drawing chemical structure - tripod.comallcee.tripod.com/lweek05.pdfkos 1110 –computers in science...

KOS 1110 – Computers in Science

Drawing Chemical Structure


You want to draw this molecule


You want to draw this reaction


You want to draw this molecule


We use Chemical Drawing Software to draw and to visualize the molecules CTS Students: “Why we need to learn to draw this molecule?” Answer: We work as a team, we help each other. The Biotech and Biomed Students might be good in synthesizing the molecules but they don’t have a strong Mathematical background, so you will need to help them, BUT in order to help them, the Mathematicians will need to know a little bit about the problem that they want to solve, to enable them to construct the model for that molecule.


List of Free and Commercial Software to Draw the Molecule

1. ACD/ChemSketch 11.0 2. DrawIt (KnowItAll – Academic Edition) 3. BKChem 4. Mol Works 2.0 5. Symyx (MDL) Draw 3.0 6. ChemDraw 11 7. Chemsitry 4-D 8.0 Lite 8. WinPLT 9. ChemPen 10. WinDrawChem 11. JChemPaint 12. MarvinSketch 13. JME Editor


We will use ChemSketch 11.0 Obtaining ChemSketch Download from http://www.freechemsketch.com Installation Click the downloaded file and follow the screen instruction


ChemSketch Tour


ChemSketch Tour

Menu

Toolbar

Drawing Toolbar


ChemSketch Tour

Element Radical


Drawing Your First Structure

1. Simple drawing

2. Drawing Double and Triple Bond

3. Deleting atom or Redo



4. Drawing polymer

5. Drawing Pseudo Atoms



6. Changing the Atom



7. Editing Atoms

8. Flipping Structures

Set Bond HorizontallySet Bond VerticallyFlip on BondFlip Top to BottomFlip Left to Right


Drawing More Complex Structure

1. Using Table of Radicals

Hexadecahydrocyclopenta[c]fluorene-3,4,5,7,8,9-haxacarboxylic acid

2. Using Ring Structure


1. Setting Charges and Defining Anion sand Cations


Cation, Anion, Free Radical+ Radical Ion, - Radical Ion, Singlet Biradical, Triplet Biradical



2. Markush Bond

3. Generating Stereo Descriptors



3. Drawing Coordination Bonds

4. Delocalized Charges and Curves


Drawing, Labelling and Mapping Reactions


Simplified Molecular Input Line Entry System

- A concise chemical notation system which allows keyboard entry (i.e. plain text, no mouse, no graphics) of molecular structure. SMILES handles common bonds (single, double, triple aromatic, ionic), any atom or isotope, odd valences, and so on

- A chemical notation that allows a user to represent a chemical structure in a way that can be used by the computer

- It is a universal nomenclature - It is widely used as a general-purpose chemical nomenclature and

data exchange format - An Australian chemist in 2025 will be able to understand a SMILES

generated by an Japanese chemist in 1985


SMILES follows 5 Basic Syntax Rules 1. Atoms and Bonds 2. Simple Chains 3. Branches 4. Rings 5. Charged Atoms


Rule One: Atoms and Bonds

- Support all element in the periodic table - Upper case letters for Non-aromatic atoms - lower case letters for aromatic atoms - Atomic symbol with more than one letter, the second letter must

be lower case Bonds

Symbol Meaning Molecule SMILES

- Single Bond CH3CH3 CC

= Double bond CH2CH2 C=C

# Triple bond C=N C#C * Aromatic bond

. Disconnected Structures NaCl Na.CL


Rule Two: Simple Chains

- Hydrogen suppressed structures, the software know how many hydrogen by reading the SMILES notation

- Atom with two letter should be enclosed in a square bracket [ ], to avoid confusion with single bond notation. (e.g. [Sc] – Scandium)


Rule Three: Branches

- The branch atom symbol should be put a parethesis - The parenthesis is placed directly after the symbol for the atom to

which is connected. Example

SMILES Molecule name

CC(O)C 2-Propanol

CC(=0)C 2-Propanone

CC(CC)C 2-Methylbutane

CC(C)CC(=O) 2-Methylbutanal

c1c(N(=O)=O)cccc1 Nitrobenzene

CC(C)(C)CC 2,2-Dimethylbutane


Rule Four: Rings

- Using numbers to identify the opening and closing of the ring atom

- Multiple rings? Used different number for different ring opening and closing

- Double, single or aromatic bond? Use the bond symbol before the ring closure number

Example

SMILES Molecule C=1CCCC1 Cyclohexene

c1ccccc1 Benzene

C1OC1CC Ethyloxiarne

c1cc2ccccc2cc1 Naphthalene


Rule Five: Charged Atoms

- Using brackets [ ] Example

SMILES Molecule

CCC(=O)[O-1] Ionized propanic acid

c1ccccn[+1]1CC(=O)O 1-Carboxylmethyl pyridinium


Drawing Apparatus


END

drawing chemical structure - tripod.comallcee.tripod.com/lweek05.pdfkos 1110 –computers in science...

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