Introduction to Organic Chemistry PDF

Introduction to organic chemistry PROF. NAFEZ ABU TARBOUSH NURSING SUMMER 2022-2023 Organic compounds and Functional groups o"Organic" means carbon-containing oThe properties of organic molecules depend on: oArrangement of the carbon skeleton, oThe presence of functional groups  Or Aroma...

Introduction to organic chemistry PROF. NAFEZ ABU TARBOUSH NURSING SUMMER 2022-2023 Organic compounds and Functional groups o"Organic" means carbon-containing oThe properties of organic molecules depend on: oArrangement of the carbon skeleton, oThe presence of functional groups  Or Aromatic X X Anhydride Group 1: Hydrocarbons Contain only carbon and hydrogen Aromatic Second group Single bonds + a carbon bonded to an electronegative atom Third group Contain C=O Anhydride Part 1: hydrocarbons (alkanes and alkenes) Alkanes Single bonds Examples: methane (CH4), ethane (CH3CH3), propane (CH3CH2CH3) In a row or in branches Different drawings can be used Condensed structures do not show bonds Isomers Molecules that have the same molecular formula (same number of atoms), but different structures (arrangements and connectivity of atoms). ◦ Constitutional isomers (structural isomers) Stereoisomers: different conformations Different three-dimensional arrangement of atoms because C-C bonds can rotate. Geometric isomers (stereoisomers) Naming organic molecules IF TWO OR MORE FUNCTIONAL GROUPS, PREFIX-PARENT-SUFFIX ORDER OF PRIORITY: 1. Carboxylic acid (highest) Parents: number of carbon molecules 2. Aldehyde Prefix: where substituents are located (methyl, 3. Ketone ethyl, etc.) 4. Alcohol Suffix: family (alkane, alcohol, ether, etc.) 5. Amine 6. Thiol 7. Alkyne = alkene 8. Alkane (lowest) Number of carbon molecules Example pentane 2-methylbutane 2,2-dimethylpropane 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 Name the longest continuous carbon chain, with the prefix “cyclo”. Examples (practice at home) X X Alkenes What are they? Alkenes are hydrocarbons that have carbon-carbon double-bond functional groups. They are said to be unsaturated. ◦ Alkanes are saturated. Fatty acid Naming alkenes The –ene suffix indicates an alkene. The longest chain chosen for the root name must include both carbon atoms of the double bond. The main chain is numbered from the carbon nearest to the double-bond atom. Cis vs. trans of 2-….ene 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. Benzene An aromatic cyclic hydrocarbon It is called benzene if it is attached to an alkane or a metal. It is named phenyl if it is attached to another functional group such as an alcohol, an aldehyde, etc. The amino acid phenylalanine Common aromatic compounds X X X Part 2: hydrocarbons (alcohols, phenols, thiols, disulfide, amines) Alcohols 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 indicated by placing the number(s). Number substituents according to position on chain, listing the substituents in alphabetical order What does OH the “t” mean? OH OH tert-Butyl alcohol t-butanol 2-pentanol heptanol Naming alcohols Alcohols may also be classified as primary, 1º, secondary, 2º & tertiary, 3º (carbons attached to the carbon with –OH).  Reactions of alcohols 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 The amino acid phenylalanine Thiols and disulfides What re they? Sulfur analogs of alcohols are called thiols or mercaptans. Strong odor ‫ الظربان‬- Skunk 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 OH HS 1-Butaneth iol 2-Methyl-1-prop anethiol 2-Sulfanylethan ol (Butyl mercaptan) (Isobutyl mercaptan) (2-Mercap toeth anol) Amines 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. Amino acids Some 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 DNA Properties of amines Amines are polar. Primary and secondary amines have H-bond donors and acceptors. Tertiary amines have no H-bond donor since they have three alkyl groups on the nitrogen. Amine salts Reaction of an amine with acid produces an ammonium salt. Salts of amines are named by changing “amine” to “ammonium”. Quaternary amines Nitrogen can also have a fourth alkyl group attached. ◦ When nitrogen is attached to four groups. This gives a positively-charged compound known as a quaternary amine. They will always carry a positive charge. Part 3: aldehydes, ketones, carboxylic acid, ester, amides, anhydrides Carbonyl groups Aldehyde -al Ketone -one Carboxylic acid -oic acid Ester -oate Amide -amide Aldehydes and ketones What are they? Belong to the carbonyl group (C=O) The carbonyl carbon of aldehydes has at least one hydrogen bonded to it. Ketones have two alkyl groups bonded to the carbonyl carbon. Sugars Properties This group is polar. The carbonyl group has a H-bond acceptor but no H-bond donor. Reactions of aldehydes and ketones (1) Oxidation ◦ Both are synthesized from the oxidation of alcohols. Aldehydes are oxidized to carboxylic acids. Sugars RCH=O + [O] RC(OH)=O Ketones do not get oxidized. Reactions of aldehydes and ketones (2) Reduction ◦ Aldehydes and ketones are reduced to alcohols. Sugars 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 Hemi-acetals can be stabilized if they form a ring structure (e.g. glucose) ◦ Addition of another alcohol forming acetal Carboxylic acids, esters, and amides 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, as well as a hydrogen bond acceptor. 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 the longest chain containing the carboxyl group. Suffix is "-oic acid“. Formula Common Name IUPAC Name HCO2H formic acid methanoic acid CH3CO2H acetic acid ethanoic acid Fatty acids CH3CH2CO2H propionic acid propanoic acid CH3(CH2)2CO2H butyric acid butanoic acid CH3(CH2)3CO2H valeric acid pentanoic acid CH3(CH2)8CO2H capric acid decanoic acid Acidity of carboxylic acids Carboxylic acids are weak acids. The name of the ionic form of carboxylic acids ends of “-ate” Buffers: Fatty acids Amino acids Salts of carboxylic acids Carboxylic acids are neutralized by bases forming salts O O NaOH _ + CH3 C OH CH3 C O Na HCl Soaps Important drugs are carboxylic acids Aspirin (salicyclic acid) Ibuprofen Anesthetics (lidocaine and benzoncaine) Formation of esters Formation of esters (esterification) by substitution of the hydroxyl Group with either the –OR of an alcohol (reversible reaction) When hydrolyzed, esters form carboxylic acid and an alcohol Waxes Triacylglycerol In esters, the –OH group of the carboxyl end is converted to –OR. Amides Amides are also derived from carboxylic acids. The -OH group of a carboxylic acid is replaced by an -NH2 group forming an amide bond. Peptide bonds Properties of amides They can form hydrogen bonds. 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 phosphoric acids can form a phosphoric acid anhydride called pyrophosphate or diphosphoric acid. A third phosphate can react with them forming a triphosphoric acid Examples: AMP ADP ATP Glucose-6- Anhydride means phosphate “without water” Diphosphate and triphosphate esters Diphosphate and triphosphates can form esters. 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.