Creating Arbitrary Alkanes

This can also be used (in a somewhat unusual way) to generate alkanes of arbitrary length from a given one. Assume, we have a butane as given. We cut off the terminal hydrogens at either end and place them in files buildingblock_upper.xyz and buildingblock_lower.xyz.

To correct for the displacement, we subtract the position of its carbon neighbor as if it were at "0,5,5".

./molecuilder -i buildingblock_upper.xyz --select-all-atoms -t "-8.3885,-1.5127,-0.89" -s buildingblock_upper.xyz --undo

In the same way we proceed with the hydrogen at the other end stored in buildingblock_lower.xyz.

./molecuilder -i buildingblock_lower.xyz --select-all-atoms -t "-12.1362,-1.5127,-0.89"

where we translate the position such that it's relative to the same carbon at "0,5,5" and additionally we have to compensate for the x distance which we set such that is bond partner would be at "x=0".

Furthermore, we cut out the first pair of carbon atoms along with the four hydrogens (not the terminal one) and store it in buildingblock_center.xyz.

./molecuilder -i buildingblock.xyz --select-atoms-inside-cuboid "2.5,5,5" --position "8.3,3,3" -s buildingblock_center.xyz

Sadly, we have to take a look here at the coordinates in the xyz file to know what to cut out. We pick a position slightly before the first carbon atom. Finally, we have to translate the section

./molecuilder -i buildingblock_center.xyz --select-all-atoms -t "-8.3885,-1.5127,-0.89"

such that the first carbon atom is at "0,5,5".

Then we may proceed as follows to produce a decane.

./molecuilder -i decane.xyz --change-box "2.4985,0,10,0,0,10" -l buildingblock_center.xyz --repeat-box "5,1,1"

where we obtained the box length from the distance of one carbon atom to its next-nearest neighbor.

That is:

• first, we use -i to store everything in a new file decane.xyz.
• Next, we set the box dimensions (--change-box) to fit with the periodicity of the alkanes, here in the x direction.
• Then, we load (-l) the atoms into this domain.
• Finally, we call --repeat-box the create five copies from the given segment containing two carbons.

At last, we need to re-attach the terminal hydrogen atoms. First the upper part, which is easier

./molecuilder -i decane.xyz -l buildingblock_upper.xyz

Then the lower part which has to be translated to its destination

./molecuilder -i decane.xyz -l buildingblock_lower.xyz --select-molecule-by-order -1 --select-molecules-atoms -t "11.24325,0,0"

where the translation factor is 4.5 times the above periodicity in the x direction.

That is:

• first, we use -i to work on the file decane.xyz where the "truncated" decane is contained.
• Then, we load (-l) the hydrogen atom into this domain, it is automatically placed into a new molecule
• We select this (last) molecule (--select-molecule-by-order) where -1 is the reverse order, 1 is first, -1 is last, -2 is second to last, ... (Note: we might as well have selected the molecule by its name buildingblock_left with --select-molecule-by-name).
• We transform the molecule selection into an atomic selection (--select-molecules-atoms) for the subsequent translation working on atoms.
• Finally, we call -t to translate the selected hydrogen atom at its final position.

And finally, we have a complete decane molecule.

Now, one may ask: Why not do this in a text editor? Of course, the duplication along with the translation of the periodic section is nice. Moreover however this approach can easily be placed in a script file and arbitrary alkanes can be produced by calling this script.

_{This has been done with version v1.1.3}