Assignment
3 - Questions in ChemSketch and PDB
Due date
Monday,
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
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
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
Structure
5
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.