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CREATED BY: Alistaire Rauch
T​H​E ​U​L​T​I​M​A​T​E ​C​H​E​M​I​S​T​R​Y ​S​T​U​D​Y​ ​G​U​I​D​E
T​E​R​M​ ​T​W​O​:
UNIT II: SMELLS
I. Smells
Chemical Compounds smell certain ways because they bind with nose receptors in different
ways causing a different smell. (The odor molecule is bonded with a neuron receptor which
travels to the brain to perceive a certain scent).
Molecular Formula/Molecular Covalent Compound​: A chemical formula of a molecular
substance that tells the types of atoms and the number of different type of atoms
Isomers​: Molecules that have the same chemical formula, but different structures overall not just
the rotation of certain branches etc.
Different types of smells
Ending of
Name
Chemical Formula Patterns
Functional Group/Other
Info
SWEET
-ate
-yl
- Usually contains 2 O atoms, 1 O in
others.
- Stringy
- hydroxyl
- ester
PUTRID
-ic...acid
- 2 O atoms in ALL
- stringy
- carboxyl
MINTY
-one
- Contains 1 O atom in ALL
- frying pan shaped
- ring structures
- ketone
- hydroxyl
FISHY
-ine
- Contains 1 nitrogen atom in ALL
- stringy
- amine
CAMPHOR
(don’t think
this
knowledge
is needed)
- double ring structure
- 1 O atom in all
- ball shaped
- examples: fenchol, camphor
- ketone
- hydroxyl
II. HONC RULE
The Honc Rule states the number of covalent bonds the main molecules can make.
Hydrogen - 1 Bond
Oxygen - 2 Bonds
Nitrogen - 3 Bonds
Carbon - 4 Bonds
Valence Electrons
Covalent Bonds Formed
Electrons needed for full shell
Hydrogen
1
1
1
Oxygen
6
2
2
Nitrogen
5
3
3
Carbon
4
4
4
III. Bonding
In molecular structures that are drawn out, a
single bond​ is represented by “a line” which is the
sharing of one pair of valence electrons. A ​double
bond​ or sharing of two valence electrons is shown by
two lines. ​Triple bond​ is three pairs of electrons
shared and shown by three lines.
IV. Isomers
An isomer is molecules that have the same chemical formula, but different structures
overall not just the rotation of certain branches etc.
An example of two isomers would be the fact that they both share the same formula of C 4H 10 .
One way that an isomer is considered different is by looking at the main structure or “backbone”
of a molecule or in this case the carbons. In butane, there are four carbons together in a single
straight chain (continuous chain) while in isobutane, there is a three carbons, while the fourth is
in the middle and pokes out. In other words, this can be compared to a train going down a rail, in
butane, there is four straight carbons without being interrupted, while in isobutane, there is three
carbons, but in order to get to the last carbon that sticks out one would have to backtrack or take
a turn.
V. Lewis Dot Structures:
A Lewis Dot Structure is a relatively accurate way to represent valence electrons being bonded
with other atoms as well as lone pairs. ​Lone pairs​ are electrons that are not being bonded. On
itself a lewis dot structure of an element just shows the valence electrons
The way to draw a lewis dot structure (molecules) is:
1. Draw the total number of
valence electrons of atoms
2. Put a pair of electrons
between each of the bonded
atoms
3. Place the remaining
electrons between the
double/triple bonds or as
lone pairs
In this example, the ​lone
pairs​ are the electrons
that are on the outside.
The bonded ones are
represented in between
the molecules.
This table shows the first
6 periods of lewis dot
structures. There is also a
common pattern where elements in the same groups have the same number of valence electrons
Octet Rule: ​This rule is for nonmetal atoms and when they combine that each atom must have a
total of eight valence electrons by sharing electrons. This picture to the right is an example of the
octet rule and how each molecule has a total of 8 valence electrons
VI. Functional Groups
This is just an overview of the main groups, these molecules are not a hundred percent accurate
because different forms can exist of each group.
A ​functional group​ is a group of molecules that molecules have in common.
Example:
Carboxyl Group:
This is a functional group that is normally associated with putrid
smelling molecules. This group is composed of mainly an ​oxygen
double bonded with a carbon along with a oxygen and
hydrogen​.
Oxygen = Carbon - Oxygen - Hydrogen
Ester Group:
This group is normally associated with sweet smelling molecules.
This is made out of an oxygen and carbon double bonded along with a
oxygen and carbon.
Oxygen = Carbon - Oxygen (- Carbon)
Amine Group:
This group is associated with the fishy smelling molecules. This is made
out of a nitrogen and carbon.
Nitrogen - Carbon
Ketone Group:
This group is associated with the minty smelling molecules. This is composed an oxygen and
carbon double bonded, along with the carbon attached to two other molecules in a single bond.
Oxygen = Carbon -----( -Carbon -carbon w/ oxygen - Carbon -R)
Aldehyde Group:
This group is associated with sweet smelling molecules
(perfume and flowery). This group has an oxygen and
carbon double bonded along with another carbon and
hydrogen.
Hydroxyl Groups:
This group is made of a hydrogen and oxygen bonded. An important compound that contains this
group would be alcohols and this normally smells medicinal and or alcoholic.
Alkane Group:
This functional group is contains one carbon with four
different bonds (seen in methane). This group can either
have no smell or a gasoline smell. An important note
about this group is that the molecular formula follows
this rule: C nH 2n+2 . Examples are shown in the picture to
the right.
Molecules also do not follow the exact groups listed
above, but tend to share features and they are called:
Esters ⇒ Ethers
Name
Compound
Type
Functional Group
Smell
-ane
alkane
alkyl
no smell/gasoline
smell
-ic acid
carboxylic acid
carboxyl
putrid
-yl -ate
ester
ester
sweet
-one
ketone
ketone
minty
-ol
alcohol
hydroxyl
medicinal
-lamine
amine
amine
fishy
VII. Naming Acids:
An acid is named by the number
of carbons in its main backbone
or chain.
When an acid is combined with
an ester it follows this:
_____-yl _____-ate
VIII. Electron Domains​:
An​ electron domain​ the space occupied by valence
electrons in a bonded pair of electrons, a lone pair of
electrons, or multiple bonded pairs.
Electron Domain Theory​ is the tendency for electrons to
be as far apart as possible (also called VSEPR or Valence
Shell Electron Pair Repulsion).
IX. Space Fillings Models:
A ​space filling model​ is a three dimensional representation
of a chemical substance that mainly displays the position of the bonds
and the atoms itself. It is also used to determine the overall structure.
Long/Stringy- Sweet
Frying Pan- Minty
Ball-Shaped- Camphor
X. Polar and Nonpolar Molecules:
Partial Charges- ​A less than full charge on part of a molecule, created by the unequal sharing of
electrons.
Polar Molecules: ​Molecules attracted to a charge because they have a
partial change on them. For example, this water molecule, has a partial
negative and partial positive charge. In other words a polar molecule
has two poles.
Nonpolar Molecule​: A nonpolar molecule is a molecule that is not
attracted to another charge. It also is a molecule that shares electrons
equally.
Intermolecular Forces​: A force of attraction that occurs between
molecules
XI. Electronegativity:
Electronegativity: ​The tendency of an atom to attract shared electrons that are involved in
bonding and it is the measurement of the ability of a molecule or atom to attract other electrons
to itself.
Dipole:​ A molecular or covalent bond with a
nonsymmetrical distribution of electrical charge
that makes the molecule or bond polar. A crossed
arrow is used to show the direction of a dipole.
The crossed end represents the partial positive
charge and the arrow is the negative end.
ELECTRONEGATIVITY CHART:
This chart displays the elements and their electronegativities respectively. It is important to know
that fluorine is the most electronegative and francium is the least. Also, the pattern of how it
increases bottom to top and left to right.
Intra versus Inter: ​Intermolecular forces occur between two molecules, and intramolecular
forces occur within the molecule.
London Dispersion Forces:​ It is the weakest intermolecular ​force​. It is a force between two
nonpolar molecules, noble gase, and some charges.
Ex:
Dipole-Dipole:​ The attraction of two partially opposite charges (polar bond). (
Ex.
Hydrogen Bonding:​ This is an intermolecular force between
two molecules, where a hydrogen connects to an oxygen,
nitrogen, or fluorine of another molecule.
RULE: R-H------:B-R
Hydrogen atom (H) must link to a nitrogen, oxygen, or fluorine
(B) of another molecule.
XII. How to decide if a molecule is overall polar
The way to decide if a molecule is overall polar is to first look at the
overall structure and whether it has ​symmetry​ around the central
molecule because then it the molecule would cancel out the dipoles.
A good example would be C F 4 . This molecule is symmetric and the
dipoles would cancel each other out.
If it ​asymmetric​, this would mean that bonds don’t cancel out.
Another way to think about this
is to look out whether there is
potentially more lone pair
electrons in one area than in another. For example in C F 4 , they are evenly displaced around
each molecule and visually it is overall equal because each fluorine is equally distanced from the
other fluorines that have lone pairs. So therefore, it is nonpolar.
While water on the hand, has a buildup of lone pairs in one and it is not evenly displaced
therefore it is polar because it has a greater chance to bond.
(Extra Material)
Ozone O3 is a weird molecule because of it
does not follow the double bonding rule (if
it did it would be a triangle shape) and
instead has two electrons that are moving
throughout the structure because it will
make the molecule more ​stable​. This
molecule looks like the “actual” one to the
right. This molecule is polar because there is
a greater group of lone pair electrons on the
right and left which can creates a partial
negative on the left and right. On the top of
the molecule it has a partial positive because
there are less electrons.
XII. Polar and Nonpolar Substances and Solubility:
Polar Molecules easily ​dissolve​ in other polar substances
such as water and alcohol. Since water is polar and so is
alcohol, they form hydrogen bonds through and this causes it
to easily dissolve into water.
On the hand polar and nonpolar do not mix well, but
nonpolar and nonpolar do mix well. A good example would
be water and oil, a polar and nonpolar substance.
Nonpolar and nonpolar molecules do attract each other and dissolve each other.
Summary:
Polar + Polar = Mix/Dissolve
Nonpolar + Nonpolar = Mix/Dissolve
Polar + Nonpolar = NO mix
Nonpolar + Polar = NO mix
LIKE DISSOLVES LIKE!
XIII. Phase, Size, Polarity etc.
Molecule
Smell
Phase
Small Nonpolar Molecules
Yes
Gas
Small Polar Molecules
Yes
Gas
Medium-Sized Polar and Nonpolar Molecules
Yes
Liquid
Large Polar and Nonpolar Molecules
No
Solid
Ionic
No
Solid
Metallic
No
Solid
Network Covalent
No
Solid
This chart displays the Molecule and its type along with the smell and phase.
Concerning that of Polar or Nonpolar molecules, the size is determined by number of carbons:
Molecules (Nonpolar and Polar)
# of Carbons
Small
X>5
Medium
5 < X < 19
Large
X > 19
XIV. Mirror-image Isomers
Mirror-Image Isomers​ are
molecules whose structures are mirror
images of each other and cannot be
superimposed on one another and due to
their different 3D structures contain
different properties and scents.
Superimposed​ means that a molecule can
be oriented in a way to fit the original
molecule. A good example from class is
D-Carvone and L-Carvone.
The simple way to determine if a molecule has a mirror isomer is to see whether a
carbon​ is surrounded or bonded to ​four​ very different groups. This does not mean a carbon is
bonded to a oxygen, fluorine, and two hydrogens, it has to be four different molecules or R
groups.
XV. Amino Acids and Proteins
Amino acids​ are molecules that contains an amine
(-NH​2​) and a carboxylic acid (-COOH) functional group. A
long strand of perhaps thousands are called ​proteins​, but
these proteins are folded into a very complex specific 3D
shape. When two amino acids bond, they bond in a similar
way to ester synthesis where a water molecule is created as
a byproduct. With this, when the long strands of amino
acids fold with the hydrophilic (polar) side facing outwards
and hydrophobic (nonpolar) side inwards. The bond is
called a ​peptide bond​.
In the human body, there are twenty different amino acids all of which contain a “left
handedness”, the reason left handed amino acids are used and not right is undiscovered, but it
may be because of how most the amino acids falling to space are more left than right.
To determine whether an amino acid is polar or nonpolar is to look at the R group of the
molecule and whether that R group is overall polar or nonpolar and the bond type as well.
Amino Acids also contain a “​chiral​” molecule which means that the molecule is not
superimposable and is thus a mirror-image isomer. It is just another way to say a mirror-image
isomer. A “​chiral center​” is the carbon molecule surrounded by four different groups
(mirror-image isomer. ​Achiral​ means an object that superimposable on its mirror image. For
example, like tetrafluoromethane (CF​4​).
Fun fact: chiral in Greek means “hand.” Your hand by the way, is not superimposable.
For an explanation better than the one I can give, check out Sal Khan:
https://www.khanacademy.org/science/organic-chemistry/stereochemistry-topic/chirality-r-s-syst
em/v/introduction-to-chirality​ (change speed to 1.25 or more if you feel like he talks too slow).
XVI. CORN
CORN is a mnemonic to determine if an amino acid is right or
left handed.
First you would want to look at the molecule from a side view,
and because they contain an amine (-NH​2​) and a carboxylic
acid (-COOH) functional group, it would would tetrahedral
overall. So look at it with the hydrogen in the middle or
sticking out at you. Then, if you go LEFT to right from CO group and it spells CORN, then it
would be LEFT handed. IF it goes to the RIGHT and spells corn, it would be RIGHT handed.