Introduction to organic Introduction to organic chemistrychemistryDr. Mamoun AhramNursingFirst semester, 2016

Organic compoundsOrganic 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 groupsFunctional 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

HydrocarbonsHydrocarbons

Contain only carbon and hydrogen

Aromatic

Second groupSecond group

Single bonds + a carbon bonded to an electronegative atom

Third groupThird group

Contain C=O

Anhydride

AlkanesAlkanes

They contain carbon and hydrogen only in single bonds.Examples: methane (CH4), ethane (CH3CH3), propane (CH3CH2CH3)

Straight versus branched Straight versus branched alkanesalkanes

Carbons can be connected in a row or in branchesNote that with more branching, physical properties are different.

boiling point is lowerNote that different drawings can be used

Condensed structures do not show bonds

IsomersIsomers

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

ConformationsConformations

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 moleculesNaming organic molecules

Prefix-parent-suffix

Parents: number of carbon moleculesPrefix: where substituents are located (methyl, ethyl, etc.)Suffix: family (alkane, alcohol, ether, etc.)

If two or more functional groups, order ot priority:

1. Carboxylic acid2. Aldehyde3. Ketone4. Alcohol5. Amine6. Alkyne = alkene7. Alkane

Number of carbon moleculesNumber of carbon molecules

ExampleExample

pentane

2-methylbutane2,2-dimethylpropane

““Common" names for simple alkanesCommon" 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)

DD

Number of carbons attached to branch point

Sec: secondaryTert: tertiary

Classification of carbon atomsClassification of carbon atoms

“R” indicates a general abbreviation of any organic substituent

Naming an alkanes 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 pointsWrite the name as a single name

SubstituentsSubstituentsIf 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

CycloalkanesCycloalkanesRing structures of alkanesThese 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)Examples (practice at home)

What are they?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 unsaturatedAlkanes are saturated

Formula and structureFormula 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 alkynesNaming alkenes and alkynesThe –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 bondThe 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 numberIn 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

ExamplesExamples

ExamplesExamples

Cis vs. trans of 2-buteneCis 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 isomerIsomers that differ only in the spatial orientation of their component atoms are called stereoisomers

Alkene polymersAlkene polymers

Polymers are large molecules made from repetitive units called monomers

Benzene Benzene

An aromatic cyclic hydrocarbon

Naming of benzene (1)Naming of benzene (1)

Molecule is named by attaching the name of the substituent as a prefix to benzene

Naming of benzene (2)Naming of benzene (2)

The prefix ortho signifies a 1,2-disubstituted benzene ringmeta signifies 1,3-disubstitutionpara signifies 1,4-disubstitutionThe prefixes o, m, and p can be used when a substance is named as a benzene derivative

Common aromatic compoundsCommon aromatic compounds

Naming of benzene (3)Naming of benzene (3)

The benzene ring is named as a phenyl group when it is a substituent

phenylethyne

What is an alcohol?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 alcoholNaming 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

2-pentanol

OH

t-butanol

OH

heptanol

Naming alcoholsNaming 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 Numbering order of compounds with more more than one functional groupthan one functional group

1. Carboxylic acid2. Aldehyde3. Ketone4. Alcohol5. Amine6. Alkyne = alkene7. Alkane

Naming alcoholsNaming alcohols

The hydroxyl group takes precedence over alkyl groups and halogen substituents, as well as double bonds, in the numbering of the parent chainAlcohols may also be classified as primary, 1º, secondary, 2º & tertiary, 3º (carbons attached to the carbon with –OH)

Reactions of alcohols (1)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)Reactions of alcohols (2)

OxidationThe product depends on the class of alcohol, 1o, 2o or 3o

1o alcohol

2o alcohol 3o alcohol

What are phenols?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?What are ethers?

Ethers are compounds having two alkyl or aryl groups bonded to an oxygen atom, as in the formula R1–O–R2Ethers contain a H-bond acceptor, O, but no H-bond donorDimethyl ether is soluble in waterDiethyl ether is miscible in waterEthers with larger alkane groups are water insolubleDiethyl ether is anesthetic

Naming ethersNaming ethers

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

The smaller, shorter alkyl group becomes the alkoxy substituent. The larger, longer alkyl group side becomes the alkane base name.

What re they?What re they?

Sulfur analogs of alcohols are called thiols or mercaptansStrong odor

NomenclatureNomenclature

The parent is the longest chain that contains the -SH groupchange the suffix -e-e to -thiol-thiolwhen -SH is a substituent, it is named as a sulfanyl group

1-Butanethiol(Butyl mercaptan)

2-Methyl-1-propanethiol(Isobutyl mercaptan)

2-Sulfanylethanol(2-Mercaptoethanol)

SH SH OHHS

2-butene-1-thiol

Naming alkyl halidesNaming alkyl halides

ThyroxineThyroxine

What are 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.

Naming aminesNaming 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 aminesNaming amines

For amines with other functional groups, the amine is considered a substituent amino group.

Naming aminesNaming amines

Secondary and tertiary amines with the same substituents (symmetrical) are named as di- and tri- alkyl amines:

Naming secondary and tertiary Naming secondary and tertiary aminesamines

If the two groups are different, then they are named as substituent amines with the parent molecules being the largestSecondary 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 aminesNaming 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 aminesProperties of amines

Amines are polarPrimary 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 aminesBasicity 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 saltsAmine 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 aminesQuaternary 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 saltsQuaternary ammonium saltsQuaternary ammonium salts are salts of quaternary ammonium cations with an anion.

Carbonyl groupsCarbonyl groups

Aldehyde -al

Ketone -one

Carboxylic acid -oic acid

Ester -oate

Amide -amide

What are they?What are they?

Belong to the carbonyl group (C=O)

Polar

The carbonyl carbon of aldehydes has at least one hydrogen bonded to itKetones have two alkyl groups bonded to the carbonyl carbon

Naming aldehydes and ketonesNaming aldehydes and ketonesThe longest C chain containing the C=O is the parent compoundThe 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 groupsWhen the aldehyde group is attached to a ring it is named as a -carbaldehyde

Properties Properties

This group is polarThe 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 Reactions of aldehydes and ketones (1) (1)

OxidationBoth are synthesized from oxidation of alcohols

Aldehydes are oxidized to carboxylic acidsRCH=O + [O] RC(OH)=O

Ketones do not get oxidized because they do not have hydrogen

Reactions of aldehydes and ketones Reactions of aldehydes and ketones (2)(2)

ReductionAldehydes and ketones are reduced to alcohols

Reactions of aldehydes and ketones Reactions of aldehydes and ketones (3)(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 hemiacetalsStability of hemiacetals

Hemi-acetals can be stabilized if they form a ring structure (e.g. glucose)

Addition of another alcohol forming acetal

What is carboxylic acid?What is carboxylic acid?

The active group of carboxylic acids is called a carboxyl group

Properties of carboxylic acidProperties of carboxylic acid

Both parts of the carboxyl group are polarThe C=O of carboxylic acids is highly polar, and is a hydrogen bond acceptorThe 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 acidsNaming 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”

ExamplesExamples

Formula Common Name IUPAC NameHCO2H formic acid methanoic acid

CH3CO2H acetic acid ethanoic acidCH3CH2CO2H propionic acid propanoic acid

CH3(CH2)2CO2H butyric acid butanoic acidCH3(CH2)3CO2H valeric acid pentanoic acidCH3(CH2)4CO2H caproic acid hexanoic acidCH3(CH2)5CO2H enanthic acid heptanoic acidCH3(CH2)6CO2H caprylic acid octanoic acidCH3(CH2)7CO2H pelargonic acid nonanoic acidCH3(CH2)8CO2H capric acid decanoic acid

ExamplesExamples

Acidity of Carboxylic AcidsAcidity of Carboxylic Acids

Carboxylic acids are weak acidsThe name of the ionic form of carboxylic acids ends of “-ate”

Salts of Carboxylic AcidsSalts of Carboxylic Acids

Carboxylic acids are neutralized by bases forming salts

CH3 C

O

OHNaOH

CH3 C

O

O_Na

+

HCl

Important drugs are carboxylic acidsImportant drugs are carboxylic acids

Aspirin (salicyclic acid)IbuprofenAnesthetics (lidocaine and benzoncaine)

Reactions of carboxylic acidsReactions of carboxylic acids

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

Esters Esters

In esters, the –OH group of the carboxyl end is converted to –OR.

Naming estersNaming 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.

AmidesAmides

Amides are derived from carboxylic acidsThe -COOH group of carboxylic acid is replaced by an -NH2 group

Naming amidesNaming 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 2Naming amides 2

Amides are classified as 1º, 2º or 3º, depending on the number of alkyl groups bonded to the nitrogenWith N substituted amides the attachment to the nitrogen must be indicated

CH3CONHCH3 is N-MethylacetamideCH3CONH(CH2CH3)2 is N,N-Diethylacetamide

ExamplesExamples

Properties of amidesProperties of amides

The melting points of unsubstituted amides are high because they can form hydrogen bonds.

Formation of amidesFormation of amides

Formation of amides by substitution of the hydroxyl Group with the NR2 of an amine

When hydrolyzed, amides form carboxylic acid and an amine.

AcetaminophenAcetaminophen

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 acidPhosphoric acid

Phosphoric acid can form three ionized forms

Phosphoester Phosphoester Alcohols react with phosphoric acid to produce a phosphate ester, or phosphoester

Anhydride linkageAnhydride 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 Diphosphate and triphosphate estersesters

Diphosphate and triphosphates can form esters

Hydrolysis of phosphateHydrolysis of phosphate

Pyrophosphate and triphosphoric acids can be hydrolyzed easily

This is just the reverse reaction of forming them

PhosphorylationPhosphorylation

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.