Organic Chemistry Lecture Notes PDF

Prepared by: Mari Jane C. Andaya, RMT, RN, LPT, MAN, Ed.D All life depends on water and compounds of carbon Organic chemicals are those compounds containing carbon(at least 1 atom). Originally organic compounds were thought to be only from ‘living matter’, ie. containing a ‘vital forc...

Prepared by: Mari Jane C. Andaya, RMT, RN, LPT, MAN, Ed.D All life depends on water and compounds of carbon Organic chemicals are those compounds containing carbon(at least 1 atom). Originally organic compounds were thought to be only from ‘living matter’, ie. containing a ‘vital force’. ( consider the symbolism of ‘organic foods’) Probably ~10 million organic compounds known! Inorganic compounds are compounds/molecules that do not contain carbon.  HYDROCARBON COVALENT BONDING H × × C H C ×H ×H × Carbon Atom H Hydrogen Atom Carbon with Hydrogen C:C C::C Carbon with Carbon C C C C C C single double triple ORGANIC STRUCTURES ( a ‘short hand’) HHH CH3 – CH2 – CH2 H-C-C-C-H or CH3 H H H-C-H H or CH3CH2CH2CH3 or all H’s understood  The Problem with Prefixes C5H12 Isomers(positional) CH3 CH3 CH2 CH2 CH2 CH3 CH3 CH CH2 CH3 CH3 C CH3 CH3 CH3 Pentane Isopentane Neopentane (Methyl butane) (Dimethyl propane)  Positional Isomers of the Alkanes # of C’s Formula # of Isomers 1 CH4 1 2 C2H6 1 3 C3H8 1 4 C4H10 2 5 C5H12 3 6 C6H14 5 7 C7H16 9 8 C8H18 18 9 C9H20 35 10 C10H22 75 15 C15H32 4347 20 C20H42 366,319  The International Union of Pure and Applied Chemistry, beginning in 1892, has attempted to systematize the naming of organic compounds. This IUPAC system for organic nomenclature is still in general use. Here are a few basic rules: 1. Find the longest continuous chain of carbon atoms and apply the appropriate ‘term’; this will be the ‘parent name’. # of C’s Parent name Derivation 1 meth- methe-(Gr.) 2 eth- aither(Gr.) 3 prop- protos + pion(Gr.) 4 but- butyrum(Lat.) 5 pent- pente(Gr.) 6 * hex- hex(Gr.) 7 hept- hepta(Gr.) 8 oct- okto(Gr.); octa(Lat.) 9 non- novem(Lat.) 10 dec- deka(Gr.); decem(Lat.)  The First 10 Straight - Chain Alkanes Name Molecular Formula Methane CH4 Ethane CH3–CH3 Propane CH3-CH2-CH3 Butane CH3-CH2-CH2-CH3 Pentane CH3-CH2-CH2-CH2-CH3 Hexane CH3-CH2-CH2-CH2-CH2-CH3 Heptane CH3-CH2-CH2-CH2-CH2-CH2-CH3 Octane CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3 Nonane CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3 CH3 Decane CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3 ▪ Undecane (11), dodecane (12) tridecane(13),tetradecane(14), pentadecane(15) hexadecane (16) heptadecane (17), octadecane (18), nonadecane(19) ▪ After C19, beyond the scope of CHEM 1003! ▪ C20H42 is eicosane ▪ At the end of the chain with the most branches ▪ 3-methylhexane  Families of compounds are compounds of similar structure and therefore similar properties. Hydrocarbons are composed exclusively of carbon and hydrogen. There are 4 sub-categories alkanes of hydrocarbons: alkenes alkynes aromatics  Hydrocarbons (Alkyl) Structure Bond “Suffix” Examples C C Single ___ane Butane, isooctane C C Double ___ene Polystyrene, propylene, -carotene C C Triple ___yne Acetylene (ethyne) ▪ Isomers! Isomers are compounds that have the same molecular formula but are ‘different’ in some aspect of their structure, eg. a. positional: structural ‘iso-’, ‘neo-’, ‘tert-’ chemical -OH & C=O vs. -COOH b. geometrical: ‘cis-’, ‘trans-’ c. 3-dimensional(stereo-): all chiral centers mirror images (D/L; +/-) only 1 center epimers ▪ Enantiomers: contain one chiral (Gr. “Chiros” =hand) center and are non-superimposable mirror images ▪ Are identical in all respects except for the direction in which they rotate plane polarized light ▪ D and L isomers ▪ Arise from tetrahedral C with 4 different substituents ▪ All naturally occuring amino acids are the L –isomers : rotate the plane of polarized light in counterclockwise direction (Why??) ▪ Enzymes: many are chiral and are only active for a specifically handed substrate ▪ Lock and key (hand in glove) mechanism for activity ▪ L-Dopa is active vs. Parkinson’s disease ▪ Its mirror image D-Dopa is inactive ▪ “Chiral synthesis” of pharmaceuticals is a multibillion-dollar operation ▪ Separations are costly and time-consuming ▪ # of isomers possible =2n. ▪ These are diastereomers: have different mp, bp ▪ Cholesterol has 8 chiral centres, hence 28= 256 possible isomers. But only one occurs naturally! ▪ 8 chiral centres ▪ Geometrical isomers ▪ Simplest examples are cis-trans isomers ▪ Differ only in the spatial arrangement of atoms geometrical isomers of cis fats (cis=same) , trans= opposite ▪ Produced by partial hydrogenation of polyunsaturated vegetable oil ▪ Are solids-give longer shelf life to products ▪ Are worse than lard (sat’d fat) for your arteries! ▪ “Banned” in NYC as of Jan 1, 2008 ▪ No, they occur naturally in small amounts in beef tallow, butter, milk ▪ Arise from microbial hydrogenation of polyunsaturated fats in the animals’ digestive system ▪ Ottawa City council has decided against a “ban” (wisely)  Organic Nomenclature - Descriptors R Examples C C C C cis- or trans- R trans R cis R fatty acids R R R PABA = para- amino benzoic acid (in R R R sunscreen) ortho- meta- para- hexane cyclo butane = cyclo pentane ▪ Contain atoms other than C and H ▪ To understand their properties, they are grouped according to the nature of these atoms and how they are bonded ▪ Classified according to reactivity and function, hence “functional groups”  A functional group is a small set of atoms, held together by covalent bonds in a specific and characteristic arrangement, that is responsible for the principal chemical and physical properties of that compound  Organic Functional Groups Functnl Grp Generic ‘Suffix’ ‘Prefix’ Examples R–X halocarbon -halide halo- PVC, perchloro- ethylene R – OH alcohol -ol hydroxy menthol, ethanol cholesterol R – OR ether -ether alkoxy Methyl-t- butyl ether (MTBE); octane enhancer nicotine amine am(ine) amino- adrenaline R – NHR cocaine  Organic Functional Groups Functnl Grp Generic ‘Suffix’ ‘Prefix’ Examples R – C = O aldehyde -al acyl citronellal retinal H formaldehyde R–C=O ketone -one ----- cortisone acetone R testosterone  Organic Functional Groups Functnl Grp Generic ‘Suffix’ ‘Prefix’ Examples R – C = O carboxylic -oic carboxyl acetic acid acid ASA OH fatty acids R – C = O ester -oate ------ phthalates OR (acid + polyester alcohol) ethyl acetate R – C = O amide -amide amido- DEET (acid+ N,N-diethyl- NR2 meta-toluamide ▪ Acetone (common solvent) is propanone ▪ Acetic acid (in vinegar) is ethanoic acid ▪ Benzene (potent carcinogen) is 1,3,5-cyclohexatriene ▪ Chloroform is trichloromethane ▪ Candle waxes are mixtures of solid saturated hydrocarbons (paraffins) and long chain (C16 or more) monoesters. ▪ Combustion in air generates CO2, H2O, heat and light ▪ Oleo Stearin or Oleo Stearate (palm vegetable wax) mp 155- 160oF ▪ Stearic acid is the common name for octadecanoic acid (C18) ▪ Oleic acid is same as stearic acid, except for a cis C=C at the C9 position of the chain ▪ Made by “overdipping” a normal candle (wax mp. 135-145 F) with a higher melting (160-170 F) ▪ Candle burns down the middle leaving a hallow rim/tube to hold the melted inner wax ▪ Or, try soaking a normal candle for 24 hours in salt water (2 tbs. salt to 2 cups water) for 24 hours ▪ Demo!! ▪ Wick absorbs the NaCl solution ▪ When the wax starts to burn, it excites the sodium electrons to a higher energy level ▪ Visible light (yellow) is given off when these electrons return to a lower E level ▪ Sodium D line at 589 nm (yellow) in visible range of 700 (red) to 400 (violet);3p to 3s ▪ Heat excites 2p electrons to 3p level ▪ Visible light (589 nm wavelength) is emitted when these electrons come down to the 3s level ▪ Recall electron configurations ▪ Na is 1s2, 2s2, 2p6, 3s1. ▪ Na+ has lost the 3s electron ▪ Red is longest wavelength, violet is shortest ▪ Flame is hotter and stronger with salt present in the wick, hence melted wax on top vaporizes and burns off before it drips down the side! ▪OBJECTIVES: ▪Explain how organic compounds are classified. ▪OBJECTIVES: ▪Identify halocarbons and the IUPAC rules for naming halocarbons. ▪OBJECTIVES: ▪Describe how halocarbons can be prepared. ▪Most organic chemistry involves substituents ▪often contain O, N, S, or P ▪also called “functional groups”- they are the chemically functional part of the molecule, and are the non-hydrocarbon part ▪Functional group - a specific arrangement of atoms in an organic compound, that is capable of characteristic chemical reactions. ▪What is the best way to classify organic compounds? By their functional groups. ▪The symbol “R” is used to represent any carbon chains or rings ▪- alkyl groups ▪Halocarbons - class of organic compounds containing covalently bonded fluorine, chlorine, bromine, or iodine ▪General formula: R-X (X = halogen) ▪Naming? Name parent as normal, add the halogen as a substituent (or prefix) - ▪The more highly halogenated the compound is, the higher the b.p. ▪Few halocarbons found in nature ▪but, readily prepared and used ▪halothane and also the hydrofluorocarbons ▪Organic reactions often much slower than inorganic reactions ▪must break strong covalent bond ▪trying to find new catalysts to use ▪ Substitution - an atom (or group of atoms) replaces another atom or group of atoms ▪A halogen (shown as “X”) can replace a hydrogen to make a halocarbon: R-H + X2 R-X + HX ▪Sunlight is often a sufficient catalyst: CH4 + Cl2 →lightCH3Cl UV + HCl ▪Treating benzene with a halogen? Halogens on carbon chains are readily displaced by hydroxide ions (OH1-) to make an alcohol + a salt: R-X + OH1- R-OH + X1- CH3-Cl + NaOH CH3-OH + NaCl Methanol + sodium chloride  CH3-I + KOH CH3-OH + KI Iodomethane Methanol CH3CH2Br + NaOH CH3CH2OH + NaBr Bromoethane Ethanol ▪OBJECTIVES: ▪Identify how alcohols are classified and named. ▪OBJECTIVES: ▪Predict how the solubility of an alcohol varies with the length of its carbon chain. ▪OBJECTIVES: ▪Name the reactions of alkenes that may be used to introduce functional groups. ▪OBJECTIVES: ▪Construct the general structure of an ether and describe how ethers are named. ▪Alcohols - a class of organic compounds with an -OH group ▪The -OH functional group in alcohols is called a “hydroxyl” group; thus R-OH is the formula ▪How is this different from the hydroxide ion? (covalent bonding with the carbon- not ionic with a metal like bases) ▪Aliphatic alcohols classified into categories according to the number of R groups attached to the carbon with the hydroxyl ▪1 R group: primary alcohol ▪2 R groups: secondary alcohol ▪3 R groups: tertiary alcohol ▪Both IUPAC and common names ▪For IUPAC: ▪drop the -e ending of the parent alkane name; add ending of -ol, number the position of -OH ▪parent is the longest chain that contains the carbon with the hydroxyl attached. ▪The hydroxyl is given the lowest position number ▪Alcohols containing 2, 3, and 4 of the -OH substituents are named diols, triols, and tetrols respectively ▪Common names: ▪similar to halocarbons, meaning name the alkyl group, then followed by the word alcohol ▪One carbon alcohol = methyl alcohol ▪More than one -OH substituents are called glycols (ethylene glycol?) ▪** Examples on page 731 ** ▪Phenols - compounds in which a hydroxyl group is attached directly to an aromatic ring. Cresol is the common name of o, m, and p isomers of methylphenol ▪Much like water, alcohols are capable of hydrogen bonding between molecules ▪this means they will boil at a higher temp. than alkanes and halocarbons with a comparable number of atoms ▪Alcohols are derivates of water; the -OH comes from water, and thus are somewhat soluble ▪Alcohols of up to 4 carbons are soluble in water in all proportions; more than 4 carbons are usually less soluble, because the longer carbon chain is more nonpolar ▪Many aliphatic alcohols used in laboratories, clinics, and industry ▪Isopropyl alcohol (2-propanol) is rubbing alcohol; used as antiseptic, and a base for perfume, creams, lotions, and other cosmetics ▪Ethylene glycol (1,2-ethanediol) - commonly sold as “antifreeze” ▪Glycerol (1,2,3-propanetriol) - used as a moistening agent in cosmetics, foods, and drugs; also a component of fats and oils ▪Ethyl alcohol (ethanol) used in the intoxicating beverages; also an important industrial solvent ▪Denatured alcohol- means it has been made poisonous by the addition of other chemicals, often methyl alcohol (methanol, or wood alcohol). ▪As little as 10 mL of methanol has been known to cause permanent blindness, and 30 ml has resulted in death! ▪The carbon-carbon single bond is not easy to break ▪In double bonded alkenes, it is easier to break a bond ▪Addition reaction- substance is added at the double or triple bond location, after it is broken ▪Addition of water to an alkene is a hydration reaction - usually occurs with heat and an acid (such as HCl or H2SO4 acting as a catalyst) ▪Note the formation of ethanol from ethene + water ▪If a halogen is added in an addition reaction, the result is a halocarbon that is disubstituted – ▪The addition of bromine is often used as a test for saturation - Addition of a hydrogen halide? - called monosubstituted halocarbon ▪Addition of hydrogen to produce an alkane is a hydrogenation reaction, which usually involves a catalyst such as Pt or Pd ▪common application is the manufacture of margarine from unsaturated vegetable oils (making them solid from a liquid) ▪The hydrogenation of a double bond is a reduction reaction, which in one sense is defined as the “gain of H” ▪ethene is “reduced” to ethane; cyclohexene is “reduced” to cyclohexane ▪A class of organic compounds in which oxygen is bonded to 2 carbon groups: R-O-R is formula ▪Naming? The two R groups are alphabetized, and followed by ether ▪Two R groups the same? Use the prefix di- ▪Diethyl ether is the one commonly called just “ether” ▪was the first reliable general anesthetic ▪dangerous- highly flammable, also causes nausea ▪ethers are fairly soluble in water ▪Alcohol used for fuel in the future? ▪OBJECTIVES: ▪Identify the structure of a carbonyl group as found in aldehydes and ketones. ▪OBJECTIVES: ▪Construct the general formula for carboxylic acids and explain how they are named. ▪OBJECTIVES: ▪Describe an ester. ▪OBJECTIVES: ▪Explain how dehydrogenation is an oxidation reaction. ▪Review: ▪alcohol has an oxygen bonded to a carbon group and a hydrogen ▪ether has an oxygen bonded to two carbon groups ▪An oxygen can also be bonded to a single carbon by a double bond ▪The C=O group is called the “carbonyl group” ▪it is the functional group in both aldehydes and ketones ▪Aldehydes - carbonyl group always joined to at least one hydrogen (meaning it is always on the end!) ▪Ketones - the carbon of the carbonyl group is joined to two other carbons (meaning it is never on the end) ▪Naming? ▪Aldehydes: identify longest chain containing the carbonyl group, then the -e ending replaced by -al, such as methanal, ethanal, etc. ▪Ketones: longest chain w/carbonyl, then new ending of -one; number it? ▪propanone, 2-pentanone, 3-pentanone ▪Neither can form intermolecular hydrogen bonds, thus a much lower b.p. than corresponding alcohols ▪wide variety have been isolated from plants and animals; possible fragrant odor or taste; many common names ▪Benzaldehyde ▪Cinnamaldehyde ▪Vanillin ▪Methanal (the common name is: formaldehyde) ▪40% in water is formalin, a preservative ▪Propanone (common: acetone) is a good solvent; miscible with water in all proportions ▪why is it a good substance used in nail-polish removers? (a powerful solvent-able to dissolve both polar & nonpolar) ▪Also have a carbonyl group (C=O), but is also attached to a hydroxyl group (-OH) = “carboxyl” group ▪general formula: R-COOH ▪weak acids (ionize slightly) ▪Named by replacing -e with -oic and followed by the word acid ▪methanoic acid; ethanoic acid ▪Abundant and widely distributed in nature, many having a Greek or Latin word describing their origin ▪acetic acid (ethanoic acid) from acetum, meaning vinegar ▪many that were isolated from fats are called fatty acids ▪General formula: RCOOR ▪Derivatives of the carboxylic acids, in which the -OH from the carboxyl group is replaced by an -OR from an alcohol: carboxylic acid + alcohol ester + water ▪many esters have pleasant, fruity odors- banana, pineapple, perfumes ▪Although polar, they do not form hydrogen bonds (reason: there is no hydrogen bonded to a highly electronegative atom!) ▪thus, much lower b.p. than the hydrogen-bonded carboxylic acids they came from ▪Can be prepared from a carboxylic acid and an alcohol; usually a trace of mineral acid added as catalyst (because acids are dehydrating agents) ▪Naming? It has 2 words: ▪1st: alkyl attached to single bonded oxygen from alcohol ▪2nd: take the acid name, remove the -ic acid, add -ate ▪All of the previous classes of organic compounds are related by oxidation and reduction reactions ▪What is oxidation-reduction? ▪Oxidation: the gain of oxygen, loss of hydrogen, or loss of e-1 ▪Reduction: the loss of oxygen, gain of hydrogen, or gain of e-1 ▪Oxidation and reduction reactions (sometimes called redox) are coupled- one does not occur without the other ▪The number of Oxygen and Hydrogen attached to Carbon indicates the degree of oxidation ▪The fewer the # of H on a C-C bond, the more oxidized the bond ▪Thus, a triple bond is more oxidized than a double bond and a single bond ▪An alkane is oxidized (loss of H) to an alkene, and then to an alkyne ▪Loss of hydrogen is called a dehydrogenation reaction ▪may require strong heating and a catalyst ▪Methane can be oxidized in steps to carbon dioxide methane methanol methanal methanoic acid CO2 ▪the more reduced (more H) a carbon compound, the more energy it can release upon oxidation ▪Alcohols can also be oxidized into other products ▪“Dr. Al K. Hall Mr. Al D. Hyde” ▪Preparing aldehydes from a primary alcohol is a problem, because they are then easily oxidized to carboxylic acids ▪Benedict’s test and Fehling’s test are commonly used for aldehyde detection – ▪OBJECTIVES: ▪Describe how addition polymers are formed. ▪OBJECTIVES: ▪Describe how condensation polymers are formed. ▪Polymers are giant molecules, not small like the ones studied earlier in this chapter ▪examples are plastics ▪Polymer- large molecule formed by the covalent bonding of smaller molecules called monomers ▪An addition polymer forms when unsaturated monomers react to form a polymer ▪ethene will form polyethylene, ▪polyethylene is easy to clean, chemically resistant- milk bottles, plastic wrap, refrigerator dishes ▪Polypropylene is a stiffer polymer, used in utensils and containers ▪Polystyrene is formed from styrene (phenylethene), and is a poor heat conductor (styrofoam ® Dow Chemical) ▪molded coffee cups and picnic coolers, insulates homes ▪Polyvinyl chloride (PVC) used for pipes in plumbing ▪Polytetrafluoroethene (PTFE, or teflon ® DuPont) is very resistant to heat and chemical corrosion ▪found on nonstick cookware; coating on bearings and bushings used in chemical reactors ▪Condensation polymers are formed by the head-to-tail joining of monomer units ▪usually accompanied by the loss of water from the reacting monomers, and forming water as a product ▪Ex: polyethylene terephthalate (PET) ▪Dacron (® DuPont), Fortrel (® Wellman), Polyesters: permanent press clothing, tire cords ▪Sheets of polyester called Mylar (® DuPont), used as magnetic tape in tape recorders and computers, as well as balloons ▪Nylon: carpet, fishing line, hosiery ▪Examples: ▪aromatic rings form Nomex (® DuPont), which is a poor electrical conductor; makes parts for electrical fixtures; flame resistant clothing for race car drivers; flame resistant building materials ▪Kevlar (® DuPont): strong and flame resistant  Plastic container code system. PERCENT OF CODE MATERIAL TOTAL Polyethylene Terephthalate 20-30 percent (PET) High Density Polyethylene 50-60 percent Polyvinyl Chloride (PVC) 5-10 percent Low Density Polyethylene 5-10 percent Polypropylene 5-10 percent Polystyrene 5-10 percent All other resins 5-10 percent 1 -- PETE (Polyethylene terephthalate) PET (or PETE) is used in the production of soft drink bottles, peanut butter jars... PET can be recycled into fiberfill for sleeping bags, carpet fibers, rope, pillows... 2 -- HDPE (High-density polyethylene) HDPE is found in milk jugs, butter tubs, detergent bottles, motor oil bottles... HDPE can be recycled into flower pots, trash cans, traffic barrier cones, detergent bottles... 3 -- V (Polyvinyl chloride) PVC is used in shampoo bottles, cooking oil bottles, fast food service items... PVC can be recycled into drainage and irrigation pipes... 4 -- LDPE (Low-density polyethylene) LDPE is found in grocery bags, bread bags, shrink wrap, margarine tub tops... LDPE can be recycled into new grocery bags... 5 -- PP (Polypropylene) PP is used in most yogurt containers, straws, pancake syrup bottles, bottle caps.... PP can be recycled into plastic lumber, car battery cases, manhole steps... 6 -- PS (Polystyrene) PS is found in disposable hot cups, packaging materials (peanuts), and meat trays... PS can be recycled into plastic lumber, cassette tape boxes, flower pots... 7 -- Other This is usually a mixture of various plastics, like squeeze ketchup bottles, "microwaveable" dishes... 1862 – First man-made plastic 1866 – Celluloid makes it’s debut 1891 – Rayon is discovered 1907 – Bakelite is invented 1913 – Cellophane causes the plastics craze 1926 – PVC is invented 1933 – Polyethylene is discovered 1933 – Saran makes it’s debut 1938 – Teflon is discovered 1939 – Nylon stockings hit market 1957 – Here comes velcro