6.03 shapes of molecules - san diego miramar...

Aug ‘171 6.03 Shapes of Molecules

6.03 Shapes of Molecules

Dr. Fred Omega GarcesChemistry 100Miramar College

Predicting Chemical Structures a Criteria for Molecular Polarity


Shapes and Sense of Smell

At the chemical level, a biological cell is a membrane bound sack filled with molecular shapes interacting in anaqueous fluid. Complex processes in an organism often begin when a molecular “Key” fits into a correspondinglyshaped molecular “lock”. The key can be a relatively small molecule circulating in a body fluid, whereas the lock isusually a large molecule, known as a biological receptor, that is often found embedded in a cell membrane. Thesurface of the receptor contains a precisely shaped cavity, or receptor site, that is exposed to the passing fluid.Thousands of molecules collide with the site, but when a molecule with the correct shape (that is, the molecularkey) lands on it, the receptor “grabs” it though intermolecular attractions, and the biological response-begins.

Let’s see how this fitting together of molecular shapes operates in the sense of smell (olfaction). A substancemust have certain properties to have an odor. An odorous molecule travels through the air, so it must come form agas or a volatile liquid or solid. To reach the receptors, it must be soluble, at least to a small extent, in the thinfilm of aqueous solution that lines the nasal passages. Most importantly, the odorous molecule, or a portion of it ,must have a shape that fits into one of the olfactory receptors sites that cover the nerve ending deep within thenasal passage. When this happens, the resulting nerve impulses travel from these needling to the brain, whichinterprets the impulses as a specific odor.

The location of olfactory receptors within the nose. A. Theolfactory area lies at the at the top of the nasal passage veryclose to the brain. Air containing the odorous molecules issniffed in, warmed, moistened, and channeled toward thisregion. B. A blowup of the region shows olfactory nerve cellsand their hair like endings protruding into the liquid-coatednasal passage. C. A further blowup shows a receptor on one ofthe endings containing at odorous molecule that matches itsshape. This particular molecule has a peppermint odor.

A B C

Link: How we smell


NCH3

Shapes of Molecules

H3CO

N

OCH3O

Herione

HO

N

OHO

Morphine

CH3O

N

OHO

CodeineCodeineMorphineHeroineMethamphetamine

Lewis Structure representation give no indication of how atoms are arranged in 3-dimensional space.How can the 3D shape of the molecule be determined from its chemical formula or its Lewis Structure?Importance of 3D chemical Structure:

Shape of molecule give rise to the unique property of the molecule.i.e., Sense of smell, taste, the potency of drugs

- all depend on the shape of the compounds


CocaineNeurotransmitters are block by cocaine up take in the receptor site.


VSEPR- Valence Shell Electron-Pair Repulsion Theory

An extension of Lewis Structure.Main premise of model-

Valence electron pair repel each other

Molecule assumes Geometry that minimizes electrostatic repulsion:

Occurs when electron pair are far apart as possible.Driving force is the Pauli exclusion principle:

2 electrons with same spin, can't occupy the same space.

Electronic Geometry is geometry around central atom in which e- e- repulsion is minimize. AEn (system)

Molecular Geometry is geometry around central atom when electron pairs are replace by bonding atoms. ABmEn (system)


Shapes for Energy Minimization

Molecules assumes a geometry that minimize electrostatic repulsion g occurs when e-pair are as far apart as possible.


VSEPR- Procedural Steps

1) Determine the Lewis Structure.a) Valence electrons for each atom in the structure.

b) Determine the number of bonds in molecule and identification the central atom

2) Determine electronic geometry (AEn system) from Lewis structure.a) Count the electron domain (region) around the central atom.

b) Arrange electron domain to minimize electron-electron repulsion.

Occurs when electron pair are far apart as possible.

c) 2-domain g linear, 3-domain g trigonal, 4-domaingtetrahedral

3) Determine molecule geometry (ABmEn system) from electronic geometry.a) The geometry is based on the position of the atoms.

b) The lone pair electrons are ignored for the molecular geometry.

i) ElecGeo-Linear AE2. MolcGeo-Linear AB2

ii) ElecGeo- Trigonal AE3. MolcGeo- Trig AB3 or Bent AB2E

ii) ElecGeo-Tetrahedral AE4. MolcGeo-tetr AB4 , pyramid AB3E or Bent AB2E2


Hubs, spokes and WheelsWhat does a wheel have in common with

molecular geometry?

A BB

..


Electron Regions and Spokes

..O C O

......

BHH

H

N OOCHH

HH

NH HH

OHH

..

..HC

HO

H C N :

OO

OC

H2N NH2

O


Electron Regions (Spokes?)

..O C O

......

BHH

H

N OOCHH

HH

NH HH

OHH

..

..HC

HO

H C N :

OO

OC

H2N NH2

O


VSEPR Table

Molecular Geometry Determination Guide

Valence Shell Electron-Pair Repulsion Theory (VSEPR) : # e- pr

AEn Electronic Geometry Bond Pair

[Coord #] non-bond AEnBm Molecular Geometry

2 AE2 EE A Linear

2 0 AB2 B A B Linear

3 0 AB3 B AB

B Trigonal

3

AE3

EE

EA

Trigonal

2 1 AB2E AB

B

..

Bent 4 0 AB4

BA

BB

B

Tetrahedral 3 1 AB3E

BA

BB

..

Pyramidal

4

AE4

A EEE

E

Tetrahedral 2 2 AB2E2 A

BB

..

..

Bent


Coordination 2: AE2 ¾® AB2

Two electron dense region around a central atom :

Examples: CO2 or BeH2

Lewis Structure Two Regions AEn ABn Molecular Geometryof e- density Ball Stick

AE2 AB2

Space filling

# e- pr AEn Electronic Geometry Bond Pair

[Coord #]

non-

bond

pair

AEnBm Molecular Geometry Bond angle

Hybrid

Examples

2 AE2

Linear

2 0 AB2

Linear

180°

sp

BeH2CO2

EE A B A B

..O C O

......

..O C O

......



[Coord #]

non-

bond

pair


Hybrid

Examples

3 AE3

Trigonal

3 0 AB3

Trigonal

120°

sp2

BF 3BCl3

2 1 AB2E

Bent

< 120°

sp2

NO2

EE

EA B A

B

B

AB

B

..

Three electron dense region around a central atom :

Examples:Lewis Structure Two Regions AEn ABn Molc’ Geometry SpaceBH3 of e- density Ball Stick filling

AE3 AB3

NO2-

AE3 AB2E

Coordination 3: AE3 ¾® AB2E , AB2

BHH

H BHH

HH H

B

H

H H

B

H

N OO N OOO

NO

O

NO


Coordination 4: AE4 ¾® AB 4 , AB3E , AB2E2Four electron dense region around a central atom :

Examples: CH4 NH3 H2O


[Coord #]

non-

bond

pair


Hybrid

Examples

4 AE4

Tetrahedral

4 0 AB4

Tetrahedral

109.5°

sp3

CH4NH4+

3 1 AB3E

Pyramidal

< 109.5°

sp3

NH3

2 2 AB2E2

Bent

< 109.5°

sp3

H2O

A EEE

E BA BB

B

BA

BB

..

AB

B..

..

CHH

HH

NH HH

OHH

H

H

N

H

HH

NH

H

O

H

H

O

H


VSEPR Table


Examples


Examples

http://www.chemeddl.org/resources/models360/models.php?pubchem=2519

N

CN

C

CC

NC

NC

C

C

O

OHH

H

HH

H

H

H

HH

N

N N

NH3CCH3

CH3

O

O

H


Examples

Caffeine

N

CN

C

CC

NC

NC

C

C

O

OHHH

HH

H

H

H

HHsp2

sp3

sp3

N

N N

NH3CCH3

CH3

O

O

H



Examples


C

C C

COH

NC

C

C

OH

CN

C

N

N

H

H

N

H HH

H

H

O

OCH3

H

AZTC

C C

COH

NC

C

C

OH

CN

C

N

N

H

H

N

H HH

H

H

O

OCH3

H

AZT


Example: Ibuprofen

http://www.chemspider.com/Chemical-Structure.36498.html


SummaryKey to determine molecular Geometry• Lewis Structure

Determine electron domain in structure.

• Electronic GeometryEstablish the AEn system.

• Molecular GeometryEstablish the ABmEn system. Determine the molecular geometry

Remember that lone pairs in the central atom shapes the geometry but do not take part molecular geometry, i.e. bent shape of water.

6.03 shapes of molecules - san diego miramar...

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