Molecular Structure:Introduction and Review

Lecture Supplement page 3

Taxol: An anticancer drug

H

OO

O

O

H3C OH3C

O

OHCH3

OO

N

H

CH3

O

O

HO

O

OH

H

CH3

CH3

Basic Questions

Organic chemistry: What is it?•The study of molecules containing carbon

Why all this fuss about carbon?•Millions of molecules known from small set of elements (northeast corner of periodic table)•Carbon is unique in its ability to form stable rings and chains

Example: Cholesterol

HO

CH3

CH3

•Carbon compounds basis for life (as we know it)

Basic Questions

•Broadly applicable to other fields: Biochemistry, pharmaceuticals, biology, etc.

•Skills learned useful elsewhere: Information organization, critical/analytical thinking, etc.

How often should I study organic chemistry?•Monday, Tuesday, Wednesday, Thursday, Friday, Saturday, Sunday…

Why should I study organic chemistry?

Basic Questions

In Chemistry 14C we expand our knowledge of organic molecular structure by exploring…

•Selected topics in structural theory: Resonance, conjugation, aromaticity, stereochemistry, etc.

•Laboratory determination of structure: Spectroscopy

•Structure controls properties: Physical, chemical, biological

•Reaction chemistry (substance substance) covered in Chemistry 14D

Basic Questions

What is molecular structure?•Molecular structure = electron distribution (in bonds, in molecule) and positions of atoms in space.

•Example: Water

O

HH

H-O-H bond angle 104.5o

O-H bond length 0.96 Å

Molecular RepresentationsHow do we draw molecules?

is a covalent bond (electron pair shared by two atoms)

• : is a lone (nonbonded) electron pair

• Carbons do not always have to be drawn

• Hydrogens can be omitted only if carbon not written as C

• All other atoms must always be shown

• Lone pairs do not always have to be shown

• Formal charges must always be shown (unless FC = 0)

• Three-dimensional geometry does not always have to be shown

bond projects outward towards viewer

bond recedes away from viewer

The Rules

CH3NH2

H C

H

N

H H

H

H

NH2

H

H

Molecular Representations

C C

H

H

H H

OH

C

H

H

C

H

H

C C C

H

H H

H

H

H

C C

H

H

C

O

OH

Queen Honeybee molecule(E)-9-hydroxydec-2-enoic acid

9-HDA

C10H18O3Molecular Formula

Name

Fully drawn out structure

OH

OH

OBond - Line notation

(CH3)CH(OH)CH2CH2CH2CH2CH2CH=CHCOOHMolecular Formula (elaborated)

Me

OH

OH

O

H3C

OH

OH

O

Napoleon: IntroKlein: Chap 1

Molecular Representations

Applying the rules: Taxol, an anticancer drug•Carbons do not always have to be drawn•Hydrogens can be omitted only if carbon not written as C•All other atoms must always be shown•Lone pairs do not always have to be shown

H

OO

O

O

H3C OH3C

O

OHCH3

OO

N

H

CH3

O

O

HO

O

OH

H

CH3

CH3

Molecular RepresentationsYour molecular model kit

•Models useful to visualize, manipulate structures in three dimensions

•Compare molecular models of molecules in this review versus their “paper” structures

•Bring models to discussion sections

•Models can be used on exams

•Models are a good habit and can be a fun toy!

•“How to use your model kit” tutorial is available on Prof. Hardinger’s course website

Molecular model kit Benzene -D-Glucopyranose

Molecular Representations

•More often you see it, more important it is

•More important it is, greater chance you might need to know its structure Common: Methane, glucose Uncommon: Taxol

•Pure memorization (the “m word”) rarely needed

Do I have to memorize these structures?

Molecular Representations

•Naming of simple molecules

•Drawing structure of simple molecules from name

•Examples:

What do I have to know about nomenclature?

2-chlorobutane Cl

CH3

OH

3-methylcyclohexanol

H

H

H H

HC

The Electron Count CountsReview Lewis structure tutorial at course web site

•H full shell = two electrons (same as He)

•2nd row elements (CNOF): Eight electrons and four bonds maximum

The "octet rule"

Pentavalent carbon very bad

•3rd row elements easily violate “octet rule”

Valence shell electron count

O P

O

O

O S often has 12 electronsP often has 10 electrons O S

O

O

O

The Electron Count Counts

Definition: The charge on an atom in a Lewis structure if the bonding was perfectly covalent and the atom has exactly a half-share of the bonding electrons. (The difference between the number of electrons “owned” by a covalently bonded atom versus the same atom without any bonds, i.e., a free atom of the same element.)

Formal Charge

Significance•Indicates electron excess or deficiency•Desire to gain or lose electrons•Electrostatic interaction between regions of charge

Determination of formal charge•Review tutorial at course web site

Formal Charge

=# of valence electrons

-# of electrons present as lone pairs

# of shared electrons+

2

The Electron Count Counts

Formal Charge Self-Test•Verify the formal charges in the following molecule:

NADCoenzyme in biological oxidation reactions

OOP

O

O

OP

O

O

OON

H2N

O

HO OHHO OH

N

NN

N

NH2

The Electron Count Counts

Formal Charge Self-Test•Verify the formal charges in the following molecule:

NADCoenzyme in biological oxidation reactions

OOP

O

O

OP

O

O

OON

H2N

O

HO OHHO OH

N

NN

N

NH2

+1

-1 -1

All other atoms in this molecule have formal charge of zero

Electrons in Bonds

…even (covalent bond)

…uneven (polar covalent bond or ionic bond)

Electronegativity (EN): Power of an atom to attract electrons to itself

High EN = strong electron attraction

Low EN = weak electron attraction

•Electron distribution can be…

Electrons in BondsPauling EN values for elements important to Chemistry 14C

H = 2.1

C = 2.5 N = 3.0 O = 3.5 F = 4.0

P = 2.2 S = 2.5 Cl = 3.0

Br = 2.8

I = 2.5

EN with distance from fluorine

Must I memorize electronegativity values?•Not necessary…just do lots of problems. Learn them by frequent use.

EN decreases

EN decreases

EN decreases

Polar Covalent BondsUneven electron distribution leads to partial charges

XY

EN (X) < EN (Y)

Result: Bond dipole or polar covalent bond

Magnitude of bond dipole influenced by...

• EN difference bond dipole

• bond length bond dipole

•Example: CH EN = 0.4 but has low polarity due to short bond length

Polar Covalent BondsUneven electron distribution leads to partial charges

•Electrostatic interaction with other ions or moleculesConsequences of bond polarity

Influences chemical, physical, and biological properties

Example: Polar H-N bond hydrogen bonding DNA base pairing

Adenine Thymine

N

N

N

N

H N

N

O

O CH3N H

H

Functional Groups

Functional group (FG): A characteristically bonded group of atoms that determines molecular properties regardless of what molecule contains it.

Why study FG?Similar functional groups similar properties

Expected skills:•Identify FG within molecules•Draw molecules with particular FG

FG Table: Thinkbook Appendix A

Identify the Functional Groups in Taxol

O O

CH3

CH3

O

H3CONHO

OH

O

H3C CH3OH

OOOH

O

CH3

O

O

H

ester

Benzene ring Alcohol

Benzene ring

ester

ether (cyclic)

AlcoholKetoneester

Alkene

Amide

Benzene ring

ester

Atomic Positions and Molecular Geometry

repulsion causes bond angle

•Larger electron cloud = stronger repulsion

•Approx. electron cloud size: H, F < lone pair, Cl, Br, I < group of atoms (CH3, OH, etc.)

bond anglee- cloud repulsion

Atoms = balls of electrons

...have mutual repulsion

...move as far apart as possible

The relationship between Lewis Structures, Valence Shell Electron Pair Repulsion Theory (VSEPR) and Hybridization

Molecular Formula ↓

Propose a good Lewis Structure (fulfill octet rule, minimize formal charges) ↓

Use VSEPR to “space out” groups as far away from each other as possible (this final geometry is referred to in the chart below as the “electron

arrangement”)↓

Choose the hybridization scheme that gives the desired geometry

• Discuss handout on hybridization

Atomic Positions and Molecular Geometry

•Four electron clouds around central atom tetrahedral shape

•Lone pair/lone pair repulsion > H/H repulsion H-O-H angle < 109.5o

H

H

H

H

OH

H

Methane

•Four electron clouds around central atom tetrahedral shape

•Equal repulsion by all H equal H-C-H angles (109.5o)

Water

109.5o

104.5o

Bonds, Molecular Geometry, and Orbitals

•Orbital: Mathematical equation that describes a volume of space in which there is a certain probability of finding an electron of a certain energy.

•Orbitals can be drawn, but have no physical reality.

•Bond example: Two H 1s orbitals (spheres) overlap to form H-H bond:

Hydrogen atoms

+

Hydrogen molecule

Covalent bonds formed by overlap of orbitals

Bonds, Molecular Geometry, and Orbitals

H (1s) + C (2s, 2px, 2py, 2pz) C-H bonds

Therefore this orbital combination incorrect

+

orthogonal

What orbitals are used for organic molecules? Example: Methane (CH4)

H-C-H bond angle 90o

H 1s + C 2px + C 2pz wrong H-C-H bond angle!

Verify with your model kit

•s + px + py + pz sp3 + sp3 + sp3 + sp3

•C sp3 + H 1s C-H bond

Bonds, Molecular Geometry, and Orbitals

•Use mathematical combinations of s, px, py, and pz orbitals to form correct

number of bonds with correct geometry•Combinations = hybrid orbitals

Hybridization scheme for atom with four electron groups•Electron group = bond or lone pair•CH4 geometry = tetrahedral; need four bonds and four hybrid orbitals•Orbital conservation: Four hybrid orbitals come from four atomic orbitals

CH

H

H

H

109.5osp3

Solution (Linus Pauling, 1931)

Molecular Conformations

Additional material available on course web site

CH3H3C

HH H

H

HH3C

HH CH3

HAcyclic molecules:

Eclipsed Staggered

Cyclic molecules:

Axial Equatorial

H

CH3

H

CH3