Electronegativity (EN) - Measure of the relative tendency of an atom to attract electrons to itself

when chemically combined with another atom. The higher the value of electronegativity, the more
it tends to attract electrons toward itself.

Polar covalent bonds occur when electron pairs are unequally shared. The difference in
electronegativity between atoms is significant. Examples of compounds having polar covalent
bonds are:

HCl EN of H = 2.1 EN of Cl = 3.0 ΔEN = 0.9

HF EN of H = 2.1 EN of F = 4.0 ΔEN = 1.9

The separation of charges makes the bond polar. It creates an electric dipole. Dipole refers to “two poles,”
meaning there is a positive and a negative pole within a molecule. Elements with the higher EN value
become the partial negative pole while elements with the lower EN value become the partial positive
pole. This makes the molecule a polar molecule Non-polar covalent bonds occur when electron pairs are
shared equally or the difference in electronegativity between atoms is less than 0.5.
Examples of substances having non-polar covalent
bonds are:

H2 EN of H = 2.1 ΔEN = 0.0 NON-POLAR MOLECULE; not a dipole

Cl2 EN of Cl = 3.0 ΔEN = 0.0 NON-POLAR MOLECULE; not a dipole

F2 EN of F = 4.0 ΔEN = 0.0 NON-POLAR MOLECULE; not a dipole

HI EN of H = 2.1 EN of I = 2.5 ΔEN = 0.4 POLAR MOLECULE; a dipole

Molecular Geometry

The valence shell electron pair repulsion theory or VSEPR theory helps predict the spatial arrangement of
atoms in a polyatomic molecule. The shapes are designed to minimize the repulsion within a molecule.

The basic shapes such as linear, bent, tetrahedral, trigonal pyramidal, trigonal planar, and octahedral.
Emphasize that symmetry plays an important role in determining the polarity of a molecule.
Give the following guidelines to determine the VSEPR shape of a molecule:
1. Determine the central atom of a molecule. The central atom is the least electronegative element.
2. Count how many valence electrons the central atom has.
3. Count how many valence electrons the side atoms have.
4. Create the appropriate Lewis structure of the molecule.
5. Using the Lewis structure as a guide, determine the appropriate VSEPR shape for the molecule.
6. Note how many electrons are shared and unshared. This will help determine the appropriate VSEPR
shape.

Lone pairs has a big factor in making a molecule polar.

Polar molecule:
H2O Bent - polar due to two lone pairs
NH3 Trigonal pyramidal - polar due to one lone pair
NO Linear - polar due to unequal sharing of electrons

Due to the two lone pairs, the water molecule has a bent shape.

Note that dots refer to unshared electrons in the Lewis structure above and a dash refers to bonding
between two electrons.
Point out the effects of lone pairs in the shape and polarity of a molecule.

Non-polar molecule
CO2 Linear
CH4 Tetrahedral
CCl4 Tetrahedral

The difference between bond polarity and molecular polarity. The presence of polar bonds does not
automatically make a molecule polar. The geometry of the molecule also plays an important role. This
can be seen in CO2 wherein the electronegativity difference of C and O is 1.0 which makes the bond
between them polar. However carbon is placed in the middle of two oxygen atoms making the molecular
structure linear. This equal distribution of polar bonds make the molecule non-polar.

Molecules are polar or non-polar based on the type of covalent bond and its molecular geometry. Mention
that one of the most practical manifestations of polarity is solubility and miscibility. Solubility refers to
the ability of a solute to dissolve in a certain amount of solvent. Miscibility is the ability of two liquids to
mix in all proportions.
Solubility, Miscibility, and Polarity. General rule that “like dissolves like” or “like mixes with like.” This
refers to substances being able to mix due to their same polarity. Water and vinegar mixed because they
are both polar substances while gasoline and oil are non-polar substances. Oil and
water, oil and vinegar, gasoline and water, and vinegar and gasoline do not mix because their polarities
are different.

Applications of polarity, VSEPR model-making

Polarity in biological examples.

The importance of the polarity of molecules by citing how many biological processes rely on polarity.
Give proteins and phospholipids as examples. Proteins are macromolecules having polar and non-polar
parts that are essential to life. Protein chains can be so long that they must bend and form a particular
shape. The shape is affected by attraction and repulsion among polar and non-polar groups. Proteins that
have an irregular shape are not able to perform biological functions well. One particular example is a
hereditary disease called sickle cell anemia wherein the red blood cell acquires the shape of a sickle or
crescent moon instead of a normal circular shape. This irregularity in shape lessens the ability of the red
blood cells to carry oxygen throughout the body.

Phospholipids on the other hand are biological macromolecules that normally form as cell
membrane. Phospholipids have a water-loving (polar) and water-fearing (non-polar) part. This
macromolecule orients itself in such a way that the polar part is oriented towards the watery
environment (outwards) while the non-polar orients itself away from the watery environment
(inwards). In this way, cells are able to perform their functions.

The four main types of intermolecular forces:

1. Ion-ion interaction
2. Dipole-dipole interaction
3. Hydrogen bonding
4. Dispersion forces also known as London forces in honor of Fritz London.

Ion-ion interaction
Ion-ion interaction exists between oppositely charged ions. It occurs between ionic compounds. Most ion
ion interaction is strong and compounds which have them have high melting and boiling points. Ions of
like charges repel while opposite charges attract. The compound orients itself in such a way as to
minimize repulsion. The strength of ion-ion interaction is inversely proportional to the square of distance
between the ions. This is the strongest intermolecular force.

Dipole-dipole interaction

Occurs between polar molecules. This is due to the partial positive pole and the partial negative pole of
the molecule. Average dipole-dipole interaction is relatively weak, around 4kJ/mol. This interaction is
effective over a very short range. The strength of dipole-dipole interactionis inversely proportional to
distance raised to the fourth power (d4).

The figure above shows the partially charged poles of the molecules, and the attraction and
repulsion between them. Both attraction and repulsion occur simultaneously.

Hydrogen Bond

Hydrogen bond is a very strong dipole-dipole interaction. Hydrogen bond occurs in polar molecules
containing H and any one of the highly electronegative elements, in particular F, O, N. Hydrogen tends to
be strongly positive due to the strong tendencies of F, O, or N to attract the electron towards it. The highly
electronegative elements make hydrogen strongly positive. Hydrogen bonding is responsible for the
unusually high boiling point and melting point of water as compared to compounds of similar molecular
weight and geometry. Typically, H-bond is in the range of 15-20 kJ/mol.

Use the properties of water to show the uniqueness of H-bonds.

The ability of water to form hydrogen bonds relates to its ability to be a universal solvent. Due to its
polarity, it is able to dissolve (or interact) with ionic compounds and polar molecules. Hydrogen bonding
is also very important to life in general as the H-bond prevents water from quickly evaporating into the
atmosphere. In freezing temperature, the H-bond causes the water molecules to form a crystal lattice
thereby increasing its volume. This is why ice floats on water. This prevents the water beneath from
cooling down further as the ice sheet acts a protective layer. This allows marine creatures to survive in
cold weather. H-bonding in water is also important in the hydration of organic molecules and in the
formation of peptide bonds within proteins.

Dispersion Forces or London Forces

Dispersion force is present in all molecules. It is the only force present in nonpolar molecules. It is very
weak and acts in very small distances. It is formed due to the attraction between the positively charged
nucleus of an atom with the negatively charged electron cloud of a nearby atom. This interaction creates
an induced dipole. The strength of dispersion forces is inversely proportional to distance raised to the 7 th
power (d7). Without dispersion forces substances would not be able to condense to liquid and solid phase.

The image above shows a lone iodine molecule having equal electron density. When several iodine
molecules are exposed to each other, an induce dipole is created. This is shown in the uneven electron
density of the iodine molecules. As the molecular weight of molecules increases (which also corresponds
to an increased number of electrons), the polarization increases due to dispersion forces. Sometimes,
dispersion forces can be stronger than dipole-dipole interaction or even H-bonding.
Surface tension

A phenomenon caused by cohesive forces (intermolecular forces) between molecules allowing liquids to
create a thin film on its surface. This causes liquids to acquire a certain shape when put on a container or
dropped on surfaces. In a container, the bulk of a liquid has a balance of intermolecular forces in all
direction. There is a net inward force on the surface since there are no liquids there. This creates surface
tension. Stronger intermolecular bonds equates to stronger surface tension. Certain insects or reptiles
being able to walk/ glide over water. (water striders, fisher spiders, basilisk lizard).

Concave meniscus

Occurs when there is stronger adhesive force between the container and the liquid than the liquid’s
molecules. The adhesive force overcomes the cohesive force of the liquid. This causes the liquid to climb
up the sides of the container.

Adhesion - interaction between different materials touching each other e.g. Tape and paper, skin and
glass, etc.
Cohesion - interaction between same materials

Convex meniscus

Occurs when there is stronger cohesive force between the liquid’s molecules than the adhesive force
between the liquid and the container. This causes the liquid to create a dome shape on its surface. The
shape of the meniscus depends on the relative strength of the adhesive and cohesive forces
experienced by the liquid and its container.

Viscosity

Viscosity is the resistance of a liquid to flow. The more viscous a liquid is the thicker its consistency. In
layman’s term it is the measure of the thickness of a liquid. In general, stronger intermolecular forces
leads to higher viscosity.Increased H-bonding, like in glycerine, results to higher viscosity. Higher surface
area or increasing molecular size also results to greater viscosity due to greater dispersion forces.
Compare the flow of honey and water on a spoon. The liquid with the longest time is the most viscous
while the one with the shortest time is the least viscous. The most viscous liquid has the stronger
intermolecular force and the least viscous liquid has the weakest intermolecular force.

Capillary action

A phenomenon wherein a liquid is able to rise up on anarrow tube. Adhesive forces between the tube and
the liquid allow the liquid to exceed its weight. The narrower the tube, the higher the liquid will reach.
Trees bring nutrients up to its leaves. Bring an image of veins or tubes within the plant/tree that act as
straws that bring nutrients up to the tree. This process is a combination of capillary action and osmosis.

Evaporation / vaporization

Evaporation is the process of turning liquid into gaseous form. Weaker intermolecular forces equates to
greater volatility.
.
Amazing Water

Point out how amazing it is that water is made from two gases that are flammable but together they make
a substance that can put out fire.These two elements bonded together allow life on earth to exist. The
ability of water to form hydrogen bonds presents many interesting properties which are useful for life.

Probable intermolecular force of attraction in the following:

1. KCl ----KCl ion-ion
2. NH3——NH3 dipole-dipole, H-bonding
3. Na2S——Na2S ion-ion
4. HF——HF dipole-dipole, H-bonding
5. MgS——MgS ion-ion
6. CH3OH——CH3OH dipole-dipole, H-bonding
7. H2——H2 dispersion forces
8. CuO——CuO ion-ion
9. SbH3——SbH3 dipole-dipole
10. CO2——CO2 dispersion forces

Boiling point - solutions with stronger intermolecular forces (IMF) have higher boiling points
thansolutions with weaker intermolecular forces. The solutions with stronger IMF holds it molecules
together stronger hence making it harder for the solution to evaporate and eventually boil.

Surface tension - this is a phenomenon wherein a liquid creates a seemingly thin film on its surface. The
stronger the IMF, the stronger is its surface tension.

Capillary action - this is the ability of fluids to rise in narrow tubes. The IMF between the surface of the
tube and the liquid allows the liquid to rise provided that the IMF between the surface and the liquid is
stronger than the cohesive forces within the liquid.

Convex and concave meniscus - a convex meniscus is formed when the cohesive forces within a liquid is
stronger than the adhesive forces between the liquid and the surface of the container. Concave meniscus
on the other hand is the opposite wherein the adhesive forces is stronger than the cohesive forces. The
cohesive and adhesive forces are both due to IMF.

Viscosity - this is the measure a liquid’s resistance to flow. Generally, the stronger is the IMF in the liquid
the more viscous it is.

Biological Macromolecules

Carbohydrate

The word carbohydrate may be broken down to carbon and hydrate. From the chemical formula of
carbohydrate, notice that the ratio of C:H:O is 1:2:1, which can be rewritten as Cn(H2O)n. Carbohydrates
can be seen as hydrates of carbon. This is a traditional but incorrect understanding of carbohydrates but it
still presents a useful picture of the molecule. Another term for carbohydrate is saccharide. This term
is derived from the Latin word saccharum referring to sugar--a common carbohydrate. Carbohydrates are
classified either as simple or complex. Simple sugars are monosaccharides and disaccharides. Complex
sugars are polysaccharides. Carbohydrates are the primary energy source of the human body. The
different saccharides that humans eat are converted to glucose which can be readily used by the body.
Around 4 kilocalories is derived from one gram of carbohydrate. Should there be an excessive
consumption of carbohydrates, the excess is converted to glycogen which is stored in the liver and in
muscles. Glycogen is a slow-releasing carbohydrate. Monosaccharide (one saccharide) Glucose Used in
dextrose, blood sugar; the form utilized by the human body Galactose Found in milk and milk products
Fructose Found in fruits and honey The above monosaccharides all have the same chemical formula of
C6H12O6 and its structure is the one that made the difference in its properties. For example, galactose
(163-169oC) has a higher melting point than glucose (148-155oC). Glucose is sweeter than galactose.
Melting point of glucose is for β-D-glucose.

Disaccharide (two saccharides)

Maltose Glucose + Glucose Found in malt
Sucrose Glucose + Fructose Found in regular table sugar, sugarcane, and sugar beet
Lactose Glucose + Galactose Found in milk and milk products
Individual saccharides are connected via glycosidic bonds. A water molecule is released when
two saccharides are combined.

Polysaccharide (many saccharides)

Starch / Amylose Composed of 250 - 400 glucose molecules connected via α-1-4-glycosidic bond
Storage form of glucose in plants

Amylopectin Like amylose but has more branches attached via α-1-6 glycosidic bond
Storage form of glucose in plants
Glycogen Composed of more glucose, more highly branched (same type of bond as amylopectin)
Storage form of glucose in animals, stored in the liver and muscles
Cellulose Composed of glucose units connected via β-1-4 glycosidic bond, linear chain arranged in a
parallel manner
Structural material in plants--cell wall in wood, wood fiber
Cannot be digested by humans

Protein
The word protein came from the Greek term proteios meaning first. One can think of protein as the
beginning of life. From egg albumin being pure protein to sperm and egg cells, we all start from proteins.
Proteins are composed of four elements, namely, carbon, hydrogen, oxygen and nitrogen. Sulfur and other
metals are sometimes also found in proteins. If carbohydrates are made up of saccharides, proteins
are made up of amino acids. An amino acid is a molecule that has an amine and a carboxyl group. Below
is the structure of an amino acid:

There are 20 amino acids. The combination of many amino acids creates protein. Amino acids are
joined together with a peptide bond. Proteins are also called polypeptides.

Enzymes function to catalyze chemical reactions. They either speed up a reaction, lower the needed
energy for a reaction to take place, or bind
substances to their specific partners. Enzymes themselves are very specific as can be seen in their shape.
Examples of enzymes are below:
1. Lipase - help in digestion of fats
2. Pepsin - help in breaking down proteins into peptides (smaller units)
3. Sucrase - also called invertase, help in the digestion of sugars and starches
Lipids

The word lipid comes from the Greek word lipos which means fat. Lipids are a family of biomolecules
having varied structures. They are grouped together simply because of their hydrophilic property (water-
fearing). They are soluble in non-polar solvents such as ether, acetone, and benzene. Lipids can be
classified into four categories:
a. Wax
b. Triglycerides
c. Phospholipids
d. Steroids

Fatty acids
Building blocks of lipids. Fatty acids are long-chain carboxylic acids that are insoluble in water. Fatty
acids can be saturated or unsaturated. Saturated fatty acids contain single bonds in its hydro-carbon chain
whereas unsaturated fatty acids contain double bonds.
Saturated fatty acids is to think of them as “saturated” with hydrogen. All the carbon molecules have two
hydrogen atoms attached to it. In unsaturated fatty acids, carbons with a double bond only have one
hydrogen atom attached to it hence being “unsaturated.” Saturated fatty acids allow their molecules to fit
close together and form strong attraction. They usually have high melting points and are solid at room
temperature. Unsaturated fatty acids are bent because of the double bond and are therefore, not as close
together as saturated fatty acids. They are often irregularly shaped. Unsaturated fatty acids have a low
melting point and are liquid at room temperature. Lipids containing either saturated or unsaturated fatty
acids somehow are able to retain these properties.

Triglyceride
Fat and oil are the most common examples of lipids. They are under triglycerides because they are
composed of glycerol and three fatty acids.

Fat refers to solid triglyceride usually from animal sources such as meat, milk, butter, margarine, eggs,
and cheese. Oil refers to liquid triglycerides from plant sources. Examples are olive oil, corn oil,
sunflower oil, and soybean oil. Animal fat contains high percentages of saturated fatty acids while plant
oil are mostly unsaturated fatty acids.

Phospholipids
Phospholipids contains glycerol, two fatty acids, and a phosphate group. Unlike other lipids,
phospholipids have a polar and non-polar end. This property allows it to transport molecules in the
bloodstream. It is also a major component in the cell membrane. The two parts of a phospholipid can be
termed as the hydrophilic head (phosphate group) and hydrophobic tail (fatty acid group). This dual
property allows phospholipids to form a phospholipid bilayer. In this configuration, the hydrophilic head
sticks out while the hydrophobic tail is tucked in and away from the watery environment. This is why
phospholipids are suitable as cell membrane.

1. Why are nucleic acids named so?

- Around 1868, Friedrich Miescher isolated an unknown weakly acidic substance from the nucleus of
white blood cells, hence the term
nucleic acid.
2. What comprises nucleic acids?
- Nucleic acids are composed of nucleotides.
3. What is another term for nucleic acids?
- Nucleic acids are also known as polynucleotides.
4. What are the three parts of a nucleotide?
- A nucleotide has a five-carbon sugar, a phosphate group and a nitrogenous base
5. What are common examples of nucleic acids?
- DNA and RNA
6. What is the primary role of DNA?
- It is the blueprint of life. Our genetic code is found in the DNA.
7. How does RNA help in protein synthesis?
- RNA helps in protein synthesis by carrying out the instructions encoded in the DNA.
8. What are the bases of DNA? of RNA?
- DNA: Adenine, Guanine, Tyrosine, Cytosine RNA: Adenine, Guanine, Uracil, Cytosine
9. How are DNA and RNA similar?
- They have the same three bases: A, G, C.
- They both have nucleotides containing one phosphate group, a five-carbon sugar, and a nitrogenous
base.
- Both are used in the manufacture of proteins
10. How are DNA and RNA different?
- DNA is double stranded while RNA is single strand
- DNA has deoxyribose for its sugar while RNA has ribose
- DNA has thymine while RNA has uracil

Collision Theory of Reaction Rates

This theory states that for reactions to occur, molecules, atoms, or ions must first collide. Not all
collisions are successful. In order for collisions to be effective collisions, particles must possess
the minimum amount of energy needed for the reaction and must collide with proper orientation.
Introduce the transition state theory.

Transition State Theory

Chemical reactions which require bond breaking and forming is accompanied by changes in potential
energy. According to the theory, the reactants must pass through a high-energy, short-lived intermediate
state called the transition state in order for reactions to occur. The kinetic energy of the particles must
overcome the potential energy needed to break and create bonds. The activation energy, Ea (or activation
barrier) is the kinetic energy needed by reactants to allow them to reach the transition state.
Bond breaking - energy is absorbed
Bond forming - energy is released

The net amount of energy in the breaking and forming of bonds determines if a reaction is
exothermic or endothermic.Activated complex quickly occurs and is temporary when the activation
energy is reached.

Exothermic reaction
C + D → CD + energy negative heat of reaction
Energy absorbed is less than the energy released. Hence, heat of reaction is negative.
Heat of reaction = Energy of products - Energy of reactants
= lower energy of product - higher energy of reactant
= negative value of Heat of Reaction
C (s) + O2(g) → CO2(g) + 393.5 kJ
C (s) + O2(g) → CO2(g) ΔH = -393.5 kJ

Endothermic reaction
A + B → AB - energy positive heat of reaction
Energy absorbed is more than the energy released. Hence, heat of reaction is positive.
Heat of reaction = Energy of products - Energy of reactants
= higher energy of product - lower energy of reactant
= positive value of Heat of Reaction
N2(g) + O2(g) + 180.5 kJ → 2NO(g)
N2(g) + O2(g) → 2NO(g) ΔH = +180.5 kJ
In endothermic reactions, energy is absorbed overall so the reactions feel cool to the touch. On the
other hand, exothermic reactions have a net release of energy so the reactions feel warm to the touch.
Energy is always part of a chemical reaction. The activation energy state for both is still the highest
energy state in the whole reaction. The transition state is also created when the activation energy is
reached. The heat of reaction is used in many things. Cite power production as an example. Coal is
reacted with oxygen in the process of combustion. This reaction produces a lot of heat (exothermic). The
heat turns water into steam that then powers the turbines. Baking bread is an endothermic reaction
wherein the dough absorbs heat from the environment in order to rise and cook properly. As more
substances are involved in a chemical reaction, more energy is either absorbed or released to the
environment.

Catalysts

Catalysts are substances that can be added to a chemical reaction to increase its reaction rate. This
allows the reaction to occur in an alternative pathway. This pathway requires lower activation energy.
Catalysts are not consumed in a reaction.

2 CO(g) + O2(g) 2 CO2(g) [reaction in catalytic converter]

The sample reaction above occurs in catalytic converters of automobiles. This reaction very quickly
converts harmful and poisonous carbon monoxide to less harmful carbon dioxide. There is no need to
discuss all the parts shown in the diagram. Only emphasize the action of the catalysts in cleaning the gas
released by the engine. The honeycomb structure increases the surface area of the catalyst making the
catalytic converter more efficient.
Other examples of catalyzed reactions are:

Requirements for effective collision

1. Proper orientation
2. Meet activation energy

Factors affecting reaction rate:

1. Concentration
2. Surface area
3. Temperature
4. Presence of catalyst