me to do this! :lol:
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Naib
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Re: The Spice must flow ...

Post by Naib »

You should. Computer models are great but there's nothing quite like holding one in your hands.
distrans
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Re: The Spice must flow ...

Post by distrans »

would have thought the DE entry was merely art and
any remotely objective analysis would have spit it out

wonder who drew it that first time...
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