1. Draw five different structures having less than 50 atoms with different functional groups and atoms. Find out their iupac names using ChemSketch software. Explain the iupac rules used to name these structures

18:01 a1/p1 Assignment 3 14/01/2013 KOS 1110 Computers in Science Assignment 3 - Questions in ChemSketch and PDB Due date Thursday, 19-8-2004, 5pm 1. Draw five different structures having less than 50 atoms with different functional groups and atoms. Find out their IUPAC names using ChemSketch software. Explain the IUPAC rules used to name these structures. (i) There is a tertiary butyl at Carbon no 1 of cyclohexane and named as tert-butylcyclohexane (ii) The longest Carbon chain of this compound is 5 Carbon which is pentane. There is bromine at Carbon no 1 and is called 1-bromo. There is double bond at Carbon no 2 and the compound named 2-ene. Two methyl group are at Carbon no 3 and 4 and it is called 3,4-dimethyl. When the named arranged alphabetically, the compound name is 1-bromo-3,4-dimethylpent-2-ene. (iii) The major structure of this compound is benzoic acid. There is one methyl group attached to the Oxygen atom at carboxyl group. Therefore, the name of the compound is methyl benzoate. (iv) In this compound, we named the aromatic compound at Carbon no 2 acts as prefixes and called 2-phenyl. The longest Carbon chain is 2 and named ethane. There is alcohol functional group at first Carbon of ethane and named ethanol. Therefore, the name of the compound is 2-phenylethanol. (v) The compound longest Carbon chain is 7 and called heptane. There is one double bond at Carbon no 3 and called hept-3-ene. There are 3 methyl groups in the compound; 2 methyl groups situated at Carbon no 2 and 1 methyl at Carbon no 6. The structure named 2,2,6-trimetyhl. Bromine atom is situated at Carbon no 3 while Chlorine atom is situated at Carbon no 4. The structure named 3-bromo-4-chloro.The configuration of atom with higher priority which are chlorine and bromine are on opposite site and the configuration is “E”. The priority group is at carbon no 3 and it is called 3E. Therefore, the whole structure named (3E)-3-bromo-4-chloro-2,2,6-trimethylhept-3-ene. 2. Explain the SMILES notation by drawing five different structures and finding out their SMILES notation using ChemSketch. (i) (ii) (iii) (iv) (v) 3. Draw five different reactions of industrial or biological importance with complete structural, stereo chemical and mechanistic details using ChemSketch. Use maximum number of options available in chemsketch. (i) Synthesis of glucose-6-phosphate in Glycolytic pathway (ii) To Prepare Nylons (iii) To prepare Dacron (iv) Transamination of pyruvate (v) To produce glycine from ethanoic acid (acetic acid) 4. Draw one experimental set up used in any laboratory or industrial preparation of any chemical or enzyme or anything using ChemSketch. Insert enough text captions with callouts to explain the apparatus. Use maximum number of options available in chemsketch, including shading options. Preparation of aldehydes and ketones 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. Use this example to explain the different features of these file formats. (i) Q5.pdb REMARK Accelrys ViewerPro PDB file REMARK Created: Tue Aug 17 18:16:49 Malay Peninsula Standard Time 2004 ATOM 1 C1 MOL 1 10.969 -10.133 0.000 1.00 0.00 ATOM 2 C2 MOL 1 14.098 -10.133 0.000 1.00 0.00 ATOM 3 C3 MOL 1 9.500 -6.574 0.000 1.00 0.00 ATOM 4 C4 MOL 1 9.627 -13.186 0.000 1.00 0.00 ATOM 5 Cl5 MOL 1 11.210 -13.186 0.000 1.00 0.00 ATOM 6 O6 MOL 1 7.600 -6.574 0.000 1.00 0.00 ATOM 7 N7 MOL 1 12.274 -8.157 0.000 1.00 0.00 TER (ii) Q5.mol ACD/Labs0816042249 7 6 0 0 0 0 0 0 0 0 1 V2000 10.9693 -10.1333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.0980 -10.1333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5000 -6.5740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6267 -13.1860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2100 -13.1860 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 7.6000 -6.5740 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.2740 -8.1573 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 3 1 1 0 0 0 0 4 1 1 0 0 0 0 5 4 1 0 0 0 0 6 3 1 0 0 0 0 7 1 1 0 0 0 0 M END (iii) Q5.xyz 7 NoName 0.000000 C 10.9693 -10.1333 0.0000 C 14.0980 -10.1333 0.0000 C 9.5000 -6.5740 0.0000 C 9.6267 -13.1860 0.0000 Cl 11.2100 -13.1860 0.0000 O 7.6000 -6.5740 0.0000 N 12.2740 -8.1573 0.0000 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 enough information about this molecule in the web page, so that others would be able to understand this structure. The length of this web page should not be less than two pages. http://www.tripod.com/alpha_digma/Q6.xyz Page 1 Question 6 Glycogen Phosphorylase Show nitrogen atoms Show oxygen atoms Show chiral carbon Show atoms 1, 4-7, and 10 Remove hydrogens Show all atoms Label atoms Label off

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