Organic chemistry in life

Here was once a time when chemists thought "organic" referred only to things that were living, and that life was the result of a spiritual "life force." While there is nothing wrong with viewing life as having a spiritual component, spiritual matters are simply outside the realm of science, and to mix up the two is as silly as using mathematics to explain love (or vice versa). In fact, the "life force" has a name: carbon, the common denominator in all living things. Not everything that has carbon is living, nor are all the areas studied in organic chemistry—the branch of chemistry devoted to the study of carbon and its compounds—always concerned with living things.The element carbon forms a vast number of compounds. 

Over 16 million carbon-containing compounds are known, and about 90% of the new compounds synthesized each year contain carbon. The study of carbon compounds constitutes a separate branch of chemistry known as organic chemistry. This term arose from the eighteenth-century belief that organic compounds could be formed only by living systems. This idea was disproved in 1828 by the German chemist Friedrich Wöhler when he synthesized urea (H2NCONH2), an organic substance found in the urine of mammals, by heating ammonium cyanate (NH4OCN), an inorganic substance. Organic chemistry addresses an array of subjects as vast as the number of possible compounds that can be made by strings of carbon atoms.

Chemistry of Life

Life on earth depends on the chemical element carbon, which is present in every living thing. Carbon is so important, it forms the basis for two branches of chemistry, organic chemistry and biochemistry. The GED will expect you to be familiar with the following terms:

Hydrocarbons - molecules that only contain the elements carbon and hydrogen (e.g., CH4 is a hydrocarbon while CO2  is not)

Organic - refers to the chemistry of living things, all of which contain the element carbon

Organic Chemistry - study of the chemistry of carbon compounds involved in life (so, studying diamond, which is a crystalline form of carbon, isn't included in organic chemistry, but studying how methane is produced is covered by organic chemistry)

Organic Molecules - molecules that have carbon atoms linked together in a straight line (carbon chain) or in a circular ring (carbon ring)

Polymer - hydrocarbons which have chained together

Separation of organic compounds

Introduction

The Separation of a mixture of organic compounds to give the pure components is of the great practical importance in chemistry. Many synthetic reactions react to give mixture of products. It is necessary to have a reasonably clear idea of how the mixture of compounds can be separated out. Almost all the compounds which have the interest of biochemical occurs naturally as components of very complex mixture from which they can be separated out only with considerable difficulty and efficiency.

Separations of organic compounds can be achieved by differences in physical and chemical properties, such as differences in boiling point, melting point etc. or by chemical means, having differences in physical properties which are regulated by chemical reactions.

Problems in Separation of organic compounds

A common problem arises in organic chemistry involves the separation of a mixture of two or three organic compounds into single compound fractions followed by the purification and identification of each organic compound.  To effect the separation of organic compounds, the chemist must make use of the different properties of the components. The phenomena such as differences in solubility, density, acid-base chemistry and reactivity are used to separate a mixture of organic compounds.

Then each component is purified and identified.  For example the carboxylic acid can react with a base such as sodium hydroxide and forms an anion which is water soluble. The neutral doesn’t react and so it remains “neutral”. The possible organic neutral compounds are separated out.

Utility of Separation of organic compounds

It is important to note that single extractions of organic compound for its separation do not necessarily yield complete separations, and that multiple extractions sometimes needed. It includes the extraction the original organic solution two times with aqueous sodium hydroxide solution to remove the acid and water soluble impurities from the organic layers of mixture.

The two aqueous extracts are then combined with each other and set aside as the aqueous sodium hydroxide fraction. The organic compound is further extracted once with distilled water to remove any water soluble impurities.  Once these extractions of organic compound are complete, the organic solution should contain only the "neutral" compound.

Structural representations of organic compounds

Introduction

The structural formula of a chemical compound is a graphical representation of the molecular structure to show that how the atoms are arranged. The chemical bonding inside the molecule is shown, either explicitly or implicitly. There are three common representations which used in publications: text, Lewis type and line-angle formula. Also many other formats are used, as in chemical databases, like SMILES, InChI and CML.

Structural formulas give a representation of the molecular structure. Chemists mostly describe a chemical reaction or synthesis by using structural formulae instead of chemical names, because the structural formulas allow the chemist to observe the molecules and the changes that occur.

Many chemical compounds are present in different isomeric forms, which have different structures but the same overall chemical formula. A structural formula indicates the arrangements of atoms in a mannered way which a chemical formula cannot do.

Text formulas

In early organic chemistry publications, when use of graphics was strictly limited, a text-based system came for describing organic structures in a line of text. Although this system tends to break down with complex cyclic compounds, it remains a easier way to represent simple structures.

CH₃^–CH₂^–OH or CH₃CH₂OH

Lewis structures

Lewis structures are flat graphical formulas which show the atom connectivity, but do not give information about the three-dimensional structure of molecules. This notation is commonly used for small linear molecules. A single line shows a single bond or single electron pair. Two and three lines show double and triple bonds, respectively. Alternatively, dots (•) are used to show single electrons. This is called as Lewis Dot Structure.

Three-dimensional structures

Several methods are present to picturize the three-dimensional arrangement of atoms in a molecule.

Fischer projection

The Fischer projection is commonly used for linear monosaccharides. The vertical backbone is implicit to form a bridge-like structure on the paper plane with the substituents sticking up.

Perspective drawings of cyclic conformations

Perspective drawing is a three-dimensional perspective of a cyclic compound, also shows the structure of the ring, as it is an example a chair conformation.

Newman projection and sawhorse projection

The Newman projection and the sawhorse projection are used for depicting the stereochemistry at two connected carbon atoms.

Skeletal formulas

Skeletal formulas are the standard information for more complex organic molecules. Carbon (C) atoms are represented by the vertices (corners) and termini of line segments which are not marked with an atomic symbol. Each carbon atom is in turn thought to bear enough hydrogen atoms to give the carbon atom four bonds.

Stereochemistry in skeletal formulas

Chiral property in skeletal formulas is denoted by the Natta projection method. Solid or dashed wedged bonds symbolize bonds pointing above-the-plane or below-the-plane of the paper, respectively.

Organic Nomenclature

A member of a large class of chemical compounds containing carbon in their molecules is organic chemical.Compounds such as simple oxides of carbon and cyanides, carbonates, including allotropes of carbon as well are considered inorganic due to some historical reasons.

The science that is concerned with all aspects of organic compounds is termed as organic chemistry and the methodology to prepare these compounds is organic synthesis.

"Organic" is an historical  name, which dates back to the first century. Vitalism was believed by western alchemists for many centuries. Vitalism was the theory which stated that  certain compounds could only be synthesized from their classical elements Earth, Water, Air and Fire by the action of a "life-force" which is possessed only by organisms. According to this theory these "organic" compounds differ fundamentally from the "inorganic" compounds that could be obtained by chemical manipulation of the elements.

There are different ways to classify organic chemicals. Natural and synthetic compounds are major distinction between them. The presence of heteroatoms can classify or subdivide organic chemicals,taking example of organometallic compound in which bonds between carbon and a metal is featured, and compounds in which bonds between carbon and a phosphorus is featured is organophosphorus.

The size of organic compounds distinguish between small molecules and polymers, this is another criteria to classify organic chemicals.

Synthesis of organic compounds from Natural compounds

Those chemicals which are produced by plants or animals are natural compounds. It may be expensive to produced some compounds artificially so they are still taken from natural sources. For examples most sugars, some alkaloids and terpenoids are included in this category, certain nutrients as vitamin B12, and those natural products which are stereoisometrically complicated molecules present in reasonable concentrations in living organisms.

Compounds such as antigens, carbohydrates, enzymes, hormones, lipids and fatty acids, neurotransmitters, nucleic acids, proteins, peptides and amino acids, lectins, vitamins and fats and oils, are of prime importance to biochemistry.

Organic chemicals: Synthetic Compounds

Synthetic compounds are those which are prepared by reaction of other compounds. They may be the compounds already found in plants or animals (semi synthetic compounds), or those which are not found naturally.

A category which includes all plastics (polymers) are organic compounds. An exception that is noticable is silicone, which comes in both category of polymer and a plastic.

Ionic radii table

What is Ionic Radii ?

Ionic radii is related to ions present in ionic substances (crystalline solids). Ions are formed when neutral atom either gain or lose electrons. The effective size of the cation (+ charged) or anion (- charged) is termed as ionic radius. It is defined as the distance between the nucleus and outermost shell of an ion or it is the distance between the nucleus and the point where the nucleus exerts its influence over the electron cloud.

Comparative size of the atoms and the cations in the table

Comparison of the ionic radii with corresponding atomic radii of the cation is always smaller than the atomic radii of the parent atom. The radius of the anion is always larger than the atomic radii of the parent atom.

Comparative size of the atoms and the cations in the table

Atom	Atomic radii (crystal radius)Ao	Corresponding cation	Ionic radii (Ao)
Li	1.52	Li+	0.59
Na	1.86	Na+	0.99
K	2.31	K+	1.33
Mg	1.60	Mg2+	0.65
Ba	2.22	Ba2+	1.35
Al	1.43	AL3+	0.50
Pb	1.75	Pb2+	1.32

Comparison of atoms and their anions in the table

Atom	Atomic radii (crystal radius)Ao	Corresponding cation	Ionic radii (Ao)
F	0.72	F­-	1.36
Cl	0.99	Cl-	1,81
Br	1.14	Br-	1.96
O	0.73	O2-	1.04
S	1.04	S2-	1.84
N	0.75	N3-	1.71
P	1.10	P3-	2.12

The Z/e Ratio and comparison of different radii

In any particular group, the ions either anions or cations increases as we move top to down, this is because the increase in the number of shell as observed in case of the atomic radius. The size of the cation decreases with the increase in the positive charge. And the size of the anion increase as the negative charge on the anion increases.

This can be explained on the basis of Z/e ratio, whenever this ratio increases, the size of the ion decreases.

Na	Na+	Cl	Cl-	Fe2+	Fe3+
Z/e=11/11=1	11/10=1.1	17/17=1	17/18=.95	26/24=1.08	26/23=1.13

Therefore the relation between the ionic radii and the ions would be:

 Na>Na⁺    Cl <Cl^-   Fe²⁺>Fe³⁺

Most reactive metals in the periodic table

Introduction :
A periodic table is an arrangement of all the known elements in vertical groups and horizontal rows so that the elements with similar physical and chemical properties are placed in the same group.In 1912, Moseley proposed the modern periodic law.  The modern periodic law states that the physical and chemical properties of the elements are periodic functions of their atomic numbers.  There are 18 vertical columns and 7 horizontal rows.The Vertical columns present in the periodic table are represented by Groups.  The horizontal rows present in the periodic table are represented by Periods.

The most reactive metals in the periodic table are:

• Lithium( Li)
• Sodium (Na)
• Potassium(K)
• Rubidium(Rb)
• Caesium(Cs)
•  Francium(Fr)

These elements are called Alkali Metals Periodic Table because their oxides and hydroxides dissolve in water to produce strong alkalies.  They are most reactive and highly electropositive elements in the periodic table.  Group first elements of the periodic table are called as alkali metals.  These are very reactive metals we cannot get freely in nature.  There is only one electron in the outer most shell of these metals.  During the formation of ionic bonding with the other elements, these elements ready to lose one electron. 

In comparison to all metals, alkali metals are more ductile, malleable and good conductors of heat and electricity.  The most reactive elements in this group are Cesium and francium.  If alkali metals are exposed to water they can explode.

Colour of alkali metals during flame test:

Metal ion	Flame colour
Lithium	Crimson red
Sodium	Golden yellow
Potassium	Lilac (pale violet)
Rubidium and caesium	Violet

Properties of Most reactive metals in the periodic table (alkali metals):

1. Alkali metals are the light metals.  Their density is low because of larger atomic volumes.
2. Alkali metals have low ionization energies because the last electron is present in the outermost s-orbital and the removal of electron is easy.
3. Due to low ionization energy , alkali metals are highly electropositive.
4. The metallic character of alkali metals increases from lithium to caesium due to low ionization energy.
5. Alkali metals are powerful reducing agents because they have very low reduction potentials.
6. Alkali metals are exposed to air, they tarnish rapidly due to the formation of oxides on the surface.  Hence they are most reactive metals kept under kerosene or paraffin oil and protected from the action of air.

Standard measurement table

Introduction:
In the metric system of measurement, designations of multiples and sub-divisions of any unit may be deduced by combining with the name of the unit the prefixes like deka to, and kilo meaning, respectively, 10, 100, and 1000, and deci, centi, and milli, meaning, respectively, one-tenth, one-hundredth, and one-thousandth.

In scientific usage, it becomes convenient to measure multiples larger than 1000 and subdivisions smaller than one-thousandth. Therefore, the following prefixes have been introduced and these are recognized worlwide:

yotta,   (Y),      meaning 10²⁴            deci,    (d),        meaning 10^-1
zetta,   (Z),       meaning 10²¹            centi,   (c),        meaning 10^-2
exa,     (E),       meaning 10¹⁸            milli,    (m),       meaning 10^-3
peta,   (P),       meaning 10¹⁵            micro, (u),         meaning 10^-6
tera,    (T),       meaning 10¹²            nano,   (n),        meaning 10^-9
giga,   (G),       meaning 10⁹             pico,    (p),         meaning 10^-12
mega, (M),      meaning 10⁶             femto, (f),          meaning 10^-15
kilo,     (k),      meaning 10³             atto,     (a),        meaning 10^-18
hecto,  (h),       meaning 10²             zepto,  (z),        meaning 10^-21
deka,  (da),      meaning 10¹             yocto,  (y),        meaning 10^-24

Units of Length

10 millimeters (mm)  = 1 centimeter (cm)
10 centimeters          = 1 decimeter (dm) = 100 millimeters
10 decimeters           = 1 meter (m)
10 meters                  = 1 dekameter (dam)
10 dekameters          = 1 hectometer (hm)
10 hectometers         = 1 kilometer (km)

Units of Liquid Volume

10 milliliters (mL)       = 1 centiliter (cL)
10 centiliters              = 1 deciliter (dL)
10 deciliters               = 1 liter
10 liters                     = 1 dekaliter (daL)
10 dekaliters             = 1 hectoliter (hL)
10 hectoliters             = 1 kiloliter (kL)

Units of Area

100 square millimeters (mm²)         = 1 square centimeter (cm²)
100 square centimeters                  = 1 square decimeter (dm²)
100 square decimeters                   = 1 square meter (m²)
100 square meters                          = 1 square dekameter (dam²) = 1 are
100 square dekameters                  = 1 square hectometer (hm²) = 1 hectare (ha)
100 square hectometers                 = 1 square kilometer (km²)

Units of Mass

10 milligrams (mg)    = 1 centigram (cg)
10 centigrams           = 1 decigram (dg) = 100 milligrams
10 decigrams            = 1 gram (g)
10 grams                   = 1 dekagram (dag)
10 dekagrams           = 1 hectogram (hg)
10 hectograms          = 1 kilogram (kg)
1000 kilograms         = 1 megagram (Mg) or 1 metric ton(t)