Chapter 4. An Introduction to Organic Compounds

Structural Formula

Drawing Lewis Structures

Don't deviate from:

C can have maximum of 4 bonds

H can only has one bond

O can has two bonds

All halides has one bond (Make sure to draw 3 sets of lone pairs)

Example: Draw Lewis structures for a) H₂O, b) CH₄, c) CO₂, and d) C₂H₆O.

a) Draw all atoms with valence electrons, and connect unpaired electrons. Then, redraw.

b) Same procedure, but notice that there are double bonds involved.

Example: Draw Lewis structures for a) H₂O,

Skeltal Structure

Since it is cumbersome to write in all the atoms in a molecule, we most often use skeltal structure to represent Lewis structure. A line represents C-C bond, and C-H bonds are eliminated from the drawing, but it is understood that all necessary C-H bonds are present.

Name	Condensed Formula	Lewis Structure	Skeltal Structure
Ethane	CH₃CH₃
Propane	CH₃CH₂CH₃
Butane	CH₃CH₂CH₂CH₃
Pentane	CH₃CH₂CH₂CH₂CH₃
Hexane	CH₃CH₂CH₂CH₂CH₂CH₃
Septane	CH₃CH₂CH₂CH₂CH₂CH₂CH₃
Octane	CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₃
Nonane	CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₃
The following shows different structures arises from the same formula
	C₂OH₄
	C₂OH₄
	C₂OH₄

Example: How many carbons and hydrogens are there in the following compounds: a) b) c) d)

Remember that Carbon can only have four bonds! The lines in the skeltal structure represent a bond between two carbon atoms.

a) By counting the edges that connect lines, you get the number of carbons. Then each of the end carbons get 3 hydrogens, while each of the inner carbons that are bonded to two other carbons get 2 hydrogens. Therefore, the compound (butane) has 4 carbons and 10 hydrogens.

b) There are 6 edges, thus 6 carbons. Whenever one has a double bond, the number of hydrogen is reduced by one hydrogen per carbon. Thus, in this case, there are 12 hydrogens.

c)5 carbons and 11 hydrogens. (Look at the butane, butadiene and butadiyne examples below for the count of hydrogens)

d)6 carbons and 12 hydrogens.

Polar Covalent Bonds, Shape, and Polarity

Ploarity

Not all covalent bonds are created equal!

The two electrons are not shared equally between two atoms. When the electrons are not shared equally, the bond is said to be polar. The polarity of a bond is decided by Electronegativity. Electronegativity is the ability of an atom to attract electron. So, higher the electronegativity, higher the partial negative charge is on the atom within the molecule.

The difference between the electronegativities of two atoms decides how polar the bond is. As indicated in the following figure, you can say that a bond is nonpolar when the difference between two electronegativity of bonded atoms are about 0 to 0.5. If the difference is large and more than 2 or so, then the bond is ionic. The difference values in between, 0.5 to 1.9 or so, are considered to be having polar bonds.

You see that there are partial charges, δ+ (we read it as partial positive) and δ- (partial negative) on the atoms. The partial charges are the ficticious charge of atoms in a molecule, derived from the electronegativity. More electronegative the atom is, more partially negative the atom is.

Example:Indicate which bonds are nonpolar, polar, or ionic. If polar, place δ+ or δ-.

All C-C and C-H bonds are nonpolar. So, all the hetero atoms, referred to non-C and non-H atoms must be considered. There are four bonds that are polar, indicated by purple color. For a given polar bond, the partial charges are also given. The bond between C-Cl is only moderately polar.

The reason that polarity of bond is important is that organic reaction can to a certain extent be predicted.

Three Dimensional Shape

From above, you know that carbon forms four covalent bonds.

Name	Example	Model	Lewis structure	3D-drawing
Tetrahedral	Methane, CH₄
Pyramidal	Ammonia, NH₃
Bent	Water, H₂O

It is quite important to understand how multiple bonded carbon behaves in terms of geometry.

Bond	Geometry	Angle
sinle	Tetrahedral	109.5°
double	Planar	120°
triple	Linear	180°

Example:The following figure shows human hormones that are dominant for female and male, respectively. They look quite similar to each other! Identify the geoemtry of each carbon whether it assumes tetrahedral (Td), planar (Pl), or linear (Ln) configuration.

First, the notation used here needs clarification. The solid tapered bonds,

, are the bonds pointing toward you out of the plane of the computer screen, and the dashed tapered bonds,

, are the bonds pointing away from you, out of the plane of the screen. At the end of the bonds there exit carbon atoms, as we have understood from how we represented skeltal structures. The ones with the hydrogen,

and

, have the same meaning, but there is no carbon there. Instead, there is a terminal hydrogen. Generally we specify such H due to symmetry of the righthandedness or lefthandedness of the molecule. This becomes very important in enzyme (protein) chemistry!

From above, all singly bonded C assumes tetrahedral configuration, all doubly bonded C assumes planar configuration, and all triply bonded C assumes linear configuration.

Click below to see the answer.

+ Geometry of androhormones

All the carbons in one of the circled areas have the same configurations.

Noncovalent Interactions

Chemical bonds are results of interactions between between atoms in a molecule. There are another level of interactions that have to do with physical processes such as liquid boiling to became gas or cooling liquid become solid. These processes are the result of interaction between molecules, thus we call them, intermolecular forces. Two types:

Molecules with permanent (partial) charges

Nonpolar molecules

Noncovalent Interactions Due to Permanent Charges

According to the electronegativity difference, Δχ, between two atoms, we can classify if the molecule has permanent partial charges as we have seen above.

Hydrogen bond is a type of interaction that shares hydrogen atom between two molecules. Water is a good example. In the following image, water molecules are connected by hydrogen bonds (in red dashed lines).

When the small molecule that possesses -OH or -NH₂ group often has hydrogen bonding.

Dipole-dipole force is due to the permanent dipole moment from polarity of bonds in the molecule. The following illustrates the interaction between molecules possessing dipolar bonds.

Noncovalent Interactions Due to Temporary Partial Charges

The outermost layer of molecule is covered with electrons. In nonpolar molecules, the situation is the same. So, the molecule is a body of minus charges, represented below as δ-. When the two nonpolar molecules approach each other, the electrons nearest to each molecules start to feel each other; there are repulsion between them because of two minus charges repel each other. If and when molecule B is "softer," then the electrons on molecule B at the side of incoming molecule would go away. Because electrons are missing at the position, the molecule develops positive charges, represented by δ+. So, the positive charge will be attracted by the minus charges of molecule A to form a stable complexation. The intermolecular interaction of this kind is said to possess London force.

Example:Indicate the type of predominant intermolecular interactions each of the following molecules posssess:

a)
b)
c)
d)
e)

a) and e) are hydrocarbons. There is no polarity to bonds. Therefore, only the London forces.

b) has C=O two places within the molecule, therefore dipole-dipole force.

c) and d) -OH and -NH₂ substituents are considered to have hydrogen bonding.

Families of Organic Compounds

Functional Group -- A group of atoms in a molecule that has specific chemical properties.

Hydrocarbons

Alkanes

Alkenes

Alkynes

Aromatic hydrocarbons

Alcohols, Phenols, and Ethers

Alcohol group contains -OH substituents.

Phenol is a -OH group is attached to aromatic ring.

Ether group contains -O- substituents. In the picture, R and R' represent some carbon containing groups.

Thiols, Sulfides and Disulfides

Thiol group contains -SH substituents. Again, R is some organic group.

Sulfide group contains -S- substituents.

Disulfide group contains -S-S- substituents.

Amines

Amine group contains N in three different arrangements


Primary (1°) amine	Secondary (2°) amine	Tertiary (3°) amine

Alkyl Halides

Halogen such as F, Cl, Br, or I is attached to tetrahedral C.

Ketones and Aldehydes

Ketone has C=O substituent

Aldehyde has O=CH substituent

Carboxylic Acids, Esters, and Amides

Carboxylic Acid has -COOH substituent

Ester has -COO- substituent

Amide has -CON- substituent

Amino acid ia an important molecule for biochemistry. It is a building block of protein. Because protein acts as structural molecules as well as reaction catalysts. Amino acid has a simple structure, which contains amine group and carboxylic acid group. Below is the structure of amino acid.

What makes amino acid unique is in the R-group. R represents some carbon-containing group, and different R makes different amino acid. There are about 20 naturally occuring amino acid. We'll look into it more in Chapter 12.

Example:Identify functional groups in the following: