General Index
Organic Structures
In this demo we'll have a look at the main organic functions from a structural point of view
It is recommended to systematically follow the demo. Buttons:
display molecular models on the left panel and radio buttons:
Execute actions on the model.
Normally the button is followed by the structural formula of the compound:
Índice
1. Saturated hydrocarbons
sp3 carbons direct their four molecular orbitals as the vertices of a regular tetrahedron, in such a way that the substituents atoms appear as far as possible from another. Such is the structure of
Next hydrocarbon in the saturated series is Ethane:
with two carbon atoms. Ethane presents one C-C bond and six C-H equivalent bonds.
If we look at the molecule along the C-C- bond, we'll see that the principle of atoms being
as far as possible from another is also seen in ethane. The six hydrogen atoms appear as the vertices of
a regular hexagon. This arrangement is known as alternating conformation and represents the
minimum energy conformation of all the organic molecules
On the contrary, the least energetically-favoured conformation is the
In this conformation we see that the hydrogen atoms bonded to one carbon hide the hydrogen
atoms bonded to the other carbon.
The saturated hydrocarbon of three carbon atoms is
Rotating the molecule we can observe the principle of alternating conformation between adjoining carbon atoms.
Next hydrocarbon in the saturated series is
We also observe in this model the principle of alternating conformation.
Having the same composition as butane (C4H10), we have
This is a skeletal isomer of butane. See that the principle of alternating conformation is also met in this molecule.
Five-carbon saturated hydrocarbon is
changing the display to spacefill,
We get an idea of the general shape of saturated hydrocarbons chains in space.
Pentane has two skeletal isomers, Methylbutane:
And Dimethylpropane:
The following structures show the general shape of saturated hydrocarbon chains:
With the mouse right button we can change the display to spacefill to get an idea of the general shape of saturated hydrocarbon chains.
2. Unsaturated hydrocarbons
Two sp2 carbons link to each other by means of a double bond. Hydrocarbons containing double bonds constitute the ethylene series.
The simplest of them is
This double bond consists in two molecular orbitals: One s (sigma) orbital and
one p (pi) orbital, each containing two electrons. These orbitals do not allow
the rotation around the bond. This causes the six atoms being in the same plane.
The next hydrocarbon in the ethylene series is
If we pass to the next hydrocarbon in the series, we find that the double bond can be
in two different positions. This is a case of positional isomerism. These isomers are 1-Butene
and 2-Butene.
In this case, given the impossibility of rotation arond the double bond, the two methyl
terminal groups can be placed in two different ways with repect to the double bond, giving geometrical isomers; one is
and the other is
This structural difference is seen in the Fatty Acids. In natural unsaturated
fatty acids, the double bond is almost invariably of the cis- type. This creates an angle in the molecule
than can be seen in
or 9-cis Octadecenoic acid. Compare this structure with the corresponding saturated
acid,
Or the trans- unsaturated isomer,
We can see that in those last cases the molecule is a straight line, without any angles.
Two sp carbon atoms can be joined by a triple bond, as is the case of
Compounds with triple bonds are rarely seen in biological media.
3. Alyciclic Hydrocarbons
When a saturated hydrocarbon chain closes on itself the resulting compunds are called
Alicyclic hydrocarbons to differentiate from the Aromatic Hydrocarbons to be treated below.
the simplest of alicyclic hydrocarbons is
Note the deviation of the C-C-C angles (60 degrees) from the 110 degrees present in a linear hydrocarbon.
This distortion is not so great in
(90 degrees), and even less in
In the
the C-C-C angles have approximately the same value as in the linear saturated hydrocarbon
chains. This structure allows us to introduce the concept of conformation: freedom of rotation around
a single bond allows the molecule to show multiple forms in space. However, some of them are more energetically-favoured
than others. Such is the case of the chair conformation.
On the contrary, in
Adjacent atoms appear in the eclypsed conformation, thus being the least energetically-favoured conformer.
The cyclic forms of the Aldohexoses adopt a very similar disposition ins space as
the chair form of cyclohexane. Such is the case of
4. Aromatic compounds
When sp2 carbons form cyclic structures the resulting compunds are the
Aromatic Hydrocarbons. The most representative of these compunds is
In benzene, the six C-C bonds are equivalent and so are the six C-H bonds. The whole molecule
is coplanar. This is due to the fact that the p orbitals of all bonds are delocalized.
Aromatic compounds can also be formed by the fusion of several rings. So,the fusion of
two benzene rings gives the hydrocarbon called
The fusion of three rings gives
And
Aromatic cycles are not necessarily formed only by carbon atoms. Some other atoms can
enter in the structure of aromatic rings, giving what we call Heterocycles. Among the biomolecules
some important heterocycles are the Pyrimidines, with two nitrogen and four carbon atoms. An example is
Other heterocyclic bases are the Purines. An example is
Purines and Pyrimidines are important constituents of the Nucleic Acids.
Other planar systems with delocalized electrons of great interest in Biochemistry
are the Porphyrins. One example is
5. Oxygen Functions
5.1 Alcohols and Phenols
The substitution of an hydrogen by a Hydroxyl group -OH in a aliphatic hydrocarbon results in the
compounds called Alcohols. If the substitution takes place in an aromatic hydrocarbon, we have the Phenols.
The simplest alcohol is Methanol:
With two carbon atoms, ve get Ethanol:
In both cases we have a Primary Alcohol, -CH2OH. When both atoms of ethane
are substituted, we get
Substitution on propane can take place in two different ways, giving positional isomers, In carbon 1 we get
A primary alcohol like methanol ant ethanol, and a Secondary alcohol if the substitution takes place in carbon 2:
Other aliphatic alcohol of great interest in Biochemistry is Propanotriol or Glycerol:
When the -OH group susbtitutes an aromatic hydrocarbon, the resulting compounds are
the Phenols. The most representative is
5.2 Aldehydes and Ketones
A further degree of oxidation is seen in these compounds, whose functional group is
carbonyl, -C=O. When this group is on a primary carbon, the compounds are called aldehydes;
on a secondary carbon, ketones.
The simplest aldehyde is Methanal or Formaldehyde:
Next in the series is Ethanal or Acetaldehyde:
Note the planarity of the aldehyde group (both carbons, oxygen and hydrogen lie on the same plane).
When the carbonyl group is on a secondary carbon atom, the resulting compounds are the Ketones.
As an example, ths structure of propanone (Acetone) is presented:
An important group of biomolecules, the Carbohydrates, are polyhydroxycarbonyl compounds, that is,
Aldehyde or ketone functions in a molecule with one or several alcohol groups.
5.3 Carboxylic acids
A greater degree of oxidation is that of Carboxylic acids, whose functional group is
carboxyl, -COOH. It is a sp2 carbon, like the carbonyl, but with a -OH group instead of a hydrogen.
The simplest carboxylic acid is methanoic (formic) acid:
Next in the series is
Monocarboxylic acids with an even number of carbons, called Fatty Acids are important components of lipids.
As an example, the estructure of Palmitic Acid (C16), with 16 carbon atoms:
Very often fatty acids are unsaturated. Such is the case of 9-cis Octadecenoic or Oleic Acid:
6. Nitrogen functions
When the -OH group of an alcohol is substituted by an amino (-NH2) group, the resulting compounds are called Primary Amines.
The simplest is Methylamine:
Next is Ethylamine:
When one of the hydrogens of the amino group is substituted by another group, we get the
Secondary Amines. It is the case of Piperidine:
The amino group is very important in biomolecules. Such is the case of Aminoacids,
monomers of Proteins. In protein aminoacids, the same carbon appears substituted by an amino group and a
carboxyl group. This is the case of L-Alanine:
the amino group in Alanine appears protonated, as -NH3+, because
this is the form at the physiological pH (7-7.4). The carboxyl group appears dissociated, as -COO-.
An example of relevant amines in biological media are the Catecholamines, hormones and
neurotransmitters. This is the structure of one of them, L-Epinephrine:
The secondary amino group appears protonated, as -NH2+-.