Editing Cahn–Ingold–Prelog priority rules (section)

==Steps for naming==
The steps for naming molecules using the CIP system are often presented as:
# Identification of [[stereocenter]]s and [[Covalent bond#Bond order|double bond]]s;
# Assignment of priorities to the groups attached to each stereocenter or double-bonded atom; and
# Assignment of ''R''/''S'' and ''E''/''Z'' descriptors.

===Assignment of priorities===
[[Absolute_configuration#By_absolute_configuration:_R-_and_S-|''R''/''S'']] and [[E–Z notation|''E''/''Z'']] descriptors are assigned by using a system for ranking priority of the groups attached to each stereocenter. This procedure, often known as ''the sequence rules'', is the heart of the CIP system. The overview in this section omits some rules that are needed only in rare cases.
#Compare the [[atomic number]] (''Z'') of the atoms directly attached to the stereocenter; the group having the atom of higher atomic number Z receives higher priority (i.e. number 1).
#If there is a tie, the atoms at distance 2 from the stereocenter have to be considered: a list is made for each group of further atoms bonded to the one directly attached to the stereocenter. Each list is arranged in order of decreasing atomic number Z. Then the lists are compared atom by atom; at the earliest difference, the group containing the atom of higher atomic number Z receives higher priority.
#If there is still a tie, each atom in each of the two lists is replaced with a sublist of the other atoms bonded to it (at distance 3 from the stereocenter), the sublists are arranged in decreasing order of atomic number Z, and the entire structure is again compared atom by atom. This process is repeated recursively, each time with atoms one bond farther from the stereocenter, until the tie is broken.

====Isotopes====
If two groups differ only in [[isotope]]s, then the larger [[atomic mass]] is used to set the priority.<ref>{{Cite web |last=Ashenhurst |first=James |date=2017-01-17 |title=Assigning Cahn-Ingold-Prelog (CIP) Priorities (2) - The Method of Dots |url=https://www.masterorganicchemistry.com/2017/01/17/determining-rs-2-the-method-of-dots/ |access-date=2022-11-18 |website=Master Organic Chemistry |language=en-US}}</ref>

====Double and triple bonds====
[[File:Cahn-Ingold-Prelog Double Bond.png|class=skin-invert-image|thumb|This example showcases the "divide and duplicate rule" for double bonds. The vinyl group (C=C) or alkene portion has a higher priority over the alkane (C−C) portion.]]
If an atom, A, is double-bonded to another atom, then atom A should be treated as though it is "connected to the same atom twice".<ref name=":0">{{Cite web |date=2014-08-05 |title=3.6 Cahn-Ingold Prelog Rules |url=https://chem.libretexts.org/Courses/Purdue/Purdue%3A_Chem_26505%3A_Organic_Chemistry_I_(Lipton)/Chapter_3._Stereochemistry/3.6_Cahn-Ingold_Prelog_Rules |access-date=2022-11-18 |website=Chemistry LibreTexts |language=en}}</ref> An atom that is double-bonded has a higher priority than an atom that is single bonded.<ref name=":0" /> When dealing with double bonded priority groups, one is allowed to visit the same atom twice as one creates an arc.<ref name=":1">{{Cite book |last=Patrick |first=Graham |title=Instant Notes Organic Chemistry |publisher=Garland Science |year=2004 |isbn=0203427610 |edition=2nd |pages=52–61}}</ref>

When B is replaced with a list of attached atoms, A itself, but not its "phantom", is excluded in accordance with the general principle of not doubling back along a bond that has just been followed. A triple bond is handled the same way except that A and B are each connected to two phantom atoms of the other.<ref name="IUPAC" />{{Rp|28}}

==== Geometrical isomers ====
If two substituents on an atom are [[Cis–trans isomerism|geometric isomers]] of each other, the ''Z''-isomer has higher priority than the ''E''-isomer. A stereoisomer that contains two higher priority groups on the same face of the double bond (''cis'') is classified as "Z." The stereoisomer with two higher priority groups on opposite sides of a carbon-carbon double bond (''trans'') is classified as "E."<ref>{{Cite book |last1=Okuyama |first1=Tadashi |title=Organic Chemistry, A Mechanistic Approach |last2=Maskill |first2=Howard |publisher=Oxford University Press |year=2014 |isbn=9780199693276 |pages=38–39}}</ref>

====Cyclic molecules====
To handle a molecule containing one or more [[Cyclic molecule|cycles]], one must first expand it into a [[Tree (graph theory)|tree]] (called a '''hierarchical digraph''') by traversing bonds in all possible paths starting at the stereocenter. When the traversal encounters an atom through which the current path has already passed, a phantom atom is generated in order to keep the tree finite. A single atom of the original molecule may appear in many places (some as phantoms, some not) in the tree.<ref name="ciprev1982">{{cite journal |last1=Prelog |first1=Vladlmir |last2=Helmchen |first2=Guenter |title=Basic Principles of the CIP-System and Proposals for a Revision |journal=Angewandte Chemie International Edition in English |date=August 1982 |volume=21 |issue=8 |pages=567–583 |doi=10.1002/anie.198205671 }}</ref>{{rp|at=572}}

=== Assigning descriptors ===
==== Stereocenters: ''R''/''S'' ====
[[File:CIP system example.svg|class=skin-invert-image|thumb|Two examples of stereocenters. The lowest substituent (number 4) is shown only by a wavy line, and is assumed to be behind the rest of the molecule. Both centers shown are ''S'' isomers.]]

A [[Chirality (chemistry)|chiral]] sp<sup>3</sup> hybridized isomer contains four different substituents. All four substituents are assigned prorites based on its atomic numbers. After the [[substituent]]s of a [[stereocenter]] have been assigned their priorities, the molecule is oriented in space so that the group with the lowest priority is pointed away from the observer. If the substituents are numbered from 1 (highest priority) to 4 (lowest priority), then the sense of rotation of a curve passing through 1, 2 and 3 distinguishes the [[stereoisomer]]s. In a [[Stereoisomerism|configurational isomer]], the lowest priority group (most times hydrogen) is positioned behind the plane or the hatched bond going away from the reader. The highest priority group will have an arc drawn connecting to the rest of the groups, finishing at the group of third priority. An arc drawn clockwise, has the ''rectus'' (''R'') assignment. An arc drawn counterclockwise, has the ''sinister'' (''S'') assignment. The names are derived from the [[Latin]] for 'right' and 'left', respectively.<ref>{{Cite book |last=Klein |first=David R. |title=Organic Chemistry |date=2013-12-31 |publisher=Wiley |isbn=978-1118454312 |edition=2nd |page=203 |language=en}}</ref><ref>{{cite journal |last1=Cahn |first1=R. S. |date=March 1964 |title=An introduction to the sequence rule: A system for the specification of absolute configuration |journal=Journal of Chemical Education |volume=41 |issue=3 |pages=116 |bibcode=1964JChEd..41..116C |doi=10.1021/ed041p116}}</ref> When naming an organic isomer, the abbreviation for either rectus or sinister assignment is placed in front of the name in parentheses. For example, 3-methyl-1-pentene with a rectus assignment is formatted as (''R'')-3-methyl-1-pentene.<ref name=":1" /> 
[[File:(1R,2s,3S)-1,2,3-trichlorocyclopentane.svg|class=skin-invert-image|thumb|left|An example of a (''s'') descriptor: (1''R'',2''s'',3''S'')-1,2,3-trichlorocyclopentane]]
A practical method of determining whether an enantiomer is ''R'' or ''S'' is by using the [[right-hand rule]]: one wraps the molecule with the fingers in the direction {{nowrap|1 → 2 → 3}}. If the thumb points in the direction of the fourth substituent, the enantiomer is ''R''; otherwise, it is ''S''.

It is possible in rare cases that two substituents on an atom differ only in their absolute configuration (''R'' or ''S''). If the relative priorities of these substituents need to be established, ''R'' takes priority over ''S''. When this happens, the descriptor of the stereocenter is a lowercase letter (''r'' or ''s'') instead of the uppercase letter normally used.<ref>{{GoldBookRef|title=pseudo-asymmetric carbon atom|file=P04921}}</ref>

==== Double bonds: ''E''/''Z'' ====
{{Main article|E-Z notation}}

For double bonded molecules, Cahn–Ingold–Prelog priority rules (CIP rules) are followed to determine the priority of substituents of the double bond. If both of the high priority groups are on the same side of the double bond ([[Cis-trans isomerism|''cis'' configuration]]), then the [[stereoisomer]] is assigned the configuration ''Z'' (''zusammen,'' [[German language|German]] word meaning "together").  If the high priority groups are on opposite sides of the double bond ([[Cis-trans isomerism|''trans'' configuration]]), then the stereoisomer is assigned the configuration ''E'' (''entgegen'', German word meaning "opposed")<ref>{{Cite book |last=International Union of Pure and Applied Chemistry. Commission on the Nomenclature of Organic Chemistry |url=https://www.worldcat.org/oclc/27431284 |title=A guide to IUPAC nomenclature of organic compounds : recommendations 1993 |date=1993 |publisher=Blackwell Scientific Publications |others=Robert Panico, Warren H. Powell, Jean-Claude Richer |isbn=0-632-03702-4 |location=Oxford |oclc=27431284}}</ref>

==== Coordination compounds ====
In some cases where [[stereogenic]] centers are formed, the configuration must be specified. Without the presence of a [[Non-covalent interaction|non-covalent]] interaction, a compound is [[achiral]]. Some professionals have proposed a new rule to account for this. This rule states that "non-covalent interactions have a fictitious number between 0 and 1" when assigning priority.<ref>{{Cite journal |last=Elguero |first=José |date=2016-12-01 |title=Is it possible to extend the Cahn-Ingold-Prelog priority rules to supramolecular structures and coordination compounds using lone pairs? |journal=Chemistry International |language=de |volume=38 |issue=6 |pages=30–31 |doi=10.1515/ci-2016-0633 |s2cid=99300397 |issn=1365-2192|doi-access=free }}</ref> Compounds in which this occurs are referred to as [[coordination compounds]].

==== Spiro compounds ====
Some spiro compounds, for example the SDP ligands ((''R'')- and (''S'')-7,7'-bis(diphenylphosphaneyl)-2,2',3,3'-tetrahydro-1,1'-spirobi[indene]), represent chiral, C<sub>2</sub>-symmetrical molecules where the rings lie approximately at right angles to each other and each molecule cannot be superposed on its mirror image.<ref name=":1" /> The spiro carbon, C, is a stereogenic centre, and priority can be assigned a>a′>b>b′, in which one ring (both give the same answer) contains atoms a and b adjacent to the spiro carbon, and the other contains a′ and b′. The configuration at C may then be assigned as for any other stereocentre. 

=== Examples ===
The following are examples of application of the nomenclature.<ref name="HartHadad2011">{{cite book|author1=Harold Hart|author2=Christopher M. Hadad|author3=Leslie E. Craine |author4=David J. Hart |title=Organic Chemistry: A Short Course|url=https://books.google.com/books?id=JasIAAAAQBAJ&pg=PA177|date=1 January 2011|publisher=Cengage Learning|isbn=978-1-133-17283-3|pages=177–}}</ref>

:{| align="center" class="wikitable skin-invert-image" width=800px
|-
!colspan="2"|''R''/''S'' assignments for several compounds
|-
|| [[File:R-bromochlorofluoroiodomethane-2D.png|center|600px]]
| valign=top| The hypothetical molecule [[bromochlorofluoroiodomethane]] shown in its (''R'')-configuration would be a very simple chiral compound. The priorities are assigned based on [[atomic number]] (''Z''): [[iodine]] (''Z'' = 53) > [[bromine]] (''Z'' = 35) > [[chlorine]] (''Z'' = 17) > [[fluorine]] (''Z'' = 9). Allowing fluorine (lowest priority, number 4) to point away from the viewer the rotation is clockwise hence the ''R'' assignment.
|-
|| [[File:L-serine-skeletal.svg|center|120px]]
| valign="top" | In the assignment of [[L-Serine|<small>L</small>-serine]] highest priority (i.e. number 1) is given to the [[nitrogen]] atom (''Z'' = 7) in the [[amino group]] (NH<sub>2</sub>). Both the [[hydroxymethyl]] group (CH<sub>2</sub>OH) and the [[carboxylic acid]] group (COOH) have carbon atoms (''Z'' = 6) but priority is given to the latter because the carbon atom in the COOH group is connected to a second oxygen (''Z'' = 8) whereas in the CH<sub>2</sub>OH group [[carbon]] is connected to a [[hydrogen]] atom (''Z'' = 1). Lowest priority (i.e. number 4) is given to the hydrogen atom and as this atom points away from the viewer, the counterclockwise decrease in priority over the three remaining substituents completes the assignment as ''S''.  
|-
|| [[File:(S)-Carvone.svg|center|80px]]
| valign=top| The stereocenter in [[Carvone|(''S'')-carvone]] is connected to one hydrogen atom (not shown, priority 4) and three carbon atoms. The isopropenyl group has priority 1 (carbon atoms only), and for the two remaining carbon atoms, priority is decided with the carbon atoms two bonds removed from the stereocenter, one part of the [[ketone|keto]] group (O, O, C, priority number 2) and one part of an alkene (C, C, H, priority number 3). The resulting counterclockwise rotation results in ''S''.
|}