1. Draw five different structures having less than 25 atoms with different functional groups and atoms. Find out their IUPAC names using ChemSketch software. Explain the IUPAC rules used to name these structures.
To name these structures, the atoms cannot exceed 50 or more than 3 cycles. The atoms that can be used are H, C, N, P, O, S, F, Cl, Br, I, Li, Na and K.
2. Explain the SMILES notation by drawing five different structures and finding out their SMILES notation using ChemSketch.
SMILES stands for Simplified Molecular Input Line Entry Specification. It is a concise chemical notation system which allows keyboard entry. Below are the examples of the Smiles notation given to some molecular structures.
3. Draw five different reactions with complete structural, stereo chemical and mechanistic details using ChemSketch.
4. Draw any one experimental set up (not discussed in the class) used in any laboratory using ChemSketch. Insert enough text captions with callouts to explain the apparatus.
This experiment is done to determine the mass of magnesium and oxygen in magnesium oxide. The magnesium oxide is burned, cooled and weighed over and over again until a constant mass is achieved.
5. What are the names of the different file formats used to save the molecular structures? Draw a molecule containing C, N and O in ChemSketch. Save this molecule in different file formats. Examine these files using any text editors. Use this example to explain the different features of these file formats.
The file formats used to save the molecular structures are .mol, .xyz and .pdb. To view the structure on the web page, go to planet.time.net.my/KLCC/mj_diana/Chemsketch.htm.
Below is the information from the text editor obtained from the mol file.
ACD/Labs0109041227
21 25 0 0 0 0 0 0 0 0 2 V2000
11.5560 -6.7131 1.3504 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8622 -6.9834 2.8240 C 0 0 0 0 0 0 0 0 0 0 0 0
11.9445 -5.3209 1.1082 N 0 0 0 0 0 0 0 0 0 0 0 0
10.7137 -6.4004 3.6251 C 0 0 0 0 0 0 0 0 0 0 0 0
11.4527 -4.5467 2.2529 O 0 0 0 0 0 0 0 0 0 0 0 0
10.2978 -5.1932 2.8880 N 0 0 0 0 0 0 0 0 0 0 0 0
13.6000 -7.9732 1.0549 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4927 -8.5411 2.5063 C 0 0 0 0 0 0 0 0 0 0 0 0
12.2305 -7.7489 0.5342 N 0 0 0 0 0 0 0 0 0 0 0 0
12.1613 -8.3712 3.0214 O 0 3 0 0 0 0 0 0 0 0 0 0
15.6707 -6.9233 1.5147 N 0 0 0 0 0 0 0 0 0 0 0 0
15.7440 -7.7899 2.6894 O 0 0 0 0 0 0 0 0 0 0 0 0
14.2873 -6.7306 1.0828 O 0 0 0 0 0 0 0 0 0 0 0 0
14.4500 -7.8288 3.3631 N 0 0 0 0 0 0 0 0 0 0 0 0
11.5244 -9.0338 0.7465 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2207 -9.1267 2.2510 C 0 0 0 0 0 0 0 0 0 0 0 0
10.3195 -9.2140 -0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.8452 -10.4879 2.6605 N p; 0 0 0 0 0 0 0 0 0 0 0 0
9.3581 -10.0651 0.6485 C ; 0 0 0 0 0 0 0 0 0 0 0 0
10.0149 -11.1093 1.6010 C ; 0 0 0 0 0 0 0 0 0 0 0 0
9.6343 -7.3223 3.6369 O 0 0 0 0 0 0 0 0 0 0 0 0
3 1 1 0 0 0 0
4 2 1 0 0 0 0
5 3 1 0 0 0 0
6 4 1 0 0 0 0
6 5 1 0 0 0 0
9 7 1 0 0 0 0
10 8 1 0 0 0 0
1 9 1 0 0 0 0
2 10 1 0 0 0 0
2 1 1 0 0 0 0
12 11 1 0 0 0 0
13 11 1 0 0 0 0
14 12 1 0 0 0 0
7 13 1 0 0 0 0
8 14 1 0 0 0 0
8 7 1 0 0 0 0
16 15 1 0 0 0 0
17 15 1 0 0 0 0
18 16 1 0 0 0 0
19 17 1 0 0 0 0
20 18 1 0 0 0 0
20 19 1 0 0 0 0
9 15 1 0 0 0 0
16 10 1 0 0 0 0
21 4 1 0 0 0 0
M CHG 1 10 1
M END
Below is the information from the text editor obtained from the xyz file.
21
NoName 0.000000
C 11.5560 -6.7131 1.3504
C 11.8622 -6.9834 2.8240
N 11.9445 -5.3209 1.1082
C 10.7137 -6.4004 3.6251
O 11.4527 -4.5467 2.2529
N 10.2978 -5.1932 2.8880
C 13.6000 -7.9732 1.0549
C 13.4927 -8.5411 2.5063
N 12.2305 -7.7489 0.5342
O 12.1613 -8.3712 3.0214
N 15.6707 -6.9233 1.5147
O 15.7440 -7.7899 2.6894
O 14.2873 -6.7306 1.0828
N 14.4500 -7.8288 3.3631
C 11.5244 -9.0338 0.7465
C 11.2207 -9.1267 2.2510
O 10.3195 -9.2140 0.0000
N 10.8452 -10.4879 2.6605
C 9.3581 -10.0651 0.6485
C 10.0149 -11.1093 1.6010
O 9.6343 -7.3223 3.6369
Below is the information from the text editor obtained from the pdb file.
REMARK Accelrys ViewerPro PDB file
REMARK Created: Fri Jan 09 13:23:25 Malay Peninsula Standard Time 2004
ATOM 1 C1 MOL 1 11.556 -6.713 1.350 1.00 0.00
ATOM 2 C2 MOL 1 11.862 -6.983 2.824 1.00 0.00
ATOM 3 N3 MOL 1 11.944 -5.321 1.108 1.00 0.00
ATOM 4 C4 MOL 1 10.714 -6.400 3.625 1.00 0.00
ATOM 5 O5 MOL 1 11.453 -4.547 2.253 1.00 0.00
ATOM 6 N6 MOL 1 10.298 -5.193 2.888 1.00 0.00
ATOM 7 C7 MOL 1 13.600 -7.973 1.055 1.00 0.00
ATOM 8 C8 MOL 1 13.493 -8.541 2.506 1.00 0.00
ATOM 9 N9 MOL 1 12.231 -7.749 0.534 1.00 0.00
ATOM 10 O10 MOL 1 12.161 -8.371 3.021 1.00 0.00
ATOM 11 N11 MOL 1 15.671 -6.923 1.515 1.00 0.00
ATOM 12 O12 MOL 1 15.744 -7.790 2.689 1.00 0.00
ATOM 13 O13 MOL 1 14.287 -6.731 1.083 1.00 0.00
ATOM 14 N14 MOL 1 14.450 -7.829 3.363 1.00 0.00
ATOM 15 C15 MOL 1 11.524 -9.034 0.747 1.00 0.00
ATOM 16 C16 MOL 1 11.221 -9.127 2.251 1.00 0.00
ATOM 17 O17 MOL 1 10.319 -9.214 0.000 1.00 0.00
ATOM 18 N18 MOL 1 10.845 -10.488 2.661 1.00 0.00
ATOM 19 C19 MOL 1 9.358 -10.065 0.649 1.00 0.00
ATOM 20 C20 MOL 1 10.015 -11.109 1.601 1.00 0.00
ATOM 21 O21 MOL 1 9.634 -7.322 3.637 1.00 0.00
TER
6. Download a molecule from the Protein Data Bank (PDB) in pdb format. Prepare a chime enhanced web page showing this molecule in two different display formats. Include some comments in the web page.
To view the molecule, go to planet.time.net.my/KLCC/mj_diana/ DNApdb.htm
7. Prepare a web page (“my class mates”) containing the names of your class mates. Link these names to their respective web pages, so that when any one clicks on these names, they should be able to visit the web pages built by your friends. Publish this web page in your web site as one of the links.
To address to view the web page is www.geocities.com/mj_diana/ classmates.htm
Class/Lab Exercises
β-Maltose
β-Cellobiose
