Generating SMILES notation

Today, we learnt about how to generate SMILES notation by using ChemSketch application. SMILES is Simplified Molecular Input Line Entry System is a specification in a form of a line notation for describing the structure of chemical species using ASCII strings. For more info click the link below:
theory on SMILES

Molecule structures can be constructed in ChemSketch and then the SMILES notation can be generated. The following is the application of SMILES on some molecules: 

SMILES	Name	SMILES	Name
CC	ethane	[OH3+]	hydronium ion
O=C=O	carbon dioxide	[2H]O[2H]	deuterium oxide
C#N	hydrogen cyanide	[235U]	uranium-235
CCN(CC)CC	triethylamine	F/C=C/F	E-difluoroethene
CC(=O)O	acetic acid	F/C=C\F	Z-difluoroethene
C1CCCCC1	cyclohexane	N[C@@H](C)C(=O)O	L-alanine
c1ccccc1	benzene	N[C@H](C)C(=O)O	D-alanine

Reaction SMILES	Name
[I-].[Na+].C=CCBr>>[Na+].[Br-].C=CCI	displacement reaction
(C(=O)O).(OCC)>>(C(=O)OCC).(O)	intermolecular esterification

PDB protein data bank

For today's class we will be educate you on the following:

The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids. The following link will educate you more on Protein Data Bank.
http://www.rcsb.org
And if you click on the link, the following page will appear on your browser. 

While RasMol is a computer program written for molecular graphic visualisation intended and used primarily for the depiction and exploration of biological macromolecule structure, such as those found in the PDB. It was originally developed by Roger Sayle in the early 90s.

RasMol is a molecular graphics program for viewing molecules. For Microsoft Windows user this program is called RasWin whereas for Apple users is called RasMac. The following link will educate you more on how to use RasWin:
Manual for RasMol

These structures such as amylase, trypsin, pepsin, protease and lipase can be search in PDB website and the molecular structure can be viewed using RasWin.

1. Protease (IQY6)

• classification: protease
• structure weight: 29715.10
• molecule: serine pretease
• polymer: 1
• type: protein
• length: 274
• Chains: A
• fragment: V8 protease
• organism: staphylococcus aureus subsp. aureus Mu50
• gene name: sspA SAV1048

2. Amylase (2TAA)

• classification: hydrolase (o glycosyl)
• structure weight: 157432.43
• molecule: TAKA-AMYLASE A
• polyymer: 1
• type: protein
• length: 478
• chains: A, B, C
• organism: aspergillus oryzae
• gene name: amy 1 amyl Taa-G1 AO090023000944 amy 2 amyll Taa-G2 AO090120000196

3. Trypsin (6PTI)

• classification: proteinase inhibitor(trypsin)
• srructure weight: 6622.57
• molecule: PANCREATIC TRYPSIN INHIBITOR PRECURSOR
• polymer: 1
• type: protein
• length: 58
• chain: A
• organism: bos taurus

 

4. Pepsin (IYX9)

• classification: hydrolase
• structure weight: 34591.93
• molecule; pepsinogen A
• polymer: 1
• type: protein
• length: 326
• chain: A
• organism: sus scrofa
• gene name: PGA

5. Lipase (4LIP)

• classification: lipase
• structure weight: 66658.37
• molecule: TRYACYL-GLYCEROL-HYDROLASE
• polymer: 1
• type: protein
• length: 320
• chain: D, E
• organism: Burkholderia cepacia
• gene name: lipA

Chem Sketch

CHEMSKETCH
Chemsketch is a molecular modeling program used to create and modify images of chemical structures. Also, there is a software that allows molecules and molecular models displayed in two and three dimensions, to understand the structure of chemical bonds and the nature of the functional groups.

FEATURES
The program offers some advanced features that allow the molecules rotate and apply color to improve visualization. It has several templates with ions and functional groups with the possibility to add text and use other tools to optimize productions created by the software.

APPLICATION
Using ChemSketch is primarily for educational use. With this program it is possible to write and perform chemical equations, diagrams laboratories and chemical structures of various entity.

We learnt to use ChemSketch by ourselves, the following are some examples on what we did such as modelling apparatus, DNA, phospholipids, orbitals and table.