workbook 01

CHEM 357 Winter 2016-Workbook01 L02 - A Musgrove Richer

Used with permission from Dr A Causton UC Chem 1

The Language of Organic Chemistry

How to Draw and Interpret Organic Structures

Structural diagrams need to include all the necessary information

Also need to reduce ldquosuperfluousrdquo information for ease of viewing structures

Drawing Hydrocarbon Frameworks

The hydrocarbon framework is made up of hydrogen and carbon atoms ONLY ndashit can be in a straight or branched chain or in a ring

Carbon can form four covalent bonds to other atoms

Hydrogen can form one covalent bond to other atoms

Steps for drawing hydrocarbon frameworks (using a five carbon chain as an example) o Notice the three dimensional shape of the molecule (which we will ignore for now)

1 Draw chains of atoms as zig-zags (to imitate the three dimensional shape)

CC

CC

C

HH HH

HH

H

HHH

H

H

2 To make the diagram above less busy miss out the Hrsquos attached to carbon atoms along with C-H bonds Occasionally the Hrsquos are included especially is they take place in a reaction or are part of a functional group (see below)

CC

CC

C

3 Now remove capital Crsquos representing carbon atoms and draw a zig-zag chain This is typically how an organic chemist draws the structure of pentane

Q1 Draw three different hydrocarbons that contain two carbon atoms Write out both the empirical formula and molecular formula for each example Hint Carbon can form single double and triple bonds with itself ndash add the appropriate number of hydrogen atoms to complete the carbon frameworks

H C

H

H

C

H

H

C

H

H

C C

H

H

H

H

H



Q2 Work out the molecular formula of the hydrocarbon molecule shown below and calculate its molecular weight

Q3 Draw ldquostickrdquo diagrams of hydrocarbon molecules with five carbon atoms (containing only single bonds) that have a 1 Single chain 2 Branched chain 3 Ring

Q4 Re-draw (and therefore ldquotidy uprdquo) the following as ldquostickrdquo representations

CH2

CH3

CH3

CH

2

CH

CH3

CH

CH2

CH2

C

H2C

H2

CH3

Wedge and hash bonds can be used to represent molecule in three dimensional space The three dimensional structure of methane (CH4) can be represented as

Wedged line points forw ard

Hashed line points behind the

plane of the paperStraight line is in the

plane of the paper



Heteroatoms

This is an atom that is neither carbon nor hydrogen

For organic chemistry this is most commonly O N F Cl Br I S P Si

These atoms are ALWAYS included in the structural drawing

Heteroatoms are generally the reactive portion of organic molecules

Q5 How many covalent bonds can be made by the following atoms O = S = N = F = Cl = Br = I =

Functional Groups

Functional groups are the key to the chemistry of molecules

Diagrams must emphasize the functional groups and let the hydrocarbon framework fade into the background

Q6 Circle amp name the functional groups in the molecule below The following structure represents ldquoNutraSweetrdquo an artificial sweetener that is 200 times sweeter than sugar (ie sucrose)

NH

O

O

NH2 O

CO2H

Q7 What is the molecular formula of this molecule



Q8 Circle amp name the functional groups in the molecule below

The structure shown below represents Astra-Zenecarsquos drug ldquoTenorminrdquo a cardiovascular -blocker for the treatment and prevention of heart disease

O

OH

N

H

Q9 What is the molecular weight of ldquoTenorminrdquo

Q10 Name the functional groups in the molecules shown below

CNNO

2Me

Me

O

CH3

CH3 O

H

Q11 Write out the molecular formula under each structure shown above

Functional Groups of Hydrocarbons

Carbon-carbon double and triple bonds are considered to be functional groups

Q12 Name the following functional groups



Interpreting Lewis Structures

The Structure of a Molecule ultimately Determines Its Bulk Properties

A molecule is a group of atoms held together by electrons to give a definite three dimensional shape

The structure and properties of the molecule are determined not only by its constituent atoms but also by how they are arranged ndash the shape of the molecule

An understanding of the fundamental principles related to the structure and bonding of atoms is essential for understanding the diverse architecture and properties of molecules

Atoms Electrons and Orbitals

Each element in the periodic table is characterized by a unique atomic number (Z) which is equal to the number of protons in its nucleus

99 of naturally occurring carbon atoms are ldquocarbon-12rdquo 1 of carbon is the isotope ldquocarbon-13rdquo For each isotope below

C

12

6 C

13

6 Q13 What is the atomic number Q14 What is signified by the mass number Q15 How many protons neutrons and electrons does each isotope have Q16 How many protons neutrons and electrons does the following ion have

C13

6

+



Organic chemists are primarily concerned only with the electrons in atoms and more importantly with the electrons in molecules

Q16 Write out the electronic configurations of Hydrogen Carbon Oxygen

Q17 How many valence electrons do the following atoms have Hydrogen Lithium Carbon Nitrogen Oxygen Chlorine

The Lewis Model of Chemical Bonding

In 1916 G N Lewis proposed that atoms combine in order to achieve a more stable electron configuration

Maximum stability results when an atom is isoelectronic with a noble gas

An ionic bond is the force of electrostatic attraction between oppositely charged ions

An electron pair that is shared between two atoms constitutes a covalent bond

Structural formulae in which electrons are shown as dots are called Lewis Structures eg H for a hydrogen atom

Sharing electrons allows atoms to become isoelectronic to a noble gas eg Two atoms of H become HH ndash filling their 1s shell

A shared electron (covalent) bond is represented by a dash ie HH becomes H-H



Q18 Draw Lewis structures for the following (show all valence electrons) F2 HCN H2O Li+Clmacr (ionic bond)

Q19 Why is the following structure not possible

Q20 Draw stick diagrams for the following (include all lone pairs of electrons)

CH3

CCH

3

OH

H

CH2

CH2

CH

2

CH2

CH2

C

CH2ClH

CH3

NCH

3

CH3

CO

CH3

O

CH3

C

H

H

H

H

H



The Shapes of Some Simple Molecules

So far covalent bonding has only been considered in two dimensions specifically o How many covalent bonds an atom can form (and why) o Drawing simple molecules using Lewis structures

What three dimensional shapes do organic molecules take and why do they assume these shapes

Types of three dimensional representations you may encounter

Application of the Valence Shell Electron Pair Repulsion (VSEPR) theory where the most stable

arrangement of groups attached to a central atom is the one that has the maximum separation of electron pairs (bonded or non-bonded)

Q21 What are the shapes of the following simple molecules

H

C H

H

HN

H

HH

H O H

B

F

FFC

O

HHO C O

Stick Model (Ethanol)

Ball-and-Stick Model

(Acetone) Space Filling Model

(Hexane)



H O

O

O

N

H O

O

O

N

Ionic Bonding


Ionic bonds are common in inorganic chemistry but rare in organic chemistry o eg NaCl

Na Cl

+ _+_

Na + Cl Na + Cl

The charge on an atom changes upon loss or gain of an electron Formal Charge for Organic Structures

To demonstrate how to calculate formal charges for individual atoms in organic molecules (with covalent bonds) consider the Lewis formula of nitric acid (HNO3) shown on the left without any charges assigned

In order to calculate the formal charge on each atom it is necessary to know how many electrons the neutral atom has in its valence shell (H = 1 C = 4 N = 5 O = 6 F = 7 etc)

Count up the number of electrons that belong to each atom o Each ldquolinerdquo in the Lewis structure represents a covalent bond ndash a shared pair of

electrons where one electron ldquobelongsrdquo to each atom on either side of the bond o Add to this the number of ldquolone pairsrdquo of electrons on each atom

H O N

O

O

6 electrons (4 from lone Pairs plus 2 from covalent bonds)



1 electron (from covalent bond)

4 electrons (4 from covalent bonds)

For the atoms in nitric acid to be considered neutral H O and N must have 1 6 and 5 electron(s) ldquobelongingrdquo to their valence shell

o The H atom has one electron ndash therefore is neutral o Two of the O atoms have six electrons - therefore are neutral o One O atom has seven electrons associate with it ndash that is one extra negatively

charged electron - therefore this atom is assigned a negative charge o The N atom has four electrons associated with it ndash that is one less negatively charged

electron - therefore this atom is assigned a positive charge

Thus the formal charges on the Lewis diagram of nitric acid are

or_

_

NOTE You should be able to look at the formal charges on an atom in an organic structure (ie the bottom left representations) and work backwards to figure out how many electrons (and lone pairs) are associated with each atom



Q22 Calculate the formal charges (if any) associated with the following structures

Q23 Add the appropriate number of electrons to the following

HC

+

H

O

H O+

N O C

H

H

H_ _

Q24 Draw a Lewis representation (and include any formal charges) of ozone O3 Q25 From you drawing comment on the expected bond lengths between each of the oxygen atoms

VERY IMPORTANT CONCEPT Resonance

Sometimes more than one Lewis structures may be written for a compounds (or ion) ndash these are known as resonance hybrids (or contributing structures)

o Consider ozone (O3) ndash the O-O-O bonds are all equal in length ndash therefore the two possible Lewis structures must represent an ldquoaveragedrdquo structure

o Notice the double-headed arrow that designates resonance structures



Q26 Draw resonance structures of ozone O3 Q27 What assumption(s) are made when ldquoreadingrdquo a resonance structure Q28 How is the concept of resonance important to interpreting the structure of benzene

NOTE By definition resonance structures differ only in the distribution of electrons in the Lewis structure - the connectivity of the individual atoms must be the same in all resonance hybrids

Q29 Draw resonance structures for the following NO3oline ion

Not a resonanceStructure

ImpossibleResonanceStructure

__

EquavlentResonanceStructure to

the one shown

DifferentResonance Structure to

the one shown



Curved Arrows

Curved arrows are used to track the flow of electrons o Full arrows are used to show the movement of a pair of electrons

OO

O OO

O

++__

o Half arrows show the movement of one electron

Cl Cl Cl Cl

Q30 Draw the curved arrows to show the electron shift between resonance structures in the amide functional group

Bad Resonance Structure but not impossible

Q31 Draw an ldquoimpossiblerdquo resonance structure for the amide functional group

Q32 Complete the following ldquoarrow pushingrdquo reaction schemes

+ Br

_



Polar Covalent Bonds and Electronegativity

Electronegativity is a measure of the ability of an element to attract electrons toward itself (when bonded to another element) - electronegative elements attract electrons

Electronegativity increases from left to right in the periodic table

Electronegativity decreases going down a group in the periodic table

The greater the difference in electronegativity between two bonded atoms - the more polar the bond

A bond can be classed as polar or non-polar - the symbols + and - are used to signify the distribution of the electron density in a polar bond

+ -

Non-Polar Bond Polar Bond

Q33 Draw a circle around the most polar molecule in the following series

H F H Cl H Br H I

Q34 Draw a circle around the polar molecule(s) in the following series H2O CH4 CO2 NH3 BF3

Q35 Draw a circle around the polar molecule(s) in the following series CH4 CH3Cl CH2Cl2 CHCl3 CCl4

Electronegativity and Resonance Structures

Among Lewis structural formulae that satisfy the octet rule and in which one or more atoms bears a formal chargehellipthe major contributor is the one in which the negative charge resides on the most electronegative atom

- -

Major Minor

Oxygen is more electronegative than nitrogen

Q36 Rank the relative importance of the following resonance contributors to ethanamide

NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__



Q37 Rank the relative importance of the following resonance contributors to the nitro functional group

RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+

Rules for Ranking Resonance Structures

MOST STABLE 1 All atoms neutral with full ldquooctetrdquo 2 All atoms with formal charges have full ldquooctetrdquo

2a More electronegative atom bears negative charge 3 Atoms present without full ldquooctetrdquo

3a More electronegative atom bears negative charge 4 Too many electrons in valence electron shell

LEAST STABLE The concept of electronegativity can help explain whyhow reactions proceed

eg SN2 nucleophilic substitution reactions ndash a one-step reaction mechanism in which the negatively charged species ldquoattacksrdquo the carbon centre that has low electron density (ie is electropositive) with the bond to the ldquoleaving grouprdquo being broken at the same time

H O

H

Br

CH3

H

H

OH

HCH

3

Br- -

Q38 In the above example why is the carbon ldquoelectropositiverdquo

Q39 Define Electrophilic Nucleophilic



Q40 Shown below is an alternate two-step mechanismthat can be proposed to the SN2 nucleophilic substitution reactions shown on the previous page Why is this proposed mechanism seriously flawed

_Br

Question to think about Q41 When looking at the reaction at the top of the page do you think the reverse reaction is possible ie products rarr reactants

H O

H

Br

CH3

H

H

OH

HCH

3

Br--



Q2 Work out the molecular formula of the hydrocarbon molecule shown below and calculate its molecular weight

Q3 Draw ldquostickrdquo diagrams of hydrocarbon molecules with five carbon atoms (containing only single bonds) that have a 1 Single chain 2 Branched chain 3 Ring

Q4 Re-draw (and therefore ldquotidy uprdquo) the following as ldquostickrdquo representations

CH2

CH3

CH3

CH

2

CH

CH3

CH

CH2

CH2

C

H2C

H2

CH3

Wedge and hash bonds can be used to represent molecule in three dimensional space The three dimensional structure of methane (CH4) can be represented as

Wedged line points forw ard

Hashed line points behind the

plane of the paperStraight line is in the

plane of the paper



Heteroatoms






Functional Groups




NH

O

O

NH2 O

CO2H






O

OH

N

H



CNNO

2Me

Me

O

CH3

CH3 O

H















C

12

6 C

13


C13

6

+



















CH3

CCH

3

OH

H

CH2

CH2

CH

2

CH2

CH2

C

CH2ClH

CH3

NCH

3

CH3

CO

CH3

O

CH3

C

H

H

H

H

H










H

C H

H

HN

H

HH

H O H

B

F

FFC

O

HHO C O




(Hexane)



H O

O

O

N

H O

O

O

N

Ionic Bonding



Na Cl

+ _+_

Na + Cl Na + Cl






H O N

O

O











or_

_






HC

+

H

O

H O+

N O C

H

H

H_ _













__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--



Heteroatoms






Functional Groups




NH

O

O

NH2 O

CO2H






O

OH

N

H



CNNO

2Me

Me

O

CH3

CH3 O

H















C

12

6 C

13


C13

6

+



















CH3

CCH

3

OH

H

CH2

CH2

CH

2

CH2

CH2

C

CH2ClH

CH3

NCH

3

CH3

CO

CH3

O

CH3

C

H

H

H

H

H










H

C H

H

HN

H

HH

H O H

B

F

FFC

O

HHO C O




(Hexane)



H O

O

O

N

H O

O

O

N

Ionic Bonding



Na Cl

+ _+_

Na + Cl Na + Cl






H O N

O

O











or_

_






HC

+

H

O

H O+

N O C

H

H

H_ _













__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--





O

OH

N

H



CNNO

2Me

Me

O

CH3

CH3 O

H















C

12

6 C

13


C13

6

+



















CH3

CCH

3

OH

H

CH2

CH2

CH

2

CH2

CH2

C

CH2ClH

CH3

NCH

3

CH3

CO

CH3

O

CH3

C

H

H

H

H

H










H

C H

H

HN

H

HH

H O H

B

F

FFC

O

HHO C O




(Hexane)



H O

O

O

N

H O

O

O

N

Ionic Bonding



Na Cl

+ _+_

Na + Cl Na + Cl






H O N

O

O











or_

_






HC

+

H

O

H O+

N O C

H

H

H_ _













__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--











C

12

6 C

13


C13

6

+



















CH3

CCH

3

OH

H

CH2

CH2

CH

2

CH2

CH2

C

CH2ClH

CH3

NCH

3

CH3

CO

CH3

O

CH3

C

H

H

H

H

H










H

C H

H

HN

H

HH

H O H

B

F

FFC

O

HHO C O




(Hexane)



H O

O

O

N

H O

O

O

N

Ionic Bonding



Na Cl

+ _+_

Na + Cl Na + Cl






H O N

O

O











or_

_






HC

+

H

O

H O+

N O C

H

H

H_ _













__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--



















CH3

CCH

3

OH

H

CH2

CH2

CH

2

CH2

CH2

C

CH2ClH

CH3

NCH

3

CH3

CO

CH3

O

CH3

C

H

H

H

H

H










H

C H

H

HN

H

HH

H O H

B

F

FFC

O

HHO C O




(Hexane)



H O

O

O

N

H O

O

O

N

Ionic Bonding



Na Cl

+ _+_

Na + Cl Na + Cl






H O N

O

O











or_

_






HC

+

H

O

H O+

N O C

H

H

H_ _













__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--










H

C H

H

HN

H

HH

H O H

B

F

FFC

O

HHO C O




(Hexane)



H O

O

O

N

H O

O

O

N

Ionic Bonding



Na Cl

+ _+_

Na + Cl Na + Cl






H O N

O

O











or_

_






HC

+

H

O

H O+

N O C

H

H

H_ _













__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--



H O

O

O

N

H O

O

O

N

Ionic Bonding



Na Cl

+ _+_

Na + Cl Na + Cl






H O N

O

O











or_

_






HC

+

H

O

H O+

N O C

H

H

H_ _













__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--





HC

+

H

O

H O+

N O C

H

H

H_ _













__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--








__


the one shown


the one shown



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--



Curved Arrows


OO

O OO

O

++__


Cl Cl Cl Cl





+ Br

_









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--









+ -



H F H Cl H Br H I





- -

Major Minor



NH2

CCH

3

O

H2N

CCH

3

O

NH2

CCH

3

O

NH2

CCH

3

O

+

+

+_

__




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--




RN

O

O

RN

O

O

RN

O

O

RN

O

O

+ + 2+







H O

H

Br

CH3

H

H

OH

HCH

3

Br- -






_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--




_Br


H O

H

Br

CH3

H

H

OH

HCH

3

Br--

workbook 01

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