The Spice must flow ...

    ❝Some of the contributions are sure to arouse controversy...❞

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Ziggy
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The Spice must flow ...

Postby Ziggy » 10 Nov 2019 14:30

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.

Image

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Not an obsessive Dune fan at all … :roll:

georgiedenbro
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Re: The Spice must flow ...

Postby georgiedenbro » 11 Nov 2019 11:23

Wish I could understand what any of that means. Nice images, though :)
"um-m-m-ah-h-h-hm-m-m-m!"

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Serkanner
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Re: The Spice must flow ...

Postby Serkanner » 11 Nov 2019 13:26

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 ...

Postby Ziggy » 11 Nov 2019 13:50

: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 ...

Postby SadisticCynic » 12 Nov 2019 07:41

Very cool. :clap:

What was the original image like? A structural formula?
Ah English, the language where pretty much any word can have any meaning! - A Thing of Eternity

Ziggy
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Re: The Spice must flow ...

Postby Ziggy » 12 Nov 2019 08:35

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 ...

Postby Naib » 12 Nov 2019 10:05

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 ...

Postby Ziggy » 12 Nov 2019 13:54

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 ...

Postby Naib » 13 Nov 2019 11:15

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 ...

Postby distrans » 17 Nov 2019 22:10

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...