unit 1 – organic chemistry - msdunlop -...

Unit 2 – Organic ChemistryChapter 1 Summary Notes – Structure and Properties of Organic Compounds

Chapter 1 – Structure and Physical Properties of Organic Compounds

Section 1.1 – Introducing Organic Compounds

The Modern Definition of Organic Compounds Organic Compounds: type of compound in which carbon atoms are nearly always

bonded t each other, to hydrogen atoms, and occasionally to atoms of a few specific elements (O, F, Cl, N, Br, S, P, I)

o Exceptions: Carbonates (CO32-), cyanides (CN-), carbides (C2

2-) and oxides of carbon (CO, CO2)

These do not contain any carbon-carbon or carbon-hydrogen bonds Inorganic Compounds: A type of compound that includes carbonates, cyanides,

carbides, and oxides of carbon, along with all compounds that do not contain carbon atoms

The Special Nature of Carbon Atoms Why is carbon so special? What is it about carbon that makes it the basis for all living

things? Recall: Carbon has four valence electrons (Electron Configuration: 1s22s22p2). This

means that the outer valence shell is exactly half full and therefore carbon can form 4 covalent bonds. These outer electrons can hybridize to sp3, sp2, and sp orbitals, which means they can form single, double and triple bonds. Additionally, carbon has intermediate electronegativity (EN = 2.5), which means it is far more likely to share electrons than to gain or lose enough electrons to form ions.

Shapes of carbon structures

Shape Hybridization Diagram and Example

Tetrahedral sp3

CH4

Trigonal Planar sp2

CH2O

Linear sp

HCN

Representing MoleculesIn organic chemistry, there are many ways to represent molecules: the molecular formula, the structural formula, the ball and stick model, and the space-filling model are some examples, each one gives different information about the molecule

of 20


For example: Ethane (C2H6)

Molecular Formula Structural Formula Ball and Stick Model Space FillingC2H6

Additionally: Chemists often abbreviate structural diagrams, because organic molecules often contain a lot of hydrogen and carbon.

Example: C4H10

vs. vs.

Structural Formula Condensed Line Structural FormulaStructural Formula

Each bend or end-point represents a carbon atom, it is assumed that there are enough hydrogens to complete the octet and form 4 bonds unless otherwise written.

Isomers Carbon atoms can form bonds with each other, which often results in long straight or

branched chains of atoms. Each carbon can also be boned to hydrogen or atoms of other elements. However, once you have enough carbons and hydrogen, the atoms can attach to each other in different ways; that is, they have the same molecular formula but they have a different structural formula

For Example: Each of the following molecules has the formula C5H12 – they all contain 5 carbons and 10 hydrogens.

Each one of these molecules would have different physical properties, because the arrangement of the atoms is different

Isomers: molecules that have the same molecular formula but their atoms are in different arrangements

Constitutional Isomers: molecules that have the same molecular formula but their atoms are bonded together in different sequences (i.e. the examples above)

of 20


Note: sometimes it is hard to tell if two molecules are isomers – remember, molecules are free to rotate, and individual atoms can rotate around a single bond.

Consider the following:

vs.

These two molecules look structurally different, as drawn. BUT, they aresimply rotated 180, or flipped horizontally

OR:

vs.

Because atoms can rotate around a single bond, these are the molecule and are not isomers of each other.

Carbon atoms can also for ring structures with three or more atoms. For example, each of the following molecules is a constitutional isomer of the formula C5H10

Stereoisomers An important property of double bonds is that they ‘lock’ a structure in place: atoms

cannot rotate around them. These make the molecule flat and rigid This leads to another type of isomer called a stereoisomer Stereoisomer: molecules that have the same molecular formula and their atoms are

bonded together in the same sequence, but differ in the three-dimensional orientations of their atoms

o There are two kinds of stereoisomers: enantiomers and diastereomers

Diastereomers Diastereomers: stereoisomer based on a double bond, in which different types of atoms

or groups are bonded to each carbon in the double bond

of 20


Example: C4H8, the molecules shown below contain a double bond between the second and third carbon

trans-2-butene cis-2-butene

The trans- isomer has the identical CH3 groups on opposite sides of the double bond, the cis- isomer has identical CH3 groups on the same side of the double bond. The groups do not have to be identical, as long as the larger groups are on the same side of the double bond, it is cis and if they are on different sides then it is trans

The difference between cis- and trans- isomers is very important, especially in metabolic processes.

Note: triple bonds do not form diastereomers

Enantiomers Enantiomers: are non-superimposable mirror images of each other. They occur when a

single carbon is bonded to four different types of atoms or groups Example: CHFClBr

A more common example of enantiomers is your hands: they are perfect mirror images but you cannot superimpose them on each other. We even distinguish between different forms by conventions of right-handed or left-handed enantiomers

Catch: these have IDENTICAL chemical properties, but are often metabolized differently, which makes this property incredibly important in pharmaceuticals and can be deadly if not taken in to account in synthesis processes

o Example: Thalidomide

of 20


Section 1.2 – Hydrocarbons

Hydrocarbons: organic compounds that contain only carbon atoms and hydrogen atoms

o Example: fossil fuels such as natural gas and gasoline

Alkanes Alkane: the simplest hydrocarbon in which all carbon atoms are joined together by

single covalent bondso Also called Saturated Hydrocarbons: hydrocarbons that contain only single

bonds, no double or triple bonds, that is, each carbon atom is bonded to the maximum possible atoms and all of them are sp3 hybridized

The simplest alkane is methane (CH4) and each additional alkane adds either a CH2 or CH3 to the chain

The general formula for a straight or branched alkane is CnH2n+2

o Therefore: if you have an alkane with 5 Carbons: C5H2×5+2 = C5H12

Methane Ethane Propane Butane

Alkanes can also have substituent groups, where an atom or groups of atoms has been substituted in place of a hydrogen, often called a side group

Naming AlkanesThe International Union of Pure and Applied Chemistry (IUPAC) has a system for naming organic compounds. Each organic compound name has the following components:

Root: denotes the number of carbon atoms in the longest continuous chain of carbon atoms

Prefix: gives the positions and names of any branches from the main chain Suffix: indicates the series to which the molecule belongs. The suffix for alkanes is ‘-ane’

Alkyl Groups: a side group based on an alkane; to name them you use the same root as the main chain, but instead of the suffix ‘-ane’ you use ‘-yl’

Number of Carbon Atoms

Root NameSide Group

Name

Number of Carbon Atoms

Root NameSide Group

Name

1 meth- methyl- 6 hex- hexyl2 eth- ethyl- 7 hept- heptyl3 prop- prop- 8 oct- octyl4 but- but- 9 non- nonyl5 pent- pent- 10 dec- decyl

of 20


Steps for Naming Alkanes

Name the following compound:

1. Identify Roota. Identify the longest continuous carbon

chainb. Find the root for the number of

carbons in the chain

The longest chain is six carbon atoms, therefore the root is hex-

2. Identify the Suffix The compound is an alkane, therefore the suffix is ‘-ane’

3. Identify the PrefixThe prefix indicates the position and type of side groups on the main chain. To identity the prefix:

a. Identify the number of carbon atoms in each side group

b. Determine the number of each side group according to the number of carbons

c. If there is more than one side group, write their names in alphabetical order

d. Find the position of each side group. Numbering must begin at the end of the chain that gives the lowest possible numbers.

e. Precede the name of each side group with the number of carbon atoms to which it is attached on the main chain. Use a hyphen to separate numbers and words, and use a comma to separate the numbers

f. Use a prefix to indicate how many of each type of side group there are if there is more than one of the same group: di, tri, tetra, penta. These additional prefixes do not affect the alphabetical order established before

a. Two side groups have one C atom, the other has two

b. The side groups with one carbon atom are methyl groups, the other side group is an ethyl group.

c. Alphabetical order: ethyl, methyld.

The compound is numbered from left to right. This gives the side numbers 3, 3, 4. The two methyls are on C-3, and ethyl is on C-4.

e. The prefix is now: 4-ethyl-3,3-methylf. The two methyl groups make the

prefix: 4-ethyl-3,3-dimethyl-

4. Name the CompoundCombine the prefix, root, and suffix.

4-ethyl-3,3-dimethylhexane

Note: no space, dash, or comma between prefix, root, and suffix

of 20


Practice 1: Name the following alkanes

a. b.

(answer: 2,3,4-trimethylpentane) (answer: 4,5-diethyl-3,6-dimethyloctane)

Drawing Alkanes

Example: Draw the line structural formula for 3-ethyl-3-methylpentane

1. Identify the rootThe root of the name gives the number of carbon atoms in the main chain

The root is pent- so there are five carbons in the main chain

2. Identify the suffix The suffix is –ane, so the compound contains only single bonds

3. Draw and number the main chain, but do not add any hydrogen atoms yet

C—C—C—C—C

4. Identify the prefix and draw the side groups

The prefix is 3-ethyl-3-methyl-. Therefore, there is an ethyl group and a methyl group attached to carbon atoms 3 of the main chain. You can place the side groups on either side of the main chain

5. Complete the condensed structural formula

6. Draw the line structural formula

Practice 2: Draw the line and condensed structures for the following molecules:

a. 3-ethyl-2-methylheptaneb. 2,3,3,-triethylpentane

Physical Properties of Alkanes Non-polar, therefore not soluble in water; but soluble in non-polar solvents like benzene Low carbon alkanes (1-4) are gases at room temperature, medium length alkanes are

liquids; long length (over 26) are solid at room temperature; property is due to increasing number of London Dispersion Forces

of 20


Alkenes Alkenes are any hydrocarbon that has at least one double bond in the carbon chain

o When a carbon has one double bond it is sp2 hybridized; when it has two double bonds it is sp hybridized

Unsaturated hydrocarbons: hydrocarbons that contain a double or triple bonds, whose carbon atoms can potential bond to additional atoms if those bonds are broken.

When naming alkenes you must include the location of all the double bonds, the carbon indicated is the lower numbered carbon

The suffix for alkenes is ‘-ene’ Remember: double bonds can result in diastereomers if different side groups are

present

Examples:

Ethene Propene 1-butene 1-butene

Trans-2-butene cis-2-butene

Note: cis-double bonds form kinks in long carbon chains (important for later)

Properties of Alkenes Non-polar, therefore do not dissolve in water; dissolve in non-polar solvents (like

benzene) Boiling points increase as more carbons are added However: alkenes have lower boiling points than alkanes of similar carbon lengths Slight difference in location and shape around the double bond change the boiling points

o But-1-ene = -6.3Co Trans-but-2-ene = 0.88Co Cis-but-2-ene = 3.71C

Naming Alkenes: The process is the exact same as naming alkanes, except the suffix is –ene; if there is more than one double bond, you must use ‘di’, ‘tri’, etc. to indicate the number, just as with alkyl prefixes

of 20


Example: Name the following alkene

1. Identify the roota. Identify the longest chain that

CONTAINS THE DOUBLE BOND(S)b. Find the root for the number of

carbons in the chain. The longest containing the double bond is five carbons, therefore the root is pent-

2. Identify the suffixa. Number the main chain by starting at

the end of the chain nearest the double bond, giving the double bond the lowest numbers possible(Note: this takes precedence over any rule for numbering alkanes)

b. If the alkene contains four or more carbons, you must give the position in the suffix.

Numbering from left to right gives the lowest possible carbon numbersThe compound is an alkene. It contains four or more carbons. The double bond is between C-2 and C-3.The suffix is -2-ene

3. Identify the prefixName the side groups on alkenes as you would for alkanes

There are two methyl groups, one on C3, the other on C4.The prefix is 3,4-dimethyl-

4. Name the compound 3,4-dimethylpent-2-ene

Practice:

a. b.

5-ethyl-3,4,5-trimethyloct-3-ene 3-ethyl-4-methylhex-2,4-diene

of 20


Practice: Draw the line structural diagram of 3-ethyl-4-methylhex-3-ene

Alkynes Alkynes are hydrocarbon that contain one or more triple bonds, these are also

unsaturated hydrocarbons General Structural Formula: CnH2n-2

Note: the presence of triple bonds means both carbons are sp hybridized, therefore the structure is linear

Triple bonds do not cause stereoisomers

Examples:

ethyne propyne but-1-yne but-2-yne

Naming and Drawing Alkynes

Example: Name the following alkyne

1. Identify the roota. Identify the longest chain that

CONTAINS THE TRIPLE BOND(S)c. Find the root for the number of

carbons in the chain.

The longest chain that includes the triple bond is five carbon atoms, so pent- is the root

2. Identify the suffixa. Number the main chain by starting at

the end of the chain nearest the triple bond, giving the triple bond the lowest numbers possible(Note: this takes precedence over any rule for numbering alkanes, and takes precedence over double bonds)

b. If the alkyne contains four or more carbons, you must give the position in the suffix.

Numbering starts at the end that gives the triple bond the lowest number, in this case C-1, the compound contains a triple bond.

The suffix is -1-yne

3. Identify the prefixName the side groups on alkynes as you would for alkynes

There is a methyl group on C-3The prefix is 3-methyl-

4. Name the compound 3-methylpent-1-yneExample: draw the following alkyne: 4-ethylhex-2-yne

of 20


Physical Properties: Have higher MP/BP then analogous alkenes and alkanes

Cyclic Hydrocarbons Cyclic Hydrocarbons are hydrocarbons that form rings These are the foundation of many biological molecules, including cholesterol and the

steroid hormones. Can be alkanes, alkenes, or alkynes (but alkyne-based rings are extremely unstable) The prefix ‘cyclo’ is added to indicate it

Examples:

Cyclopropane Cyclobutane Cyclopentane Cyclohexane

Naming Cyclic HydrocarbonsExample:

1. Identify the rootDetermine the root of carbon atoms in the ring in order to find the root. This is the same as the straight chain alkane, alkene, or alkyne with the same number of carbon atoms, preceded by cyclo-

There are five carbon in the ring, therefore cyclopent- is the root

2. Identify the suffixDetermine whether the molecule has all single bonds, at least one double bond, or at least one triple bond. The suffix is –ane, -ene, or –yne accordingly. It is not necessary to indicate the location of the double or triple bond, because they are assumed to be on C-1

The ring has one double bond, therefore the suffix is –ene

3. Identify the prefixNote: if there are no side groups, then it is not necessary to indicate the position of the side groups; however if there are, then the double or triple bond must be between C-1 and C-2, numbering must go according to that

The prefix is 3,4-dimethyl-

4. Name the compound 3,4-dimethylcyclopentane

Physical Properties: MP/BP are slightly higher than analogous straight chain hydrocarbons

of 20


Aromatic Hydrocarbons Benzene: a cyclic aromatic hydrocarbon, C6H6, in which all six carbon-carbon bonds are

intermediate in length between a single and double bond; results from delocalized electrons in sp2 hybridized orbitals (unhybridized p-orbitals form the delocalized p-electrons)

o Results from the resonance structures formedo Unusually stable

NOTE: because of the sp2 hybridization, benzene rings are FLAT

Structural Diagram Alternating resonance forms Resonance hybridShowing delocalized e-

Aromatic Hydrocarbons: compound that contains only carbon and hydrogen and based on the structure of benzene

Aliphatic hydrocarbon: compound containing only carbon and hydrogen in which carbon atoms form chains and/or non-aromatic rings

Naming and Drawing Aromatic HydrocarbonsNote: the root for ALL aromatic hydrocarbons is benzene

1. Identify the rootThe root is -benzene

-benzene

2. Identify the prefixa. Determine the position number of the

side groups in order to write the prefix. The carbons in a benzene ring are numbered if there is more than one side group

b. Prioritize alkyl groups with six or fewer carbons in alphabetical order. Then continue to number in the direction of the nearest side group

c. Write the prefix as you would for any other hydrocarbon

There are two methyl groups and one ethyl group. Numbering is counterclockwise to give the lowest numbers.

1-ethyl-2,3-dimethyl-3. Name the compound 1-ethyl-2,3-dimethylbenzene

If a benzene ring is present as a side group off an alkyl chain, then it is called a phenyl group

of 20


Example: Name the following compound

(answer: 3-phenylheptane)

Physical Properties of Aromatics:

Benzene is a liquid at room temperature, and is a common solvent for non-polar compounds

Often have very similar MP/BP to aliphatic compounds with the same number of carbons

These compounds often have strong odours

Section 1.2 – Hydrocarbons, Summary

of 20


Section 1.3 – Hydrocarbon Derivatives Organic compounds are classified according to their functional groups Functional gropu: in a molecule, a certain gropu of atoms responsible for chemical

reactions that are characteristic of the moleculeo Responsible for chemical and physical properties of the moleculeso Change the suffix or the prefix of the compound

Hydrocarbon Derivative: a a compound made up of carbon atoms and at least one other atom that is not hydrogen

Functional Group and the Suffix/Prefixes

Organic Compound General Formula For Functional Group

Prefix or Suffix

AlcoholHydroxyl group

-ol

Haloalkane(X=halogen)

Prefix varies with halogenF = fluoro; Cl = chloro; Br = bromo; I = iodo

Aldehyde

(formyl group)

-al

Ketone

(carbonyl group)

-one

Carboxylic Acid

(carboxyl group)

-oic acid

Ester

(carboxyl group)

-oate

Ether(alkoxy group)

-oxy; -yl

Amine

(amine group)

-amine

Amide

(amide group)

-amide

Note: R, R’, and R’’ can represent either a hydrogen or unspecified hydrocarbon chains

of 20


Alcohols An alcohol group consists of a hydroxyl functional group (-OH). Examples: methanol, ethanol, propan-1-ol, propan-2-ol, ethylene glycol (OH-CH2CH2OH)

Types of Alcohols – the type of alcohol is determined by the number of carbons attached to the carbon the hydroxyl group is attached toPrimary Carbon attached to one other

carbon(alcohol group is at the end of the chain)

Butan-1-ol

Secondary Carbon is attached to two carbons(alcohol group is the middle of the chain)

Butan-2-olTertiary Carbon is attached to three

carbons(alcohol is at a branch point)

2-methylbutan-2-ol

Naming and Drawing Alcohols Names are based off the parent alkane (basic hydrocarbon structure), but the suffix is “-

ol” instead of “-ane”, you must number where the alcohol groups is; if multiple OH groups exist, then use greek prefixes as well (“diol”, “triol”…)

Alcohols must be numbered to give the lowest numbers (they take priority over alkyl groups)

Name the following alcohols:

Draw the line and condensed structures of 4-methylpentane-1,2-diol

Properties of Alcohols Hydroxyl groups is very polar, so small alcohols are polar (i.e. methanol and ethanol are

completely miscible in water); solubility decreases as the hydrocarbon chain becomes longer

Boiling points are higher due to stronger intermolecular forces Very toxic and can cause blindness or death

of 20


Haloalkanes Hydrocarbon that contains at least on halogen Artificial and often not found in living system Examples: Tricholormethane (chloroform); chlorofluorocarbons (CFCs) used in

refrigerants Part of the prefix:

o Fluoro; chloro; bromo; iodo

Naming and Drawing Haloalkanes Name the following (make sure to number so that halogens with biggest mass have lowest numbers IF THERE IS AMBIGUITY and that in the prefix, the halogens are alphabetical

Name the following compound:

Draw the line structural formula of 4-bromo-2-chloro-3-fluoro-5-methylhexane

Properties of Haloalkanes Only the smallest haloalkanes are slightly soluble in water; all others are insoluble in

water Boling/Melting points are higher than analogous alkanes Really toxic

Aldehydes Contain a carbonyl functional (C=O) group at the end of a chain; carbonyl group contain

a carbon double bonded to an oxygen, but the when it is at the end of a chain it is called a formyl group (shorthand: CHO); analogous to primary alcohols

Example: formaldehyde Given the suffix –al; aldehydes must be on carbon 1

Naming and Drawing AldehydesName the following aldehydes

of 20


Draw the line and condensed structures of 5-ethyl-4-methyl-octanal

Physical Properties Carbon-hydrogen bonds are not polar even though C-O bonds are, therefore there are no

hydrogen bonds to each other, although they can H-bond with water Boiling points are lower than analogous alcohols, but larger than analogous

hydrocarbons Small ones are soluble in water Pungent odour

Ketones Contain a carbonyl group in the middle of a chain; analogous to secondary alcohols Examples: propanone (acetone, nail polish remover, simplest ketone); strong odours Ketoacidosis Suffix = -one; longest chain must contain ketone group Must number where the ketone is if there are more than 4 carbons

Naming and Drawing KetonesName the following ketones

Draw the structure of 5,5-dimethylheptan-3-one

Properties of Ketones No hydrogens, therefore no hydrogen bonds; similar boiling points to aldehydes 15 or more carbons = waxy solid at room temperature

Carboxylic Acids Combination of alcohol and carbonyl group = carboxyl group; -COOH Carboxylic acids contain carboxyl groups Example: ethanoic acid (acetic acid, vinegar), citric acid (3-carboxy-3-

hydroxypentanedioic acid), tartaric acid Weak acids Carboxyl groups take up three bonds for carbon, so they must be on the end of a chain,

parent chain must include COOH group, always on carbon 1

of 20


Naming and Drawing Carboxylic AcidsName the following carboxylic acids

Properties of Carboxylic Acids The C=O and –OH groups are both very polar, which make these the most polar of the

functional groups. Can hydrogen bond with water and with one another High boiling and melting points

o Alkane < aldehyde ketone < alcohol < carboxylic acid Short-chain are liquid at room temp; longer chains are waxy solids 1-4 C = completely miscible in water Solubility decreases with increased carbon length Weak acids, therefore turn litmus paper red; conduct electricity in water

Esters Occur when a carboxylic acid and an alcohol combine in a reaction called a condensation

reaction (similar to a synthesis reaction) General formula: -RCOOR’ (R represents any hydrocarbon chain Esters smell surprisingly pleasant

Naming and Drawing Esters The first part of the name comes from the name of the ‘alcohol’ side, the second part

comes from the ‘carboxylic acid’ side

Draw the line structure of butyl propanoate

Properties of Esters Somewhat polar, but have no OH group to make hydrogen bonds with; lower MP/BP

than corresponding alcohols and carboxylic acids Smaller esters are liquid, waxy solids for larger ones Volatile compounds (which cause them to generate their aromas)

of 20


Ethers Hydrocarbon derivative with an -O- in the middle of the carbon chain, the general

formula is –ROR’-, where the R and R’ are any alkyl groupo R is the longest hydrocarbon chaino -OR’ is the side group

The group is called an alkoxy group Examples: ether (diethyl ether); methyl tertiary butyl ether (MTBE, a gasoline additive)

and many aerosols, solvent, and plasticisers

Naming and Drawing Ethers

Draw the condensed structural formula of 2-methoxy-4-methylpentane

Properties of Ethers The ether gropu is slightly polar (because it forms a V so the dipoles do not cancel out) Not at polar as others hydrocarbon derivatives Ethers with 2 or 3 carbons are a gas, but otherwise they are waxy solids Can form H-bonds with water. Therefore small ethers are soluble in water

Amines Contain single bonded N atoms bonded to at least one carbon

o Primary amine = bonded to 1 Co Secondary amine = bonded to 2 Co Tertiary atoms = bonded to 3 C

Examples: adrenaline, the DNA bases (adenine, cytosine, thymine, guanine) and many other biologically significant molecules

Based off the compound ammonia Smell very bad You must indicate when a carbon chain is attached to a nitrogen for secondary and

tertiary amines Use the longest hydrocarbon chain as a parent chain

Naming and Drawing Amines

Draw the structure of N-ethylpentan-3-amine

of 20


Properties of Amines Primary and secondary amines are very polar and can H-bond; but tertiary amines have

no N-H bonds so no H-bonds Primary and secondary amines have relatively higher boiling points compared to similar

ethers and alkanes Small amines are soluble in water

Amides Contain the functional group –C=ON-

o Carbon double bonded to an oxygen and single bonded to a nitrogen The nitrogen can be attached to either one or two more alkyl chains

o Primary = one C chain, nothing attached to No Secondary = one C chain, one C chain attached to No Tertiary = one C chain, two C chains attached to N

Examples: acetaminophen, penicillin, form the backbone of all proteins, dimethylformamide, nylon and polyacrylamide

General:

Naming and Drawing Amides

Draw the line structure of N,N-diethyl-2-ethylpentanamide

Properties of Amides Primary and secondary amides can form H-bonds Therefore, higher than analogous compounds Otherwise, similar properties to amines and other hydrocarbon derivatives

NOTE about polarity:

amide > acid > alcohol > ketone aldehyde > amine > ester > ether > alkane

of 20

unit 1 – organic chemistry - msdunlop -...

Documents