Assignment #3

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 compresses using winzip and sent to me as one file with the name “3yourname.zip” before the due date along with the printed assignemnt.  Publish these files in your web pages before the due date and when you are sending the assignments, send me the web page links to these pages.

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 .

A.

             (2E)-5,5-dimethyl-4-oxohex-2-enenitrile

             B.

             2-amino-N-[1-formyl-2-(1H-imidazol-5-yl)ethyl]propanamide

            C.

            (2-methylhydrazino)acetaldehyde

D.

(2,5-diamino-5-oxopentylidene)(1,1-dimethyl-2-oxoethyl)oxonium

E.

2-amino-1-(3-phenylcyclooctyl)propan-1-one

-     To use generate name from a structure, select the required structures and choose this command. The generated name for the structure or mixture will appear under the lower structure as a text string in one line.

-     However, the structure to be named can contain no more than 50 atoms (H, C, N, P, O, S, F, Cl, Br, I, Li, Na, K) and no more than 3 cycles.

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

            A.

c21C(NC(Nc2ncn1)=O)=O

B.

CCOPOCC

             C.

              OC1C(C(C(O1)CO)O)O

D.

F[P-](F)(F)(F)(F)F

E.

C1(OC(C(C(C1O)O)O)O)CO

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.

A.

B.

C.

D.

E.

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.

Experiment : To determine the boiling point of a solution.

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 .

1)format pdb:

C  6.3584 -0.5460  0.0000:

      REMARK   Accelrys ViewerPro PDB file

REMARK   Created:  Thu Aug 19 14:39:02 Malay Peninsula Standard Time 2004

ATOM      1  C1  MOL     1       4.176  -4.326   0.000  1.00  0.00             

ATOM      2  C2  MOL     1       1.994  -3.066   0.000  1.00  0.00             

ATOM      3  O3  MOL     1      -0.189  -4.326   0.000  1.00  0.00             

ATOM      4  C4  MOL     1       6.358  -3.066   0.000  1.00  0.00             

ATOM      5  N5  MOL     1       4.176  -6.846   0.000  1.00  0.00              

ATOM      6  O6  MOL     1       8.541  -4.326   0.000  1.00  0.00             

ATOM      7  C7  MOL     1       6.358  -0.546   0.000  1.00  0.00             

TER

2)with format xyz:

NoName  0.000000

C  4.1761 -4.3260  0.0000

C  1.9936 -3.0660  0.0000

O -0.1888 -4.3262  0.0000

C  6.3584 -3.0660  0.0000

N  4.1761 -6.8460  0.0000

O  8.5408 -4.3260  0.0000

3) format mol:

Molecule-1

  DSViewer          3D                             0

  7  6  0  0  0  0  0  0  0  0999 V2000

    4.1761   -4.3260    0.0000 C   0  0  0  0  0  0  0  0  0  0

    1.9936   -3.0660    0.0000 C   0  0  0  0  0  0  0  0  0  0

   -0.1888   -4.3262    0.0000 O   0  0  0  0  0  0  0  0  0  0

    6.3584   -3.0660    0.0000 C   0  0  0  0  0  0  0  0  0  0

    4.1761   -6.8460    0.0000 N   0  0  0  0  0  0  0  0  0  0

    8.5408   -4.3260    0.0000 O   0  0  0  0  0  0  0  0  0  0

    6.3584   -0.5460    0.0000 C   0  0  0  0  0  0  0  0  0  0

  2  1  1  0  0  0

  4  1  1  0  0  0

  5  1  1  0  0  0

  3  2  2  0  0  0

  6  4  1  0  0  0

  7  4  1  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.  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 .  

DNA molecule in polyhedron style            DNA molecule in ball & stick