Module 1: Introduction to Organic Compounds PDF

ADVANCED CHEMISTRY MODULE 1 Introduction to organic compound LEARNING OUTCOMES At the end of this module, the students should be able to: a. Discuss the history...

ADVANCED CHEMISTRY MODULE 1 Introduction to organic compound LEARNING OUTCOMES At the end of this module, the students should be able to: a. Discuss the history and relevance of organic chemistry; b. Describe how the structure of carbon affects the type of bond it forms; c. Name the functional groups used as basis for naming organic compounds; d. Write the nomenclature of organic compounds using the IUPAC system and draw their different structural formula; and e. Write a reflection on the uses of common organic compounds as home remedies that may help boost the immune system as protection against Covid-19 during this pandemic. INTRODUCTION Organic chemistry is a branch of chemistry that deals with the study of compounds of carbon. It deals with the scientific study of the composition, structure, properties and preparation of carbon-based compounds, hydrogen and their derivatives. Today, 98% of all known compounds are organic. There are natural and synthetic organic compounds. Carbohydrates, fats, vitamins, proteins and DNA are examples of natural organic compounds. Rubbers, plastics, perfumes, inks, soap, explosives, pesticides are some of the various products of synthetic organic compounds. Lesson 1: History and relevance of organic chemistry Jöns Jacob Berzelius first used the term “organic chemistry” in 1807. He believed that organic compounds can be derived from living organisms. He believed in Vitalism - the idea that organic compounds could only originate from living organisms through the action of some vital force. This belief was known as the Vital Force Theory or Vitalism (vital means “life force”). Friedrich Wöhler (1828), a former student of Berzelius, synthesized urea (an organic compound present in the urine of living organisms) from heating ammonium cyanate (an inorganic compound). It is now called the “Wöhler synthesis”. The synthesis of urea proved that organic compounds can also be produced in the laboratory using inorganic materials. His discovery led to the downfall of the Vital Force Theory. Figure 1: Synthesis of Ammonium cyanate to produce ammonia, a synthetic organic compound.  ADVANCED CHEMISTRY From the discovery of Wöhler, two historical scientific ideas came out: 1. The Vital Force theory was disproved since organic compound can be produced or synthesized from inorganic substances, and 2. The discovery of isomerism – the possibility of a substance to have two or more different structure but with the same chemical formula like the ammonium cyanate (CH4N2O) and urea (CH4N2O) as illustrated above. Friedrich August Kekulé von Stradonitz, was recognized as the principal founder of the theory of chemical structure. His theory was based on the following ideas: 1. The valence of carbon is always four, 2. Carbon atoms can combine with one another to form chains of any length and complexity, and 3. The study of reaction products can provide information about chemical structure. Figure 2: Friedrich Wohler (1800-1828) Figure 3: Friedrich August Kekule (1829- converted ammonium cyanate to urea 1896) established the tetravalence of carbon and the structure of benzene. The Important products of Organic Compounds Organic compounds are essential to our daily lives. We produce and consume products of organic compounds every day from the food on our tables, the medicines that we take in when we are sick, the clothes we wear, the fertilizer for our plants, the vitamins for our livestock etc. Our understanding on organic compounds will help us improve our way of living through its various products. Various Fields or Areas Important Products of Organic Compounds Food Flour, sugar, bread, meat, dairy products Health Medicine: antibiotics like penicillin and streptomycin; pain relie ver like ibuprofen and morphine; antihistamine Textiles (Clothings) Cotton, silk, nylon, wool Agriculture Pesticides, insecticides, fertilizer (urea) Household Bath soaps, vinegar, soy sauce, plastics, paints Table1: Some important products of organic compounds produced by various fields or areas.  ADVANCED CHEMISTRY Lesson 2: The Carbon atom and Organic compounds There are some compounds that are considered as inorganic but contain carbon like carbon monoxide (CO), carbonic acid (H2CO3), cyanate (CNO-) and carbonate (CO32-) because their properties resemble those of inorganic compounds. Table 2 shows the difference between organic compounds and inorganic compounds. ORGANIC COMPOUNDS INORGANIC COMPOUNDS There are more organic compounds. Lesser in number compared to organic compounds Most are not soluble in water (polar solvent) Generally, soluble in water and are rarely but soluble in nonpolar solvents. soluble in nonpolar solvents. Ex. oil and water are insoluble Ex. muriatic acid and water are soluble Poor conductors of electricity (nonelectrolyte) Compounds that are electrolytes can conduct Electricity (electrolyte) Ex. water and salt solution/brine solution Low boiling point and melting point, High boiling point and melting point. Low density. High density. Ex. Oil float in water Ex. Iron rod sink in water Generally, flammable and produce carbon Generally, non-flammable dioxide and water. Ex. water Ex. When gasoline, diesel or sugar is burned The type of bond is covalent bond. The type of bond is covalent bond and ionic bond Have long and complex chain of molecules. Don’t have chain and complex formula. Ex. Octane (CH3CH2CH2CH2CH2CH2CH2CH3) Ex. table salt (NaCl), water (H2O), carbon monoxide (CO), oxygen gas (O2) Table 2: Differences between organic compound and inorganic compounds Predicting the types of Bond One way of predicting whether a compound is covalent bond (polar covalent bond or non-polar covalent bond) or ionic bond is by getting the electronegativity difference between the bonded atoms using the periodic table of elements. Table 3 shows the electronegativity difference of covalent and ionic bonds. Type of bonds Electronegativity Difference a. Covalent Bond Non-polar covalent bond 0 – 0.4 Polar covalent bond 0.5 – 1.8 b. Ionic bond greater than 1.9 Table 3: Electronegativity differences Example: Classify whether the given bonds are non-polar covalent, polar covalent or ionic. a. O-H * 3.5 – 2.1 = 1.4 * polar covalent bond b. C-H * 2.5 – 2.1 = 0.4 * non-polar covalent bond c.Na-F * 4.0 – 0.9 = 3.1 * ionic bond  ADVANCED CHEMISTRY The Carbon Atom Why is carbon atom the foremost component of organic compounds? Why is carbon such a special element? It is because of its versatility. The properties of carbon atom make it a unique atom. Carbon atoms can strongly bond with other carbon atoms and with atoms of other elements. Carbon atoms can also form large number of covalent bonds. Its uniqueness can produce numerous organic compounds including all kinds of chained or ringed molecules. Table 4 shows the properties of carbon atom. Properties of Carbon Atom  Carbon is  The electron  Forms 4 stable  Carbon bonds  It has the 6th configuration single bonds with itself allotrope or element is making it a different 1s22s22p2 Example: unique atom forms  Atomic no. is 6  It has 4 Example: Examples: valence Allotropes of  Atomic electron carbon mass is 12 methane gas 1. Diamond, hardest mineral 2. Graphite, CH3CH2CH2CH3 used as pencil Butane “lead” Table 4: Properties of Carbon Atom Lesson 3: Functional groups Functional Group is a specific grouping of atoms within a molecule that has its own characteristic and property regardless of the other atoms attached to the molecule. It is the reactive part of the molecule. General formula (R-X) is consist of carbon skeleton and the functional group. R is the carbon skeleton attached to a functional group (X). There are different functional groups (see table 5 below) like alcohol, ether, carboxylic acid, aldehyde and ketone. Figure 4 shows an illustration of the components of a functional group given propanol and ethyl methyl ether as examples. Figure 4: Illustration of the components of functional group  ADVANCED CHEMISTRY Classes of Organic Compounds and their Functional Groups Table 5: Classes of Organic Compounds and their Functional Groups https://www.rit.edu.resources  ADVANCED CHEMISTRY Lesson 4: Structural formula and Nomenclature of organic compounds Ways of Writing the Formula of Organic Compounds 1. Molecular Formula shows the total number of each atom present in the molecule. Ex. butane C4H10 octane C8H18 2. Structural Formula shows how the atoms bond to another atom. a. Expanded Structural Formula shows how all the atoms are bonded. *In writing the expanded structural formula, always remember that carbon is tetravalent which means it has 4 valence and that it can form 4 stable bonds whether single, double or triple bond. With this, always check the number of bonds you will form. There should be four bonds. Ex. butane octane b. Condensed Structural Formula is an abbreviation of the expanded structural formula showing no bonds. *Consider the expanded form of butane above, look at the first carbon, count the number of hydrogen atom attached to it and so with the second, third and fourth carbon then write in a condensed form following how butane was drawn. Ex. butane CH3CH2CH2CH3 octane CH3CH2CH2CH2CH3CH2CH2CH3 c. Skeleton Structural formula shows only the carbon–carbon bond (C-C bond). Ex. butane C–C–C–C octane C–C–C–C–C–C–C–C d. Line Structural Formula represents the molecule using line. *Each vertex represents carbon and the segment (line) is the type of bond. Ex. butane  ADVANCED CHEMISTRY octane Some examples of organic compounds 1. Open chain compounds Organic Molecular Expanded Condensed Skeleton Line Compound Compound Structural Structural Structural Structural Formula Formula formula Formula Propane C3H8 CH3CH2CH3 C–C–C 1 - butene C4H8 CH2=CHCH2CH3 C=C–C–C 1 - butyne C4H6 CH=CHCH2CH3 C=C–C–C 2 -butene C4H8 CH3CH=CHCH3 C–C=C–C 2. Cyclic or closed chain compounds Organic Molecular Expanded Skeleton Line Structural Compound Compound Structural Structural Formula Formula formula cyclopropane C3H6 C4H6 1 - cyclobutene Write the formula (molecular and structural) of hexane and cyclohexane. Hexane Cyclohexane  ADVANCED CHEMISTRY Using the IUPAC System in Naming Organic Compounds In writing the nomenclature of organic compounds using the International Union of Pure and Applied Chemistry (IUPAC) System, there are three parts that you need to identify. These are the prefix – parent – suffix. a. Prefix tells what and where the substituents are located. Substituents are ions attached to the main chain or ring. Locants are numbers assigned to each carbon in the main chain or ring which tell the position of the substituent group. b. Parent tells the number of carbon present in the carbon chain. The Parent chain is the main chain of carbon. It is the longest chain of carbon. Below are the prefixes and their number of carbons. Prefixes Number of carbons Prefixes Number of carbons hex 6 meth 1 hep 7 eth 2 oct 8 prop 3 non 9 but 4 dec 1 pent 5 Infix tells what type of carbon – carbon bond (C-C bond) is present in the parent chain. Infix The C-C bond -an- All the bonds are single -en- 1 or more double bonds -yn- 1 or more triple bonds c. Suffix tells the class of compounds where the substance belong. Sufix Class of compounds -e Hydrocarbon -ol Alcohol -al aldehyde -one ketone -oate esters -amide amide -amine Amine -oic acid Carboxylic acid  ADVANCED CHEMISTRY Some examples: Expanded Organic No. of Type of Class of Structural Compound Carbon bond Compound Formula Propane propane prop – 3 an – single bond e – hydrocarbon 1 – butane 1 - butene but – 4 (1) en – double e – hydrocarbon bond in the first carbon 1 - butyne 1 - butyne but – 4 (1) yn – triple e – hydrocarbon bond in the first carbon 2-chloropentanol 2-chloropentanol pent –5 an – single bond ol – alcohol 2-chloro *Chlorine is attached to the second carbon More illustrations: Propene Pentyne 3 carbons 5 carbons 1 c-c double bond 1 c-c triple bond a hydrocarbon a hydrocarbon Butanoic acid hexanal 4 carbons 6 carbons 1 c-c single bond 1 c-c single bond A carboxylic acid an hydrocarbon Identify the names of these organic compounds using the given descriptions. 8 carbons 7 carbons 1 c-c single bond 1 c-c single bond an acetone A ketone