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Chemistry

FAQ

What is SciFinder?

SciFinder is a system that provides integrated, user-friendly access to several Chemical Abstracts Service databases plus Medline:

  • Chemical Abstracts (CAPLUS, bibliographic data, 1907-present)
  • Registry (chemical structures, biosequences, and names, with associated property and spectral data)
  • CASREACT (single and multistep organic reactions, 1840-present),
  • CHEMLIST (regulatory information on chemicals)
  • CHEMCATS (commercial availability of chemicals from major suppliers)
  • MARPAT (generic Markush chemical structures from patents)
  • MEDLINE (biomedical literature, 1946-present)

You can search more than 33 million references by topic, author, CAS Registry Numbers, patent number, and CAS abstract number. More than 56 million chemical substances may be searched by chemical name, structure, Registry Numbers, and molecular formula. You can also do substructure searches for substances and more than 42 million organic reactions.

How does the Research Topic query work?

The Explore by Research Topic option presents a single text box that looks like Google's, but SciFinder's search algorithms function VERY differently from those of standard web search-engines. SciFinder uses a proprietary, highly complex (and somewhat mysterious) natural language query algorithm that breaks your query into a set of discrete concepts, searches them against the database indexes, and then presents you with a selection of result options. Here is a very brief list of important searching points unique to SciFinder -- these apply to no other database tools or web search engines.

    • Compose a natural-language query phrase with at least two distinct concepts, linked with prepositions. Examples: 
      • single walled carbon nanotubes in thin film transistors
      • synthesis of fluorescein derivatives
      • determination of arsenic in wood pulp

    • SciFinder uses prepositions as connectors to parse query into component concepts; prepositions are not analyzed for their linguistic meaning. Example: in SciFinder, 'determination of arsenic' is the same as 'determination in arsenic' unless you choose the more restrictive "as entered" phrase results.

    • Avoid typing long, complex queries: as with all databases, simpler is usually better. Try to keep your query straightforward, with no more than 3 or 4 distinct concepts. A query that is too complex will usually result in few if any hits. If your topic is inherently complex, start with a simple search of the most important concept or two, then narrow down the results using the Analyze or Refine options.

    • SciFinder ignores the Boolean operators AND and OR, treating them as ordinary words instead. However, inserting NOT will usually work to eliminate concepts you don't want.

    • Slight differences in the way your phrase a query can retrieve markedly different results, so you may want to try your search several different ways if your first results aren't satisfactory. Try to avoid including generic or meaningless words that may limit your results unnecessarily. Think about what keywords are likely to be used in titles and abstracts relevant to your topic, and stick with those.

    • If you want to search an exact phrase, type the phrase without quotation marks (which are ignored), and select the first option in the results list: "X references were found containing 'A B C' as entered." You will only see this option if there was an exact match of your search string in the database. Note that none of the algorithmic processes described below will have been performed on this exact "as entered" phrase.

    • SciFinder auto-truncates your words in most cases, so common wildcard symbols like * or # will be ignored. Sometimes autotruncation includes totally irrelevant terms in your results. Redoing your search with a NOT qualifier sometimes gets rid of a specific unwanted term. See below for more explanation.

    • SciFinder is case-insensitive. AIDS = aids.

    • Using general keywords does not automatically retrieve more specific concepts. Example: 'metals' will not also retrieve 'gold' or 'platinum', etc. You can enter them them as synonyms though.

    • You can include up to three synonyms in parentheses, separated by commas, following the word in question. Example: 'lead poisoning in humans (men, women)'. You don't need to do this for simple plurals -- SciFinder truncates most plurals automatically and includes both in your results. SciFinder also uses an internal thesaurus of synonyms, so you'll occasionally see words you didn't search included in your results.

    • SciFinder recognizes and translates some abbreviations and British vs. American spellings. Examples: 'NMR' = 'nuclear magnetic resonance'; 'color' = 'colour' etc. Abbreviations that are ambiguous or non-standard will not be translated in this way.

    • Chemical names included in topic queries are automatically searched in the synonym index of the Registry file, and if an exact match is found that compound's Registry number is added to your query. However, the more complex the chemical name, the less likely an exact match will be found, due to vagaries of nomenclature and punctuation. It's better to start a chemical name search under the Explore Substances tab.

  • You can use a Registry Number in the Topic query box, but for best results you should start with the Substance Identifier option under the Explore Substances tab instead. For example, you can type 'synthesis of 5467-78-6' in the topic box, but it would be more precise to type the number in the Substance Identifier box and then limit reference retrieval to articles on Preparation.

Summary: The Research Topic option is meant to be user-friendly and inclusive, and to retrieve good results for almost all types of queries, rather than a highly precise search mechanism for expert searchers. For more information, consult the Help pages.

How are records in a results set sorted?

The default sort for references is by the database accession number, which is essentially the same as reverse-date: newest documents are on top, the oldest at the bottom. (Records from Medline are always below records from CAPLUS, also sorted in reverse chronological order.) You can re-sort a results set by author, document title, citing references, or reverse publication year.

SciFinder does not sort reference answers by "relevance" algorithms. To increase relevance you can select the "closely associated with each other" set from the results histogram before displaying your answers, or you can use the Refine function to narrow and focus a results set.

Substance records are (as of December 2011 release) default-sorted by relevance, which should bring the closest matches to the top. It is also useful to re-sort by Number of References, which will bring the best-known and most-cited substances to the top. You can re-sort by reverse Registry Number, which means that the most recently reported substances - which usually have few or no references - are on top.

How can I limit a substance answer set that's too large?

The Refine and Analyze tools allow you to narrow your substance results by a number of criteria, including additional structure component, metal- or isotope-content, property data or commercial supplier information, etc. For instructions and examples see CAS' How To Guides page.

How do I search for chemical names?

Carefully. Under Explore Substances, select the "Substance Identifier" option. Chemical nomenclature in general is very complex, and follows different sets of rules. CAS uses its own nomenclature rules to assign systematic names to chemical substances, and their rules have changed substantially over the years. The Registry database indexes the current official CA Index Name for all substances, along with any former CA Index Names and various synonyms and trade names that have been used in the literature. However, Registry is not a comprehensive source of chemical names and trade names.

It's straightforward to search by well-known common names (ex. acetic acid, cyclohexane, acetaminophen), familiar trade names (ex. Taxol), and common abbreviations (ex. MTBE). Searching systematic names is less reliable because of the many possible variations in a name string. In general, the longer the systematic name the less likely you'll find it by typing it exactly.

SciFinder looks first for an exact match to the name as you type it. If it finds an exact match, it displays only that compound, and no others. For example, if you search for "Gallopamil" it will retrieve the one compound that has that exact name, but it will NOT retrieve compounds where "Gallopamil" is a segment of a longer name, such as "Gallopamil hydrochloride" (or any salts or multicomponent compounds). If it doesn't find an exact match, it next looks for the string you entered as a segment within a name. It will retrieve all such partial matches. For long names, you'll have a better chance of getting a hit if you break it up into discrete segments than if you type it all as a single unbroken string. SciFinder will retrieve all the compounds that have names including all the segments, and you can browse these for the one you want. If you get too many hits, add locants to some segments to narrow the possibilities. For example, to search for 

2-(3-buten-1-yl)-2,3,4,9-tetrahydro-1H-Pyrido[3,4-b]indole-1-carboxylic acid

type some of the identifiable functional group segments, in any order, separated by spaces: 

3-buten-1-yl   2,3,4,9-tetrahydro   1H-pyrido   1-carboxylic

and you'll get a table of matches to browse. It is not currently possible to browse an alphabetical index of names in SciFinder.

As with all chemical database tools, the chemical name is not the ideal way to search for a compound because of the complexity and inconsistency of chemical nomenclature and the diversity of synonyms and trade names used in the literature. Never rely on a name search when doing a comprehensive search for a compound. The rule of thumb is, when in doubt, draw it!

How do I transfer a Registry structure into the drawing module to modify it?

View the Registry compound record with the structure in question. Click on the structure diagram and choose "Explore by chemical substance" (or reaction). The structure will be imported into the drawing module and can be modified for further searching. This is a useful shortcut to drawing a complex structure. Another shortcut is to enter a SMILES or InChI string in the drawing panel, which SciFinder will translate into a 2-D structure for you to modify and search.

How do I search for the preparation of a compound?

SciFinder offers a few ways to do this.

  • On the Explore Substances page:
    1. Do a search by Registry Number, structure, molecular formula, or chemical name. If you wish, you can pre-limit the search to preparation by selecting that option from the Studies menu.
    2. Mark the compound(s) in the results table that you wish to explore further. Click "Get References".
    3. On the limiting menu, select the Preparation role. (Registry numbers in document records where a preparation method is described are assigned this role. The Preparation role has been retroactively added to Registry numbers back to 1907.)
  • You can use Explore Reactions and draw your target compound as a product, along with any starting materials or reactants you wish to include. One nice feature of this method is that the experimental procedures section from selected journals is displayed directly in SciFinder, allowing you to determine applicability of a reaction more quickly.
  • On the Explore by Research Topic page, enter a phrase query with a Registry Number (preferred) or common name (less accurate): 
    • preparation of 12345-67-8
    • synthesis of chloroaldehyde

To search for specific synthetic pathways, see the Synthetic Pathways Overview.

How do I search by molecular formula?

Molecular formulas, while imprecise, can give you searching options not possible any other way. But you do have to understand how CAS derives and indexes the MF in Registry records.

  • Single component substances: Under Explore Substances/Molecular Formula tab, enter the formula in any element order but add up all the atoms (ex. Benzoic acid is C7 H6 O2 not C6H5COOH). SciFinder will parse and order the formula and ask you for clarification if it's ambiguous. Searches are not case-sensitive unless the symbols are ambiguous. Spaces between the elements are optional.
  • Multicomponent substances (salts, mixtures, hydrates, etc.): Separate the individual components with a dot. (Ex. Sodium benzoate is indexed as C7H6O2 . Na. See the explanation under salts below).
  • Polymers: Component formulas are in parentheses, separated by dots, with an x following. Ex.: (C8 H8 . C4 H6)x
  • Alloys: Elements are listed in alphabetical order, separated by dots. Ex.: Cr . Fe . Mo . Ni

Molecular formula searches often retrieve large numbers of hits. You can use the Analyze/Refine tool and draw part of the structure to narrow them down, or try another kind of search.

How do I search for salts?

Salts are often best searched by molecular formula, and CAS treats most of them as multicomponent substances composed of a free acid and a base. Simple salts like NaCl (= ClNa) are straightforward. The formulas of more complex inorganic, organometallic and organic salts are indexed as "dot-disconnect" compounds under the following scheme:
    Fc . NFa 
where Fc is the molecular formula of the cation (or acid), Fa is the anion (or base) formula, and N is the number of anions - which can be a whole number or a fraction. Examples:

  • Sodium benzoate, i.e. the sodium salt of Benzoic acid [C7 H5 Na O2] is searched as: C7 H6 O2 . Na
  • Calcium phosphate, i.e. the calcium salt of Phosphoric acid [Ca3(PO4)2] is searched as: Ca . 2/3 H3 O4 P
  • Organometallic salts: ex. C16 H36 N . 1/4 C8 Mo N8

This unique format of formula parsing is based on the sorting in the old CA printed formula indexes, where all salts of a particular acid would be grouped under the parent acid's alphabetic formula. This policy doesn't make as much sense in the digital environment, but it is still the operating principle.

You can also search for salts by drawing the exact structure of either the free acid or the base, or both together as separate fragments.

How do I search for organometallic compounds?

Doing structure searches for organometallic and coordination compounds in SciFinder is a challenge. If you're looking for an exact structure, it's sometimes easier to use the molecular formula option instead. (A name search is generally not a good approach.) If you're drawing the structure, always select "Show precision analysis" before running the search. Then select the "conventional structure" subset of the results. (Note: precision analysis is not available if there is stereochemistry, or for similarity searches.) There's also a limiter for coordination compounds that you can check if you wish. Another tip: Turn off valency analysis in the drawing applet's preference pane so that the system doesn't keep bothering you about nonstandard valencies as you draw. It will still ask you to confirm the nonstandard valency before doing the search, and just click OK to proceed as drawn.

For a more extensive overview of searching for inorganic compounds, go here.

How do I search for polymers?

CAS registers most polymers as multicomponent substances composed of one or more monomers. You can search by name, monomer structure or formula and limit retrieval to polymers in the Class(es) menu. Search for general classes of polymers as a research topic.

Molecular formulas of polymers are indexed as monomer formula(s) within parentheses, followed by an x: (C8 H8)x ; (C8 H8 . C4 H6)x etc.

Structure searching for copolymers in SciFinder involves executing a search for one monomer as an exact structure, then refining the results by adding another monomer. It's best to start with the less common monomer. Polymers with undefined structures obviously can't be searched by structure, but must be found with name and class terms instead. For instructions and examples see the Polymer Searching Overview on the SciFinder Solutions web site. More in-depth documentation can be found here.

How do I search for labelled compounds?

By structure: Search for all labelled analogs of a given (sub)structure by drawing and searching the structure, then using Refine to limit to isotope-containing substances. It's not possible in SciFinder to search for a specific label at a specific position, however. 
By molecular formula: Deuterated or tritiated analogs can be searched as D or T within the formula; these isotopes are double-posted with H in the MF field. Ex.: C5 H D6 N = C5 H7 N.

What is Precision Analysis?

When you draw a substructure, you should get in the habit of checking the "Show Precision Analysis" box before running the search. (It's not the default, nor is it possible to analyze by precision after running the search, although this is an often-requested improvement.) When you check the box and click Search, SciFinder will show you a pop-up box with a selection of "candidates" to choose from, to make your results more precise. Precision analysis is not available if there is stereochemistry, or for similarity searches. But it's important when searching for metal-containing organic compounds.

  • "Conventional Substructure" means those structures that contain the substructure exactly as drawn, i.e., the closest matches to what you've drawn. In most searches this is what you should select, especially if retrieval is large.
  • Closely and loosely associated structures and tautomers often will outnumber the "conventional" kind, and nobody but CAS is quite sure what the difference between "closely" and "loosely" is.
  • Other results approximately related to the substructure as drawn.

How can I remove multicomponent substances from my answer set?

After drawing the structure, select "Single component" from the Characteristics menu. This will in many cases substantially reduce your number of hits. This option has to be selected before the structure search is run; it's not a Refine option.

How do I find property values for a compound?

There are two approaches in SciFinder to search for documents that might contain specific kinds of property data for a compound. The most straightforward way is to use the compound's Registry Number in a research topic query, e.g. "vapor pressure of 104-76-7", and view the results where the concepts are "closely associated with one another." The other way, which is preferable if you don't already know the RN, is to use Explore Substances to find the compound record, click Get (all) References, and then use the Refine/Topic feature to enter the name of the desired property to narrow the results further. (Don't select the Properties role when getting references unless you're fairly sure the data was reported after 1967. The substance roles have not been applied retroactively to the pre-1967 segment of the CAPLUS file.) See this page for more details.

Can I search for chemical substances by property value(s)?

Only indirectly. Many substance records in the Registry file contain calculated or experimental property data. These data points are not directly searchable in SciFinder -- for example, you can't do a search for all compounds with a particular melting point. But you can refine a substance set by experimental property values given in the substance record(s). See the help pages for more information. Experimental property data in Registry come mostly from the literature; predicted properties are generated by algorithms from ACD Labs.

How do I find spectra for a compound?

IR, NMR (predicted from ACD Labs and experimental from BioRad-Sadtler), and some MS spectra for many compounds are included in a substance's Registry record. Searching for documents containing spectral data works basically the same as a property value search (above). See this page for more details.

Can I find current regulatory information on substances?

Yes. Do a search for the substance and locate its Registry record. Then click on the "Get Regulatory Info" link or the  button to pull up that compound's CHEMLIST record.

Why do some substances show zero references?

Although most Registry compound records come from CAS' indexing of the literature, some compounds are registered via other sources and are not necessarily represented by any indexed literature. Third-party chemical libraries, catalogs, and databases from various external agencies, as well as hypothetical ring parents are also included. For more information see CAS's STN Guide article on this topic.

How do I search for chemical reactions?

Select "Explore Reactions" from the task menu. Draw a reaction scheme including one or more reactants/reagents, a reaction arrow, and a product (sub)structure. You can focus your substructure search more narrowly and avoid error messages or too many hits by using the locking tools, mapping atoms, and defining reaction sites (bonds broken or formed) in the drawing module. You can also apply pre-limits such as solvent, number of steps, classification, year, etc. Click "Get Reactions" to run the search in the CASREACT database. Results are sorted by relevance. For more information see the How to guides.

Where does SciFinder's reaction information come from?

The CASREACT file primarily contains reaction information derived from journals indexed in the Organic sections (which include organometallics) of Chemical Abstracts since 1985 and patents since 1991.

Are the cited references in the CA record searchable?

Yes. Cited references (representing the works appearing in the article's bibliography) are included in CA bibliographic records back to 1996. Most are hyperlinked to the corresponding record in CA -- just click on the citation to go to that record.

To find later documents that cite a specific work or group of works (such as by author), pull up a group of records, select one or more (or just use the entire results set), and click "Get Citing" in the task bar. This will pull up a set of documents (post-1996) that cited the selected original(s).

How do I search for older (pre-1967) literature?

The 1907-1966 segment of the CAPLUS file is searchable by Research Topic, Author, and most other fields. All indexing data for chemical substances from the 1st through 7th Collective Indexes have been added and algorithmically matched with Registry Numbers.

Note: If you start from a chemical substance record, click Get References, and then select from the Roles menu (Adverse effect, Analytical study, etc.), you will retrieve results only from the 1967+ file segment. Chemical Roles for Registry Numbers have NOT been retroactively applied to pre-1967 CA records, with the exception of the Preparation role, which has been added back to 1907. The interface and the help pages do not make these important distinctions clear.

CAS is selectively adding bibliographic records for pre-1907 literature from other sources. 

Can I search CA abstract numbers in SciFinder?

Abstract records from 1967 to present can be searched by abstract number (e.g. 101:59753) in the Document Identifier tab. Abstract numbers from 1907-1966 are not searchable or displayable in SciFinder.

Does Chemical Abstracts index translation journals?

Originally, up to about 1995, CAS indexed only the original journals (mostly Russian), and ignored their English translation counterparts. Starting in 1995 CAS began to switch to selected translations when they were apparently simultaneous and complete. 

What patents does CAS cover?

Worldwide chemical patents and applications are thoroughly indexed and cross-referenced in SciFinder. CAS policy is to index the first published patent document (usually a non-U.S. application) in a family, and subsequent granted patents and other applications are listed in the Patent Family table in the full record:

For coverage details, see the CAS Patent Coverage page.

The SciFinder interface is not intended for comprehensive patentability (prior art) searching, which should be done by experienced patent searchers using specialized databases. The academic usage terms prohibit using SciFinder for any profit-making purpose, regardless of one's academic status or affiliation.

How can I remove patents from my results?

Click the Refine tab from a results screen, then choose Document Type, and select from the menu only those types of documents you wish to see.

What are Markush structures?

Markush structures are generic chemical structures drawn according to patent claims conventions and found in chemical patents worldwide. They are distinct from the precise structures found in the Registry database, and are searched separately in the MARPAT file using the Markush structure option under the Explore Substances tab. An example from Wikipedia:

The MARPAT file contains more than 800,000 searchable Markush structures from patents covered by CAS from 1961 to the present (records from 1961-87 derived from French INPI data), and is updated daily. Markush structures include organic and organometallic molecules reported in patents from countries covered by Chemical Abstracts, except Korea. Not included are alloys, metal oxides, inorganic salts, intermetallics, and polymers.

Drawing a Markush structure uses the same applet, but some options are not available. Unlike a Registry search, results from a Markush search in SciFinder are CAPLUS bibliographic records for patents, rather than actual structure hits, which you never actually see. (You don't see the source MARPAT records either.) Sometimes it will not be obvious why a particular CAPLUS patent record was retrieved based on the structure you entered. Registry numbers are not highlighted in the indexing. You may or may not see a matching structure graphic embedded in the abstract. You may have to refer to the full text of the patent itself to determine its relevance. When you do a Markush structure search, you are NOT searching the Registry file; to do a complete novelty search, you must search a structure using both options. While Markush structure conventions are easy for chemists to understand, the computer algorithms that match them to specific target structures are very complex.

Remember that SciFinder is not intended to serve as a tool for professional patentability searching, which must be carried out by patent experts using databases designed for that purpose.

How can I remove the Medline records from my results?

Medline records are sorted separately in results sets, and come after the hits from CAPLUS. After you get a list of references, click the Refine tab, then select the Database button and select CAPLUS. Medline records are often duplicates of CAPLUS records in the same set. SciFinder allows you to remove duplicates from your results set. You can also set your Preferences to automatically remove Medline duplicates.

Can I set up an Alert to send me new records?

Yes, you can set up a Keep Me Posted alert within your account. See the How To Guides for instructions.

Can I save answer sets from session to session?

Yes. You can save a results set (references, substances, or reactions) on the CAS server, or export them to a local disk, then combine a future results set with that saved set if you wish. By employing various options of Combine, Intersect, or Remove, you can manipulate and customize the information contained in these combined answer sets.

What is the SciPlanner?

The SciPlanner is a feature that provides a flexible whiteboard-like workspace where you can save and organize information from SciFinder substance, reaction, and bibliographic records. For example, you can copy and arrange multiple reaction schemes, with links to their full details, and the planner will let you combine them in creative ways and add associated references. You can print-to-PDF in order to share a planner layout with others.

Is there a way to email records to my colleagues?

Not directly; SciFinder does not have an email feature. First you must export selected records to a file on your computer, then email the file as an attachment. RTF is a good format to save in. Or you can just copy and paste directly into the body of an email.

Some features don't work on my browser.

SciFinder requires your computer to have the current version of Java installed and active. There can be unexpected compatibility problems between SciFinder and specific Java/JRE versions, especially with the structure editor, so if you are having trouble try switching to a different browser (IE, Firefox, or Safari).

What if I forget my password?

When you log in, click the "forgot password" link. When you register the first time, you have to answer a secret question. Provide that answer again and CAS will email your password to your registered email address. The library does not have access to your password. You are not allowed to create a new user account.