CHEM 116BL (Laverman, Spring 2024): SciFinder-n

SciFinderⁿ  Opening Screen

Note that the default opening screen is set for substance searching. If you have previously searched in this account, your recent search history will display below the search window.\

Breakdown of the Opening Screen

In the upper left is the CAS SciFinder-n logo. T

On the left are three vertically-arranged dots. Clicking on them opens a drop-down menu:

This enables the user to switch freely among CAS products. Note that you or your institution must subscribe to the product in question to access it, and at the moment, UCSB subscribes to SciFinder-n., CAS Analytical Methods and CAS Formulus. Switching from one to another requires logging in again, but the same CAS ID and password works for all three.

In the upper right are three options:

• Clicking on  Alerts takes you to a list of the search alrts you have created, if any, where you can view results, modify and update searches, etc.
• Clicking on Saved takes you to various saved items.  See below.

• Projects -  Takes you to a list of projects you have created, and where you can creat new projects. Projects allow you do store references from multiple SciFinder-n searches, including references, substances, and reactions. You projects may be shared with collaborators who also have SciFinder-n accounts. For more inforamtion, see below.
• Saved - Takes you to a list of your saved aswersets.
• History -  Takes you to a list of your recent searches, arranged most recent first. The list may be filtered by search type (such as substances or references) and by date range.
• Downloads - A feature not yet activated, which allows you to view all your downloads in one place.
• Submit feedback - Lets you send comments to the SciFinder-n staff.

• Clicking on your name opens a drop-down menu:
  • What's New? takes you to a list of the most recent updates to the SciFinder-n interface.
  • Help and Support opens a new tab, with FAQs and searchable help information on using SciFinder-n.
  • My CAS Profile allow you to manipulate details of your SciFinder account
  • Settings allows you to set personal preferences for the way SciFiner-n searches and displays results.  See screenshot below. 
  • Log out lets you log out of your current session. (Note: Always be sure to log out when using public workstations!)

Search Options

Below the previous section is the menu for selecting whcih time of search you wish to do. By default, the highlighted choice whill be whichever type of search you did last. The currently selected option is underscord (as with References in the image above.)

• All - All finds substances, reactions, references, and suppliers that match your query. You can enter search terms that identify the subject of interest (e.g., keyword, research topic, document identifier, patent information, substance name, CAS Registry Number) or draw/import a structure query.
• Substances - Find substances by substance name, CAS Registry Number, and document identifier (e.g., patent number) or chemical structure. Use Advanced Search to find substances by molecular formula, substance property, and experimental spectra.  Substance searching will be discussed in detail in Lectures 13 and 14.
• Reactions - Find reactions by substance name, CAS Registry Number, and document identifier (e.g., patent number)  or chemical structure that identifies a substance that participates in the reaction. Reaction searching will be discussed in detail in Lecture 15.
• References - Find references by keyword, research topic, document identifier, patent information, substance name, CAS Registry Number or chemical structure. Use Advanced Search to search by author, journal, or organization. Searching by topic will be discussed in detail in lecture 12, while other forms of reference searching will be discussed in detail in this lecture below.
• Suppliers - ind suppliers by substance name or CAS Registry Number or chemical structure. .  Supplier searching will be discussed in detail in Lecture 13.

Additional Search Options

• Retrosynthetic Analysis - Takes you to the SciFinder-n retrosynthesis tools which uses AI and the CAS substance and reaction databases to allow you to create retrosyntheitc paths to both known and predicted substances. See Lecture 15 for details.
•  Search CAS Lexicon - The CAS Lexicon is the hierarchical ordering of the CAS concepts assigned by CAS indexers to references. For more details, see Lecture 12.
• Search CAS Biosequences - Search for biosequences (proteins, polynucleotides) using various sequence searching options, such as BLAST. See Lecture 13 for more details.

 

Searching for Substances

• This is the opening screen for substance searching in SciFinder-n. In the CAS databases, chemical substances include: simple organic and inorgagic substances, polymers, biomacromolecues (such as proteins and nucleic acids), metals and alloys, mixtures and more. Each substance receives its own CAS Registry Number (about which more below), including isotopically-labeled substances, stereoisomers, salts and ions of differing charges.
• As indicated, you can use the search box to search by:
  • Chemical Name - This includes trade names (e.g. Teflon), generic drug names (e.g. ibuprofen), common chemical names (acetone), acronyms (EDTA), systematic chemical names, and CAS inverted chemical names.
    • If you search by a single word chemical name, you may also retrieve substances in which your term is apart of the name. If you wish to retrieve only the single substance, put the word in quotes.
    • Chemical name searching may not retrieve all the variations on a substance, such as stereochemical variants, isotopically-labeled substances, the mineral version of a salt, etc.
    • You can use the  asterisk wildcard to truncate single word names, and use quotation marks to enclose phrases.
    • You can enter multiple chemical names at the same time to find multiple substances.They must be separated by a space, not by commas or any other punctuation.
  • CAS Registry Numbers - This is the Chemical Abstracts Service ID number for substances. Like a Social Security number, or a UCSB perm number, the number contains no information about its subject. It is purely an identifier..
  • Note: At present, you cannot directly search other chemical identifiers, such a SMILES strings,  orInChI numbers . You can use InChI keys to search  in SciFinder-n. (see thedfrop-down menu of search options.) You can, however, use SMILES or InChI identifiers in the structure drawing tool to generate a starting structure for searching. See lecture 14.
  • Document identifiers - Patent numbers, DOIs PubMed IDs and CAS Accession Numbers can be used to retrieve the substances contained in the document identified.
• You may also enter a DOI for a document, PubMed ID, CAS Accession Number (CAN) or a patent number, and retrieve the substances indexed in that document or patent.
• To the right of the search box is the Draw button. Clicking it opens the SciFinder-n structure drawing tool, for finding substances by chemical structure. This will be discussed extensively in Lecture 14.
• Below the search box is the link for Advanced Search, which will be discussed in detail below. You can use it to search by: You can add multiple advanced search fields if desired  Unlike the advanced search fields in Reference searching, fields in Substance searching are automatically combined with AND.

 

Searching by Research Topic

 

• Searching for references by keyword in SciFinder-n is similar in many respects to searching in other scholarly databases like Web of Science. For instance:
  • You can combine terms with the Boolean operators AND, OR, NOT and parentheses. Example: (oxidation OR reduction) NOT combustion
  • You can combine terms as a specific phrase using quotation marks, for esample "nuclear magnetic resonance"
  • You can use wildcard characters, asterisk * or question mark ? to generalize your searches.  For example:
    • photosynth* finds photosynthesis, photosyntheses, photocynthetic
    • alumin?um finds aluminum, aluminium
• You can add additional search fields, conecting them with AND, OR or NOT, including fields like author, organization, etc.
• SciFiner-n is also capable of handling natural language phrases, such as  oxidation of secondary alcohols to ketones. SciFinder-n will automatically do truncation and insert necessary connectors. Note that the results of a natural language search may not be identical to those of an equivalent Boolean search.
• However, there are also things which SciFinder-n does uniquely, such as:
  • In addition to titles and abstracts, keyword searches search indexer-selected keywords, CA concept headings and MeSH subject headings.
  • It automatically searches for CAS abbreviations when it encounters a word which could be abbreviated, and vice versa.
  • It automatically searches for some synonyms of common chemical terms. For example, searching for NMR will also find nuclear magnetic resonance. 
  • Most importantly, when you search a chemical name as a keyword, it will detect that it is a chemical name, and also search the CAS Registry Number for that substance, greatly increasing the comprehensiveness of the search. Each document record has in-depth substance indexing. See examples below, and more about CAS Registry Numbers in Lecture 13.

Keyword Searching Example

• Let's say I wanted to search for the topic, electrochemistry of nickel or cobalt phthalocyanines.
• , You might enter that exact phrase, but you can also use something like this, electrochem* AND (nickel OR ccobalt) AND phthalocyan*, using either the Boolean operators, and parentheses to group the terms.
• Note below how, as I start to type the phrase, SciFinder-n provides a drop-down autocomplete list of possiber terms.

• The list of terms suggests strongly that I might want to use the asterisk wildcard to get all the terms starting with electrochem*
• Here's the completed search phrase:

 

• Note that the drop-down list of terms does not appear as you add additional terms to the same line.  If you wish to verify your terms, you could add additional lines and add each set of synonymous terms on its own line. 
• Now I click the Search icon. After the sstem completes its search, I obtain the initial results set below.

 

• Note the following points about the reference answer set display above:
  • Search terms are highlighted..
  • SciFinder-n has retrieved a large answer set BUT note at the upper left that it has not displayed the full answer set. The "most relevant" answer set is 2,439 answers. If I click on the Load More Results button, it goes to 2,801.
  • SciFinder-n expects that the user will get large answer sets, and use the Relevance sort, and the Filter options to home in on the desired answers.
  • Note that a new Filter options has appeared:
    • Substance Role  This is because we have searched on one or more chemical substance terms. In the drop-down list, only roles pertaining to the substances which we searched on appear, and the numbers reflect how many answers have each role. Note, too, that a substance may be assigned more than one role in a given document record. Note that the substance roles displayed in the left-hand column are broad roles, e.g. Uses. If you click on the View All link the table of roles will include more specific roles, e.g. Analytical Reagent Use.
    • CAS Solutions - Shows which records also appear in CAS Analytical Methods and Formulus.
    • Formulation Purpose - Shows purposeses in formulations for the substances found, such as Coating materials and Drug delivery systems.
  • Below is the Concepts filter table for this answer set. This is a powerful refinement tool for my search

• Note how, unsurprisingly, there are many "electrochem" terms among the most common concepts.
• Note, too, how you may find related terms that you might want to consider to broaden or refocus your search, like cyclic voltammetry (an electrochemical technique) and metallaphthalocyanines.
• You may select as many of the concept headings as you like, then click the Apply button to filter your results to just those documents that have those concepts in their indexing. You may use the Search tab to help find relevant concepts when you have a long list. See example below. In this case, I searched electro* and then clicked the Select All on Page box to select them all at once.

 

• After applying, the Searched concepts above, and applying the Substance Role, Analytical Study, my answer set is narrowed to 261 answers. Below is the full document record for one of the answers.

• Note that all the keywords searched are highlighted, in title, abstract, keywords, concept headings and substance records.
• Note that in the substance records, the roles for each substance as they are given in the document appear. Note also, that both the general roles that appear in the Filters list (such as Analytical Study) and more specific roles appear. These more specific rolesdon't show up in the drop-down list of roles, but do show up in the table of roles when you click "Show all", and can be used to refine from there..
• Note that Metallopthalocyanines is highlighted in the concept headings, even though we didn't search it directly, SciFinder-n's built-in "smarts" searched for it anyway. Also note, that since it is a class of compounds, stubstance roles are applied to it as well as to specific substances.

 

Searching for Substances

• This is the opening screen for substance searching in SciFinder-n. In the CAS databases, chemical substances include: simple organic and inorgagic substances, polymers, biomacromolecues (such as proteins and nucleic acids), metals and alloys, mixtures and more. Each substance receives its own CAS Registry Number (about which more below), including isotopically-labeled substances, stereoisomers, salts and ions of differing charges.
• As indicated, you can use the search box to search by:
  • Chemical Name - This includes trade names (e.g. Teflon), generic drug names (e.g. ibuprofen), common chemical names (acetone), acronyms (EDTA), systematic chemical names, and CAS inverted chemical names.
    • If you search by a single word chemical name, you may also retrieve substances in which your term is apart of the name. If you wish to retrieve only the single substance, put the word in quotes.
    • Chemical name searching may not retrieve all the variations on a substance, such as stereochemical variants, isotopically-labeled substances, the mineral version of a salt, etc.
    • You can use the  asterisk wildcard to truncate single word names, and use quotation marks to enclose phrases.
    • You can enter multiple chemical names at the same time to find multiple substances.They must be separated by a space, not by commas or any other punctuation.
  • CAS Registry Numbers - This is the Chemical Abstracts Service ID number for substances. Like a Social Security number, or a UCSB perm number, the number contains no information about its subject. It is purely an identifier..
  • Note: At present, you cannot directly search other chemical identifiers, such a SMILES strings,  orInChI numbers . You can use InChI keys to search  in SciFinder-n. (see thedfrop-down menu of search options.) You can, however, use SMILES or InChI identifiers in the structure drawing tool to generate a starting structure for searching. See lecture 14.
  • Document identifiers - Patent numbers, DOIs PubMed IDs and CAS Accession Numbers can be used to retrieve the substances contained in the document identified.
• You may also enter a DOI for a document, PubMed ID, CAS Accession Number (CAN) or a patent number, and retrieve the substances indexed in that document or patent.
• To the right of the search box is the Draw button. Clicking it opens the SciFinder-n structure drawing tool, for finding substances by chemical structure. This will be discussed extensively in Lecture 14.
• Below the search box is the link for Advanced Search, which will be discussed in detail below. You can use it to search by: You can add multiple advanced search fields if desired  Unlike the advanced search fields in Reference searching, fields in Substance searching are automatically combined with AND.

Searching by Chemical Name; Substance Answer Sets

Entering a chemical name (in the example below, the trade name, "aspirin" opens a dropdown menu of possible stustances whose names start with aspirin.

Below is a substance search using four common names of over-the-counter analgesic and anti-inflammatory drugs. Note how the names are separated by space, not commas or other punctuation.

• Note that in SciFiner-n, you can use Boolean operators, wildcards and parentheses in Substance name searching Wildcard searching only truncates the specific term to which it is applied, not the whole of a complex name. However, the terms you enter may be searched within names. Pay close attention to your results sets to determine whether you are retrieving the answers you expect to get from your name search.
• Below are he results of that search.

 

• Looking at the display above, notice:
  • Since we searched by chemical name, the name(s) searched are the names displayed in the brief record(s), e.g. Acetaminophen.
  • Just below the description of the search terms are the buttons to retrieve References, Reactions and Suppliers associated with the (selected) substances in the answer set.
  • Further to the right, are the icons for Download, E-mail and Save and Alert. For Substances, the download options are Excel, PDF, RTF and SDF. SDF stands for Substance Description File. Note that there are limits on how many substances you can dowload; for most formats it's 1000 records, for Excel files it's 100 records at a time. If you have a larger answer set, you'll need to break it up into smaller chunks.
  • To the immediate right of the Filter Behavior header is the number of substances in the answer set (4)
  • Further to the right is the drop-down Sort menu. The default sort is Relevance. Also available are CAS Registry Number (RN), Molecular Formula, Molecular Weight, Number of References, (all in ascending or descending order) and Number of Suppliers descending order only.) Sorting by CAS RN is essentially sorting by when the substance was added to the Registry database, the larger the number, the more recent the addition. 
  • To the right of that is the Record View drop-down menu. Dafault is Partial; option is Full.
• To the left are the Filter options for Substances. As with References, you may opt to either Filter by or Exclude a given parameter.  Again, only options that are relevant to your answer set appear. As with References, the top five possibilities display. If there are more, click on See More to get up to 10 answers, or a full table.
  • Search within Results - Lets you open the structure drawing tool to search within the answer set for a particular structure of substructure and require or exclude that structure. Note that with small answer sets (that is, almost anything less than the full Registry file), even small structure fragments can be successfully searched.
  • Reaction Role - What roles in reactions does a substance play? Product, Reactant, Reagent, Catalyst, Solvent. If a substance appears in a given role in even one reaction, it will be listed here.
  • Reference Role - This is the counterpart to the Substance Role filter for References. If a substance has a given role in at least one reference, it will appear here. To view the table of all Reference Roles for substances in the answer set, click the View all link.
  • Bioactivity Data - Which substances in the set have Structure-Activity Relationship or ADMET data (note, this option may go away when the CAS Life Sciences product is launched.)
  • Commercial Availability - whether or not suppliers are avaiable for a substance
  • Number of Components - Salts, mixtures, copolymers, alloys, etc. will have more than one component.
  • Molecular Weight - Lets you specify a range of molecular weights to filter your results.
  • logP - You can filter by a range of the octanol/water partition coefficients.
  • Stereochemistry - Is there at least one stereochemical center in the answer structure?
  • Element -  What elements are present in a substance in the set?
  • Functional Groups - You may bilter by (or exclude) a number of common organic functional groups, such as "Carboxylic acid" or "Amide"
  • Aromatic Rings - The number of aromatic rings present in the substance
  • Substance Class - Examples: Organic/Inorganic Small Molecule, Polymer, Biosequence, Mixture, etc.
  • Isotopes - Are there any isotopically-labelled substances in the answer set?
  • Metals - Do any of the substances in the answer set contain metals?
  • Experimental Property - Lists the experimental properties (not the values of the properties) available for substances in the answer set.
  • Experimental Spectrum -  Lists the types of experimental spectra available for substances in the answer set.
  • Bioactivity Indicator - Lists biological activities that have been studied for substances in the answer set.
  • Target Indicator - Lists biological targets (e.g. enzymes) for which substances in the answer set have been studies.
  • Regulatory Data by Country/Region - Is regulatory information available in the database for substances in the answer set, broken down geographically.
  • Regulatory Data by List - Same as the above, but broken down by list, such as EINECS or NIOSH.
  • Reference Availability - Whether or not there are literature references available for the substance. While most CAS Registry substances have literature refernces, some, such as some substances registered for regulatory agencies, do not.
• Below the filter list is Filter Content Report, which generates an Excel spreadsheet of selected filter data for this answer set.
• On the right are the brief records for the substances in the answer set. Note that right-clicking on links here, as elsewhere in SciFinder-n, will open a new tab or window containing the linked information. This can be handy for moving back and forth between an answer set and individual answers.
  • At the top of each record is a set of three dots.  Clicking on them given the options to Save the  substance record, or to add it to a Project. Projects allow you to gather results from multiple different searches into a single saved location in your account.
  • Just below that is the CAS Registry Number (or CAS RN) for the substance. Clicking on the RN will take you to the full record for the substance (see below for examples.)
  • To the right of the RN is an Expand link, which displays a more extensive brief record (see below for the aspirin record.) This view adds key physical property data (where available) anda link to the experimental properties and spectra table for the substance.

• Next you see the 2-D structure of the substance. Stereochemical bonds, if any, are indicated. Note that structures are only displayed i there is a known structure for the substance, and it contains 255 or fewer non-hydrogen atoms. Thus, most biosequences do not have a displayable 2-D structure. If you click on the structure, you get a pop-up "quick view" of the substance record (see below). The quick view includes
  • the CAS RN,
  • a brief name,
  • the 2-D structure diagram, and links to
  • Get Substance Detail s(the full substance record),
  • Get Bioactivity Data, the SAR and ADMET data, if any,
  • Get Reactions (all reactions in which the substance is indexed),
  • Synthesize (all reactions in which the substance is a product),
  • Start Retrosynthetic Analysis (see Lecture 15 for a discussion),
  • Get References (all references in which the substance is indexed), and
  • Get Suppliers (all suppliers in the database for the substance.)
  • The Edit Structure link opens the structure drawing tool and enters the substance's structure as a starting point for creating a new structure search.
  • - Reset + affect the displayed size of the structure diagram
  • The Download icon lets you download the structure as an image, molecular structure file, or SMILES string.

• Teturning to the brief record, below the structure are:
  • Molecular Formula in Hill order. Hill order is carbon, then hydrogen, then all other elements in alphabetical order. If carbon is not present, then all elements, including hydrogen, are in alphabetical order
  • Substance Name - in this case, the name which was used as a search term.
  • Links to References, Reactions and Suppliers in which the substance appears.

CAS Registry Numbers

     CAS Registry Numbers were first assigned to substances by Chemical Abstracts Service in the 1960s when they created a computerized database of substances to aid their indexers in determining whether a substance in a document they were indexing had previously appeared in the literature. CAS RNs are of the form: xxx-xx-x where the first number is 2-7 digits long, the second number is always two digits long and the third number is a check digit generated by an aloorithm from the previous digits insuch a way that most common mistakes in entering an RN would generate an invalid RN, rather than the RN for the wrong substance.  

     Every unique chemical substance gets its own RN, including stereoisomers, isotopically-labeled substances, mixtures, etc. One excepption to this is that polymers which only differ in chain length or molecular weight do not get different RNs, nor do plastics which differ only in how tey were processed. This is a long-standing CAS indexing policy, somehwat to the regret of scientists working in the plastics industry.

     Note that CAS RNs are purely identification numbers, and do not convey any information about the structure or properties of the substances they represent. Most RNs are assigned by indexers in the course of indexing documents. Some are assigned at the request of chemical manufacturers or government agencies, and represent substances which have no published references. Note, too, that CAS RNs are the property of Chemical Abstracts Service and are not in the public domain. Reaction to this led to the creation of the InChI system (International Chemical Identifier) as an alternative which would be freely available to anyone.

Substance Detail (Full Substance Records)

Below is the substance detail for aspirin

 

 

• From the top: 
  • CAS Registry Number
  • Links to References, Reactions, Suppliers for this substance. To the right, the Download, E-mail, and Save options
  • 2-D Structure Diagram (Clicking on the structure gives the same pop-up window as clicking on the structure in the brief record shown above.)
  • Molecular Formula in Hill order  To the right of that are the standard Safety Warning Symbols that apply t the substance. Clicking on them takes you to the GHS Hazard Statements section below.
  • CAS Systematic Chemical Name (in inverted order)
  • Key Physical Properties (properties shown varies depending on the substance. These are fairly typical for a common organic molecule.)
  • Then a series of drop-down lists, beginning with:
    • Other Names and Identifiers These include the canonical SMILES string, InChI number and InChI key, where available, and any trade, generic and other chemical names used for the substance. This list can be VERY long - polyethylene has over 1000 names in its list!
    • Experimental Properties - These are given in tabular form. divided into tabbed sections by type of property. These sections will vary depending on what is available for the substance. Each property may or may not give actual numeric values, and may or may not have conditions associated with them (such as pressure for boiling points). All will have a link to the reference from which the property information was obtained.)
    • Experimental Spectra - These two are listed in tabular form. If a spectrum listed says View then the specrum itself is available in SciFinder-n. Click on the link to get the spectrum, with source detail. The spectrum may be scrolled up and down in size, or shifted left to right or up and down by clicking and dragging for better viewing. The spectrum may be freely downloaded as a JPG image. The SciFinder-n spectra do not, in general, give peak assignments. If the spectrumd does not say vieew, then it will link to the SciFinder-n record for the source document.
    • Structure Activity Relationships
    • Absorption, Distribution, Metabolism and Excretion Data
    • Toxicity Data
      • The three above sets of data are from the CAS Life Sciences product, and may cease to be available in SciFinder-n once CAS Life Sciences launches.  The data in each category are in tabular form, and may be orted by any of the data categories. All provide source references for each data entry, linked to the CAS record for the document.
    • Predicted Properties - This table of properties is calculated from the chemical structure with software creaated by ACDLabs and licensed by CAS. Among the tabbed lists for aspirin, you will see one labeled "Lipinski". These are named for Christopher Lipinski, who, while at Pfizer, described a set of five properties which could be used to determine whether a given chemical would be orally active as a drug. These involve molecular weight, acid-base properties and the relative solubility in water vs. organic solvents.
    • Predicted Spectra - These are also generated by ACDLabs software, and may be downloaded like the experimental spectra mentioned above.
    • Bioactivity Indicators - A hierarchical list of the broad and narrow bioactivities described in the literature for the substance. Each bioactivity has the number of current documents containing the information. Clicking on the name of the boactivity creates a Reference list of the relevant documents, which may then be maniupulated like any other SciFinder-n reference list.
    • Target Indicators - Hierarchical list of the proteins (including enzymes) with which the substance has been shown to interact. Like the bioactivity indicators, the number of papers is shown for each protein target, and clicking on the link generates a Reference list of those papers. Note: For a widely-tested drug like aspirin, this list is VERY LONG!
    • Regulatory Information - Lists the names under which is substance is known in national regulations, and the countries which regulate it, and the names of the documents in which the regulation appears. This information is derived from the CAS database, CHEMLIST. Note that SciFinder-n does not contain, or link to, the actual regulatory documents.
    • GHS Hazard Statements - GHS is an acronym for Globally Harmonized System. GHS label hazard statements are phrases that describe the nature of hazardous products and the degree of hazard. They're further organized and identified by GHS hazard statement codes, or H codes. You can learn more about the GHS hazard statements at the List of GHS Hazard Statements and How to Choose site. Users can filter the GHS table by code, hazard statement, class, and/or source to find the right information.
    • Additional Details - (not visible in the image above) Includes a list of  Document Types in which the substance is referenced; Substance Classes to which it belongs, and Deleted CAS Registry Numbers. Deleted RNs occur when an indexer identified a substance in a document as a new substance, assigned a RN, and it is later found to be the same as a previously known substance. The newer RN is then deleted from the Registry file. However, since it is still attached to the original document(s), SciFinder=n automatically searches all the deleted RNs when you search for references to a substance - so you don't miss out on anything!.

Sample Records for Other Classes of Substances

Polymers/Plastics

 

• Above is the Substance Detail for a styrene-butadiene copolymer, 
• Note how the two monomers are treated as individual components of the polymer. Some polymers are graphically described with the structure repeating units (SRU) instead.
• Note the molecular formula gives the two monomers in descending order of molecular formula in Hill order, enclsed in parentheses with an x subscript. Molecular formulas for SRU polymers use an n subscript. Both the n ad x indicate an indeterminate length polymer.
• Note how the systematic name is written. Copolymers use "copolymer with"; homopolymers use "homopolymer"  There are also Registry Numbers ofr "block" and "graft" polymers.
• If you open the drop-down list, ote how the Experimental Properties include categories relevant to plastics, such as Flow and Diffusion and Mechanical.

Biosequence

See below the substance recrd for human insulin, with the Sequence Details section expanded:

• Note how there is no structure diagram given. Human insulin has more than 255 non-hydrogen atoms, so the Registry Record cannot record a 2D structure for the molecule. However, see the Sequence Details section.
• Note that below the name, it is identified as a Protein/Peptide Sequence, the total sequence length (in amino acids) as well as the lengths of the two sub-chains, the protein is identified as Multichain, and there is a link to Related Sequences. Since CAS assigns separate Registry records for each distinct protein or polynucleotide, and sell as distinguishing by source organism, there are many other "insulin" records besides the one we tretrieved. Clicking on the link creates a Substance answer set of all the related sequences.
• In Sequence Details, you get the amino acid sequences for each subchain, as well information on the number, types and locations of modifications to the chairs (in this case the Cys-Cys bridges between the two subunits.) The sequences are gtiven in standard one-letter codes for each amino acid, familiar to protein chemists. Polynucleotide chains use the standard A,T,C,G, and U

Alloys and Tabular Inorganics

• Above is the Substance Detail for a Registry record for Monel alloy.
• Note the tabular composition display. This is common for metal alloys, as well as some other types of nonstoichiometric inorganic substances, like the high-temperature superconducting perovskites. The first column lists the components (usually elements, though occasionally metal oxides), the second column the molar percentage (or range of percentages) of each component, and the third column the CAS RN for the component.
• Below that is the molecular formula in Hll order. Notice that there are no subscripts given for the elements. Below that is the number of components, and the CAS systematic name. The element with the highest molar percentage is considered the "base" of the alloy,  The percentage ranges for it and the other elements are included in the name.
• Again, note the the Experimental Properties categories given are ones appropriate for a metal alloy, such as Electrical and Mechanical.

Salts

• As mentioned in Lecture 110, the CAS Registry system has a unique system of nomenclature for inorganic oxyacids and organic acids. Originally created to group salts of such acids alphabetically with the parent acid in printed indexes, this system bases names and molecular formulas and structure diagrams of salts as derivatives of the parent asid.

• In the example above, disodium hydrogen phosphate is treated as a mixture of phosphoric acid with two sodium atoms. Note the effect oh the molecular formula, index name and structe diagram.

Mixtures

• Above is the Substance Detail for a mixture of metformin and glipizide (two drugsoften used for the treatment of hypertension, that is, high blood pressure, in humans.)
• Note that in addition to the mixture Registry Number, the structures and Registry Numbers for each component of the mixture are given.
• The molecular formula gives the Hill order molecular formula of each component in descending alphabetical order. Note that no specific rations of the two components are given. (CAS now has a database, Formulus, that gives detailed information on formulations, including states of matter, coatings and the like, for drugs and agrochemicals. It is a separate producton theSciFinder Discovery platform, aimed at industrial users. However, when you retrieve references for substanceswhich in in formulations, you will see a Filter for formulation information appear. This can be useful on identifying which documents have detailed formulation information int heir full text. Formulus will be discussed in detail in Lecture 15)
• Typically, for mixtures there is no experimental or  predicted property information given, but for mixtures used as drugs or agrochemicals, there is frequently bioactivity indicator data.

Advanced Substance Search (Molecular Formulas, Substance Properties, Experimental Spectra)

 

• Just below the main keyword search window in Substance Search is a link to the Advanced Substance Search (see image above), Note that some of the otions listed have arrows by the name. This indicates sub-menus for that option.  See below..
• Advanced search fields include:
  • Molecular Formula - Molecular formulas are generally entered in Hill oder. Polymers, salts and mixture have special formats.
  • CAS Registry Number. Note the arrow opening Substance RN and Component RN options.
  • Chemical Identifier. Note the arrow opening Chemical Name and InChI Key options.
  • Document Identifier - Searching by document identifier (DOI, PubMed ID, CAN, etc.) will retrieve all substances indexed in the selected document.
  • Patent Identifier - Searching by patent identifier (patent number, application number) will retrieve all substances indexed in the selected patent.
  • Experimental Spectra
    •  . Valuees are in ppm Currently, searchable experimenal spectra include:
      • Proton NMR
      • Carbon-13 NMR
      • Nitrogen-15 NMR
      • Fluorine-19 NMR
      • Phosphorus-31 NMR
    • You may enter specific peaks in ppm, or ranges of ppm. Examples are given.
  • Bioactivity Data - one one chemical identifie or disease may be searched at a time
    • Target
    • Ligand
    • Disease
  • Biological
    • Bioconcnetration Factor (predicted) - specific values or ranges
    • Median Lethal Dose (experimental) in mg/kg specific values or ranges. Note that you cannot specify the organism.
  • Chemical Properties
    • Koc (predicted)
    • LogD (predicted)
    • LogP (predicted)
    • Mass Intrinsic Solubility (predicted) g/L
    • Mass Solubility (predicted) g/L
    • Molar Intrinsic Solubility (predicted) mol/L
    • Molar Solubility (predicted) mol/L
    • Molecular Weight
    • pKa (predicted)
    • Vapor Pressure (predicted) Torr
  • Density
    • Density - can search both experimental and predicted values, or experimental values only g/cm3
    • Molar Volume (predicted) cm3/mol
  • Electrical (experimental only)
    • Electrical conductance - S
    • Electrical conductivity - S/cm
    • Electrical resistance - ohm
    • Electrical resistivity - ohm*cm
  •  -Lipinski (predicted only) - These are properties used to predict potential drug applications.
    • Freely Rotatable Bonds
    • Hydrogen Acceptors
    • Hydrogen Donor/Acceptor Sum
    • Hydrogen Donors
  • ​​​​​​​Magnetic
    • ​​​​​​​Magnetic Moment (experimental) - muB
  • ​​​​​​​Mechanical
    • ​​​​​​​Tensile Strength (experimental)  - Mpa
  • ​​​​​​​Optical and Scattering
    • ​​​​​​​Optical Rotatory Power (experimental) - degrees
    • Refractive Index (experimental)
  • ​​​​​​​Structure Related
    • ​​​​​​​Molar Surface Area (predicted) - A2
  • ​​​​​​​Thermal
    • Boiling Point (experimental and predicted, or experimental only) Note that SciFinder-n does not allow you to - specify the pressure at which the bp is measured. - kdeg C
    • Enthalpy of Vaporization - kJ/mol
    • Flash Point - deg C
    • Glass Transition Temperature - def C
    • Melting Point - deg C
• ​​​​​​​​​​​​​​Note that new searchable properties are added from time to time. Also note that for property values, units are specified. (In STNext, the searcher can choose which unit system to use. SciFinder-n does not have any units conversion facility.)
• Also note, unlike Reaxys and STNext, SciFinder-n does not allow you to specify conditins, such as pressure for boiling points.
• ​​​​​​​Advanced substance search fields may be combined with structure drawing searching. See Lecture 14 for mroe information.

• SciFinder-n does not have any units conversion facility.
• ​​​​​​​Advanced structure search fields may be combined with structure drawing searching. See Lecture 14 for more information.

Searching Substances by Structure

• When you click on the Draw button next to any search window, the SciFinder-n structure drawing tool will open. See below:

 

• Note the drop-down menu at top. SciFinder-n offers two built-in structure editors: CAS Draw and ChemDoodle. This lecture will focus on CAS Draw. You can also use external structure drawing programs, such as ChemDraw which can export a structure as a MOL file. See Import below. ChemDraw Professional integrates directly with SciFinder-n for easy transfer of structure information.

•  Top horizontal row of icons
  • New - start drawing a new structure
  • Import - Enter the name of a saved CXF or MOL file that you wish to modify or search in SciFinder-n.
  • Export - Once you have crated a structure, you can export it as a CXF or MOL file.
  • Save as Template - You can save the structure in the current structure drawing window as a template to reuse as a starting point for structure building and searching.
  • Center Structure - Moves the structure you have drawn to the center of the drawing field
  • Cut
  • Copy
  • Paste
  • Undo
  • Redo
  • Preferences - Lets you set bond lengths and angles as you prefer. This only affects the way structures display; it has no effect on searching.
  • Keyboard shortcuts - Opens a list of single-keystroke shortcuts that can save time for the experienced user.

• Text template window - You may enter a CAS Registry Number, SMILES string or InChI, then click Enter, and the identified structure will appear in the structure drawing field or you to modify or search.
• Search window to import structures from CAS Registry Numbers, SMILES strings or InChI Keys  
• The grey bar above the search window will display error messages and suggestions in cotext.

• Furthest-left  vertical tool bar  Note that when you clickion one of these icons, a description of its function appears in the main drawing window.
  • Lasso - Select objects by clicking on them, or clicking and dragging a line around them.
  • Pencil - Draw or change atoms or bonds 
  • Atoms  - Opens a periodic table from which you may select any atom to draw with the Pencil tool. Selected atoms show up in the window just below the drawing field. When you hover your cursor over an element in the table, it will display the atomic number, element name (in English), atomic weight, and the column and row names to which it belongs, see below. Use the close button when you are done selecting atoms. Note, too, that deuterium and tritium are available at the bottom of the table.

• Variables - List of available variables: See below.

• Select fragment attachment - Assign an attacment point or points to a fragment for use in R-groups (se below).
• Add positive charge - Lets you add one or more positive charges to a structure you'v drawn. This does not affect searching.
• Repeating Groups - If you wish to specify a repeating group in your structure, dfaw it, then shoose this tool and draw a selection box around the group. A window will appear in the horizontal bar above the drawing window where you can specify a range of how many repeats, from 0 to 20.
• Variable attachment points - Used to allow variation in where a given subsituent may be attached to a ring system. Create the ring system structure, then creae the substituent separate from the ring(s). Now click on the Variable Attachment tool, then on the substituent, then on each atom on the ring system where you wish to allow th substituent to be attached. Note that this does not mean that multiple copies of the substituent will necessarily be attached. The substituent will be shown as connected by dotted lines to the selected ring atoms.See example below.
• Map atoms - Designate corresponding atoms in reactants and products
• Bonds formed/broken - Clickon a bond in a reactant or product to indicate that the bond is broken or formed in the reaction.

Second left-hand vertical tool bar:

• Rectangle selection tool - Click ion the upper left hand corner of the area you wish to enclose and select, then drang to the lower right hand cordner and release, to select all the atoms and bonds within the rectangle.
• Eraser -Delete atoms and bonds
• Shortcuts - Opens a table of "shortcut" symbols for commonly used functional groups, such as Me, Et, NO2, etc. Note that if you use ashortcut group in drawing your structure in a substructure search, no further substituion is allowed on the shortcut group. Note that a few shortcuts appear in two different forms. This makes no difference in searching, but can be used to get a better appearance in the structure diagram. Note the recently added list of common protecting groups at the bottom of the table. To see the structrue diagram corresonding to a shortcut, hover your cursor over the abbreviation.

• R-groups - These are "build your own" variable groups. You may create up to 20 different R-groups per structure (R1, R2, R3 etc.) selecting from Atoms, Variables and Shortcuts.  Note that the option to nclude structure fragments in the R-group is greyed out as no structure fragments have been designated yet.  See below for more infomration.

• Structure Templates - These are a set of pre-defined structures which you can use as starting points for structure drawing. See the full list of structure types below, and an example of one of the types in full. Note that you can create you own user-defined templates using the Save as Template tool mentioned above. Note, too, that you can seaerch all the templates by name to find a particular one. See the opening table, and the expanded Alkaloids example.

 

• Add negative charge - See "Add positive harge" above.
• Chain - Click and drag this tool to create a chain of single-bonded carbon atoms.
• Substance role in reactions - Click on an atom and designate whether the structure fragment it is in is a reactant, product or other
• Lock rings - Clicking on this icon displays a menu of several tools: Click on an atom in a ring to designate that no additional ring fusion on tht ring is allowed.. Lock atoms forbids non-hydrogen substitution on te atom; Rotate fragment and Flip fragment. These last two only affect the appearance of the display, and do not influence searching.
• Add reaction arrow - Click and drag to create a reaction arrow, with reactants to its left, and products to its right.

Bertical tool bars on the righthand side of the drawing window:

• These provide access to commonly used atoms and bond types. Note that some boxies have an arrow in the lower right-hand corner. These indicate that more choices appear when you click on the box.
  • C = Carbon; H = Hydogen (Click on the arrow for Deuterium and Tritium)
  • O = Oxygen; S= Sulfur
  • N = Nitrogen; P = Phosphorus
  • Cl = Chlorine (click on arrow for Fluorine, Bromine, Iodine); Si = Silicon
  • Single bod; Double bond (Click on arrow for Triple bond and Unspecified bond.)
  • Stereo bond up (Click on arrow for Stereo bond down, Stereo double bond up, Stereo double bond down); Cis=trans double bond.
  • Cyclopentane ring; Cyclopentadiene ring
  • Cyclohexane ring; Benzene ring
  • Cycloheptane ring; 3-15 soded romg

Multiple Points of Attachment

This tool allows you to specify that a given atom/group may be attached at multiple possible points on a ring structe. To do so, draw the ring structure, then draw the desired atom/group as an unattached fragment, and clig on the  Multiple Points of Attachment tool, then click on the fragment, and draw lines to the desired ring atoms.  Below is an example using a Cl atom and a naphthalene ring.

Note  how the resulting structure shows  a solid line from the Cl tothe center of one of the naphthalene rings, with dotted lines going to the selected ring atoms.

Structure Fragments in R-Groups

To create an R-group including structure frangments, first draw each individual frgment you wish to create. In the example below, I created an amide group, a triphenylsilyl group and a alkyl, sulfonyl group.  Then, click the Fn tool, and click on the point of attachment you desire on each fragment. Note that if you want to use a fragment as a bridging group, you can create multiple points of attachment on the same fragment.

 

Note how each attachment point is labeled, and the fragment as a whole hs an F-number assigned.

Then, click on the R tool, choose an unused R number, and select the atoms, variables shortcuts or fragments you wish to include in the R group. Fragments will appear in a table at the bottom of the R-group window.  In this case, R1 includes fluorine, trifluoromethyl, and the three structure fragments I drew.  I could now close the window and attach R1s wherever I want in my desired molecular structure for searching.

Drawing Structures

With the tools above, drawing structures in SciFinder-n is relatively straightforward. SciFinder automatically checks for "normalized" bonds in aromatic structures or tautomers.

Some general tips -- While you can do most functions in any order, I prefer to do the following:

• Plan out your structure before you start drawing. Think about whether you are doing an exact structure search or substructure search. Are there templates you can use? Think ahead as to what groups can be represented by shortcuts. Note that SciFinder (and the underlying database) do not allow substituents to be attached to most shortcuts.
• Is there a known substance that you can use as a starting point, rather than drawing from scratch? If so, look up the substance in SciFinder-n and click on its structure diagram, then select "Edit Structure". Alternatively, if you can find its CAS Registry Number , SMILES string or InChi number, you can enter it in the CAS Draw search window and pull it up that way.
• Whe starting from scratch"
  • Draw any ring structures in the compound first.
  • Then draw/attach chains as needed.
  • Then change any atoms into heteroatoms, variables, shortcuts, R-groups as necessary.
  • Then modify bonds as needed. This is where you can add stereochemistry if desired.
  • Then consider any added restrictions: locking down substitution at some sites or locking out ring fusion.
• Previewing substructure searches is a good idea to make sure you're getting the kind of results you anticipated.

Structure Drawing Example: Ruthenium(2+)​, tris(2,​2'-​bipyridine

As an example, let's take a look step-by-step at the drawing of the structure of feropolone (Note: the screenshots below were made with the Java structure editor, but the process is the same with the non-Java editor):

First, use the ring drawing tools (right-hand tool bar) below the drawing board to draw in the ring portions of the structure -- the benzene ring tool for the six benzene rings :Note that the precise  positioning is not important - I've laid them out similar to the final 2-D structure for convenience.

Now, use the Pencil tool to draw bonds connecting pairs of benzene rings to create three biphenyls. Note that as the Pencil tool touches an existing atom or bond, that atom or bond is highlighted. Hold the mouse putton and go to the corresponding atom on the adjacent ring. As you do so, a bond will appear. When you reach the other atom, the bond will link the two rings.

Continuing with the pencil tool, select N from the list of common elements on the right-hand tool bar and change one carbon on each ring in the ortho position to the biphenyl bond to a nitrogen.  Now, you have three 2,2'-bipyridyls.

Now, we can use the Atom button,(the periodic table icon on the left-hand tool bar)  to open the periodic table and select Ru  and close the periodic table. Note how the window to the left of the buttons now shows a Ru. That is the current atom that will appear when you draw. Now, move the pencil tool cursor to the center of the circle of bipyridyls and click to place a ruthenium atom there.

Now use the pencil tool to connect the Ru atom to each of the six nitrogens, one at a time. Now, your structure is drawn. You could use the + tool in the left-hand menu bar to add a +2 charge to the Ru, but charge assignments are not used in searching by SciFinder-n.

Now, click OK to return to the search screen.

 

Note how the structure Edit icon is now highlighted. Click the Search icon to carry out the sturure search. You can ad additional substance search terms (keywords, property values, etc.) before launching the search.

 

Searching Structures

When you click the Search button, you gett a display of thesbustance answers in the SciFinder-n database that match your query. The default sort order is Relevance though you can select other sort orders. Note, too, on the left, that there are three answer sets created by your search:

• As drawn - Structure containing the drawn structure, but with no additional substitution on the structure itself. However, the answer set can include strucutres with different stereochemistries, salts (in this case, since the main structure is a cation, you can get salts with a range of different anions), isotopically-labelled comounds, and mixtures containing the basic structure.
• Substructure - This answer set includes all of the structures in the "As drawn" set, plus all those in which additional substituents are attached to the original strcuture.
• Similarity - This answer set uses an alogrithm to select structure similar to the one drawn They may have additional sutsituentsor fewer atoms, or some replaced by different elements (suc as a Co in place of the Ru). The similarity algorithm ranks the results by a percent similarity. Similarity searching is frequently used in drug discovery searchesto turn up compounds that might have similar biological activity to the starting structure.

"Filters" allows you to limit your search results to certain types of substances or to exclude certain types of substances. Note that you can apply multiple filters to the same answer set. Filters can be removed as well.

Filtering Substance Answer Sets

The previous tab, "Substance Searching", lists the various filters available for substance answer sets. Note that a filter category only appears if it is applicable to the answer set in question. If the number of possibilities in a given option is small, they will be listed in order of descending occurrence. If they are larger, you'll see a "View All" link, which will open a table of all the possibilites. For esample, here's the table of Reference Roles for the Ru*bipy)3 answer set above:

Note that the roles can be lised either in descending order by occurrence cunt, or alphanumberically.  If you select more than one option from the table, they are, in effect "OR"ed together. If you want to "AND" roles together, apply them one at a time.

Structure Search Within Results -- Why, you might ask, would I want to refine one structure search with a second structure search? Why not just do the structure search you wanted in the beginning. The answer is that some types of structure search are too general to run on the full database. But if you can create a smaller subset of substances to run your desired structure against, you can be successful. The subset can be created by either structure or molecular formula searching, or by using the Get Substances option on a document answer set. Also, by starting with a more general search, you can filter for a particular structure option, then back up and try a different option.