Representing Chemical Reactions in SL

[Jean-Claude Bradley]

Andrew Lang and I have been discussing the representation of molecules reacting in Second Life in the form of 3D animation.  I am continuing the conversation on the mailing list so we can get input from others.

 

This is the Ugi reaction that I discussed with Jessica

http://usefulchem.wikispaces.com/Exp086

 

The Ugi reaction has several steps.

http://en.wikipedia.org/wiki/Ugi_reaction

 

We can just start with first step, which is the reaction of the amine (5-methylfurfurylamine) with the aldehyde (benzaldehyde).

Andy - do you need someone to create the HIN files or is that enough info?

 

It also has nice pictures of the final product crystals so we can show the molecule in that form as well.

--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University

http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com

[Jean-Claude Bradley]

Tony,

That might helpful, although probably not directly because it has to be recreated in Second Life.  Andy - do you have experience with ChemSketch?

 

Jean-Claude

 

On 7/16/07, Tony at ChemSpider <tony...@gmail.com> wrote:

JC,

The 3D viewer connected to ChemSKetch has a "movie mode" so that you
can generate 3D animations. It might be useful in the context you
describe. The ACD/Labs app scis can help you if you need assistance.
Let me know and I can connect you.

[Hiro Sheridan]

I don't have any experience with chemsketch though it might compliment
what we're trying to do in SL.
I'll see if we I can do the first reaction.
Andy (Hiro)

On Jul 17, 5:06 am, "Jean-Claude Bradley"

<jeanclaude.brad...@gmail.com> wrote:
> Tony,
> That might helpful, although probably not directly because it has to be
> recreated in Second Life. Andy - do you have experience with ChemSketch?
>
> Jean-Claude
>

[Hiro Sheridan]

Can somone post links to the chem data files of the molecules
involved.
I can only find 2d (flat) versions. Any 3d version that openbabel
recognizes will do.
Andy (Hiro)

[Jessica Colditz]

Hi,
I posted the "hin" files under the Files tab for all six compounds.

-Jessica

[Jean-Claude Bradley]

Hiro - Jessica used ChemSketch to do a quick 3D minimization then exported as mol then coverted to hin using OpenBabel.

 

Jessica,

If you use email to reply to the messages to the list then you can attach files as an alternative to uploading them on the mailing list page.

 

[Andrew Lang]

Thanks Jessica. I'll take a look soon.

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[Puppy Friend]

What's the name of the imine? What should we call it in SL?

On Jul 23, 6:28 pm, "Andrew Lang" <gameshon...@hotmail.com> wrote:
> Thanks Jessica. I'll take a look soon.
>
>
>
> >From: "Jean-Claude Bradley" <jeanclaude.brad...@gmail.com>
> >Reply-To: drexel...@googlegroups.com
> >To: drexel...@googlegroups.com
> >Subject: [Drexel Island] Re: Representing Chemical Reactions in SL
> >Date: Mon, 23 Jul 2007 16:34:05 -0400
>
> >Hiro - Jessica used ChemSketch to do a quick 3D minimization then exported
> >as mol then coverted to hin using OpenBabel.
>
> >Jessica,
> >If you use email to reply to the messages to the list then you can attach
> >files as an alternative to uploading them on the mailing list page.
>

> >On 7/23/07, Jessica Colditz <jmcold...@hotmail.com> wrote:
>
> > > Hi,
> > > I posted the "hin" files under the Files tab for all six compounds.
>
> > > -Jessica
>
> >--
> >Jean-Claude Bradley, Ph. D.
> >E-Learning Coordinator for the College of Arts and Sciences
> >Associate Professor of Chemistry
> >Drexel University
>
> >http://drexel-coas-elearning.blogspot.com
> >http://drexel-coas-talks-mp3-podcast.blogspot.com/
> >http://usefulchem.blogspot.com
>

> _________________________________________________________________http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_m...

[Puppy Friend]

Regarding the imine file that Jessica uploaded to the group? I think
the oxygen atom should be carbon right?
See: http://flickr.com/photos/7863441@N05/885654540/

[Jean-Claude Bradley]

No that should be an oxygen in the furan ring  - everything looks fine there!

The 2 D structures are here

http://slurl.com/secondlife /Drexel/223/196/26

Andy/Hiro - could you please put the first 3 molecules on that platform just on top of the 2D structures?

 

If we wanted to do an animation that is chemically correct, it would have to look like this:

http://www.cem.msu.edu/~reusch/VirtualText/amine1.htm

(scroll to bottom of page and click on the link marked:

To see an animated mechanism for imine formation   click

 

If Jessica makes the HIN files of all the intermediates in that mechanism, would that be enough for you to complete the animation in Second Life? (This reminds me of Peter Murray-Rust's use of animations based on CMLReact - maybe he can comment about using that in a systematic way in the future....)

 

As for the name, we'll just call it the imine intermediate for our purposes.  The full IUPAC, SMILES, InChI should be put in:

http://secondlifemolecules.wikispaces.com/

Jessica could you do that please?

 

[Andrew Lang]

I have rezzed the molecules over the 2d images on drexel island
(http://slurl.com/secondlife/Drexel/223/196/26).
They are copyable so you can play with them. If you want to make them stop
spinning, just remove the script from inside.

I'd like to do an animation that is chemically correct, I think that would
be cool.
Is the following what happens or am I making it more complicated than it
really is?:
(I'm looking at
http://www.cem.msu.edu/~reusch/VirtualText/mechism/aminerx/iminefm.htm)

1. Start with Benzaldehyde.
2. Along comes RNH2 and they join together (I would need a data file for the
joined together molecule).
3. A Hydrogen atom jumps from the Nitrogen to the Oxygen (I would need a
data file for this molecule).
4. H2O leaves (I would need a data file for this molecule and the water
molecule too to make sure everything has consistent angles, sizes, etc.)
5. Along comes another RNH2 and steals a Hydrogen leaving the Imine (I would
need a data file for the RNH3, the Imine is already done)

Just for my interest, do the intermediate molecules exist for a long time?
Do they have names?
How do they know this is what really happens?

Andy/Hiro

>From: "Jean-Claude Bradley" <jeanclaud...@gmail.com>
>Reply-To: drexel...@googlegroups.com

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[Jean-Claude Bradley]

Wow - they look really good - the spinning is helpful to get a better idea of their 3D shape.

Yes you have the basic idea - Jessica will upload the hin files shortly.  She will optimize the conformation for each intermediate in ChemSketch so that might give us a better idea of what acutally happens.  It would be nice if physical chemists could comment at some point about how we are doing this.

 

The neutral intermediate with an O and an N on the same carbon is called a carbinolamine. But usually we just number the intermediates to talk about them unambiguously.  In monitoring our systems, we have never observed the formation of a carbinolamine in any significant concentration by NMR.  Under different conditions I think people have been able to trap them and that is how mechanisms can be investigated.  But it is not a trivial thing to completely determine a mechanism like this experimentally.  Also note that the mechanism will change depending on the pH.  When we preform the imine there is no added acid catalyst so that will be a bit different than when acid is present.

 

On 7/24/07, Andrew Lang <games...@hotmail.com> wrote:

I have rezzed the molecules over the 2d images on drexel island

( http://slurl.com/secondlife/Drexel/223/196/26).

[Hiro Sheridan]

Looking forward to the molecules, Jessica will you upload them to the
files area?

When they have observed the carbiolamine, have they noted the hydrogen
in both positions? Or does the water detach as soon as the hydrogen
jumps?

On Jul 24, 3:18 pm, "Jean-Claude Bradley"

<jeanclaude.brad...@gmail.com> wrote:
> Wow - they look really good - the spinning is helpful to get a better idea
> of their 3D shape.
> Yes you have the basic idea - Jessica will upload the hin files shortly.
> She will optimize the conformation for each intermediate in ChemSketch so
> that might give us a better idea of what acutally happens. It would be nice
> if physical chemists could comment at some point about how we are doing
> this.
>
> The neutral intermediate with an O and an N on the same carbon is called a
> carbinolamine. But usually we just number the intermediates to talk about
> them unambiguously. In monitoring our systems, we have never observed the
> formation of a carbinolamine in any significant concentration by NMR. Under
> different conditions I think people have been able to trap them and that is
> how mechanisms can be investigated. But it is not a trivial thing to
> completely determine a mechanism like this experimentally. Also note that
> the mechanism will change depending on the pH. When we preform the imine
> there is no added acid catalyst so that will be a bit different than when
> acid is present.
>

> On 7/24/07, Andrew Lang <gameshon...@hotmail.com> wrote:
>
>
>
>
>
>
>
> > I have rezzed the molecules over the 2d images on drexel island

> > (http://slurl.com/secondlife/Drexel/223/196/26).

> > They are copyable so you can play with them. If you want to make them stop
> > spinning, just remove the script from inside.
>
> > I'd like to do an animation that is chemically correct, I think that would
> > be cool.
> > Is the following what happens or am I making it more complicated than it
> > really is?:
> > (I'm looking at
> >http://www.cem.msu.edu/~reusch/VirtualText/mechism/aminerx/iminefm.htm)
>
> > 1. Start with Benzaldehyde.
> > 2. Along comes RNH2 and they join together (I would need a data file for
> > the
> > joined together molecule).
> > 3. A Hydrogen atom jumps from the Nitrogen to the Oxygen (I would need a
> > data file for this molecule).
> > 4. H2O leaves (I would need a data file for this molecule and the water
> > molecule too to make sure everything has consistent angles, sizes, etc.)
> > 5. Along comes another RNH2 and steals a Hydrogen leaving the Imine (I
> > would
> > need a data file for the RNH3, the Imine is already done)
>
> > Just for my interest, do the intermediate molecules exist for a long time?
> > Do they have names?
> > How do they know this is what really happens?
>
> > Andy/Hiro
>

> http://drexel-coas-elearning.blogspot.comhttp://drexel-coas-talks-mp3-podcast.blogspot.com/http://usefulchem.blogspot.com- Hide quoted text -
>
> - Show quoted text -

[Jessica Colditz]

I've attached all of the HIN files for the structures involved in the imine
formation process. I've also attached the JPEG image of the overall process
that Khalid submitted earlier, only I added numbers next to each of the
structures that correspond to their HIN file names. Let me know if there
are any problems with the files.
-Jessica

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[Chris Landau]

Hiro,

Are you using some sort of open-source script to generate the in-world molecules?

They look great!

Best,

Chris Landau

(SL: Clement Greenberg)

Chris Landau

Lead Designer

N Formation Design, LLC

3D . CUSTOM . INTERACTIVE

www.nformationdesign.com

chris@nformationdesign.com

215-253-5631(office)

216-526-4443 (cell)

landauchris (Skype)

[Andrew Lang]

Chris,
i am using my own script. I will release it as open SLedware as soon as I
pretty the code up a bit and write some instructions.
Andy/Hiro

>ch...@nformationdesign.com

>215-253-5631(office)
>216-526-4443 (cell)
>landauchris (Skype)
>
>
>
>>

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[Andrew Lang]

Thanks Jessica!

I've built all the molecules. What is interesting is that when one thing
changes, like when the hydrogen moves to the oxygen, everything sort of
rearranges itself and moves too. Even when they join together initially,
some relative positions and angles change.

This means there is no simple animation. I will try to do something. It may
not be as pretty (smooth looking) as I envisioned initially. To do it
better, I would have to write a script that animated every atom and bond
individually at each stage. Though possible, that would be a lot of work.

I'll let you know when I have something worth showing.

Andy/Hiro

><< 1 >>

><< 2 >>

><< 3 >>

><< 4 >>

><< 5 >>

><< 6 >>

><< 7 >>

><< 8 >>

><< iminemech.jpg >>

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[jcb]

Andy,
Yes, the hybridization changes at some atoms and many angles shift.
If you manage to solve this in a general way we could populate Second
Life with several organic chemistry mechanisms that look more
realistic than the 2D representations everyone learns from books. But
I agree that it is probably not trivial to solve.

Jean-Claude

[jcb]

Andy - thanks for adding some more molecules to the SL molecules wiki
http://secondlifemolecules.wikispaces.com

That's a nice collection of molecules you have on Nature Island!
http://slurl.com/secondlife/Second%20Nature/103/50/23/

Jean-Claude

[Hiro Sheridan]

yw. A couple of questions on the chemical reaction:

1. Is it important to show molecules 5 & 6 (OH-)? Would it be OK to go
from molecule 4 to molecules 7 (H20) & 8 (Imine)?

2. The jpeg showing the mechanism is a little different than the other
description:
http://www.cem.msu.edu/~reusch/VirtualText/mechism/aminerx/iminefm.htm
Why is this?

Andy

On Jul 31, 9:50 am, jcb <jeanclaude.brad...@gmail.com> wrote:
> Andy - thanks for adding some more molecules to the SL molecules wikihttp://secondlifemolecules.wikispaces.com
>
> That's a nice collection of molecules you have on Nature Island!http://slurl.com/secondlife/Second%20Nature/103/50/23/

>
> Jean-Claude
>
> On Jul 27, 4:15 pm, jcb <jeanclaude.brad...@gmail.com> wrote:
>
>
>
> > Andy,
> > Yes, the hybridization changes at some atoms and many angles shift.
> > If you manage to solve this in a general way we could populate Second
> > Life with several organic chemistry mechanisms that look more
> > realistic than the 2D representations everyone learns from books. But
> > I agree that it is probably not trivial to solve.
>
> > Jean-Claude
>

> > On Jul 27, 3:59 pm, "Andrew Lang" <gameshon...@hotmail.com> wrote:- Hide quoted text -

[Jean-Claude Bradley]

Andy,

The reason that mechanism is different is that it is acid catalyzed, while the one Jessica gave you is under basic conditions.  The mechanism changes depending on conditions, like acidity.  There may also be different mechanisms competing.  For example, going from molecule 4 to 7 and 8 would involve loss of H+ and -OH at the same time.  I think that is plausible, even if it is not the dominant pathway.  For what we are trying to do that is probably ok.  As I have said before, it would be great to get some constructive criticism and debate about the mechanism that we display from some physical chemists who happen to stop by Drexel Island :)

 

Actually, not to confuse the issue further, but sometimes we run the reaction by mixing the acid at the same time as the aldehyde and amine.  Under those circumstances, the mechanism from the Reusch book would apply. (Although it turns out that imine formation is not complete under those circumstances in most cases - more on that later on the UsefulChem blog)
 

Jean-Claude

[Hiro Sheridan]

I have set up a 3d model of the mechanism here: slurl.com/secondlife/
Drexel/147/141/24/
Image here: http://flickr.com/photos/7863441@N05/969563014/

What do you think?

- Hiro/Andy

On Jul 31, 2:03 pm, "Jean-Claude Bradley"

<jeanclaude.brad...@gmail.com> wrote:
> Andy,
> The reason that mechanism is different is that it is acid catalyzed, while
> the one Jessica gave you is under basic conditions. The mechanism changes
> depending on conditions, like acidity. There may also be different
> mechanisms competing. For example, going from molecule 4 to 7 and 8 would
> involve loss of H+ and -OH at the same time. I think that is plausible,
> even if it is not the dominant pathway. For what we are trying to do that
> is probably ok. As I have said before, it would be great to get some
> constructive criticism and debate about the mechanism that we display from
> some physical chemists who happen to stop by Drexel Island :)
>
> Actually, not to confuse the issue further, but sometimes we run the
> reaction by mixing the acid at the same time as the aldehyde and amine.
> Under those circumstances, the mechanism from the Reusch book would apply.
> (Although it turns out that imine formation is not complete under those
> circumstances in most cases - more on that later on the UsefulChem blog)
>
> Jean-Claude
>

[jcb]

Just to update this thread:
We have accomplished our goal of demonstrating a chemical reaction in
Second Life
http://usefulchem.blogspot.com/2007/08/chemical-reactions-in-second-life.html

> >http://drexel-coas-elearning.blogspot.comhttp://drexel-coas-talks-mp3...- Hide quoted text -

[Eloise Pasteur]

Sneaking it into the SLogosphere too

http://www.secondlifeinsider.com/2007/08/03/chemistry-comes-alive/

EL.

>>> mp3...- Hide quoted text -

[Andrew Lang]

Thanks El. Excellent article!

>From: Eloise Pasteur <eloise...@gmail.com>
>Reply-To: drexel...@googlegroups.com
>To: drexel...@googlegroups.com
>Subject: [Drexel Island] Re: Representing Chemical Reactions in SL

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[Hiro Sheridan]

Here's an email from my physical chemist friend (I am trying to get
him to join the group):

It is a great way to view mechanisms!!!!! I have suggested several to
various department members, and George T. thinks it would be a great
way to teach stereochemistry!

I guess I did not see the water separation, and I agree that it would
be better to keep it there as I especially like the "back" feature.
You just need Hyperchem text descriptions of the various transition
states of the mechanism to create the 3D mechanism, correct? I think
it would be great for SN1/SN2 reactions and E1/E2 reactions as
stereochemistry is important there.

> Learn.Laugh.Share. Reallivemoms is right place!http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us- Hide quoted text -

[Jean-Claude Bradley]

Hiro - great!  I'd love to see more chemists join.  There was also some very positive feedback at the SciFoo conference.  Definitely more mechanisms will be useful and I'll be using them in the fall with my CHEM241 orgo class.  As your friend mentions, some mechanims like SN2 would be particularly useful to display in second life because of the important 3D effects going on.

It would be helpful to get a few chemist volunteers to help populate Second Life with mechanisms.  I am sure we can streamline the process as we move forward.  Also, Peter Murray-Rust has developed CMLReact, which represents chemical reactions in XML - maybe we could write a convertor to import existing mechanisms. (Peter, I'm not sure if you're on this list so I am copying you)

I'll be organizing a demo of the reaction online for those interested shortly and will post here with the time and slurl.

Jean-Claude

[Hiro Sheridan]

I've have received feedback from several physical chemists at ORU
about the mechanism.

1. It would be cool to show and animate the 'energy profile diagram'
along with the mechnism. This I think this should be easy, provided
you have the diagram :).
2. It would be cool to show and animate the 'charge distribution'
along with the mechanism. I think this would be very difficult but is
something we should consider for the future.
Thay also had some concerns that ChemSketch might not be very accurate
but it was not too big a deal.
The said that not only would the mechanisms be educational but having
students create mechanisms in SL would be awesome, I know I have
learned a lot. :)

On SL in general, it ranged from the very excited, to the intrigued,
to it's from the Devil!

> Learn.Laugh.Share. Reallivemoms is right place!http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us- Hide quoted text -

[Jean-Claude Bradley]

answers below

On 8/8/07, Hiro Sheridan <games...@hotmail.com> wrote:

I've have received feedback from several physical chemists at ORU
about the mechanism.

1. It would be cool to show and animate the 'energy profile diagram'
along with the mechnism. This I think this should be easy, provided
you have the diagram :).

 

I don't have the energy diagram handy but, yes it could be useful if someone wanted to contribute it. 

2. It would be cool to show and animate the 'charge distribution'
along with the mechanism. I think this would be very difficult but is
something we should consider for the future.

 

Yes that is missing - a simple thing would be to add a minus and plus signs on the intermediate. I don't know it you can easily do that.

Thay also had some concerns that ChemSketch might not be very accurate
but it was not too big a deal.

 

True - for a real calculation you would use more sophisticated programs but for this purpose I think you'll get most chemists to agree that it is adequate.  Chemsketch is free and easy to use.

The said that not only would the mechanisms be educational but having
students create mechanisms in SL would be awesome, I know I have
learned a lot. :)

 

I'm sure Jessica has learned something from helping out with this.  This will likely be one of my extra credit options for my fall classes.  If several teachers did the same thing and we pooled our reactions (or at least kept track of them with the seconlifemolecules wiki) we could quickly have some great content - 3D Wikipedia style

On SL in general, it ranged from the very excited, to the intrigued,
to it's from the Devil!

 

Well part of it is owned by the Devil - have you seen Beth's island on Dante's Inferno ? :)

[Jessica Colditz]

I've attached all of the converted HIN files for the remaining molecular
structures involved in the Ugi synthesis. I named them according to what
level platform the molecules appear on in SL, along with what type of the
molecule it is (it should be the same as what appears on the posters in SL).

-Jessica

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[Jean-Claude Bradley]

Absolutely Peter - I would be happy to help you with that.

Contact me to set up a time if you don't see me online when you're ready.

Hopefully we can get a few more chemists to join.  The ACS has just set up a booth today in the Chemistry Corner.

 

Jean-Claude

 

On 8/15/07, Peter Murray-Rust <peter.mu...@googlemail.com> wrote:

On 8/7/07, Jean-Claude Bradley < jeanclaud...@gmail.com> wrote:

Hiro - great!  I'd love to see more chemists join.  There was also some very positive feedback at the SciFoo conference.  Definitely more mechanisms will be useful and I'll be using them in the fall with my CHEM241 orgo class.  As your friend mentions, some mechanims like SN2 would be particularly useful to display in second life because of the important 3D effects going on.

It would be helpful to get a few chemist volunteers to help populate Second Life with mechanisms.  I am sure we can streamline the process as we move forward.  Also, Peter Murray-Rust has developed CMLReact, which represents chemical reactions in XML - maybe we could write a convertor to import existing mechanisms. (Peter, I'm not sure if you're on this list so I am copying you)

I am on this list and would love to have collaborators in SL. First JC was going to show me how to get some clothes on.

P.

Drexel University

http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com