Chem 111 Lecture Week 13 Organic Chemistry PDF

Inorganic and Organic Chemistry Week 13 TOPICS/CONTENT ▪ The Chemistry of Carbon Atom ▪ Structure and Isomerism ▪ Functional Groups ▪ Classification of Functional Groups ▪ Importance of Functional Groups Overview: Carbon: The Backbone of Life Although cells are 70–95% water, the rest consist...

Inorganic and Organic Chemistry Week 13 TOPICS/CONTENT ▪ The Chemistry of Carbon Atom ▪ Structure and Isomerism ▪ Functional Groups ▪ Classification of Functional Groups ▪ Importance of Functional Groups Overview: Carbon: The Backbone of Life Although cells are 70–95% water, the rest consists mostly of carbon-based compounds Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds Organic chemistry is the study of carbon compounds. Organic chemistry is the study of compounds that contain carbon. Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms  Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized these compounds Mechanism is the view that all natural phenomena are governed by physical and chemical laws Can organic molecules form under conditions believed to simulate those on the early Earth? Carbon atoms can form diverse molecules by bonding to four other atoms. Electron configuration is the key to an atom’s characteristics. Electron configuration determines the kinds and number of bonds an atom will form with other atoms. The Formation of Bonds with Carbon With four valence electrons, carbon can form four covalent bonds with a variety of atoms. This tetravalence makes large, complex molecules possible. In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape. However, when two carbon atoms are joined by a double bond, the molecule has a flat shape.  The electron configuration of carbon gives it covalent compatibility with many different elements. The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules. Carbon atoms can partner with atoms other than hydrogen; for example: Carbon Dioxide: CO2 Urea: CO(NH2)2 Molecular Diversity Arising from Carbon Skeleton Variation Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape The structural formula of a compound tells us the arrangement or the graphic representation of atoms in the molecule of a compound. Ways of depicting the alkane 3-ethyl-2-methylhexane. Isomers Isomers are compounds with the same molecular formula but different structures and properties: Structural isomers have different covalent arrangements of their atoms Geometric isomers have the same covalent arrangements but differ in spatial arrangements Enantiomers are isomers that are mirror images of each other Types of Isomerism Constitutional Isomers of C4H10 and C5H12 Compounds have the same molecular formula but different structural formula Sometimes more than one type of isomerism occurs in the same molecule. The more carbon atoms there are, the greater the number of possible isomers Structural Isomers - Chain caused by different arrangements of the carbon skeleton similar chemical properties slightly different physical properties more branching = lower boiling point Structural Isomers - Chain There are two structural isomers of C4H10. Differences Between Chain Isomers Structural Isomers - Positional molecule has the same carbon skeleton molecule has the same same functional group... BUT the functional group is in a different position have similar chemical properties / different physical properties Structural Isomers - Positional Position of a Double Bond in Alkenes Structural Isomers - Positional Position of a Halogen in a Haloalkane Structural Isomers - Positional Relative Positions on a Benzene Ring Structural Isomers – Functional Group molecules have same molecular formula molecules have different functional groups molecules have different chemical properties molecules have different physical properties Structural Isomers – Functional Group Alcohols and Ethers Structural Isomers – Functional Group Aldehydes and Ketones Structural Isomers – Functional Group Carboxylic Acids and Esters Geometric Isomers Enantiomers Enantiomers Enantiomers are important in the pharmaceutical industry. Two enantiomers of a drug may have different effects. Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules. Most organic compounds are classified based on their specific groups and the bonding of the atoms that render their general properties. These specific groups are known as functional groups. Hydrocarbons Hydrocarbons are compounds that contain only carbon and hydrogen atoms. They may be described as saturated or unsaturated. Saturated hydrocarbons are those in which all carbon-carbon bonds are single bonds; unsaturated hydrocarbons hydrocarbons contain one or more carbon- carbon multiple bonds (double bonds, triple bonds, or both). The three types of hydrocarbons are alkanes, alkenes, and alkynes. Hydrocarbons Alkanes Straight-Chain Alkanes Straight-chain alkanes are named according to the number of carbon atoms they contain. With the exception of the first four compounds (methane, ethane, propane, butane) whose names have historical origins, the alkanes have Greek prefixes to reflect the number of their carbon atoms. The suffix identifies the molecule as an alkane. Alkanes are commonly used as fuels. Methane, ethane, propane, and butane are all components of natural gas. Propane and butane are the major gases in liquefied petroleum gas (LPG). Hydrocarbons Alkanes Straight-Chain Alkanes Hydrocarbons Alkanes Hydrocarbons Alkanes Branched Alkanes Carbon atoms can also bond to three or four other carbon atoms, resulting in branched chains. Each carbon in a molecule is described as primary, secondary, tertiary, or quaternary based on the number of carbon atoms bonded to it. It is primary if it is bonded to only one carbon atom, secondary if bonded to two carbon atoms, tertiary if bonded to three carbon atoms, and quaternary if bonded to four carbon atoms. Hydrocarbons Alkanes Branched Alkanes Hydrocarbons Alkanes Branched Alkanes The longest continuous carbon chain of a branched hydrocarbon is known as the parent alkane. All the other elements or groups that replace an H atom in the parent alkane are regarded as substituents. An alkane substituent is called an alkyl group. Hydrocarbons Alkanes Branched Alkanes Hydrocarbons Alkanes Branched Alkanes Butane and 2-methylpropane are described as structural isomers, which are compounds that have the same molecular formula but different arrangement of atoms. Notice that both compounds have the molecular formula C4H10. Hydrocarbons Alkanes Branched Alkanes However, butane is straight-chained, while 2-methylpropane is branched. The two alkanes, being two different compounds, differ in melting point, boiling point, and chemical reactivity. Hydrocarbons Alkanes Branched Alkanes In general, the more branched the hydrocarbon is, the lower is its boiling point compared to its less branched isomer. Hydrocarbons Alkanes Branched Alkanes Drawing structural isomers can be done systematically by considering all possible parent chains that can be derived from a given molecular formula. Consider butane and 2-methylpropane. For butane, the two possible parent chains are the four-carbon straight chain and the three-carbon chain. The four-carbon chain is considered as one isomer of butane. The other isomer is formed by attaching the alkyl group (CH3) to the second C of the three-carbon parent chain.. Note that placing the alkyl group to the first or third C atom will just result to the four-carbon isomer. Sample Problem 1 Draw the isomers of hexane (C6H14). Hydrocarbons Alkenes Alkenes, having double bonds in their structures, are unsaturated hydrocarbons with the general formula ethene (ethylene) 𝐧 𝟐𝐧 Straight-chain alkenes use the same prefixes as alkanes, but end in Examples are ethene (ethylene) and 2-pentene. Ethene is responsible for the ripening of fruits; 2-pentene is an organic solvent. 2-pentene Hydrocarbons Alkenes As nonpolar compounds, alkenes are insoluble in water and soluble in nonpolar solvents. They show trends in boiling points similar to alkanes. Hydrocarbons Alkenes Alkenes may exhibit or , in which the atoms are joined in the same order but have different arrangement in space. The cis isomer has the bulky (non-H) substituents of the double-bonded carbon on the same side of the molecule. In the trans isomer, these bulky substituents are oriented oppositely. Hydrocarbons Alkynes Alkynes are also unsaturated hydrocarbons having the formula 𝐧 𝟐𝐧 𝟐 They contain triple bonds in their ethyne structure. Straight-chain alkynes also use the Greek prefixes, but a suffix of. Alkynes are nonpolar and exhibit the same trends in boiling point and physical state as the other hydrocarbons. The simplest and smallest alkyne is ethyne, 2-pentyne more commonly known as acetylene, which burns with pure oxygen, producing the intense in welding torches. Hydrocarbons Cycloalkanes Cycloalkanes are saturated hydrocarbons in which the carbon atoms are connected in a cyclic arrangement. They are usually represented as polygons; each corner corresponds to a carbon atom attached with two hydrogen atoms. Cycloalkanes follow the general formula 𝐧 𝟐𝐧. They are named by adding the prefix before the name of the open-chain compound having the same number of carbon atoms as there are in the ring. The simplest cycloalkanes is cyclopropane, which is used as inhalation anesthetic. Cycloalkanes are nonpolar. Their boiling points generally increase as more carbon atoms are present in the ring. Hydrocarbons Cycloalkanes Hydrocarbons Aromatic Hydrocarbons Aromatic hydrocarbons or arenes are compounds that contain a benzene ring in their structure. Most aromatic hydrocarbons are nonpolar and are generally used as solvents for other nonpolar substances. Benzene, a six-carbon ring with formula 𝟔 𝟔 , is the simplest arene. Hydrocarbons Aromatic Hydrocarbons The term “aromatic” is derived from the characteristically strong and pungent smell emitted by most arenes. Among these substances are naphthalene (commonly known as mothballs) and toluene. Naphthalene is used as insect repellent. Toluene is an ingredient of petroleum products, lacquers, paints, and adhesives. Halogen-Containing Compounds Organic compounds may also contain other elements aside from carbon and hydrogen. Some of these alkyl halides, where carbon atoms are bonded with halogens. Halogen-Containing Compounds Alkyl Halides Alkyl halides are hydrocarbons in which one or more hydrogen atoms around a carbon atom have been replaced by halogen atoms. They have the general formula , where is an alkyl group and is a halogen. The successive substitution of chlorine atoms to each hydrogen of methane forms different alkyl halides. methane methyl chloride methylene chloride chloroform carbon tetrachloride BP: −𝟏𝟔𝟒𝐨 𝐂 BP: −𝟐𝟒. 𝟐𝐨 𝐂 BP: 𝟒𝟎𝐨 𝐂 BP: 𝟔𝟏. 𝟕𝐨 𝐂 BP: 𝟕𝟔. 𝟓𝐨 𝐂 Halogen-Containing Compounds Alkyl Halides The melting point and boiling point of alkyl halides increase as their molecular mass rises. Methyl chloride has the least number of chlorine atoms and, thus, has the lowest molecular mass and boiling point among the given alkyl halides. Carbon tetrachloride, with the greatest molecular mass, has the highest boiling point. In general, alkyl halides have higher melting and boiling points compared to hydrocarbons with comparable molecular masses. methane methyl chloride methylene chloride chloroform carbon tetrachloride BP: −𝟏𝟔𝟒𝐨 𝐂 BP: −𝟐𝟒. 𝟐𝐨 𝐂 BP: 𝟒𝟎𝐨 𝐂 BP: 𝟔𝟏. 𝟕𝐨 𝐂 BP: 𝟕𝟔. 𝟓𝐨 𝐂 Halogen-Containing Compounds Alkyl Halides Alkanes where hydrogen atoms are substituted with chlorine and fluorine are collectively called chlorofluorocarbons (CFCs). These compounds, widely used before as refrigerants and as foaming agents for plastics, are known ozone-depleting substances whose uses are now being controlled and reduced. Oxygen-Containing Compounds Some hydrocarbon derivatives have oxygen-containing functional groups, in which the oxygen either (1) participates in two single bonds (alcohols, phenols, and ethers); (2) participates in a double bond (aldehydes and ketones); or (3) participates in single bonds and another in a double bond (carboxylic acids and its derivatives). Oxygen-Containing Compounds Alcohols and Phenols Alcohols are compounds that have a hydroxyl group ( ) bonded to a carbon atom and which makes them polar. They have the general formula. They may be classified as primary (1o), secondary (2o), or tertiary (3o) depending on the number of substituents (R) bonded to the carbon atom with group. Oxygen-Containing Compounds Alcohols and Phenols Alcohols are named by appending the suffix to the hydrocarbon name from which it is derived. For example, methane becomes methanol, which is an alternative engine fuel. Similarly, ethanol is derived from ethane and is used as a disinfectant, wine ingredient, and fuel. Both methanol and ethanol are primary alcohols. Oxygen-Containing Compounds Alcohols and Phenols Phenols are similar to alcohols except that the hydroxyl group is attached to a carbon of a benzene ring. They are also named with the same suffix as alcohols. Phenols are more phenol soluble in water and have higher boiling points than alcohols of similar molecular mass. The simplest example of a phenol is monohydroxybenzene (also known as phenol), which is used as an antiseptic and a raw material for making plastics and aspirin. Another example is hydroquinone, a skin bleaching agent in personal care products. hydroquinone Oxygen-Containing Compounds Ethers Ethers are compounds with the general formula where and are hydrocarbon groups, which may be the same or different. An example of ether with similar and is diethyl ether, which is used as an organic solvent and sometimes as anesthetic. Its name “diethyl” indicates the two ethyl groups attached to the oxygen atom. The last name “ether” is a standard term for all ethers. Methyl phenyl ether is an example of asymmetrical ether, or ether with dissimilar hydrocarbon diethyl ether methyl phenyl ether groups. (similar R and R’) (dissimilar R and R’) Oxygen-Containing Compounds Ethers The boiling points of ethers are generally higher than those of hydrocarbons, but lower than those of alcohols of comparable molecular mass. Ethers are more soluble in water than hydrocarbons but less soluble than alcohols because of the absence of polar groups. Oxygen-Containing Compounds Aldehydes and Ketones Both aldehydes and ketones contain the carbonyl ( ) group. The difference lies on the substituents attached to the carbon atom of the carbonyl; aldehydes contain R and H, while ketones have R and R’ groups. Oxygen-Containing Compounds Aldehydes and Ketones Aldehydes and ketones are named by replacing the terminal of the corresponding alkane name with and , respectively. For example, methanal is the corresponding aldehyde of methane, and propanone is the corresponding ketone of propane. Methanal is the simplest aldehyde and is usually available 40% aqueous solution known as formalin used to preserve biological specimens. Propanone, commonly known as acetone, is a solvent for plastics and a nail polish remover. Oxygen-Containing Compounds Aldehydes and Ketones Compared to their corresponding alkanes and alcohols, aldehydes, and ketones have higher boiling points because of the presence of carbonyl groups, but lower than those of alcohols due to the absence of the hydroxyl groups. methane methanal (formaldehyde) propane propanone (acetone) BP: −𝟏𝟔𝟒𝐨 𝐂 BP: −𝟏𝟗𝐨 𝐂 BP: −𝟒𝟐𝐨 𝐂 BP: 𝟓𝟔𝐨 𝐂 Oxygen-Containing Compounds Aldehydes and Ketones All aldehydes and ketones with more than three carbon atoms are soluble in nonpolar solvents, while those with less than three are soluble in water in all proportions. Boiling Points of Derivatives of Propane Classifications Compound Formula Boiling Point (oC) Alkane Propane CH3CH2CH3 Aldehyde Propanal CH3CH2CHO Ketone Propanone CH3COCH3 Alcohol 1-propanol CH3CH2CH2OH Oxygen-Containing Compounds Carboxylic Acids Carboxylic acids contain the carboxyl functional group and have the general formula shown on the right. Compared to other compounds of similar molecular mass, carboxylic acids have higher melting and boiling points because of their polar nature. They are soluble in water, but their solubility decreases as the number of carbon atoms increases. Oxygen-Containing Compounds Carboxylic Acids methanoic acid Simple open-chain carboxylic acids are (formic acid) named by replacing the terminal of the corresponding alkane name with and adding the word acid. ethanoic acid Examples are methanoic acid and (acetic acid) ethanoic acid, which are derivatives of the alkanes methane and ethane, respectively. Ethanoic acid, commonly called acetic acid, is an ingredient of vinegar. Methanoic acid is secreted by ants. This acid causes the sting in their bites. citric acid Oxygen-Containing Compounds Esters Esters are almost similar in form to carboxylic acids except that the H in the carboxylic acid is replaced with another alkyl group The general formula for esters is given below. Oxygen-Containing Compounds Esters The names of esters are derived from the name of the alkyl group attached to oxygen followed by the carboxylic acid name whose suffix is replaced with. Ethyl acetate, used as an artificial food flavoring because of its fruity smell, contains an ethyl and a carboxylic acid groups. methyl acetate Oxygen-Containing Compounds Esters Esters have lower boiling points compared to carboxylic acids. Those with relatively lower molecular mass are soluble in water, while those containing more than four carbons have limited solubility. Nitrogen-Containing Compounds Common organic compounds that contain nitrogen include amines and amides, each group with a different general formula. Nitrogen-Containing Compounds Amines Amines are derived from ammonia 𝟑 whose hydrogen atoms are replaced by hydrocarbon groups. They may be classified either as primary 𝟐 , secondary 𝟐 , or tertiary 𝟑 depending on the number of substituents attached to the nitrogen atom. Nitrogen-Containing Compounds Amines Amines are named using those of the substituent groups bonded to nitrogen, then adding the suffix The prefixes and are used for identical alkyl groups. The simplest primary amine is methylamine, used in making pharmaceuticals, insecticides, and surfactants. It has one methyl group. Dimethylamine and trimethylamine has two and three methyl groups, respectively. Dimethylamine is used as a solvent, while trimethylamine is responsible for the unpleasant smell of decomposing plants and animals. Nitrogen-Containing Compounds Amines BP: 𝐨 BP: 𝐨 BP: 𝐨 All amines are soluble in water. They generally have low boiling points, which increase as molecular mass increases. Nitrogen-Containing Compounds Amines Caffeine and nicotine are examples of complex amines. Caffeine is naturally present coffee beans and tea leaves, while nicotine is present in cigarettes. Both compounds are known stimulants. caffeine nicotine Nitrogen-Containing Compounds Amides Amides are another derivative of carboxylic acids and have the general formula given below: Amides have high melting points and are soluble in water because of their relatively polar nature. Nitrogen-Containing Compounds Amides Simple amides are named after their corresponding carboxylic acids; changing the ending (common names) or the ending (IUPAC names) of the acid to. Examples are methanamide and ethanamide. Methanamide is a raw material in manufacturing herbicides and pesticides. Ethanamide is used as a solvent and plasticizer.  Nitrogen-Containing Compounds Amides formic acid formamide (methanoic acid) (methanamide) acetic acid acetamide (ethanoic acid) (ethanamide) CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE (may be written HO—) In a hydroxyl group (—OH), a The carbonyl group ( CO) When an oxygen atom is hydrogen atom is bonded to an consists of a carbon atom double-bonded to a carbon oxygen atom, which in turn is joined to an oxygen atom by a atom that is also bonded to bonded to the carbon skeleton of double bond. an —OH group, the entire the organic molecule. (Do not assembly of atoms is called confuse this functional group a carboxyl group (—COOH). with the hydroxide ion, OH–.) NAME OF Alcohols (their specific names Ketones if the carbonyl group is Carboxylic acids, or organic COMPOUND usually end in -ol) within a carbon skeleton acids Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Ethanol, the alcohol present in Acetone, the simplest ketone Acetic acid, which gives vinegar alcoholic beverages its sour taste Propanal, an aldehyde FUNCTIONAL Is polar as a result of the A ketone and an aldehyde may Has acidic properties PROPERTIES electrons spending more time be structural isomers with because the covalent bond near the electronegative different properties, as is the between oxygen and hydrogen oxygen atom. case for acetone and propanal. is so polar; for example, Can form hydrogen bonds with These two groups are also water molecules, helping found in sugars, giving rise to dissolve organic compounds two major groups of sugars: such as sugars. aldoses (containing an aldehyde) and ketoses (containing a ketone). Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion). CHEMICAL GROUP Amino Sulfhydryl Phosphate Methyl (may be STRUCTURE written HS—) The amino group The sulfhydryl group In a phosphate group, a A methyl group consists of a (—NH2) consists of a consists of a sulfur atom phosphorus atom is bonded to carbon bonded to three nitrogen atom bonded bonded to an atom of four oxygen atoms; one oxygen hydrogen atoms. The methyl to two hydrogen atoms hydrogen; resembles a is bonded to the carbon skeleton; group may be attached to a and to the carbon hydroxyl group in shape. two oxygens carry negative carbon or to a different atom. skeleton. charges. The phosphate group P (—OPO32–, abbreviated ) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). NAME OF Amines Thiols Organic phosphates Methylated compounds COMPOUND EXAMPLE Glycine Glycerol phosphate Because it also has a Cysteine In addition to taking part in carboxyl group, glycine 5-Methyl cytidine many important chemical is both an amine and Cysteine is an important reactions in cells, glycerol a carboxylic acid; sulfur-containing amino 5-Methyl cytidine is a phosphate provides the compounds with both acid. component of DNA that has backbone for phospholipids, groups are called been modified by addition of the most prevalent molecules in amino acids. the methyl group. cell membranes. FUNCTIONAL Acts as a base; can Two sulfhydryl groups Contributes negative charge Addition of a methyl group PROPERTIES pick up an H+ from can react, forming a to the molecule of which it is to DNA, or to molecules the surrounding covalent bond. This a part (2– when at the end of bound to DNA, affects solution (water, in “cross-linking” helps a molecule; 1– when located expression of genes. living organisms). stabilize protein internally in a chain of Arrangement of methyl structure. phosphates). groups in male and female Cross-linking of Has the potential to react sex hormones affects cysteines in hair with water, releasing energy. their shape and function. proteins maintains the curliness or straightness (nonionized) (ionized) of hair. Straight hair can Ionized, with a be “permanently” curled charge of 1+, under by shaping it around cellular conditions. curlers, then breaking and re-forming the cross-linking bonds.  Carboxyl STRUCTURE NAME OF Carboxylic acids, or organic COMPOUND acids EXAMPLE FUNCTIONAL Has acidic properties PROPERTIES because the covalent bond between oxygen and hydrogen is so polar; for example, Acetic acid, which gives vinegar its sour taste Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).  Amino STRUCTURE NAME OF Amines COMPOUND EXAMPLE FUNCTIONAL Acts as a base; can PROPERTIES pick up an H+ from the surrounding solution (water, in living organisms). Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; (nonionized) (ionized) compounds with both groups are called amino Ionized, with a charge acids. of 1+, under cellular conditions.  Sulfhydryl STRUCTURE NAME OF Thiols COMPOUND (may be written HS—) EXAMPLE FUNCTIONAL Two sulfhydryl groups can PROPERTIES react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Cysteine Cross-linking of cysteines in hair proteins maintains the Cysteine is an important curliness or straightness of sulfur-containing amino hair. Straight hair can be acid. “permanently” curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds.  Phosphate STRUCTURE NAME OF Organic phosphates COMPOUND EXAMPLE FUNCTIONAL Contributes negative charge to PROPERTIES the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of Glycerol phosphate phosphates). Has the potential to react with In addition to taking part in many water, releasing energy. important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes.  Methyl STRUCTURE NAME OF Methylated compounds COMPOUND EXAMPLE FUNCTIONAL Addition of a methyl group to PROPERTIES DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects 5-Methyl cytidine their shape and function. 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. Sample Problem 1 Name the functional group and state the type of organic compound Functional Group: carbonyl Type: aldehyde Sample Problem 2 Name the functional group and state the type of organic compound Functional Group: carboxyl (carbonyl and hydroxyl) Type: carboxylic acid Sample Problem 3 Name the functional group and state the type of organic compound Functional Group: hydroxyl Type: alcohol