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.

 

 

The IUPAC Rules

i.                     The longest carbon chain in the molecule was determined. The number of carbon was counted using the Greek preferences (meth, eth, pop, but, pent, hex, hept, etc.) and followed by the suffix name of the functional group.

ii.                   The attached shorter name then was named.

iii.                  To locate the position of the substituent group, the longest carbon chain was named consecutively from one end to another, starting from the end that will give the lowest number to the substituent.

 

 

Structure 1

 

 

a. numbering with lowest possible numbers, alphabetically

b. the exceptional aromatics can serve as parent name with principal

     substituents assumed to be on carbon 1.

 

 

Structure 2

 

 

    1. count the number of carbon atoms in the ring and use the parent name for that number of carbons. In this case, the name is cyclohexane
    2. name and number the substituents. Here is 1,3,5 bromo
    3. the same substituents occurs more than once in the compound.the prefixes tri is used

 

 

Structure 3

 

a.       aldehydes are named by using the suffix- al

b.      the parent chain must be  the longest continous carbon chain that contains the –CHO group  – pentanal

c.       the carbonyl carbon is always numbered as carbon 1.

d.      name and number  each atom  attached to the parent compound.-2,3-cloro                 

e.       two same substituents occur-the prefixes di is used

 

 

 

 

 

 

Structure 4                                              

 

 

 

 a. used suffix –ene for double bond

  b. parent chain :cyclohexene

  c. position of double bond: carbon-1 and 4 :1,4-diene

  d. substituents :3,6 dimethyl

 

 

structure 5

 

                                                                      

 

a.       The main chain is benzoic acid, as the functional group must be included in the longest carbon chain.

b.      The substituent is isobutyl at carbon number 4.

c.       The numbering starts at -COOH as the functional group.

 

 

 

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

 

SMILES (Simplified Molecular Inpit Line Entry Specification) is a universal nomenclature. It is widely used as general-purpose chemical nomenclature and data exchange format. SMILES is a concise chemical notation system which allows keyboard entry (i.e. plain text, no mouse, no graphic) of molecular structure. SMILES handles common bonds (single, double, triple, aromatic, ionic) any atom or isotope, add, valences and so on.

The following atomic symbols are several valid SMILES notations.

 

C

methane

(CH4)

P

phosphine

(PH3)

N

ammonia

(NH3)

S

hydrogen sulfide

(H2S)

O

water

(H2O)

Cl

hydrochloric acid

(HCl)

 

 

 

 

CC

ethane

(CH3CH3)

C=O

formaldehyde

(CH2O)

C=C

ethene

(CH2=CH2)

O=C=O

carbon dioxide

(CO2)

COC

dimethyl ether

(CH3OCH3)

C#N

hydrogen cyanide

(HCN)

CCO

ethanol

(CH3CH2OH)

[H][H]

molecular hydrogen

(H2

 

 

Structure 1

 

 

 

  1. Number is used for the ring. Number the atoms on each side of a break with the same number.

      b.   The branched group is placed in parentheses.

 

Structure 2

 

 

a. Number is used for the ring. Number the atoms on each side of a break with the same number.

b . Hydrogen is not showed.

 

 

Structure 3

 

           

a. atoms and any charges are placed in brackets

 

Structure 4

 

  1. pound sign(#) for triple bond.

 

 

Structure 5

 

  1. the branched group is placed in parentheses.
  2. Equal sign (=) for double bond.
  3. The upper case for aliphatic; lower case for aromatic. The second letter of any symbol is always lower case.

 

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.

 

Reaction 1

 

Reaction 2

 

                                                                                                            chloroethane

 

 

 

 

 

 

 

 

Reaction 3.

 

Reaction 4

 

 

Reaction 5

 

 

 

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.

 

 

AN ACID BASE TITRATION APPARATUS

 

 

 

 

 

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.

     

     The different file formats used to save the molecular structures are:

          1. mol

          2. xyz

          3. PDB

 

 

mol.Format

  ACD/Labs0819041456 

 

 14 14  0  0  0  0  0  0  0  0  1 V2000

    7.8575   -5.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    9.0794   -6.4409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   10.3014   -5.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   11.5233   -6.4409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   12.7453   -5.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   13.9672   -6.4409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   10.3014   -4.3244    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

    9.0794   -7.8518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

   11.5233   -7.8518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   12.7453   -8.5573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   10.3014   -8.5573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   12.7453   -9.9683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   10.3014   -9.9683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

   11.5233  -10.6738    0.0000 C   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  4  1  0  0  0  0

  6  5  1  0  0  0  0

  7  3  1  0  0  0  0

  8  2  2  0  0  0  0

 10  9  1  0  0  0  0

 11  9  2  0  0  0  0

 12 10  2  0  0  0  0

 13 11  1  0  0  0  0

 14 12  1  0  0  0  0

 14 13  2  0  0  0  0

  4  9  1  0  0  0  0

M  END

 

 

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. 

 

 

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.