ChemSketch and SMILES :)

Assalamualaikum everyone! We hope that you're in a good health and thanks for stopping by!~

We are excited to meet the new lecturer, Dr. Raihan Musa. The day before the class, which is on Monday, we were given a task by Dr. Raihan (through Whatsapp) to install a software called ChemSketch. We were asked to install the software because we need to use it in class.

Dr. Raihan made a game using this software. There are 2 groups; Pisang, and Jaguar. We were asked to draw these 4 molecules. And...the group with most students who finished draw the structures faster is...Pisang. Haha!

Next, Dr. Raihan asked us to search for the apparatus used in laboratory. Awesome, isn't it? If we were going to do a lab report and then were asked to draw the set-up of the experiment, we could just use this ChemSketch!

 The picture below are the structure of carbohydrates. If we were to draw carbohydrates in our assignments and reports, we could just use this template too. So we don't have to burden ourselves by drawing the hard carbohydrates structure. Just choose and click on the structure in the template below and Walla! you're done. Hehe, thank God this software exists! <3 there are lots of other tools and templates inside the ChemSketch, do check them out!

After the ChemSketch lesson, Dr. Raihan taught us SMILES. She did not teach us how to smile but the name of the lesson is SMILES. Haha >.< oh yeaaa...you didn't know what SMILES is, did you? :P hehe. SMILES is the abbreviation for Simple Molecular Input Line Entry System. It is used to translate a chemical's three-dimensional structure into a string of symbols that is easily understood by computer software.

Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as [Au] for gold.

Bonds between aliphatic atoms are assumed to be single unless specified otherwise and are implied by adjacency in the SMILES string. Although single bonds may be written as "-", this is usually omitted. For example, the SMILES for ethanol may be written as C-C-O, CC-O or C-CO, but is usually written CCO. Double and triple are represented by the symbols '=' and '#' respectively as illustrated by the SMILES O=C=O (carbon dioxide) and C#N (hydrogen cyanide).

Ring structures are written by breaking each ring at an arbitrary point (although some choices will lead to a more legible SMILES than others) to make an acyclic structure and adding numerical ring closure labels to show connectivity between non-adjacent atoms. For example, cyclohexane and dioxane may be written as C1CCCCC1 and O1CCOCC1 respectively. For a second ring, the label will be 2. For example, decalin (decahydronaphthalene) may be written as C1CCCC2C1CCCC2.

Aromatic rings such as benzene may be written in one of three forms:

1. In Kekulé form with alternating single and double bonds, e.g. C1=CC=CC=C1,
2. Using the aromatic bond symbol ":", e.g. C:1:C:C:C:C:C1, or
3. Most commonly, by writing the constituent B, C, N, O, P and S atoms in lower-case forms 'b', 'c', 'n', 'o', 'p' and 's', respectively.

In the latter case, bonds between two aromatic atoms are assumed (if not explicitly shown) to be aromatic bonds. Thus, benzene, pyridine and furan can be represented respectively by the SMILES c1ccccc1, n1ccccc1 and o1cccc1.

Pheww! That's a lot!!

Dr. Raihan announced that, on the next Tuesday, we have a quiz on this topic >.< there will be 4 questions with a total mark of 10. Do wish us the best in answering the quiz! See you again next week :-)