CHEMSKETCH

What is CHEMSKETCH?

Chemsketch is a drawing package software that allows you to draw chemical structure, lewis structures, 3D structures, space filling models and others.

This program provide you with two mode, first, structure mode and draw mode. Structure mode is used when you want to draw a skeletal structure of the compound by choosing the element compound provided in atom toolbar. An example, glucose, 1-cyclohexene. 
First step, click the cyclohexane  on reference toolbar, then put it in the workspace area.

Then, choose C from the atom toolbar, click at the carbon atom in the ring, hold and drag upwards. if you unhold the mouse button, the methyl group will automatically appeared.

Next, to create the double bond, just simply click at any carbon-carbon single bond, then double bond would appear.

  If you want to draw the orbital from the chemsketch template, click template windows, then choose orbitals, then you can choose which orbital you want to use.

However, you can customize your own skeletal structure or if you want to draw lipid, firstly. you must change the mode to draw mode first.

Then you can draw your own skeletal structure by using draw tools provided.

If you want to download this program, please visit http://chemsketch.soft32.com/free-download/

For your information, the tutorial is already provided. If you want to open the tutorial, follow this instruction below:

SMILES

Simplified Molecular Input Line Entry Specification (SMILES)

What is SMILES?

• A specification for unambiguously describing the structure of chemical molecules using ASCll strings.
• Widely used and computationally efficient.
• Uses atomic symbols and a set of intuitive rules.
• Uses hydrogen-suppressed molecular graphs (HSMG)

Canonical SMILES	ISOMERIC SMILES
a type of SMILES specification includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation common appilcation: indexing and ensuring uniqueness of molecules in a database.	a type of SMILES specification includes extensions to supprt the specification of isotopes, chirality, and configuration about double bonds. allow rigorous partial specification of chirality.

Grapgh Based definition

• Printing the symbol nodes encountered in a depthfirst tree traversal of a chemical graph.
• Chemical graph:
1. Trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree.
2. Numeric suffix labels are included to indicate the connected nodes on where the cycles have been broken.
3. Use Parentheses to indicate points of branching on the tree.

SMILES Bonds

• Single*	-
  Double	=
  Triple	#
  Aromatic*	:

SMILES Branches

• Represented by enclosure in parentheses
• 
  

ccc (cc) co

2-Ethyl-1-butanol

• Branches can be nested or "stacked" to any depth:

• 	cc (c) c (=o) c (c) c	2,4-dimethy-3-pentanone
  	occ (ccc) c (c(c)c) ccc	2-propyl-3-isoprophyl-1-propanol
  	os (=o) (=s) o	thiosulfate

  
  
• The SMILES branch/chain rules allow nested parenthetical expressions (branches) to an arbitrary depth.

SMILES Symbols/ Atoms

• String of alphanumeric characters and certain punctuation symbols.
• Terminates at the first space encountered when read left to right.
• The ORGANIC SUBSET:
• B, C, N, O, P, S, F, Cl, Br, I
• Aliphatic or noraromathic carbon: C
• Atom in aromatic ring: lowercase letter
• Designate ring closure with pairs of matching digits, e.g:
• c1ccccc1 is benzene
• C1CCCCC1 is Cyclohexane

SMILES Charges

• Charge is specified by a "+n" where "n" is a number; if the number is missing, it means either +1 or -1 as appropriate.
• Also specify attached hydrogens and chargers in square brackets.
• Number of attached hydrogens is the symbol H followed by optional digit.

• [H+]	proton
  [OH-]	hydroxyl anion
  [OH3+]	hydronium cation
  [FE++]	iron(ll) cation
  [Cl-]	chloride anion
  [Cu+2]	copper cation
  [Cu++]	copper cation

  
  

SMILES Cylic Structures

• Break one single or one aromatic bond in each rings
• only numbers 1-9 are used
• A number should appear only twice
• For example:
• Napthalene: c12ccccc1cccc2

SMILES Fragments

• Nitro	N(=O)(=O)
  Nitrate	ON(=O)(=O)
  Nitrite	ON(=O)
  Sulfonic Acid	S(=O)
  Cyanide/Nitrile	C#N
  Azide	N=N#N
  Azido	N+=N-

  
  

SMILES Conventions

• Avoid two consecutive left parentheses if possible.
• Strive for the fewest number of possible branches.
• Tautomeric bonds are not designated; enter the appropriate form.

Other Restrictions

• A branch cannot begin a SMILES notation.
• A branch cannot immediately follow a double-bond or triple-bond symbol.
• Example: C=(CC)=C is invalid, but
• C(=CC)C or C(CC)=C are valid SMILES.

Disconnected Structures

• The dot '.' symbol (also called a "dot bond") is legal most places where a bond symbol would occur, but indicates that the atoms are not bonded.
• The most common use of the dot-bond symbol is to represent disconnect and ionic compunds.

• 	[Na+] . [Cl-]	sodium chloride
  	Oc1ccccc1.NCCO	phenol, 2-amino ethanol
  	[NH4+] . [NH4+] . [O-] S (=O) (=O) [S-]	diammonium thiosulfate

• The dot can appear most places that a bond symbol is allowed.
• Although dot-bonds are commonly used to represent compunds with disconnected parts, a dot-bond does not itself mean that there are disconnected parts in the compound.

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

*You can also refer to other websites about the Simplified Molecular Input Line Entry Specification (SMILES):

• http://www.opensmiles.org/spec/open-smiles-3-input.html

XML

Introduction to XML (Extensible Markup Language)

• was design to describe data and focus what data is.

was created to structure, store, and transport information.

• with XML, we can invent our own tag, an example like <to> and <from> which are not defined in any XML standard.
• XML is not a complement to HTML as it is a software- and hardware-independent tool for carrying information.
• difference between XML and HTML:
• 
  

XML	HTML
Designed to transport data, with focus on what data is.	Design to display data with focus on how data looks looks.
About displaying information.	About carrying information.

How can XML be used?

• used widely in aspects of web development often to simplify data storage and sharing.
• XML separates data from HTML.
1. data can be stored in separate XML files.
2. with a few lines of JavaScript, you can read an external XML files and update the data content without interrupt the HTML data.
• since  data is stored in text format, thus easier to expand or upgrade to new operating system, new applications, or new browsers, without losing data.
• Foundation for several next-gen Web technologies sucg as XHTML, WSDL, WAP. WML, RSS, RDF, OWL and SMIL.
• XML documents form a tree structure that start at "the root"and branched to "the leaves"

• An example of XML data:

The syntax Rules:

• All element must have a closing tag.

• XML tag are case sensitive, thus tag <Letter> is different with tag <letter>.
• Opening and closing tags must be written with the same case.

• XML must be properly nested within each other. If you compare the XML with HTML, XML are properly nested within each other.

XML	HTML
<b><i>This text is bold and italic</i></b> -properly nested	<b><i>This text is bold and italic</b></i> -not properly nested.

• must contain one element called parent. This element is called root element.

• just like HTML, XML also can have attributes in name/value pair just like in HTML, and must always be quoted.

The predefined entity references in XML:

Command	Explanation
<!-- This is a comment -->	comment in XML which is  similar to HTML command.
HTML:Hello            my name is Tove Output: Hello my name is Tove	XML white-space in a document is not  truncated. However, in  HTML, multiple white-space truncates the character to one single white-space.

• new line is stored depend on the type of operating system used:

Type of operating system applications	How XML store a new line
Windows applications	stored as a pair of characters: carriage return (CR) line feed (LF)
Unix applications	stored as a line feed character (LF)
Macintosh applications	use only a carriage return (CR) character to store a new line.

XML Element

• An XML element is everything from (including) the element's start tag to (include) the element's end tag.
• can contain other elements, simple text or a mixture of both.
• can also have attributes.

Example of the XML element.

• from the example above, only book have attribute (catogery="CHILDREN")

XML Naming Rules:

• can contain letters, numbers, and other characters.
• cannot start with number or punctuation character.
• cannot start with xml.

XML extensible:

• XML element can be extended to carry more information.

XML Attributes

• XML attributes must always be quoted either single or double quote, both can be used.
• an example:

                            <person sex="female">    or      <person sex='female'>

• if the attribute value itself contain double quotes you can use single quotes, an example:

<gangster name='George "Shotgun" Ziegler'>   or  <ganster name="George &quot;Shotgun&quot; Ziegler">

XML validation

• XML with correct syntax is "Well Formed" XML
1. document must have root element ,
2. element must have closing tag, 
3. tag must case sensitive,
4. element must properly nested,
5. Attribute must quoted.
• XML validated against a DTD is a "Valid" XML

That's all about XML, for more detail, please do visit http://www.w3schools.com/xml/

Protein DAta Base (PDB)

Have you seen molecules such as protein and nucleic acid in 3D structure?
Well, for us biologist, it is a norm. For your information, there is an organization who keep all the information, structures of the molecules which had been submitted by biologist and biochemist across the globe. Worldwide Protein Data Bank is the name of the organization.
So, for our new entry, we are going to share some types of molecules which are stored within the PDB.

Molecules	Description
Prolyl Oligopeptidase	belongs to a distinct class of serine peptidase a large cytosolic enzyme involve in maturation and degradation of peptide hormones and neuropeptides details : http://en.wikipedia.org/wiki/Prolyl_endopeptidase
Thermolysin	a thermostable neutral metalloproteinase enzyme details : http://en.wikipedia.org/wiki/Thermolysin
Oligopeptidase	cleaves to peptide but not protein play essential role as hormones details: http://en.wikipedia.org/wiki/Oligopeptidase
Signal Peptidase	converts some secretory and some membrane proteins to their mature form details: http://en.wikipedia.org/wiki/Signal_peptidase
Collagenase	break peptide bonds in collagen details: http://en.wikipedia.org/wiki/Collagenase

So do you understand?if you do then you are the one we are looking. For further information please go to http://www.rcsb.org/
Well  goodbye!! See you again!!

HTML??? Use HTML to construct a webpage???

HyperText Mark up Language or well known throughout the world as HTML... but the "computer people" would understand it as the language of the internet.. still blur right?how about we show some pictures for us to understand more on these "HTML" word.

So the simple HTML document begins with "<html>" which indicate as an opening as an opening tag of the document.
Then, construct the content of your document by inserting "<body>" .
To start the overall story of the document, we should included "<header>" or as seen in our notepad as h1. This would be the header of your document. Don't forget to include the close tag as "</header>" or </h1> in the notepad.
The next thing is that the text paragraph which we indicate in the notepad as "<p>".
After all, you can replace the "My first Paragraph" in our example to any text that your are desire.
To close the content of the paragraph, include the "</p>".
Finally, to finalize the body content of your html document put the tag of "</body>" and "</html>" as seen in the example given.

To make an unordered list, we begin with the <ul> tag. Each list we qwish to add begin with <il>. Thus this item will mark with disc bullets. Before that, make sure we specify the type of bullet we wish to use. To end the list, we write </ul> tag.

however, if we wish to create html ordered list, we begin with <ol> tag and ended list with </ol> tag. If we replace "disc" with "A" letter, thus disc bullet will change qto letter order, such as the first item is A, the second item is B, and so on.

 

Last but no least, if we wish to emphasize text categories and subcategories, we use nested list. To create it, we type <ul> tag below the item we wish to emphasize the categories of that item. An example in the picture above, we want to emphasize the type of tea, the black tea and the green tea.

If we wish to add link, we add " <a href="(web link)"> (description) </a>. See the picture below for the clear view. Simple right. Make sure we add <p> before we write this command and end it with </p>.

Finally, if we wish to add picture to this HTML, we must add this command.

 <img src="(image directory)" alt="(image description)"

width="(size of image)" height="(size of image)" />

"Src" refers to the source of an image we wish to add, and specify the size we wish to adjust. For the image directory, we can just simply add the url image to it.

This is the overal collection of tag that are being used in this tutorial.

Tag	Description
<html>, </html>	describe the web page
<h>, </h>	describe the header of the content of the web page
<p>, </p>	describe the paragraph of the content
<ol>, </ol>	describe the ordered list of the item
<ul>, </ul>	describe the unordered list of the item.
<body>, </body>	describe the content of the web page.

That's all the steps we should know to construct a webpage using notepad.

Our First day in IIUM Kuantan..

three happy stooges

Assalamualaikum.. and hi to all!!! Alhamdulillah, For 2 years we strive for this moment For 2 years we suffer for this moment For 2 years we stay up all night for this moment At last, on the 19th of August 2013, we had been offered to kuantan. And our journey begins on 3rd September 2013...

our journey begin

TAARUF PROGRAMME!!!!! We thought 3 days of it are not enough for us to taaruf with IIUM Kuantan. We are expecting MORE. However, hours of briefings are enough to taaruf with IIUM Kuantan.

if you are smart enough, find us.. :)

LEADING THE WAY.. We are inspired by this song. One of us cried when we sang this song. Such a beautiful song for the closing ceremony.

Forever in our HEART.

4 FLAT!!! it is our dream to grasp it. so it us time for us to study. see you later. Assalamualaikum and good bye.

focus focus focus

OUR STUDY PLAN!!

	MONDAY	TUESDAY	WEDNESDAY	THURSDAY	FRIDAY	SATURDAY	SUNDAY
DAY	STUDY	STUDY	STUDY	STUDY	STUDY	SHOPPING	SLEEP
NIGHT	STUDY	STUDY	STUDY	STUDY	STUDY	SLEEP	SLEEP