SciFinder client overview

• About the SciFinder client
• Search guide/tutorial

SciFinder Client

New to SciFinder? Take a look at the web version!

The client version is currently available on all Library PCs. You can also download the software onto a PC in your department or work area, however the client can not be used from off campus. To download the client software, head to the Library catalogue record for SciFinder and follow the prompts.

To obtain a copy of the site.prf file, please contact Ursula Henderson, the Research Librarian for Chemistry.

Search guide/tutorial

• Exact structure
• Substructure
• Reaction
• Molecular formula
• Chemical name and registry number
• Topic
• Author
• Verifying a reference
• Analysing, refining or combining searches
• Displaying, printing and saving references

Exact structure searching

Searching compounds through their structures is useful when molecular formula searching results in too many isomers. As an example of a simple exact structure search, imagine you want to find articles on the synthesis of:

Step 1. Building and searching the structure

If the Explore window is not showing, click New Task on the menu bar at the top. Choose Explore, then Explore Substances - Chemical Structure to reach a structure drawing window.

	The vertical tool palette along the left of the structure drawing window has a number of tools for drawing rings, chains etc. Hold the cursor above each icon to see its function. Note the Erase tool. To delete a mistake, click the Erase tool then click the bond or node to be deleted. Alternatively, undo a step with the Undo command on the Edit menu. Place the first benzene ring: click the Benzene ring tool, move the resulting ring cursor to the centre of the window and click. Fuse the second benzene ring to the first: place the same ring cursor in the middle of the right bond of the first ring until the bond becomes highlighted, then click. Add the one-carbon chain: click the Chain tool, place the cursor on the relevant ring node until the node becomes highlighted, click and drag the cursor away from the ring until you see a chain length of 1, then release the mouse button. Add the two-carbon chain: repeat for the second chain but drag until you see a chain length of two. To reverse the orientation of the chain, hold the shift key while dragging the cursor. Add the double bond chain: add a one carbon chain as above to the middle node of the two-carbon chain. You now have the structure skeleton:
Now change atoms and bonds. The horizontal tool palette at the bottom of the window has common bond and atom icons. Other atoms and shortcuts are on the vertical tool palette.
Change the single chain bond to a double bond: Click the Double Bond icon on the horizontal palette, place the cursor on the single bond and click. Change C to N and O: click N on the horizontal tool palette, place the cursor on the appropriate ring atom and click. Repeat for the other N and the O. Change C to Me: click (without releasing the mouse button) the Shortcut menu tool on the vertical palette, drag to Me and release the mouse button. Click the appropriate node. You now have the required structure: Note: You can also create double bonds and non-carbon nodes in a single step. Simply click the appropriate bond or atom, then create it with the Chains tool.

Step 2. Getting Substances

After building the structure

• Click Get Substances
• Choose Exact search
• Click OK.

You get the structures and registry numbers of matching substances. As well as the main substance of interest, an exact structure search may find stereoisomers, isotopically labelled forms or components of multicomponent substances such as salts and mixtures.

Click the adjacent microscope icon to show other details such as names or click the adjacent box to select a substance.

Step 3. Getting Journal article references

• Click Get References.
• You can choose All references or limit to one of the listed types.
• In this example, for synthesis, choose References associated with and Preparation, then OK.

Substructure searching

Substructure searching lets you find any substances which contain a core substructure. You can also do a similarity search for substances similar to a drawn structure.

Starting with a substructure:

you can find substances such as:

Step 1. Build the structure.

Use structure building commands to build the structure. On the vertical tool palette, there are extra commands that let you specify what atoms, groups or ring fusion can occur at a node. Click:

	then click a node to block substitution at that node
	then click a ring to block further ring fusion.
	then choose a variable group such as a halogen, alkyl group etc and click the node you want to atttach it to.
	then enter atoms, shortcuts or variable groups to define an R group, and click the node you want to attach it to.
	then click a node and specify in the window at the top the number of repeats to specify variable chain lengths or ring sizes
	then click a substituent and drag to each required ring node to define the attachment of the substituent to any of multiple points on a ring.

You can build a structure such as the one below, which defines the kinds of attachments you want at certain nodes:

Step 2. Getting substances

After building the structure:

• click Get Substances
• choose Substructure search.
• You can also choose Filters to exclude certain categories e.g. isotopes, polymers.
• Click OK to get a list of substances.
• If the substance list is too large, click the Analyze or Refine button.

Analyzing lets you define more exactly the substances in the result e.g. what atoms are attached at certain nodes, what ring skeletons are allowed. Refining lets you limit by the presence, for example, of another structure or of metals or of property data.

Step 3. Getting journal article references

Click Get References. You can choose All references or limit to one of the listed types. In this example, for synthesis, choose References associated with and Preparation, then OK.

You get a list of brief references to journal articles and other materials. See Displaying, printing and saving references, Analyzing and Refining searches below.

Reaction searching

You can search chemical reactions through a structure search. Reactant and/or product and functional groups can be specified and searches can be refined by yield. Both exact structures and substructures can be searched.

Step 1. Build the structures involved in the reaction.

Then use the reaction icons in the vertical tool palette to indicate reaction characteristics. Hold your cursor over each icon to see its function. You do not need to use all icons. Click:

	then click between structures to add a reaction arrow.
	then click under a structure to add a reaction role (reactant, product) to it.
	then click in the window if you want to specify that a functional group (aldehyde etc) is also present in the reaction; you can add reaction roles to functional groups.
	then click a bond to mark that it must be modified in a reaction. This can limit the results too much: use it only when really necessary.
	then click the appropriate reactant node which becomes numbered. Then click the appropriate product node which gets the same number. Only reactions in which the marked reactant node is converted to the marked product node will be retrieved. This can limit the results too much: use it only when really necessary.

With these commands you can draw a reaction between substructure fragments such as:

Step 2. Getting reactions.

• After building the structure and labelling its components, click Get Reactions
• Select any required Filters and variable only at specified positions or substructures
• Click OK.
• A reaction summary with literature reference is given. Click the microscope icon for an expanded view. Click a structure to get its details or reactions.
• Click Analyze/Refine to limit the set of reactions by structure, product yield, number of steps, reaction classification, catalyst, solvent etc.

Step 3. Getting journal article references

Click Get References. You can choose All references or limit to one of the listed types. In this example, for synthesis, choose References associated with and Preparation, then OK.

You get a list of brief references to journal articles and other materials. See Displaying, printing and saving references, Analyzing and Refining searches below.

Molecular formula searching

Searching by molecular formula is quick for formulae without a large number of isomers. To do this:

• If the Explore window is not showing, click New task on the menu bar at the top.
• Choose Explore
• Explore Substances - Molecular Formula.
• Enter a molecular formula e.g. C7H5BrO2S and click OK.

• You can enter the formula in any order e.g. C7H5SO2Br or C7H5BrO2S
• Case does not matter unless the formula becomes ambiguous e.g. enter Si for silicon since SI or si could be read by the system as SulphurIodine.
• Multicomponent substances such as salts, mixtures and polymers are represented by dot formulae

You get the structure and registry number of matching substances. Click the microscope icon to show other details. Select the substances you want by clicking their boxes.

Click Get References, choose All references or one of the listed types and OK to get a list of brief references. See Displaying, printing and saving references, Analyzing and Refining searches below.

Chemical name and registry number searching

You can search by systematic chemical names, common names, trade names, acronyms and CAS registry numbers. To do this:

• If the Explore window is not showing, click New Task on the top menu bar.
• Choose Locate
• Then Locate Substances
• Enter substance names or registry numbers

• Enter exact names not name fragments e.g. benzene will find benzene but not chlorobenzene.
• Enter each name or number on a separate line.
• Names can be in upper or lower case.
• Include spaces and punctuation in systematic names.
• Enter Registry numbers with or without hyphens. [Registry numbers such as 50-00-0 are assigned by Chemical abstracts to each substance.]

You get the structure and registry number of matching substances. Click the microscope icon to show other details. Select the substances you want by clicking their boxes.

Click Get References, choose All references or one of the listed types and OK to get a list of brief references. See Displaying, printing and saving references, Analyzing and Refining searches below.

Topic searching

Use the Research Topics search to look for information in areas such as: techniques, processes, theoretical concepts or classes of substance.

To search by topic:

• If the Explore window is not showing, click New Task on the top menu bar.
• Choose Explore
• Then Explore Literature - Research Topic
• Enter the words - or phrase - that represent your topic and click OK.

For example:
isolation of peptides from frogs (rana, litoria)
[Note: where 'rana' and 'litoria' are frog genus names].

Search TIPs

• Do not use the Boolean operators AND and OR that are used in most other databases.
• Use a simple English phrase or sentence and be prepared to change it after examining your search results.
• Adjacent words e.g skin peptides are retrieved from the same sentence.
• There is no truncation symbol: the database may automatically truncate terms.
• If you want two or three concepts all to be present, use prepositions such as an, at, of, with and phrases such as effect of X on Y; if possible, avoid and.
• Place alternative terms (synonyms) in brackets e.g. frogs (rana, litoria); avoid listing them with and or or between; the database has an internal dictionary and adds some synonyms, word forms, abbreviations and spellings automatically.
• Use not and except to eliminate unwanted topics, but be wary of throwing the baby out with the bath water; place 'not' carefully - the query is read left to right.
• Do not use phrases that share a word e.g. use chiral reduction (chiral hydrogenation) not chiral reduction (hydrogenation).
• Use upper or lower case or both.
• Specific substances are normally better searched through one of the Chemical substance search options.

At the search results screen:

You'll get a screen of candidate combinations of the terms. Decide which of the combinations you want and click its adjacent box. You can choose more than one. In this example, we want isolation and peptides to be present with either frogs or rana or litoria, so the most likely candidates are:

those containing both of the concepts "isolation" and "peptides", and at least one of the concepts "frogs", "rana" or "litoria" with the concepts closely associated.

those containing both of the concepts "isolation" and "peptides", and at least one of the concepts "frogs", "rana" or "litoria" with the concepts anywhere within the reference.

Here the first result may miss some useful references because the terms have to be near each other but will produce fewer irrelevancies; the second result may give more irrelevant references e.g. peptides from another organism in an article that also mentions frogs, but is likely to miss fewer useful ones.

Or one of the other candidates may be better e.g. perhaps without the term 'isolation'. There is no such thing as an ideal search: look carefully at the search result candidates and experiment with alternatives. It's often better to avoid adjacent term phrases since they generate fewer candidate combinations to choose from e.g. you get more choice entering 'peptides from frogs' than 'frog peptides'.

Click Get References to get a list of brief references to journal articles and other materials. See Displaying, printing and saving references, Analyzing and Refining searches below.

Author searching

• If the Explore window is not showing, click New Task on the top menu bar.
• Click Explore
• Then Explore Literature -Author Name.
• Enter Last name, First Initial and click Get References to get a list of brief references. See Displaying, printing and saving references, Analyzing and Refining searches below.

Verifying a reference

Sometimes a reference in the literature turns out to have wrong page numbers, year etc. To find its correct details:

• choose Locate
• then Locate Literature - Bibliographic Information.
• Enter the author and/or title words and/or journal name and click OK to get a list of matching references.

Analyzing or refining or combining search results

SciFinder has useful ways to analyze and refine results. At the list of references, click Analyze or Refine References. Choose either

• Analyze references to find the frequency of certain kinds of term in the reference; for example, analysis by indexing terms can be a useful source of search terms; analysis by CA sections allows a search to be limited to broad subject categories; analysis by journal name lets you limit a search to a given journal.
• Refine references to limit to, for example, another set of search terms (through Research Topic), document types (patent, journal article etc), year.
• Categorize to refine the result by subject categories and terms

You can also narrow your result by combining the current result set with an earlier saved result set - see Scifinder guide: How to combine answer sets.

Displaying, printing and saving references

You can:

• look at full details of any article: click its microscope icon; within the full view, click a registry number for details of a substance or Patent Family information for related patents; click a cited reference (for articles from 1999 onwards) to view its full details.
• look at full details of all articles: choose one of the options on the View menu.
• mark useful articles for later saving, printing or redisplaying: click their adjacent boxes.
• click the computer icon against an article or patent to reach the full electronic text; this link will not always lead directly to the electronic full text; if it doesn't, search the journal title directly in the Library catalogue.
• get related references that cite the articles, references cited in the articles, substances or reactions indexed in the articles.
• remove duplicate Medline references already in the result as Chemical abstracts references.

To save results to a disk,

• Click Save As....
• Click Options to specify all or selected answers
• Click Save.