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Aids in visualizing atomic level phenomena Options
 
Spiralout
#1 Posted : 8/25/2020 11:59:07 PM

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Hey folks,

I'm not sure if there's been a thread about this before but if there has been I haven't been able to find one .

Does anyone have any programs (or favorite programs ) which model atoms, molecules, ions, electrons etc? It looks like there are a large handful of them, at least more than I expected there to be, listed on Wikipedia; I have no idea which might be most fruitful or useful though . My main goal is to help visualize these things .. I'm able to see them in my head but it would be nice to verify that Im looking at them somewhat realistically .


 

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downwardsfromzero
#2 Posted : 8/26/2020 1:01:13 AM

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Because I use open source software, I use GChemPaint for organic structures. It only crashes sometimes Big grin
For 3D molecules I use Avogadro which is quite nice once you get used to it.

At the atomic/electronic level I haven't any recommendations as that's outside my range of interest for modelling. Ditto for anything to do with ms windows or apple.
Ora, lege, lege, lege, relege et labora

“There is a way of manipulating matter and energy so as to produce what modern scientists call 'a field of force'. The field acts on the observer and puts him in a privileged position vis-à-vis the universe. From this position he has access to the realities which are ordinarily hidden from us by time and space, matter and energy. This is what we call the Great Work."
― Jacques Bergier, quoting Fulcanelli
 
Spiralout
#3 Posted : 8/27/2020 2:55:30 PM

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Thanks for the reply. Opensource /free is exactly what I'm looking for . I've installed gabedit but haven't had time to try to figure out to use it.. I remember using jmol at some point but I only used it very minimally.

I will try those two you mentioned ; I've heard of avogrado , it looks like that is one of the more popular ones?



 
downwardsfromzero
#4 Posted : 8/28/2020 4:51:57 PM

Peeing into the abyss

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Avogadro is quite effective if you want a 3D view. It also does simple aminations [if only!] animations, and has a tool that corrects the geometry of a structure after drawing it. It was a bit fiddly to start with but I was learning mostly by trial-and-error, and the correction tool was what I had been looking for all along.

I typically use GChemPaint for drawing reaction schemes and 2D molecules because that's what I've installed. I'll emphasize again, on my machine at least it can crash so regular saves are advised. Everything else it does more than acceptably well.

https://en.wikipedia.org...ext&oldid=968832974 is perhaps worth a look through; I'm not sure why the list of web-based modelling systems got so abruptly curtailed. It seems there was some kind of edit war going on Neutral

Attached is an example of a structure drawn with Avogadro.
downwardsfromzero attached the following image(s):
DMT.jpg (8kb) downloaded 60 time(s).
Ora, lege, lege, lege, relege et labora

“There is a way of manipulating matter and energy so as to produce what modern scientists call 'a field of force'. The field acts on the observer and puts him in a privileged position vis-à-vis the universe. From this position he has access to the realities which are ordinarily hidden from us by time and space, matter and energy. This is what we call the Great Work."
― Jacques Bergier, quoting Fulcanelli
 
Spiralout
#5 Posted : 8/29/2020 1:00:23 AM

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Hey,

Thanks. So I'm not exactly sure what I'm looking for (given my ignorance on the subject) but obviously seeing the structures is one thing.. If I could actually watch certain reactions play out I think that would be helpful in understanding it.. Like today I was wondering exactly what is going on when you add an "acid" or "base" to water.. When you add a base; does it break down the hydronium molecules and make 2 "new" h20 molecules for every 1 h30 molecule? Anyways.. seeing this played out visually seems like it would be useful.

I've installed avogadro on one system and I'm getting a file error; I'm trying it on another one now. I've installed gabedit ( think it's called) and been able to have it pull up some pre-programmed (or "drawn"Pleased compounds but haven't figured out anymore of it. It looks like a pretty complex GUI.

 
downwardsfromzero
#6 Posted : 8/29/2020 8:31:20 PM

Peeing into the abyss

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That's a more complex level of molecular animation you're looking for, by the sounds of it. A 3D view of proton transfer? Protons will be dancing their way through the solution continuously whether it's an acid or a base that has been added.

Water is a very dynamic substance. Here's a video illustrating it somewhat, I've no idea what program he used for the modelling:


Quote:
When you add a base; does it break down the hydronium molecules and make 2 "new" h20 molecules for every 1 h30 molecule?
Pretty much.
The simple equation is H3O+ + OH¯ → 2H2O

In aqueous solution the ions are surrounded by a solvation sphere of about six water molecules although, as said, this is dynamic - as well as being subject to widely differing interpretations.

[I've just noticed I've installed Gabedit a while ago but completely forgotten to try it out Embarrased Thanks for bringing it back to my attention; I've looked at a few things it interfaces with and don't like the look of the licensing agreements and password access that some of them have. It'll take a bit more poking around to find the open source plugins but this is (yet another) something I've been meaning to check out anyhow. There should be something more to share in this thread as my exploration of the possibilities continues.]
Ora, lege, lege, lege, relege et labora

“There is a way of manipulating matter and energy so as to produce what modern scientists call 'a field of force'. The field acts on the observer and puts him in a privileged position vis-à-vis the universe. From this position he has access to the realities which are ordinarily hidden from us by time and space, matter and energy. This is what we call the Great Work."
― Jacques Bergier, quoting Fulcanelli
 
Spiralout
#7 Posted : 2/3/2021 9:50:19 PM

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Hey downwards,

I took a bit of a hiatus from the chemistry stuff but now I'm back at it. I've begun to develop a bit of an ability to visualize this stuff in my minds eye but am now at a point of the studies where I'm doing more "macro" (although still tiny; right?) stuff; the way bonds are kept in place etc. I'm on VESPR and resonance and stuff like this.. I'm going to need to go back to the beginning of the book to get a better understanding of the wavefunction, light, photon stuff, but I'm just plowing ahead for the time being.


I noticed that microsoft edge (and probably just bing) have some limited aids for some molecules but nothing too useful. I use Brave & ddg normally so it isn't enough for me to open it up often. Have you played around with any more of these programs? I've put them basically entirely on the backburner because, by the time I go to look something up online, or try to figure out a program, I would have been more productive by just visualizing it myself and thinking about it a bit more.

 
 
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