DINA BTE. MOHD KAMAL

0432716

SECTION 1

DR. IBRAHIM ALI NOORBATCHA

BMATHSC

dimkazz_03@yahoo.com

http://dimkazz.tripod.com

ASSIGNMENT 3

KOS 1110 COMPUTER IN SCIENCE

-2005-

KOS 1110 Computers in Science

Assignment 3 - Questions in ChemSketch and PDB

Due date Monday, 12-9-2005, 10AM

Instructions: For question numbers 1-4 after drawing the structures, reactions and the apparatus, put them in one MS Word file sequentially, along with the questions. For question number 5, the complete answer should be prepared as a HTML file. All the files, including the pdb files should be compressed using winzip and sent to me as one file with the name “3yourname.zip” before the due date along with the printed assignment. Publish these files in your web pages before the due date and when you are sending the assignments, indicate the web page links to these pages. Use as many options as possible, including colour in all the drawings.

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.

IUPAC Rules:

1. Identify the longest carbon chain. This chain is called the parent chain.

2. Identify all of the substituents (group appending from the parent chain)

3. Number the carbon of the parent chain from the end that gives the substituents the lowest numbers when comparing a series of number,the series that is the “lowest” is the one which contains the lowest number at the occasion of the first difference. If two or more chains are in equivalent positions, assign the lowest number to the one who which will come first in the name.

4. If the same substituent occurs more than once, the location of each point on which the substituent occurs is given. In addition, the number of times the substituent group occurs is indicated by a prefix. (di, tri,tetra,etc.)

5. If there are two or more different substituent they are listed in alphabetical order using the base name (ignore the prefixes). The only prefix which is used when putting the substituents in alphabetical order is iso as in isopropyl or isobutyl. The prefixes sec- and tert- are not used in determining alphabetical order except when compared with each other.

6. If chain of equal length are competing for selection as the parent chain, then the choice goes in series to:

i. The chain which has the greatest number of side chains.

ii. The chain whose substituent has the lowest-numbers.

iii. The chain having the greatest number of carbon atoms in the smaller side chain.

iv. The chain having the least branched side chains.

A cyclic (ring) hydrocarbon is designated by the prefix cycle- which appears directly in front of the base name.

2. Explain the SMILES notation by drawing five different structures and finding out their SMILES notation using ChemSketch.

SMILES Notation

o Use ordinary atomic symbols.(B,C,N,O,P,S,Cl,Br,I- used as shown)

o Other atoms and any charges are placed in brackets.(eg: [N+])

o The upper case for aliphatic; lower case for aromatic. A second letter of any symbol is always lower case.

o Bond need not to be specified except:

- Equal sign (=) for double bond

- Bound sign (#) for triple bond

- A period separates disconnected structures (ions or complexes)

o A branched group is placed in parentheses. Branches can be nested if desired.

o To make a ring path linear, one bond must be broken for each ring.

- Number the atoms on each side of break with the same number.

- Any number can be re-used after that ring is closed.

3. Draw five different reactions with complete structural, stereo chemical (use shaded or wedge bonds) and mechanistic (use different types of arrows) 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.

PREPARING ETHANOL USING DISTILLATION METHOD

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 and print these files using any text editors. Use this example to explain the different features of these file formats.

To save molecular structures, 3 different file formats used are

a. mol file

b. pdb file

c. xyz.file

1) .mol file

For the mol file,the number of atom and the whole of bonds of this molecule is shown. There is also the information about the connectivityof whether it is single or double bonds and x,y,z coordinates.

ACD/Labs0909051341

7 7 0 0 0 0 0 0 0 0 1 V2000

9.6819 -8.2083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

12.1291 -6.4304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

14.5762 -8.2083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

13.6415 -11.0852 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

10.6166 -11.0852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.8051 -7.2736 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

12.1291 -3.4055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

2 1 1 0 0 0 0

3 2 1 0 0 0 0

4 3 1 0 0 0 0

5 1 1 0 0 0 0

5 4 1 0 0 0 0

6 1 1 0 0 0 0

7 2 1 0 0 0 0

M END

2) .pdb file

This PDB format emphasize more information about protein. The numbering of atom is automatic in x,y,z coordinates. There is also chain identifier and chain residue number. The first line is kind of remark or comment.

REMARK Accelrys ViewerPro PDB file

REMARK Created: Sat Sep 10 12:17:39 Malay Peninsula Standard Time 2005

ATOM 1 C1 MOL 1 12.248 -10.384 0.000 1.00 0.00

ATOM 2 C2 MOL 1 15.344 -8.135 0.000 1.00 0.00

ATOM 3 C3 MOL 1 18.440 -10.384 0.000 1.00 0.00

ATOM 4 N4 MOL 1 17.257 -14.023 0.000 1.00 0.00

ATOM 5 C5 MOL 1 13.431 -14.023 0.000 1.00 0.00

ATOM 6 N6 MOL 1 8.609 -9.202 0.000 1.00 0.00

ATOM 7 O7 MOL 1 15.344 -4.308 0.000 1.00 0.00

TER

3) .xyz file

this format stated the molecule’s name, show the total number of atom and identifies each of them in x,y,z coordinates.

7

NoName 0.000000

C 12.2482 -10.3841 0.0000

C 15.3440 -8.1348 0.0000

C 18.4398 -10.3841 0.0000

N 17.2573 -14.0234 0.0000

C 13.4307 -14.0234 0.0000

N 8.6088 -9.2016 0.0000

O 15.3440 -4.3082 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. Write one paragraph about this molecule in the web page.

<html>

<head>

<title>Assignment 3: chemsketch & PDB (HEMOGLOBIN (VAL BETA1 MET, TRP BETA37 TYR) MUTANT)

</title>

</head>

<body bgcolor="#FFFFFF">

<h2>Question 6: 'Example enhanced web document with Chime'</h2>

<embed src="1A00.pdb"height=120 width=120 display3D=ball&stick>

<p>

The display type has been set to ball and stisck.

<p>

<embed src="1A00.pdb"height=120 width=120 display3D=spacefill

startspin=true spinY=15;

<p><br><br>

The display type is set to spacefill and the molecule is started off rotating.

(You can turn off the rotation by using the pop-up menu.)

<p>

</body>

</html>

7. Prepare a web page (eg. “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.