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Introduction to Organic Chemistry. Chemical Bonding and Reactions. Scientific Method. A systematic approach to research Hypothesis: a tentative explanation for a set of observations and experiments Law: a description of a phenomenon that allows for general predictions

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Introduction to Organic Chemistry

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Introduction to Organic Chemistry

Chemical Bonding and Reactions

Scientific Method

  • A systematic approach to research

  • Hypothesis: a tentative explanation for a set of observations and experiments

  • Law: a description of a phenomenon that allows for general predictions

  • Theory: a well-established explanation for scientific data; not fully tested; can be disproven

  • Experiments: systematic observations and measurements performed under controlled conditions

Classification of Matter

  • Matter is any physically present substance that has a mass and occupies space

  • Matter is composed of atoms and molecules


  • An element is a singlesubstance in its simplest form that cannot be split into any more separate substances by chemical means

  • Everything around us is comprised of chemical elements

  • 112 elements, 90 of them naturally occurring

  • Only 25 of these are essential for the human body

  • Hydrogen (H), carbon (C), oxygen (O) and nitrogen (N) make up of ~97 % of body weight and 99 % of total atoms

  • Elements are made of atoms

Periodic Table

  • Periodic table is a chart in which elements with similar physical and chemical properties are grouped in a periodic way

  • The elements are arranged according to their atomic number

  • In a periodic table, horizontal rows are called periods and vertical groups are called groups

  • Elements within each group have similar chemical and physical properties

  • Groups 1-2 and 13-18 are called main group elements (also called 1A through 8A groups)

  • Groups 3-12 are called transition group elements (also called 3B through 12B group elements)

Periodic Table

Descriptive Names for Groups in the Periodic Table

  • 1A – alkali metals: lithium, sodium, potassium are most common, very reactive against air and water, hydrogen (H) is also in this group, but it is not a metal

  • 2A – alkaline earth metals: magnesium and calcium are the most abundant in nature among the group, found mainly as minerals

  • 7A – halogens: fluorine, chlorine, bromine, iodine are the most common – halogens react readily with metals to form salts (sodium chloride, calcium chloride)

  • 8A – noble gases: helium, neon, argon, krypton, xenon, radon – they are very unreactive gases – also called inert gases, they are present in monoatomic form

  • Transition metals (B group elements) – contain many of the common metals, such as iron, nickel, copper, cobalt, zinc, platinum, gold, silver

Essential Elements for the Body

Classification of Elements

17 nonmetals

8 semimetals

Atoms and Atomic Theory

  • The smallest unit (particle) of an element is atom

  • Atom is made up of subatomic particles; protons, neutrons and electrons – number of these determine the characteristic of an atom


  • Atomic Number (Z):number of protons (or electrons in a neutral atom) in an atom

  • Mass Number (A): (number of protons) + (number of neutrons)

Atoms and Ions

  • Ions:gain electron – anion, lose electron – cation(fluoride, F-; sodium cation, Na+)

  • Atoms form ions as part of their reaction with other atoms to form molecules.

  • The readiness with which an atom gains or loses electrons dictates its reactivity

  • F + 1e- F-





Neutral fluorine


Fluorine anion

9 protons, 10 electrons

9 protons, 9 electrons

Isotopes of Atoms

  • Isotopes:atoms with the same number of protons and electrons, but different number of neutrons 16O, 17O, and 18O

  • Elements are present in nature as mixtures of their isotopes

  • Chemical behaviors of isotopes are identical, nuclear properties might be different; radioactivity

  • Atomic mass of an element is the weighted average mass of all the isotopes – not same as mass number

  • 35Cl (~75.8%) and 37Cl (~24.2%) – atomic mass is 35.45

  • Isotopes are important in

  • biology and medicine

  • Radioactive isotopes are used

  • for monitoring biochemical activity

Representation of Atoms: Lewis Symbols

  • Representing atoms by showing only the valance electrons

  • Electrons (valance) are represented as dots around the chemical symbol of the atom

  • Dots can be placed on the 4 sides of the chemical symbol – place one electron each side, then start to add remaining electrons

Each unpaired dot is available

for bonding with other atoms

Atomic Orbitals and Energy Levels

  • Electrons of an atom are found in discrete shells around the nucleus – from closest to the nucleus to the farthest (valance shell)

  • These shells also correspond to energy levels;

    (n = 1, n = 2 etc.)

  • The energy level corresponds to the period number at the periodic table (hydrogen, n = 1, period 1)

    (Lithium, n = 2, period 2)

Valance shell

Calcium (Ca) is in the 4th period

Atomic Orbitals and Energy Levels

  • 1) Principal energy levels: Shown as n = 1, 2, 3 etc. – total electron capacity of a principal energy level is equal to 2(n)2

    (for n=1, capacity 2 e-, for n=1, capacity 8 e-, for n = 3 capacity 18 e-)

  • 2) Sublevels:Within each principal energy level, there is a set of equal-energy orbitals – designated as s, p, d, f

    (Both principal energy level and type of sublevel is specified for describing the location of an electron)

  • 3) Orbital: Sublevels have atomic orbitals, which is a specific region of a sublevel where electron is located (probability of finding the electron is high);

  • 4)An orbital can have maximum 2 electrons

Octet Rule

  • Octet rule; atoms react in such a way that they have eight electrons in their valance (outermost) shell (more stable configuration)

  • This configuration of 8 electrons in the valance shell is also known as “noble gas configuration”

  • Noble gases (group 8A) are not reactive, since they have their valance shells already filled with 8 electrons (Helium is an exception and has 2 electrons in its only shell)

  • Other atoms lose/gain or share electrons to achieve the more stable noble gas configuration

  • By using octet rule, we can predict the

  • chemical changes between atoms

Shapes of Orbitals

1 kind of s,

3 kind of p,

5 kind of d


Electron configuration and Aufbau Principle

  • 1st principal energy level (n = 1) - 1s

  • 2ndprincipal energy level (n = 2) – 2s 2p

  • 3rdprincipal energy level (n = 3) – 3s 3p 3d

  • 4thprincipal energy level (n = 4) – 4s 4p 4d 4f

  • Aufbau principle:electrons fill the lowest-energy orbital that is available first

How to write the electronic configuration of an atom?


  • 1) Start filling the orbitals from the lowest energy; (1s orbital is the lowest energy orbital)

  • 2) Each principle energy level contain n sublevels and each sublevel contain certain number of orbitals

  • 3) No more than 2 electrons can be placed in an orbital

    For example, 1s < 2s < 2p < 3s < 3p is the order of energy for the first three principal levels

    Be: 1s2 2s2

    O: 1s2 2s2 2p4

    Ne: 1s2 2s2 2p6

    Mg: 1s2 2s2 2p6 3s2

Molecular Interactions: How do molecules form?

  • Substances that are made of more than one element are called compounds, e.g. water (H2O) and carbon dioxide (CO2)

  • Valance electrons ;The valence shell holds the electrons located furthest from the nucleus

  • Valance electrons are important because; the rearrangement and redistribution of valence electrons between atoms enable atoms to ‘bond’ to one another

  • Full valance shell is the most stable form for an atom

  • The principal aim of chemical bond formation is to generate full valence shells

Valance shell

Chemical Bond Formation

  • There are two types of chemical bonding:

  • In a “covalent bond” one or more pairs of electrons are shared equally between the atoms

  • In an “ionic bond” electrons are totally transferred from one atom to another

  • Two non-metal atoms will react to form a covalent compound

  • A non-metal will react with a metal to form an ionic compound

1) Covalent Bond: Sharing of Electrons

  • In covalent bonding electrons are shared between atoms

  • The two orbitals with the valance electrons should overlap for covalent bond formation

  • This way the atoms sharing electrons gain full valance shell – more stable (octet rule)

  • Atoms which are linked by covalent bonds form discrete units called molecules; the smallest part of a single element (O2) or a compound (such as glucose, C6H12O6)

  • The molecular formula show the composition of one molecule of a covalent compound

C3H8S (1-thiol), odour of onion

C6H12O6 (glucose), sugar

2) Ionic Bond: Transfer of Electrons

  • Ionic bonds are formed when one or more electrons are fully transferred from one atom to another – one atom becomes positively charged (cation) another becomes negatively charged (anion)

  • The attraction between the oppositely charged cations and anions makes the the ‘ionic bond’ between the ions - electrostatic interaction

  • Ionic compounds exist as extended lattices–a network of cations and anions

  • Ionic compunds have an overall charge of zero due to equal number of positive and negative charges within the compound

Covalent Bonds: Single and Multiple Bonds

  • Types of covalent bonds: Sigma (γ) and pi (π) bonds

  • Single or multiple bonds can form between two atoms

  • Single bonds are always sigma bonds

  • Single bond – one sigma bond

  • Double bond – one sigma bond + one pi bond

  • Triple bond – one sigma bond + 2 pi bonds

Polar Covalent Bonding and Electronegativity

  • Although there is no electron transfer in covalent bonding, the atoms making the covalent bond might have partial charges

  • In a heteroatomic molecule, the electron distribution around the molecule is not even; electrons are not shared equally – this gives partial charges to atoms

  • Electronegativity is the measure of the ability of an atom to attract electrons in a chemical bond

  • Electronegativity determines which of the atoms in a molecule will be partially negative and which will be partially positive

Chemical Bonding vs. Non-covalent (Intermolecular) Interactions

  • Non-covalent interactions are weak interactions between molecules

  • Non-covalent interactions determine physical properties such as boiling point, melting point, density etc.

  • These interactions are very important in biological systems (assembly of lipid bilayers, packing of genome etc.)

  • Although they are weak, multiple non-covalent interactions occur at the same time between two molecules to give a large overall effect

Type of Non-covalent Interactions

1) Electrostatic Interactions

2) Van der Waals Forces

3) Hydrogen bonding

4) Hydrophobic Interactions

1) Electrostatic Interactions (Coulomb Interaction)

  • Opposite charges attract, like charges repel

  • Due to polar covalent bonds – one part of the molecule has partial negative and one part has partial positive charge – these molecules are said to have dipole

  • Ion-dipole and dipole-dipole interactions are types of electrostatic interactions

  • Not all molecules with polar bonds are indeed polar – such as CO2

2) Van der Waals Interactions

  • 1) Dispersion forces: Interactions between all molecules due to induced dipole – the only form of non-covalent interaction between nonpolar molecules such as methane,

  • These interactions are due to temporary dipoles and short-lived

  • 2) Dipole-dipole İnteractions: Non-covalent interactions that occur between polar molecules due to attraction between opposite partial charges on the molecule

  • These interactions are due to permanent dipole of molecules and are long-lived

2) Van der Waals Interactions

  • 3) Steric Repulsion: Repulsion between two molecules due to close proximity of their electrons


  • Van der Waals interactions is the sum of the dispersion forces, dipole-dipole interactions and steric repulsions

  • Distance and medium are two important parameters that determine the magnitude of Van der Waals interactions

3) Hydrogen Bonding

  • What is hydrogen bonding?:A hydrogen atom covalently bound to an oxygen (O), nitrogen (N) or fluorine (F) atom can interact with an unshared electron pair on another oxygen, nitrogen or fluorine atom to form a hydrogen bond

    1) A hydrogen atom must be bonded to an atom of oxygen, nitrogenor fluorine

    2) This hydrogen atom must interact with a lone pair on an atom of oxygen, nitrogen or fluorine

  • Hydrogen bonds are relatively weak compared to covalent bonds, but stronger than Van der Waals interactions

  • Hydrogen bonding is a special type of dipolar interaction

Hydrogen bonding between water molecules

Changing of The Three States of the Matter

  • The extent of physical (non-covalent) interactions between molecules determines the physical state of a substance; solid, liquid, gas

  • Solid > liquid > gas (the order of the strength of non-covalent interactions)

  • The physical state of a substance can be changed by altering the number of non-covalent interactions between its molecules; this is achieved by giving or taking energy from the substance – generally by heat energy

Three States of Matter

  • As we increase the energy of a substance, its molecules exhibit greater degree of movement and finally overcome the attractive forces holding the molecules together

  • Polar molecules have higher melting and boiling points, non-polar molecules have lower melting and boiling points

    (water b.p. =100 °C vs. methane b.p.= -161 °C)

Chemical Reactions

  • A chemical reaction involves breaking of bonds between atoms (reactants) and the formation of new bonds to form products

  • It is the movement of valence electrons that lies at the heart of many chemical reactions

  • In formation of molecules, valence electrons are shared between atoms in such a way that all atoms complete full valence shells (octet rule)

  • In a chemical reaction, reactants and products react in precise amounts (stoichiometry)

  • Stoichiometry is indicated by numbers in front of the chemical formula in the reaction scheme

    6 CO2 + 6 H2O → C6H12O6 + 6 O2 (photosynthesis)

    6 : 6 1 : 6


Nucleophiles and Electrophiles

  • A nucleophile (Nu– or Nuδ–), is an electron-rich species, which has a valence electron pair (which may be a non-bonding pair) that can be donated to form a covalent bond

  • An electrophile (E+ or Eδ+), is an electron-poor species, which can accept a complete electron pair and share it with the nucleophile to form a covalent bond

Oxidation and Reduction Reactions

  • In oxidation and reduction reactions (also called redox reactions) oxidation of one molecule is couple to the reduction of the other molecule

  • A nucleophile can donate an electron(s) to an electrophile such that the nucleophile will lose electrons and the electrophile will gain electrons

  • The species that loses electron becomes oxidized and the species that gains electron becomes reduced

  • In many cases;

  • loss of hydrogens is oxidation and gain of hydrogens is reduction;

  • loss of oxygen is reduction, gain of oxygen is oxidation

  • There are many examples of redox reactions in biology; for example many oxidation

  • reactions of organic compounds are couple to reduction of cofactors such as NAD+ or FAD

Mechanism of a Reaction

  • The reaction mechanism tell us how electrons are redistributed during the change from reactants to products

  • A reaction goes through certain stages to form the product

  • These stages determine the mechanism of the reaction

  • Mechanism is the type of the changes of reactant into products (number of steps, nature of reaction etc.)

Mechanism of a Reaction

  • A reaction might be one step or multiple steps

  • Consider a one step mechanism:

    A + B  C

  • Reactants do not go into products suddenly; instead goes through a transition state

  • Transition state is the highest point of energy of a reaction

  • In transition state some bonds are partially broken and some bonds are partially formed

Transition States and Intermediates

  • Consider a multi-step reaction:

  • Reactants form an intermediate compound at each step and at the last step the product is formed

  • In a multi-step reaction, formation of each intermediate goes through a transition state

  • Intermediates are more stable than transition states and have a longer life-time

Types of Reaction Mechanisms

1) Substitution

2) Addition

3) Elimination

4) Condensation

1) Substitution

  • In a substitution reaction, an atom on the reactant is replaced by a different atom

  • A + B - X ----> B + A - X (A is substituted with B)

  • A substitution reaction can be nucleophilic or electrophilic

  • Nucleophilic substitution reactions are more common

Nucleophilic Substitution

  • If a nucleophile attacks the parent molecule where substitution occurs, this reaction is called nucleophilic substitution reaction

  • A nucleophilic substitution reaction can occur in one or two steps

2) Addition

  • In an addition reaction, two molecules combine to give one single product; the product contains all the atoms of both molecules

  • A + B ---> AB

  • The most common type of addition reactions is addition of small molecules to the carbon-carbon double bond of alkenes - double bond acts as a nucleophile and the adding molecule acts as an electrophile

  • Addition of a nucleophile to the carbon-oxygen double bond (carbonyl bond – a common functional group) is also a common addition reaction

3) Elimination

  • In an elimination reaction, a molecule loses some of its part to form a compound with a double bond and the eliminated part becomes a new molecule:

  • An elimination reaction is the reverse of an addition reaction

  • Elimination reactions result in the formation of a double bond in a molecule

  • Elimination reactions can proceed through a one-step or two-step mechanism

4) Condensation

  • In a condensation reaction, two molecules combine together to give a large product and a small product:

  • A-X + B-Y  A-B + X-Y (minor small product)

  • Condensation provides a way of joining two molecules together to form a larger product

  • In many cases, the eliminated small product is water (also called dehydration reactions)

  • Many examples in biology; amino acids combine to from proteins, nucleic acids combine to form DNA/RNA – all condensation reactions

5) Hydrolysis

  • The reactions in which large molecules are broken down into smaller molecules through reaction with water; large molecules react with water and split into two

  • Opposite of condensation

  • Don’t mix hydration and hydrolysis!; in hydration water adds to a molecule and there is no splitting into smaller molecules

  • One of the most important hydrolysis reaction in biology is hydrolysis of ATP molecules

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