Lesson 4 - SMILES (Introduction to SMILES, and how to make SMILES notaiions using ChemSketch)

Bismillahirrahmanirrahim and good morning.

     Alhamdulillah, praise to Allah, we still have a chance to live in His blessing. Well, today we has learned new thing which is SMILES.At first, we had thought that Smiles is this:

However, this SMILES that we learned is different, it is about SMILES notations.  What is SMILES? SMILES is an acronym for Simplified molecular-input line-entry system. It is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules (source : HERE). 

     This SMILES notation is widely used and also very efficient computationally.It uses atomic symbol and a set of intuitive symbols. Furthermore, it uses hydrogen-suppressed molecular graphs (HSMG), which basically men=ans that for example, in writing molecular formula (for example, propane), instead of writing the chemical structure as follows :

We just write it as CCC. This is what we called HSMG in SMILES notations, as we neglect the hydrogen atoms.

     In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses "the brackets ()" are used to indicate points of branching on the molecular structure. For example, 2-methylpentane an be written as CC(C)CCC. For molecular bondings, we use symbols as follows :

• for single bond we use - symbol (can be omitted)
• for double bond we use = symbol
• for triple bond we use # symbol
• For arimatic we use : symbol (also can be omitted)

     

     For branches, as stated before, we can use parenthesis to indicate them. The parenthesis symbol can be either nested or stacked. Example of branched molecules :

• CC(O)CC is 2-Butanol
• OCC(C)C is iso-Butanol
• OC(C)(C)C is tert-Butanol

     Then, for aliphatic carbon, we use big capital C and for aromatic one, we use small capital c. For atomic charges, we can specify the atoms and the charges in a square brackets. For examples : 

• [H⁺] proton
• [OH^-] hydroxyl anion
• [OH₃⁺] hydronium cation
• [Fe²⁺] iron(II) cation
• [NH₄⁺] ammonium cation

     For SMILES Cyclic Structures, we can degign notaions by breaking one single or one aromatic bond in each ring and number it in any order

–Designate ring-breaking atoms by the same digit following the atomic symbol

Numbers indicate start and stop of ring :

• Same number indicates start and end of the ring, entered immediately following the start/end atoms
• Only numbers 1 –9 are used
• A number should appear only twice
• Atom can be associated w. 2 consecutive numbers, e.g., Napthalene: c12ccccc1cccc2

There are few restrictions in doing SMILES notations :

     Avoid two consecutive left parentheses if possible

     Strive for the fewest number of possible branches

     Tautomeric bonds are not designated; enter the appropriate form

     A branch cannot begin a SMILES notation

     A branch cannot immediately follow a double-or triple-bond symbol

     Example: C=(CC)C is invalid, but

     C(=CC)C or C(CC)=C are valid SMILES

For isomeric and chiral SMILES :

     Isomeric configuration indicated by forward and backward slashes: / \

     Examples:

          –trans-1,2-dibromoethene: Br/C=C/Br

          –cis-1,2-dibromoethene: Br/C=C\Br

     Chirality indicated by the “@” symbol

     Then, we will demonstrate how to use SMILES notations by using ChemSketch..

• GENERATING SMILES NOTATION FOR BENZYLAMIDE

By using ChemSketch, firstly, we click structure and we choose benzene diagram. We continued by clicking the carbon symbol and linked the bond of carbon to the benzene ring. Lastly, we click the nitrogen symbol and connected to the structure. To notate the structure, we click draw then go to the tools and choose generate and then click SMILES notation. At the end, the notation of the structure given as follows :

• GENERATING SMILES NOTATION FOR FLUORENE 

Generate Fluorene compound using the template provided in the Chemsketch

Using Draw mode, highlight the compound.

 Then, select ‘Tools’ in the Menu Bar.

Choose, ‘Generate’ in the ‘Tool’.

  Lastly, select SMILES notation.

 Finally, the SMILES notation is generated.

In addition, repeat (2) until (4) and select ‘Name for Structure’ to generate the structure’s name.

• GENERATING SMILES NOTATION FOR PARACETAMOL

Draw the N-(4-hydroxyphenyl)acetamide or paracetamol using a chemsketch. Open structure mode and click C for carbon, O for OH and N for NH which are situated on the left side. Click the benzene ring structure on the right side to create a benzene ring.Open tools on chemsketch and select generate then select name for structure to insert the name. Select generate again and this time select SMILES notation to put the notation.

Lesson 3 : PDB - Protein Data Bank

Bismillahirrahmanirrahim...

     Alhamdulillah, for our today's KOS1110 class, we had learned about Protein Data Bank, aka PDB. What is PDB? PDB basically means is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. These proteins and nucleic acids are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome. All of these proteins and nucleic acids structures are commonly obtained by X ray Crystallography, NMP spectroscopy, and so on.

     The PDB archive is available at no cost to users. The PDB archive is updated each week at the target time of Wednesday 00:00 UTC (Coordinated Universal Time).

     The PDB was established in 1971 at Brookhaven National Laboratory under the leadership of Walter Hamilton and originally contained 7 structures. After Hamilton's untimely death, Tom Koetzle began to lead the PDB in 1973, and then Joel Sussman in 1994.  In 1998, the Research Collaboratory for Structural Bioinformatics (RCSB) became responsible for the management of the PDB. In 2003, the wwPDB was formed to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community. It consists of organizations that act as deposition, data processing and distribution centers for PDB data.

     In addition, the RCSB PDB supports a website where visitors can perform simple and complex queries on the data, analyze, and visualize the results. For more details about PDB, all of us can find it at this website.

     The PDB data format is made to contain coordinate. The main data format of PDB is mmCIF. mmCIF is a dictionary containing 2500 definitions. Furthermore, it also contain syntax such as "_chem_comp_link.details". And finally PDB which confirmed by syntax can be loaded by the system.

     The examples of software for PDB is pdb_extract, ADIT, and Validation Suite. The details of the softwares are as follows :

pdf_extract	Extract info from output of crystallographic, and merge it into mmCIF
ADIT	It has two types, which is web-based and standalone tools. Its function is to assemble, edit, validate, and deposition structural data
Validation Suite	Create reports

     For more information about PDB you can go to the website http://www.rcsb.org/. All the PDB datas are stored in this website.

     RasMol is a program for molecular graphics visualisation. It is a sophisticated, yet user-friendly, molecular graphics program for viewing molecules. The program is provided as freeware,available for internet downloading, by Roger Sayle in 1992 at the BioMolecular Structures Group of Glaxo Research & Development (UK). It is used by hundreds of thousands of users world-wide to view macromolecules and to prepare publication-quality images. Rasmol can be obtained by downloading from the internet as it is programmed as an open source program. 

     Difference between Rasmol and RASWIN. When the RasMol is compiled for use by Microsoft Windows users, it is called RASWIN.

     Then, we will show 5 types of proteins which we had got them from the RCSB PDB website  The 5 types of proteins are :

• Amylase
• Trypsin
• Pepsin
• Protease
• Lipase

 The details of the 5 proteins are as follows :

• Amylase (1BAG)

Classification: Alpha Amylase 

Structure Weight: 48016.77 

Molecule: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE 

Polymer: 1 

Type: protein 

Length: 425 

Chains: A EC#: 3.2.1.1 

Mutation: E208Q 

Details: COMPLEXED WITH MALTOPENTAOSE 

Organism: Bacillus subtilis 

Gene Names: amyE amyA BSU03040 

• Pepsin (3PSG)

 

 

Classification: Hydrolase(acid Proteinase Zymogen) 

Structure Weight: 39551.90 

Molecule: PEPSINOGEN 

Polymer: 1 

Type: protein 

Length: 370 

Chains: A EC#: 3.4.23.1 

Organism: Sus scrofa 

Gene Name: PGA 

• Trypsin (7PTI)

 

Classification: Proteinase Inhibitor (trypsin) 

Structure Weight: 6558.45 

Molecule: BOVINE PANCREATIC TRYPSIN INHIBITOR 

Polymer: 1 

Type: protein 

Length: 58 

Chains: A 

Organism: Bos taurus 

• Protease (3B4R)

Classification: Hydrolase 

Structure Weight: 50019.76 

Molecule: Putative zinc metalloprotease MJ0392 

Polymer: 1 

Type: protein 

 Length: 224 

Chains: A, B EC#: 3.4.24 

Fragment: Site-2 Protease residues 1-224 

Organism: Methanocaldococcus jannaschii 

Gene Name: MJ0392 

• Lipase (1GT6)

Classification: Lipase 

Structure Weight: 59218.33 

Molecule: LIPASE 

Polymer: 1 

Type: protein 

Length: 269 

Chains: A, B EC#: 3.1.1.3 

Mutation: YES 

Details: OLEIC ACID 

Organism: Thermomyces lanuginosus 

Gene Name: LIP

Chemsketch: A powerful tool for scientists especially chemists.

Bismillahirrahmanirrahim..............

     Well hello there world! Hopefully we are all fine with the blessing from Allah SWT. Amiin.

     In our second class of KOS1110 we had learned something new. Before tht, do you remember what we have learned in our first classwhich is bout HTML, right? Yes, insyaAllah. and for this week we had learned something which is totally different from HTML which is to use the software namely "ChemSketch".

Figure 1 : ChemSketch - the basic.

     As a scientist, we must get used to this application as it serves a useful service for us to generate chemical compound either organic or inorganic or polymer compounds and also other uses such as making atomic orbital, DNA, lipids, energy diagram and much more. For example, ChemSketch. ChemSketch has a lot of functions which enables us to make all uses mentioned earlier, and also can help scientists (and also science students) to do what is commonly cannot be done using normal software such as drawing chemical structure, drawing set up of apparatus and so on. The basic background of the ChemSketch is as shown in Figure 1.

     We had learned 6 uses of ChemSketch in the our second KOS1110 class, which were :

• Drawing energy diagram
• Making atomic orbitals
• Drawing apparatus (Vacuum distillator)
• Drawing DNA - two-chain DNA strand
• Drawing Lipids and Micells
• Making tables (which shows the compositions and densities of some chemical compounds)

     Unlike the first HTML assignment which we had done it individually, this ChemSketch assignment we had done it in group. The uses of ChemSketch that we had learned and done in the assignment are as shown in Table 1 below :

Uses	Images	Descriptions
Drawing energy diagram		Energy diagram normally used to sketch the flow of energy along a series of chemical reaction, also can determine the activation energy and also either the reaction is endothermic or exothermic, and many more
Making atomic orbitals		Atomic orbitals has their own respective shapes, which are determined by l number of uantum number. For example, p orbital is the orbital with l=1, and d orbital ith l=2. Meanwhile, pi-bonding orbital is formed when two electrons from two atoms overlap side-by-side to form covalent bonding (pi bonding only occurs in two atoms which has more than one bonding, the other type is sigma-bonding)
Drawing apparatus (Vacuum distillator)		A vacuum distillation is used when the boiling point of the compound (or the solvent) is too high (Tb>150 oC) in order to distill the compound (or the solvent off) without significant decomposition. For more information, you can click HERE
Drawing DNA - two-chain DNA strand		Double-stranded DNA is simply two chains of single- stranded DNA, positioned so their "bases" can interact with each other. At left is a cartoon depiction of double-stranded DNA. The sugar-and-phosphate 'backbone' is depicted in red, and the bases are depicted in blue. Importantly, the two strands travel in opposite directions; hence the structure is said to be "anti-parallel". The bases in the middle "pair up" with bases on the opposite strand, so that a type 'A' nucleotide is always opposite a type 'T', and 'G' is opposite 'C'. The attraction between the paired nucleotides is fairly weak, but when there is a whole string of them, it adds up to enough strength to hold the strands together.
Drawing Lipids and Micells		Micelles are lipid molecules that arrange themselves in a spherical form in aqueous solutions. The formation of a micelle is a response to the amphipathic nature of fatty acids, meaning that they contain both hydrophilic regions (polar head groups) as well as hydrophobic regions (the long hydrophobic chain). Micelles contain polar head groups that usually form the outside as the surface of micelles, and the hydrophobic tails are inside and away from the water since they are nonpolar.
Making tables		The table shows us the compositions of atoms of three different elements, which are benzene, naphthalein, and also qounoline

     Those shown in Table 1 are some descriptive explanations in what we had done with ChemSketch in the previous class. We hope that all of us can get benefits from the information given above.

     To conclude, after we had learned ChemSketch, we felt that this sofware can help us very much in order for us as Applied Chemistry students especially for drawing chemical structure, drawing mechanisms and many more. This is because there are a lot of functions that ChemSketch can do to help us, the uses shown in Table 1 only shows some of it. There are a lot of other functions of this software which we are yet to discover, (InsyaAllah we'll try to discover it). This malicious varieties functions of ChemSketch software make it suitable as this post's title which is "Chemsketch: A powerful tool for scientists especially chemists".

Wallahu a'lam

Lesson 2 : CHEM Sketch

Bismillahirrahmanirrahim..............

     Well hello there world! I ask how are you? ("aku tanya apa khabar" direct manglish trenslation...haha). Hopefully we are all fine with the blessing from Allah SWT. Amiin.

     Well, well well well.... In our second class of KOS1110 we had learned something new. Before tht, do you remember what we have learned in our first class? About HTML, right? Yes exactly, pandai anak mama. Haha (bila nak masuk tajuk daa....). And...this week we had learned something which is totally different (really?) from HTML which is to use the software ChemSketch What is ChemSketch?

(for full update please click HERE)

Lesson 1 : HTML.

Bismillahirrahmanirrahim...

     Alhamdulillah we had successfully went through our first KOS1110, aka Computer in Science class at 12th February 2015. This class is taught by Dr Noraslinda binti Muhamad Bunnori from Biotech Department, KOS. InsyaAllah Dr Linda will teach us for the first 7 weeks, and the other 7 weeks will be taught by Dr. Khairul Bariyah. (bila la nak masuk html ni). Ok. And Alhamdulillah, in our first and foremost class we had learned about HTML.

Image 1 : Dr Linda - our beloved KOS1110 lecturer.

      First of all, what is HTML? We often heard this word, but do we know the meanings of these lovely acronym? Literally, HTML is acronym for "Hypertext Markup Language". Conceptually, HTML basically means the language used to design web pages. In the other word, HTML is the language, or coding language designated for the web pages. Each and everything which appear in the website, including this article, are made up of various codes of HTML, which are then translated to the readable language as all of us can see now. The example of HTML :

Image 2 : HTML the basic

      In this class, we have learned and practised 5 elements of HTML coding. First of all, the introduction. In the introduction, we had learned and practised the basic HTML coding, the opening, closing of HTML coding, and to change the font size using HTML. The HTML are as shown as in Image 2. The result of those coding is :

My First Heading

My first paragraph.

Alhamdulillah, our first HTML coding. Yeah...(hehe)

     Then, the second one is to do list; ordered and unordered list. Unordered list is the list which is unordered (absolutely. haha). Just kidding. It is the list which is not in ordered manner, such as in numbered order, or alphabetical order etc. The example of unordered list is bullet list, and the example of HTML for unordered list is :

Image 3 : Unordered List

And when we transferred to normal language, it will become as follows ;

Disc bullets list:

• Apples
• Banana
• Lemons
• Oranges

Other than that, there are ordered list (alphabetical, numbered, etc). The example of HTML coding for ordered list : 

Image 4 : Ordered List

Can you see the differrence? <ul> coding for unordered list, while <ol> for ordered list. And the result is...tadaa (sorry for the wrong spelling...haha) : 

Letterss list:

1. Apples
2. Banana
3. Lemons
4. Oranges

Besides that, there are also nested list, which is  as we can call as "list of the list". The following is the example of nested list : 

Image 5 : Nested List

And........the result is....... :

A nested List:

• Coffee
• Tea
  • Green Tea
  • Chrysanthemum Tea (Fattah's favourite tea)
• Milk

     After that, we also has learned how to link text, using HTML. For example, to link certain text to other text, paragraph or chapter etc, or to do hyperlink to websites. The following is the example of HTML of linking to other chapter :

Image 6 : Linking to other text/chapter

From Image 6, can you see the highlighted coding? If not, please wear spectacles (haha). The highlighted one is the coding to link to another text/chapter which is Chapter 4. Plus, if you can see at the Chapter 4, there are also coding <a name="C4"> for the usage of the linkage text above. Clicking the text 'See also Chapter 4" will direct you to the Chapter 4.

Other than that, we also had a (like) competition. To do hyperlink to Facebook account. The first three person will get extra mark. Alhamdulillah, Fattah from our group is among the three person. How we do the hyperlink code to our FB account? This is the example :

Image 7 : Linking to websites

And the result is : 

Name ; Abdul Fattah bin Mohd Khiruddin

(if you press the link, it will directly link you to Fattah's Facebook account)

     For the last two elements, we had learned to put images and also for constructing tables. For putting image, there was also competition. Alhamdulillah, we also had winner from our group. Congratulations to brother Muhammad Azzubair bin Azeman. The example of the image coding (that we had learned) is :

Image 8 : HTML for image that we had learned

Apart of that, we also had learned to construct table, using HTML. In fact, if you want to make a table in Blogger itself for your blog post, you must use HTML. This is because, there is no button for making table in making blog post, unlike inserting image, making list etc. Therefore, you must learn HTML to make table in your blog. The example of HTML for making table : 

Image 8 : HTML for making table

And the result is : 

Without cellpadding:

First	Row
Second	Row

With cellpadding:

First	Row
Second	Row

   
     Finally, we had given task to make a HTML coding which is consists of all elements of what we had learned in the class. the task is to make a table, which consists all the Kulliyyahs in IIUM Kuantan (with hyperlink to their respective Kulliyyah website in IIUM portal), with their respective deans (including their pictures, name and email), and also the list of departments in the respective Kulliyahs (using unordered list). We had given about an hour to complete the task.

     As conclusion, Alhamdulillah we had finished our first class last two week. We are sorry for all the mistakes we had done in the class, as well as in the assignment. Hopefully all of us will do the best, insyaAllah. Let's learn knowledge for the sake of Allah. May Allah bless us. Amiin.....

Ready for the next class.... :-D

TUAN GURU NIK AZIZ, AN ORBITUARY

Nik Aziz, an obituary

Datuk Nik Aziz Nik Mat speaking at a "ceramah" before the last general election. It was to be his last campaign as he stepped down as Kelantan MB shortly after GE13. – The Malaysian Insider pic, February 12, 2015.

     Datuk Nik Abdul Aziz Nik Mat’s death marks the loss of one of PAS’s most iconic and influential leaders – he was a cleric who has helped shape the course of the Islamist party for over three decades, and was a politician so unlike any other politician the country has seen.

     Throughout his lifetime, Nik Aziz always struck a humble figure. Despite having the most powerful position in a party that boasted about one million members, and retaining the Kelantan menteri besar post for over two decades, the religious teacher was content staying in his old kampong house and driving around in his own car.

     His gentle, subdued manner belied his fiery, bordering on zealous, determination to turn Kelantan into the first state in Malaysia to implement the controversial Shariah criminal law, as well as his instrumental role in overthrowing a former PAS president and turning the party around.

Even as his health deteriorated during his last months, the PAS spiritual adviser did not neglect his party during the recent Pengkalan Kubor by-election in Kelantan, and turned up at a PAS ceramah to deliver a brief but rousing speech.

     Born on January 10, 1931 in Pulau Melaka, Kota Baru, Nik Aziz began his studies in pondok schools under the guidance of religious teachers around Kelantan and Terengganu before pursuing his tertiary education in Islamic university Darul Uloom Deoband, in India.

     He obtained his Bachelor of Arts in Arabic Studies and Master of Arts in Islamic Jurisprudence from Al-Azhar University, Egypt.

     He returned to Malaysia in 1962 and served as a religious teacher in Kelantan, earning him the popular nickname “Tok Guru”.

     Five years later, Nik Aziz joined PAS and won the Kelantan Hilir parliamentary seat in a by-election that same year, a seat that he held until 1986.

     He witnessed the transition PAS underwent under the leftist pan-Islamism leadership of Burhanuddin al Helmy, to the Malay nationalist-leadership of Asri Muda, who took over the presidency in 1970 and nearly dragged the party to its early demise.

     Asri’s most controversial decision was to announce PAS’s alliance with Umno and its entry into the ruling coalition in 1972, ostensibly to strengthen Malay unity. But the move was doomed from the beginning, as many members and leaders unhappy with the decision either left or were purged from the party.

     But the PAS-Umno partnership was shortlived: a disagreement between the two parties over the Kelantan menteri besar post saw PAS exit the alliance just five years later, and Kelantan, PAS’s long-treasured jewel, fell to Barisan Nasional (BN) in the 1978 general election.

     Nik Aziz was appointed Kelantan state commissioner immediately after PAS lost the state to Umno.

     It was Nik Aziz’s bitter, first-hand experience dealing with the fallout between Umno and PAS that has kept the two parties from venturing into another alliance decades later, despite fringe voices urging for a unity government.

     Nik Aziz and the new generation of leaders, did not stand idly by as Asri led the party to one of its worst electoral losses in history; he, Abdul Hadi Awang and the other clerics in the party sought to reorient PAS as an Islamic party led by the ulama faction.

     Asri was ultimately pressured to resign from the party, and in 1990, under the leadership of former PAS president Datuk Fadzil Noor, the party wrested back Kelantan and Nik Aziz was appointed menteri besar.

     A year later, he succeeded former PAS president Yusof Rawa as the party’s spiritual advisor after the former passed away.

     Nik Aziz held the position of menteri besar until May 6, 2013, a day after the 13th general election concluded. Throughout his 23 uninterrupted years of service, Kelantan remained a PAS stronghold even as Perak, Terengganu and Kedah fell to BN after they were briefly captured by the party.

     No other PAS leader could boast being a menteri besar for such a long period of time; PAS president Abdul Hadi Awang was the Terengganu menteri besar for only one term, before losing the state to Barisan Nasional in the 2004 general election.

     After relinquishing his menteri besar post, Nik Aziz continued to play an important role in both PAS and Pakatan Rakyat (PR) as the party’s spiritual adviser.

     During the Selangor menteri besar crisis last year, which saw PAS threatening to break away from PR, Nik Aziz put his foot down and maintained that the party would remain with the opposition pact, even as other PAS leaders floated the idea of cooperating with Umno.

     But now with his passing, the future of PAS and its role in PR is no longer so certain, and with it, the possibility of an alternative coalition to take over Putrajaya. – February 12, 2015.

- See more at: http://www.themalaysianinsider.com/malaysia/article/nik-aziz-an-obituary#sthash.JTR5fEEn.dpuf

OUR FAVORiTE EXPERIMENT (TLC)

        Thin-layer chromatography (TLC) is a simple, quick, and inexpensive procedure that gives the chemist a quick answer as to how many components are in a mixture. TLC plate is a sheet of glass, metal, or plastic which is coated with a thin layer of a solid absorbent (usually silica or alumina). A small amount of the mixture to be analyzed is spotted near the bottom of this plate.

        The TLC plate is placed in a shallow pool of a solvent in a developing chamber so that only the very bottom of the plate is in the liquid. The liquid, or the eluent, is the mobile phase, and it slowly rises up the TLC plate by capillary action.

(The picture used is copied from the internet)

To view the components of the mixture, the TLC plate is placed with solid iodine in a glass jar.

(The picture used is copied from the internet)

If  the components cannot be viewed after using iodine, ultraviolet ray can be used to view the components.

     (The picture used is copied from the internet)

For TLC demonstration, watch TLC demonstration in Youtube by searching  Introduction to Thin Layer Chromatography

       In conclusion, TLC is a useful method in separating mixtures according to their polarity. For further information on TLC, refer website: http://www.chemguide.co.uk/analysis/chromatography/thinlayer.html