Constraints and the Chiral Error Function

The distance matrix representation is the same for a molecule and its mirror image, so it is impossible to obtain only one optical isomer with embedding. This alone is not a serious problem because the entire molecule can be inverted if necessary. However, there can also be problems with relative stereo- 

Chiral constraints also can be used on united atom models that do not include hydrogens in this case, the chiral constraint includes three nonhydrogen substituents and the asymmetric carbon itself. For structures whose absolute configuration is unknown, chirality can be sampled randomly by simply omitting the chiral constraint at asymmetric carbons of unknown configuration. 3 

Chiral constraints are also used to maintain planarity by constraining four atoms to have zero volume. Because the chiral volume is more sensitive than the distance error term to minor variations from planarity, it is used to constrain planar groups more accurately. 

A minimum of three chiral constraints are used to maintain planarity at unsaturated bonds (aromatic, amide, ester, etc.) atoms 1-2-3-4, 1-5-6-3, and 

A chiral constraint plus a distance constraint also can be used to constrain nonplanar torsional angles. The 1-4 distance constraint cannot define a torsional angle by itself for example, 90° and —90° have the same 1-4 distance, but their tetrahedral volumes are equal in magnitude but opposite in sign. 

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