Chemistry of

covalent

bonds

Unit 2: SMELLS

Molecular Structure and

Properties

How do elements combine that have

similar electronegativities?

Combine in fixed ratios.

Hydrogen peroxide

Glucose C6H12O6

*the combination of two or more different kinds of atoms.

Property of almost all elements – the ability to

combine with other elements and form

compounds*

In a compound, the different elements lose

their individual chemical properties.

Compounds and Chemical Formula

Compounds often have common names such as

water or salt - but are also named by their formula

which tell what elements make up the compound

and in what proportion.

For example, a molecule of

water is made up of two

hydrogen atoms for every one

oxygen atom. H2O

Law of conservation of mass

Mass is not created or destroyed during a chemical reaction or physical change – but it can change form.

Compounds can be

separated based on their size

and charge.

The reactions/actions of elements

that share electrons

How compounds form -

Electron arrangement determines

the chemical properties of an atom

e- move around

the nucleus in

specific energy

levels

Each energy level

(shell) is

numbered starting

closest to the

nucleus.

This is called the energy

level’s “quantum number”

Max. # of e- in each energy level calculated

by the formula: 2n2 (where n is the quantum number)

Each atomic orbital and the electrons in it are associated with

a specific amount of energy, and the farther an electron is

from the nucleus the greater its

energy (very important).

*The electrons in the outermost (highest) E level.

It is the outermost electrons that determine the chemical properties of the element. (very important)

These outermost electrons are the one’s that are

involved in bonding.

Chemistry of an element depends almost entirely

on the number of its valence electrons.

Chemical Bonding

A chemical bond results from strong electrostatic interactions between two atoms.

The nature of the atoms determines the kind of bond.

Atoms bond to achieve

stability – reach a stable

OCTET

Predicting types of bonds

How do you predict what type of bond will from between atoms?

Notice the location of the elements in the Periodic Table. As a rule, elements on the right (non-metals) share electrons with each other (covalent bonds) and elements on the left tend to donate electrons to elements on the right (ionic bonds).

What factors determine if an atom forms a covalent or ionic bond with another atom?

The number of electrons

in an atom, particularly the

number of the electrons

furthest away from the

nucleus determines the

atom’s reactivity and

hence its tendency to form

covalent or ionic bonds.

If enough energy is applied, either by another

element or by external photons, electrons can be

pushed so far that they escape the attraction of the

nucleus

Losing an electron is called ionization

Ionic Bonding

Losing/gaining an electron is called ionization

An ion is an atom that has either a net positive or net

negative charge.

cation

It is possible that, as two

atoms come close, one

electron is transferred to the

other atom.

The atom that gives up an

electron acquires a +1

charge and the other atom,

which accepts the electron

acquires a –1 charge.

The two atoms are attracted

to each (opposite charges

attract) resulting in an IONIC

bond.

3 Biologically Important Properties

of Ionic Compounds

Ionic compounds are soluble in water.

In aqueous

solution, an

ionic compound

dissociates

into its ions.

The

dissociated

ions in

aqueous

solution give

the solution the

ability to

conduct

electricity.

Metallic Bonds

Metallic bonds occur when metal atoms share electrons.

Electrons in the outer shells float together loosely and form a “sea” electrons.

This also explains why metals are

good conductors

The outer electrons are so weakly bound to metal

atoms that they are free to roam across the entire

metal. Having “lost” their outer electrons, individual

metal atoms are more like positive ions in a swarm

of communal electrons.

Metallic bonding

Lesson 1: Sniffing Around

Molecular Formulas

What does chemistry have to do with

smell?

Smell appears to be related to molecular

formula and chemical name.

Lesson 2: Molecules in Two

Dimensions

Structural Formulas

Key Question

How can molecules with the same molecular

formula be different?

You will be able to:

• describe the difference between

structural formulas and molecular

formulas

• recognize isomers

Molecular formula: The chemical formula

of a molecular substance, showing the types of

atoms in each molecule and the ratios of those

atoms to one another.

Covalent Bonds

A chemical bond that involves sharing a pair

of electrons between neutral atoms in a

molecule in order to achieve an octet in the

valence shell.

In covalent bonding the attraction for electrons is similar for two atoms.

COVALENT bonds result from a strong

interaction between NEUTRAL atoms

Each atom donates an electron resulting in a

pair of electrons that are SHARED between

the two atoms

For example, consider a hydrogen molecule, H2. When the two hydrogen, H, atoms are far apart from each other they are not attracted to each other. As they come closer each “feels” the presence of the other.

The electron on each H atom occupies a volume that covers both H atoms and a COVALENT bond is formed.

Once the bond has been formed, the two electrons are shared by BOTH H atoms.

COVALENT bonds result from a strong interaction

between atoms of similar electronegativity and

electron affinity.

Each atom

donates an

electron

resulting in a

pair of

electrons that

are SHARED

between the

two atoms

Generally, elements with similar electronegativity form covalent bonds

Atoms can bond forming single, double,

triple and even quadruple covalent bonds.

ethene

O

H

H

Structural formulas indicate kind, number and arrangement of bonds using a line to represent a shared e- pair

One word of warning: hydrogen behaves with a divided personality. While it is traditionally placed in the periodic table above lithium, and can form ions (as in the case of acids), it typically forms covalent bonds. And remember: As with all generalizations, there are exceptions.

3 Biologically Important Properties

of Covalent Compounds

Because the angles formed between covalently

bonded atoms are specific and defined -

biological molecules formed with covalent

bonds have definite and predicable shapes.

glucose

matter Anything that has mass and takes up space.

Bond energy.

Covalent bonds represent chemical potential energy

that can be used in biological reactions. An example of

this are the phosphoanhyride bonds of ATP.

A covalent bond STORES energy

– so breaking those bonds

releases energy that can be used

for the needs of living organisms.

Polarity

polar covalent bonds are extremely important because

of the unique properties exhibited by molecules with

these kinds of bonds. (this is particularly true for living

organisms)

The structure of

covalent

molecules:

Structural

Formulas

Structural formulas indicate kind, number and arrangement of bonds using a line to represent a shared e- pair

remember

Drawing structural

formulas

• First identify the valence electrons.

• Draw Lewis dot structures

• Apply the octet rule to determine where and

how many bonds will form.

• Replace shared electrons with line.

• Leave dots for lone pairs of electrons

• Represent the correct geometry.

• First identify the valence electrons.

• Draw Lewis dot structures

• Apply the octet rule to determine where and

how many bonds will form.

• Replace shared electrons with line.

• Leave dots for lone pairs of electrons

• Represent the correct geometry.

Let’s try some!

Drawing structural

formulas

Bonded pair: A pair of electrons that are shared

in a covalent bond between two atoms.

Lone pair: A pair of valence electrons not involved

in bonding within a molecule. The two electrons

belong to one atom.

After bonding, each atom has a

total of eight valence electrons

surrounding it. (H exception)

Draw the Lewis dot structure for the two

covalently bonded molecules shown here.

Explain how you arrived at your answer.

a. O2 b. NH3

Draw the molecular structure for the two

covalently bonded molecules shown here.

Explain how you arrived at your answer.

from the text:

The HONC 1234 rule and the octet rule both help you figure out Lewis dot structures and structural formulas.

Both the HONC 1234 rule and the octet rule can be satisfied by using double and triple bonds appropriately.

It is not possible to create a triple-bonded oxygen compound, according to the HONC rule.

There are exceptions to the bonding rules laid out here.

A Puzzling Activity

Each puzzle piece contains the correct

number of valence electrons for that atom. It

also contains the appropriate number of tabs

for bonding.

Structural formulas show how the atoms in a molecule are connected.

A molecular formula can be

associated with more than one structural formula.

Isomers

The structural formula for certain molecules can differ.

Compounds with the same molecular formula but different structural formulas

are isomers.

C4H8O2

chemical compounds

which have a common

chemical formula, but not a

common structure.

This gives isomers different chemical properties

C5H12

structural isomers

• show a different arrangement in covalent bonds

• Usually occur in differences in the arrangements of the carbon

skeleton.

• Locations of double bonds may vary also

Differ in covalent arrangement

OR

location of double bond

Geometric isomer

• differences in arrangements of atoms around a double bond.

(double-bonded carbons do not exhibit rotation).

• When molecules/functional groups are found on the same side

of a double bond, this is known as the "Cis" configuration

• When atoms/functional groups are located on opposite sides

of a double bond, this is called the "trans" configuration

trans-2-butene cis-2-butene

Example in the biological

world

This is a schematic diagram of

a rod cell. The stacked disks

contain rhodopsin, the complex

of opsin protein and 11-cis-

retinal.

The nerve fires a signal to the

brain as a result of retinal

isomerization passed along to a

connecting nerve cell, creating

an electrical impulse

interpreted as visual

information by the brain.

Upon absorption of a

photon in the visible

range, 11-cis-retinal

can isomerize to all-

trans-retinal.

Note how the size

and shape of the

molecule change as

a result of this

isomerization.

optical isomers

when 4 different

atoms/functional

groups occur

around a single

carbon

This results in molecules which are "mirror images"

of each other, but NOT IDENTICAL.

The resulting molecules do not function the same.

Amino acids & proteins often show this feature.

Biological systems usually can identify and use the correct form,

the other is usually ignored.

dextro = right

levo = left

The two forms of an enantiomer are known as the "L"

form or the "D" form

Example in the biological

world

Laboratory tests after the

thalidomide disaster showed

that the 'S' enantiomer was

teratogenic but the 'R' isomer

was an effective sedative. It is

now known that even when a

selective sample of

thalidomide is created, it can

cause racemizing. This

means that both enantiomers

are formed in a roughly equal

mix in the blood. So, even if a

drug of only the 'R' isomer

had been created, the

disaster would not have been

averted.

Thalidomide

phocomelia

polarity Electron position in a covalently bonded molecule

Polar covalent bonds are a particular type of covalent

bond.

In a polar covalent bond, the electrons shared by the atoms spend

a greater amount of time, on the average, closer to one nucleus

(in this example- Oxygen) than the other nucleus (in this case

Hydrogen). This is because of the geometry of the molecule and

the great electronegativity difference between the two atoms.

Polar covalent bonds

Chlorine is clearly to the right of carbon. Carbon is however fairly central. Electrons in a bond between these two elements are shared (covalent), but they are not shared equally. The shared electrons (one from Cl, one from C) would spend more of their time under the influence of chlorine, being farther right, but are not completely lost to carbon (as they would be to sodium).

Consider, carbon (C) and chlorine (Cl).

The electrons

being shared are

held closer to the

Cl than to the C

giving the

molecules

slightly charged

areas.

In a polar covalent bond, the electrons shared

by the atoms spend a greater amount of time,

on average, closer to one of the nucleus’ of

one of the atoms.

This is because of the geometry of the molecule and

the great electronegativity difference between the two

atoms.

The result of this

pattern of unequal

electron association is

a charge separation in

the molecule, where

one part of the

molecule has a partial

negative charge and

the other has a partial

positive charge.

(You should note this molecule is not an ion because there is no exchange of electrons, but there is a simple charge

separation in this electrically neutral molecule.)

Polar covalent bonds are extremely important in

biological systems because they allow the

molecules to form another kind of weak bond….

The biological importance of

polar covalent bonds is that

these kinds of bonds can

lead to the formation of a

weak bond called a

hydrogen bond.

Hydrogen bonds

How are they formed? a hydrogen bond is

formed when a charged part of a molecule

having polar covalent bonds forms an

electrostatic (as in positive attracted to

negative) interaction with a substance of

opposite charge. Molecules that have

nonpolar covalent bonds do not form

hydrogen bonds.

Important. Hydrogen bonds are extremely important in

biological systems. Their presence explains many of the

properties of water. They are used to stabilize and

determine the structure of large macromolecules like proteins and nucleic acids. They are involved in the

mechanism of enzyme catalysis.

Strength. Hydrogen bonds are classified as weak

bonds because they are easily and rapidly formed and

broken under normal biological conditions.

What classes of compounds can form hydrogen

bonds? Under the right environmental conditions, any

compound that has polar covalent bonds can form

hydrogen bonds.

Polar/nonpolar

lab

Water

Water is the most abundant

molecule in the body. Water

forms the internal ocean that

baths every cell of the human

body. It makes up around 65%

of the body weight. The water

molecule is composed of one

atom of oxygen and two atoms

of hydrogen held together by

covalent bonds.

The polarity of water plays a critical role

in all living and nonliving systems

The shape of the water

molecule and the

atoms in it give water a

special property called

polarity. This means

that one end of the

molecule is slightly

positive while the other

end is slightly negative.

Special properties of water

Water exhibits some very special and unique

properties that make it a critical compound.

Special Properties of Water.

Polar: H bonding, adhesion and cohesion.

High specific heat.

Universal Solvent.

High Surface Tension.

Has capillary action.

Po

larity

pro

pe

rties

Polarity gives

water several

special

properties that

are very

useful for

living

organisms :

COHESION

ADHESION

HYDROGEN

BONDING

Universal Solvent

In a solution one or more substances are dissolved. The dissolved

substances are called solutes. The water which dissolves the

solutes is called the solvent.

Notice how the

negative ends of water

attract sodium

and the positive ends

attract chloride.

Water is so effective at dissolving substances that

it is referred to as the universal solvent.

Water is an example of

a molecule that has

polar covalent bonds

and engages in

hydrogen bonding.

hydrogen bond

They are simply a special type of powerful dipole-

dipole attraction.

Hydrogen bonds are caused by dipole

attraction between two molecules containing

hydrogen bonded to small electronegative

elements (N, O or F).

Hydrogen Bonding

The dipole forces are attracted.

A low-energy bond forms.

This attractive force is what

gives water its cohesive and adhesive properties.

Molecules that have nonpolar covalent bonds

form hydrogen bonds.

Cohesion

Water attracted to other water.

This is caused by hydrogen bonds that form between

the slightly positive and negative ends of neighboring

molecules. This is the reason why water is found in

drops; perfect spheres.

Surface Tension Surface tension is the name we give to the

cohesion of water molecules at the surface of a body of water.

Water Strider

Can You Float A Paper Clip?

water has the ability to support small objects. The hydrogen bonds between neighboring molecules cause a “film” to develop at the surface.

Breaking The Surface Tension What happened when you added a drop of

detergent?

Why?

The detergent has phosphate in it. The phosphate attracts to the water molecules and breaks the surface tension.

adhesion

Water can also be

attracted to other

materials. This is

called adhesion.

(Remember adhesive

tape picks up things)

What do you observe when you placed a drop of water onto a piece of wax paper?

Why do you think it is this shape?

007 Science

You only

Live Twice

What is happening?! Water is not attracted to wax paper

(there is no adhesion between the drop and the wax paper). Each molecule in the water drop is attracted to the other water molecules in the drop. This causes the water to pull itself into a shape with the smallest amount of surface area, a bead (sphere). All the water molecules on the surface of the bead are 'holding' each other together or creating surface tension.

Capillary Action

Capillary action

is related to the

adhesive

properties of

water.

Capillary action is when water moves up a cylinder.

the water molecules are attracted to the straw molecules.

When one water molecule moves closer to the straw molecules the other water molecules (which are cohesively attracted to that water molecule) also move up into the straw.

What is happening with the straw demonstration?

Capillary action is limited by gravity and the size of

the straw. The thinner the straw or tube the higher

up capillary action will pull the water.

This explains how a meniscus forms in a cylander.

Apply these properties to answer WHY the

meniscus is different.

glass plastic

(wax)

Plants and Capillary Action Plants take advantage of capillary action to

pull water from the soil into themselves.

From the roots water is drawn through the plant by another force, transpiration.

Specific Heat

Water has a high heat capacity.

Specific heat (a measure of heat capacity),

is the heat required to raise the temperature

of 1 gram of water 1°C.

Water, with its high heat capacity, changes

temperature more slowly than other

compounds that gain or lose energy.

• Water’s resistance to sudden changes in temperature

makes it an excellent habitat (organisms adapted to narrow

temperature ranges may die if the temperature fluctuates widely).

• The heat retaining properties of water provide a much

more stable environment than is found in terrestrial

situations. AND Fluctuations in water temperature occur

very gradually (seasonal extremes are small).

Water As a Habitat

Hydrogen bonds are extremely

important in living systems

Hydrogen bonds are

responsible for the

unique properties of

water and they loosely

pin biological

polymers like proteins

and DNA into their

characteristic shapes.

Hydrogen bonds are classified as weak bonds

because they are easily and rapidly formed

and broken under normal biological

conditions.

An electron density plot for the H2 molecule

shows that the shared electrons occupy a

volume equally distributed over BOTH H atoms.

Electron Density for the H2 molecule

non-polar In addition to polar covalent

bonds, there are nonpolar

covalent bonds.

In biological systems, if a molecules has a predominance of

nonpolar covalent bonds, that substance is hydrophobic. (very important)

Nonpolar covalent bonds

The hydrophobic effect is another unique

property of water caused by the hydrogen

bonds.

The hydrophobic effect is particularly important

in the formation of cell membranes.

Hydrophilic properties are very important because

they allow molecules to be soluble in water.

(because most living organisms are mostly water – this is

a good thing)

Hydrophilic properties (between polar molecules)

amphipathic molecules

Molecules with a polar/ionized region at one end

and a non-polar region at the other end

hydrophilic hydrophobic

If amphipathic molecules are

mixed with water, the molecules

form clusters with the polar

(hydrophilic) regions at the

surface, where they will come

into contact with water, and the

non-polar (hydrophobic) regions

nestled in the center of the

cluster away from contact with

water. The arrangement will

increase the overall solubility in

water.

Hydrophilic:

Hydrophobic:

Example: mix salad oil with water—shake to break H bonds

but as these bonds reform between water molecules, they

push the oil molecules out of the way-the oil tends to

cluster together in drops or as a layer on the water’s

surface-thereby exposing less surface area to the water

Bond strength

In biological systems, covalent bonds are called strong

bonds. This means that they are not normally broken

under biological conditions unless by enzymatic

catalysis.

This is in opposition to weak bonds such as ionic bonds

which are easily broken under normal biological

conditions of temperature and pressure.

Van der Waals interactions

probably the

most basic type

of interaction.

Any two

molecules

experience Van

der Waals

interactions.

due to the spatial orientation of the molecules,

the attractive forces outweigh the repulsive

ones.

Even macroscopic surfaces experience

VDW interactions

VDW forces are electrostatic in nature

strongest

weakest

covalent

ionic

hydrogen

Van der Waals