Beilstein & Gmelin Commander (Version 6) Guide
Find spectra, reactions and chemical, physical & biological properties of chemical substances
- Beilstein – organic & some organometallic substances
- Gmelin – inorganic & organometallic substances, incl. alloys, ceramics, coordination compounds, glasses, minerals, & polymers
Contents
Beilstein
Gmelin
Beilstein
Find spectra, reactions and chemical, physical & biological properties of organic and some organometallic chemical substances.
What is Beilstein?
A chemical database containing:
- chemical identities of millions of organic chemical compounds (structure, formula, name, registry numbers, etc.)
- chemical, physical and biological properties of those compounds
- millions of organic chemical reactions
- literature references to the compounds, properties and reactions
- 1771 - present coverage of the chemical literature with quarterly updates
The Beilstein/Gmelin database server for UM is mounted at the University of Wisconsin Library. UM campus computers may access Beilstein or Gmelin via the Internet using Beilstein Commander software, either directly or via UM Library Terminal Services.
What is Beilstein good for?
- search by chemical structure - you don’t need to know the chemical name [use the Structure Editor]
- search by chemical reaction - specify product(s), starting material(s)
- hyperlinks between compounds, literature citations, and reactions
- search by chemical name, formula, property, etc. [use Easy Data Search]
- search for properties and reactions of isotopically labeled compounds
- search for radicals, ions, and other variants of a molecule
- search for molecules isolated from natural products (e.g. from a particular plant)
- find original literature references to properties and reactions
- broad coverage of the organic chemistry journal literature
What doesn’t Beilstein cover?
- Polymers (such as peptides over 2 units). See Gmelin for inorganic polymers.
- Most inorganic compounds. Search the Gmelin database for these.
- Most organometallic compounds (check Gmelin). Beilstein substances generally may contain the elements H, Li, Na, K, Rb, Cs; Mg, Ca, Sr, Ba; B, Si, N, P, As, O, S, Se, Te; F, Cl, Br, or I in addition to carbon.
- Chemical patent literature after about 1980. Use SciFinder Scholar for patent coverage.
- After 1980, coverage may be less comprehensive. Currently about 180 journals are covered (listed at http://www.beilstein.com/support/journal.shtml). In the 1980s, only about 85 journals were covered, then about 120 in the early 1990s. In 1994, coverage of ecology, toxicology and pharmacy journals was expanded.
- Newly published reactions/compounds/properties may take 6+ months to be entered into the database.
- Chemical Abstracts Registry numbers are not listed for substances newly listed by Chemical Abstracts after the mid-early 1990s.
Getting Started
How do I get Beilstein Commander software?
- On UM Library public computers: www.lib.umich.edu/help/ts/resources/beil.html and click on the Use Beilstein link. This uses the UM Library Terminal Services server to run the Beilstein software and display it to your computer. Note that LitLink links to fulltext articles are NOT available via the UM Terminal Services version.
- Use of the Beilstein Commander software itself is recommended for office, lab, dorm, etc. computers (MS-Windows, or Macintosh up to MacOS 9.1 or Classic Mode under OS-X) on the UM campuses. To install/upgrade:
- Print the Installation Notes and Troubleshooting Notes before installing: links from http://minerva.library.wisc.edu/
- ID/Passwords needed for UM install (UM Library login required) are available at http://pk.lib.umich.edu/BBH8338.html
- Download the Commander software from http://minerva.library.wisc.edu/
- Under Options-Startup Tasks in the main Commander Menu bar, check the MDL Crossfire and Structure Editor boxes.
- The UM Library Terminal Services version is also available for installation. This is recommended for remote usage (you will be asked for a UM library login when using it remotely). See: http://www.lib.umich.edu/help/ts/resources/beil.html
- Tip: you may find either the Terminal Services or full software versions using the library's Search Tools - Find Databases page.
- LitLink software for MS-Windows computers is also available for installation (http://minerva.library.wisc.edu/) to provide deeplinks to the fulltext of retrieved articles.
Prepare your search
- On the main MDL Crossfire Commander screen, use the Select Database menu bar to choose between the Beilstein (note: the code BS070400AE would stand for the 2007, 4th quarter release of Beilstein) and Gmelin databases.
- You may search both Beilstein and Gmelin at the same time, although (a.) the Easy Data Search forms won’t be available and (b.) structure searches will miss some Gmelin records which do not include structures.
- Use the Structure Editor to draw a chemical structure or chemical reaction.
- Use an Easy Data Search form or the Fact Editor on the main Commander window left side to enter keywords (e.g. molecular formula, author last names, publication year), properties (e.g. melting point between 100 and 110 degrees C.), or combinations.
- You may also use the Text Search box in the main Commander window for general keyword searches. Note: keywords are automatically truncated, e.g. a search on woods also retrieves woodson, woodside, etc.
Submitting your search
- After you have prepared your search/query, use the blue Start Search button in the lower right of the main window to start the search.
Structure Searching (using the Structure editor)
- Use the Structure Editor. Click on the Structure Editor icon in the main Commander window. Be sure that you are using the MDL CrossFire Commander Structure Editor (note: the default MDL ISIS/Draw is not supplied with the download). If you get a “”Failed to transfer structure to ISIS Draw ...etc.” error message, go to the main MDL CrossFire Commander window, choose the Options menu and select the MDL Crossfire Structure Editor.
- The EditMode menu should have checkmarks by the Structure and Organic options and the View menu have checkmarks by the Standard Bar, Function Bar, Toolbox, and Status Bar options.
- Tip: Commander defaults to looking for a single-component exact structure match except stereochemistry (default finds all stereoisomers).
- Tip: Individual hydrogens do NOT usually need to be drawn.
- Use the top bar to specify type of atom (C, N, O, etc. or choose from periodic table), type of bond (single, double, etc.), type of ring (e.g. benzene) or templates (pre-drawn structures). Use the tools on the left side to draw/edit (the pencil tool), erase, select (the box or lasso), etc.
- To draw an atom, click on the pencil tool icon, then on the element symbol (e.g. S for sulfur). Click where you would like the atom to appear in the window.
- To draw a ring, click on the desired ring from the button bar, and then drag the resulting highlighted ring to the desired location. Deselect by clicking outside the highlighted area.
- To draw a bond connecting two existing atoms: choose the pencil tool, and then click on the desired type of bond (e.g. double bond) in the button bar. Move the pencil tool over the first atom until a small “A” appears on the pencil, click and drag the pencil until it is over the second atom (again, a small “A” will appear on the pencil when you are over the atom) and release.
- To draw a new atom and connect to an existing atom, use the pencil tool to click on the element symbol in the toolbar, then on the type of bond you want to draw. Click in the drawing area at the desired location, hold the mouse button and drag the pencil to the atom you want to connect to (an “A” appears on the pencil) and release the mouse button.
- To change a bond, select the bond by moving the drawing tool (pencil) over the bond until a B appears on the pencil and then click. Choose from the options available (type of bond, stereochemistry) in the Bond Attributes window.
- To change an atom, move the pencil until an A appears on the pencil, then choose an option (e.g. change a C to an O, change the number of attached hydrogens allowed) in the resulting Atom Attributes window. Shortcut: to just change the atom label, e.g. C to S -- click on the type of atom you want to change it to (e.g. S) in the Function bar, hold the shift key down, and click on the existing atom you want to change.
Substructure search
To allow unlimited substitution at a particular atom (instead of assuming the vacant positions have all hydrogen atoms), change the Atom Attributes default Free Sites setting of zero (0) to maximum (MAX).
To allow unlimited substitution at all atoms, use the Free Sites checkbox to the right of the structure editor box on the main window.
Specifying stereochemistry
- Select a bond. Use the resulting Bond Attributes window to change the bond stereochemistry (e.g. stereo up, stereo down, double steric, etc.).
- Before starting the search, change the default Stereo setting Off to Absolute, Relative or Racemic depending on your requirements using the Stereo pulldown list in the main window to the right of the structure search box.
Use the red crossed arrows shortcut button to return to the main Commander window to start your search.
Reaction Searching (using the Structure editor)
Tip: If looking for preparations of a specific compound, it is usually best to start out by specifying only the desired product. If that gives too many results, then try specifying starting materials(s) in addition to the product(s).
Tip: Beilstein searches may miss a particular reaction if you specify starting material(s) that the author treated as intermediate steps. Example: if you are looking for B --> D, but the author treated the reaction as A --> D (with intermediate steps/products B and C implied), Beilstein will NOT retrieve that reference using a B --> D search.
- Use the Structure Editor to draw the structures of the product(s) and/or starting material(s) of the reaction you are looking for.
- Switch to the Reaction Mode using the EditMode menu.
- Highlight a particular compound structure (e.g. the one you want to be the product) using either the Lasso or Select (dashed box) tool, then click on the “Product” button on the top button bar. Repeat for the other Products or Reactants (use the Reactant button).
- You may specify more than one reactant. You may specify reactants only, to find out the product(s), or specify both reactant(s) and product(s).
- If you want two chemical groups (substructures) to be included in the same Reactant (or Product), highlight them both and click on the Product (or Reactant) button.
- If you make a mistake in assigning a role, such as assigning a structure as a reactant that should have been a product, use the lasso or select tool to highlight that structure, then click on the Undefine button.
Tips to narrow the search results. Note: use the following sparingly as they may slow the search down considerably:
To specify that a particular bond is to be made, broken or changed during the reaction:
- Use the pencil tool to select the bond.
- Choose from the options in the resulting window to specify that the bond is to be broken, etc.
Atom Mapping: to require that a specific atom in a reactant becomes a particular atom in a product.
- Using the pencil tool, click and hold the mouse button on the desired atom and connect it to the corresponding atom in the product (a dashed line appears).
- If you make a mistake, use the “Delete All Atom Mappings” button on the top buttonbar. More than one set of atoms may be mapped, if necessary.
When you have finished creating your query, use the red crossed arrows shortcut button to return to the main Commander window and start your search.
Keyword Search / Browse
Easy Data Search (EDS) SearchForms
EDS Searchforms are listed on the left panel of the main Commander window and designed to make it easier to do some types of keyword searches. Some of the most useful EDS forms are:
Ident. Data (Substance identification data): Use when you know a molecular formula, chemical name or part of a name, registry number (either Chemical Abstracts or Beilstein), etc. of a substance.
- click in a box (e.g. Molecular formula)
- then click on the magnifying glass icon next to the box to choose from a list (browse) available searchterms.
Bibliographic Data: Use to search for articles by author lastname (note that initials are occasionally, but not always used), publication year, journal name, or article title/abstract words.
- When you have finished creating your query, select the OK button to return to the main window and then start your search.
Tips:
- To pick from a list of possible keywords: click on the magnifying glass, and type the beginning letters of the term you want to look for, then pick from the resulting list.
- Using more than one box/term requires both terms to be present (a logical AND).
- To find all terms beginning with a particular word/string, use the Starts With option if available, or use an “ * ”; for example: Chemical Name (CN) = taxol* would find any chemical names that begin with taxol, e.g. taxol C, taxol-7-xyloside.
- For completeness, use the format “lastname*” to search for article authors, as listing of author firstnames/initials are inconsistent in the database. The search form will do this for you if you choose the Starts With option.
Text Search Box
Enter keywords into the Text Search box on the main window. Choose the radio button “in bibliographic fields” to search only words in the article title, author, etc.
- Words are automatically made singular (terminal “s” is removed) and searched right-truncated (find all words beginning with the same characters).
- The Preliminary Results window lets you choose whether to search the words in the Structures, Reactions, or Bibliographic sections of data. To change the default truncation, and logic settings, use the Options button in the Preliminary Results window.
Fact Editor (Table)
The Fact Editor allows more powerful and flexible keyword search/browses than the pre-defined EDS form searches. It also lets you recombine/re-use previous answer sets.
There are two pieces of information needed for each logical piece of your search:
- Field Name: tells the database which piece of information you are looking for (e.g. RN which stands for CAS registry Number). This can also be the name of an existing answer set (e.g. .Q03).
- Field Value: the actual value to look for in that field, e.g. 100-52-7.
To see what Field Names are available:
- Click in the Field Names box, then select the List Values button (5th from right).
- Use the Find button to look for a particular Field Name, example: search on “melt” to see that the Field Name/abbreviation is “Melting Point (MP)”
- OR browse the tree of datafields to see what Field Names are available (e.g. NMR for Nuclear Magnetic Resonance or MF for Molecular Formula)
- Click on the desired Field Name in the list, then click the OK button. This pastes the label abbreviation (e.g. MP) for the field you want into the Fact Editor. Tip: If you know the abbreviation for the Field Name you need, it may be typed directly into the box.
Entering Field Values:
- Use the adjacent Field Value box. Enter the term/value you want to search for, e.g. C13H18O3 for a MF (molecular formula) search or Corey* for an AU (author) search.
- To select from a list of search values/terms for (browse) a particular field, click in the Field Name box, use the F2 function key (or click on the List Values shortcut button), and type the beginning characters of the term you want to check for. To select a term for use, click on the term, then on OK.
- If you want to add another term to the search query, tab to the Operator box, double-click and choose AND, OR, NOT, NEAR, NEXT to tell the search how to combine your terms. Note: do NOT use operators within a single Field Value box.
- Tab to the next Field Name box and repeat the process for entering the Field Name and Value until all your search terms are entered.
Wildcards/Truncation. Search for terms beginning with same base word.
Symbol |
Action |
* |
find any number of characters |
? |
find one character |
?? |
find two characters |
Field Name |
Field Value |
Finds these words: |
BF |
*leu*em* |
antileukemic, leukemic, leucemic, leukemia, etc. |
BF |
inhibitor? |
inhibitor, inhibitors as Biol Function words |
AU |
Corey* |
Corey; Corey, E.J.; etc. as author terms |
Group together terms using parentheses. Example: (MF C13H18O3 OR MF C11H14O3) AND Pharm.com inhib*. Use the F3 function key to open an editing window and set the parentheses using the keyboard.
When you have finished creating your query, select the OK button to return to the main Commander window and then start your search.
Combination Searches
Combining previous answer sets
Use the Fact Editor (Table) to combine two previous answer sets. Tip: you may combine different search types [Fact Editor and Structure; Author and Structure, etc.].
- Click in the FieldName box and use the List Hitsets shortcut button (hexagon shaped, 4th from the right) to see a list of available hitsets.
- Doubleclick on the answer set you want to use (e.g. the 3rd search this session would be Query 3, Q03), then choose a Boolean operator (e.g. AND) and then a second answer set (e.g. Q04).
- Note: if you wish to directly enter the answer set numbers into the form, a period is required before the “Q” ( .Q03 rather than Q03).
Structure plus Fact/EDS
- Draw the structure in the Structure Editor, go to the main Commander window and wait for the structure to be pasted to the search screen.
- Then go to the Fact Editor/EDS Forms, prepare the search, and return to the main window.
- Submit the search.
Displaying the Results (Hits)
Ordinarily, the desired display-type of results (compound, reaction, or citation) will be set automatically for you in the “Display as” box: e.g. a reaction editor search query will automatically retrieve answers in reaction format. You may change the “Display as” setting, if you prefer.
After the search is completed, your answer set will appear in the display Hits window. Select a specific answer.
To navigate within an answer:
- Be certain that you are looking at the entire answer. Go to the View menu, and check that All Fields has a checkmark next to it. You can then scroll through the entire answer or go directly to the portion of interest.
- Choose Field Availability from the View menu.
- Browse to select the field that you are interested in (e.g. MP for melting point). It may be easier to find the section you want if you select the Order-alphabetical by name” button.
- Click on the desired Field Name/Code, then on OK, and the program will scroll to that section of the answer.
- Tip: Sometimes it is helpful in scanning the answers to look at several at a time. Make use of the “change short/full” shortcut button (eighth from the right) to see several structures at a time. Double-click on the one that is of interest. To reset the number of rows/columns, use the Options menu to choose select Short Rows and Columns.
- Tip: To look at previous answer(hit) sets, use the left Display Hits navigation column to choose a different hitset or answer within a hitset.
- Tip: To turn the structure display on/off, choose Structure under the View menu.
- Tip: usually only what is displayed will be printed.
Exporting Results to Endnote, ProCite
- Use Display Hits for a citation record. To convert a citation in a substance/reaction display to a citation display, click on the Citation Number link.
- Click the Export button on the bar (or choose Export on the File menu).
- Choose EndNote/ Procite/ Reference Manager from the list. (note: this exports only the citation information without the abstract).
- Click on Start Export button and choose from All, Current Hit, Selected Hits only. Click on Start button.
- Choose where to save the exported data. Click the Save button.
- For additional information and UM support for EndNote/ProCite, see http://www.lib.umich.edu/knc/howto/citationdata.html
Printing the Results (Hits)
Many of the answers can be very, very long. Please customize display before printing.
Print Only Selected Section(s) of the answer you want (e.g. all the melting point data for a particular substance):
- Use the View menu (in Display Hits) and click on the Field Availability option.
- A box listing available data for that search result appears. A checkbox appears to the left of each property/field name.
- Click the checkboxes so a checkmark appears next to the sections you wish to print/display. Uncheck (leave blank) boxes next to those you don't want. Tip: it may be quicker to use the Remove All Checkmarks button and only check the ones you want.
- For substance results: be sure to include IDE (Substance) so you know which substance the properties belong to.
- Click on "Apply selections to User View".
- When finished, use the View menu to return the setting to "All fields".
Print Only Selected Fact(s)/Reactions
- Choose the desired fact(s) by clicking the “Select Fact for printing or copying” box (a small empty box, middle of three icons, to the right of the fieldname). It is recommended for substance answers to also check the box next to the Substance field, so that you can identify what property data belongs to which substance.
- Click the Print button.
- Selected Facts should already be checked. If not, check that box and click OK.
- If you choose specific facts from more than one substance in a hitset, ALL of those selected (checked off) facts will be printed.
Change Font-size when printing an answer
- Choose Print button; then choose Select Fonts button.
Select a Reaction from a Substance answer
- In viewing the search results, use the red hyperlink [an underlined number to the right of the text “Reaction ID” at the beginning of the data for a particular reaction] to select that reaction to view/print. This is useful when there are many different reactions listed for a particular compound, but you only want to print data for a few specific reactions.
- To print only specific reaction examples (e.g. the first and third), check off the “Select fact for printing or copying” box as noted in Print Only Selected Facts section above.
Hyperlinks
There are a number of different-colored hyperlinks useful in navigating the search results and finding related information.
- Red hyperlink - an underlined red number to the right of the text “Reaction ID”. The reaction hyperlink lists all other indexed cases of that reaction.
- Green hyperlink - an underlined green number to the right of the text “Ref. 1” or “Ref. 29”, etc. The article record hyperlink lists all the compounds and reactions indexed from that article
- Black hyperlink - an underlined black number to the right of the text “Reactant BRN”. Starting Materials hyperlink connects to the data for the properties and reactions of the starting substance.
- Blue hyperlink - an underlined number to the right of the phrase “Product BRN”. product hyperlink connects to the record for the properties and reactions of the product substance.
- LitLink hyperlink –requires installation of LitLink software (windows only, NOT available for Macs or via Terminal Services).
HitSet Navigation
Display Hits has a HitSet navigation tool on the left side of the window. Use it to choose from previous answer sets, or to navigate to particular answers within sets (4th substance of 212), or to get to particular sections of a single answer (melting point of 3rd substance of 143 for first hitset Q01).
Logging Off
- The program may ask you if you want to “Save changes to untitled document” or “Save history”. Answer No.
Finding the Original Article
For articles not available via LitLink, remember that you will likely need to search the UM Library catalog (Mirlyn) to find which (if any) UM library has the journal and what the call number of the journal is. Use a title search (t = beginning of exact title of the journal). If the article is not in the UM libraries’ collections, then current UM faculty, staff, or students may request a copy of the article via InterLibrary Loan.
Sample Beilstein journal citation:
Ref. 1 5507850 ; Journal; Hirao, Toshikazu; Mori, Makoto; Ohshiro, Yoshiki; JOCEAH; J. Org. Chem.; EN; 55; 1; 1990; 358-360.
This indicates that Reference 1 is
- article number 5507850 in the database
- a journal article
- the three authors are Hirao, Mori, and Ohshiro
- the CODEN (a standard acronym/code for the journal name) is JOCEAH
- the abbreviated journal title is J. Org. Chem.
- the journal is in English (EN)
- the article is in volume 55, issue number 1, pages 358-360, and published in 1990.
Use a journal abbreviations reference book to lookup the abbreviation as Journal of Organic Chemistry, then search Mirlyn by Title Begins With ... for journal of organic chemistry) to see which library has that title and the volume/issue you need.
Citing information you find
If you go to the original article to find the information you need, then you should cite the original article [example: Hirao, T. et. al. J. Org. Chem. 55, 358-360 (1990)] rather than citing the Beilstein database/handbook.
If you make direct use of information directly from the database (e.g. the melting point is listed directly), be sure to note that the original article was not looked at, e.g.
Hirao, T. et. al. J. Org. Chem. 55, 358-360 (1990) as reported in the Beilstein Crossfire database, 4th Quarter 2002 update.
Use an appropriate citation format according to whichever style guide you are using, e.g. the ACS Style Guide.
Relationship of Online Database to print Handbook
You may have a reference to the print Beilstein Handbook of Organic Chemistry. If you know the structure of the substance being referred to, it is sometimes easiest to just do a structure search for that substance. When viewing an answer or using the Fact Editor, the print handbook reference is in the Beilstein Reference (SO) field; example:
| Beilstein Reference (SO field) |
What it means |
| 5-24-03-00290 |
5th Supplement (call number QD251 .B4223 1942 Suppl.5), vol. 24, part 3, p. 290 |
| 2-07-00-00846 |
2nd Supplement (call number QD251 .B422 1942 Suppl. 2), vol. 7, p. 846 |
FAQs & Tips
Online Help & Additional Documentation
- Context-sensitive online help is available when Commander has been installed directly on your own machine (not available thru the UM Library Terminal Services version). Choose Contents under the Help menu.
- Additional documentation & product info at http://www.beilstein.com and at links on University of Wisconsin Library download page http://minerva.library.wisc.edu/
Author Searches
Use the author: contains Lastname in the EDS Bibliographic Data Form (or the equivalent Fact Editor format “Lastname*”) to search for article authors, then check through the results to eliminate unwanted answers.
- Example, for E.J. Corey, use: AU = corey*
This finds all occurrences of the last name corey regardless of first name, initials, etc (even though it may also retrieve last name = coreyi or david r. corey articles). Why do it this way? Searches on “corey, e*” will miss cases where the first name/initial was not entered into Beilstein/ Gmelin or where a comma was not used. Note: initials, commas, and firstnames are entered inconsistently into the database. Only “corey” may be listed even though the original article listed a firstname and sometimes commas are omitted.
Searching for specific double-bond stereochemistry
- Use the Structure Editor to draw the structure.
- Use the pencil-tool to click on the double-bond you want to specify exact stereochemistry for. You’ll know the cursor is in the right place when a small “B” appears on the pencil.
- Choose “double-steric” from the list of bond-types on the right side of the Bond Attributes window.
- Before submitting the search, change the default pulldown Stereo setting Off to Absolute, Relative or Racemic in the main window to the right of the structure search box depending on your requirements.
- Continue with the rest of your structure drawing / search as usual.
Do all the substances in Beilstein have a CAS Registry Number listed?
No. You may have searched for your compound using a Chemical Abstracts Registry Number and the system didn’t find any answers. When this happens, also try a structure or name search. Molecules added to the database since the mid 1990s may not have a CAS Registry Number listed, if the CAS registry number is new since 1993-4.
Include or exclude isotopically labeled atoms in a search
Starting with Commander Version 6, the default setting is to exclude isotopic variations from search results. To allow isotopic variation at any/all atoms of the substance, check the Allow: Isotopes box to the right of the Structure Editor section of the main window.
To search for isotopic labeling at specific atoms:
1. Use the Structure Editor; click on the specific atom that you want to specify as isotopically labeled.
2. In the resulting Atom Attributes window, choose the desired specific atomic mass (note: NIM = Naturally-occurring Isotopic Mixture - NIM) from the pull-down list in the Mass box.
3. To search for specific labeled hydrogen atoms, they must be explicitly drawn and set to the desired mass/isotope.
Substances Isolated from Natural Products
Choose Fact Editor (Table) under the Easy Data Search choices. The Isolation from Natural Product (INP) field lists plant or animal names (species name or sometimes a common name, e.g. tobacco) that a substance has been reported to be isolated from, e.g. INP hypericum
will find any reports of substances isolated from various species of the hypericum genus, which includes St. John’s Wort.
Substructure from any natural product: A combination search of
- a Fact Editor (Table) search using Field Name INP and a blank Field Value with
- a Structure Editor substructure search (e.g. a benzofuran ring with unlimited substitution on the furan ring)
will find substances in the database, which have been isolated from any natural product and contain htat substructure. It will not include any cases where a substance has only been produced solely by chemical synthesis. Examining the INP field in an answer will indicate what species the substance was isolated from.
Spectra availability
Not every substance listed in the database has spectral data or any other particular type of data reported for it. There are over a hundred different possible data fields. Some substances may have only one or two properties reported, but others may have many more properties reported. To retrieve only those answers that have the type of data you are looking for (in this case spectra), try this strategy:
Combination search of
- a Fact Editor search using only a Field Name (SPE for any spectra type, or IR, NMR, or UV, etc. for specific types of spectra) with the field Value left blank AND
- a Structure Editor substructure search (e.g. a benzene ring with one halogen and a 3-alkyl group)
will produce only the substances in the database matching that substructure which have data reported for that type of spectra, i.e. it won’t find any substance unless there is spectral data reported for it. Note: this technique works for only a few data fields, not all.
How to draw a nitro group (and other functional groups)
Use the Structure Editor with the default settings. Draw the nitro group (RNO2) using a nitrogen with two double-bonded oxygens attached. Using single nitrogen-oxygen bonds will NOT retrieve the desired answers containing the nitro grouping.
Tip for other functional groups: if uncertain about how to draw a bond (single or double, with charges or without) try using an un-specified bond type (Bond attribute = Any), then browse the results to find the one you are interested in, then re-submit the search using the revised bond type.
How to exclude/include radicals, ions/charges, and multi-component substances
Starting with Commander Version 6, the default setting is to exclude charge, radical, and multi-component variations from search results. To allow variation at any/all atoms of the substance, check the appropriate Allow: box to the right of the Structure Editor section of the main window.
To allow variations at specific atoms:
- Use the Structure Editor; click on the specific atom.
- In the resulting Atom Attributes window, choose the desired value for the specific attribute, e.g. charge = +2
Heterocyclic compounds or enols (searching for tautomers)
Starting with Commander Version 6, the default setting is to include tautomer variations (typically isomers where a proton and double bond have shifted positions) in the search results. This is important in obtaining more complete retrieval for many heterocyclic ring systems. If too many extra answers appear, tautomers search may be turned off using the checkbox to the right of the Structure Editor section of the main window.
How to enter a Molecular Formula
Remember that a molecular formula MUST have the elements in a standard order, called Hill order. First listed is carbon (C), then hydrogen (H), then the rest of the elements in alphabetical order.
Examples: OK not OK
C13H17BrClF3 F3CCClBrCH2 or C13H17F3BrCl
C3H8S H3CSCH2CH3 or H8C3S
German chemical terms
Some of the older records contain German terms. A brief German-English dictionary of commonly used chemical terms is available at http://www-sul.stanford.edu/depts/swain/beilstein/bedict1.html
Gmelin
Find spectra, reactions and chemical, physical & biological properties of inorganic & organometallic chemical substances, including alloys, ceramics, coordination compounds, glasses, minerals, & polymers
What is Gmelin?
A chemical database containing:
- chemical identities for over 1.6 million inorganic and/or organometallic chemical substances (structure, formula, name, registry numbers, etc.), including some polymers (11,000+), alloys (55,000+), minerals (3200+), zeolites, and ceramics/glasses (14,000+).
- chemical, physical and biological properties of those compounds
- over a million chemical reactions
- literature references to the substances, properties and reactions
- coverage of 1772 - current chemical literature, with a partial gap for 1995-99 (being worked on). Includes 8th ed. of the Gmelin Handbook and about 112 inorganic, organometallic, physical chemistry, and physics journals since 1984.
A Gmelin substance must contain at least one of the following elements/types. As long as the substance contains one of the listed elements, it may also include elements that are not on the list.
| Any actinides |
Any noble gases |
B, Al, Ga, In, Tl |
Po, At |
Sb, Bi |
| Any lanthanides |
Any transition metals |
Ge, Sn, Pb |
Be, Ra |
Fr |
What is Gmelin good for?
- search by chemical structure - in many cases, you don’t need to know the chemical name [use the Structure Editor]
- search by chemical reaction – specify product(s), starting material(s)
- hyperlinks between compounds, literature citations, and reactions
- search by chemical name, formula, property, etc. [use Fact Editor]
- search for properties and reactions of isotopically labeled compounds
- search for radicals, ions, and other variants of a molecule
- find original literature references to properties and reactions
- broad coverage of the inorganic/organometallic chemistry journal literature. For a list of journals covered: http://www.beilstein.com/support/journal_gmelin.shtml
What doesn’t Gmelin cover?
- Chemical patent literature after 1977.
- Organic compounds (try the Beilstein database instead)
- Substances that do not contain one of the “Gmelin elements” (see above list).
- Some 1995-1999 articles in covered journals. Indexing had ceased for a few years. This backlog has been worked on since 2000 and will eventually be caught up.
How do I get to Gmelin?
- Gmelin CrossFire uses the same search software as Beilstein does. Version 6 allows one to search both Gmelin and Beilstein simultaneously, although some search features (the EDS forms) will not be available in this case.
- Check the box in the “Select Database” section in the upper left of the main screen. Note: the code GM0704 would stand for the 2007, 4th quarter data release.
Differences between Gmelin and Beilstein Searches
Drawing Conventions
Coordination bonds in coordination compounds are always drawn as sigma bonds, e.g. a ferrocene will be drawn as having 10 individual Fe-C bonds, one to each of the carbons in the two cyclopentadienyl rings.
Searching for Substances in Gmelin
Not all compounds in Gmelin have a structure (i.e. connection tables represented as drawings) listed. Examples include simple salts (NaCl), alloys, or polymers. You CANNOT retrieve data on these substances using a structure query.
It is often more effective to use the Fact Editor to search for Gmelin compounds. A molecular formula search, sometimes in combination with other datafields will often be practical, as there tend to be fewer compounds in the database having a single formula than there are in Beilstein.
Some inorganic compounds may be represented in the database in multiple forms (e.g. crystalline forms, alternate bonding representations, etc.), so structure searching on a particular way of representing a structure may not retrieve some data. For example, a metal-cyclopentadienyl compound may be represented separately as a two-component cyclopentadienyl complex or as a single-component metal-bonded cyclopentadienyl compound.
- To find a specific substance in Gmelin, a molecular formula (MF) Fact Editor search will often give more comprehensive results than a simple structure search.
- For more comprehensive retrieval in substructure searches, draw any component that might remotely be considered a separate ligand separately.
Fact Editor
Field Names are different from and more numerous than those used in Beilstein. Always use the “List Values” shortcut button to check the exact form of Field Name or Field Code.
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