Block 1 Introduction to Organic chemistry

This topic forms the basis for which the three blocks later on organics (including
spectroscopy) will be built upon, thus it is absolutely essential that students
familiarize and consolidate upon their knowledge of the main concepts described
below. This set of notes will include a mixture of content from your course guide,
lecture slides as well as drawing relevant content from the textbook
Fundamentals of Organic Chemistry 6
th
edition by McMurry and Simanek. The
aim of this is to provide a whole picture and inspire interest for those passionate
about chemistry. However, vital ideas of which you will definitely need to revise
and drill in firmly into your heads will be explicit pointed out.

Organic chemicals are Molecules

Organic chemicals are predominantly molecules; exceptions include compounds
such as the carboxylate ion or ethoxide ion, which do contain ionic characters.
Thus we begin our tutorial by exploring the important features to bear in mind
when describing a particular molecule.

Features of a molecule:

Molecules are formed by covalent bonds, which themselves are the sharing of
electrons. The aim of this alliance between individual atoms in achieving the
molecular state is to gain an outer shell (full valence). When we consider how
many bonds an atom can make, we need to firstly consider how many outer
electrons it already has, and subsequently deduce how many further electrons it
will need.

Lets consider the reaction below:



The nitrogen atom in ammonia needs three more electrons as it already has five
to start with and thus it forms an alliance with 3 hydrogen atoms via single
bonds, which means that each atom is donating one electron to the bond. Double
bonds are thus the investment of two electrons each from each atom, Triple
bonds: three electrons from each. *Why cant a quadruple bond form?

Notice however, N also has a lone pair in its valence; this simple means a pair of
electrons not involved in a particular bond. This lone pair will have vital roles in
the organic chemistry reactions to come.

The combination of NH3 and H+ is a unique one. This is an example of a
formation of a new covalent bond, but whats special about it? Well, if you look
closely, NH3 is providing both electrons to the new bond while H+ has nothing to
donate. This type of bond is called a dative bond, in which one atom provides
both electrons to the newly formed covalent bond. This type of relationship will
also be quite prevalent in reactions to come.

Thus in summary, when inspecting a particular molecule we should be observant
of features such as:
Covalent bond; and whether is it a single, double or a triple bond.
Lone pairs
Presence of dative bonds

New concept:
There are molecules that have an unpaired electron in their outer shells and
these are called free radicals. As you can imagine, due to the instability of the
lone electron, these molecules will be extremely reactive. They are presented in
the manner below, and play a vital role in the Free Radical Substitution reaction
discussed in the next tutorial.

This is an example of the formation of chlorine free radicals.


Covalent bonds
So if covalent bonds make up molecules, what are some features of a bond we
need to be aware of?
Bond energy and bond length
Bond polarity
Bond geometry

Bond energy and length are inversely proportional. These terms and concepts
pertinent will not be a part of CHEM110.

Bond polarity
Bond polarity is the result of the difference in electronegativity between the
atoms involved in the bond. Electronegativity is a feature possessed by all atoms
to different extents, and describes the ability of the bonded atom to pull the
bonded electrons towards itself. Thus you can imagine, the higher the
electronegativity of an atom, the more potent it is at pulling the electrons
towards itself and thus making its surrounding region slightly more negative
than the neutral state we expect it to be.

The rule of electronegativity is based on atomic structure and presents itself in
the way below:


Thus atoms, N, O and F exhibit the highest amounts of electronegativity and will
show delta (-) in any bond that it is involved in. *Whats the exception?

Why bond polarity?

The appreciation of polarity is crucial for the discussion of two further concepts:
boiling point and solubility.

Boiling point:
The determinant of variation in boiling points between different organic
molecules is the type of intermolecular force present. Note although the type of
intermolecular force present is determined by the type of covalent bond present;
the term intermolecular is specific in describing the forces between molecules
and not within. It is essential that you acknowledge that in boiling a substance,
we are not interrupting covalent bonds (intra-molecular bonds), you are
breaking down the intermolecular forces.

Important learning point:
A molecule with polar bonds does not necessarily have to be a polar molecule,
why?







Polarity of molecule Type of intermolecular forces
Non-polar:
1.No polar bonds present
2. Symmetrical molecule
Temporary dipole forces
Polar Permanent dipole forces
Presence of Hydrogen bonds Hydrogen bonds

When we consider molecules with purely temporary dipole-dipole forces
present, the bigger the molecular mass the higher the boiling point. Thus butane
will have a higher boiling point than ethane. *How do you think the boiling point
of pentane will compare to 2-methylbutane?

However if we consider two molecules with the same molecular mass, but
different types of intermolecular forces present, the rank of the strength of
intermolecular forces will follow that:

H-bonds > Permanent dipole-dipole > Temporary dipole dipole

The reasoning of this is quite intuitive. The absence of a permanently polar
molecule will lead to a weakened intermolecular attraction as electro-staticity
between the (-) and (+) dipoles between neighboring molecules will be short-
lived. Permanent dipole-dipole forces will provide a more concrete
intermolecular adhesion. Finally, H-bonds which is strictly defined as the:

The presence of Hydrogen bonded to one of the following atoms: N, O, F.

Will provide the most intensive intermolecular force. One can consider H-bond
as an extreme type of permanent dipole-dipole as from the table above, you can
see that N, O and F are the most electronegative atoms in the periodic table and
thus such molecules will establish a very prominent permanent dipole. *Despite
so, how do you think the presence of an ionic bond will compare to H2O (H-
bond) in terms the boiling point?

Specific examples are discussed in the table on the following page.

Solubility:

The concept of solubility is really founded upon this fundamental concept that:

Like dissolves Like.

Solvents that contain similar intermolecular forces as the solute will readily
accept that solute and vice versa. This information is encrypted in the table
below. *Why do some of these molecules, despite having compatible bonds to
water, only dissolve with carbon chains up to three or seven?




Compound type Relative
polarity
Reasoning Water
solubility
Hydrocarbons (CH) 1 Nonpolar molecule and
thus only exhibit
temporary dipole
forces
Insoluble
Halides (CX) 2 Permanent dipole
present but quite weak
Ethers (COC) 3 Permanent dipoles but
stronger than one
above due to presence
of oxygen atom
Esters/aldehydes/ketones
(C=O)
4 Permanent dipole force
present, however a C=O
bond exhibits a
stronger bond polarity
than C-O from ethers.
This is due to the fact
that there are more
electrons between the
two atoms and thus
allows distortion of a
more rich electron field
by the oxygen atom.
Up to three
carbon in chain
Amides (COHN) 5 Permanent dipole + H-
bond
Up to seven
carbons in
chain Amines (NH) 6 H-bonds present
Alcohols (OH) 7 H-bond present also,
but stronger than the
one above due to fact
that oxygen is more
electronegative than
nitrogen.
Carboxylic acids (COOH) 8 H-bond involving
oxygen + permanent
dipole (C=O)
Carboxylate and amine
salts (COO-)/(NH3+)

8


These are on the top of
the food chain, due the
presence of complete (-
)/(+) charges on the
oxygen and nitrogen
compared to molecules
above which only
exhibit delta (-)/(+)s.






Bond geometry:

Hybridization
notation
Carbon configuration Shape Bond
angle
Sp3

Tetrahedral 109.5
Sp2

Trigonal
planar
120
sp

linear 180
*Can you think of another bonding configuration of carbon that will also provide
the linear shape?

Key learning point:

This table is very crucial, and remembering the information contained within
will be key to attaining some easy marks. The background and derivation of
hybridization notations will not be examined and thus the majority of
information below will not be examinable but merely provide the overall picture
for those with more interest. Important things are highlighted and need to be
learned as normally.

The theory of hybridization:

Lets begin by looking at the electron configuration of carbon: 1s2 2s2 3px1 3py1
3pz0. Immediately we realize that there is no way carbon can form four bonds if
it only has two single electrons available in its electron configuration. Thus the
achievement of four equivalent bonds in methane and so on will rely on the
reasoning provided by the hybridization theory.

1. Electron promotion
In this step, the atom promotes an electron from the 2s orbital to the empty
2py orbital, and now we have four single electrons occupying four individual
orbitals.

2. Hybridization

i)sp3
The atom raises the energy level of the 2s orbital and lowers the energy level of
the three 2p orbitals so that they are all at the same energy state. They atom has
HYBRIDIZED one s orbital and three p orbitals and this is why it is given the term
sp3. Consequently, the four bonds this carbon atom will make with the usage of
these four orbitals will be equivalent in energy and allow the formation of a
tetrahedral shape.

Key learning point:
The formation of covalent bonds has always been known to students as the
sharing of electrons; this concept is modified in this course as the overlapping of
orbitals. Thus in this context, after the process of hybridization, the orbitals with
the electrons that they possess will go on to OVERLAP with another orbital. In
methane, this would be hydrogen. Through overlap, the newly formed bond will
contain an electron from each atom, thus the idea of sharing remains the same.
When hybridized orbitals overlap, the orientation under which it happens can be
in two ways:
1. If the orbitals overlap head to head they will form a sigma bond
2. if the orbitals overlap side to side they will form a pi bond.

In this scenario of a sp3 carbon, the carbon will have four sigma bonds. This is
because the inter-nuclear axis between carbon and the four hydrogens is the
preferred site of orbital overlap and thus overlap will always be head to head
where possible.


ii)sp2

In this case, the atom will hybridize one s orbital and 2 p orbitals, leaving
another p orbital un-hybridized. The hybridized orbitals will undergo overlap as
above, forming sigma bonds. At this instant, the remaining p orbital will be
forced form another type of bond, that does not take place along the internuclear
axis as it has already been taken by an existing sigma bond. It can only form a
side-to-side orbital overlap up and below the pre-existing sigma bond; a pi bond.

Key learning point:
A sigma bond + a pi bond = a double bond.

iii)

In this case, the atom will hybridize one s orbital and one p orbital, leaving two p
orbitals un-hybridized. The hybridized orbitals will form sigma bonds and the p
orbitals will form two pi bonds, one above and below the pre-existing sigma
bond, and the other in front of and behind the sigma bond.

Key learning point:

One sigma bond + two pi bonds = a triple bond

Questions:
1. why is the carbon in =C= also considered sp?
2. why cant a carbon atom have a quadriple bond?






Nomenclature, DBE and skeletal formula:

In terms of the different functional groups that this course will cover, we will
take a slightly different approach in discussing each functional group specifically
and in detail when we get to it instead of introducing them all at the same time.
Students should definitely revise the organics part of their high-school
curriculum in preparation for block one, because even though it wont include
specific reactions, it will include nomenclature and formulae presentation.

In terms of nomenclature, a quick debrief of the principles that you should stick
to will be:
1. Identify longest carbon chain.
2. Identify side groups.
3. Identify the side group with the highest priority, and number carbons
from the side which this group is closes to.
4. Attach correct prefixes and suffixes according to side groups present.


DBE:
DBE stands for double bond equivalents. One can think of it literally as the total
number of double bonds and structures equivalent in character to double bonds
which can be considered to be a triple bond or a ring. We will explore this
concept in more detail below.

The concept of DBE is really to deduce the level and pattern of saturation.
Whether it is the presence of a double bond or a triple bond or a ring, it will
reduce the number of hydrogens present and thus alter the molecular formula
significantly, thus they are collectively considered to be DBE. We can find out the
DBE in two ways:

By inspection:
This method of investigating DBE requires that we count the number of double
bonds, triple bonds and rings in the displayed/skeletal formula. Note:
1 double bond = 1 DBE
1 ring = 1 DBE
1 triple bond = 2DBE

Key learning point: we can only find out DBE by inspection if the molecule is
presented to us in its displayed or skeletal formula (maybe also structural),
because only these presentations will specifically show the positions and
numbers of the structures relevant.

By Calculation:


DBE = (2n4+n3-n1+2)

The subscripted numbers imply the number of atoms, which can form the stated
number of maximum bonds. Thus n4 represents all the numbers of carbon
atoms, n3 represent the number of nitrogen atoms and n1 represent the total
numbers of hydrogen atoms and halogen atoms.

DBE provides a good tool for getting a quick impression of the type of functional
groups that might be present, and it will be very handy in the topic of
spectroscopy.

Skeletal formula:

This is a crucial component of your assessment in CHEM110, it requires you to
extend your knowledge of the variety of formulae used in organic chemistry.
Organic molecules in reality are big and complex, therefore this form of formula
provides a more compact and dense way of illustrating a molecule.

The process of translation from any other formular to a skeletal formula follows
that:
1. Any joint or end of a line represents the presence of a carbon atom.
2. Any carbon atoms or hydrogen atoms directly joined to a carbon are not
shown.

Handy note: this seems like a short set of rules, but it is really hard not to make
mistakes, thus plentiful of exercises will be really crucial.











Isomerism
* Insert tree of isomerism here















































Constitutional isomerism

A fancy term of structural isomerism that you learned in highschool. It is defined
to be molecules with the same molecular formula but different structural
formula or more specifically different atom-to-atom bonding sequence.

key learning point:
this means that consititutional isomers can be functionally the same or different,
i.e. C3H6O can be an aldehyde or a ketone.


Stereoisomerism

This encompasses all categories of isomerism in which the isomers have the
same molecular and structural formula but have different spatial arrangements.


Configurational isomerism
To interconvert between the isomers of this type, one has to physically break a
bond and reattach it at another position.


Geometric isomerism

These isomers arise due to restricted rotation around a bond. The most common
example that students are aware of is alkenes, but the structure not to be
overlooked is rings that also restrict complete bond rotation.

Students are expected to build upon their previous interactions with the Cis-
Trans system and work with the E/Z system. This system provides a more
comprehensive way of dealing with this class of isomers as it allows the presence
of four different substituents on both carbons involved in the double bond. The
same applies to rings.

The principles of assigning priorities (discussed on next page) are as follows:
1. Consider the two groups on the same carbon, and prioritize them as
either Hi or Lo.
2. If both His are on the same side, it will be considered Z, if they are on the
opposite side, it will be considered E.

Key learning point: the two groups on the same carbon involved in the double
bond must be different.

Handy note: E is for Deefferent.





Enantiomers:

These are isomers, which are mirror images that arise from a carbon
simultaneously joined to four different groups. This carbon is known as a chiral
carbon or a stereocentre, and the two isomers might seem similar but they are
actually different as mirror images are non-superimposable.

One enantiomer will rotate plane-polarized light to the left, this is known as
laevorotatory, the other will rotate plane-polarized light to the right and this is
known as dextrorotatory. A mixture containing exactly 50:50 of each is known as
a racemic; it will not rotate plane-polarized light. Distinguishing enantiomers is
an important process especially in the drug industry as one can be much more
potent than another.

One is expected to work with the R/S system when considering a stereocentre;
the principles are as follows:

1. Prioritize the four groups. ( Discussed below)
2. Have the lowest group turning directly away from you and thus the
remaining three should point at you like a steering wheel.
3. If the priorities rank down in a clockwise manner, it is considered R, if it is
anti-clockwise, it will be considered S.

Handy note: R for turning to the Right i.e. clockwise.


Assigning priorities:
1. The higher the atomic number of the immediate atom bonded to the C, the
higher the priority.
2. If the atomic number of the immediate atoms discussed above is the
same, then one should keep inspecting downstream until a clear
difference can be established.
3. Atoms bonded by a double bond or a triple bond can be considered as
being bonded to an equivalent number of single bonds.


Conformational isomerism:

Isomers arise due the rotation around single bonds.



Diastereomers

Stereoisomers, which are, not mirror images. This is a perplexing topic and one
shouldnt spend too much time reading upon this. However one should be aware
of its definition and what that implies in context: is covers geometric and
conformational isomers in theory.