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/