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 Model VSEPR 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 S1 Lewis & VSEPR structures 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 - F F F S F A VSEPR structure helps us to: convert 2D “flat” Lewis structure into 3D molecular shape S F F F F S2
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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.
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
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;