BONDING IN ORGANIC MOLECULES

General Chemistry I 1

BONDING INORGANIC MOLECULES

7.1 Petroleum Refining and the Hydrocarbons

7.2 The Alkanes

7.3 The Alkenes and Alkynes

7.4 Aromatic Hydrocarbons

7.5 Fullerenes

7.6 Functional Groups and Organic Reactions

7.7 Pesticides and Pharmaceuticals

7CHAPTER

General Chemistry I


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Organic Chemistry:the study of the compoundsof carbon

7.1 PETROLEUM REFINING AND

THE HYDROCARBONS

Hydrocarbons:compounds of carbon andhydrogen


7.2 THE ALKANES309

Normal alkanes, n-alkanes

~ straight-chain (linear) alkanes, CnH2n+2


Fig. 7.1. Bonding in alkanes involves sp3 hybridized orbitals.

Fig. 7.2. Rotation about C–C bond variable conformations

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‘staggered’ conformer ‘eclipsed’ conformer

(sp3-sp3)(sp3-s)(sp3-s)

Conformers (conformations) are isomers that can be interconverted via bond rotations. They are stereoisomers.


310

Two conformations of C16H34

Londondispersion

force


Fig. 7.5. Fractional distillation of petroleum.

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Cyclic Alkanes: Carbon atoms arranged in rings

Cyclopropane, C3H6 Cyclobutane, C4H8 Cyclohexane, C6H12

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- cycloalkanes have one ring: CnH2n

- angle strain energy reducing the stability of small rings (< C5) CCC bond angle smaller than the sp3 tetrahedral angle of 109.5o

angle strainedunstrained


Fig. 7.7. Conformations of cyclohexane. (a) Chair. (b) Boat.

Cyclohexane, C6H12

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C

CC

C

CC

H2C

H2CCH2

CH2

CH2

H2C

or or

H HH

H

H H

HH

HHH

H


Branched-Chain Alkanes and Isomerism

Fig. 7.8. Two isomeric hydrocarbons with the molecular formula C4H10.(a) Butane. (b) 2-Methylpropane (branched chain isomer).

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-Branched chain hydrocarbons contain only C-C and C-H single bonds, but not in a straight chain. They are constitutional(structural) isomers of normal alkanes. Isomers are different structures with the same molecular formula.

Constitutional isomers have different atomic connectivities: they can be interconverted only by bond-breaking and bond-making processes.


ISOMERS

CONSTITUTIONALISOMERS

STEREOISOMERS

Branch isomersPosition isomersFunctional groupisomers

Geometric isomersOptical isomersConformers

Differ in atomicconnectivity

Have same atomicconnectivity, butdiffer in spatialarrangement ofatoms

Slide 17

Slide 18

Slides 4 & 8

Slide 9

Slide 18

Slide 33

Interconversion of all isomers, except conformers, requiresbond breaking and remaking


Nomenclature for isomeric alkanes (IUPAC: International Union of Pure and Applied Chemistry)

1. Find the longest (backbone) alkane chain (= root, named

according to slide 3)

2. Alkyl groups (branches)

Methyl –CH3 Ethyl –CH2CH3

Propyl –CH2CH2CH3 Isopropyl –CH(CH3)2

3. Numbering of carbon atoms

(lowest number for the attached position)

4. Prefixes for many alkyl groups

di-, tri-, tetra- , penta-

5. Alphabetical order for different alkyl groups

(E.g. ethyl before methyl before propyl)

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EXAMPLE 7.1

Name the following branched-chain alkane:

1 3 4 5 62

4-ethyl-2,4-dimethylhexane

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Octane number

Straight-chain alkanes burn very unevenly “knocking”

Heptane (octane number, 0) Isooctane (octane number, 100)

Octane number, 90 90% (by vol) isooctane + 10% heptane

Anti-knocking additive: tetraethyllead, Pb(C2H5)4 (now banned!)

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7.3 THE ALKENES AND ALKYNES314

Unsaturated hydrocarbons

Alkene ~ double bonds E.g. Ethene (Ethylene), C2H4

Alkyne ~ triple bonds E.g. Ethyne (Acetylene), C2H2

Fig. 7.10. Reaction with KMnO4.(a) No reaction with hexane.(b) Redox reaction with 1-hexene. Products: MnO2 and CH3(CH2)3CH(OH)CH2OH


Ethylene, H2C=CH2

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Acetylene, HC≡CH315


Optical isomerism and chirality

Fig. 7.9. Non-superimposable optical isomers of a molecule CHBrClF.

Optical isomers:

Non-superimposable mirror image structures are called

enantiomers

Same physical properties but with different optical activity

Chemical properties can differ when they interact with other

optically active molecules → Pharmaceutically important! Optical activity:

Rotating the plane polarized light clockwise or anti-clockwise

Chirality (handedness) ~ C*: chiral center

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Position isomers of alkenes and alkynes

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C4H8: CH2=CH-CH2-CH3 CH3-CH=CH-CH3

C4H6: HCC–CH2–CH3 H3C–CC–CH3

1-butyne 2-butyne

1-butene 2-butene

Geometric isomers of alkenesE.g. 2-butene


Fig. 7.14. Configurational change of the trans isomer of 2-butene to its cis isomer upon absorbing UV light. * transition.

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Fig. 7.13. The overlap between the two p orbitals decreases when the2-butene molecule is twisted about the C=C bond.


Polyenes

1,3-butadiene, CH2=CH–CH=CH2

Fig. 7.15. The four MOs formed from four 2pz AOs in 1,3-butadiene. Only the twolowest orbitals are occupied in the ground state.

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conjugated electron

system


7.4 AROMATIC HYDROCARBONS319

Benzene, C6H6

Fig. 7.16. The six molecular orbitals for benzene.


BTX (benzene-toluene-xylene)

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- hydrodealkylation: from toluene to benzene, 550-650 oC, 40-80 atm

(1,2; 1,3; 1,4-dimethylbenzenes)(methylbenzene)


Reforming reactions: producing BTX aromatics from straight chain alkanes

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7.5 FULLERENES322

- Buckminsterfullerene: the third allotrope of carbon

- a whole family of closed-cage carbon molecules


“for their discovery of fullerenes”

Robert F. Curl, Jr. Harold W. Kroto Richard E. Smalley

The Nobel Prize in Chemistry 1996323


Carbon nanotubes : one of the purest carbon forms

• Single-walled nanotubes (SWNTs)

- a single graphite sheets wrapped into a cylindrical tube

• Multi-walled nanotubes (MWNTs)

- an array of concentrically nested nanotubes

Baughman, R. H. et al. Science 2002, 297, 787

Carbon Nanotubes (CNTs)323


Graphene-Based Materials

D. Li et al. Science 2008, 320, 1170

• graphenes – monolayers of carbon atoms arranged in a honeycomb network

• simply prepared by pulling an atomic layer off of a graphite crystal with a piece of sticky tape

• a giant aromatic macromolecule that conducts both electricity and heat well in two dimensions

• high specific surface area, high mechanical strength comparable to CNTs

• production cost lower than that of CNTs

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7.6 FUNCTIONAL GROUPS AND ORGANIC REACTIONS

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Halides R–X (X = F, Cl, Br, I) Halo-

Free radical chain reaction

Cl2 → 2 Cl ∙ (initiation)

Cl ∙ + CH4 → HCl + ∙ CH3 (propagation)

∙ CH3 + Cl2 → CH3Cl + Cl ∙ (propagation)

CH4 + Cl2 CH3Cl + HClo250 400 C, h

Addition and elimination reactions

ClCH2CH2Cl CH2=CHCl + HClo500 C, charcoal

CH2=CH2 + Cl2 → ClCH2CH2Cl

vinyl chloride (chloroethene)monomer of PVC

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chloromethane

+ other products

1,2-dichloroethane


Alcohols R–OH – OH group -ol, hydroxy-

Methanol (methyl alcohol), CH3OH

CH4(g) + H2O(g) → CO(g) + 3 H2(g) (reforming reaction) CO(g) + 2 H2(g) → CH3OH synthesis gas

Ethanol (ethyl alcohol), C2H5OH

CH2=CH2 + H2O → CH3CH2OH

CH3CH2CH2OH: 1-propanol (propyl alcohol)

CH3CH(OH)CH3: 2-propanol (isopropyl alcohol)

CH3CH(OH)CH2CH3: 2-butanol or 2-hydroxybutane

2H O 4HSO

+H

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Position isomers


Types of Alcohols

Primary alcohol: RCH2–OH

ethanol

Secondary alcohol: R2CH–OH

2-butanol

Tertiary alcohol: R3C–OH 2-methyl-2-propanol tertiary-butyl alcohol or tert-butanol (CH3)3COH

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Phenols C6H5OH or Carbolic acid Weak acid, but stronger than EtOH

Partial oxidation of benzene, distillation of coal

Toxic: lethal dosage, 1g

Major Synthetic Process (the cumene process)

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Ethers R–O–R’ –O– group

CH3CH2–O–CH2CH3, diethyl

ether

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- methyl t-butyl ether (MTBE)

- cyclic ethers: epoxides

E.g. epoxyethane (ethylene oxide)

Alcohols and ethers of same molecular formula arefunctional group isomersE.g. ethanol (CH3CH2OH) and dimethyl ether (CH3OCH3), both C2H6O


Aldehydes

“Formalin” : aqueous solution of HCHO preservation of biological specimens

‘Sick house syndrome’

-CHO group –al

▶ HCHO, methanal (formaldehyde)

▶ CH3CHO, ethanal (acetaldehyde)

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Fig. 7.23. Bonding in formaldehydeinvolves sp2 hybrid orbitals of bothC and O.

(H)RC

O

H

C O

H

H

(sp2-sp2)(sp2-1s) sp2


Ketones –one

(CH3)2CO, propanone (acetone)

Good solvent, miscible with water

Oxidation of secondary alcohol:

CH3CH2CH2COCH3, 2-pentanone

CH3CH2COCH2CH3, 3-pentanone

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>CO group

RC

O

R'

Position isomers


Carboxylic Acids R–COOH –oic acid

▶ Carboxyl group:

HCOOH, methanoic acid (formic acid)

CH3COOH, ethanoic acid (acetic acid)

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C

O

OH


Esters

Product of the reaction between a carboxylic acid and an alcohol

Ethyl ethanoate (ethyl acetate)

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Fragrant odors, flavors of fruits

–oate

R

C

O

OR'


★ Fats

Hydrogenation of oils (esters of cis-unsaturated fatty

acids)

Saturated fats with higher m.p.:

→ solid, good for baking and extended shelf-life

Remaining double bonds converted from

cis to trans isomers → bad for health!

+ 6H2 → saturated fats

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Triglyceride ester


Amines334

Primary amine: RNH2

Secondary amine: R2NH Tertiary amine: R3N

Condensation product of an amine with a carboxylic acid

◆ Amides: R–(CO)–(NH)–R’ -CONH- group -amide (or amido-)

an amide

>N- group –amine (or amino-)N

R'(H)

(H)R'' R Weak bases


Amino acids, NH2–R–COOH ~ bifunctional molecules

Glycine, NH2CH2COOH

α-amino acid, +H3NCH2CO2– (pH = 7)

Peptide

~ Condensation product of two or more amino acids Peptide bonds –(CO)–(NH)– (amide bonds)

Functional Groups in Proteins332

‘zwitterion’


Protein ~ Polypeptide

primary, secondary, tertiary, quaternary structures

tertiary structure of theenzyme chymotrypsin

binding of phenylalanine in the active site of chymotrypsin

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expanded view of theactive site of chymotrypsin


7.7 PESTICIDES AND PHARMACEUTICALS

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Insecticides ( 살충제 )

First-generation

Copper, Lead, Arsenic, Nicotine → aphid

Second-generation

DDT (dichlorodiphenyltrichloroethane):→lice

Methyl parathion

Third-generation

Target oriented, environmentally degradable

E.g. sex attractant, Juvenile hormone ~

Methoprene


Herbicides ( 제초제 )

2,4-D (2,4-dichlorophenoxyacetic acid) 2,4,5-T (“Agent Orange,” or 2,4,5-trichlorophenoxyacetic

acid) → Defoliant used during Vietnam war

→ Contains trace amount (10 ppb) of TCDD

TCDD (“dioxin,” or 2,3,7,8-tetrachlorodibenzo-p-dioxin)

Extremely toxic ! Waste-burning incinerator

→ major source of dioxin in the environment

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Analgesics ( 진통제 )

Aspirin (acetylsalicylic acid)

Analgesic (pain reliever), Antipyretic (reduces fever),

Prevents heart disease (thins the blood)

Carboxylic acid Irritates stomach

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Acetaminophen (4-acetaminophenol)

“Tylenol” ~ weakly acidic phenol


Much more powerful pain relievers

Morphine ~ natural product from “opium poppy” Codeine ~ also cough suppressant and analgesic Heroin ~ 3,6-diacetylmorphine

2~3 times powerful than morphine and more addictive

Morphine Codeine Heroin

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A Little Joke on Nomenclature

A research chemist walked into a pharmacy and asks, “Do you have (5,6)-7,8-didehydro-4,5-epoxy-3-methoxy-17-methylmorphinan-6-ol?”The pharmacist scratched her head and said, “Do you mean codeine?”“That’s it!”, said the chemist, “I can never remember that word!”


Antibacterial Agents (Antibiotics) Sulfanilamide

Bacteria mistake sulfanilamide for p-aminobenzoic acid

→ Interferes with bacteria’s synthesis of folic acid, Penicillin ~ natural product formed by certain molds

~ Total synthesis by John C. Sheehan (1957)

~ Fermentation (more economic)

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“Steroid nucleus” 3 six-atom rings and 1 five-atom ring

Cholesterol ~ synthesized in the liver from acetate units

via the ‘mevalonate pathway’. It is the biological precursor

to most other steroids

Cortisone ~ secreted from adrenal glands

~ controls metabolism of sugars, fats, and proteins

Progesterone, Estrogen

~ Female sex hormones, oral contraceptives

Testosterone ~ male sex hormone

Steroids: derived from cholesterol

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10 Problem Sets

For Chapter 7,

4, 12, 20, 28, 30, 32, 40, 44, 46, 50

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BONDING IN ORGANIC MOLECULES