ChemSpider is presently under maintenance.
We are adding new capabilities as we move from beta release.
The site is still working but you might experience some issues. Please bear with us.
HELP PAGE
It was quite common for anyone stepping onto a spider web to get into some sticky situations. On this help page we will help you navigate your way to a solution. Sometimes there is a shortcut to successfully freeing yourself from confusion and we recommend that you try the Frequently Asked Questions pages first.
Access to ChemSpider-related Manuals
We have made available a number of manuals online and the ChemSpider manual specifically will be updated on an ongoing basis as we add more capabilities. All manuals are available under the Help Tab and available via these links. Simply Click on the 
associated with each manual.
The ChemSpider Manual
The Structure Drawing Applet Manual
The ChemSketch Manual
A Short Description of ChemSpider
ChemSpider, in its present form, is limited
to searching chemically related information. The searches are presently biased
to exact structure, substructure and similarily structure searches as well as
chemical names. ChemSpider has been enhanced with a series of calculated
properties associated with the chemical structures and can be mined according
to these properties also. A breakdown of the types of searches that are
feasible at present is given below.
Exact Structure
SubStructure
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In order to perform an exact structure search,
the molecule needs to be submitted using any of the input methods available.
Presently molecules can be input by pasting in a SMILES or InChI string, uploading
a molfile or using the ACD/Structure Drawing Applet or the PC-based ChemSketch package to
submit your query. The search options allow you to match stereo
configurations, isotopes and charges by selecting the appropriate flags -
stereo and charges are matched by default.
In order to perform a substructure
search the appropriate substructure should be input via pasting of the
appropriate SMILES or InChI string, should be sketched in the Java Molecular
Editor or Structure Drawing Applet (SDA). The SDA offers greater flexibility
in searching using the appropriate definitions for undefined bonds and atoms
as defined in the manual. PC-based searches can also be
launched via the ACD/ChemSketch integration. ChemSpider locates all
molecules containing the drawn substructure and displays as a hit list
NOT AVAILABLE IN BETA RELEASE
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Systematic Names
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Since chemical names can exist in either
systematic format (IUPAC or CAS style are the most common) or as trivial
names, trade names, synonyms and registry numbers a textual input can result
in a very large hit list. In order to perform a name-based search simply type
in the appropriate string for searching. For example, a common chemical name
("acetone"), a systematic chemical name
("2,2-dimethyl-3-ethylpentane"), trade name ("Sudafed"),
IUPAC name, or CAS Number.
For common names and trade names, you can
use the asterisk * as a wildcard character. For example, "*propane"
will find 1,1,3,3-tetramethoxypropane and hundreds of other chemical names
that have a prefix before the word "propane". (For IUPAC names, you
must enter the whole name).
NOT AVAILABLE IN BETA RELEASE |
When the initial hit list appears it is
possible to select the details hyperlink to provide an expanded view of
available information. This expanded view includes structure properties,
calculated properties and links to vendors and associated databases.
Chemical Editors
At the time of release ChemSpider will accept chemical structure inputs in various forms. These are SMILES strings, InChI codes, molfiles, via the Structure Drawing Applet (ACD/SDA) or via the PC-based ACD/ChemSketch (NOT AVAILABLE IN BETA RELEASE) structure drawing software. ChemSpider may be enchanced in the future to include support for ChemDraw (CambridgeSoft) and ISISDraw (MDL).
InChI
An InChI (IUPAC International Chemical Identifier) is a string of characters capable of uniquely representing a chemical substance. It is derived from a structural representation of that substance in a way designed to be independent of the way that the structure was drawn therefore ensuring that a compound will always produce the same identifier. InChI is fast becoming adopted by cheminformaticians around the world as a flexible structure exchange format. For further details about InChI please refer to the Unofficial InChI FAQ page.
SMILES
SMILES (Simplified Molecular Input Line Entry System) is a
line notation for entering and representing chemical structures and
reactions. SMILES contains the same information as an extended connection
table and is very compact relative to other methods of representing chemical structures.
For details regarding SMILES strings please refer to the SMILES Tutorial.