org.openscience.cdk.stereo

Class Stereocenters

java.lang.Object

org.openscience.cdk.stereo.Stereocenters

public final class Stereocenters
extends Object

Find atoms which can support stereo chemistry based on the connectivity. Stereocenters are classified as True when they have constitutionally different ligands and Para ("resemble") stereo centers with constitutionally identical ligands. Some examples of para-centers are listed below. Non and potential stereogenic atoms are also indicated. The method partially implements the rules described by [Razinger, Marko and Balasubramaniam, Krishnan and Perdih, Marko and Munk, Morton, Stereoisomer Generation in Computer-Enhanced Structure Elucidation, J. Chem. Inf. Comput. Sci, 1993, 33:812-825, doi:10.1021/ci00016a003]. Para centers are identified in isolated rings (more common) but are not currently found in fused systems (e.g. decalin), spiro linked 'assemblages' or acyclic interdependent centers. Accepted Stereo Atoms This atoms accepted as being potentially stereogenic are those defined in the InChI Technical Manual [Unknown BibTeXML type: InChITechManual]. These are: Tetrahedral Stereochemistry:

• Carbon - 4 valent, 4 sigma bonds
• Silicon - 4 valent, 4 sigma bonds
• Germanium - 4 valent, 4 sigma bonds
• Tin - 4 valent, 4 sigma bonds
• Nitrogen cation - 4 valent,4 sigma bonds
• Phosphorus cation - 4 valent, 4 sigma bonds
• Arsenic cation - 4 valent, 4 sigma bonds
• Boron anion - 4 valent, 4 sigma bonds
• Nitrogen - 5 valent, 3 sigma and 1 pi bond
• Phosphorus - 5 valent, 3 sigma and 1 pi bond
• Sulphur - 4 valent, 2 sigma and 1 pi bond
• Sulphur - 6 valent, 2 sigma and 2 pi bonds
• Sulphur Cation - 3 valent, 3 sigma bonds
• Sulphur cation - 5 valent, 3 sigma and 1 pi bond
• Selenium - 4 valent, 2 sigma and 1 pi bond
• Selenium - 6 valent, 2 sigma and 2 pi bonds
• Selenium Cation - 3 valent, 3 sigma bonds
• Selenium cation - 5 valent, 3 sigma and 1 pi bond
• Nitrogen - 3 valent, 3 sigma bonds and in a 3 member ring

N, P, As, S or Se are not stereogenic if they have a terminal H neighbor or if they have 2 neighbors of the same element (O, S, Se, Te, N) which have at least one hydrogen. Consider: P(O)(=O)(OC)OCCC. Phosphines and arsines are always stereogenic regardless of H neighbors Double Bond Stereochemistry: The following atoms can appear at either end of a double bond.

• Carbon - 4 valent, 2 sigma and 1 pi bond
• Silicon - 4 valent, 2 sigma and 1 pi bond
• Germanium - 4 valent, 2 sigma and 1 pi bond
• Nitrogen - 3 valent, 1 sigma and 1 pi bond
• Nitrogen cation - 4 valent, 2 sigma and 1 pi bond

Examples of Para Stereocenters

• inositol - has 9 stereo isomers, O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O myo-inositol
• decalin - has 2 stereo isomers, C1CC[C@H]2CCCC[C@H]2C1 (not currently identified)
• spiro/double-bond linked ring - InChI=1/C14H24/c1-11-3-7-13(8-4-11)14-9-5-12(2)6-10-14/h11-12H,3-10H2,1-2H3/b14-13-/t11-,12- (not currently identified)
• An example of a para-center not in a cycle C[C@@H](O)[C@H](C)[C@H](C)O (not currently identified)

It should be noted that para-centers may not actually have a configuration. A simple example of this is seen that by changing the configuration of one center in C[C@@H](O)[C@H:1](C)[C@H](C)O removes the central configuration as the ligands are now equivalent C[C@@H](O)[CH:1]](C)[C@@H](C)O

Author:

John May

Source code:

master

Belongs to CDK module:

standard

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Stereocenters.Stereocenter Defines the type of a stereocenter.
static class	Stereocenters.Type

Method Summary

Modifier and Type	Method and Description
Stereocenters.Type	elementType(int v) Obtain the type of stereo element support for atom at index v.
boolean	isStereocenter(int v) Is the atom be a stereocenter (i.e.
static Stereocenters	of(IAtomContainer container) Determine the stereocenter atoms in the provided container based on connectivity.
Stereocenters.Stereocenter	stereocenterType(int v) Determine the type of stereocenter is the atom at index v.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

of

public static Stereocenters of(IAtomContainer container)

Determine the stereocenter atoms in the provided container based on connectivity.

 IAtomContainer container = ...;
 Stereocenters  centers   = Stereocenters.of(container);
 for (int i = 0; i < container.getAtomCount(); i++) {
     if (centers.isStereocenter(i)) {

     }
 }
 

Parameters:

container - input container

Returns:

the stereocenters

elementType

public Stereocenters.Type elementType(int v)

Obtain the type of stereo element support for atom at index v. Supported elements types are:

• Stereocenters.Type.Bicoordinate - an central atom involved in a cumulated system (not yet supported)
• Stereocenters.Type.Tricoordinate - an atom at one end of a geometric (double-bond) stereo bond or cumulated system.
• Stereocenters.Type.Tetracoordinate - a tetrahedral atom (could also be square planar in future)
• Stereocenters.Type.None - the atom is not a (supported) stereo element type.

Parameters:

v - atom index (vertex)

Returns:

the type of element

isStereocenter

public boolean isStereocenter(int v)

Is the atom be a stereocenter (i.e. True or Para).

Parameters:

v - atom index (vertex)

Returns:

the atom at index v is a stereocenter

stereocenterType

public Stereocenters.Stereocenter stereocenterType(int v)

Determine the type of stereocenter is the atom at index v.

• Stereocenters.Stereocenter.True - the atom has constitutionally different neighbors
• Stereocenters.Stereocenter.Para - the atom resembles a stereo centre but has constitutionally equivalent neighbors (e.g. inositol, decalin). The stereocenter depends on the configuration of one or more stereocenters.
• Stereocenters.Stereocenter.Potential - the atom can supported stereo chemistry but has not be shown ot be a true or para center.
• Stereocenters.Stereocenter.Non - the atom is not a stereocenter (e.g. methane).

Parameters:

v - atom index.

Returns:

the type of stereocenter