What is Organic Chemistry......?

 Organic Chemistry is the chemistry of the carbon compounds. At the earlier days the chemical compounds were divided into two classes, Inorganic and Organic depending upon where they had come from. The compounds those were obtained from minerals are known as Inorganic compounds; Organic compounds were those obtained from the materials produced by living organisms. Even after it had become clear that these compounds did not had to come from living organisms but could be made in the laboratory, it was convenient to keep the name organic to describe carbon based compounds. The division between inorganic and organic compounds has been retained to this day.

Today, although many carbon compounds can be isolated from living sources, most of them  synthesized. They may also be synthesized from inorganic substances like carbonates or cyanides, but more often from other organic compounds. The petroleum and the coal , which are the large reservoirs of organic compounds from which simple organic compounds  can be obtained. Since we study the organic chemistry as a special field, what is so special about organic compounds from compounds of all the other hundred-odd elements of the periodic table? because there are so very many compounds of carbon , and their molecules can be so large and complex. The number of carbon contain compounds are many times greater than the number of carbon free compounds. As well as carbon atoms can attach themselves to one another forming all most all size of chains and rings, but which can not be done by other elements or atoms.
These chains and rings can have branches and cross-links. To the carbon atoms of these compounds there are attached other atoms chiefly Hydrogen, but also Fluorine, Chlorine, Bromine, Iodine, Oxygen, Nitrogen, Sulfur, Phosphorus and many others.

Fundamentals

1. Structure and Properties
2. Energy of Activation; Transition State
3. Alkanes
4. Alkyl halides
5. Alcohols and Ethers
6. Role of the Solvent
7. Alkenes
8. Conjugation and Resonance
9. Alkynes
10. Cyclic Aliphatic Compounds
11. Aromaticity
12. Aromatic-Aliphatic Compounds
13. Aldehydes and Ketones
14. Carboxylic Acids
15. Functional Derivatives of Carboxylic Acids
16. Amines
17. Phenols
18. Carbanions

Selected Topics

1. Molecular Orbitals
2. Symphoria, Neighboring Group Effects
3. Polymers and Polymerization
4. Stereochemistry
5. Reaction Types and Mechanisms
6. Spectroscopy
7. Heterocyclic Compounds
8. Aryl Halides

Biomolecules 

1. Lipids, Fats and Steroids
2. Carbohydrates, Monosaccharides
3. Carbohydrates, Disaccharides and Polysaccharides
4. Proteins and Nucleic Acids, Molecular Biology

Spectroscopy

 Spectroscopy

When an organic chemist confronted with an unknown compound, he sets out to find the answer to the question : what is this? There are so many steps for the identification of the organic compounds; determination of molecular weight and molecular formula; detection of the presence or absence of certain functional groups; degradation to simpler compounds; conversion into derivatives. Nowadays the modern instruments help us to see more clearly the new things we shall met, and to recognize them more readily when we encounter them again.


The structures of the organic compounds can be readily found out by spectroscopy methods using the instruments called spectrometers. The organic spectroscopy is the study of how photons are absorbed by organic molecules. There is a relationship between the molecular structure and the type of the the photons' absorbance. By studying this relationship informations can be obtained about the molecules.

• The Mass Spectroscopy
• The Electromagnetic Spectrum
• The Infrared Spectroscopy
• The Visible and the Ultraviolet Spectroscopy
• The Nuclear Magnetic Resonance (NMR) Spectrum
• NMR Number of Signals
• NMR Chemical Shift
• NMR Peak Area and Proton Counting
• NMR Coupling Constants
• Carbon-13 NMR (CMR) Spectroscopy
• CMR Splitting
• CMR Chemical Shift
• The Electron Spin Resonance (ESR) Spectrum

                                                                                                                                             

                The Mass Spectroscopy                 

The mass spectrometer is used in this method. In here the molecules are bombarded with a beam of high energetic electrons, so that the molecules are ionized and broken up into many fragments, some of which are positive ions. Each type of ion posses its own ratio of mass to charge, or m/e value. for most of the ions the charge is 1, therefore m/e is the mass of the ion. 

In the mass spectrometer, a signal is produced by the detector for each value of m/e ; the intensity of each signal provide us the relative abundance of the ion producing the signal. A plot showing the relative intensities of signals at the various m/e value is called a mass spectrum, which is highly characteristic for a particular compound. The largest peak is called as the Base Peak; its intensity taken as 100.

mass spectra of the Phenol

mass spectra of  2-pentanol

Mass spectra can be used generally for two purposes, (a) To prove the identity of two compounds and (b) To help establish the structure of a new compound.

 If we measure the mass spectrum of an unknown compound and find it to be identical with the spectrum of a previously reported compound, then we can end up with that (almost beyond the shadow of doubt) the two compounds are identical. There are two or more compounds can show identical physical properties; melting point, refractive index, boiling point, conductivity, etc.. but mass spectrum varies from one another.

When an electron is removed from a molecule, it produces a parent ion or molecular ion; M+ whose m/e value is definitely, the molecular weight of that particular compound, because the charge is1.

In general most elements occur naturally as isotopes, so that the molecular weight that one usually measure and work with it is the average atomic weights of the element. But this is not for the molecular weight that is obtained from mass spectrum. Each isotope results a different peak in mass spectrum.

Electromagnetic spectrum

The Electromagnetic Spectrum

The Electromagnetic Spectrum (EM) is consist of radiation of a wide range of wavelengths (λ). According to the Quantum Mechanics, all these radiations have a dual and seemingly contradictory nature. EM radiations have the properties of both wave and particle. So that these radiations can be described in the terms of its wavelength (λ) or its frequency (ν). It can also be described as if it consisted of particles called quanta or photons. Photons are known as quantized energy.

 

The EM radiation travel through a vacuum at the same velocity(c), called the velocity of light; which is 2.99792458 Χ 10⁸ ms^-1. The frequency of a wave is usually given by Hertz (Hz). The energy of a EM radiation is directly proportional to its frequency,

E = hν

where,

h = Planck's constant, 6.63 x 10^-34 J s

ν = the frequency (Hz)

E = energy

This means that the higher the frequency of radiation the greater is its energy.

Since, ν = c/λ, the energy of a EM radiation inversely proportional to its wavelength.

               E = hc/λ

where, c = velocity

When the energy of these EM radiations are bombarded with the organic molecules, the energy is absorbed by the molecules and they shows transitions in their energy levels. The molecules are in continuous motion and these motions can be resolved into different component as below,

• Rotational energy :- this is the energy due to the rotation of the molecule resolving about an axis of its gravity.

• Vibrational energy :- This is the energy due to the vibration of the molecule.

• Electronic energy :- This is the energy that possessed by the electron from its definite energy levels.

• Nuclear spin energy :- This the energy due to the spin of the nuclei of the molecule.

There are various energy levels in the molecules according to their energy type, they are; Rotational energy level, Vibrational energy level, Electronic energy level, and the Nuclear energy level.

E_electronic > E_vibrational > E_rotational > E_{nuclear spin} ; this means that the EM radiation with higher energy can effect the electronic transitions and the EM radiation with lower energy can effect the nuclear spin transitions. This can be illustrated by following table as well,

Radiation type	Wavelength/cm	Energy	Transition effect
Radio	104 - 106	10-10 - 10-8	Nuclear spin
TV	102	10-6	Nuclear spin
Radar	1	10-4	Nuclear spin
Microwaves	10-1	10-3	Rotational
far IR	10-2	10-2	Vibrational
near IR	10-4	1.24	Vibrational
Visible	10-5	1.55 - 3	Electronic
UV	10-6	4	Electronic
X-ray	10-8	104	Electronic
γ- ray	10-10	106	Nuclear
Cosmic ray	10-12	108	Nuclear

Visible and the UV spectroscopy

  The Visible and the Ultraviolet Spectroscopy  

In the Electromagnetic (EM) spectra , the far UV is in the region of the wavelength (λ) 4nm – 200nm, the near UV is in the region of the λ of 200nm – 400nm and the visible light exist in the range of the λ 400nm – 800nm. When the EM radiation in the UV or visible region is passed through an organic compound, a portion of the radiation is usually absorbed by compound. The energy of the absorbed radiation from these regions are used to electron transitions from lower electronic energy levels to higher electronic energy levels. The magnitude of the absorption of this radiation depends on the wavelength of the radiation and the structure of the molecules.

The UV – Visible spectrometers are the instruments those used to measure the absorbance of the radiation at each wavelength of the visible and UV regions. In general the absorbance of the wavelength of 200nm – 800nm can be measured by most of the visible-UV spectrometers, so the far UV is less useful in the spectroscopic methods as its wavelength range is from 4nm to 200nm. In these instruments, a beam of visible/UV radiation (200nm-400nm and 400nm-800nm) is directed through a solution of the compound being analyzed. Also, these instruments are design to make a comparison of the intensities of Incident light (I₀) and the transmitted light (I), to produce a graph plot of the Wavelength of the entire region versus the Absorbance (A) of light at each wavelength. Such a graph is called an Absorption Spectra.

The absorption at a particular wavelength is defined by the equation;

A = log(I₀/I)

It is also can be derived from the Beer Lambert's law , which says that,

I = I₀ x -ЄCl

log(I/I₀) = -ЄCl

log(I₀/I) = ЄCl

So that,

A = log(I₀/I) = ЄCl

Where,

A- observed absorbance

Є- molar absorptivity or molar extinction coefficient

C- molar concentration of the sample

l- length of the sample tube

I₀- intensity of incident light

I- intensity of transmitted light

The wavelength of maximum absorption (λ_max) and the maximum molar absorptivity (Є_max) are differ from one compound to another. Most of the absorption bands (or peaks) in the absorption spectra are broad because, each electron energy level has associated with its many vibrational and rotational energy levels. Thus, electronic transitions may occu from any of several vibrational and rotational energy levels of one electronic level to any of several vibrational and rotational states of a high electronic levels.

Alkenes and non-conjugated dienes usually have λ_max below 200nm which is out of the range of visible-UV spectrometers. But the compounds with conjugated multiple bonds have λ_max longer than 200nm. For example, Ethene gives a λ_max at 171nm, 1,4-pentadiene gives a λ_max at 178nm and 1,3-butadiene gives a λ_max at 217nm.