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ORGANIC CHEMISTRY. Naming Saturated Hydrocarbons. The International Union of Pure and Applied Chemistry (IUPAC) names for the first 12 "straight-chain" or "normal" alkanes are:. Alkanes and Cycloalkanes. The simplest saturated hydrocarbons are called alkanes.

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naming saturated hydrocarbons
Naming Saturated Hydrocarbons
  • The International Union of Pure and Applied Chemistry (IUPAC) names for the first 12 "straight-chain" or "normal" alkanes are:
alkanes and cycloalkanes
Alkanes and Cycloalkanes
  • The simplest saturated hydrocarbons are called alkanes.
  • Methane, CH4, is the simplest alkane.
  • The alkanes form a homologous series.
    • Each member of the series differs by a specific number and kind of atoms.
alkanes and cycloalkanes4
Alkanes and Cycloalkanes
  • The alkanes differ from each other by a CH2 or methylene group.
  • All alkanes have this general formula.


  • For example ethane, C2H6 , and propane, C3H8 , are the next two family members.
alkanes and cycloalkanes5
Alkanes and Cycloalkanes
  • Isomers are chemical compounds that have the same molecular formulas but different structures.
  • Two alkanes have the molecular formula C4H10.
    • They are a specific type of isomer called structural isomers.
  • Branched-chain alkanes are named by the following rules.
naming saturated hydrocarbons6
Naming Saturated Hydrocarbons
  • Choose the longest continuous chain of carbon atoms which gives the basic name or stem.
  • Number each carbon atom in the basic chain, starting at the end that gives the lowest number to the first group attached to the main chain (substituent).
  • For each substituent on the chain, we indicate the position in the chain (by an Arabic numeric prefix) and the kind of substituent (by its name).
    • The position of a substituent on the chain is indicated by the lowest number possible. The number precedes the name of the substituent.
  • When there are two or more substituents of a given kind, use prefixes to indicate the number of substituents.
    • di = 2, tri = 3, tetra = 4, penta = 5, hexa = 6, hepta = 7, octa = 8, etc.
  • The combined substituent numbers and names serve as a prefix for the basic hydrocarbon name.
  • Separate numbers from numbers by commas and numbers from words by hyphens.
    • Words are "run together".
naming saturated hydrocarbons7
Naming Saturated Hydrocarbons
  • Alkyl groups (represented by the symbol R) are common substituents.
    • Alkyl groups are fragments of alkanes in which one H atom has been removed for the connection to the main chain.
    • Alkyl groups have the general formula CnH2n+1.
  • In alkyl groups the -ane suffix in the name of the parent alkane is replaced by -yl.
    • A one carbon group is named methyl.
    • A two carbon group is named ethyl.
    • A three carbon group is named propyl.
  • Three alkanes have the formula C5H12.
    • There are three structural isomers of pentane.
    • n-pentane 2-methylbutane 2,2-dimethylpropane
alkanes and cycloalkanes8
Alkanes and Cycloalkanes
  • There are five isomeric hexanes, C6H14.

n-hexane 2-methylpentane 3-methylpentane

2,2-dimethylbutane 2,3-dimethylbutane

  • The number of structural isomers increases rapidly with
  • increasing numbers of carbon atoms.
  • The boiling points of the alkanes increase with molecular weight.
alkanes and cycloalkanes9
Alkanes and Cycloalkanes
  • Cyclic saturated hydrocarbons are called cycloalkanes.
    • They have the general formula CnH2n.
  • Some examples are:



  • The three classes of unsaturated hydrocarbons are:
  • alkenes and cycloalkenes, CnH2n
  • alkynes and cycloalkynes, CnH2n-2
  • aromatic hydrocarbons
  • The simplest alkenes contain one C=C bond per molecule.
    • The general formula for simple alkenes is CnH2n.
  • The first two alkenes are:
  • Each doubly bonded C atom is sp2 hybridized.
  • The sp2 hybrid consists of:
    • two s bonds (single bonds) and
    • one s and one p bond (double bond)
  • The systematic naming system for alkenes uses the same stems as alkanes.
  • In the IUPAC system, the -ane suffix for alkanes is changed to -ene.
    • Common names for the alkenes have the same stem but use the suffix -ylene is used.
  • In chains of four or more C atoms, a numerical prefix shows the position of the lowest-numbered doubly bonded C atom.
    • Always choose the longest chain that contains the C=C bond.
  • Polyenes contain two or more double bonds per molecule.
  • Indicate the number of double bonds with suffixes:
    • -adiene for two double bonds.
    • -atriene for three double bonds, etc.
  • The positions of the substituents are indicated as for alkanes.
  • The position of the C=C bond(s) is/are given the lowest number(s) possible.

1,3-hexadiene 1,2,5-hexatriene


  • Cycloalkenes have the general formula CnH2n-2.
  • Examples are:
  • cyclopentene
  • cyclohexene
  • Alkynes contain CC bonds.
  • The simplest alkyne is C2H2, ethyne, or acetylene.
    • Alkynes with only one C  C bond have the formula CnH2n-2.
  • Each carbon atom in a C  C bond is sp hybridized.
    • Each sp hybrid contains two  bonds and two  bonds.
    • The carbon atom will have one single bond and one triple bond.
  • Alkynes are named like the alkenes except that the suffix -yne is used with the characteristic stem
    • The alkyne stem is derived from the name of the alkane with the same number of carbon atoms.

3-heptyne 2-octyne

aromatic hydrocarbons
Aromatic Hydrocarbons
  • Historically, aromatic was used to describe pleasant smelling substances.
  • Now it refers to benzene, C6H6,and derivatives of benzene.
    • Other compounds that have similar chemical properties to benzene are also called aromatic.
  • The structure of benzene, C6H6, is:
  • Coal tar is the common source of benzene and many other aromatic compounds.
  • Some aromatic hydrocarbons that
  • contain fused rings are:
  • napthalene
resonance in benzene
Resonance in Benzene
  • C6H6 has two resonance structures with alternating double bonds.
  • The π electrons are delocalized over the ring.
  • C–C single bond = 154 pm
  • C=C bond = 134 pm
  • CC bonds in benzene = 139 pm

Resonance structures of benzene, C6H6 Abbreviated representation

of resonance structure

π electrons delocalized

other aromatic hydrocarbons
Other Aromatic Hydrocarbons
  • Many aromatic hydrocarbons contain alkyl groups attached to benzene rings (as well as to other aromatic rings).
  • The positions of the substituents on benzene rings are indicated by the prefixes:
    • ortho- (o-) for substituents on adjacent C atoms
    • meta- (m-) for substituents on C atoms 1 and 3
    • para- (p-) for substituents on C atoms 1 and 4

m-xylene o-xylene p-xylene

general properties and reactivity of alkanes alkenes and alkynes
General Properties and Reactivity of Alkanes, Alkenes, and Alkynes
  • Alkanes Consist of C–C and C–H bonds that are strong, not polar, and not easily attacked by nucleophiles or electrophiles, so reactivity is limited
  • The multiple bond of an alkene produces geometric isomers (cis and trans)
      • Cis and trans isomers of alkenes behave as distinct compounds with different chemical and physical properties
  • The hydrogen atom of a terminal alkyne can be removed as H+,forming anacetylide ion (R–CC–)
    • Acetylide ions are potent nucleophiles used for making longer carbon chains by a nucleophilic substitution reaction
  • Rotation about the carbon-carbon multiple bonds of alkenes and alkynes cannot occur without breaking a bond, which constitutes a large energy barrier to rotation. Alkenes and alkynes are prepared by elimination reactions
  • Arenes undergo substitution rather than elimination due to stability from delocalization of their  electron density, and are poor nucleophiles
organic halides
Organic Halides
  • A halogen atom may replace almost any hydrogen atom in a hydrocarbon.
  • The functional group is the halide (-X) group.
  • Examples include:
    • chloroform, CHCl3
  • 1,2-dichloroethane, ClCH2CH2Cl
  • para-dichlorobenzene
alcohols and phenols
Alcohols and Phenols
  • The functional group in alcohols and phenols is the hydroxyl (-OH) group.
  • Alcohols and phenols can be considered derivatives of hydrocarbons in which one or more H atoms have been replaced by -OH groups.
  • Phenols are derivatives of benzene in which one H has been replaced by replaced by -OH group.
  • The stem for the parent hydrocarbon plus an -ol suffix is the systematic name for an alcohol.
  • A numeric prefix indicates the position of the -OH group in alcohols with three or more C atoms.
  • Common names are the name of the appropriate alkyl group plus alcohol.
alcohols and phenols21
Alcohols and Phenols
  • Ethyl alcohol (ethanol), C2H5OH, is the most familiar alcohol.
  • Phenol, C6H5OH, is the most familiar phenol.
alcohols and phenols22
Alcohols and Phenols
  • Alcohols can be classified into three classes:
  • Primary (1°) alcohols like ethanol have the -OH group attached to a C atom that has one bond to another C atom.



  • Secondary(2°) alcohols have the –OH group

attached to a C atom that has bonds to

2 other C atoms.

  • For example,2-propanol:




  • Tertiary (3°) alcohols have the –OH group attached to a C atom that is bonded to 3 other C atoms.
  • For example, 2-methyl-2-propanol





alcohols and phenols23
Alcohols and Phenols
  • Alcohols are named using the stem for the parent hydrocarbon plus an -ol suffix in the systematic nomenclature.
  • A numeric prefix indicates the position of the -OH group in alcohols with three or more C atoms.
    • Common alcohol names are the name of the appropriate alkyl group plus the word alcohol.

1-pentanol 2-pentanol 3-pentanol

1-pentyl alcohol 2-pentyl alcohol 3-pentyl alcohol

alcohols and phenols24
Alcohols and Phenols
  • There are several isomeric monohydric acyclic (contains no rings) alcohols that contain more than three C atoms.
  • There are four isomeric four-carbon alcohols.

1-butanol 2-butanol

2-methyl-1-propanol 2-methyl-2-propanol

alcohols and phenols25
Alcohols and Phenols
  • There are eight isomeric five-carbon alcohols.
alcohols and phenols26
Alcohols and Phenols
  • Polyhydric alcohols contain more than one -OH group per molecule.
alcohols and phenols27
Alcohols and Phenols
  • Phenols are usually called by their common (trivial) names.
  • Ethers may be thought of as derivatives of water in which both H atoms have been replaced by alkyl or aryl groups.
  • Ethers are not very polar and not very reactive.
  • They are excellent solvents.
  • Common names are used for most ethers.
general properties and reactivity of alcohols and ethers
General Properties and Reactivity of Alcohols and Ethers
  • Alcohols and Ethers
    • Have “bent” structures and are able to hydrogen-bond
    • Are good solvents for organic compounds
  • Alcohols are prepared by
    • the addition of water to the carbons of a double bond or by substitution of an alkyl halide by hydroxide, a potent nucleophile
    • he reduction of compounds containing a carbonyl functional group ( CO)
    • Undergo two major types of reactions: those involving cleavage of the O–H bond, which produces an acid, and those involving cleavage of the C–O bond occurring under acidic conditions where the –OH is first protonated followed by a nucleophilic substitution
  • Phenols are more acidic than alcohols because of interactions between the oxygen atom and the ring
  • Ethers are prepared by
    • a substitution reaction in which the highly nucleophilicalkoxide ion (RO–) attacks the carbon of the polarized C–X bond of an alkyl halide (R´ X)
    • Unreactive because they lack the –OH unit
aldehydes and ketones
Aldehydes and Ketones
  • The functional group in aldehydes and ketones is the carbonyl group.
aldehydes and ketones31
Aldehydes and Ketones
  • Except for formaldehyde, aldehydes have one H atom and one organic group bonded to a carbonyl group.
  • Ketones have two organic groups bonded to a carbonyl group.
aldehydes and ketones32
Aldehydes and Ketones
  • Common names for aldehydes are derived from the name of the acid with the same number of C atoms.
  • IUPAC names are derived from the parent hydrocarbon name by replacing -e with -al.
aldehydes and ketones33
Aldehydes and Ketones
  • The IUPAC name for a ketone is the characteristic stem for the parent hydrocarbon plus the suffix -one.
  • A numeric prefix indicates the position of the carbonyl group in a chain or on a ring.
general properties and reactivity of aldehydes and ketones
General Properties and Reactivity of Aldehydes and Ketones

• Aldehydes and ketones

  • Contain the carbonyl functional group
  • Are prepared by
    • the oxidation of alcohols
    • reducing a carboxyl group (–CO2H) to a carbonyl group, which requires a good reducing agent
  • Characterized by nucleophilic attack at the carbon atom of the carbonyl functional group and electrophilic attack at the oxygen atom
  • React with organometallic compounds that contain stabilized carbanions such as the Grignard reagents (RMgX, where X = Cl, Br, ), which convert the carbonyl functional group to an alcohol and lengthen the carbon chain
  • Aromatic aldehydes have intense and characteristic flavors and aromas, and many ketones also have intense aromas
  • Ketones are found in hormones responsible for sex differentiation in humans
  • Amines are derivatives of ammonia in which one or more H atoms have been replaced by organic groups (aliphatic or aromatic or a mixture of both).
  • There are three classes of amines.

General Properties and Reactivity of Amines

  • Tertiary amines form cations in which all four H atoms are replaced by alkyl groups and are called quaternary ammonium salts, which can be chiral if all four substituents are different
      • Alkylamines can be prepared by nucleophilic substitution reactions of polar alkyl halides with ammonia or other amines
      • Reactions of amines are dominated by two properties:
        • the ability of amines to act as weak bases and
        • their tendency to act as nucleophiles, both resulting from the lone pair of electrons on the nitrogen atom
      • Amines behave as bases by accepting a proton from an acid to form an ammonium salt
      • Amines can react with any electrophile
      • Aryl amines are weaker bases than alkylamines because the lone pair of electrons on nitrogen interacts with the  bonds of the aromatic ring
carboxylic acids
Carboxylic acids contain the carboxyl functional group.

The general formula for carboxylic acids is:

R represents an alkyl or an aryl group

Carboxylic Acids
  • IUPAC names for a carboxylic acid are derived from the name of the parent hydrocarbon.
    • The final -e is dropped from the name of the parent hydrocarbon
    • The suffix -oic is added followed by the word acid.
  • Many organic acids are called by their common (trivial) names which are derived from Greek or Latin.
carboxylic acids39
Carboxylic Acids
  • Positions of substituents on carboxylic acid chains are indicated by numeric prefixes as in other compounds
    • Begin the counting scheme from the carboxyl group carbon atom.
  • They are also often indicated by lower case Greek letters.
    •  = 1st C atom
    •  = 2nd C atom
    •  = 3rd C atom, etc.
nomenclature of carboxylic acids
Nomenclature of Carboxylic Acids
  • Dicarboxylic acids contain two carboxyl groups per molecule.
carboxylic acids41
Carboxylic Acids
  • Aromatic acids are usually called by their common names.
  • Sometimes, they are named as derivatives of benzoic acid which is considered to be the "parent" aromatic acid.
general properties and reactivity of carboxylic acids
General Properties and Reactivity of Carboxylic Acids
  • Can be prepared from the oxidation of alcohols and aldehydes or through the reaction of a Grignard reagent with CO2, followed by acidification
  • Reactions of carboxylic acids are dominated by their polar carboxyl group and their acidity
  • Reactions with strong bases produce carboxylate salts
  • Less susceptible to nucleophilic attack due to delocalization of bonding over three atoms (O–C–O)
  • Substitution of the –OH of a carboxylic acid produces derivative compounds with different tendencies to participate in resonance with the CO functional group
  • Resonance structures have significant effects on the reactivity of carboxylic acid derivatives, but their influence varies, being least important for halides and most important for the nitrogen of amides
  • Two important carboxylic acid derivatives are esters and amides
general properties and reactivity of ester carboxylic acid derivatives
General Properties and Reactivity of Ester Carboxylic Acid Derivatives
  • Have the general formula RCO2R´, where R and R´ can be any alkyl or aryl group
  • Prepared by the reaction of an alcohol (R´OH) with a carboxylic acid (RCO2H) in the presence of a catalytic amount of strong acid (an electrophile); this protonates the doubly bonded oxygen atom of the carboxylic acid (a nucleophile) to give a species that is more electrophilic than the parent carboxylic acid
  • The nucleophilic oxygen atom of the alcohol attacks the electrophilic carbon atom of the carboxylic acid and a new C–O bond is formed

–General overall reaction


R–C + R´OH  R–C + H2O


–If an ester is heated with water in the presence of a strong acid or base, the reverse reaction will occur, producing the parent alcohol, R´OH, and either the carboxylic acid, RCO2H (under acidic conditions), or the carboxylate anion, RCO2– (under basic conditions)

general properties and reactivity of amide carboxylic acid derivatives
General Properties and Reactivity of Amide Carboxylic Acid Derivatives

– The two substituents on the amide nitrogen can be hydrogen atoms, alkyl groups, aryl groups, or any combination of two of those species O



– Are prepared by the nucleophilic reaction of amines with other, more electrophilic carboxylic acid derivatives, such as esters

– Are unreactive because of  bonding interactions between the lone pair of electrons on nitrogen and the carbonyl group, which inhibits free rotation about the C–N bond

– Stability of amide bond is important in biology because they form the backbones of peptides and proteins


When compounds contain more than one functional group, the order of precedence determines which groups are named with prefix or suffix forms. The highest precedence group takes the suffix, with all others taking the prefix form. However, double and triple bonds only take suffix form (-en and -yn) and are used with other suffixes.


Reactivity of Organic Molecules

  • The reactivity of a molecule is affected by the degree of substitution of the carbon bonded to a functional group; the carbon is designated as primary, secondary, or tertiary

– Primary carbon is bonded to only one other carbon and a functional group

– A secondary carbon is bonded to two other carbons and a functional group

– A tertiary carbon is bonded to three other carbons and a functional group

  • Identifying the transient species formed in a chemical reaction, some of which are charged, enables chemists to predict the mechanism and products of the reaction

Reactive Intermediates

  • When cleaving a C–H bond, the most common species formed is C+,called a carbocation, which has only six valence electrons and is electron deficient

– A carbocation is an electrophile, a species that needs electrons to complete its octet

– A tertiary carbocation is more stable than one that is primary because it increases electron density at the carbocation

  • Adding an electron to a free radical produces a carbanion, a negatively charged carbon with eight valence electrons
    • A carbanion is a nucleophile, an electron-rich species
    • Carbanions are destabilized by groups that donate electrons, so a tertiary carbanion is less stable than a primary one
common organic reactions
Common Organic Reactions
  • Five common types of organic reactions:
  • Substitution (SN1, SN2)– one atom or group of atoms in a substance is replaced by another atom or group of atoms from another substance. A typical substitution reaction is the reaction of hydroxide ion with methyl chloride (nucleophilic substitutionreactions):

CH3Cl + OH–  CH3OH + Cl

  • Elimination (E1, E2)– in which adjacent atoms are removed, or “eliminated,” from a molecule with the formation of a multiple bond and a small molecule are called elimination reactions
  • Addition – the components of a species A–B are added to adjacent atoms across a carbon-carbon multiple bond is called an addition reaction

HCl + CH2CH2  CH3CH2Cl

  • Free-radical reactions – the best known is the reaction of a saturated hydrocarbon with a halogen: CH3CH3 + Br2  CH3CH2Br + HBr
      • Free radical reactions occur in three stages: initiation,propagation, and termination
        • At high temperature or in the presence of light, the weak Br–Br bond generates Br atoms
        • A bromine atom attacks ethane, producing a free radical, which reacts with a bromine molecule
        • combination of two bromine atoms, of two ethyl radicals, or of an ethyl and a bromine radical
        • Oxidation-reduction reactions – are common in organic chemistry and can be identified by:
    • An increase in either is an oxidation, whereas a decrease is a reduction
    • An increase in the number of hydrogens in a hydrocarbon is an indication of a reduction
    • In compounds with a carbon-nitrogen bond, the number of bonds between the C and N atoms increases as the oxidation state of the carbon increases


CH2–CH2  CH2CH2 + A–B

  • Isomers have identical composition but different structures
  • Three forms of isomerism
    • Conformational
    • Constitutional (or structural)
    • Stereoisomerism
  • Conformational
    • Differences in three-dimensional structure resulting from rotation about a  bond are called differences inconformation, and each different arrangement is called a conformational isomer
  • Constitutional
    • Same empirical formula but different atom-to-atom connections
  • Stereoisomerism
    • Same atom-to-atom connections but different arrangement in space.
      • Geometric - Geometric isomers can occur when there is a C=C double bond.
      • Optical - Optical isomers are molecules with non-superimposable mirror images. Such molecules are called CHIRAL. Pairs of chiral molecules are enantiomers. Chiral molecules in solution can rotate the plane of plane polarized light.
conformational isomers
Conformational Isomers

• Differences between the conformations are depicted in drawings called Newman projections

  • A Newman projection represents the view along a C–C bond axis, with the carbon that is in front shown as a point and the carbon that is bonded to it shown as a circle; the C–H bonds to each carbon positioned at 120º from each other; the hydrogen atoms nearest the viewer are shown bonded to the front carbon, and the hydrogen atoms farthest from the viewer are shown bonded to the circle
  • In one extreme, the eclipsed conformation, the C–H bonds on adjacent carbon atoms are parallel and lie in the same plane
  • In the other extreme, the staggered conformation, the hydrogen atoms are positioned as far from one another as possible; the staggered conformation is the most stable because electrostatic repulsion between the hydrogen atoms on adjacent carbons is minimized
conformational isomers53
Conformational Isomers
  • Newman projections are useful for predicting the stability of conformational isomers
    • The eclipsed conformation is higher in energy than the staggered conformation because of electrostatic repulsions between hydrogen atoms
    • The staggered conformation is the most stable because electrostatic repulsion between the hydrogen atoms on adjacent carbons is minimized
    • Longer-chain alkanes can also be represented by Newman projections and rotation can occur about each C–C bond in the molecule; Newman projections are useful for revealing stericbarriers to rotation at a particular C–C bond due to the presence of bulky substituents
structural constitutional isomers
Structural (Constitutional) Isomers

In the conversion of one constitutional isomer to another, at least one bond must be broken and reformed at a different position in the molecule

stereoisomers geometric



Stereoisomers: Geometric

Geometric isomers can only occur when there is a C=C double bond. Geometric isomers differ in the relative placement of substituents in a rigid molecule; members of an isomeric pair are either cis or trans, with interconversion between the two forms requiring breaking and reforming one or more bonds; their structural differences causes them to have different physical and chemical properties and to exist as two distinct chemical compounds

stereoisomers optical
Stereoisomers: Optical
  • Optical isomers are molecules with

non-superimposable mirror images.

  • Such molecules are called CHIRAL
  • An achiral object is one that can be superimposed on its mirror image
  • Pairs of chiral molecules are enantiomers.
  • Chiral molecules in solution can rotate the plane of plane polarized light
  • Optical isomers have identical physical properties, although their chemical properties may differ
  • A chiral solution that contains equal concentrations of a pair of enantiomers is called a racemic mixture, where the rotations cancel one another and the solution is optically inactive

Lactic acid

  • Chirality generally occurs when a C atom has 4 different groups attached.
chirality handedness in nature
Chirality: Handedness in Nature

These molecules are non-superimposable mirror images.


• Interactions of enantiomers with other chiral molecules

  • In living organisms, every molecule with a stereocenter is found as a single enantiomer, not a racemic mixture
  • At the molecular level, our bodies are chiral and interact differently with the individual enantiomers of a particular compound
  • Only one enantiomer of a chiral substance interacts with a particular receptor, initiating a response; the other enantiomer may not bind at all, or it may bind to another receptor, producing a different response
the molecules of life
The Molecules of Life

• All the functional groups described are found in the organic molecules that constitute and maintain every living organism on Earth

  • Most organic molecules that are chiral have at least one carbon atom that is bonded to four different groups

– This carbon is designated by an asterisk in structural drawings and is called a chiral center, chiral carbonatom, asymmetric carbon atom, stereogenic center, or stereocenter

• The most abundant substances found in living systems belong to four major classes:

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids



Monosaccharides - simple sugars,  with multiple hydroxyl groups.

Based on the number of carbons (e.g., 3, 4, 5, or 6) a monosaccharide is a triose, tetrose, pentose, or hexose, etc.

Disaccharides - two monosaccharides covalently linked

Oligosaccharides - a few monosaccharides covalently linked.

Polysaccharides - polymers consisting of chains of monosaccharide or disaccharide units (starches and cellulose)




































• Carbohydrates are the most abundant of the organic compounds found in nature; they constitute a substantial portion of food consumed to provide energy.

• Carbohydrates are polyhydric aldehydes or polyhydric ketones

– The simplest carbohydrates consist of unbranched chains of three to eight carbon atoms; one carbon is a carbonyl carbon and the others are bonded to hydroxyl groups

– The structure of a carbohydrate can be drawn either as a hydrocarbon chain, known as a Fisher projection, or as a ring, or cyclic form, called a Haworth projection

– The two cyclic forms in a Haworth projection are called anomers

  • Haworth projections represent the cyclic sugars as having essentially planar rings, with the OH at the anomeric C1 extending either:
  • below the ring (a)
  • above the ring (b).
sucrose and ribose

Deoxyribose, the sugar in the DNA backbone.

Sucrose and Ribose

Sucrose, common table sugar, has a glycosidic bond linking the anomeric hydroxyls of glucose and fructose. Because the configuration at the anomeric carbon of glucose is a (O points down from the ring), the linkage is designated a(1®2). The full name is a-D-glucopyranosyl-(1®2)b-D- fructopyranose.

sugars related to alcohols
Sugars: Related to Alcohols
  • Sugars are carbohydrates, compounds with the formula Cx(H2O)y.

What is the difference between a and b D-glucose?

Glycosidic bonds: The anomeric hydroxyl group (axial) and a hydroxyl group of another sugar or some other compound can join together, splitting out water in a condensation reaction to form a glycosidic bond.

R-OH + HO-R'-->R-O-R' +H2O



  • Characterized by their insolubility in water

– Form a family of compounds that includes fats, waxes, vitamins, and steroids

– Fatty acidsare the simplest lipids and have a long hydrocarbon chain that ends with a carboxylic acid functional group

1. Saturated fatty acids — the hydrocarbon chains contain only C–C single bonds that stack in a regular array

2.Unsaturated fatty acids — have a single double bond in the hydrocarbon chain (monounsaturated) or more than one double bond (polyunsaturated); double bonds give fatty acid chains a kinked structure, which prevents the molecules from packing tightly

  • Unsaturated fatty acids
    • Melting point lower than that of a saturated fatty acid of comparable molecular mass
    • Double bonds can be hydrogenated in an addition reaction that produces a saturated fatty acid or oxidized to produce an aldehyde or carboxylic acid
    • Are the starting compounds for the biosynthesis of prostaglandins,hormonelike substances

• Waxes are esters produced by nucleophilic attack of an alcohol on the carbonyl carbon of a long-chain carboxylic acid

• Triacylglycerolsare esters that are used by the body to store fats and oils and are formed from one molecule of glycerol and three fatty acid molecules

  • Steroids are lipids whose structure is made up of three cyclohexane rings and one cyclopentane ring fused together; presence of various substituents on the basic steroid ring structure produces a family of steroid compounds with different biological activity
    • Cholesterol is a steroid found in cellular membranes and is the starting point for the biosynthesis of steroid hormones, including testosterone, the primary male sex hormone, and progesterone, which helps maintain pregnancy
fats and oils
Fats and Oils

R = organic group with NO C=C bonds

C12 = Lauric acid

C16 = Palmitic acid

C18 = Stearic acid

What is the functional group in a fat or oil?

R = organic group with C=C bonds

C18 = oleic acid

fats and oils69

C=C bond

Fats and Oils

Fats with C=C bonds are usually LIQUDS

Oleic acid: a monounsaturated fatty acid

trans fatty acids

C=C bond

Trans Fatty Acids
  • Oleic acid is a mono–unsaturated cis-fatty acid
  • Trans fatty acids have deleterious health effects.
  • Trans fatty acids raise plasma LDL cholesterol and lower HDL levels.


• Proteins are biologically active polymers formed from amino acids linked together by amide bonds; in addition to an amine group and a carboxylic acid group, each amino acid contains a characteristic R group

  • The nature of the R group determines the particular chemical properties of each amino acid

• All the amino acids found in proteins are chiral compounds except glycine, which suggests that their interactions with other chiral compounds are selective

• Some proteins are enzymes that catalyze biological reactions

peptides and proteins
Peptides and Proteins



– H2O


Adding more peptide links ---> PROTEIN


Nucleic Acids

• Nucleic acids are the basic structural components of DNA and RNA, the biochemical substances found in the nuclei of cells that transmit the information needed to direct cellular growth and reproduction

• Structures are derived from nitrogen-containing cyclic compounds called pyrimidines and purines, which can hydrogen-bond through the lone electron pair on nitrogen (in pyrimidine and purine) or through the hydrogen of the amine (in purine)

• When a pyrimidine or purine is linked to a sugar by a bond called a glycosidic bond, a nucleoside is formed; addition of a phosphoric acid group to the sugar produces a nucleotide



Ribose Deoxyribose




Cytosine Thymine Uracil

Adenine Guanine

Connects #9 Nitrogen to #1 carbon of sugar to form a nucleoside

Connects #1 Nitrogen to #1 carbon

of sugar to form a nucleoside

Connects to #5 carbon of a nucleoside to form a nucleotide

Joins to nucleotides at the #3 carbon to make DNA and RNA (nucleic acids)


coordination compounds
Coordination Compounds
  • Transition metal complexes are important in biochemistry and is an active area of research.
  • Catalytic cofactors: Many reactions require trace elements as catalytic cofactors.
    • Zinc is required in over 200 reactions including synthesis of proteins, taste perception, prostrate reproductive health, metabolizing alcohol, and protecting against copper and heavy metal toxicity such as cadmium and lead. Zinc occurs in greater amounts than any other trace mineral except iron.
    • Manganese is required to synthesize connective tissue and bones (collagen).
    • Oxidation/reduction: Some metal ions, particularly iron, copper, and manganese are involved in the energy metabolism of cells. Iron is involved in the electron transport that ultimately converts oxygen to water. Copper participates in electron transport as well as synthesis of nerve membranes and formation of collagen.
    • Oxygen binding and transport: Oxygen is carried by the red cells of the blood from the lungs bound to hemoglobin which contains iron at its active heme center. Oxygen is released to the tissues where it is picked up by a similar protein, myoglobin, before it accepts electrons and protons to form water.
    • Metabolic regulation: Iron, copper and zinc can regulate the activities of protein and nucleic acid synthesis. Proper immune response requires these trace elements.
    • Structural integrity: The three dimensional architecture of proteins and nucleic acids depends upon zinc and manganese as well as iron and copper. These metals bind and hold large molecules in active configurations. An example is the requirement of zinc for proper conformation of the taste- bud proteins in the tongue. Without zinc, taste and smell are lost. Iodide is incorporated into the amino acids which synthesize thyroid hormones.
important terms
Important Terms
  • A ligand is a Lewis base that coordinates to a central metal atom or ion.
  • A donor atom is the atom in a ligand that donate a lone pair of electrons to form a coordinate covalent bond.
  • A unidentate ligand is a ligand that can bind through only one atom.
  • A polydentate ligand is a ligand that can bind through more than one donor atom.
      • There are known examples of bidentate, tridentate, quadridentate, quinquedentate, and sexidentate ligands.
  • Chelate complexes are complexes that have a metal atom or ion and polydentate ligand(s) that form rings.
  • The coordination number is the number of donor atoms coordinated to a metal atom or ion.
  • A coordination sphere includes the metal atom or ion and the ligands coordinated to it. The coordination sphere does not include uncoordinated counter ions.
important terms78
Important Terms
  • For the complex compound K3[Co(CN)6] the coordination number is _________, and the coordination sphere is _______.

Rules for Naming Complex Species

  • Cations (+ ions) are named before anions (- ions).
  • Coordinated ligands are named in alphabetical order.
    • Prefixes that specify the number of each kind of ligand (di = 2, tri = 3, tetra = 4, penta = 5, hexa = 6, etc.) are not used in alphabetizing
    • Prefixes that are part of the name of the ligand, such as in diethylamine, are used to alphabetize the ligands.
  • For complicated ligands, especially those that have a prefix such as di or tri as part of the ligand name, these prefixes are used to specify the number of those ligands that are attached to the central atom.
    • bis = 2 tris = 3 tetrakis = 4 pentakis = 5 hexakis = 6
  • The names of most anionic ligands end in the suffix -o.
    • Examples of ligands ending in –o are:
      • Cl-chloro S2-sulfido O2-oxo
  • The names of most neutral ligands are unchanged when used in naming the complex.
    • There are several important exceptions to this rule including:
      • NH3 ammine H2O aqua
  • The oxidation number of a metal that exhibits variable oxidation states is designated by a Roman numeral in parentheses following the name of the complex ion or molecule.
  • If a complex is an anion, the suffix "ate" ends the name.
    • No suffix is used in the case of a neutral or cationic complex.
    • Usually, the English stem is used for a metal, but if this would make the name awkward, the Latin stem is substituted. ferrate instead of ironateplumbate instead of leadate
important terms80
Important Terms

Typical Simple Ligands

  • Name the following compounds:



  • Write formulas for the following compounds:

potassium hexacyanochromate(III)

tris(ethylenediammine) cobalt(III) nitrate

  • The structures of coordination compounds are controlled primarily by the coordination number of the metal.
  • Usually the structures can be predicted by VSEPR theory (Chapter 8).
    • The geometries and hybridizations for common coordination numbers are summarized in this table.
  • Sketch the shape of the hexacyanaochromate(III) ion.
isomerism in coordination compounds
Isomerism in Coordination Compounds
  • Isomers . two or more forms of a compound having the same composition

• Structural isomers involve different atom to ligand bonding sequences.

        • hydration isomers isomers
          • exchange water as ligand

and hydrate

        • ionization isomer
          • exchange ion between ligand and anion
        • coordination isomers
          • denote an exchange of ligands between the coordination spheres of the cation and anion.
        • linkage isomers
          • different ligands or different

attachment of ligands

• Stereoisomers (identical bonding)

• geometrical isomers

• optical isomers

coordination sphere


structural constitutional isomers87
Structural (Constitutional) Isomers
  • Hydrate isomersare a special case of ionization isomers in which water molecules may be changed from inside to outside the coordination sphere.
  • For example:
    • [Cr(OH2)6]Cl3 vs.
    • [Cr(OH2)5Cl]Cl2. H2O vs.
    • [Cr(OH2)4Cl2]Cl2. 2H2O
  • Note whether the water molecule(s) are inside or outside the coordination sphere.
  • [Cr(OH2)6]Cl3 [Cr(OH2)5Cl]Cl2. H2O
  • [Cr(OH2)5Cl]Cl2. H2O [Cr(OH2)4Cl2]Cl2. 2H2O
structural constitutional isomers88
Structural (Constitutional) Isomers
  • Ionization (Ion-Ion )Exchange Isomers
    • [Pt(NH3)4Cl2]Br2 compared to [Pt(NH3)4Br2]Cl2
    • Note where the Cl’s and Br’s are in the structures, that is what makes these two species isomers.
  • [Pt(NH3)4Cl2]Br2 [Pt(NH3)4Br2]Cl2
structural constitutional isomers89
Structural (Constitutional) Isomers
  • Coordination isomers denote an exchange of ligands between the coordination spheres of the cation and anion.
  • For example look at these two isomers:

[Pt(NH3)4][PtCl6] vs [Pt(NH3)4Cl2][PtCl4]

  • The isomeric distinction is whether the ligands are on the cation or the anion.
structural constitutional isomers90

bonding via N nitro-bonding via O nitrito-

bonding via C cyano-bonding via N isocyano-

bonding via S thiocyanato-bonding via N isothiocyanato-

Structural (Constitutional) Isomers
  • Linkage isomerismif a ligand contains more than one atom with a free electron pair, the ligand may be bound to the central atom via the different atoms.
  • [Co(NH3)5ONO]Cl2 [Co(NH3)5NO2]Cl2
  • Stereoisomers are isomers that have different spatial arrangements of the atoms relative to the central atom.
  • Complexes with only simple ligands can occur as stereoisomers only if they have coordination numbers equal to or greater than four.
  • Geometrical or positional isomersare stereoisomers that are not optical isomers.
  • Cis-trans isomers have the same kind of ligand either adjacent to each other (cis) or on the opposite side of the central metal atom from each other (trans).
  • Note where the ligands are positioned relative to the central atom.
  • Other types of isomerism can occur in octahedral complexes. Complexes of the type [MA2B2C2] can occur in several geometric isomeric forms:
    • trans- trans- trans-
    • cis- cis- cis-
    • cis- cis- trans-
stereoisomers geometric92
Stereoisomers - Geometric

cis- [Pt(NH3)2Cl2] trans-[Pt(NH3)2Cl2]


trans-diammine-trans-diaqua-trans-dichlorocobalt(III) ion

cis-diammine-cis-diaqua-cis-dichlorocobalt(III) ion


trans-diammine-cis-diaqua-cis-dichlorocobalt(III) ion

cis-diammine-cis-diaqua-trans-dichlorocobalt(III) ions


cis-diammine-trans-diaqua-cis-dichlorocobalt(III) ions

  • Octahedral complexes can exhibit another type of geometric isomerism
    • - mer-fac isomerism.
    • mer isomerism involves all three similar ligand lying in the same plane, or meridianl like a globe.
    • fac facial involves a grouping of three similar ligands that are arranged on a triangular face of the octrahedron
  • fac and mer-Co(NH3)3Cl3
  • Optical isomers are mirror images of each other that are not superimposable.
  • The cis-diammine-cis-diaqua-cis-dichlorocobalt(III) ion has two different forms called optical isomers or enantiomers.
  • Separate equimolar solutions of the two isomers rotate plane polarized light by equal angles but in opposite directions.
    • The phenomenon of rotation of polarized light is called optical activity.
  • These are the optical isomers of:

cis-diammine-cis-diaqua-cis-dichlorocobalt(III) ion