organic chemistry i dr. pahlavan chapter 3 organic

Organic Chemistry I Dr. Pahlavan

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CHAPTER 3 – Organic compounds;

Alkanes and Their Stereochemistry

A . Functional Groups

Functional groups are structural units within organic compounds that are defined by specific bonding

arrangements between specific atoms. The structure of capsaicin, the compound responsible for the heat in

peppers, incorporates several functional groups, labeled in the figure below and explained throughout this

section.

I. Functional groups are group of atoms within a molecule that have a characteristic chemical behavior.

II. The chemistry of every organic molecule is determined by its functional groups.

III. Functional groups described in three categories;

A. Functional groups with carbon – carbon double and triple bonds.

B. Functional groups which carbon forms a single bond with an electronegative atom, (C – X).

C. Functional groups with a carbon – oxygen double bond (C = O).

Alkanes, Alkenes, and Alkynes

Alkanes, alkenes, and alkynes are all classified as hydrocarbons, because they are composed solely of carbon

and hydrogen atoms. Alkanes are said to be saturated hydrocarbons, because the carbons are bonded to the

maximum possible number of hydrogens - in other words, they are saturated with hydrogen atoms. The double

and triple-bonded carbons in alkenes and alkynes have fewer hydrogen atoms bonded to them - they are thus

referred to as unsaturated hydrocarbons.

Alkenes (sometimes called olefins) have carbon-carbon double bonds, and alkynes have carbon-carbon triple

bonds. Ethene, the simplest alkene example, is a gas that serves as a cellular signal in fruits to stimulate

ripening. (If you want bananas to ripen quickly, put them in a paper bag along with an apple - the apple emits

ethene gas, setting off the ripening process in the bananas).


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Ethyne, commonly called acetylene, is used as a fuel in welding blow torches.

Alkenes have trigonal planar electron geometry while alkynes have linear geometry. Furthermore, many alkenes

can take two geometric forms: cis or trans. The cis and trans forms of a given alkene are different molecules

with different physical properties there is a very high energy barrier to rotation about a double bond.

In the example below, the difference between cis and trans alkenes is readily apparent and we will learn naming

in next chapters.

Aromatics The aromatic group is exemplified by benzene (which used to be a commonly used solvent on the organic lab,

but which was shown to be carcinogenic), and naphthalene, a compound with a distinctive 'mothball' smell.

Aromatic groups are planar (flat) ring structures, and are widespread in nature. We will learn more about the

structure and reactions of aromatic groups in future chapters.

Haloalkanes (alkyl halides) When the carbon of an alkane is bonded to one or more halogens, the group is referred to as a alkyl

halide or haloalkane. Chloroform, CHCl3, is a useful solvent in the laboratory, and was one of the earlier

anesthetic drugs used in surgery. Dichlorodifluoromethane, CCl2F2 (Freon -12) was used as a refrigerant and

in aerosol sprays until the late twentieth century, but its use was discontinued after it was found to have harmful

effects on the ozone layer. Bromoethane, C2H5Br, is a simple alkyl halide often used in organic synthesis.


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Alcohols and Thiols

In the alcohol functional group, a carbon is single-bonded to an OH group (the OH group, by itself, is referred

to as a hydroxyl). Except for methanol, all alcohols can be classified as primary, secondary, or tertiary. In

a primary alcohol, the carbon bonded to the OH group is also bonded to only one other carbon. In a secondary

alcohol and tertiary alcohol, the carbon is bonded to two or three other carbons, respectively. When the

hydroxyl group is directly attached to an aromatic ring, the resulting group is called a phenol. The sulfur analog

of an alcohol is called a thiol (from the Greek thio, for sulfur).Alcohols, phenols, and thiols.

The deprotonated forms of alcohols, phenols, and thiols are called alkoxides, phenolates, and thiolates,

respectively. A protonated alcohol is an oxonium ion.

In an ether functional group, a central oxygen is bonded to two carbons. Below is the structure of diethyl ether,

a common laboratory solvent and also one of the first compounds to be used as an anesthetic during operations.

The sulfur analog of an ether is called a thioether or sulfide.

Ethers and sulfides

Phosphate and its derivative functional groups are ubiquitous in biomolecules. Phosphate linked to a single

organic group is called a phosphate ester; when it has two links to organic groups it is called a phosphate

diester. A linkage between two phosphates creates a phosphate anhydride.

Aldehydes, ketones, and imines

There are a number of functional groups that contain a carbon-oxygen double bond, which is commonly

referred to as a carbonyl. Ketones and aldehydes are two closely related carbonyl-based functional groups that

react in very similar ways. In a ketone, the carbon atom of a carbonyl is bonded to two other carbons.


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In an aldehyde, the carbonyl carbon is bonded on one side to a hydrogen, and on the other side to a carbon. The

exception to this definition is formaldehyde, in which the carbonyl carbon has bonds to two hydrogens.A group

with a carbon-nitrogen double bond is called an imine, or sometimes a Schiff base (in this book we will use the

term 'imine'). The chemistry of aldehydes, ketones, and imines will be covered in later chapters.

Carboxylic acid derivatives

When a carbonyl carbon is bonded on one side to a carbon (or hydrogen) and on the other side to an oxygen,

nitrogen, or sulfur, the functional group is considered to be one of the ‘carboxylic acid derivatives’, a

designation that describes a set of related functional groups. The eponymous member of this family is

the carboxylic acid functional group, in which the carbonyl is bonded to a hydroxyl group. The conjugate base

of a carboxylic acid is a carboxylate. Other derivatives are carboxylic esters (usually just

called 'esters'), thioesters, amides, acyl phosphates, acid chlorides, and acid anhydrides. With the exception

of acid chlorides and acid anhydrides, the carboxylic acid derivatives are very common in biological molecules

and/or metabolic pathways, and their structure and reactivity will be discussed in detail in later chapters.

A single compound often contains several functional groups, particularly in biological organic chemistry. The

six-carbon sugar molecules glucose and fructose, for example, contain aldehyde and ketone groups,

respectively, and both contain five alcohol groups (a compound with several alcohol groups is often referred to

as a ‘polyol’).


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The hormone testosterone, the amino acid phenylalanine, and the glycolysis metabolite dihydroxyacetone

phosphate all contain multiple functional groups, as labeled below.

Hormone testosterone has only three functional groups.

Exercise - Identify the functional groups (other than alkanes) in the following organic compounds. State

whether alcohols and amines are primary, secondary, or tertiary.

Try this.


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Amines

Amines are characterized by nitrogen atoms with single bonds to hydrogen and carbon. Just as there are

primary, secondary, and tertiary alcohols, there are primary, secondary, and tertiary amines. Ammonia is a

special case with no carbon atoms.

One of the most important properties of amines is that they are basic, and are readily protonated to

form ammonium cations. In the case where a nitrogen has four bonds to carbon (which is somewhat unusual in

biomolecules), it is called a quaternary ammonium ion.

Note: Do not be confused by how the terms 'primary', 'secondary', and 'tertiary' are applied to alcohols and

amines - the definitions are different. In alcohols, what matters is how many other carbons the alcohol carbon is

bonded to, while in amines, what matters is how many carbons the nitrogen is bonded to.

Nitriles

Finally, a nitrile group is characterized by a carbon triple-bonded to a nitrogen.


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Common Organic Functional Groups

B. Alkanes and Alkanes Isomers

Isomerism are in Branched Alkanes. The smallest branched alkane is isobutene.Two different molecules

which have the same molecular formula are isomers. Isomers which differ in the connectivity of bonds are

constitutional isomers, or structural isomers. Isobutane is a constitutional isomer of n-butane.

Alkanes of the same formula cab have different arrangement of atoms. Such different arrangements are known

as

Isomers. Two isomers of C4H10 are shown below.


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Types of Formula

Butane

1. Molecular formula C4H10 2. Electron Dot Structural Formula

3. Open Structural FormulA 4. Condensed Structural Formula

5. Line Bond Structural Formula (Skeletal Formula)

Example – Isomers.

1) Pentane, C5H12 (has three isomers)

2) Hexane, C6H14 (has five isomers)


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C. Alkyl Groups

In organic chemistry, an alkyl substituent is an alkane missing one hydrogen. The term alkyl is intentionally

unspecific to include many possible substitutions. An acyclic alkyl has the general formula of CnH2n+1.

The IUPAC system requires first that we have names for simple unbranched chains, as noted above, and

second that we have names for simple alkyl groups that may be attached to the chains. Examples of some

common alkyl groups are given in the following table. Note that the "ane" suffix is replaced by "yl" in naming

groups. The symbol R is used to designate a generic (unspecified) alkyl group.

Alkanes can be described by the general formula CnH2n+2. An alkyl group is formed by removing one hydrogen

from the alkane chain and is described by the formula CnH2n+1. The removal of this hydrogen results in a stem

change from -ane to -yl. Take a look at the following examples.

Common Alkyl Groups


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IUPAC Rules for Alkane Nomenclature

Here is a simple list of rules to follow. Some examples are given at the end of the list.

1. Identify the longest carbon chain. This chain is called the parent chain.

2. Identify all of the substituents (branches attached to the parent chain)

3. Number the carbons of the parent chain from the end that gives the substituents the lowest

numbers.

4. If the same substituent occurs more than once, the location of each point on which the substituent

occurs is given. In addition, the number of times the substituent group occurs is indicated by a

prefix (di, tri, tetra, etc.).

5. If there are two or more different substituents they are listed in alphabetical order using the base

name (ignore the prefixes). The only prefix which is used when putting the substituents in

alphabetical order is iso as in isopropyl or isobutyl. The prefixes sec- and tert- are not used in

determining alphabetical order except when compared with each other.

6. If chains of equal length are competing for selection as the parent chain, then the choice goes in

series to:

a) the chain which has the greatest number of side chains.

b) the chain whose substituents have the lowest- numbers.

c) the chain having the greatest number of carbon atoms in the smaller side chain.

d)the chain having the least branched side chains.

7. A cyclic (ring) hydrocarbon is designated by the prefix cyclo- which appears directly in front of

the base name.

In summary, the name of the compound is written out with the substituents in alphabetical order followed by the

base name (derived from the number of carbons in the parent chain). Commas are used between numbers and

dashes are used between letters and numbers. There are no spaces in the name.

Example s


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More Examples

Writing structures

Try these;

a. Give name; b. Give Structure : 6- ethyl -2-methyl -5-isopropylnonane


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V. Properties of Alkanes

Alkanes are organic compounds that consist entirely of single-bonded carbon and hydrogen atoms and lack

any other functional groups. Alkanes have the general formula CnH2n+2 and can be subdivided into the

following three groups: the linear straight-chain alkanes, branched alkanes, and cycloalkanes. Alkanes are

also saturated hydrocarbons. Alkanes are the simplest and least reactive hydrocarbon species containing only

carbons and hydrogens.

The number of carbon atoms present in an alkane has no limit. Greater numbers of atoms in the molecules will

lead to stronger intermolecular attractions (dispersion forces) and correspondingly different physical

properties of the molecules. Properties such as melting point and boiling point usually change smoothly and

predictably as the number of carbon and hydrogen atoms in the molecules change.

Physical Properties

Non-polar and colorless compounds

Insoluble in water

Less dense than water and so will float on top of the water

Dissolve in organic solvents and in each other

Low melting point and boiling point

The melting and boiling points of the shorter chain alkanes is low, but the melting and boiling of

increase as the number of carbon atoms in the carbon chain increases.

Chemical Properties

Alkanes are relatively unreactive.

Alkanes do not react with strong acids, bases, oxidizing agents (oxidants) or reducing agents

(reductants).

Alkanes combust (react rapidly with oxygen) releasing energy, which makes alkanes useful as

fuels.(see combustion of hydrocarbons and heat of combustion)

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Combustion reactions occur when oxygen reacts with another substance and gives off heat and light.

Burning coal, methane gas, and sparklers are all common examples of combustion reactions.

Examples:

a) Methane, CH4(g) + 2O2(g) CO2 (g) + 2H2O(g)

b) Sugar, C6H12O6 + 6O2 6CO2 + 6 H2O

c) Propane, C3H8 + 5O2 3CO2 + 4H2O

d) Butane, 2 C4H10 + 13O2 8 CO2 + 10 H2O

e)

f)


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Halogenations substitutions

Alkanes will react with halogens such chlorine gas and bromine water in the presence of

ultraviolet light.

Types carbons;

Types Hydrogens

Substitution increases from 30

> 20 > 1

0

Examples;

a)

b)

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c)

Identify the number of primary, secondary, and tertiary carbon and hydrogen in the

following compounds.

I. Conformations of alkanes and ehtane

Conformation of Alkanes deals with the isomers of alkanes that form due to slight changes in their structure, especially in their carbon-carbon bonds. The conformations start with ethane and occur in all alkanes higher than ethane.

Conformational isomerism involves rotation about sigma bonds, and does not involve any differences in the

connectivity or geometry of bonding. Two or more structures that are categorized as conformational isomers,

or conformers, are really just two of the exact same molecule that differ only in terms of the angle about one or

more sigma bonds.

Ethane Conformations

Although there are seven sigma bonds in the ethane molecule, rotation about the six carbon-hydrogen bonds

does not result in any change in the shape of the molecule because the hydrogen atoms are essentially spherical.

Rotation about the carbon-carbon bond, however, results in many different possible molecular conformations.


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In order to better visualize these different conformations, it is convenient to use a drawing convention called

the Newman projection. In a Newman projection, we look lengthwise down a specific bond of interest – in this

case, the carbon-carbon bond in ethane. We depict the ‘front’ atom as a dot, and the ‘back’ atom as a larger

circle.

The six carbon-hydrogen bonds are shown as solid lines protruding from the two carbons at 120°angles, which

is what the actual tetrahedral geometry looks like when viewed from this perspective and flattened into two

dimensions.

The lowest energy conformation of ethane, shown in the figure above, is called the ‘staggered’

conformation, in which all of the C-H bonds on the front carbon are positioned at dihedral angles of 60°relative

to the C-H bonds on the back carbon. In this conformation, the distance between the bonds (and the electrons in

them) is maximized.

If we now rotate the front CH3 group 60°clockwise, the molecule is in the highest energy ‘eclipsed'

conformation, where the hydrogens on the front carbon are as close as possible to the hydrogens on the back

carbon.

This is the highest energy conformation because of unfavorable interactions between the electrons in the front

and back C-H bonds. The energy of the eclipsed conformation is approximately 3 kcal/mol higher than that of

the staggered conformation.


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Another 60°rotation returns the molecule to a second eclipsed conformation. This process can be continued all

around the 360°circle, with three possible eclipsed conformations and three staggered conformations, in

addition to an infinite number of variations in between.

Dihedral angle, as defined by the highlighted(red) hydrogens in ethane rotating the back carbon through 360o,

clockwise.

The carbon-carbon bond is not completely free to rotate – there is indeed a small, 3 kcal/mol barrier to rotation

that must be overcome for the bond to rotate from one staggered conformation to another. This rotational barrier

is not high enough to prevent constant rotation except at extremely cold temperatures.


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The potential energy associated with the various conformations of ethane varies with the dihedral angle of the

bonds, as shown below.


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Butane Conformations

The hydrocarbon butane has a larger and more complex set of conformations associated with its constitution

than does ethane. Of particular interest and importance are the conformations produced by rotation about the

central carbon-carbon bond (C2 – C3). Among these we shall focus on two staggered conformers (B & D)

and two eclipsed conformers (A & C), shown below in several stereo-representations.

As in the case of ethane, the staggered conformers are more stable than the eclipsed conformers by 2.8 to 4.5

kcal/mol. Since the staggered conformers represent the chief components of a butane sample they have been

given the identifying prefix designations anti for A (most stable, least energy) and gauche for B.

In butane the gauche-conformer is less stable than the anti-conformer by about 0.9 kcal/mol. This is due to a

crowding of the two methyl groups in the gauche structure, and is called steric strain or steric hindrance.

The following diagram illustrates the change in potential energy that occurs with rotation about the C2–C3 bond

in butane.


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Questions - Consider 2-methylbutane, view the molecule along C2-C3 bond and provide a Newman projection

which represent each of the following;

1) lowest energy conformer 2) highest energy conformer 3) gauche conformer

4) eclipsed conformer 5) anti conformer 6) staggered conformer

7) graph the potential energy versus dihedral angle

organic chemistry i dr. pahlavan chapter 3 organic

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