Organic compounds

Naming of organic compounds is based on a fairly fixed set of rules, followed to a certain extent. This means that in the systematic naming you can encounter having multiple options when finding the name. IUPAC, which is the body in charge of the the rules for naming, has its own favorites, obviously, but it is not mandatory to follow IUPAC's recommendations. There is only one demand when it comes to systematic naming: it has to be unambiguous.

In principle you can find a systematic name for all organic molecules, but in reality, you reach a point where the systematic naming becomes so convoluted and difficult that use a workaround. The workaround will be shown later on this page. Naming of an organic molecule is done in the following order:

1. The longest chain of C-C bonds (including double and triple bonds) is the molecule's main chain, BUT:
   • If you have a functional group, the chain containing the functional group will automatically be the molecule's main chain.
   • If you have multiple functional groups, the chain containing the most functional groups will be the main chain.
   • If you have multiple chains containing the same number of functional groups, the prioritized list for functional groups is followed.
2. Double and triple bonds are noted. If you have Z/E or cis/trans isomery, this is noted as well.
3. Find the functional group(s) on the main chain. The primary functional group (the group that rankt highest on the prioritized list in the list of functional groups) will determine the ending (suffix) on the name, and any remaining functional groups will be noted as prefix(es). The position of the primary functional group determine the numbering of the carbon atoms.
4. Find the side chains. Side chains are mentioned in alphabetical order, if there is more than one, and not the same type. For cyclic compounds, the primary functional group defines what is cis/trans isomers on the ring.
5. In case of optic isomery, this is mentioned last.

Note:

• If the name contains a number, denoting the position and combined side chains, these are separated using a dash and brackets, to make it decipherable, e.g. 3-(2-oxocyclohexyl)propanoic acid.
• If you have more than one of the same functional group, the positions are separated using a comma, even if they are at the same position.
• If you have multiple positions with cis/trans or Z/E isomery, these are mentioned in the same order as the placement of the functional groups.

The names for chains can be found here, the names for functionalities and functional groups can be found here.

As a general rule we are looking for the longest C-C chain, the main chain, however, a shorter chain with more functional groups will take precedence as the main chain. This problem will addressed further down. Starting with the basics, this is the molecule ethane:



You have 2 carbon, and only single bonds. If we have 6 carbon instead,



it is thus called hexane (6 carbon = hex). If the chains are linear, we call them aliphates.


The chains do not have to be linear. If they form a circle, we call them cyclic compounds or aromates, depending on the construction. Aromates have conjugated double bonds only, in the ring formation, so they become flat, cyclic compounds may contain comjugated parts, but they are not flat

If the atoms in the molecule forms a circle, you add cyclo before the chain. This molecule



is thus named cyclohexane.


Getting a bit ahead of things, some cyclic compounds that have their own common name, due to complexity and being widely used. Crown ethers is one of these.

The ending of the name reflects the content of single, double and triple bonds. The endings are:

• ane = only single bonds
• ene = one or more double bonds
• yne = one or more triple bonds

If the position of the double or triple bonds is ambiguous without specifying the position, you must specify the position. Let us take a look at a couple of examples, so it makes sense.

If we have 2 carbon, we can have all three types of bonds:

ethane	ethene	ethyne

As seen, the double and triple bonds can only be in one place. Specifying the position would thus be redundant. If we have a C4 chain, positioning becomes relevant. Here the double and triple bonds can be place between position 1 and 2 or 2 and 3, which we specify as 1-ene, 2-ene, 1-yne and 2-yne:

but-1-ene	but-2-ene	but-1-yne	but-2-yne

The rules for naming were changed in the 1990's, so you can still encounter references to the old rules for naming. Here you placed the position of the binding before the chain length, i.e. the four molecules shown above would be named 1-butene, 2-butene, 1-butyne and 2-butyne. Phonetically the new names do not work as well as the old ones, so the old systematic names like 2-propanole instead of propane-2-ol, are still used.

If you have multiple double og tripe bonds, the positions are separated using a comma, and you give the ending the prefixes di, tri, etc. This molecule:



is thus named penta-1,4-diene.

Double bonds and cyclic compounds are locked in position, so you have a relative orientation of up and down, if you have 2 or more substituents to position. If a molecule is drawn like this:



you cannot tell the difference, but if the molecule is drawn like this, with a slightly more correct rendering of the three dimensional structure:



you can see, that there is a difference whether the two carbon atoms next to the double bond are one the same side of the double bond, this is called cis or Z. If they are placed on opposide sides, i.e. like this:



it is called trans or E.

Similarly we have the two isomers of cyclohexane-1,2-diol:


Left: cis-cyclohexane-1,2-diol. Right: trans-cyclohexane-1,2-diol. (the suffix ol referring to the functional groups alcohol (-OH). There is more about alcohols and other functional groups in the next section).

Beware that for cyclic compounds, you only use cis/trans. It is one of the differences between cis/trans and Z/E, and being not the only one, let ud start by getting this settled, as it is important.


Z/E and cis/trans has the same function, but you have some fundamental differences, and the two nomenclatures cannot do exactly the same things. Therefore, there will be molecules where you can only use one of the two nomenclatures. Z is short for zusammen (i.e. together) and E is short for entgegen (i.e. opposite). cis is latin for on this side and trans is latin for on the other side.

• For cyclic compounds you can only ise cis/trans. Here cis and trans refer to the functional groups being on the same side or on opposite sides of the plane formed by the rings.
• For double bonds, cis/trans orients accorting to the 2 atoms of the same type on each side of the double bond. Usually it is carbon, but is can also be something else, e.g. 2 hydroxy groups. If you do not have two atoms of the same type on each side of the double bond, you cannot use cis/trans, but have to use Z/E instead.
• Z/E orients according to the atom's position in the periodic system (Cahn-Ingold-Prelog or CPI priority), so this nomenclature can handle double bonds with 3 or 4 different atoms on the double bonds.
• cis/trans cannot handle special constructs e.g. like cumulenes. Here you need to use Z/E nomenclature.

Traditionally the cis/trans nomenclature has been used, and it it still accepted in general. IUPAC prefer the Z/E nomenclature for the molecules where you can use both, but there is no formal requirement to use one or the other nomenclature.


So, if we look at this molecule:



it will be named (E)-hex-2-ene (new nomenclature) or trans-hex-2-ene (old nomenclature).

If you have multiple double bonds, e.g.



the names will be (Z,E)-hexa-2,4-diene (new nomenclature), or cis,trans-hexa-2,4-diene (old nomenclature), as the first double bond, on the 2 position, is Z/cis and the other one, on the 4 position, is E/trans.

In some places, people prefer specifying the Z/E positions, e.g. (2Z,4E)-hexa-2,4-diene. If there is any doubt about which Z and E belongs where, you obviously have to do it like this, to make the naming unambiguous, but otherwise you can leave out the specification of the position.


As ther is a difference between cis/trans and Z/E isomery, let us take a look at an example where the difference becomes visible:



At cis/trans the two carbon are placed in the trans position, so according to the cis/trans nomenclature, the molecule is (trans)-2-Hexene-3-ol. According to the Z/E nomenclature, the atoms in the four positions around the double bond are ranked accordong to their position in the periodic system, and oxygen has a higher number than carbon, so the highest ranking atoms on each side of the double bond have the same orientation, i.e. Z, and the molecule's name is therefore (Z)-2-Hexene-3-ol. So, for the cis/trans nomenclature, it is a trans compound, whereas for the Z/E nomenclature, the molecules is equivalent to being a cis compound.


For cyclic compounds, you regard the ring, formed by the atoms, as a plane, and you orient cis and trans according to the plane. The Z/E nomenclature is not used for cyclic compounds. A molecule like this



is thus named trans-cyclopentane-1,2-diol (the suffix ol referring to the functional groups alcohol (-OH). Functional groups is the next part).

Side chains and functional groups can be a bit tricky, as they have an inherent hierarchy, and the functional groups can appear on the side chains. There is a few general rules to keep in mind:

• Aliphatic side chains are named by using the ending -yle. For alkanes, -ane is changed to -yle, whereas alkeners and alkynes -yle is added, i.e. -enyle and -ynyle respectively.
• For non-aliphatic side chains, you need to know the specific name for that particular type, e.g. a benzene ring is called phenyle.
• Almost all functional groups has a name as prefix and suffix. Prefix is the name of the functional groups when not the main functional group. Suffix is the name of the group, when it is the main group. Therefore, a molecule can only have one suffix, but multiple præfixes is fine.
• For the functional groups, there is a hierarchy, specifying which group is the dominating, in case of multiple functional groups. The most oxidized group is the dominating group.
• The numbering of the positions must be as low as possible. The dominating functional group determines which carbon is number 1. The functional group does not have to be situated on carbon number one, but the position have to have the lowest possible number.

Naming of side chains and functional groups contains a lot of conditional requirements, so looking at a few examples to learn the nomenclature, is the most sensible approach.

We start with a simple molecule:



The procedure for naming is:

1. We have 3 carbon and only single bonds, so the name will be something containing propane (prop = 3 carbon, -ane = single bonds).
2. The molecule contains an OH group, which is an alcohol (see funfunctional groups). There is only one functional group, so it will be the dominating group and has to be written as a suffix. Therefore it will have the ending -ol. Therefore the molecule will be named someting containing the word propanol (notice that we remove the e at the end of propane, before adding -ol).
3. The alcohol group is placed on the carbon at the end of the chain, which is carbon number 1 or number 3, depending on which end we start counting from. We need to have the lowest possible number in the name, so we specify it as position 1. The name of the molecule is thus propan-1-ol. Note: Not all functional groups require a specification of the position, as they can only be in one position on the chain, e.g. aldehydes and carboxylic acids.

If we take a look at a slightly more complicated molecule:



Starting from the top:

1. We have 4 carbon and only single bonds in the carbon chain, so the name will be something containing butane (but = 4 carbon, -ane = single bonds).
2. The molecule contains an OH group, which is an alcohol group, and a C(=O)OH group, which is a carboxylic acid. The carboxylic acid has the highest rankt, so that will be written as the suffix, i.e. the name will be something -oic acid. So the molecule will be named something with butanoic acid.
3. The alcohol group now has to written as præfix, i.e. hydroxy. We can now expand the name to hydroxy-butanoic acid.
4. The position of the carboxylic acid specifies where carbon number 1 is placed, and carboxylic acids can only be at the end of a chain. The only instance where a you encounter a carboxylic acid group having another number than 1, is if you have multiple acid groups (an example is shown further down). The alcohol group is thus placed on carbon number 3. Therefore the name will be 3-hydroxy-butanoic acid.

Adressing the problem regarding multiple carboxylic acid groups. If there is only 2, and they are on the main chain, e.g. glutaric acid:



it is quite simple:

1. Der er 5 carbon og kun enkeltbindinger, så det bliver noget med pentan.
2. Der er 2 carboxylsyrer, så vi kan udvide navnet til pentandisyre.
3. Det er nødvendigvis kun den ene der kan have nummer et, hvilket betyder at den anden må sidde på nummer 5. På den anden side, er molekylet en alifat, så der er kun to ender hvor carboxylsyrerne kan sidde. Så selv om man kunne få den tanke, at molekylet skulle hedde pentan-1,5-disyre, er det tilstrækkeligt blot med pentandisyre for at have et entydigt navn.

Nu skal det hele jo ikke være simpelt, så hvad gør man med de lidt mere komplicerede arkitekturer med carboxylsyrer? Citronsyre er et godt eksempel på flere muligheder, og hvor UIPAC foretrækker en anden navngivning end den helt stringente. Lad os se på citronsyre, som ser således ud:



Vi har nu tre syregrupper, hvoraf en sidder på en sidekæde.

1. Som altid ser vi efter den længste kæde med flest substituenter. Det er muligt at vælge mellem en disyre med 4 carbon (yderste og midterste syregruppe) eller en disyre med 5 carbon (de 2 yderste syregrupper), så det bliver nødvendigvis de 5 carbon. Molekylet må derfor hedde noget med pentandisyre.
2. Den midterste syregruppe (på position 3) bliver nu degraderet til at være sidekæde. Så kommer den til at hedde 3-carboxy, og det fulde navn bliver noget med 3-carboxy-pentandisyre.
3. Alkoholgruppen på position 3 kommer også til at figurere som præfix, dvs. hydroxy, og fordi substituenterne listes alfabetisk (efter nummerrækkefølgen) bliver det noget med 3-carboxy-3-hydroxypentandisyre.
4. Selv om de to carboxylsyrer kun man sidde endestillet, er der mange der godt kan lide at angive deres nummer, dvs. 3-carboxy-3-hydroxypentan-1,5-disyre. Det er ikke forkert navngivning, det er bare heller ikke strengt nødvenigt

IUPAC betragter citronsyren på denne måde:

1. Den længste kæde med flest substituenter (stamhydridet) er 3 carbon med 3 carboxygrupper på. Molekylet må derfor hedde noget med propan.
2. De tre syregrupper bliver nu en specifik navngivet gruppe, dvs. en carboxylsyre (her tricarboxylsyre fordi der er 3 af dem), på propanen, der sidder på positionerne 1, 2 og 3. Molekylet kommer så til at hedde noget med propan-1,2,3-tricarboxylsyre.
3. Alkoholgruppen på position 2 kommer til at figurere som præfix, dvs. hydroxy, så navnet bliver 2-hydroxypropan-1,2,3-carboxylsyre.

Er det så forkert med 3-carboxy-3-hydroxypentandisyre som systematisk navn? Nej, navnet er godt nok, det er bare ikke det navn som IUPAC foretrækker.Derfor: Vær opmærksom på om der bliver bedt om et systematisk navn eller IUPAC-navnet, der KAN være en forskel!


Lad os se på endnu et molekyle, hvor navngivningen kan være lidt tricky:



Hvis vi starter fra en ende af:

1. Den længste carbonkæde er 7 carbon, så man kunne forledes til at tro, at molekylet burde hedde noget med heptan. Men, hvis vi skal følge reglerne stringent, er den længste carbonkæde med flest funktionelle grupper fra carboxylsyren til aldehydet. Hovedkæden bliver således 3 carbon lang, dvs. propan.
2. Molekylet indeholder en CHO-gruppe, som er en aldehydgruppe, og en C(=O)OH-gruppe som er en carboxylsyre. Carboxylsyren har den højeste prioritet, så den kommer til at figurere som suffix, dvs. syre. Molekylet skal altså hedde noget med propansyre.
3. Aldehydgruppen er nu nødt til at stå som præfix, dvs. oxo. Vi kan nu udvide navnet til oxopropansyre.
4. Syregruppen kan kun sidde yderst, og som den højst prioriterede funktionelle gruppe, definerer dette hvor carbon nummer 1 er placeret. Aldehydgruppen sidder således på carbon nummer 3, og navnet bliver da 3-oxopropansyre.
5. Den sidste gruppe er alifatisk kæde på 5 carbon, dvs. pentan. Som sidekæde kommer den til at hedde pentyl, og den sidder på position 2. Molekylet kommer så, fordi substituenterne listes alfabetisk, til at hedde 3-oxo-2-pentylpropansyre.

Dette er hvis man følger reglerne stringent. Mere pragmatisk, og lige så entydigt (og dermed lige så korrekt) er:

1. Der er to funktionelle grupper, en carboxylsyre og et aldehyd, og af disse er carboxylsyren den funktionelle gruppe med højest prioritet.
2. Den længste carbonkæde der sidder på syren er 7 carbon, så molekylet hedder noget med heptansyre.
3. Aldehydgruppen er nu nødt til at stå som præfix. Methanal som en sidelæde hedder formyl, så vi kan nu udvide navnet til formylheptansyre.
4. Syregruppen kan kun sidde yderst, og som den højst prioriterede funktionelle gruppe, definerer dette hvor carbon nummer 1 er placeret. Aldehydgruppen sidder således på carbon nummer 2, og navnet bliver da 2-formylheptansyre.

Navngivningen af aromatiske forbindelser fungerer efter samme principper som alifatiske og cyckliske forbindelser. Benzen med en enkelt substituent hedder således:

Hydroxybenzen	Methylbenzen

Hvis der er flere substituenter, er det den hovedfunktionelle gruppe der bestemmer nummereringen, og navngivningen følger den normale procedure for navngivning.

En speciel ting der hører til aromatiske forbindelser er brugen af ortho-, meta- og para- i stedet for positionsangivelserne 1, 2 og 3 ved flere substituenter. På skrift forkorter man gerne ortho-, meta- og para- til o-, m- og p-. Bemærk at ortho-, meta- og para- er med kursiv i den kemiske retsskrivning. Ligeledes vil man ofte opleve halvsystematiske navne som f.eks. 3-nitro-toluen fordi methylbenzen har trivialnavnet toluen, og toluen er det navn der bruges mest, f.eks.

2-aminohydroxybenzen ortho-aminohydroxy-benzen	1,3-dimethylbenzen meta-dimethylbenzen m-xylen	2,4,6-trinitromethylbenzen 2,4,6-trinitrotoluen (TNT)

Nitrogenet i aminer og amider tillader flere bindinger. For aminer taler man om sekundære og tertiære aminer, afhængig af om der er 2 eller 3 substituenter på. Man kalder dem også for N-substituerede aminer. For amider har man en orientering i forhold til carbonylgruppen, der er en del af amidgruppen. Her taler man, analogt til aminerne, om N-substituerede amider og sekundære og tertiære amider.

Aminernes navngivning følger de almindelige regler for navngivning med længste kæde med flest substituenter som hovedkæden. Hvis vi starter med en primær amin som ethylamin:



Hvis vi sætter en methylgruppe på nitrogenet, kommer det til at se således ud:



Dette er N-methyl-ethylamin. Sætter vi en methylgruppe mere på, kalder man det N,N'-dimethyl-ethylamin. Hvis der ikke er tvivl om placeringerne, som f.eks. ved triethylamin:



angiver man ikke N,N'.


Analogt til aminerne, kan vi med amiderne starte med ethylamid:



Hvis vi sætter en methylgruppe på nitrogenet, kommer det til at se således ud:



Dette er N-methyl-ethylamid. Sætter vi en methylgruppe mere på, kalder man det N,N'-dimethyl-ethylamid.

Med amider skal man være lidt opmærksom, da amidet har en orientering. Man ser det f.eks. ved dette molekyle:



Her er den længste kæde på 3 carbon, men carbonylgruppen, som er en del af amid som funktionel gruppe, sidder på ethyl-kæden, så det bliver til en N-propyl-ethylamid.

Optisk isomeri kræver en 3D-tegning og en rumlig forståelse af et molekyle, hvis man skal kunne se det. Hvis vi ser på pentan-2-ol i en 2D-tegning, ser således ud:



Vi kan se, at carbon i position 2 har fire forskellige substituenter, så der er to optiske isomerer af molekylet. Vi kan ikke se hvilken af de to der er tale om, og det kunne være en racemisk blanding. Det kræver en rumlig angivelse af hvorledes bindingerne er arrangeret, at kunne se hvilken isomer man har. Det kunne f.eks. være sådan her:



Substituenten med den laveste placering, i dette tilfælde H, kan nu flyttes ind i baggrunden bag det optiske center, så de tre andre substituenter peger ud i rummet mod læseren. Vi kan nu nummerere de tre substituenter der peger ud i rummet efter deres placering i det periodiske system, med den højeste placering som nummer 1:



Hvis nummereringen 1 til 3 er med uret, er orienteringen R (Right), og mod uret er orienteringen S (Sinister). Orienteringen er i dette tilfælde, som det kan ses af figuren, mod højre, dvs. en R-form. Stoffet må da være en (R)-pentan-2-ol.

Hvis man arbejder med store og komplekse molekyler, hvor det kan være svært at overskue de optiske centre, eller der er flere optiske centre markerer man dette ved at skrive positionen foran de respektive orienteringer f.eks. (2R,3S)-2,3-dibromopentan.

Optisk isomeri af denne type bruges kun til monosaccharider, og kræver en markering af hvad der er i planet og ud af planet ligesom i R/S-isomeri. I mod-sætning til R/S-isomeri er der indbygget en orientering i metoden. Når man tegner molekylet, er det i en lodret række med det mest oxiderede carbon øverst. Hvis man skal tegne glucose-molekylet gør man således:



L/D-isomerien afgøres på det optisk aktive carbon med det højeste nummer. Hvis OH-gruppen vender mod højre er det D-formen, og mod venstre er det L-formen. I det viste eksempel er det C(5) der har det højeste nummer, og her vender OH-gruppen mod højre. Der er derfor tale om D-glucose.