chapter 9_part 1_4 pages per slide

1

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 ModelVSEPR Model

Molecules are not “flat” as we draw their Lewis structures.

Lewis structure shows the distribution of valence electrons in a molecule and how atoms are connected to each other, but doesn’t provide any information about bond angles, or shape of the molecule in 3D space.

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

VSEPR = Valence Shell Electron Pair Repulsion

S1Lewis & VSEPR structuresLewis & VSEPR structures

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

FF

F

S

F

A VSEPR structure helps us to: convert 2D “flat” Lewis structure into 3D molecular shape

SF F

F F

S2

2

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

Regions in space where valence electron density can be found areknown as “electron domains” (E.D. in the following slides).

Bonding domains (BP) Non- bonding domainsSingle (1 shared e- pair)Double (2 shared e- pairs)Triple (3 shared e- pairs)

Lone (unshared) pair of e- (LP)One lone pair e-

BP e- is localized between two nuclei; LP e- is on a single atom.

S3VSEPR ModelVSEPR Model 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:

LP – LP > LP – BP > BP – BP

Molecular geometry (or shape): considering the arrangement of atoms around a central atom.

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

S4

Five Basic VSEPR GeometriesFive Basic VSEPR GeometriesS5

Linear SpeciesLinear Species

All atoms lie in a straight line The angle between the three atoms is 180º Examples: BeCl2, CO2 , N3

-

No non-bonding (LP) electrons on central atom

2 E.D.S6

3

Non-equivalent resonance structures for CO2:

O C O(+) (-)

O C O(+)(-)

O C O(0) (0)(0)

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

O C O

Lewis Structure of COLewis Structure of CO22

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

- + - -+

C OPolar bonds

S7Trigonal Planar SpeciesTrigonal Planar Species A central atom is surrounded by three atoms All atoms are in the same plane

Bond angle = 120º Examples: BCl3, CO3

2- (resonance form)

3 E.D.S8

(-)(-)

(0)

(-)

(-)

(0)

(-)

(-)(0)

2 2 2

Equivalent resonance forms of carbonate group:

OC

O

O

(-2/3)

(0)

Hybrid

2-

(-2/3)

(-2/3)

Lewis Structure of COLewis Structure of CO3322--

For equivalent resonance forms, take the Hybrid structure to use

for VSEPR geometry.

S9Bent Species with a Trigonal Planar GeometryBent Species with a Trigonal Planar Geometry

A central atom with one lone-pair e- is bonded to two atoms

Bond angle < 120º Examples: SnCl2; O3 and NO2

- (resonance forms)

3 E.D.

Bent

Consider resonance!

>

S10

4

Lewis Structure of OLewis Structure of O33

O O O O O O

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

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

O O OHybrid structure:

(-)(+)(0) (-) (+) (0)

(+)(-1/2) (-1/2)

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

S11Tetrahedral SpeciesTetrahedral Species

A central atom surrounded by four other atoms occupying the vertices of a tetrahedron.

Examples: CH4, CCl4, PO43- (resonance form) Bond angle = 109.5º

4 E.D.S12

Trigonal Pyramidal Species with a Tetrahedral GeometryTrigonal Pyramidal Species with a Tetrahedral Geometry

A central atom with one lone-pair e- is surrounded by three atoms.

Bond angle < 109.5º Examples: NH3, IO3

- (resonance form)

N

H H H

4 E.D.

S13Bent Species with a Tetrahedral GeometryBent Species with a Tetrahedral Geometry

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

4 E.D.

Bent

S14

5

Tetrahedral GeometriesTetrahedral Geometries

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

4 E.D.

Molecular shapes/ geometries:

Bent

VSEPR geometry = Tetrahedral

S15Trigonal BiTrigonal Bi--pyramidal Speciespyramidal Species

A central atom surrounded by five other atoms

Examples: PF5

Bond angle:between two equatorial bonds = 120ºbetween two axial bonds = 180ºbetween an axial and equatorial bonds = 90º

5 E.D.

An equatorial bond

An axial bond

Two axial and one equatorial ligands are in one plane.

Behind the plane

In front of the plane

One pyramid on top

One pyramid below

S16

SeasawSeasaw Species with a Trigonal BiSpecies with a Trigonal Bi--pyramidal Geometrypyramidal Geometry

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

5 E.D. Bond angle: < 120º, < 180º, < 90º Examples: SF4

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

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

S17TT--Shaped Shaped Species with a Trigonal BiSpecies with a Trigonal Bi--pyramidal Geometrypyramidal Geometry

5 E.D.

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

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

S18

6

Linear Linear Species with a Trigonal BiSpecies with a Trigonal Bi--pyramidal Geometrypyramidal Geometry

5 E.D. A central atom with three lone-pairs of electrons is surrounded by two other atoms. Bond angle: 180º Examples: XeF2

S19VSEPR geometry: Trigonal BiVSEPR geometry: Trigonal Bi--pyramidalpyramidal

A central atom surrounded by five other atoms

Bond angle:between two equatorial bonds = 120ºbetween two axial bonds = 180ºbetween an axial and equatorial bonds = 90º

5 E.D.

An equatorial bond

An axial bondMolecular geometry = Trigonal bi-pyramidal

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

Molecular geometry = Seesaw

S20

VSEPR geometry: Trigonal BiVSEPR geometry: Trigonal Bi--pyramidalpyramidal 5 E.D.

Molecular geometry = T-Shape

Molecular geometry = Linear

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

Bond angle: < 180º, < 90º

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

S21Lewis Structure for ILewis Structure for I33

--

I3- anion has totally 22 valence electrons:

(3 x 7) + 1 (negative charge) = 22 e- = 11 pairs of e-

III

VSEPR: TetrahedralMolecular shape: Bent

After distributing the valence electrons and determining FC:

(0)

I I I(-) (0)

I I I(0) (-)(0)

A B

I I I(0)(-)(0)

C

VSEPR: Trigonal bi-pyramid

Molecular shape: LinearConfirmed by experiment

I I I

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

Hybrid of A and B

S22

7

Possible electron arrangements for IPossible electron arrangements for I33-- 5 E.D.

Lone pairs are only 90º apart. Lone pairs are 120º apart.

Molecular geometry =

VSEPR geometry =

S23 TBP GeometriesTBP Geometries

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

5 E.D.

TBP = Trigonal bi-pyramidal

VSEPR geometry = Trigonal bi-pyramidal

Molecular geometries/ shapes:

S24

Examples: SF6

Octahedral SpeciesOctahedral Species

A central atom is surrounded by six other atoms.

6 E.D.

Bond angle:between opposite groups = 180ºbetween adjacent groups = 90º

S25Square PyramidalSquare Pyramidal Species with an Octahedral GeometrySpecies with an Octahedral Geometry

6 E.D. A central atom with one lone-pair of e- is surrounded by five atoms

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

-

XeF

F

F

F

O

S26

8

Square PlanarSquare Planar Species with an Octahedral GeometrySpecies with an Octahedral Geometry

6 E.D. A central atom with two lone-pair electrons is surrounded by four other atoms.

Bond angle: 180º, 90º Examples: XeF4, BrO2F2

+

S27Possible electron arrangements for XeFPossible electron arrangements for XeF44

A central atom with two lone-pair electrons is surrounded by four other atoms.

Lone pairs of e- are only 90ºapart.

Lone pairs of e- are 180ºapart.

Molecular geometry = VSEPR geometry =

6 E.D.S28

Octahedral GeometriesOctahedral Geometries 6 E.D.

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

Molecular geometries/ shapes:

VSEPR geometry = Octahedral

S29StereochemistryStereochemistry

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

Behind the plane


Behind the plane


In the plane

S30

9

Molecular shape of larger molecules

Coordinate Covalent Bond

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

Methane: A small moleculeMethane: A small molecule

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

No. of electron domains = 4 No. of lone-pairs on central metal = 0

VSEPR geometry = tetrahedralMolecular shape/ geometry = tetrahedral

Think of the covalent bond as the electron density existing between the two atoms.

S31

Larger Molecules: EthaneLarger Molecules: Ethane In ethane (H3C-CH3), there are two central atoms (surrounded by at least two other atoms):

No. of electron domains around CNo. of lone -pair e- around CVSEPR geometry

Molecular shape / geometry

C1 C2

C2

C1

S32EthaneEthane

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.

VSEPR structure

C C

H

H

H

HH

H

S33

10

Larger Molecules: EthyleneLarger Molecules: Ethylene

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

No. of electron domains around CNo. of lone -pair e- around CVSEPR geometry


C1 C2

C1

C2

“Overall” ethane molecular shape:

S34Larger MoleculesLarger Molecules

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

No. of electron domains around C atoms = No. of lone -pair e- around C atoms =

VSEPR geometry around each C atom:

“overall” molecular shape =

S35

Larger Molecules: MethanolLarger Molecules: Methanol

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

No. of electron domains around atomNo. of lone -pair e- around atomVSEPR geometry


C O

Lewis structure VSEPR structure

or

S36Larger Molecules: AcetoneLarger Molecules: Acetone

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

Lewis structure VSEPR structure

12

3



C1 C2 C3

S37

11

QuestionQuestion

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

CN N HHH

H

O

Molecular shape

Molecular shape around N =

S38Larger Molecules: Acetic AcidLarger Molecules: Acetic Acid

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



C1 C2

1 2

1

O1

VSEPR structure

S39

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

+ CH

H

H

C

O

O Na+

+H2O

Na+ OH-

Lewis structure

Larger Molecules: Acetic AcidLarger Molecules: Acetic AcidS40 Functional groupsFunctional groups

Functional group

HydroxylAlcohol

Ketone

Aldehyde

Amine

Name Functional group Name

Amide

Carboxylic acid

Ester

C-O-H

C

O

HO

CC C

N

C-N

O

H

C-O-H

O

O

C O CC

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

S41

12

QuestionQuestion

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

S42Coordinate Covalent BondCoordinate Covalent Bond

Electron deficient means lacking electron; not having octet

Electron sufficient means having enough electron; having octet or more….

B

H H

H

HNH

H

B

H H

H

HNH

H

S43

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

Coordinate Covalent BondCoordinate Covalent Bond

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

B

H H

H

HNH

H

B N+

VSEPR geometry:

Molecular geometry:

After bond formation, we cannot tell where was the origin of the shared electrons!

S44Where did you see this before? Where did you see this before?

Demonstration # 1: Dissolving Na2O in water

S45

PracticePractice

Questions 9.82 and 9.83 of your textbook show the structures of two large molecules. For each central atom in these structures, determine:

A) Number of electron domainsB) VSEPR geometry (around each central atom)C) Molecular geometry (around each central atom)D) Bond angle

13

Molecular dipole

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

Molecular Shape in Larger Molecules: The Importance of “Molecular Shape” in Biological Systems

Practice Problems: 9.63, 65, 66, 67

Bond DipolesBond Dipoles

HF

Atoms with different electronegativity values will share bonding e-

unequally.

Red / hot spot = High valence e-

density

F2

Blue spot = Low valence e-

density

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

HF HCl HBr HI

+ -

S46

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

Electric field OFF

+

+

-

-

+-

Random dipolesElectric field ON

+

+

+ -

-

-+

-

-

+

-

-+

+

+ -

Oriented dipoles

-

+

S47Molecular polarityMolecular polarity Just as bonds can be polar, molecules with more than two atoms

can also be polar.

b) Solubility (e.g. polar solvents can dissolve polar molecules; also water can dissolve ionic compounds because it is polar)

Molecular polarity plays an important role in:

a) Reactivity (in biochemical/ chemical reactions; where is it attacked?)

H2O a polar molecule

Hydrated ions (dissolves)

Ionic crystal lattice

+

-

++

-

-

++

+

+

+ +

+

S48

14

Molecular polarityMolecular polarity

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

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

A molecule with polar bonds may be either polar or non-polar

CH3ClH2O H2C=O NH3

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.

+ -

S49Molecular polarityMolecular polarity 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.

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

As first approximation, one can consider the overall molecular dipole () as vector sum of individual bond dipoles.

Non-polar

+

= 0 = 0

- + -

S50

BF3

B

F

F F3


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

Non-polar

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.

= 0

S51What is What is ““symmetrysymmetry””??

S52

15

Molecular polarityMolecular polarity Many molecules are non-polar and have no molecular dipole

moment even though they contain polar bonds. These molecules have “symmetrical” shapes.

All the five basic VSEPR geometries have “symmetrical” shapeswhen all of the domains attached to them are identical.

CO2

BCl3 CCl4

S53Molecular polarityMolecular polarity Carbon tetrachloride (CCl4) has polar C-Cl bonds,

but no overall dipole moment because the individual bond dipoles cancel.

Resultant of thesetwo bond dipoles is


Non-polar = 0

A tetrahedral molecule with four identical bonds is non-polar (e.g. CH4)

S54

Molecular polarityMolecular polarity 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.

S55Molecular polarityMolecular polarity 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.

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

C-H = 0.4(2.5 – 2.1)

C-Cl = 0.4(2.9 – 2.5)



-+ Molecular dipole

Polar ≠ 0

+

-+

-

S56

16


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

-

+

-

+

+

--

+Molecular dipole

C-H = 0.4 C-Cl = 0.4S57

Molecular polarityMolecular polarity Chloroform (CHCl3) and formaldehyde (H2C=O) have polar bonds and

are polar molecules ( ≠ 0).

-

+

C-H = 0.4 C-Cl = 0.4

-

+

C-O = 3.5 – 2.5 = 1.0

-

+

-

+Molecular dipole

S58

Molecular polarityMolecular polarity Formaldehyde (H2C=O) is used to “fix” biological samples.

Chloroform (CHCl3) makes one unconscious.

S59Molecular polarityMolecular polarity

C-Cl = 2.9 – 2.5 = 0.4

C-F = 4.1 – 2.5 = 1.6

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

-+



+

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

S60

17


-

+

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

N-H = 1.0(3.1 – 2.1)

Polar bonds

Polar molecule≠ 0

-

+

Molecular dipole

S61Molecular polarityMolecular polarity Water has two polar O-H bonds; these dipole moments do not cancel,

making water a polar molecule.

-

+Molecular

dipole

+

-

Polarity of the water molecules helps ionic compounds to dissolve.

S62

Molecular polarityMolecular polarity S63QuestionQuestion

Which of the following molecules is polar?

A) SF6 B) PCl5 C) both D) neither

S64

18

QuestionQuestion

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

S65QuestionQuestion

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

S66


Non-polar = 0

Non-polar = 0

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

S67Predicting molecular polarityPredicting molecular polarity

1) Determine the Lewis structure2) Determine the VSEPR geometry3) Determine bond polarity and bond dipoles based on differences in

electronegativities between the two atoms ()4) If there is no polar bond, the molecule is non-polar ( = 0)5) 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.

6) 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.

7) 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.

+ - S68

19

The Importance of “Molecular Shape” in Biological Systems

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

Peptide (or amide) bond in peptides and proteins Peptide (or amide) bond in peptides and proteins

Proteins consist of amino acids, connected via peptide bonds

R

C-terminus

N-terminus

Amino acid

Peptide bond

S69

Peptide (or amide) bondPeptide (or amide) bond

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

S70

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

Resonance in a peptide (or amide) bondResonance in a peptide (or amide) bond Resonance forms:

A B

Carbon = trigonal planargeometry (3 electron domains)

Nitrogen = trigonal pyramidalgeometry (4 electron domains)

In structureA, we expect: In structure B, we expect:

Nitrogen = planar (3 electron domains)

Carbon = planar (3 electron domains)

S71

20

Average structure:

Resonance in a peptide (or amide) bondResonance in a peptide (or amide) bond

A B

Experiments show that C, N and O are in a plane!

Delocalization of electron density (4 e-) in the plane of C, O, N atoms

Amide bond’s shape:planar

S72Fatty acidsFatty acids

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

Saturated fatty acid “overall” molecular

shape: chain

S73

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

Physical properties of fatty acids depends on the chain lengthand the number of double bonds.

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

S74Drawing VSEPR Geometry for Larger MoleculesDrawing VSEPR Geometry for Larger Molecules

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

C

C

C

C

HH

H

H

H H

H

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

3) Identify central atoms

2) Keep lone-pair e-

C

2

3

4

5

1O

O1/21/2

S75

21

Drawing VSEPR Geometry for Larger MoleculesDrawing VSEPR Geometry for Larger Molecules

Drawing VSEPR geometry for an unsaturated fatty acid

C

C

C

C

C

HH

H

H

H H

H

1/21

2

3

4

5

O

O1/2

S76 DNADNA

Purine bases

Pyrimidine basesNuc

leot

ide

unit

Deoxyribonucleic acid (DNA)

S77

“Overall” DNA molecular shape:

double helix

S78Active Site in HemoglobinActive Site in Hemoglobin

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.

Each red blood cell contains 640 million hemoglobin molecules!

Hemoglobin contains iron.

S79

22

Iron is surrounded by four N donors in a porphyrine ring.

Heme in Greek = blood

Hemoglobin is a tetramer:

Hemoglobin = Heme + globin protein

4 x heme + 4 x globin protein

Knowing the structure of hemoglobin helps to understand how O2 is transported.

OO

Active Site in HemoglobinActive Site in HemoglobinS80

EnzymesEnzymes

In a chemical reaction some bonds are broken and some formed.

For a reaction to happen, reactants should collide effectively!

A + B C + DReactants Products

A reaction can go faster by increasing temperature.

Chemical reactions in our body happen at 37 ºC.

Enzymes facilitate and increase the speed of many complicated chemical reactions in our body.

Without enzymes, many biological reactions would have been too slow at body’s temperature!

S81

Active Sites in EnzymesActive Sites in Enzymes

Enzymes are very specific: Specific enzyme for a specific reaction

Enzymes are very efficient: Biological reactions work better in a

cell than in a big reactor!

The shape of a substrate molecule should fit to the active site of that specific enzyme (like Lock & Key)

Enzymes are very selective: Only one type of product is produced

Shape of substrate is important!

S82Active Sites in EnzymesActive Sites in Enzymes

Example: Carbonic anhydrase speeds up both reactions:

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

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

HCO3- + H+ H2CO3 H2O + CO2

In lung (low CO2)

S83

23

CO2 + H2O H+ + HCO3-

HCO3- + H+ H2CO3 H2O + CO2

- + -

S84ChiralChiral compounds compounds Imagine 4 different groups bonded to a central carbon atom.

These 4 groups can be arranged in two different ways in space:

A BAtom-atom connections are the

same in optical isomers

A & B are mirror images, and cannot be overlapped (like our left/ right hands)

A & B are optical isomers (rotate polarized light in opposite directions)

Compounds that contain a C atom connected to 4 different groups are called Chiral compounds.

A & B are isomers: they have the same molecular formula.

S85

Polarized LightPolarized LightS86

Ref: Whitten, “Chemistry”, 8th Ed., Chapter 25

Interaction of Interaction of ChiralChiral Compounds w/ Polarized LightCompounds w/ Polarized Light

Optical activity:The ability of the chiral molecule to rotate the plane of polarized light.

Chiral molecules are optically active.

S87

24

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

Almost all aminoacids are chiral!(except glycine, R = H) DNA double-helix is

right-handed

Our Body is Our Body is ChiralChiral! ! S88

(S)-thalidomide (R)-thalidomide

Drug for morning sickness in pregnant women

Causes birth defects

The Tragedy of ThalidomideThe Tragedy of Thalidomide

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

S89

SummarySummary

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

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

SummarySummary

In coordinate covalent bonding, the shared electrons in the bond come from only one of the two atoms.

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

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.

C1

C2

C3

H

H

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