Chemistry notes
Dr. Ezihie
MBCHBORGANICCHEMISTRY.ppt1) Organic Chem …………. Stanley H. Pine
2) Organic chem …………..Morrison & Boyd.
3) Organic chemistry ………….David Baker &
Robert Engel
5) Principles of Physical
and Organic Biological Chem ……………John R. Holum
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Molecular formula
C2H6
C3H8
C4H10
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NEWMAN PROJECTION FORMULA
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Potential energy diagram for rotation about the carbon–carbon bond in ethane. Two of the hydrogens are shown in red and four in green so as to indicate more clearly the bond rotation.
The gauche and anti conformations
of butane shown as ball-and-spoke models (left) and as Newman projections (right). The gauche conformation is less stable than the
anti because of the van der Waals strain between the methyl groups.
Emil Fischer projection
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Another common representation of organic molecules especially in carbohydrate chemistry is the HAWORTH PROJECTION FORMULA
Glucose
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WEDGE FORMULA
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WHICH FORMULA TO USE?
In biochemistry a combination of several molecular representation is used sometimes for brevity and sometimes to clarify some aspects of reaction mechanism
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STRUCTURAL ISOMERISM IN ALKANES
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| Molecular formula | No. structural isomers |
| CH4 | 1 |
| C2H6 | 1 |
| C3H8 | 1 |
| C4H10 | 2 |
| C5H12 | 3 |
| C6H14 | 5 |
| C7H16 | 9 |
| C8H18 | 18 |
| C9H20 | 35 |
| C10H22 | 75 |
| C15H32 | 4,347 |
CLASSIFICATION OF HYDROCARBONS
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ALKANES
Alkanes are aliphatic of alicyclic hydrocarbons in which every carbon is bonded to four other atoms through the use of sp3 molecular orbitals. Alkanes are also known as paraffin's of saturated hydrocarbons. Saturated hydrocarbons have the general formula CnH2n+2
The term cycloalkane is used to describe saturated and cyclic hydrocarbons which have the empirical formula CnH2n
Alkanes are relatively stable to chemical reactions though at higher temperatures in the presence of catalyst alkanes can fragment to smaller products
Because of their inertness alkanes are used as solvents.
Their physical state depends on their molecular weight
Alkanes are:
Non polar and hence immiscible with water
Less dense than water (density <1.0g/ml)
Alkanes which differ by one methylene –CH2- are said to form a homologous series. The boiling point of hydrocarbons in a homologous series increase regularly as the chain of the hydrocarbon increases
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Classes of carbon atoms
It is extremely useful to classify each carbon atom of an alkane with respect to the number of other carbon atoms attached to it.
In a similar manner each hydrogen atoms is classified depending on the carbon atom to which it attached.
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NOMECLATURE OF ALKANES
The naming of alkanes utilizes trivial historic names for simple low molecular weight alkanes., however for large molecule, Latin or Greek prefixes are used. The number of the carbon atoms are counted and the name of the alkane is derived from that number
I.e.:
IUPAC NOMECLACLATURE
The fundamental criteria of naming a chemical compound is by the IUPAC system.
- In this system the longest continuous sequence of the carbon atoms in the molecule is the basis for the parent name of the aliphatic hydrocarbon. This parent name is assigned according to Greek terminology.
- A second prefix is employed to designate the structure of the side chain groups attached to the parent chain
- The position of the side chain is indicated by Arabic numeral and the numeral is chosen in such a way that the lowest numeral is used.
- The order of the side chain naming is given alphabetically.
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REACTION OF ALKANES
Alkanes are relatively unreactive to many reagents, but when heated in excess oxygen they liberate carbon dioxide and water.
CnH2n+2 + Xs O2 nCO2 + n+1H2O +DH (Heat)
- Alkanes undergo pyrolysis when heated at 400-600oC with or without a catalyst to give hydrogen and smaller fragments of alkanes and alkenes
Alkane heat H2 + Alkane + alkenes
- Alkanes undergo halogenation when heated at 250-400oC in the presence of halides to form alky halides
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Mechanism of halogenation
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ALKENES AND ALKYNES
Alkenes are unsaturated hydrocarbons they contain less hydrogen than the corresponding alkanes.
The simplest member of the alkene family is ethylene
In ethylene molecule the double bond is made up of a s bond and the other is made up of a p bond. In the formation of ethylene , carbon is sp2 hybridized and hence forms s bonds which are oriented in space at 120o and the molecule id flat
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The bonding (p) and antibonding (p*) molecular orbitals of ethylene. The wave function changes sign (red to blue) on passing through a nodal surface. The plane of the molecule is a nodal surface in both orbitals; the antibonding orbital has an additional nodal surface perpendicular to the plane of the molecule.
H
H
H
H
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The bond length is significant shorter and stronger the the corresponding CH3CH3
| ETHANE | ETHYLENE | ACETYLENE | |
| C-C/Ao | 1.53 | 1.34 | 1.21 |
| C-H/Ao | 1.112 | 1.103 | 1.079 |
| ENERGY Kj/Mole | 347 | 610 | 836 |
The double bonds in an alkene may cumulated as in Allene( Propadiene)
Or the double bond may be conjugated as in 1,3- Butadiene
In naming alkenes the position of the double bond is indicated by the use of Arabic numeral.
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Cycloalkenes and their derivatives are named by adapting cycloalkane terminology to the principles of alkene nomenclature.
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A double bond is said to be more substituted if it has substituents other than hydrogen surrounding it.
Substituted alkenes exist as Geometric Isomers.
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Cis–trans stereoisomerism in alkenes is not possible when one of the doubly bonded carbons bears two identical substituents. Thus, neither 1-butene nor 2-methylpropene can have stereoisomers.
The terms “cis” and “trans” are ambiguous, however, when it is not obvious which substituent on one carbon is “similar” or “analogous” to a reference substituent on the other.
Fortunately, a completely unambiguous system for specifying double bond stereochemistry has been developed based on an atomic number criterion for ranking substituents on the doubly bonded carbons. When atoms of higher atomic number are on the same side of the double bond, we say that the double bond has the Z configuration, where Z stands for the German word zusammen, meaning “together.” When atoms of higher atomic number are on opposite sides of the double bond, we say that the configuration is E. The symbol E stands for the German word entgegen, meaning “opposite.”
Example
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The cis/trans Isomerism also exist in cycloalkane. Consider the Haworth projection of cyclopentane.
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ALKYNES
Alkynes are the most unsaturated hydrocarbons. In alkynes the molecule has triple bond and the involved carbon has sp hybridization the bond has one sigma bond and two p bonds which are oriented at right angles to each other. The simplest member of the series is Acetylene C2H2
The molecule is linear and the bonds are shorter than in alkanes. The triple bond confers to the molecule some degree of acidity and one of the hydrogen can be easily donated
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REACTION OF ALKENES
1.Alkenes are readily hydrogenated under pressure in the presence of a catalyst (Pt,Pd) or with nickel
H
CH2=CH2 CH3CH3
Some chemical compounds can reduce only the olefinic bond. E.g. Diimide
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CH2=CH2 + H2O CH3CH20H
250-300oC, D
ADDITION OF HYDROGEN HALIDE TO ALKENES
Anti Markonikov addition of hydrogen halides
Sulfuric acid adds to alkenes to produce sulphates
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CHEMICAL REACTION OF ALKYNES
Electrophilic addition In alkynes
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ALCOHOLS AND ALKYLHALIDES
Alcohol and alkyl halides are versatile organic compounds from which nearly every other organic compound can be synthesized.
Alcohol are of great importance in biology and different types of alcohols are found in both animals and plants.
An alcohol may be considered as a derivative of water with an H being replaced by an alkyl functional group.
HOH ROH
R May be unsaturated or saturated alkyl functional group or another alcohol.
Important alcohols found in living organism include cholesterol glucose and many sugars
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Phenol
Note
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ALKYHALIDES
Alkyl halides are compounds in which one or more halogen atoms are bonded to carbon atoms. These compounds are generally covalent. Alkyl halides are not abundant in nature and many are synthesized in industrial chemical plants and used as solvents , drugs, insecticides etc.
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Most of the alkyl halides are water insoluble with boiling points comparable to the hydrocarbon of similar molecular weight from which they have been derived.
The halogen atom contributes a lot to the molecular weight and the density of the compound for example CH3I is a liquid. Except for the monochlorohyrocarbons most of the alky halides are denser than water
IUPAC NOMENCLATURE OF ALKYL HALIDES
The IUPAC rules permit alkyl halides to be named in two different ways, called functional class nomenclature and substitutive nomenclature. In functional class nomenclature the alkyl group and the halide ( fluoride, chloride, bromide, or iodide) are designated as separate words. The alkyl group is named on the basis of its longest continuous chain beginning at the carbon to which the halogen is attached.
Substitutive nomenclature of alkyl halides treats the halogen as a halo- ( fluoro-, chloro-, bromo-, or iodo-) substituent on an alkane chain. The carbon chain is numbered in the direction that gives the substituted carbon the lower locant.
When the carbon chain bears both a halogen and an alkyl substituent, the two substituents are considered of equal rank, and the chain is numbered so as to give the lower number to the substituent nearer the end of the chain.
IUPAC NOMENCLATURE OF ALCOHOLS
Functional class names of alcohols are derived by naming the alkyl group that bears the hydroxyl substituent (-OH) and then adding alcohol as a separate word. The chain is always numbered beginning at the carbon to which the hydroxyl group is attached. Substitutive names of alcohols are developed by identifying the longest continuous chain that bears the hydroxyl group and replacing the -e ending of the corresponding alkane by the suffix ol. The position of the hydroxyl group is indicated by number, choosing the sequence that assigns the lower locant to the carbon that bears the hydroxyl group.
Hydroxyl groups take precedence over (“outrank”) alkyl groups and halogen substituents in determining the direction in which a carbon chain is numbered.
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CLASSES OF ALCOHOLS AND ALKYL HALIDES
Alcohols and alkyl halides are classified as primary, secondary, or tertiary according to the classification of the carbon that bears the functional group (Section 2.10). Thus, primary alcohols and primary alkyl halides are compounds of the type RCH2G (where G
is the functional group), secondary alcohols and secondary alkyl halides are compounds of the type R2CHG, and tertiary alcohols and tertiary alkyl halides are compounds of the type R3CG.
BONDING IN ALCOHOLS
Orbital hybridization model of bonding in methanol. (a) The orbitals used in bonding are the 1s orbitals of hydrogen and sp3- hybridized orbitals of carbon and oxygen. (b) The bond angles at carbon and oxygen are close to tetrahedral, and the carbon–oxygen bond is about 10 pm shorter than a carbon–carbon single bond.
Carbon–oxygen and carbon–halogen bonds are polar covalent bonds, and carbon bears a partial positive charge in alcohols (d+C-Od-) and in alkyl halides (d+C-Xd-). The presence of these polar bonds makes alcohols and alkyl halides polar molecules. The dipole moments of methanol and chloromethane are very similar to each other and to water.
Electrostatic potential maps of methanol and chloromethane. The most positively charged regions are blue, the most negatively charged ones red. The electrostatic potential is most negative near oxygen in methanol and near chlorine in chloromethane.
The most striking aspect of the data, however, is the much higher boiling point of ethanol compared with both propane and fluoroethane. This suggests that the attractive forces in ethanol must be unusually strong. Figure 4.4 shows that this force results from a dipole–dipole attraction between the positively polarized proton of the OH group of one ethanol molecule and the negatively polarized oxygen of another. The term hydrogen bonding is used to describe dipole–dipole attractive forces of this type. Hydrogen bonding occurs only when hydrogen is attached to OH or NH
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Thiols
- Many thiols have disagreeable odors
- Used to detect gas leak
- Found in onions, oysters, garlic and oysters
Onions CH3CH2CH2-SH 1-propanethiol
Garlic CH2= CHCH2-SH 2-propene-1-thiol
Skunk spray
CH3 trans-2-butene-1-thiol
CH = CH
CH2SH
Ethers
- Contain an -O- between two carbon groups
- Simple ethers named from -yl names of the attached groups and adding ether.
CH3-O-CH3 dimethyl ether
CH3-O-CH2CH3 ethyl methyl ether
CHEMICAL REACTION OF ALKYL HALIDES
Alkyl halides are among the most versatile organic compounds known, through their use a wide variety of organic compounds can be synthesized. The halide ion being a weak base is easier to displace from the carbon skeleton in a reaction known as Nucleophilic substitution. The ease of displacement is:
I > Br > Cl > OH2+ > F
Nucleophilic substitution
In nucleophilic substitution a nucleophile which has two lone pairs of electrons approaches a molecule and displace another nucleophile viz
N: + R:X X: + R:N
:
:
:
:
:
- Alkyl halides are hydrolysed to alcohol by boiling aqueous alkali
RX + KOH ROH + KX
The mechanism involved is either SN1 or SN2
2) Alkyl halides are reduced by dissolving metals to alkanes
RX RH + HX Zn/Acid
3) Alkyl halides undergo rearrangement when heated at 300oC
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4) When alkyl halides are heated with ethanolic ammonia under pressure a mixture of amine are produced
RX + NH3 HX + RNH2
RNH2 + RX HX + R2NH
R2NH + RX HX + R3N
R3N + RX HX + R4N+
- Alkyl halides produce alkyl cyanides when heated with ethanol potassium cyanide
RX + KCN RCN + KX
- Alkyl halides form esters when heated with silver salts of carboxylic acids
The acid may be organic inorganic
7) Formation of ethers: heating of an alkyl halide with sodium alkoxide leads to the formation of ethers
8) Alkyl halides reacts with ethanolic sodium hydrogen sulfide to produce thioalcohol and thioethers
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9) Alkyl halides form alkenes when heated with ethanolic potassium hydroxide
The special reaction which takes place in this transformation is known as Elimination reaction
All elimination reaction introduce double bonds into a hydrocarbon– Elimination depends on the existence of a good leaving group attached to the molecule and basically this leaving group is a nucleophile. Elimination can take place on the carbon the so called 1,1-elimination or on the vicinal carbons : the 1,2-elimination. We will concentrate on the 1,2- elimination mechanism of chemical reaction.
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In the 1,2-elimination mechanism a base usually an alkoxide abstracts a proton b to the leaving group.
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In E1-elimination mechanism, a slow heterolysis reaction takes place to produce a carbocation this is followed by a fast abstraction of the hydrogen by the base
Slow
Fast
:Br
REACTION OF ALCOHOLS
1) Alcohols reacts with inorganic acid halides to produce haloalkanes or esters,the product depends on the specific reaction condition used. This reactions proceed in a sequence of Lewis acid/Lewis base reaction steps.
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MECHANISTIC STEPS
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2) Alcohols can act as Bronsted acids as well as Lewis bases, most alcohols have a pKa in the region of 15-19.
Sodium metal and other electropositive metals dissolve in alcohol to give the corresponding alkoxide
2Na + CH3CH2OH H2 + CH3CH2ONa
Alcohol react with strong acids to produce a protonated alcohol called oxonium ion.
CH3CH2OH + H2SO4 HSO4- + CH3CH2OH2+
Ethoxide
OXIDATION OF ALCOHOLS
Oxidation can be defined as loss of electrons or loss of hydrogens in a molecule while reduction can be considered a reverse of this statement
A hydrocarbon is said to be oxidized if it is attached to a more electronegative atom than the carbon carrying the substituents.
The following rules are important in assigning oxidation states of an organic molecule:
- The oxidation state of a carbon changes by -1 for each bond to a less—electronegative atom such as hydrogen.
- The oxidation state of carbon changes by +1 for each bond to a more electronegative atom such as a heteroatom.
- Double and triple bond count two and three times respectively
- Bonds between carbon atoms are not counted in the determination of oxidation State.
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ALDEHYDE AND KETONES
Aldehydes are compounds with the general structural formula RCHO, While ketones have the general molecular formula RR’CO the group R and R’ may be aliphatic alicyclic or aromatic
The distinguishing feature of both Aldehyde and ketone is the presence of the carbonyl functional group. This group determines the chemistry of these compounds. Bonding in the carbonyl group is by both s and p bonds. The functional group is flat and has some considerable polarity.
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Some naturally occurring aldehydes and ketones.
STRUCTURE AND BONDING: THE CARBONYL GROUP
Two notable aspects of the carbonyl group are its geometry and its polarity. The carbonyl group and the atoms directly attached to it lie in the same plane. Formaldehyde, for example, is planar. The bond angles involving the carbonyl group of aldehydes and ketones are close to 120°. At 122 pm, the carbon-oxygen double bond distance in aldehydes and ketones is significantly
shorter than the typical carbon–oxygen single bond distance of 141 pm in alcohols and ethers.
Differences in the electron distribution of (a) ethylene and (b) formaldehyde. The region of highest electrostatic potential (red ) in ethylene lies above and below the plane of the atoms and is associated with the electrons. The region close to oxygen is the site of highest electrostatic potential in formaldehyde.
NOMENCLATURE
The names of aldehydes and ketones are derived from the common names of the corresponding carboxylic acids by replacing –ic with aldehyde. The carbon atoms are numbered by giving them the Greek letters a, b, g, d, e etc.
The longest chain carrying the –CHO group is considered the parent structure. In the IUPAC system the numbering starts from carbon bearing the CHO group and the name of the aldehyde is given by replacing –e for the corresponding alkane by –al.
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For ketones the carbonyl group is in the middle of the chain. The simplest ketone is acetone. A ketone in which the carbonyl group is attached to a Benzene ring is called a Phenone. According to the IUPAC system of nomenclature the longest chain carrying the carbonyl group is taken to be the parent structure and is named by replacing the –e of the alkane by –one. The position of various groups are indicated by Arabic numbers with the carbonyl carbon given the carbon number one.
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PHYSICAL PROPERTIES OF ALDEHYDES AND KETONES
The Polar carbonyl makes aldehydes and ketones polar compounds and hence they have higher boiling point than alkanes of comparable molecular weight. However compared to alcohols and carboxylic acids aldehydes and ketones have lower boiling points because of the absence of hydrogen bonds between aldehydes and ketones molecules.
The lower aldehydes and ketones are soluble in water because of hydrogen bond between solute and water molecules. Formaldehyde is a gas (bp -21oC) and is handled as a solution in water as formalin
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*****(DONT BOTHER TO READ)**** REACTIONS THAT YIELD ALDEHYDES AND KETONES
*****(DONT BOTHER TO READ)**** REACTIONS THAT YIELD ALDEHYDES AND KETONES
CHEMICAL REACTION OF ALDEHYDE AND KETONES
The most important chemical property of the carbonyl group is its tendency to undergo nucleophilic addition reactions of the type represented in the general equation shown below. A negatively polarized atom or group attacks the positively polarized carbon of the carbonyl group in the rate-determining step of these reactions. Grignard reagents, organolithium reagents, lithium aluminum hydride, and sodium borohydride, for example, all react with carbonyl compounds by nucleophilic addition.
Many reagents which reacts with carbonyl functional groups are actually nucleophile electrophile pair Nu:E The nucleophile can react with the carbonyl carbon while the electrophile can react with the carbonyl oxygen
AdN reaction
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Many addition reactions are catalyzed by acids. The conjugate acid produced din the reaction is a more reactive electrophile than the neutral carbonyl an hence many nucleophile attack this carbon.
1) Cyanides reacts with aldehydes to form cyanohydrins. Cyanohydrins are common in nature . They are found in cherries, peaches, plums and apricots
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2) Haloacid addition produce halohydrins.
3) Alcohols add to aldehydes to produce acetals. Acetal formation is a reversible reaction and the equilibrium constant is less than 1 however formation of cyclic acetals has a very high equilibrium constant making these acetals stable. Hemiacetal and hemiketal formation play important roles in carbohydrate chemistry.
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4) Addition of Hydrides (H:-)
Hydrides are nucleophiles they can only be generated from special reagents notable NaBH4 and LiAlH4. These reagents are used in organic chemistry as powerful reducing agents.
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5) Primary amines react with aldehydes and ketones to produce compounds possessing carbon nitrogen double bond known as Imines or Schiff bases
Imines are not very stable though they are important intermediates in some reactions.
Formation of imines is catalyzed by acids