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 propane as given. We cut off the terminal hydrogens at either end and place them in files buildingblock_upper.xyz

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

where we translate the position such that its carbon bond partner would be at "0,5,5".

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,-0.6293,-0.89"

where we again translate the position such that its carbon bond partner would be at "0,5,5".

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. 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 lower part, which is easier

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

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

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

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 this approach can easily be placed in a script and arbitrary alkanes can be produced.