UNIVERSITI MALAYSIA SABAH SCHOOL OF SCIENCE AND TECHNOLOGY ORGANIC CHEMISTRY PRACTICAL I (SK 10301) EXPERIMENT 2: MOLECULAR MODELING:

ISOMERS, CONFORMERS AND STEREOISOMERS

Group Members : Daphne William Apin Daryl Ng Chuan Yao Fatin Binti Sualin Ili Shazwani Binti Idris Jagadeesh A/L Dewedree Title of Experiment Lecturer Demo Date of Experiment Date of Submission : : : : : (BS10110079) (BS10110080) (BS10110110) (BS10110151) (BS10110157)

Molecular Modeling: Isomers, Conformers and Stereoisomers Prof. Madya Dr. Suhaimi Md. Yassir Ms. Joyce Kristy Primus 4th October 2011 11th October 2011

Objectives : To become familiar with the 3-dimensional structures of organic molecules, especially the tetrahedral structure of alkyl carbon atoms and the planar structures of alkenes. To be able to construct the 3-dimensional models for organic compounds and draw the formulas. Introduction : Determination of shapes of organic molecules is difficult even through the most powerful microscopes other than by the usage of Nuclear Magnetic Resonance(NMR) Spectoscropy. Hence to help in the research of this field, molecular model kit is developed. Molecular models are very useful in testing hypotheses, in understanding physical and chemical properties, and also in visualizing the overall structure of an organic molecule. In this experiment, ball and stick models are used to represent atoms and bonds in molecules and organic molecules structures are built by utilizing the balls and sticks given. Different isomers of organic molecules are also able to be constructed by using these models. Isomers are molecules with the same molecular formulas but different structural formulas. Structural isomers are compounds with different connections among their atoms. Different conformations of molecules can be formed by merely rotating groups around a bond without breaking any bonds, which is also named as conformers. Materials : Molecular model kit.

Elements and bonds represented in the Organic Model Kit Color Black White Red Yellow Green Blue Method : 1. Models for the diatomic molecules hydrogen (H2), chlorine (Cl2), and hydrogen chloride (HCl) were constructed. What are the bond between atoms represent? Models for the diatomic molecules hydrogen ( ), chlorine ( ), hydrogen Element Carbon Hydrogen Oxygen Nitrogen Chlorine Bromine Number of bonds 4 1 2 3 1 1

chloride (HCl) are constructed.

HCl
H H

Cl

Cl

Cl

The bonds between the two atoms are composed of carbon-carbon single bond, which consists of sigma bond. 2. What is the octet rule and how does it explain the tendency of oxyegen to form two bonds whereas chlorine, for example, forms only one bond? The octet rule says that atoms tend to gain, lose or share electrons so as to have eight electrons in their outer electron shell. Electronic configuration of oxygen:

Oxygen tends to form two bonds because it needs another two electrons to achieve its octet configuration since it has 6 valence electrons and two unpaired electrons at -orbital as shown above. Electronic configuration of chlorine:

Chlorine needs another one more electron to achieve octet configuration since it has 7 valence electrons or one unpaired electron as shown above. 3. Models for methane (CH4) and Propane (CHCl3) were constructed. Models for Methane ( ) and chloroform ( ) were constructed.

The shape formed is tetrahedral.

4.

Models for ethane (C2H6) and propane (C3H8) were constructed.

There is no other way to construct these molecules since they have carbon numbers not more than 3, whereby isomerism can only occur with minimum 4 carbon atoms.

H H H C C

H H H H

H C H

H C H C

H H H

Ethane
5. Their structures were sketched. A model for butane (

Propane

Model for butane (C4H10) was constructed. Find another way to construct butane.

) was constructed.

There are two ways of constructing a molecule with the molecular formula

H CH3 C H

H C H CH3 CH3

CH3 C H CH3

Buthane
6.

2-methyl-propane

Ethanol and methyl ether both have empirical formula C2H6O but different structures. The molecules were constructed and the structures were drawnt. Models for Ethanol and methyl ether are constructed.

Ethanol and methyl ether have the same empirical formula linkage.
CH3 CH2 OH

O but different

structural formulas. Ethanol is an alcohol and has an OH group. Ether has a -OCH3 O CH3

Ethanol 7.

Methyl ehter

Models for diatomic oxygen and for carbon dioxide were built. How many double bonds do these molecule have?

Oxygen molecule has 1 double bond whereas carbon dioxide molecule has 2 double bonds.
O O O

Oxygen 1 double bond

8.

Carbon dioxide 2 double bonds

What formula will you predict for octane? Some up the general expression.
Name Methane Ethane Propane Butane Pentane Hexane Heptane Octane As shown on the table, every increase of carbon atom by 1, the number of hydrogen atoms increases by 2. Therefore, the general formula for this kind of hydrocarbon is . consisting of a ring of six C groups, Molecular formula

9.

a) A hydrocarbon with the formula the formula constructed.

was constructed using the molecular model kit. Then, another hydrocarbon with consisting of six CH groups with alternating single and double

bonds between the carbons, was constructed. Cyclohexane and benzene were

The benzene ring consists of six carbon atoms bonded in a flat or planar hexagonal ring. Each carbon is bonded to one hydrogen because of the three alternating double bonds. This reveals that each carbon is bonded to 3 others atoms and one of them is a double bond. Hence the molecular geometry at each carbon is trigonal planar as each carbon is hybridized.

H H C H H C C H H C

H H C C H H H H

2D plan view of benzene

2D plan view of cyclohexane

Hence the whole ring is flat as compared to the cyclohexane, which is hybridized, will give rise to a tetrahedral shape for each of the carbon atom. Each carbon atom is bonded to two carbon atoms and two hydrogen atoms in carbon-carbon single bond. Therefore, cyclohexane is not as flat as benzene. In short, benzene has 3 carbon-carbon single bonds and 3 carbon-carbon double bonds while cyclohexane have 6 carbon-carbon single bonds only.

b) The smallest unit of units have made without straining the bonds. Cyclopropane c) Years ago, chemists tried to create a Cubane molecule, which consist of 8 carbon atoms with 2 hydrogen atoms attached to each carbon. However, this molecule are proved to be unstable.

H H H C H C H H C C

H H C C H H C H C

H H

H H

Cubane in theory The carbon atoms in Cubane are where it supposed to be

Cubane in practical hybridized and have an angle of , (tetrahedral). Hence, the carbon-carbon single

bonds are too highly strained, which in return, causes more internal energy is generated renders it becomes very unstable. Therefore, the cubane structure will easily rupture at most of the conditions. The cubane in practical also proves that cubane with each carbon bonded to 2 hydrogen atoms are impossible to be made as each carbon by max could only be bonded to 4 atoms or groups. However, although cubane in practical is able to be synthesized, researches shown that even though still remains as highly reactive compound i.e. unstable. is kinetically stable, its

10.

a) Model of molecule that has single bond in center and four different atoms attached to it was constructed. It mirror image was constructed.

The two mirror pairs are not identical since the enantiomers are not superimposable and remain as distinct compound. b) The model was placed on the paper. Position of each touching atom was marked. The positions of atoms were marked. The result showed that none of the molecules fitted each other. c) A model that has a carbon atom in the centre but only three different atoms attached to it, that is, that has two of one kind of atom instead of four different atoms or groups.

d) Part b was tried with the model from part c. The result showed that the molecules fitted each other.

e) Carbons that have fewer than three different atoms were predicted. Carbons that have fewer than three different attached atoms would not give distinct left and right-handed forms. From the results of part a to part d. A rule on determination on left and righthanded forms could be formulated: 1. Identify the attached atom or groups of the highest priority. 2. Follow by the second priority to the lowest one. 3. If the arrow pointed clockwise, it is a (R)-handed form. Inversely, if the arrow pointed anti-clockwise, it is a (S)-handed form. For example: 2-bromobutane

f) A model of lactic acid was constructed.

Lactic acid

A 2D plan view of lactic acid is shown as below:

H HO C O C* CH3 OH

lactic acid
The carbon atom with the asterisk(*) has four different groups attached to it. Hence, it exists as the chiral carbon center that has two forms, (R)-Lactic acid and (S)-lactic acid.

g) Based on its structure, carvone wold be chiral was predicted. The structure of carvone:

Note: * = chiral centre The asterisk(*) shown that the indicated carbon has four different groups attached to it. Hence, optical isomerism occurs.

(R)-Carvone

(S)-Carvone

The two groups isomers. When and vice versa.

and ( atom is at the front, (

are at different side at each of the group is at the back

h) Left and right-handed forms of thalodimide were constructed.

The structure of thalodimide:

Thalodimide The different forms of thalodimide will cause different effects. Although theories stated that (R)-enantiomer is capable to cure morning sickness while (S)enantiomer is the one responsible for birth defects, however not much proofs and evidence are concrete enough to prove the theories.

The main difference is the position of the group that is attached to the nitrogen atom on the pentagonal carbon ring. Researches shown that (S)-thalodimide fits neatly into the major groove at the DNA purine sites. Therefore, it is greatly believed that (S)-enantiomer will hinder the function of purine during DNA replication processes. Therefore, causing physiological malfunction or birth defects. However, evidence shown that taking either one of the enantiomers at a time greatly reduced the chance of having birth defects.

O NH N O

O NH N O

(S)-thalidomide

(R)-thalidomide

Pre-Laboratory Questions-Experiment 2 1. How do you distinguish between molecular formula, empirical formula (simplest), and structural formula of benzene? (Draw structure) Molecular formula Empirical formula : :

Structural formula

The molecular formula and simplest formula could be distinguished by the subscripted number at C and H atoms. The empirical formula is a formula only showing the simplest ratio of carbon to hydrogen atom. Hence, a ratio of 1:1 is

denoted for empirical formula of benzene as compared to molecular formula, which shows the actual numbers of carbon and hydrogen bonded together. Structural formula is different from the two formulas as it shows how the carbon and hydrogen atoms bonded in benzene. 2. How do you distinguish between geometrical and structural isomers? Give example. Geometrical isomers occur only with a presence of carbon-carbon double bond, which in return will produce cis- and trans-isomers. They both of have the same molecular formulas but different position of the atoms or groups that attached to the two double bonded carbons Structural isomers are isomers that have the same molecular formulas but with different structural formulas, or, in another words the position of some of the atoms or groups are different from each of the structural isomers. For example, butane with molecular formula and butane with molecular formula
H H3C C H H C H CH3

that has structural isomers

that has geometrical isomers.

H H3C C H C CH3

2-butene

Butane
H CH3 H3C C H CH3 H3C C C CH3 H H C H3C C H CH3

cis-2-butene

trans-2-butene

2-methyl-propane
3. Why should the properties of structural isomers differ?

This is because of the arrangement of the position of the atoms of the compound, which results in different physical properties. For example the melting point of pentane and 2, 2-dimethyl-propane are different as the arrangement are different.
H H3C C H H C H H C H CH3 H3C

CH3 C CH3 CH3

Pentane

2,2-dimethyl-propane

Although both have the same number of carbons, they differ in their molecular shape. Pentane has a linear shape whereas 2, 2-dimethyl-propane gives a spherical shape. The melting point of pentane is higher because it has a larger surface area of contact as compares to 2, 2-dimethyl-propane which is spherical. Hence, the Van der Waals forces become stronger as Van der Waals forces is directly proportional to the surface area of contact of the organic molecules. Therefore, more heat is needed to overcome the intermolecular forces before any change of physical properties can occur. 4. Draw the skeletal formula for the following compound.

H3C H H3C C CH3 CH C H

CH3

CH3

Answer:

5.

Draw all the possible cyclic isomers for C4H8 and name all the isomers.

CH3

Cyclobutane

Methyl-cycloprapane