SCH 102. Dr Albert Ndakala. Mobile: Office: Basement of Chemistry (B-6)

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1 SCH 102 (INTRODUCTION TO ORGANIC CHEMISTRY, CHEMISTRY OF ALKANES AND CYCLOALKANES) Dr Albert Ndakala Mobile: Office: Basement of Chemistry (B-6) B.Pharm Lecture Timetable Lab Timetable Tuesday 8-9 am (ChemLab) Thursday 2-5 pm (ChemLab) Wednesday 2-3 pm (ChemLab) Slide Notes: 1

2 Course Outline (1) Introduction to Organic Chemistry. (2) Bonding in Organic Compounds: The Concept of Hybridization. (3) Overview of the Intramolecular and Intermolecular Forces in Organic Molecules. (4) Alkanes: Nomenclature, Structural Isomers, Conformational Isomers, Occurrence in fossil oils, Oil refining, Uses and Reactions. (5) Cycloalkanes: Nomenclature, Conformational Analysis and Reactions. (6) Overview of the Types of Organic Reactions. (7) Basic Concepts of Organic Reaction Mechanisms. (8) Overview of Stereochemistry. 2

3 Course Evaluation (a) Continuous Assessment Tests: Two CATs covering: (i) Alkanes and Cycloalkanes and (ii) Reaction Types, Reaction Mechanisms and Introduction to Stereochemistry (20 Marks). (b) Practicals (10 Marks). (c) Final Exam (70 Marks). 3

4 Reference Books Organic Chemistry by Francis A. Carey Organic Chemistry by John McMurry Fundamentals of Organic Chemistry by T. W. Solomons Organic Chemistry by Paula Bruice Organic Chemistry by Jonathan Clayden 4

5 A Word of Advice to the Student This introductory course on organic chemistry will begin by looking at the type of bonding (covalent bonding) in organic compounds arising from the sharing of electrons. In forming covalent bonds with other elements, we will see how the concept of hybridisation guides in rationalizing why carbon is tetravalent. We will broadly cover the first class (alkanes and cycloalkanes) of organic compounds and their reactions. Reaction mechanisms will be introduced to rationalize how organic reactions take place in transforming starting materials to products. Lastly, we will look at the 3-dimensional aspects of organic molecules in the topic on stereochemistry to appreciate the significance of the arrangement of atoms in space in diverse processes in life. 5

6 INTRODUCTION TO ORGANIC CHEMISTRY 6

7 What is Organic Chemistry? Organic chemistry, in its simplest definition, is the study of organic compounds (the compounds of carbon). However, there are compounds of carbon (carbon dioxide (CO 2 ), carbon monoxide (CO) and various carbonates) that are not considered organic compounds. 7

8 The Organic Chemists Periodic Table In actual practice, organic compounds are the compounds carbon forms with hydrogen, in addition to derivatives incorporating nitrogen, oxygen, sulphur etc (brown elements in the periodic table below). 8

9 Sample Organic Compounds The examples below illustrate the rank and file of organic compounds that combine carbon and elements such as hydrogen, nitrogen, oxygen, halogens, phosphorus and sulphur. Given the diversity of organic compounds and their vast applications in life, anyone who has an interest in the practice of medicine and the biological sciences should have a strong background in organic chemistry. 9

10 What is the Significance of Organic Chemistry in Life? The compounds of carbon are the central substances which living things. For example: drive some of the most crucial processes in i. DNA: The giant molecules that contain all the genetic information for a given species are generated from nucleic acids. ii. Proteins: blood, enzymes, muscle and skin are composed of amino acids. iii. Together with oxygen in the air we breathe, carbohydrates in our diets furnish the energy that sustains life. 10

11 Life is Significantly Organic Chemistry Not only are we composed largely of organic compounds (proteins), derived from and nourished by them (proteins and carbohydrates), we also live in the Age of Organic Chemistry. Examples: The clothing we wear are made of cotton (cellulose) or nylon, which are organic compounds. Automobile tires derived from rubber are also organic. Medicines such as asprin and paracetamol that cure and relieve suffering are also organic. 11

12 What is the Importance of Organic Chemistry to a Pharmacist? A significant proportion of drugs for chemotherapy against diverse diseases are organic compounds. For example: 12

13 BONDING IN ORGANIC COMPOUNDS 13

Bonding Background Although, the concept of bonding has diverse meanings in different settings, an interaction that establishes greater synergy in a system remains the

14 Bonding Background Although, the concept of bonding has diverse meanings in different settings, an interaction that establishes greater synergy in a system remains the central theme. However, we will restrict our discussion to chemical bonding: the formation of a lasting interaction based on stable forces of attraction between two or more atoms. 14

Since the noble gases are especially stable as atoms having a filled valence shell of electrons, by bonding, atoms attain a stable noble

15 Bonding Why do atoms bond with each other? The chemical bond arises from reorganization of the valence electrons of an atom to attain a complete octet. Since the noble gases are especially stable as atoms having a filled valence shell of electrons, by bonding, atoms attain a stable noble gas electron configuration. For example, the sodium atom ionizes to form a positively charged sodium ion with the electronic configuration of neon, a noble gas. vs The electron reorganization in bonding atoms may lead to two types of bonds: Ionic and covalent bonds. 15

Ionic Bonding The Process An ionic bond is based on electrostatic forces of attraction between atoms with opposite charges arising from transfer of electrons from one element to

16 Ionic Bonding The Process An ionic bond is based on electrostatic forces of attraction between atoms with opposite charges arising from transfer of electrons from one element to another. This is the form of bonding found in sodium chloride. An ionic bond results from reorganization of electrons in atoms that have a large difference in electronegativity. 16

Covalent Bonding The Process Covalent bonding, on the other hand, results from the sharing of electrons between atoms of the same or near similar electronegativity.

17 Covalent Bonding The Process Covalent bonding, on the other hand, results from the sharing of electrons between atoms of the same or near similar electronegativity. For example, when joining two hydrogen atoms, three types of interactions occur: Repulsive interactions (electron-electron or protonproton) and attractive interactions (proton-electron) A covalent H-H bond is the net result of the attractive and repulsive electrostatic forces in the two atoms. 17

Covalent Bonding The Process In the formation of covalent bonds, the octet configuration is achieved by sharing of the valence electotons of the bonding atoms.

18 Covalent Bonding The Process In the formation of covalent bonds, the octet configuration is achieved by sharing of the valence electotons of the bonding atoms. Note that in the nitrogen molecule, each of the nitrogen atoms of the molecule has a full octet of electrons. Covalent bonding is the principal type of bonding in all the organic compounds that we will study. 18

19 Types of Covalent Bonds There are two types of covalent bonds (sigma bonds and pi-bonds) depending on how the bonding orbitals overlap. The sigma bonds (σ-bonds) are formed from end-on overlap between s-s, s-p or p-p orbitals. 19

20 Types of Covalent Bonds Pi-bonds (ᴨ-bonds) on the other hand are formed from the side-by-side overlap between two p orbitals. Note that sigma (σ) bonds have shared electron density directly between the bonding atoms, along the bonding axis. The electron density in Pi (π) bonds lies above and below, or in front and in back of the bonding axis, with no electron directly on the bonding axis, since 2p orbitals do not have any electron density at the nucleus. With this background, let us then start looking at the element carbon to rationalize the nature of the covalent bonds it forms in organic molecules. 20

21 Carbon on the Periodic Table There are only about 100,000 inorganic compounds from about 110 elements, yet there are over 18,000,000 organic compounds (compounds of carbon). Why so! What is so special about carbon that it has become an element of significant interest in organic chemistry? Carbon is in group 4 in the periodic table with the electronic configuration shown below: 21

22 What is so unique about the bonding in carbon compounds? Carbon has four electrons in its outermost shell and requires four more electrons during bonding to complete the octet requirement. Carbon is tetravalent, that is, forms four bonds. The tetravalent carbon can only be explained if the electrons in carbon are excited as shown below: 22

23 What is so unique about the bonding in carbon compounds? Moreover, carbon can use one or more of its valence electrons to form bonds with other carbon atoms. We will look further at these bond types when covering the topic on hybridization. 23

24 Bonding in Organic Compounds Covalent Bonding in Methane Carbon has, outside its nucleus, six electrons. The ground state electronic configuration of carbon is therefore: This, however, represents the ground state of the carbon atom in which only two unpaired electrons are available for bond formation with other atoms i.e. At first sight carbon may appear to be only divalent. 24

25 Bonding in Organic Compounds Atomic Orbitals of Carbon The atomic orbitals in the valence shell of carbon that would be populated by electrons and important in the bonding of carbon are shown below: 25

26 Bonding in Organic Compounds Covalent Bonding in Methane In the excited state, carbon has four unpaired electrons and can form four bonds. Consider the formation of methane from carbon where a typical C-H bond has a bond strength of 100 Kcal/mol Net energy = (400 97) Kcal/mol = 303 Kcal/mol. With net energy released, the formation of methane from carbon and hydrogen is energetically feasible. 26

27 Bonding in Methane (CH 4 ) The Facts What is the nature of the four C-H bonds in methane? Since excited carbon utilizes two different types of orbitals (2s and 2p) for bonding purposes, one may expect methane to have two kinds of C-H bonds. In fact this is not the case. A large amount of evidence shows that all four C-H bonds of methane are identical and the bond angles are o. This is consistent with a tetrahedral bondangle. How does one reconcile this apparent equivalence in bonds? 27

28 Bonding in Methane (CH 4 ) Rationale: Hybridization The bonding orbitals of carbon are neither purely s or p orbitals but a hybrid or mixture of s and p orbitals. Hybridization is the combination of two or more atomic orbitals to form the same number of hybrid orbitals, each having the same shape and energy. Since three p orbitals are mixed with one s orbital, we refer to the orbitals as sp 3 hybridized orbitals, meaning that each one of the orbitals has one-fourth (25%) s character and three fourths (75%) p character. 28

Bonding in Methane (CH 4 ) Rationale: Hybridization Each bond in methane is formed by the overlap of an sp 3 hybrid orbital of carbon with a 1s orbital of hydrogen.

29 Bonding in Methane (CH 4 ) Rationale: Hybridization Each bond in methane is formed by the overlap of an sp 3 hybrid orbital of carbon with a 1s orbital of hydrogen. The four bonds point to the corners of a tetrahedron. All four C-H bonds are sigma bonds because the electron density is concentrated on the axis joining C and H and are formed by head-on overlap of orbitals. 29

30 Bonding in Ethane (C 2 H 6 ) sp 3 Hybridization The structure of ethane can be rationalized by assuming that the two carbon atoms bond to each other by sigma overlap of an sp 3 hybrid orbital of each carbon atom. Structure of ethane 30

31 Bonding in Ethene (C 2 H 4 ) sp 2 Hybridization of Carbon Carbon, in its excited state, can also undergo sp 2 hybridization leaving a single p orbital unhybridized. While hybridized orbitals overlap end-on to sigma bonds (σ bonds), unhybridized p orbitals overlap sideby-side to form pi (π) bonds. 31

The remaining unhybridized p orbitals on adjacent carbons will overlap side-by-side to form the pi (π) bond of

32 Bonding in Ethene (C 2 H 4 ) sp 2 Hybridization of Carbon In the ethane molecule, sp 2 hybridized orbitals will overlap end-on to form three sigma bonds (σ bonds). The remaining unhybridized p orbitals on adjacent carbons will overlap side-by-side to form the pi (π) bond of ethene. + Recall that the electron density in a π-bond is farther from the two nuclei to which they are weakly held. Consequently, π-bonds are weaker and easily broken than σ-bonds. 32

Bonding in Ethene (C 2 H 4 ) Perspectives The carbon-carbon double bond is rigid and bond rotation can not occur. For rotation to occur, the π-bond must be broken.

33 Bonding in Ethene (C 2 H 4 ) Perspectives The carbon-carbon double bond is rigid and bond rotation can not occur. For rotation to occur, the π-bond must be broken. The energy barrier for bond rotation in ethene is 235 kj/mol while for ethane is only 12 kj/mol. The rigidity of the double bond gives rise to the possibility of stereoisomerism (geometric isomerism), commonly called cis-trans isomerism in alkenes. The cis isomer can not interconvert into the trans isomer unless through a chemical reaction. 33

34 Bonding in Ethyne (C 2 H 2 ) sp Hybridization of Carbon Carbon, in its excited state, can also undergo sp hybridization leaving two p orbitals unhybridized. 34

35 Bonding in Ethyne (C 2 H 2 ) sp Hybridization of Carbon These sp hybridized orbitals overlap to form sigma bonds (σ bonds). The number of π bonds that can form will be dependent on the number of unhybridized p orbitals available 2 for sp hybridized carbons (the two π bonds will be perpendicular to each other). Alkynes have a linear geometry with C-C bond angle of 180 o. 35

Comparison of Bond Strengths and Lengths The influence of Hybridization Since the s orbitals are lower in energy than p orbitals, the electrons in s orbitals are held more closely to the

36 Comparison of Bond Strengths and Lengths The influence of Hybridization Since the s orbitals are lower in energy than p orbitals, the electrons in s orbitals are held more closely to the nucleus than electrons in p orbitals. Generally, the more s character the bond, the more tightly held the bond. This explains the relative bond lengths and strengths for each hybridization combo. 36

37 Functional Groups in Organic Chemistry The concept of hydridization also explains the structures and bonding of carbon to other elements such as nitrogen and oxygen to provide a diversity of reactive groups (functional groups) that have a strong influence on organic chemistry. 37

38 Practice Questions Hybridization in Procainamide Determine the hybridisation at the labelled atoms (a-e) of the cardiac antiarrhythmias (shortness of breath) drug. 38

Types of Covalent Bonds

Types of Covalent Bonds There are two types of covalent bonds (sigma bonds and pi-bonds) depending on which atomic orbitals overlap and how they overlap to form a bond. A sigma bond (σ-bond) is formed