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+-.




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