Organic Chemistry: An Introduction

Academic Boot Camp

Curtis P. Martin

July 20, 2016

Reading

http://www.chem.ucalgary.ca/courses/350/Carey5th/Carey.html

What is Organic Chemistry?

“… a chemistry subdiscipline involving the scientific study of thestructure, properties, and reactions of organic compounds and organicmaterials, i.e., matter in its various forms that contain carbon atoms”

-Wikipedia

Carbon: Why So Special?

Multiple possible shapes

Bonds to itself very nicely (practically infinitely)

Four valence electrons

Forms covalent bonds with MANY other atoms

Especially hydrogen

Review: Molecular Shapes

Methane:

Acetone:

Ethyne:

Tetrahedral

Trigonal planar

Linear

Carbon: Why So Special?

Multiple possible shapes

Bonds to itself very nicely (practically infinitely)

Four valence electrons

Forms covalent bonds with MANY other atoms

Found EVERYWHERE in nature

Drawing Organic Molecules

Every organic molecule has carbon

Why explicitly draw them then?

Hydrogens are cumbersome

So many… 99% of which can be assumed

Don’t show hydrogen atoms on carbon atoms

Only specify “heteroatoms,” i.e. atoms other than carbon

Isomerism

Organic Molecules: Alkanes

Organic molecules which:

Have only carbons and hydrogens (hydrocarbons)

Contain only single bonds

Systematic naming conventions

IUPAC- “International Union of Pure and Applied Chemists”

# of C atoms Prefix

1 Meth-

2 Eth-

3 Prop-

4 But-

5 Pent-

6 Hex-

Organic Molecules: Alkanes

Organic molecules which:

Have only carbons and hydrogens (hydrocarbons)

Contain only single bonds

Systematic naming conventions

IUPAC- “International Union of Pure and Applied Chemists”

C4H10 C4H10

Ethane Propane

Butane

vs.

Butane?

Organic Molecules: Alkanes

Organic molecules which:

Have only carbons and hydrogens (hydrocarbons)

Contain only single bonds

Systematic naming conventions

IUPAC- “International Union of Pure and Applied Chemists”

C4H10 C4H10

Ethane Propane

Butane

vs.

2-methylpropane

Constitutional Isomers

Organic Molecules: Alkanes

Single bonds allow rotation

C4H10 C4H10

Butane

vs.

Butane

Organic Molecules: Alkanes

Single bonds allow rotation

Newman projections

Butane

vs.

Butane

Rotamers

Organic Molecules: Alkenes

Organic molecules which:

Have only carbons and hydrogens (hydrocarbons)

Contain at least one double bond

Systematic naming conventions

IUPAC- “International Union of Pure and Applied Chemists”

Ethene Propene

1-butene 2-butene2-methylpropene 2-butene

Organic Molecules: Alkenes

Organic molecules which:

Have only carbons and hydrogens (hydrocarbons)

Contain at least one double bond

Systematic naming conventions

IUPAC- “International Union of Pure and Applied Chemists”

Ethene Propene

1-butene2-methylpropene 2-trans-butene

2-cis-butene

cis-trans diastereomers

Organic Molecules: Alkynes

Organic molecules which:

Have only carbons and hydrogens (hydrocarbons)

Contain at least one triple bond

Systematic naming conventions

IUPAC- “International Union of Pure and Applied Chemists”

Ethyne

Organic Molecules: Cyclic Hydrocarbons

All previous rules apply… add “cyclo” prefix

hexane cyclohexane

cyclohexene

1,3-cyclohexene

1,3,5-cyclohexene

C6H14 C6H12

Organic Molecules: Cyclic Hydrocarbons

All previous rules apply… add “cyclo” prefix

hexane cyclohexane

cyclohexene

1,3-cyclohexadiene

1,3,5-cyclohexatriene

C6H14 C6H12

Organic Molecules: Aromatics

All previous rules apply… add “cyclo” prefix

1,3,5-cyclohexatriene 1,3,5-cyclohexatriene benzene

Delocalized electrons

Additions to base organic molecules

Heteroatoms

Functional groups yield different properties

Electronegativity => dipole moments

Atomic size => steric interactions

Bond order => flexibility and entropy

Functional Group Name Structure

Alkyl halide Alcohol -ol

Ether -ether

Aldehyde -al

Ketone -one

Carboxylic acid -oic acid

Ester -ester

Amine -amine

Organic Molecules: Functional Groups

Reaction mechanisms

Describe how atoms and electrons move as reaction occurs

Show motion of atoms, electrons, bonds, etc. via arrows

Double headed and single headed arrows mean motion of two and one electron, respectively

Transition state: point during reaction coordinate at which system energy is at a maximum

Organic Reactions

Nucleophilic Substitution: SN2

Nucleophile: molecule which “likes” positive centers

Negatively charged atoms/molecules

Highly polar molecules

Lewis bases- electron donation

Takes place in one single step

Transition state:

Nucleophile: molecule which “likes” positive centers

Negatively charged atoms/molecules

Highly polar molecules

Lewis bases- electron donation

Takes place in one single step

Transition state:

Nucleophilic Substitution: SN2

What’s different in this reaction?

Nucleophilic Substitution: SN1

What’s different in this reaction?

“Steric hindrance” Bulky groups around positive site hinder attack by nucleophile

Nucleophilic Substitution: SN1

What’s different in this reaction?

“Steric hindrance” Bulky groups around positive site hinder attack by nucleophile

Nucleophilic substitution occurs via a different mechanism in this case SN1 reactions

Nucleophilic Substitution: SN1

SN1 reaction mechanism:

Nucleophilic Substitution: SN1

Slow and reversible

Diene + “dienophile” = cyclic hydrocarbon system

Dienophile is a molecule which “likes” dienes… typically alkenes with electron withdrawing groups

Useful for synthesizing medicines

Won Nobel Prize in 1950

Diels-Alder Cycloaddition

Proton Nuclear Magnetic Resonance Spectroscopy (1H-NMR)

Good for determining carbon skeleton and hydrogen environment

Infrared Spectroscopy (IR)

Good for determining presence of functional groups

Ultraviolet-visable Spectroscopy (UV-Vis)

Good for determining double/triple bonds

Mass Spectrometry (MS) Good for determining the molecular formula

Compound Validation

Induced magnetic field (mis)aligns protons

Protons also have spins: ½ and -½

Specific radio frequencies excite protons to higher energy state

Return to lower E state induces electrical signal

Signal dependent upon:

Nuclear Magnetic Resonance (NMR)

Induced magnetic field (mis)aligns protons

Protons also have spins: ½ and -½

Specific radio frequencies excite protons to higher energy state

Return to lower E state induces electrical signal

Signal dependent upon:

Nuclear shielding <- electrons shield protons from magnetic field

Nuclear Magnetic Resonance (NMR)

Induced magnetic field (mis)aligns protons

Protons also have spins: ½ and -½

Specific radio frequencies excite protons to higher energy state

Return to lower E state induces electrical signal

Signal strength dependent upon:

Nuclear shielding <- electrons shield protons from magnetic field

Peak splitting <- other, nearby protons affect spectra

Nuclear Magnetic Resonance (NMR)

Chirality

thalidomide (S)-thalidomide (R)-thalidomide

“Handedness”

Chirality

thalidomide (S)-thalidomide (R)-thalidomide

Engineering Context: Medicine

Imatinib: 4-[(4-methylpiperazin-1-yl)methyl]-N-(4-methyl-3-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide

Engineering Context: Medicine

Imatinib:

Treatment for chronic myelogenous leukemia

Cancer of the white blood cells

Caused by presence of “Philadelphia chromosome”

4-[(4-methylpiperazin-1-yl)methyl]-N-(4-methyl-3-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide

Engineering Context: Energy

Crude Oil

Engineering Context: Energy

Crude Oil: A mixture of organic compounds

Alkanes Cycloalkanes Aromatics Asphaltics

Average Composition

(by weight)30% 49% 15% 6%

Questions?

Next time:

Reactions!

Homework #3:

Due Wednesday, July 27

Exam #2:

Thursday