Fundamentals of Organic Chemistry PDF

 CONTENTS Page Part (1) Introduction 5 CHAPTER (1) 8 FUNDAMENTAL PRINCIPLES CHAPTER (2) 21 HYDROCARBONS CHAPTER (3) 49 ALDEHYDES AND KETONES CHAPTER (4) 63 CARBOXYLIC ACIDS CHAP...

 CONTENTS Page Part (1) Introduction 5 CHAPTER (1) 8 FUNDAMENTAL PRINCIPLES CHAPTER (2) 21 HYDROCARBONS CHAPTER (3) 49 ALDEHYDES AND KETONES CHAPTER (4) 63 CARBOXYLIC ACIDS CHAPTER (5) 72 AMINO ACIDS -3-  CHAPTER (6) 79 HYDROXY COMPOUNDS CHAPTER (7) 91 CARBOHYDRATES Part (2) Qualitative Organic Chemistry 103 Tables -4-  ‫رؤٍت انكهَت‬ ‫تتطهع كهَت انتربَت جبيعت انًُوفَت ‪ ،‬أٌ تكوٌ رائذة ويتًَزة‬ ‫فٌ يجبل انتعهَى ‪ ،‬وانبحج انتربوً ‪ ،‬وخذيت انًجتًع‪ ،‬يحهَب ً‬ ‫وإقهًََب ً‬ ‫رسبنت انكهَت‬ ‫تهتزو كهَت انتربَت ‪ -‬جبيعت انًُوفَت ‪ ،‬بتخرٍج يعهًٍَ قبدرٍٍ‬ ‫عهي تهبَت احتَبجبث سوق انعًم انتربوً بًستوى يتًَز ‪،‬‬ ‫وإَتبج بحوث تربوٍت تتواكب يع انتطوراث انًستًرة ‪ ،‬وَقم‬ ‫انًعرفت انتربوٍت نخذيت انًجتًع ‪ ،‬وتًَُت انبَئت‪.‬‬ ‫‪-5-‬‬  INTRODUCTION Organ = Greek word for life hemistry of living things- both animals and plants Organic chemistry is a discipline within chemistry which involves the scientific study of the structure, properties, composition, reactions, and preparation of chemical compounds consisting primarily of carbon and hydrogen, which may contain any number of other elements, including nitrogen, oxygen, the halogens as well as phosphorus, silicon and sulfur Organic chemistry is the study of carbon compounds except carbon monoxide, carbon dioxide (CO2), carbonates (Na2CO3), hydrogencarbonates (NaHCO3), carbides (CaC2) and cyanide NaCN, bonds Natural Sources of Organic Compounds Living things: carbohydrates, proteins, fats, deoxy ribonucleic acids (DNA), vitamins, antibiotics and a variety of organic products obtained from living things. Crude oil or coal: fractional distillation produces alkanes, alkenes, alkynes and aromatic hydrocarbon. Organic Chemistry in everyday life: Organic molecules are at the heart of life of both the existence of life on earth and the possibility of life elsewhere. Organic chemistry is the chemistry of carbon compounds, which are the central to life on this planet. Carbon compounds include: deoxy ribonucleic acids (DNA), the giant helical molecule that contain all our genetic information, the proteins that catalyze all of the reactions in our body and constitute the essential compounds of our blood, muscle and skin. Organic substances are pretty crucial in our lives. All other major types of biological molecules (lipids, carbohydrate hormones, -6- neurotransmitters) are organic molecules, and they are needed for life. We live in an age of organic chemistry; everything we use or around us in this world evolve from organic Chemistry. The food we eat, the clothes we wear, the water we drink. If there is no organic chemistry there is no life. There is no art, science or industry where knowledge of organic chemistry is not applied. The importance of organic chemistry is briefly outlined below. 1- Study of life processes, they possess exclusive biological roles, many of them are direct carrier, participant, or products of processes occurring in living organisms or live enzymes, hormones, vitamins, and the like, are biological catalyst, initiator, and regulator of these processes. 2- In daily life: we find ourselves in strange panorama of things that are connected with organic chemistry.  Food: starch, fats, proteins, vegetables, etc.  Clothes: cotton, wool, silk, etc.  Fuels: Kerosene, gasoline, diesel oil, coal, etc.  Medicine: penicillin, streptomycin, etc.  Drugs: morphine, cocaine, LSD, etc.  Insecticides: DDT, gammexane, etc.  Dyes: reactive, vat, disperse, acid, etc.  Stationery: pencil, paper, writing ink, etc.  Rubber and Plastic: polyethylene, PMMA, etc.  Leather and wood products.  Refrigerants.  Paints and varnishes. -7-  3- In industry: Knowledge of organic chemistry is necessary in many important chemical industries: Pharmaceuticals. Explosives. Preparation of foods. Soil fertilizers. Paper industry. Sugar industry. Manufacture of solvents. Dyes manufacture. Synthetic rubber and plastics. Petroleum and petrochemical industries. Manufacture of biomedical and dental materials https://www.rroij.com/open-access/impact-of-the-organic-chemistry-in- our-daily-life.pdf Key Takeaway  Organic chemistry is the study of carbon compounds, nearly all of which also contain hydrogen atoms. Concept Review Exercises Classify each compound as organic or inorganic. a. C3H8O b. CaCl2 c. Cr(NH3)3Cl3 d. C30H48O3N Answers -8-  a. organic b. inorganic c. inorganic d. organic Exercises 1. Classify each compound as organic or inorganic. a. C6H10 b. CoCl2 c. C12H22O11 2. Classify each compound as organic or inorganic. a. CH3NH2 b. NaNH2 c. Cu(NH3)6Cl2 -9-  CHAPTER (1) FUNDAMENTAL PRINCIPLES D rawing Organic Structures and The Unique Nature of Carbon: Carbon atoms link together to form chains of varying length, branched chains and rings of different sizes Catenation: Ability of atoms in forming stable bonds with itself, hence joining up into chains or rings. e.g. carbon and hydrogen atoms join up to form. Ability to Form Multiple Bonds: Electronic configuration of carbon (ground state) : 1s22s22p2 Carbon (ground state Each carbon atom has four unpaired electrons when excited Tend to form four covalent bonds - 10 -  Carbon (excited state) https://www.youtube.com/watch?v=nemBHAzHpag - 11 - Organic chemists use a variety of ways to write structural formulas. The most common types are: 1- The dot structure: Show all of the valence electrons. It is tedious and time consuming. H :O: H O ·· :: H:C:H H:C:H H C C ·· H O H H 2- Dash-structural formulas: It is easier to write and show us how does the structure and the order in which atoms are attached. OH CH3 CH3 CH3 CH3 CH3 H3 C CH3 CH3 CH3 CH3 CH3 CH3 3- Condensed formula: It is still easer to write and when we become more familiar with it, it will impart all the formation that is contained in either the dot or dash structure. CH3-CH2-OH CH3-CH2- CH2-COOH 4- Bond line (zigzag): - 12 -  STRUCTURAL ISOMERISM Isomers are molecules that have the same molecular formula, but have a different arrangement of the atoms. 1) Chain Isomerism These isomers arise because of the possibility of branching in carbon chains. For example: There are two isomers of butane, C4H10. In one of them, the carbon atoms lie in a "straight chain" whereas in the other the chain is branched. Pentane, C5H12, has three chain isomers: 2) Position isomerism In position isomerism, the basic carbon skeleton remains unchanged, but important groups are moved around on that skeleton. For example, there are two structural isomers with the molecular formula C3H7Br. In one of them the bromine atom is on the end of the chain, whereas in the other it's attached in the middle. - 13 - Another similar example occurs in alcohols such as C4H9OH These are the only two possibilities provided you keep to a four carbon chain, but there is no reason why you should do that. You can easily have a mixture of chain isomerism and position isomerism - you aren't restricted to one or the other. So two other isomers of butanol are: You can also get position isomers on benzene rings. Consider the molecular formula C7H7Cl. There are four different isomers you could make depending on the position of the chlorine atom. In one case it is attached to the side-group carbon atom, and then there are three other possible positions it could have around the ring - next to the CH3 group, next-but-one to the CH3 group, or opposite the CH3 group. 3) Functional group isomerism - 14 - In this structural isomerism, the isomers contain different functional groups - that is, they belong to different families of compounds (different homologous series). A molecular formula C3H6O could be either propanal (an aldehyde) or propanone (a ketone). Aother common example is illustrated by the molecular formula C3H6O2. Amongst the several structural isomers of this are propanoic acid (a carboxylic acid) and methyl ethanoate (an ester). https://www.chemguide.co.uk/basicorg/isomerism/structural.html https://www.youtube.com/watch?v=NgzFok_BA_0 https://www.youtube.com/watch?v=8kSwpdhEHQs Classification of organic Compounds Organic compounds are divided into five categories: 1. Aliphatic compounds: Compounds which consist of open- chain of carbon atoms are called aliphatic compounds compounds. There is no limit to the number of atoms involved, Examples are: Ethane CH3-CH3 - 15 -  Propane CH3-CH2-CH3 Ethyl alcohol CH3-CH2-OH Acetic Acid CH3-COOH n-Butylamine CH3-CH2-CH2-CH2-NH2 2. Saturated and Unsaturated Compounds: Compounds which contain only carbon and hydrogen are called hydrocarbons: A hydrocarbon is said to be saturated if it contains only C-C single bond. A hydrocarbon is said to be unsaturated if it contains C=C or C≡C multiple bonds: Examples are: Ethane CH3-CH3 Ethylene CH2=CH2 Acetylene CH≡CH The term unsaturation is also sometimes used to describe a compound containing multiple bonds between other pairs of atoms e.g. C=O, C≡N. 3. Aromatic compounds: Benzene and all compounds that have structures and chemical properties resembling benzene are called aromatic compounds. Examples are: each corner represents CH group Benzene Aniline Naphthalene 4. Alicyclic Compounds: Cyclic compounds which consist only of carbon atoms called alicyclic or carbocyclic compounds, Examples are: each corner represents CH2 group Cyclopropane Cyclobutane Cyclohexane - 16 - 5. Heterocyclic Compounds: Cyclic compounds in which the ring atoms are of carbon and some other element (for example, N, S or O) are called heterocyclic compounds: Examples are: N N N Oxirane Pyridine Quinoline Functional groups A functional group is defined as an atom or a group of atoms that effectively determines the chemical properties of an organic compound. The functional group is the reactive part of an organic molecule. Double and triple bonds are considered as functional groups. Other examples include -Cl, -Br, OH, NH2, CHO, >C=O groups. The functional group is the action group. The hydrocarbon portion of the molecule remains inert. - 17 - The R represents a carbon based group. https://www.chem.fsu.edu/chemlab/chm1046course/functional.html - 18 -  Organic compounds may contain one functional group, two functional groups, three functional groups, or more than three functional groups. Example: A multifunctional compound like the drug molecule morphine may have several functional groups http://www.dynamicscience.com.au/tester/solutions1/chemistry /organic/functionalgroupsnaming.html Homologous Series: A homologous series is a series of compounds that have the same functional group, and each member differs from the next member by a – CH2 – unit in their formula. For example, ethanol and propan-1-ol contain the same functional group –OH and they have similar chemical properties. Therefore they are classified into the same homologous series — alcohols - 19 - Bonds in organic compounds The bonds in organic compounds are generally covalent bonds. Sigma and pi bonds are types of covalent bonds that differ in the overlapping of atomic orbitals. This overlap occurs in two major ways, giving rise to two primary types of covalent bonds, i.e. sigma and pi bonds. 1- The Sigma (σ) Bond This type of covalent bond is formed by head-to-head overlapping of atomic orbitals along the internuclear axis. Sigma bonds are the strongest covalent bonds, owing to the direct overlapping of the participating orbitals. Generally, all single bonds are sigma bonds. Sigma bonds in organic compounds can be formed via the following combinations of atomic orbitals:  s-p Overlapping Here, one half filed s orbital overlaps with one half-filled p orbitals along the internuclear axis, forming a covalent bond. This condition is illustrated below. This type of overlapping can be observed in methane. CH4 molecule features 4 sigma bonds, formed by the overlap of the four p orbitals belonging to the carbon atoms and the 1s orbitals of the four hydrogen atoms. https://www.youtube.com/watch?v=lTrJD9vEWk4  p-p overlapping In this condition, one half-filled p orbital from each participating atom undergoes head-on overlapping along the internuclear axis. This type of overlapping is illustrated below. - 20 -  2- The Pi (π) Bond Pi bonds are formed by side to side lateral overlap of two atomic orbitals along a direction perpendicular to the internuclear axis. This type of covalent bonding is illustrated below. Pi Bonds are generally weaker than sigma bonds, owing to the significantly lower degree of overlapping. Generally, double bonds consist of one sigma and one pi bond, whereas a typical triple bond is made up of two π bonds and one σ bond. It is important to note that a combination of sigma and pi bonds is always stronger than a single sigma bond. Difference Between Sigma and Pi Bonds The key differences between sigma and pi bonds are tabulated below. Sigma Bond Pi Bond The overlapping orbitals must The overlapping orbitals can be pure or hybrid be unhybridized These bonds are strong and have high bond These bonds are relatively energies. weak. Must exist along with a sigma Can exist independently bond. https://www.youtube.com/watch?v=jPUb8AHWK-s - 21 -  Exercise How Many Pi Bonds Exist in Double and Triple Bonds? A triple bond consists of two pi bonds and one sigma bond. A double bond contains one sigma and one pi bond. Single bonds are always sigma bonds. What are the Possible Combinations of Orbitals in Sigma Bonds in organic compounds? The common overlap conditions that result in sigma bonds are: 1. s-p overlap 2. p-p overlap What is the Number of Sigma and Pi bonds in a Benzene Molecule? The benzene ring consists of six carbon-carbon single bonds, all of which are sigma bonds. Additionally, there exist six carbon-hydrogen sigma bonds. Therefore, the total number of sigma bonds in a benzene molecule is 12. The aromatic features alternating double bonds between carbon atoms. Therefore, the total number of pi bonds in a benzene molecule is 3. https://www.youtube.com/watch?v=Vqx9a2aU99c https://www.youtube.com/watch?v=ftw16bkTkRM https://www.chemguide.co.uk/basicorg/isomerism/structural.html ORGANIC REACTIONS Generally chemical reaction defines as broken of bonds and formation of new one. Breaking bonds: A covalent bond, joining atoms in an organic molecule, consists of two electrons. Such a group is referred to as an electron pair. Reactions in organic chemistry proceed through the sequential - 22 - breaking and formation of such bonds. Organic chemists recognize two processes for the breaking of a chemical bond. These processes are known as homolytic cleavage and heterolytic cleavage. (A) Homolytic bond cleavage: Homolytic bond cleavage is a process where the electron pair comprising a bond is split, causing the bond to break. This is denoted by two single barbed curved arrows pointing away from the bond. The consequence of this process is the retention of a single unpaired electron on each of the atoms that were formerly joined by a bond. These single electron species are known as free radicals. Heterolytic bond cleavage: Heterolytic bond cleavage is a process where the electron pair that comprised a bond moves to one of the atoms that were formerly joined by a bond. The bond breaks, forming a negatively charged species (an anion) and a positively charged species (a cation). The anion is the species that retains the electrons from the bond while the cation is stripped of the electrons from the bond. - 23 - https://www.youtube.com/watch?v=hGc1J5S7mqU https://www.youtube.com/watch?v=1UCGRWwEAN8 Mechanism of Organic Reactions A reaction mechanism is a detailed description of how bonds are broken and formed as starting material is converted into product. A reaction can occur either in one step or a series of steps. Kinds of Organic Reactions: The reactions of organic compounds can be classified into 4 types as follows: 1. Substitution Reactions 2. Addition Reactions 3. Elimination Reactions 4. Rearrangement Reactions 1. Substitution Reactions: Substitution reactions are those reactions in which an atom or group of atoms directly attached to a carbon in the substrate molecule is replaced by another atom or group of atoms. For example, - 24 -  H H UV H C H + Cl2 H C Cl + HCl Light H H A hydrogen atom of the methane molecule is replaced by a chlorine atom. H H H2 O H3C C Br + NaOH H C OH + NaBr H H Ethyl bromide Ethyl alcohol In the above reaction, the bromine atom of ethyl bromide is substituted by a hydroxy group. 2- Addition Reactions: Addition reactions are those in which atoms or groups of atoms are simply added to a double or triple bond without the elimination of any atom or other molecules. In these reactions, at least one π bond is lost while two new σ bonds are formed. Double bonds become saturated, and triple bonds are converted into double bonds or may become saturated by further addition. - 25 - Elimination Reactions: Elimination reactions are those which involve the removal of atoms or groups of atoms from two adjacent atoms in the substrate molecule to form a multiple bond. Elimination reactions may be regarded as reverse od addition reactions. In these reactions, two σ bonmds are lost and a new π bond is formed. Saturated compounds become unsaturated. For example, H H H H + Zn H C C H H C C H Br Br Ethylene 1,2-Dibromoethane - 17 -  4- Rearrangement Reactions: Rearrangement reactions involve the migration of an atom or group of atoms from one site to another within the atom molecule. The product is always the structural isomer of the original compound. For example, The rearrangement of ammonium cyanate to urea in aqueous solution at 50 °C: https://allen.in/jee/chemistry/hybridization-of-carbon https://byjus.com/jee/hybridization-of-carbon/ https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Organic_Chemistry_I_(Cortes)/05%3A_ Orbital_Picture_of_Bonding- _Orbital_Combinations_Hybridization_Theory_and_Molecular_Orbitals/5.02%3A_Orbital_Hybridiza tion_Theory https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Organic_Chemistry_I_(Cortes)/05%3A_ Orbital_Picture_of_Bonding- _Orbital_Combinations_Hybridization_Theory_and_Molecular_Orbitals/5.04%3A_Hybridization_of_ Carbon - 18 -