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Introduction to organic chemistry Dr. Mamoun Ahram Nursing Summer semester, 2015 Organic compounds Organic chemistry the chemistry of carbon compounds. They consist of one or more elements covalently bonded to carbon atoms "Organic" means carbon-containing Functional groups The distinctive properties of organic molecules depend on: arrangement of carbon skeleton, the presence of functional groups. Functional groups: groups of atoms attached to carbon skeleton, which have a characteristic structure and chemical reactivity. Or Aromatic Anhydride Hydrocarbons Contain only carbon and hydrogen Aromatic Second group Single bonds + a carbon bonded to an electronegative atom Third group Contain C=O Anhydride Alkanes They contain carbon and hydrogen only in single bonds. Examples: methane (CH4), ethane (CH3CH3), propane (CH3CH2CH3) Straight versus branched alkanes Carbons can be connected in a row or in branches Note that with more branching, physical properties are different. boiling point is lower Note that different drawings can be used Condensed structures do not show bonds Isomers Isomers are molecules that have same molecular formula, but different structures Constitutional isomers (also known as structural ismers): isomers of different atom connectivity (note boiling point) Structural Formulas for C4H10O Isomers Conformations Organic molecules have different conformations. (three-dimensional arrangement of atoms) This is because C-C bonds can rotate. These are called geometric isomers (or stereoisomers). Naming organic molecules Prefix-parent-suffix If two or more functional groups, order ot priority: Parents: number of carbon molecules 1. Carboxylic acid Prefix: where substituents 2. Aldehyde are located (methyl, ethyl, 3. Ketone etc.) 4. Alcohol Suffix: family (alkane, 5. Amine alcohol, ether, etc.) 6. Alkyne = alkene 7. Alkane Number of carbon molecules Example pentane 2,2-dimethylpropane 2-methylbutane “Common" names for simple alkanes The iso structural unit consists of two methyl groups attached to a common carbon (When this unit is present in an alkane or alky group, the common name starts with the prefix iso) Number of carbons attached to branch point D D Sec: secondary Tert: tertiary Classification of carbon atoms “R” indicates a general abbreviation of any organic substituent Naming an alkanes Name the parent (look for longest hydrocarbon chain) Number the carbon atoms (begin near the branch point) Identify and name the branch points Write the name as a single name Substituents If there are substituents of the same kinds, identify their positions, and then use the prefixes di-, tri-, tetra, etc. to indicate how many are present. If there are substituents of different kinds present, name them in alphabetical order (e.g. ethyl before methyl) Prefixes such as di-, tri-, tetra-, etc. are ignored when alphabetizing Cycloalkanes Ring structures of alkanes These have the general formula, CnH2n Name the longest continuous carbon chain, with the prefix “cyclo” If it has a substituent attached to one of the carbons, then this carbon is number 1 If two substituents are attached, then you start with the one that has alphabetical priority. Examples (practice at home) What are they? Alkenes are hydrocarbons that have carbon-carbon double bond functional groups Alkynes are hydrocarbons that have carbon-carbon triple bond functional groups They are said to be unsaturated Alkanes are saturated Formula and structure Alkane R–CH2–CH2–R CnH2n+2 This is the maximum H/C ratio for a given number of carbon atoms Alkene R–CH=CH–R CnH2n Each double bond reduces the number of hydrogen atoms by 2 Alkyne R–C≡C–R CnH2n-2 Each triple bond reduces the number of hydrogen atoms by 4 Naming alkenes and alkynes The –ene or -yne suffix indicates an alkene or alkynes (cycloalkene or cycloalkynes) The longest chain chosen for the root name must include both carbon atoms of the double bond The root chain must be numbered from the end nearest a double (or triple) bond carbon atom. If the double (or triple) bond is in the center of the chain, the nearest substituent is used to determine the end where numbering starts The smaller of the two numbers designating the carbon atoms of the double bond is used as the double bond locator. If more than one double bond is present the compound is named as a diene, triene or equivalent prefix indicating the number of double bonds, and each double bond is assigned a locator number In cycloalkenes (or cycloalkynes) the double bond carbons are assigned ring locations #1 and #2. Which of the two is #1 may be determined by the nearest substituent rule Examples Examples Cis vs. trans of 2-butene In the cis isomer the methyl groups are on the same side; whereas they are on opposite sides in the trans isomer Isomers that differ only in the spatial orientation of their component atoms are called stereoisomers Alkene polymers Polymers are large molecules made from repetitive units called monomers Benzene An aromatic cyclic hydrocarbon Naming of benzene (1) Molecule is named by attaching the name of the substituent as a prefix to benzene Naming of benzene (2) The prefix ortho signifies a 1,2-disubstituted benzene ring meta signifies 1,3-disubstitution para signifies 1,4-disubstitution The prefixes o, m, and p can be used when a substance is named as a benzene derivative Common aromatic compounds Naming of benzene (3) The benzene ring is named as a phenyl group when it is a substituent phenylethyne What is an alcohol? A hydrocarbon derivative in which one or more hydrogens of a parent hydrocarbon have been replaced by a hydroxyl or alcohol functional group, OH Naming alcohol Select the longest carbon chain containing the hydroxyl group. Derive the parent name by replacing the -e ending of the corresponding alkane with –ol. Number the chain from the end nearer the hydroxyl group. The position of the hydroxyl group(s) on the parent chain is(are) indicated by placing the number(s) Number substituents according to position on chain, listing the substituents in alphabetical order OH OH OH t-butanol 2-pentanol heptanol Naming alcohols If there is more than one hydroxyl group (-OH), the suffix is expanded to include a prefix that indicates the number of hydroxyl groups present (-anediol, -anetriol, etc.) Numbering order of compounds with more than one functional group 1. 2. 3. 4. 5. 6. 7. Carboxylic acid Aldehyde Ketone Alcohol Amine Alkyne = alkene Alkane Naming alcohols The hydroxyl group takes precedence over alkyl groups and halogen substituents, as well as double bonds, in the numbering of the parent chain Alcohols may also be classified as primary, 1º, secondary, 2º & tertiary, 3º (carbons attached to the carbon with –OH) Reactions of alcohols (1) Dehydration If OH is attached to a secondary carbon, the major product has the greater number of alkyl groups directly attached to the double-bond carbons. Reactions of alcohols (2) Oxidation The product depends on the class of alcohol, 1o, 2o or 3o 1o alcohol 2o alcohol 3o alcohol What are phenols? Derivatives of hydroxybenzene 2-bromophenol 2-chloro-5-methylphenol 2-chlorophenol (o-chlorophenol) 2-methylphenol 3-methylphenol 4-methylphenol What are ethers? Ethers are compounds having two alkyl or aryl groups bonded to an oxygen atom, as in the formula R1–O–R2 Ethers contain a H-bond acceptor, O, but no H-bond donor Dimethyl ether is soluble in water Diethyl ether is miscible in water Ethers with larger alkane groups are water insoluble Diethyl ether is anesthetic Naming ethers The smaller, shorter alkyl group becomes the alkoxy substituent. The larger, longer alkyl group side becomes the alkane base name. Alkyl Group Name Alkoxy Group Name CH3– Methyl CH3O– Methoxy CH3CH2– Ethyl CH3CH2O– Ethoxy (CH3)2CH– Isopropyl (CH3)2CHO– Isopropoxy (CH3)3C– tert-Butyl (CH3)3CO– tert-Butoxy C6H5– Phenyl C6H5O– Phenoxy What re they? Sulfur analogs of alcohols are called thiols or mercaptans Strong odor Nomenclature The parent is the longest chain that contains the -SH group change the suffix -e to -thiol when -SH is a substituent, it is named as a sulfanyl group 2-butene-1-thiol SH SH 1-Butaneth iol 2-Methyl-1-prop anethiol (Butyl mercaptan) (Isobutyl mercaptan) OH HS 2-Sulfanylethan ol (2-Mercap toeth anol) Naming alkyl halides Thyroxine What are amines? Amines are derivatives of ammonia with alkyl groups substituting for hydrogen atoms. Amines are characterized by the number of R groups bound to the nitrogen. Naming amines 1o amines are given the family name of the alkyl group and amine is added as a suffix: CH3NH2 (a primary amine): methyl amine Secondary and tertiary amines are named by alphabetizing the R groups and then adding amine This is a 2o amine with two different R groups, ethyl and methyl. This is ethylmethylamine. This is a 3o amine. This is ethyldimethylamine Naming amines For amines with other functional groups, the amine is considered a substituent amino group. Naming amines Secondary and tertiary amines with the same substituents (symmetrical) are named as di- and trialkyl amines: Naming secondary and tertiary amines If the two groups are different, then they are named as substituent amines with the parent molecules being the largest Secondary amines can be named by replacing the -e of the parent group with the word amine and then using an upper case N to designate that the second alkyl group is on the nitrogen atom N-methyl-1-propanamine N,N-dimethylethanamine Naming amines Rings that contain atoms other than carbons are called heterocycles. There are a number of important heterocyclic amines. In each case the nitrogen is assigned the number 1 in the ring. There are only a few common names for amines Properties of amines Amines are polar Primary and secondary amines have H-bond donors and acceptors, so they are held together by H-bonds. Tertiary amines have no H-bond donor, since they have three alkyl groups on the nitrogen. Basicity of amines Amines are significantly more basic than water. They produce hydroxide ion and ammonium ions when dissolved in water. In blood, amines exist as ammonium ions. Amine salts Reaction of an amine with an acid produces an alkylammonium salt. Salts of amines are named by changing “amine” to “ammonium” and adding the name of the negative ion to the end of the word. Quaternary amines Nitrogen can also have a fourth alkyl group attached. When nitrogen is attached to four groups, it is called amino cation. This gives a positively-charged compound known as a quaternary amine. They will always carry a positive charge, regardless of the pH of the surrounding solution. Quaternary ammonium salts Quaternary ammonium salts are salts of quaternary ammonium cations with an anion. Carbonyl groups Aldehyde Ketone Carboxylic acid Ester Amide -al -one -oic acid -oate -amide What are they? Belong to the carbonyl group (C=O) Polar The carbonyl carbon of aldehydes has at least one hydrogen bonded to it Ketones have two alkyl groups bonded to the carbonyl carbon Naming aldehydes and ketones The longest C chain containing the C=O is the parent compound The parent compound is given the suffix "-al" for aldehyde or "-one“ for ketone C-1 is always the C=O carbon in aldehydes. In ketones, C=O carbon is lowest number possible. C=O has precedence over -OH groups When the aldehyde group is attached to a ring it is named as a -carbaldehyde Properties This group is polar The carbonyl group has a H-bond acceptor but no H-bond donor This makes aldehydes and ketones slightly soluble in water and having lower boiling point that alcohols Low toxicity (ketones)-highly toxic (small aldehydes like formaldehyde) (R) (R) Reactions of aldehydes and ketones (1) Oxidation Both are synthesized from oxidation of alcohols Aldehydes are oxidized to carboxylic acids RCH=O + [O] RC(OH)=O Ketones do not get oxidized because they do not have hydrogen Reactions of aldehydes and ketones (2) Reduction Aldehydes and ketones are reduced to alcohols Reactions of aldehydes and ketones (3) Addition (conversion C=O to C-O) forming hemiacetals (having both an –OH group and an ether –OR group) and acetals (having two –OR groups) Reversible reaction Stability of hemiacetals These are also generally unstable, but hemi-acetals can be stabilized if they form a ring structure (e.g. glucose) Addition of another alcohol forming acetal What is carboxylic acid? The active group of carboxylic acids is called a carboxyl group Properties of carboxylic acid Both parts of the carboxyl group are polar The C=O of carboxylic acids is highly polar, and is a hydrogen bond acceptor The O-H of the carboxyl group is also highly polar, and contains a hydrogen bond donor, Hd+, as well as a hydrogen bond acceptor, Od- They have higher boiling points than similar alcohols, due to dimer formation. Naming carboxylic acids The carboxyl group always occurs at the end of the molecule, making it C1 Family name is longest chain containing the carboxyl group Suffix is "-oic acid" Carbonyl groups appearing in carboxylic acids are called "oxo" and hydroxy groups are named "hydroxy“ Simple dicarboxylic acids have the general formula HO2C– (CH2)n–CO2H (where n = 0 to 5) and end with “-dioic acid” Examples Formula HCO2H Common Name formic acid IUPAC Name methanoic acid CH3CO2H acetic acid ethanoic acid CH3CH2CO2H propionic acid propanoic acid CH3(CH2)2CO2H CH3(CH2)3CO2H CH3(CH2)4CO2H butyric acid valeric acid caproic acid butanoic acid pentanoic acid hexanoic acid CH3(CH2)5CO2H enanthic acid heptanoic acid CH3(CH2)6CO2H caprylic acid octanoic acid CH3(CH2)7CO2H pelargonic acid nonanoic acid CH3(CH2)8CO2H capric acid decanoic acid Examples Acidity of Carboxylic Acids Carboxylic acids are weak acids The name of the ionic form of carboxylic acids ends of “-ate” Salts of Carboxylic Acids Carboxylic acids are neutralized by bases forming salts O CH3 C OH NaOH HCl O CH3 _ + Na C O Important drugs are carboxylic acids Aspirin (salicyclic acid) Ibuprofen Anesthetics (lidocaine and benzoncaine) Reactions of carboxylic acids Formation of esters (esterification) by substitution of the hydroxyl Group with either the –OR of an alcohol (reversible reaction) Esters In esters, the –OH group of the carboxyl end is converted to –OR. Naming esters Esters are named with the alkyl group from the alcohol, followed by the acid name changed to "oate”. The group attached to (C=O) is the parent. Hydrolysis of esters Formation of carboxylic acid and an alcohol Amides Amides are derived from carboxylic acids The -COOH group of carboxylic acid is replaced by an NH2 group Naming amides The name is derived from the acid by replacing the "oic acid" ending by "amide“ A common amide is ethanamide, CH3CONH2 (acetamide) The simplest amide is methanamide (HCONH2) If the chain is branched, the carbon in the -CONH2 group counts as the number 1 carbon atom. Naming amides 2 Amides are classified as 1º, 2º or 3º, depending on the number of alkyl groups bonded to the nitrogen With N substituted amides the attachment to the nitrogen must be indicated CH3CONHCH3 is N-Methylacetamide CH3CONH(CH2CH3)2 is N,N-Diethylacetamide Examples Properties of amides The melting points of unsubstituted amides are high because they can form hydrogen bonds. Formation of amides Formation of amides by substitution of the hydroxyl Group with the NR2 of an amine Hydrolysis of amides Formation of carboxylic acid and an amine Acetaminophen It is an amide that also contains a hydroxyl group. It reduces fever, but unlike aspirin, it is not an anti-inflammatory agent and does not induce internal bleeding. It is used in individuals prone to bleeding or recovering from surgery or wounds. Overdoses of acetaminophen can cause kidney and liver damage. Phosphoric acid Phosphoric acid can form three ionized forms Phosphoester Alcohols react with phosphoric acid to produce a phosphate ester, or phosphoester Anhydride linkage Two phosphorioc acids can form a phosphoric acid anhydride called pyrophosphate or diphosphoric acid A third phosphate can react with them forming a triphosphoric acid Diphosphate and triphosphate esters Diphosphate and triphosphates can form esters Hydrolysis of phosphate Pyrophosphate and triphosphoric acids can be hydrolyzed easily This is just the reverse reaction of forming them Phosphorylation Phosphorylation is the transfer of phosphate from one molecule to an alcohol group of another molecule. This is an important reaction in biochemistry because and energy-rich molecule is formed. Hydrolysis of pyrophosphate and triphosphoric acids, releases energy.