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Figure 5 Structure of aspirin, composed from two sub-molecules.
Two named sub-molecules are defined, which can then be referenced to compose the complete molecule.
The chemfig package allows us to define sub-molecules that we can reuse as parts of larger assemblies.
However, a naive first attempt fails (Figure 6A), since it connects the wrong atoms between successive sub-molecules.
The submol mechanism operates essentially through string substitution; therefore, subsequent sub-molecules are simply connected across the last and first atoms of their respective main chains.
In order to place those connecting bonds correctly, we thus need to take control of the entry and exit atoms for the sub-molecules.
Figure 5 illustrates this with a simple hand-coded example, in which the aspirin molecule is built using two sub-molecule definitions, named acetyl and benzoate, respectively.
Note that, in the sub-molecule definition generated for Figure 6C, the primary amino group was manually changed to a secondary one.
We can use the -l phe or --submol-name=phe opthen to render the phenylalanyl-residue to a named sub-molecule definition (using the name phe).
In A, mol2chemfig was allowed to arbitrarily pick the first and last atoms of the sub-molecule's main chain, which causes the connecting bonds to be misplaced.
Ellipsometric measurements reveal that the enzymes formed sub-molecule layers, and the thickness of the film shows a linear relationship with the number of assembled layers, demonstrating a spatially well-ordered manner in multilayer structure.
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