Organic Chemistry

January 6, 2021July 8, 2026 SR

Introduction| Definition of Organic chemistry

Organic chemistry deals with the study of carbon compounds and the reactions involving carbon. The carbon valency of 4 means Carbon can form a maximum of four covalent bonds. This allows different kinds of chemical bonding to occur namely single, double and triple bonds. This is also related to the hybridization and the reactivity of carbon and these functional groups and will be further examined in more detail. Alkanes (alkane functional group) contain SINGLE carbon-carbon and carbon-hydrogen bonds. Alkenes have carbon-carbon DOUBLE bonds while alkynes have carbon-carbon TRIPLE bonds. The presence of atoms of other elements (heteroatoms) such as O, N, Halogens, S, P in the organic compounds introduces other functional groups in organic chemistry. The subject of organic chemistry is broad and usually involves the following basic topics .

Lewis structures and VSEPR theory

Lewis structure is a simple way of writing the structure of an organic compound. This is done by using the sum total of number of outermost electrons in the atoms involved in the bonding.

VSEPR theory represents simple covalent chemical bonds with straight lines. The number of outermost electrons around an atom in a chemical compound is used to find the hybridization and the geometry. Lone pairs are electron pairs not involved in any chemical bonding, and they are represented by two dots. Shared pairs (also known as Bonding pairs) are electron pairs between two atoms involved in a chemical bond formation.

Moreover, each type of bonding has a specific shape or orientation in space, and this is called the geometry of the compound. The molecular geometry is a simple form of the electronic geometry of a molecule.

Formal charges and Resonance structures

FORMAL CHARGE CALCULATION

Formal Charge of atom in a compound = [Number of valence electrons in a neutral atom ] – [Number of lone pairs on the atom in the compound structure] – [Number of bonding pairs ]

FORMAL CHARGE = [group number of atom on periodic table -Number of free electrons on the atom in a molecule-number of bonds around the atom.]

Example formal charge of Carbon atom in CO₂, O=C=O:

Carbon has 4 outermost electrons =group number is 4., There is no lone pair electron on the Carbon, so the number of lone pair electrons on Carbon in CO₂ is zero. The open structure O=C=O shows that the Carbon in CO₂ has 4 bonds or 4 bonding electrons around it.

Therefore, Formal Charge of Carbon in CO₂ = 4-0-4=0

Resonance

This involves the shift of electron density by moving lone pairs or bonding pairs without breaking any chemical bond. This can change the formal charge on atoms in a compound and also lead to writing of different resonance structures for certain compounds. Most stable resonance structure is also known as the lowest energy; this is also called most preferred structure and is the structure with the least number of formal charges.

How to calculate formal charges and write resonance structures of molecules

Reaction mechanisms in Organic chemistry

This is referring to details of the stages of the chemical reactions of chemical compounds. Common terms that are used are Nucleophilic Substitution methods (SN₁ and SN₂) and the Elimination methods (E₁ and E₂). Most reactions occur due to differences in electron density around atoms and subsequent electrostatic rearrangements to form new bonds. As a result of this, there are two main common reactive groups and these called Nucleophiles and Electrophiles.

Nucleophiles are atoms or group of atoms in a molecule that are electron rich. These are also Lewis bases and they donate electrons to form new bonds. A base is an atom or group that can pick hydrogens (or protons) attached to other atoms. Some of these can be shown as H₂O, OH-, RO-, CH₃CH₂CH₂CH₂–

Leaving groups are atoms or groups that can hold electrons or negative formal charge by having high polarizability or resonance stabilization can act as good leaving groups. Some of these are ; H₂O, Cl-, CO₂, Br-

Electrophiles are atoms or group that do not have sufficient electrons and can bond by accepting electrons or associating with electron rich groups. Examples of this are; Ammonium NH₄⁺ , H₃O^+, NO⁺, Lewis acids; FeCl₃

Substitution and Elimination reactions

There are two common substitution reactions, and they are called SN₁ and SN₂ reactions. In SN1 occur in two steps; a) the formation of charged intermediate ionic species. b) formation of final neutral molecule. However, SN₂ occur in one concerted step to form products. This results in change of stereochemistry at reaction center. E₁ is an elimination reaction involving two stages as in SN₁ but E₂ is a single step reaction as in SN₂.

The numbers 1 and 2 in the terminology refers to the rate dependence on the reactants. SN₁ reaction rate is determined by how fast the single one intermediate ion is formed from the reactants. This implies SN₁ reaction rate depends on the concentration of only one of the reactants. SN₂ reaction rate depends on how fast two reactant molecules react to form products. This implies SN₂ reaction rate depends on the concentration of the two reactants. Similarly, the same situation is true of E₁ and E₂.

Reaction mechanisms in Organic chemistry

Analytical techniques in organic chemistry

(IR):Infra Red spectroscopy

This is used commonly to identify functional groups and is based on the wavenumbers by which they absorb infrared radiation. For instance, the carbonyl groups show around 1800 to 1650 cm-¹ depending on what is attached to it. The hydroxyl group is usually broad ranging at 3300 to 3000cm-¹ . A hydrogen attached to an alkane carbon is usually at 3000cm-¹ while that in alkene is 3200cm-¹ and that for an alkyne is over 3300cm-¹. This difference in wavenumbers is due to the stiffness or strength of the C-H bond.

Stronger and shorter bonds require more energy to vibrate and therefore have higher wavenumbers. This also explains slight differences in wavenumbers of O-H, N-H and C-H. The O-H is slightly shorter and stiffer than N-H, which is also stiffer and shorter than C-H due to atomic size and orbital overlap. The other factor involved is the reduced mass of the atoms forming the bond. If the bond is the same between two atoms, then the reduced mass takes effect. Atoms of lower mass or weight vibrate at higher wavenumbers than heavier atoms.

An example is stretching vibrations of O-H, N-H and C-H occur at higher frequencies than C-O, C-N and C-C.

HOW TO ANALYZE IR SPECTRA OF ORGANIC COMPOUNDS

NMR: Nuclear Magnetic Resonance

The atoms of some elements have nuclei spins. Therefore, this allows them to absorb and emit energy when placed in a magnetic field. This emitted energy is transformed into electrical display on computers to be used to analyze the compound. This is called NMR spectroscopy, and it is a very important method of analysis in organic chemistry.

Atoms of different elements display different signals, and this depends on the chemical environment in which they are found. Examples of atoms of elements that show NMR activity are as follows ; H, C, O, N, F and S.

HOW TO ANALYZE NMR SPECTRA OF ORGANIC MOLECULES

UV-VIS : Ultra Violet spectroscopy

Chromophores are chemical bonds or functional groups in a compound can absorb UV radiation. Some examples of this include double and triple bonds, benzene and similar ring systems. Electrons are excited to higher energy levels when the compound absorb UV energy . However , the energy is emitted when electrons fall to lower energy ground state . The ability of a compound to absorb UV energy is used UV spectroscopy .

The absorbance A or transmittance can be calculated to find the molar absorptivity of the compound. A = ε c l where ε is the molar absorptivity, c is the molarity and l is the pathlength of 1.0 cm.

Moreover, this can similarly be used to analyze inorganic compounds that contain transition metals.

HOW TO ANALYZE UV-VIS SPECTRA OF ORGANIC COMPOUNDS

MS : Mass spectroscopy

The mass of a compound can be obtained from the mass of the total mass of atoms that make the compound. The elements with different isotopes have percent abundance that appear as different peaks in the spectrum. Isotopes of hydrogen are protium H, Deuterium D, and Tritium T. Carbon isotopes are C-12, C-13, and C-14. Oxygen isotopes are O-16, O-17 and O-18. These can be used to identify the atoms in a compound. In addition to this , it is has been found that a compound will breaks apart due to some methods used. The fragments are ionized and identified as peaks in a mass spectroscopy and this is a common procedure in organic chemistry. Examples of fragments and their masses include benzene -77, H2O -18 etc.