Cycloalkanes Directory Reference

Detailed Description

The cycloalkanes are molecules that include loops of carbon atoms. The presence of a loop constraint makes CuikSuite specially adequate tool to analyze their conformational space.

Note that the formulation we use here for the cycloalkanes is not based on distances (as we did in our JCC paper), but on vectors and rotation matrices, as in our more recent TRO paper.

Moreover, note that in the formulation of the cycloalkanes, we use a variant of the formulation described in our recent TRO paper. We do not use orthonormal reference frames for the links but we use the two vectors aligned with the rotation axis coincident in each carbon to defined a non-orthogonal reference frame. This produces equation sets that can be easily simplified avoiding numerical issues.
The generalization to use non-orthonormal reference frames whe it is advantageous is applied in general and not only in these examples, howerver the effect is specially relevant in the cycloalkanes.

Please, check the individual files for details on these experiments:

References

Files

file  Bicyclohexane.world [code]
 A cycloalkane with a two rings of 6 carbons.
 
file  Cycloheptane.world [code]
 A cycloalkane with a 7 carbon loop.
 
file  Cyclohexane.world [code]
 A cycloalkane with a 6 carbon loop.
 
file  Cyclooctane.world [code]
 A cycloalkane with a 8 carbon loop.