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Offline ragnarokas

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MC simulation of polymer growth
« on: November 09, 2021, 02:33:13 AM »
I am writing an MC model of polymer growth upon irradiation in C++, but because I have no chemical background, I really need to consult experts in this area from time to time, and I am hoping that this forum will be the place to do so.

For the time being, I'm interested in methacrylic acid. The monomer is approximated as a cuboid with dimensions of 2x4x8 angstroms.
- is the size more or less accurate? It should be related to the monomer's space occupation
- at what angles do these monomers connect to one another? It is said to be about 120 degrees along their main plane (X axis ?) and can be rotated at random angles along Y and Z axis.

I would be grateful if someone who is ok in such details could provide accurate data and consult me as simple google won't helping much.

Offline Borek

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Re: MC simulation of polymer growth
« Reply #1 on: November 09, 2021, 03:59:56 AM »
It would probably most beneficial to you to use some ball and stick model to build the compounds you are interested in and to get some intuition about  possible shapes. Once you know the shape atom distances for a given kind of a bond are to a good approximation constant, so finding possible dimensions is just a matter of reasonably simple geometry.

Depending on what you need you can try to estimate the molecule size from known shape and bond lengths (although you need to add a bit, as the distance between atoms in adjacent molecules is always larger than the bond lenghts), you can also try to estimate molecule volume from teh density (through molar mass and Avogadro's number). 2x4x8 Å is definitely in the right ballpark, but whether it is accurate enough depends on the application.

Angle part is a bit more difficult to address, as the molecule is not rigid, some bonds can freely rotate. That's where the ball and stick models come handy to help understand what is going on.
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Offline ragnarokas

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Re: MC simulation of polymer growth
« Reply #2 on: November 09, 2021, 09:48:16 AM »
Thanks a lot for your answer.

The approximations are ok for my model, it is intended to be a coarse scale one. I need at least some approximations.
So the size is moreless ok, as I understand - that's great.

So where could I look for the information, how exactly the methacrylic monomers connect betweens themselves? Again - approximations are just fine. I need some basic info, not looking into some specific cases, etc.

 - at what angles they connect to each other along the line; -
- at what angles the branches start to connect to the main line;
- I am looking for predefined ones  - if other can rotate freely, that's just perfect.

Sorry for my expressions as non-chemist

Offline Borek

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Re: MC simulation of polymer growth
« Reply #3 on: November 09, 2021, 05:04:54 PM »
Yes, teh size looks more or less in the correct ballpark.

I really, really suggest you try ball and stick models. You will learn much more in five minutes playing with them than we can explain in hours of writing.

Unfortunately I am on my cell now and a better answer would be way too time consuimng to edit. Still, the only thing I can show is how the atoms in the dimer ara arranged, you would still need to find the angles that fit your model from the molecule geometry.
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Offline ragnarokas

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Re: MC simulation of polymer growth
« Reply #4 on: November 10, 2021, 02:55:21 PM »
Ok I see that everything is much more complex and there is no just a simple answer I wanted. This is typical when you have no knowledge about topic :)

 - What do you exactly mean by "try ball and stick models"? How exactly I can play(=try) them, where?
-  Maybe it is possible to simulate the needed polymer chain with, for example, Amsterdam software or Materials Studio?
- Maybe there are some sketches/schematics/drawings how the particular polymer chains?

As for now I think I have an idea ( the connecting bonds should be at 109.5 degrees while the monomer itself can be randomly rotated ), just would like to be able to compare my results with smth. Thank you very much for your time ,
A.

Offline Borek

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Re: MC simulation of polymer growth
« Reply #5 on: November 10, 2021, 03:36:08 PM »
Ok I see that everything is much more complex and there is no just a simple answer I wanted. This is typical when you have no knowledge about topic :)

I think you came to a right place, while at the moment I am on vacations and cut away from my usual tools, I do have some experience in simulations (although I admit I did them back in eighties, with software written from scratch).

Quote
What do you exactly mean by "try ball and stick models"? How exactly I can play(=try) them, where?

https://en.wikipedia.org/wiki/Ball-and-stick_model

I am afraid living in BFE I am not able to suggest any particular set that you could buy, but even using modeline balls and matchsticks or toothpicks will help.

Quote
-  Maybe it is possible to simulate the needed polymer chain with, for example, Amsterdam software or Materials Studio?
- Maybe there are some sketches/schematics/drawings how the particular polymer chains?

Many ways to skin that cat, definitely. I could do some sketches and scan them for you - but not before Tuesday.
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