Identifying the Molecule in Fig.A and Fig.B - John

[John37309]

Any idea that this molecule is?

Fig.A shows the molecule and the electron orbitals and bonds.
Fig.B is the same image with very approximate bond angles and molecular geometry angles. All the angles are close approximations.
The angles are written in black and the number of electrons are in navy blue.

I honestly don't know what elements are used in the molecule. Any ideas, thoughts, guesses, pointers, anything that might help me identify what the molecule is would be helpful. Even identifying part of the molecule would be helpful.

Thanks guys,
John.

 

[SpectraCat]

What does the data represent? Is it experimental data, or just some artists rendering of idealized concepts? For example, what is the meaning of the little dots & triangles in the centers of the larger regions?

 

[John37309]

SpectraCat,
Thanks for replying!

Its a drawing from an old researchers note book. The man who drew the picture is dead now, so i can't ask him what he drew, R.I.P. I scanned the drawing and made a new drawing to clear things up a bit.

As you suggest, i think it might be an idealised concept of some type of molecule or compound. There was no real written explanation. Its possible that this molecule is used to coat the outer surface of a glass lens of some type. It was for some type of optical amplification device.

This would be my personal speculation;
The full molecule seems to have 3 smaller molecules. Each of the 3 smaller molecules has 2 bold "shells", at least that's what I'm describing them as. I speculate that the bold double shells could be the torus shaped Dz2 electron orbitals seen here; http://en.wikipedia.org/wiki/File:D4M0.png , We might be looking from the top down on the molecule so we see the two torus rings maybe. Might be some type of hybrid orbital with the S shells. That might mean at least one of the atoms in each of the smaller molecules would be from the d-block of the periodic table, elements greater than element 21, Scandium. Or p-block elements 31 to 54. But that's a guess!

Inside the bold double shells there are 3 dots with 2 triangles between each of them. I speculate that they are the nucleus of 3 atoms and the triangles are types of covalent bonds between the atoms. In Fig.B i added rough measurements for the angles. The first small molecule has four 90 degree angles which might mean the molecular geometry of the bonds are linear, the 3 atoms might be bonded in a straight line. The other 2 small molecules might have bent bond angles because the angles do not equal 180 degrees.

I speculate that all the other half circles are electron orbital lobes stacked one inside the other, some have 2 lobes, some have 3 lobes, some have 4 lobes. Inside each lobe is a triangle showing the 3 dimensional angle that particular set of lobes connects onto that part of the molecule. In other words, the whole thing might be a 3 dimensional image of a molecule flattened out into 2 dimensions, but also included is enough electron orbital information to tell you properties of the individual atoms or the molecule itself.

I speculate that all of the electron lobes you see would connect to either the top of the molecule facing you, the bottom of the molecule away from you, or some have angles connecting to the sides of the molecule at various angles.

I would appreciate if you would have a wild guess, any guess would help. Blow your mind and take a guess out of the blue.

John.

 

[SpectraCat]

SpectraCat,
Thanks for replying!

Its a drawing from an old researchers note book. The man who drew the picture is dead now, so i can't ask him what he drew, R.I.P. I scanned the drawing and made a new drawing to clear things up a bit.

As you suggest, i think it might be an idealised concept of some type of molecule or compound. There was no real written explanation. Its possible that this molecule is used to coat the outer surface of a glass lens of some type. It was for some type of optical amplification device.

This would be my personal speculation;
The full molecule seems to have 3 smaller molecules. Each of the 3 smaller molecules has 2 bold "shells", at least that's what I'm describing them as. I speculate that the bold double shells could be the torus shaped Dz2 electron orbitals seen here; http://en.wikipedia.org/wiki/File:D4M0.png , We might be looking from the top down on the molecule so we see the two torus rings maybe. Might be some type of hybrid orbital with the S shells. That might mean at least one of the atoms in each of the smaller molecules would be from the d-block of the periodic table, elements greater than element 21, Scandium. Or p-block elements 31 to 54. But that's a guess!

Inside the bold double shells there are 3 dots with 2 triangles between each of them. I speculate that they are the nucleus of 3 atoms and the triangles are types of covalent bonds between the atoms. In Fig.B i added rough measurements for the angles. The first small molecule has four 90 degree angles which might mean the molecular geometry of the bonds are linear, the 3 atoms might be bonded in a straight line. The other 2 small molecules might have bent bond angles because the angles do not equal 180 degrees.

I speculate that all the other half circles are electron orbital lobes stacked one inside the other, some have 2 lobes, some have 3 lobes, some have 4 lobes. Inside each lobe is a triangle showing the 3 dimensional angle that particular set of lobes connects onto that part of the molecule. In other words, the whole thing might be a 3 dimensional image of a molecule flattened out into 2 dimensions, but also included is enough electron orbital information to tell you properties of the individual atoms or the molecule itself.

I speculate that all of the electron lobes you see would connect to either the top of the molecule facing you, the bottom of the molecule away from you, or some have angles connecting to the sides of the molecule at various angles.

I would appreciate if you would have a wild guess, any guess would help. Blow your mind and take a guess out of the blue.

John.

I honestly have no idea, but what it kinda looks like is an experimental difference density map from x-ray diffraction data. I can't really speculate more as to what molecule it might be unless you can provide some more context. What sorts of information accompany the picture in the notebook?

 

[John37309]

I honestly have no idea, but what it kinda looks like is an experimental difference density map from x-ray diffraction data. I can't really speculate more as to what molecule it might be unless you can provide some more context. What sorts of information accompany the picture in the notebook?

Your guess is good. I'm just doing some Google searches on those words.

Some extra info and speculation;
1. Its something to do with the chemical element tellurium (100% probability).
http://en.wikipedia.org/wiki/Tellurium . Now that's a broad statement, tellurium is a very popular and versatile element! I'm 100% confident its related to tellurium or some telluride compound, molecule, crystal, whatever. That could mean one of the elements in the image is tellurium, but tellurium, element 52, would theoretically have 52 electron lobes. But the total number of electrons in the image is less than 52. This leads me to the conclusion the elements used in the molecule have smaller atomic numbers because it looks to me like there might be 9 individual atoms in the image. I'm struggling to see a tellurium atom in the image cos there just isn't enough electron lobes. But maybe he only drew enough information to indicate that one of the atoms is tellurium. Either way, tellurium is some how involved in what this thing does.

2. Its possible the molecule or compound is used to "coat the surface" of paratellurite, α-TeO2 glass; http://en.wikipedia.org/wiki/Tellurium_dioxide (30% probability)

3. Its possible the molecule or compound actually IS paratellurite, α-TeO2 glass. (20% probability). Paratellurite, α-TeO2, is used as an acousto-optic material; http://en.wikipedia.org/wiki/Acousto-optic . Tellurite glasses have also been shown to exhibit Raman gain up to 30 times that of silica, useful in optical fibre amplification.

4. Paratellurite, α-TeO2 glass suffers from Alpha decay; http://en.wikipedia.org/wiki/Alpha_decay . This is why i'm about 90% confident the molecule is used as a coating on the surface of a piece of α-TeO2 glass. Or that the molecule or compound actually IS α-TeO2 glass. But i just can't see it in that image.

5. (90% probability), Light or possibly infrared light passes through this molecule/compound/crystal, it might be amplified and might be modulated to encode digital or analogue information for electrical or radio transmission.

6. I'm 90% confident its a 3 dimensional molecule, but the molecule is flattened into 2 dimensions to make it easier to draw.

7. The 9 "dots" could be the 1s electron orbitals surrounding a nucleus. Or they could represent the nucleus itself, I'm not sure.

Extra info about tellurium;
--------------
Tellurium (52) Electron configuration can be written in 2 ways;
1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p6 4d10 5s2 5px2 5py2
or
[Kr] 4d10 5s2 5p4
Splitting them up;
1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p6 4d10 5s2 5px2 5py2
--------
Total s electrons= 10; 1s2 2s2 3s2 4s2 5s2
Total d electrons= 20; 3d10 4d10
Total p electrons= 22; 2p6 3p6 4p6 5px2 5py2
Overall total = 52
-----------
I made this image of the tellurium electron orbitals

----------
Here is the molecule again;

--------
And the bond angles; (The angles are only aproximate!)

Note; Worth noting that I'm far from being an expert in chemical engineering. My education background is electrical as opposed to chemical.

Please do speculate, please do say what your thinking. No matter how silly the thought is. I need the feedback because I'm stuck. Please try to find fault in what I'm saying here. Criticise me, please!

John.

 

[Borek]

Were the numbers on the drawing?

I guess question I am asking is - what is the original part of the drawing, what is added by you? Or is it all taken from the original? Why do you think digits are numbers of electrons?

 

[John37309]

Were the numbers on the drawing?

I guess question I am asking is - what is the original part of the drawing, what is added by you? Or is it all taken from the original? Why do you think digits are numbers of electrons?

Hi Borek,
Thanks for replying!

There are no numbers or letters on the original drawing, the original is just visual imagery, its what is seen in Fig.A ! The image you see with numbers and angles are just me trying to interpret the original drawing. The original drawing is just the red shaded shapes, dots and triangles.

So the digits are added in by me to point out the fact that some lobes have 2 orbitals, some have 3 orbitals, and some have 4 orbitals. Also, the extra drawing with the 360 degree protractor and the 2:3:4 angles are also me interpreting the image, its me that added that bit.

John.

 

[SpectraCat]

Can you explain why you think that the image represents a molecular structure? It doesn't really look like one to me .. except perhaps for some sort of difference density map, as I mentioned earlier. In your reconstructed image, you have shown some of the lobes as intersecting/overlapping? Is that your interpretation, or is that what the original image showed?

Is the original image a sketch, or is it computer generated?

 

[John37309]

Can you explain why you think that the image represents a molecular structure? It doesn't really look like one to me .. except perhaps for some sort of difference density map, as I mentioned earlier. In your reconstructed image, you have shown some of the lobes as intersecting/overlapping? Is that your interpretation, or is that what the original image showed?

Is the original image a sketch, or is it computer generated?

The original image is a very carefully drawn sketch, he must have spent quite a bit of time drawing the original. Its was not a quick slap-together sketch. He was looking for perfection in the original drawing.

Yes, very observant. I did actually interpret the original drawing and yes, i personally added and made the lobes overlap into each other and if the lobes pointed toward the central molecule, i did interpret the drawing and i completed the lobes so they intersect inside another part of the drawing. This is the only real extra part i added to the drawing. In the original, the lobes do NOT continue inside each other or inside the central bit.

I suppose i could also say that the 3 large blobs with the 3 dots inside them, in the original drawing, they were more like a torus than the way you see them in my drawing as shaded the whole way through to the middle. They are quite distinctly oblong torus shapes in the original drawing.

Q; "Can you explain why you think that the image represents a molecular structure?"

A; Yes, its a personal assumption. It might not be a molecule at all if you can suggest something else. I assume its a molecule simply because the "lobe" things have a striking similarity with the way many chemists draw electron orbitals. Its the way the lobes are stacked one inside the other leads me to that conclusion.

So i went off and started learning about VSEPR theory; http://en.wikipedia.org/wiki/VSEPR_theory . Electrons repel each other, but they also stack themselves around each other in shells as shown in the atomic orbitals page; http://en.wikipedia.org/wiki/Atomic_orbital . Different artists draw that orbital stacking in different ways. So that's why i think the lobes are electron orbitals. I'm very open minded to an alternative suggestion.

EDIT; I searched google images for the words "difference density map", and yes, that could be it! Maybe!

EDIT 2; I'm lying! To be honest, i have interpreted the actual lobes themselves. On the original, they are just drawn as "arcs". I personally interpreted them as being complete lobes, like a cloud. But in the original, they were not drawn as clouds, they were just drawn as outer arcs.

John.

 

[John37309]

Ok, so far the best i have come up with from google image searches is this page;
http://smu.edu/catco/research/van-der-waals.html

The drawings on that page look very close to my drawing. So it seems probable that maybe my drawing might be showing these van-der-waals surfaces.

One of the drawings from that page that looks similar to my drawing;
[PLAIN]http://smu.edu/catco/research/images/van-der-waals-3.png

The drawing is not a perfect match, but the drawing method looks similar. Either way, these things are still plots of electron orbitals and the bonds between the atoms. My drawing just has the added extra of angular information with the triangles.

The following page also has a similar image; http://ursula.chem.yale.edu/~chem125/125/answ/a198/a198.html
The guy says the image is from "X-ray diffraction from a single crystal to determine total electron density";
Here it is;
[PLAIN]http://ursula.chem.yale.edu/~chem125/125/answ/a198/Image65.gif

It also looks like my image.

John.

 

[DrDu]

Can't you post a scan of the original drawing?

 

[SpectraCat]

Ok, so far the best i have come up with from google image searches is this page;
http://smu.edu/catco/research/van-der-waals.html

The drawings on that page look very close to my drawing. So it seems probable that maybe my drawing might be showing these van-der-waals surfaces.

One of the drawings from that page that looks similar to my drawing;
[PLAIN]http://smu.edu/catco/research/images/van-der-waals-3.png

The drawing is not a perfect match, but the drawing method looks similar. Either way, these things are still plots of electron orbitals and the bonds between the atoms. My drawing just has the added extra of angular information with the triangles.

The following page also has a similar image; http://ursula.chem.yale.edu/~chem125/125/answ/a198/a198.html
The guy says the image is from "X-ray diffraction from a single crystal to determine total electron density";
Here it is;
[PLAIN]http://ursula.chem.yale.edu/~chem125/125/answ/a198/Image65.gif

It also looks like my image.

John.

Yes, but that "extra information" you added is very misleading to an expert ... we are used to looking at plots like the one in your post above, not your original sketch. The overlapping of the lobe and the added triangles make it look very weird. Still, without further annotation, even if you posted a scan of the original drawing (that would be helpful by the way), it is unlikely that we could be of much assistance. All covalent molecules are held together by "shared" electrons, and the changes in electron density between the atoms can be represented using contour plots. Looking at the contours doesn't give any information about what the molecule actually is ... not without quite a bit of additional information anyway.

 

[John37309]

I can't scan the original drawing, I'm not allowed, and i will have to arrange another trip away to get access to the notebook again. This will take time.

I can give you more information about the way its drawn, or a more specific angle of one of the triangles, or i can draw a better representation of the lobes from what's in my head, but in reality, the drawing with no written text is exactly what the original looks like.

Please have your best wild speculation guess at what it might be. There is a Hugh quantity of information in the drawings you see.

I see what looks like 3 smaller molecules, with covalent bonds, represented by triangles, and what looks to me like s orbitals, p orbitals, and possible d orbitals. There may also be some type of hybridisation going on in the drawing between the different orbitals. Let's be clear here, the triangles are original! And they are drawn precisely as you see them in that drawing. The triangles in the original drawing actually physically have little bends in the triangles themselves, just as you see them. And the triangles are also not lined up with each other in nice neat lines, this is how the original is drawn, kinda "scraggy" if you want to describe it that way.

Please do try to speculate. I know this drawing is not what convention would dictate in classical chemistry and in textbooks. As i said, i believe the original scientist attempted to flatten a 3D drawing into 2 dimensions.

Its possible he was only drawing the valence electrons or something like that. But yes i agree with you guys, i can't actually find any drawing on the internet that is drawn this way. The drawing is unique!

John.

 

[John37309]

Here is a question;
Down the middle of the molecule, i see what looks like trigonal bipyramidal geometry, just like this;

Except my molecule is unusual. It has 2 lobes, 3 lobes and 4 lobes in the middle bond. Does anyone know any molecule where that could happen? with the 2:3:4 electron configuration surrounding a bond? Its possible that central part of the molecule might be bent at a right angle pushing the 2:3:4 lobes out the back of the right angle to one side.

John.