It’s surprisingly frustrating knowing exactly what you need to do but finding that learning to do it just takes time. It’s like learning to play an instrument. At first what you play sounds awful, but after a while you can have a recital, where people can even have some enjoyment of your playing, even if no one thought you could be a professional.
So here is my first ‘recital’ of a helical array of monolignols:
It’s still quite flawed as the science goes but it already illustrates the basic concept of the folding of toroidal aggregates of molecules. When illustrated the above way, the volume taken up by the molecules isn’t properly shown. A decent estimate of this would be to include a Van der Waals surface, like what you can add when using a software like Avogadro.
However, I can’t send this Van der Waals surface data from Avogadro to Blender. I think I can manually, or semi-manually, be able to add these surfaces to the Blender File, but for now I’ll just have to ignore them.
Okay, now that I’ve owned up to not portraying the fully true arrangement of monolignols in this structure, what am I saying?
First of all, for simplicity while there are three main monolignols, I’m portraying softwood with this model, like the coniferous trees of Finland: pine and spruce. In softwood the monolignols are 95 % coniferyl alcohol (below), which means that ignoring the rest of the monolignols isn’t that big of an error.
And after that I don’t really have to make large concessions. The model assumes that the alcohols, or the OH at the end of the long chain (called propenol, when the OH is included) form hydrogen bonds with the OH connected to the hexagon (called phenol when the OH is included). This is just common knowledge for a chemist, and you really don’t need to prove it (although you can, if you wish).
The only tiny thing that I must assume is that the monolignols don’t magically fly as individual molecules from where they are biosynthesized via the phenylpropanoid pathway to the secondary cell wall, which gives structure to plants. What I hypothesize is that for the monolignols to pass through the cell membrane, they need to form a donut-shaped aggregate, or a toroidosomes, which is cleaved from the cell membrane as a single unit. Here's a very rough illustration of the closed slinky structure of the monolignol helix.
Here I only show monolignols in one turn of the helix, with a bending helix acting as a stand-in for the rest of the monolignols. Once these closed slinkies exit the cytoplasmic membrane, they tend to aggregate with a ‘deck shuffle’ analogy, where the individual turns of the helix fold together, like this.
And you end up with a hexagonal lattice, like this:
I already have a manuscript that I stopped working on in August 2022, when I realized that I needed to devote my effort to the Theory of Everything. That manuscript is now even more relevant than it was over a year ago, as I now know what bits I don’t have to explain at all, because the concept of the supramolecular shell means that not only is do monolignols for supramolecular structure, but everything in cells.
Before the Theory of Everything I felt compelled to try to explain every last bit of the theory, but now I’m content with depicting the rough outline first and only then bother with the tricky parts.
In the coming weeks (and probably months), I’ll be sharing with you much more of the theory of lignin, but I think this is good enough for now.
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