CHEM 201 Lectures 02 & 03 Dr. F.

Jalilehvand Chapter 9 Chemical Bonding & Molecular Structure Part 1

Practice Problems from the end of Chapter 9 (textbook) Chapter 9, Sections 9.1 & 9.2 (pp. 339 349) Molecules are three-dimensional with shapes that are built from five basic arrangements; Molecular shapes predicted with VSEPR model

Molecular geometry (shape) for small molecules VSEPR Model

Practice Problems: 9.50, 51, 54, 56, 94

VSEPR Model
Molecules are not flat as we draw their Lewis structures.

S1

Lewis & VSEPR structures

A Lewis structure shows:
which atoms are present in the molecule how the atoms share electrons to achieve totally 8 valence e-

S2

Lewis structure shows the distribution of valence electrons in a molecule and how atoms are connected to each other, but doesnt provide any information about bond angles, or shape of the molecule in 3D space.

A VSEPR structure helps us to:

convert 2D flat Lewis structure into 3D molecular shape

VSEPR = Valence Shell Electron Pair Repulsion

VSEPR model translates a Lewis structure into a molecular geometry, and helps us to predict the shapes of covalently bonded molecules or polyatomic ions.

F S F

F F

F F S

F F

Electron domains
In a Lewis structure, the central atom is surrounded by groups of valence electrons, which occupy areas in space.

S3

VSEPR Model

S4

The structure around a given atom is determined principally by minimizing electrostatic repulsion between valence electron domains. The electron domains position themselves as far apart (in direction) as possible.
Electrostatic repulsions are highest among two sets of non-bonding (lone-pair) electron pairs:

Regions in space where valence electron density can be found are known as electron domains (E.D. in the following slides).
BP e- is localized between two nuclei; LP e- is on a single atom.

Bonding domains (BP)

Single (1 shared pair) Double (2 shared e- pairs) Triple (3 shared e- pairs) e-

Non- bonding domains

Lone (unshared) pair of One lone pair ee(LP)

LP LP > LP BP > BP BP

VSEPR (electron-pair or electron-group) geometry: considering the arrangement of all valence e- domains (bonding and non-bonding) around a central atom. Molecular geometry (or shape): considering the arrangement of atoms around a central atom.

Five Basic VSEPR Geometries

S5

Linear Species 2 E.D.

All atoms lie in a straight line The angle between the three atoms is 180 Examples: BeCl2, CO2 , N3 No non-bonding (LP) electrons on central atom

S6

Lewis Structure of CO2

Non-equivalent resonance structures for CO2:

S7

Trigonal Planar Species 3 E.D.

A central atom is surrounded by three atoms All atoms are in the same plane
Bond angle = 120 Examples: BCl3, CO32- (resonance form)

S8

(-)

(+)

(0)

(0)

(0)

(+)

(-)

Best Lewis structure for CO2 is the one with all formal charges = 0

- + O C O

+ C

Polar bonds

For non-equivalent resonance forms, take the BEST Lewis structure to use for VSEPR geometry.

Lewis Structure of
(0) 2

CO32(-) 2 (-) 2

S9

Bent Species with a Trigonal Planar Geometry

A central atom with one lone-pair e- is bonded to two atoms
Bond angle < 120 Examples: SnCl2; O3 and NO2- (resonance forms)

S10

Equivalent resonance forms of carbonate group:

3 E.D. >

(-)
(-2/3)

(-)
2-

(-)

(0)

(0)

(-)

O C
(-2/3)

(0) O

For equivalent resonance forms, take the Hybrid structure to use for VSEPR geometry.
Consider resonance!

Bent

Hybrid (-2/3)

Lewis Structure of O3
(0) (+) (-) (-) (+)

S11

Tetrahedral Species 4 E.D.

A central atom surrounded by four other atoms occupying the vertices of a tetrahedron. Bond angle = 109.5
Examples: CH4, CCl4, PO43- (resonance form)

S12

Experimental evidence for O3 shows both O-O bonds have equal length.

(0)

The real structure is a hybrid of the two resonance structures.

(-1/2)
Hybrid structure:

(+)

(-1/2)

Electron domains around central O atom = 3 VSEPR geometry = Trigonal planar Molecular geometry = Bent

S13 Trigonal Pyramidal Species with a Tetrahedral Geometry A central atom with one lone-pair e- is surrounded by three atoms.
Bond angle < 109.5 Examples: NH3, IO3- (resonance form)

Bent Species with a Tetrahedral Geometry 4 E.D.

S14

4 E.D.

A central atom with two lone-pairs of electrons is surrounded by two other atoms. Bond angle << 109.5 Examples: H2O

N
Bent

Tetrahedral Geometries 4 E.D.

Molecular shapes/ geometries:

S15

Trigonal Bi-pyramidal Species 5 E.D.

A central atom surrounded by five other atoms Two axial and one equatorial ligands are in one plane. Bond angle: between two equatorial bonds = 120 between two axial bonds = 180 between an axial and equatorial bonds = 90
Examples: PF5
One pyramid on top

S16
An axial bond

All molecules shown here have 4 electron domains around the central atom.

An equatorial bond

VSEPR geometry = Tetrahedral

Bent

Behind the plane

In front of the plane

One pyramid below

S17

S18

Seasaw Species with a Trigonal Bi-pyramidal Geometry Bi A central atom with one lone-pair of e- is surrounded by four atoms
Bond angle: < 120, < 180, < 90 Examples: SF4

T-Shaped Species with a Trigonal Bi-pyramidal Geometry Bi-

5 E.D.

A central atom with two lone-pairs of electrons is surrounded by three other atoms.
Bond angle: < 180, < 90 Examples: ClF3

5 E.D.

The lone-pair of e- occupies the equatorial position.

Sizes and electronegativities of exterior atoms (e- density on bonds) also affect bond angles.

The lone-pair e-s occupy the equatorial positions.

S19

Linear Species with a Trigonal Bi-pyramidal Geometry Bi A central atom with three lone-pairs of electrons is surrounded by two other atoms.
Bond angle: 180 Examples: XeF2

VSEPR geometry: Trigonal Bi-pyramidal Bi-

5 E.D.

S20
An axial bond

Molecular geometry = Trigonal bi-pyramidal

5 E.D.

A central atom surrounded by five other atoms

Bond angle: between two equatorial bonds = 120 between two axial bonds = 180 between an axial and equatorial bonds = 90 Molecular geometry = Seesaw

An equatorial bond

A central atom with one lone-pair of e- is surrounded by four atoms Bond angle: < 120, < 180, < 90

VSEPR geometry: Trigonal Bi-pyramidal BiMolecular geometry = T-Shape

5 E.D.

S21

Lewis Structure for I3 I3- anion has totally 22 valence electrons: (3 x 7) + 1 (negative charge) = 22 e- = 11 pairs of e After distributing the valence electrons and determining FC:

S22

A central atom with two lone-pairs of electrons is surrounded by three other atoms.
Bond angle: < 180, < 90

(-)

(0) (0)

(0)

(0) (-)

(-1/2) (0) (-1/2)

I
Molecular geometry = Linear

A
(0) VSEPR: Trigonal bi-pyramid I Molecular shape: Linear Confirmed by experiment (-)

B
(0)

Hybrid of A and B

A central atom with three lone-pairs of electrons is surrounded by two other atoms.
Bond angle: 180

I I I
VSEPR: Tetrahedral Molecular shape: Bent

Possible electron arrangements for I3- 5 E.D.

S23

TBP Geometries 5 E.D.

TBP = Trigonal bi-pyramidal
All molecules shown here have five electron domains around the central atom. Molecular geometries/ shapes:

S24

Lone pairs are only 90 apart. Molecular geometry = VSEPR geometry =

Lone pairs are 120 apart.

VSEPR geometry = Trigonal bi-pyramidal

Octahedral Species 6 E.D.

A central atom is surrounded by six other atoms.
Bond angle: between opposite groups = 180 between adjacent groups = 90 Examples: SF6

S25

Square Pyramidal Species with an Octahedral Geometry

Bond angle: < 180, < 90 Examples: XeOF4, BrOF4-

S26

A central atom with one lone-pair of e- is surrounded by five atoms

6 E.D.
O F F Xe F F

Square Planar Species with an Octahedral Geometry

S27

Possible electron arrangements for XeF4 6 E.D.

S28

A central atom with two lone-pair electrons is surrounded by four other atoms.
Bond angle: 180, 90 Examples: XeF4, BrO2F2+

6 E.D.
Lone pairs of e- are only 90 apart.

A central atom with two lone-pair electrons Molecular geometry = VSEPR geometry = is surrounded by four other atoms.
Lone pairs of e- are 180 apart.

Octahedral Geometries 6 E.D.

All molecules shown here have six electron domains around the central atom. Molecular geometries/ shapes:

S29

Stereochemistry
Stereo- means 3-dimensionality. Stereochemistry concerns the relative spatial arrangement of atoms within molecules.

S30

VSEPR geometry = Octahedral

Behind the plane In front of the plane

Behind the plane In front of the plane In the plane

Methane: A small molecule

In methane (CH4), there is only one central atom:

S31

Molecular shape of larger molecules Coordinate Covalent Bond

Think of the covalent bond as the electron density existing between the two atoms. No. of lone-pairs on central metal = 0 No. of electron domains = 4 VSEPR geometry = tetrahedral Molecular shape/ geometry = tetrahedral

Chapter 9, Section 9.2 (pp. 341 349) Chapter 8, Section 8.6 (pp. 326 327)

Larger Molecules: Ethane

In ethane (H3C-CH3), there are two central atoms (surrounded by at least two other atoms): C1 C2

S32

Ethane H H H C C H H H

S33

C1
No. of electron domains around C No. of lone -pair e- around C VSEPR geometry Molecular shape / geometry

C2

VSEPR structure
Black H atoms and black lines are in the same page as two C atoms. Blue H atoms are behind the page. Red H atoms are in front of the page.

Larger Molecules: Ethylene

In ethylene (H2C=CH2), there are two central atoms: C2 C1

S34

Larger Molecules
In H3C-CH2-CH2-CH2-CH3, there are five central atoms:

S35

C1
No. of electron domains around C No. of lone -pair e- around C VSEPR geometry Molecular shape / geometry

C2

Overall ethane molecular shape: No. of electron domains around C atoms = No. of lone -pair earound C atoms = VSEPR geometry around each C atom: overall molecular shape =

Larger Molecules: Methanol

In methanol (CH3OH), there are two central atoms:

S36

Larger Molecules: Acetone

In acetone, CH3-CO-CH3, there are non-central atoms:

S37

or Lewis structure VSEPR structure Lewis structure

VSEPR structure

C
No. of electron domains around atom No. of lone -pair e- around atom VSEPR geometry Molecular shape / geometry

O
No. of electron domains around atom No. of lone -pair e- around atom VSEPR geometry Molecular shape / geometry

C1

C2

C3

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Question
Draw the VSEPR structure for urea, H2N-CO-NH2, with the following Lewis strcuture.

S38

Larger Molecules: Acetic Acid

In acetic acid (CH3COOH), there are three central atoms:

S39

O H N H C N H
Molecular shape No. of electron domains around atom No. of lone -pair e- around atom VSEPR geometry Molecular shape around N = Molecular shape / geometry

2 1

H
VSEPR structure

C1

C2

O1

Larger Molecules: Acetic Acid

O C O

S40

Functional groups
Functional group Name Functional group Name

S41

The COOH part of acetic acid is directly involved in chemical reactions.

+ Na+

C-O-H Na+ +H2O C

Hydroxyl

O
Alcohol

C-N O

OH

C H

O C O C N C
Ketone Amine

Amide

Lewis structure

Aldehyde

C-O-H O C

Carboxylic acid

C O C

Ester

Learn the VSEPR and molecular geometry around each central atom (practice on bond angles).

11

Question
What is the VSEPR geometry around B and N atoms in H3B-NH3.

S42

Coordinate Covalent Bond

S43

Electron deficient means lacking electron; not having octet Electron sufficient means having enough electron; having octet or more.

H H B H

H N H H

H H B H

H N H H

Coordinate Covalent Bond

In this type of bonding, the shared electrons
come from only one of the two atoms.

S44

Where did you see this before?

Demonstration # 1: Dissolving Na2O in water

S45

Bonding between B-N atoms in H3B-NH3 is coordinate covalent.

H H B H

H N H H Practice
Questions 9.82 and 9.83 of your textbook show the structures of two

After bond formation, we cannot tell where

was the origin of the shared electrons!

+
VSEPR geometry: Molecular geometry:

large molecules. For each central atom in these structures, determine: A) Number of electron domains B) VSEPR geometry (around each central atom) C) Molecular geometry (around each central atom) D) Bond angle

12

Bond Dipoles
Molecular dipole
Atoms with different electronegativity values will share bonding eunequally. + Blue spot = Low valence edensity

S46

Molecular Shape in Larger Molecules:

The Importance of Molecular Shape in Biological Systems

Red / hot spot = High valence edensity

F2
Practice Problems: 9.63, 65, 66, 67

HF

The greater the difference in electronegativity, the more polar is the bond.

Chapter 9, Section 9.3 (pp. 349-352) Molecular Symmetry Affects the Polarity of Molecules (Biological aspects from sources other than textbook)

HF

HCl

HBr

HI

Bond Dipoles
The orientation of a polar molecule in an external electric field:

S47

Molecular polarity
Just as bonds can be polar, molecules with more than two atoms can also be polar. Molecular polarity plays an important role in:

S48

+
- + + + Electric field OFF Random dipoles + + + + + + +

a) Reactivity (in biochemical/ chemical reactions; where is it attacked?) b) Solubility (e.g. polar solvents can dissolve polar molecules; also water can dissolve ionic compounds because it is polar)
+ + + + + + +

+ -

Electric field ON Oriented dipoles

Ionic crystal lattice

Hydrated ions (dissolves)

H2O a polar molecule

13

Molecular polarity
The distribution of the valence electrons in a molecule affects its behaviour and interactions with other molecules.

S49

Molecular polarity

S50

A molecule has a net dipole moment if its centers of + and charge are separated. The (red) side with higher e- density is highly reactive.

Molecular polarity is determined by the magnitude and orientation (/ direction) of the bond dipoles in the molecule (i.e. bond angles), which depends on the molecular shape. As first approximation, one can consider the overall molecular dipole () as vector sum of individual bond dipoles.

+
H2O CH3Cl H2C=O NH3

+ =0

As first step in determining whether a molecule is polar or not, check if the molecule has polar covalent bonds. A molecule with only non-polar bonds will be a non-polar molecule A molecule with polar bonds may be either polar or non-polar

Non-polar = 0

In CO2, the bond dipoles are equal in magnitude, but exactly in opposite directions. The overall dipole moment is = 0.

Molecular polarity
In BF3, the bond dipoles are equal in magnitude, but cancel because of the molecular symmetry. The overall dipole moment is = 0.

S51

What is symmetry?

S52

F
3

BF3 B F

Non-polar = 0
Sum of the two vectors is equal but opposite to the 3rd one; they cancel each other. A molecule has zero dipole moment when the bond dipoles cancel, i.e. molecule is non-polar.

14

Molecular polarity
Many molecules are non-polar and have no molecular dipole moment even though they contain polar bonds. These molecules have symmetrical shapes.

S53

Molecular polarity
Carbon tetrachloride (CCl4) has polar C-Cl bonds, but no overall dipole moment because the individual bond dipoles cancel. A tetrahedral molecule with four identical bonds is non-polar (e.g. CH4)

S54

BCl3

CCl4

Non-polar

CO2
All the five basic VSEPR geometries have symmetrical shapes when all of the domains attached to them are identical. Resultant of these two bond dipoles is

=0
Resultant of these two bond dipoles is

Molecular polarity

S55

Magnitude of a bond dipole depends

Molecular polarity

on between the two atoms.

S56

In molecules with trigonal bi-pyramidal or octahedral geometries sometimes the bonded atoms are not identical, but arranged in the form of a basic shape (e.g. linear or trigonal planar). Such molecules may be non-polar as long as the arrangement of atoms leads to an electronically balanced, symmetrical structure.

When all atoms attached to a central atom are not the same, the molecule may be asymmetric (not symmetric), and electronically unbalanced. Then polar molecules may result. In dichloromethane (CH2Cl2) the individual bond dipoles do not cancel.

C-H = 0.4
- (2.5 2.1)
Resultant of these two bond dipoles is

C-Cl = 0.4
(2.9 2.5)

Resultant of these two bond dipoles is Polar 0

Molecular dipole

15

Molecular polarity

C-H = 0.4

C-Cl = 0.4

S57

Molecular polarity

C-H = 0.4

C-Cl = 0.4

S58

CH2Cl2 and CH3Cl are examples of polar molecules ( 0).

Chloroform (CHCl3) and formaldehyde (H2C=O) have polar bonds and are polar molecules ( 0).

+ + + +
Molecular dipole

+ -

+
Molecular dipole

C-O = 3.5 2.5 = 1.0

Molecular polarity
Formaldehyde (H2C=O) is used to fix biological samples. Chloroform (CHCl3) makes one unconscious.

S59

Molecular polarity
CF2Cl2 has polar bonds with different dipole moments and is a polar molecule ( 0).

S60

C-Cl = 2.9 2.5 = 0.4 C-F = 4.1 2.5 = 1.6

Resultant of these two bond dipoles is

Magnitude of a bond dipole depends on between the two atoms.

Resultant of these two bond dipoles is

16

Molecular polarity

S61

Molecular polarity

S62

When non-bonding domains (lone pairs) are present and bond dipoles do not cancel, polar molecules may result.

Water has two polar O-H bonds; these dipole moments do not cancel, making water a polar molecule.

N-H = 1.0
(3.1 2.1)

Molecular dipole

+ +
Molecular dipole

Polar bonds Polar molecule 0 + +

Polarity of the water molecules helps ionic compounds to dissolve.

Molecular polarity

S63

Question
Which of the following molecules is polar? A) SF6 B) PCl5 C) both D) neither

S64

17

Question
Is SF4 a polar molecule? A) YES B) NO

S65

Question
Is BrF3 a polar molecule? A) YES B) NO

S66

Molecular polarity

S67

Predicting molecular polarity

S68

When non-bonding domains (lone pairs) are present and bond dipoles cancel each other, non-polar molecules may result.

1) Determine the Lewis structure 2) Determine the VSEPR geometry 3) Determine bond polarity and bond dipoles based on differences in 4) 5) electronegativities between the two atoms () If there is no polar bond, the molecule is non-polar ( = 0) If the bonds are polar, use the shape of the molecule to decide if the bond dipoles (vectors) cancel out. Check the vector sum of individual bond dipoles. If they cancel, the molecule is non-polar. If the molecule has one of the basic VSEPR geometries, with all electron domains occupied by the same atoms, the electron distribution is balanced by its symmetry, and it is non-polar. If the molecular shape is asymmetric, the overall distribution of its valence e- density is likely to be unbalanced, resulting in a polar molecule ( 0), with separation of + and charges.

Non-polar = 0

6)

7) Non-polar = 0

18

Peptide (or amide) bond in peptides and proteins

Proteins consist of amino acids, connected via peptide bonds Peptide bond

S69

The Importance of Molecular Shape in Biological Systems

N-terminus The following slides are for your information only (not Exam material): S-73, S-74 S-77 to S-84 S-86 to S-89

C-terminus

R Amino acid

Peptide (or amide) bond

Amide bond is a dehydration reaction; it forms when COOH group reacts with NH2 group, releasing a water molecule.

S70

Resonance in a peptide (or amide) bond

Resonance forms:

S71

A
In structure A, we expect: Nitrogen = trigonal pyramidal geometry (4 electron domains) Carbon = trigonal planar geometry (3 electron domains)

B
In structure B, we expect: Nitrogen = planar (3 electron domains) Carbon = planar (3 electron domains)

Structure A with FC = 0 on C, O, N atoms = Best Lewis structure

19

Resonance in a peptide (or amide) bond

S72

Fatty acids
Most of the fat in meat and dairy products is saturated fat (saturated means there is no double C=C or triple CC bond) In fatty acids (FA), a carboxyl group is attached to a long hydrocarbon chain (14-24 carbons; 16-18 is more common).

S73

A
Experiments show that C, N and O are in a plane! Average structure:
Delocalization of electron density (4 e-) in the plane of C, O, N atoms

Amide bonds shape:

planar

Saturated fatty acid overall molecular shape: chain

Fatty acids
Unsaturated fatty acids have one or more double C=C bonds.

S74

Drawing VSEPR Geometry for Larger Molecules

Drawing VSEPR geometry for an unsaturated fatty acid (contains C=C bond)
1/2

S75

Corn oil contains 86% unsaturated FA and 14% saturated fatty acids.

O
1/2

C H H H Physical properties of fatty acids depends on the chain length and the number of double bonds. H C

O H

1) Draw the best Lewis, or the hybrid resonance structure

2) Keep lone-pair e3) Identify central atoms

C3 C4 C H
5

20

Drawing VSEPR Geometry for Larger Molecules

Drawing VSEPR geometry for an unsaturated fatty acid

S76

DNA

S77
Deoxyribonucleic acid (DNA)

C H H H H C

1 2

O 1/2 H

Nucleotide unit

1/2

Pyrimidine bases

C3 C4 C H
5

Purine bases

S78

Active Site in Hemoglobin

S79

In large molecules, chemists focus on specific atoms or group of atoms that get involved in chemical reactions, and are active sites.
Hemoglobin transports oxygen (O2) from the air in the lungs to tissues and muscles. Hemoglobin is in the blood cells, and is responsible for their red color. Hemoglobin contains iron.

Overall DNA molecular shape: double helix

Each red blood cell contains 640 million hemoglobin molecules!

21

Active Site in Hemoglobin

Knowing the structure of hemoglobin helps to understand how O2 is transported. Hemoglobin = Heme + globin protein Hemoglobin is a tetramer: 4 x heme + 4 x globin protein Iron is surrounded by four N donors in a porphyrine ring.

S80

Enzymes
In a chemical reaction some bonds are broken and some formed. For a reaction to happen, reactants should collide effectively!

S81

A+B
Reactants

C+D
Products

O O

A reaction can go faster by increasing temperature. Chemical reactions in our body happen at 37 C. Enzymes facilitate and increase the speed of many complicated chemical reactions in our body.

Heme in Greek = blood

Without enzymes, many biological reactions would have been too slow at bodys temperature!

Active Sites in Enzymes

S82

Active Sites in Enzymes

S83

Enzymes are very specific: Specific enzyme for a specific reaction The shape of a substrate molecule should fit to the active site of that specific enzyme (like Lock & Key) Shape of substrate is important! Enzymes are very selective: Only one type of product is produced Enzymes are very efficient: Biological reactions work better in a cell than in a big reactor!

Example: Carbonic anhydrase speeds up both reactions:

CO2 + H2O HCO3- + H+

H+ + HCO3- In tissue (high CO2) H2CO3 H2O + CO2

In lung (low CO2)

Carbonic anhydrase is a metalloenzyme; it has a Zn(II) ion is its active site (shown in white).

22

S84

Chiral compounds
Imagine 4 different groups bonded to a central carbon atom.

S85

Compounds that contain a C atom connected to 4 different groups are called Chiral compounds. These 4 groups can be arranged in two different ways in space: A & B are mirror images, and cannot be overlapped (like our left/ right hands) A & B are isomers: they have the same molecular formula. A & B are optical isomers (rotate polarized light in opposite directions)

CO2 + H2O HCO3- + H+ H+ + HCO3H2CO3 H2O + CO2

Atom-atom connections are the same in optical isomers

Polarized Light

S86

S87

Interaction of Chiral Compounds w/ Polarized Light

Chiral molecules are optically active.

Optical activity: The ability of the chiral molecule to rotate the plane of polarized light.
Ref: Whitten, Chemistry, 8th Ed., Chapter 25

23

Our Body is Chiral!

S88

The Tragedy of Thalidomide

S89

Proteins/ enzymes, carbohydrates and nucleic acids in our body are chiral.

10,000 20,000 children affected by this drug during 1957-1961.

Almost all aminoacids are chiral! (except glycine, R = H)

DNA double-helix is right-handed

(S)-thalidomide Causes birth defects

(R)-thalidomide Drug for morning sickness in pregnant women

Summary
There are five basic VSEPR geometries (defined by considering all electron domains: bonding and non-bonding).

Summary
For molecules with more than one central metal, define the VSEPR and
molecular geometries around each centre.

In coordinate covalent bonding, the shared electrons in the bond come

from only one of the two atoms. When drawing the VSEPR geometry for tetrahedral C atoms, place the two backbone bonds in the plane; and both on one side of the C atom.

H H

C C2

The molecular shapes are obtained from VSEPR electron-pair geometries by considering that nonbonding LPs are invisible, and occupy positions with less repulsion.

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