SATURATED HYDROCARBONS OR ALKANES

Alkanes belong to a group of organic substances known as Hydrocarbons called so since they are made of carbon and hydrogen only. Alkanes are called saturated hydrocarbons since besides carbon carbon single bonds, other valence are occupied by hydrogen atoms. Consequently they contain the maximum number of hydrogen atoms.

• Aliphatic alkanes and
• Cyclic alkanes or Cycloalkanes

Aliphatic alkanes form a group of linear and branched alkanes.

Cycloalkanes: Whose carbon atoms arranged in a ring or a cyclic structure.

OCCURENCE OF ALKANES

A large number of alkanes are from natural gases and petroleum (crude oil) whose origin is attributed to the fermentation of cellulose from decayed plants dead many years ago.

NOMENCLATURE OF ALKANES 

All alkanes respond to the general formula CnH2n+2 where ech member differ from the preceding one by one carbon and two hydrogens. Compound that differ in this way are said to form an homologous series. When an alkane molecule has a linear structure or unbranched chain is called normal alkane and is said to to have a normal structure and when it is branched, is called isostructure.

NOTE

• when a carbon atom is attached or linked to a unique atom of carbon, is called primary carbon.
• when it is linked to two other carbon atoms is called secondary carbon.
• when it is linked to three other carbon atoms is called tertiary carbon.
• Finally when a carbon atom is linked to four different carbon atoms is called quaternary carbon.

ISOMERISM IN ORGANIC COMPOUNDS

In organic chemistry, we distinguish two types of isomerism: structural isomers and stereoisomers. Isomerism is the existence of compounds that have the same molecular formula but different arrangements of atoms; those compounds are called Isomers. Isomers have different physical or/and chemical properties and the difference may be great or small depending on the type of isomerism.
                                  STRUCTURAL ISOMERS
In structural isomers we distinguish:

1. Chain isomers: Molecules with the same molecular formula but different arrangement of atoms or different chain length.
   
2. Positional isomers: Molecules have the same molecular formula but with different position of unsaturation or other functional groups
3. Functional isomers: Where we have the same empirical formula into different classes
   

                            STEREOISOMERS

Note that in this type of isomerism, molecules have the same empirical formula and the same connection of atoms but different arrangement in space. We distinguish two types: geometric isomers and diastereoisomers.
GEOMETRIC ISOMERS:  The order of atoms bonding is the same but different arrangement in space (geometry is different). We distinguish Cis/Trans isomers and E/Z isomers.

• Cis/Trans isomers:  When carbon atoms are connected by single bond, we have free rotation which is impossible when double bond is present.
  Sothat for molecules of the type 
  Exist in two forms: The two R may be on the same side (Cis-isomers) or on opposite sides (Trans-isomers) with respect to the position of double bonds.
• E/Z isomers: The Cis/Trans system is applicable to the disubstituted alkenes, for a tri or tetra substituted alkenes this system is no longer applicable and contary the E/Z system is used.
  

In cases like this we use the Cahn-Ingold-Prelog convention based on priority of groups. On each carbon belonging to the double bond, we choose an atom or group of atoms of high priority. The priority is given to the atoms according to their atomic masses.

* When atoms of high priority are on the same side, the alkene is of Z-configuration, from the german word Zusammen meaning together.

* When atoms of high priority are on opposite sides, the alkene is of E-configuration, from the german word Entgegen meaning opposite.

CAHN- INGOLD- PRELOG (CIP) RULES OF PRIORITY

1. Atoms of higher atomic mass are of higher priority.
2. When we have identical atoms attached to the atom belonging to the double bond, you have to compare the following atoms till the point where appears the difference.
3. For an atom linked to the other one by multiple bonds, this will give priority.
   

DIASTEREOISOMERS OR OPTICAL ISOMERS

This is applicable to the asymmetric carbon. According to Vant Hoff and Lebel, a carbon with four different substituents is called asymmetric carbon or chiral carbon. Chemicals with chiral carbon show two isomers which are mirror images of each other but non superimposable known as optical isomers.

To name these isomers, we assign priorities to the groups according to the Cahn-Ingold-Prelog.

High priority (1)

Low priority (2)

The above isomers are said to have R or S configurations. We impose the rotation to the molecule such that the atom of priority (4) is oriented towards behind the plane in the axis of the viewer. If the eyes see the sequence of atoms of priority (1), (2), (3) in the clockwise direction (dextrose) and the configuration of chiral carbon is R (rectus) to mean right. If the eyes see the sequences in the counterclockwise direction, the configuration of that chiral carbon is S (sinister) to mean left.

OPTICAL ACTIVITY
Nonsuperimposable mirror image molecules are called enantiomer (from the greek enantion which means opposite). Enantiomers share many of the same properties:
They have the same boiling points, the same melting points, and the same solubilities. All physical properties are the same except those that arise from how groups are boned to the asymmetric carbon are arranged is space. One of them is their interaction with polarized light.
What is polarized light?
Normal light consist of electromagnetic waves that oscillate in all directions. Plane of polarized light or simply polarized light in contrast, oscillate only in a single plane passing through the path of propagation. Polarized light is produced by passing normal light through a polarizer such as polarized lens or Nicol prism.

When polarized light passes through a solution of achiral molecules, the right emerges from the solution with its plane of polarization unchanged. Achiral molecule does not rotate the plane of polarization, it is said to be optically inactive.
But when polarized light passes through a solution of a chiral compound, the light emerges with its plane of polarization changed. Chiral compounds rotates the plane of polarization either in clockwise or counterclockwise direction.

If an enantiomer rotates the plane of polarized light in clockwise direction, its mirror image will rotate the plane of polarized light exactly the same amount counterclockwise.
A compound that rotates the plane of polarization clockwise, it is called dextrogyre (dextrorotatory), indicated by (+). And when an optically active compound rotates the plane of polarized light counterclockwise it is called Levogyre (levorotatory) indicated by (-).
Dextro and Levo are latin prefixes for "to the right" and "to the left" respectively.
Sometimes lowercase d and l are used insted of (+) and (-).
Do not confuse (+) and (-) with R and S. The (+) and (-) symbols indicate the direction in which an optically active compound rotates the plane of polarized light whereas R and S indicate arrangement of groups about an asymmetric carbon. Some compounds with the R configuration are (+) and some are (-). A mixture of equal amounts of two enantiomers (+) and (-) is caleed a "racemic mixture" or a "racemate". Racemic mixtures do not rotate the plane of polarized light since their rotations cancel.

DISCRIMINATION OF ENANTIOMERS BY BIOLOGICAL MOLECULES

ENZYMES:
Enantiomers react in the same way with achiral reagents. But chiral molecules recognizes  only one enantiomer sothat if a synthesis is carried out using a chiral reagent or a chiral catalyst, only one enantiomer will undergo the reaction. The example of a chiral catalyst is an enzyme for example D-aminoacid oxidase that catalyses the reaction of the R enantiomer and leaves the S enantiomer unchanged.

RECEPTORS:
A receptor is a protein that binds a particular molecule. Because a receptor is chiral it will bind one enantiomer better than the other. many drugs exert their physiological activity by binding to receptors. If the drug has an asymetric carbon, the receptor will preferentially bind to one of the enantiomers. Note that in drugs, enantiomers can have the same physiological activity, different degrees of the same activity or very different activity.
Thalidomide tradegy:
Thalodomide is a sedative which has been used in pregnant women with anxiety.

Later on they discovered the the drug was teratogenic (cause malformation in new babies). They found the medicine to have two optical isomers R and S. One of then S, is a good sedative whereas mixed with R due to errors in synthesis even in small amount R causes malformation to new babies and since then the medicine was removed on the market. Recently, Thalidomide was approved in some diseases like leprosy and melanomas.

TYPES OF ORGANIC FORMULAS

Organic chemists have a number of ways to write the formula for organic molecules.

1. Empirical formula: This formula gives the minimum  ratio of atoms in the compound. sometimes the empirical formula is equal to the molecular formula.Ex: CH₃ may represent CH₃CH₃ or (CH₃)x2
2. Molecular formula: Shows the total number of atoms in a given compound Ex: CH₃CH₃ stands for C₂H₆
3. Condensed formula: Shows no bonds in the molecule Ex: CH₃CH₂CH₂CH₂CH₂CH₂CH₃
4. Displayed or developed formula: Show all bonds 
5. Skeletal formula: Use zigzag lines to represent molecules where each summit stands for carbon atom.      

STRUCTURE OF AN ATOM

An atom

CLASSIFICATION OF ORGANIC COMPOUNDS

Since a large number of organic compounds exist, their classification based on their structure became necessary.
Organic compounds are broadly classified as follows

Aliphatic compounds: are straight chain or branched chain compounds
                                  Example: CH₃CH₂CH₂CH₂CH₃
Cyclic compounds: These are compounds in which carbon atoms are joined to form ring or cycle.
These can be homocyclic in which the ring or cycle is made of carbon atoms only and heterocyclic when the ring incorporate other atoms than carbon like N, O, P, S etc.

Aromatic compounds: These are special types of compounds, they include benzene and related compounds (benzenoids). Like alicyclic compounds, aromatic compounds may contain an hetero atom and called heterocyclic aromatic compounds.

Non-benzenoic compounds include tropone.

INTRODUCTION TO ORGANIC CHEMISTRY

The life of human beings, animals and plants depends upon a large number of molecules from

the simplest like󠀥 H₂O, O₂ to the complex macromolecules like hormones, proteins, amino acids

etc through chemical interactions.

The common factor for each of these compounds is the carbon backbone upon which these

molecules are built. All organic compounds contain carbon but not all carbon containing

molecules are organic!

Even though some compounds like Na₂CO₃, CO, CO₂ contain carbon they are not considered to be organic, for a compound to be organic must fulfill the following requirements:

• Organic compounds are covalently bonded
•  They are mainly not soluble in water and are poor electrolytes
•  They have low fusion point and boiling points, many of them are liquids at room temperature
•  They possess the density close to unity
•  They are easily decomposed by heat tᵒ > 500ᵒC
• They are almost all combustible

Organic chemistry is a part of chemistry that studies compounds of carbon since organic compounds are mainly made of Carbon. In addition other elements include Hydrogen, Oxygen, Nitrogen, Sulfur, Halogens etc.

Till 19th century Chemists believed that only living matter, animals and plants, can only produce

organic compounds, the so called ―vitalism theory

But the production of Urea 

by heating ammonium cyanate in the

laboratory by WÖller changed the atmosphere since then many organic chemicals started to be

also synthesized in the laboratory. This was the death of Vitalism theory.

OCCURENCE OF CARBON
Carbon is found in the environment both as an element and in its combined form. Although carbon ranks about 17th in abundance by mass among the elements in the earth’s crust. It is exceedingly important because it is found in all living matter. Carbon is present in the body tissues and fluids and in the food we eat. It is also found in common fuels such as coal, petroleum, natural gas and wood.
Depending upon the internal arrangement of atoms in pure carbon we can distinguish two forms of carbon:

• Amorphous carbon: charcoals, peat
• Crystalline carbon: diamond, graphitE

STRUCTURE AND UNIQUE PROPERTIES OF CARBON

Carbon is the first member of group 14, and has mostly non-metallic properties. In its ground state carbon has an electronic configuration of 1s², 2s², 2p².

It has four electrons more than Helium and four electrons fewer than Neon; this means that the formation of carbon ions is energetically impossible under normal conditions. Its electronegativity and position in the periodic table indicates that carbon shares electrons to attain a filled outer shell, and that it bonds covalently in almost all its elemental forms and compounds.

It is seen from the above configuration that carbon can only form two covalent bonds like in CO C=O but in its many compounds, carbon is tetravalent like in methane CH₄.

How to explain such behavior?

Because 2s and 2p orbitals are approximately of the same energy level, one electron move from

2s to 2p and 227 Kjmol-1 of energy is sufficient to promote 1electron from 2s orbital to 2p

orbital.

BOND ENERGY, CATENATION AND MOLECULAR SHAPE

The number and strength of carbon atoms bonds leads to its outstanding ability to catenate which

allows it to form a multitude of chemically and thermally stable chain, ring, and branched

compounds.

ALLOTROPES OF CARBON

Carbon occurs in several solid allotropic forms that have dramatically different properties.

• Diamond: this is a colorless, crystalline solid form of carbon. It is the hardest material

known; it is the densest form of carbon, about 3.5 times more dense than water. It also

has an extremely high boiling point (greater than 3500ᵒC).

• Graphite: It is a soft, black, crystalline form of carbon that is a fair conductor of electricity.
•  Fullelenes: They are dark colored solids made of spherically net worked carbon atoms cages. It is a C60 compound resemble to a soccer ball. The uses of which are not well known.

PHYSICAL CHEMISTRY

ORGANIC CHEMISTRY

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