How can I determine the width of one molecule of a substance?

April 18, 2008 8:57 AM

What is the width of a single molecule of Tartrazine? Brilliant Blue FCF?

It's for something I'm writing for my website. I really have no idea how to even start looking into this, though I've gathered it depends greatly on the shape of the molecule and is difficult to pin down to a number due to electrons moving and such. So I'm just looking for a rough estimate.

posted by jwells to science & nature (6 comments total)

Well, you'll want to start with bond lengths, which themselves are not exact and vary depending on the molecule there in. Based on these, and the structures shown, I'd say, as very rough estimates, 1800pm for tartrazine and 2200pm for Brilliant Blue FCF, assuming by "width" you mean the greatest distance from any one atom in the molecule to any other.
posted by DevilsAdvocate at 9:10 AM on April 18, 2008 [1 favorite]

There are a couple of problems with your question. The majority of molecules are not symmetric so will have different dimensions - are you looking for the longest side, or the shortest, or an average of all three.

The classic way of doing this is to measure the volume of a drop and then place it on a surface where it will spread out to a layer one-molecule thick - oil on water for example - and measure the size of the circle produced. Tartrazine is water soluble unfortunately so you'd need a different "non-solvent".

To really solve the problem DevilsAdvocate is right on the money. You need to find the appropriate bond lengths (which are centre-of-atom to centre-of-atom) and the angles between the bonds and do some trig along whichever axis you're interested in to find the overall length. You will need to include space for van der Waal's on the ends as as well.
posted by alby at 11:33 AM on April 18, 2008

You can get the mol file or some other coordinate file of the molecule and open it in jmol. from there you can get a rough estimate of lengths etc. using the ruler functions. That would actually be really easy to do. I did a quick search and wasn't able to easily find it- but it should be around, the picture on the wiki entry was made from one so someone has it.

In fact, I just did it- and it says that the total length is about 1.9 nm longest, but you should check for yourself, it seems a bit small but I don't really have a feel for this stuff yet. Also the input file is planar, and that seems odd, as this doesn't seem like a planar molecule.
posted by Large Marge at 12:20 PM on April 18, 2008

You could generate the coordinates yourself with a program like ACD ChemSketch Freeware. Draw the molecule, then from the Tools menu choose 3D Structure Optimization. Export the coordinates as a MOL file (File menu -> Export...) then, as Large Marge mentions, use a program like jmol to open it and measure the desired dimension. You could also use Mercury (from the Cambridge Crystallographic Data Centre), which also can import MOL files, and doesn't require you to install Java.
posted by hangashore at 1:54 PM on April 18, 2008

I'm practically ready to take a crack at Chemistry one more time (between HS and College I'm still not comfortable with it). With programs like these I might be able to understand it! Thanks all! I got what I needed and a whole lot more. Especially enjoyed how the answers built on each other. I ended up pulling the .mol file from chemexper.com, 3D'ing it in ACD, and then measuring in JMOL. I did try sketching it in ACD but it's a bit beyond me.
posted by jwells at 7:58 AM on April 19, 2008

Ha ha! This reminds me of my Biochemistry I exams. We had to estimate the size in Angstroms [10^(-10) m] of many things.

If you have the chemical structure (which you do via Wikipedia), then going by bond lengths as mentioned above is the best way. Folks above have said the same things; here's what I'd do on an exam (to get full credit):

First, mentally observe the longest point in the molecule of interest (like wiht Tartrazine, from one S to the other). Then, look up all the bond lengths necessary (S-C, C=C, C=N, N=N, etc.), and all the radii of the atoms that make up the chain (commonly, they're called Van der Waals radii). It turns into a simple add-'em-up problem, which, while not the greatest activity for a sunny Saturday afternoon, probably beats tinkering with computer programs (though maybe that's more your thing). Add all the lengths + 2(radius) of each atom, and you should get a rough estimate in Angstroms.

The answer won't be exact when you're looking at ring structures in your answer, but you shouldn't be off by too much. An intrepid/lazy chemist might even look up recorded sizes of smaller molecules contained within the one in question (like, say, a ring strucutre), and just add them all together. And as my professor always said, if you state your assumptions clearly then you'll get full credit.
posted by BenzeneChile at 12:03 PM on April 19, 2008