1. Write down condensed and molecular formula for the following compounds:
 
            (a) Pentane:
 
                       H   H  H   H  H
                        |     |    |     |    |
                  H--C--C--C--C--C--H
                        |     |    |     |    |
                       H   H  H   H  H
 

Solution:

Step1: divide atom groups along main chain: C--C--C--C--C

Step 2: write down formula for each group: CH₃,   CH₂,  CH₂,  CH₂,  CH₃ .
Step 3: Combine them into condensed formula: CH₃CH₂CH₂CH₂CH₃ 
Step 4: Combine atoms of the same element and align the atom symbol acording to convention: C₅H₁₂.

Solution:

Step 1: divide atom groups along main chain: N--C--C--O:

                            H      H      O
                             |         |       ||
                       H--N-   -C-   -C-   -O--H
                                      |
                                     H

Step 2: write down formula for each group: NH₂,   CH₂,  CO,  HO  (COOH)
Step 3: Combine them into condensed formula: NH₂CH₂COHO (NH₂CH₂COOH).
Step 4: Combine atoms of the same element and align the atom symbol acording to convention: C₂NH₅O₂.
Note:

 O
  ||                   is commonly named as COOH.
 C--O--H

Solution:

Step 1: divide atom groups along main chain:

                            H
                             |
                       H--C-   -N--H
                             |        |
                            H      H

Step 2: write down formula for each group: CH₃,   NH₂
Step 3: Combine them into condensed formula: CH₃NH₂.
Step 4: Combine atoms of the same element and align the atom symbol acording to convention: CNH₅.

(d) How many bonds are connected to a C, N, O or H  atom? (You may have noticed that the same number of  bonds are connected to an atom of the same element).

Answer:

4 bonds are connected to C, 3 to N, 2 to O, and 1 to H atom. This is a very common feature and it is called the Octet rule.

2. In each of the following pair of bonds, predict which is shorter:

      (a) C=O or C--C
      (b) C=N or C=O
      (c) C-H or N-H
      (d) N-H or O-H
 

 Based on the bond length table given in the lecture, the answers can be given as:

(a) C=O is shorter
(b) C=O is shorter
(c) N-H is shorter
(d) O-H is shorter

You may notice from the Table that in most cases double bond is shorter than single bond, triple bond is shorter than double bond.
 

Answer:
Wireframe, ball-and-stick, spacefill.

4. What are the steps in ISIS draw to save a XYZ coordinate file into a .mol file?
 

Answer:
File => Export => Molfile, and then type in a .mol  file name such as file.mol

5. What are the three features of stereochemistry?
 

Answer:

            Configuration (atom organization).
            Conformation (atom spatial arrangement).
            Shape (Surface landscape, steric packing)

6. Describe the purpose of the software Rasmol.  What are the steps to open a xyz coordinate file in
      Rasmol?  How to change the display mode in Rasmol?
 

Answer:

Rasmol displays 3D graphics of a molecule in a variety of modes.

The steps for opening xyz ccordinate file: File=>Open=>List Files of Type=>MDL Mol File Format=>(Select File).

The steps for changing display mode: Display=>(Make selection).
 

Answer:

Bond stretching: E = S _bonds k_b (r - r₀)²

Torsion: E = S _torsions A [ 1 + cos(nt-f)]

Electrostatic interaction:  S _i S _jq_i q_j / r_ij