Chemistry 184/284: Chemical Literature

Lecture 5: Beilstein and Gmelin

Beilstein and Gmelin

• These two series represent attempts to gather into data collections every piece of significant information in the organic and inorganic literature, respectively.
• While both began in the 1800's in Germany, they take significantly different approaches to organizing their data.

Beilstein Handbook of Organic Chemistry

(Ref QD 251 .B4)

• Begun in 1880's by Friedrich Konrad Beilstein.
• Went through three complete editions before the current series began in 1918.
• Most of Beilstein is in German; the current (5th) supplement is in English.

Organization of Beilstein

• Beilstein attempts to cover the entire organic chemical literature published within a given period:
• When dealing with such a huge volume of literature, the organization of such a work is necessarily complex.
• The Beilstein handbook is divided chronologically, then, within each period, divided by a chemical classification scheme.
• Chronological Organization
  • Hauptwerk (H) "Basic Series" Up to 1909
  • Ergangzungswerk (E) "Supplement"
    • E(I) - 1910-1919
    • E(II) - 1920-1929
    • E(III) - 1930-1949
    • E(IV)- 1950-1959
    • E(V) - 1960-1979
  • E(III) and E(IV) overlapped in production, so their heterocycle volumes were merged.
• Organization by Chemical Class
  • Beilstein records are for individual compounds. To facilitate browsing, related compounds are grouped into "volumes" (which may occupy several physical books).
  • The classification rules remain constant for all supplements, so if a compound is found in Vol. 22 in (H), it's in Vol. 22 in all the supplements as well.

Details of Chemical Class Organization

• To use Beilstein in print, it is necessary to know how compounds are placed into volumes.
• While there are indexes for the Handbook, they are divided by volume as well!
• The three largest divisions are:
  • Acyclics (e.g. methane, ethane) in Volumes 1-4
  • Isocyclics (e.g. cyclooctane, benzene) in Volumes 5-16
  • Heterocyclics (e.g. pyridine, THF) in Volumes 17-27
• Within the three broad groups, compounds are assigned to volumes based on the functional groups present, such as: -OH, -COOH, =O, -NH2
• In heterocycles, the number and type of ring heteroatoms is also relevant.
• See the table below for a complete summary.

Contents of the 27 Volumes of the Beilstein Handbook

Organization within Volumes

• Within each volume, compounds are arranged first in order of increasing unsaturation, e.g. ethane before ethene before ethyne.
• Then, by increasing molecular size, e.g. ethane before propane before butane.
• Then by:
  • increasing degree of substitution,
  • increasing "size" of substituents.

Choosing Between Possible Volumes

• If a compound might be placed in two or more possible volumes (e.g. it contains both a heterocyclic and an isocyclic component), then additional rules apply.
• Principle of Latest Entry -- If a compound might be located in two or more places, it will appear in the highest numbered volume of the possibilities.
• Parent Compounds vs. Derivatives -- Certain types of compounds are considered parent compounds; others as derivatives. A derivative is listed following the parent compound from which it is derived.
• The trick then becomes how to identify which is the "parent" for the compound in question.

Identifying Parent Compounds

• Three rules are used to identify parents vs. derivatives.
• Non-Functional Substitution
  • Certain groups are always considered derivative:
    • Halogens (F, Cl, Br, I)
    • Nitro (NO2), Nitroso (NO), Azido (N3)
  • The parent compound is determined by replacing the group with H or OH, depending on chemical common sense:
    • CH3CH2Cl --> CH3CH3 ...but...
    • CH3COCl --> CH3COOH
• "Chalcogen Substitution"
  • Sulfur, selenium and tellurium are "replaced" by oxygen to find the parent compounds, except in the oxyacid groups (e.g. -SO3H, -SO2H)
    • Me2S is considered a derivative of Me2O
    • Thiophene is considered a derivative of furan.
• Functional Substitution
  • Whenever two "pieces" of a compound are connected by a heteroatom (O, N, S, etc.), break it up by formal hydrolysis.
  • The resulting fragment with the "latest entry" becomes the parent compound of the starting compound. Example:
    • MeCOOMe --> MeCOOH + MeOH
    • Acetic acid is Vol.2; Methanol is Vol. 1
    • Therefore Methyl acetate is Vol. 2.
  • Another example: Feropolone (C24H32O6)
    
    
    • Step 1: "Hydrolyze" at the oxygen in the bridging chain.
      
      
    • Step 2: Check which key features each fragment has
      • Left: Isocycle with oxo, two hydroxy groups --> Volume 10
      • Right: Heterocycle with one ring O, oxo and hydroxy groups --> Volume 18
    • By Principle of Latest Entry, the fragment which appears in Volume 18 controls the entry for the compound as a whole.
    • Step 3: Go to Volume 18 and check the appropriate name or formula index.
  • For more detailed description and more examples, see How to Use Beilstein, SEL Ref Area QD251.B43 B45 1978.
• Remember to always use the easy way when you can! Many sources, including the Aldrich Catalog, CRC Handbook, HODOC, Merck Index, etc. give references to the Beilstein Handbook and their indexes are easier to use! Note that they will usually only give the reference for one of the supplement series - but once you have the basic volume, tracking the compound to its other Beilstein references is easy.

Beilstein Record Content

• A compound record in Beilstein will cover all the published data on the compound within the appropriate period.
• Therefore, the amount of information in a given compound's record is dependent on the amount of research done; old data is not repeated.
  • Example: Pyridine , in E(V) 1960-79, has a 19 page entry, plus an additional 38 pages of salts and addition compounds.
• Some physical data -- mp, bp, density, etc. -- is given directly.
• Preparations are summarized.
• References only are given for some info.
• Remember that in H-E(IV), all text is in German. Also, in those volumes, journal abbreviations are in Beilstein style, e.g. B for Chemische Berichte, Am. Soc. for JACS
• If you need help with the German terms/abbreviations, see the Beilstein dictionary at http://www-sul.stanford.edu/depts/swain/beilstein/bedict1.html. A print copy is available at the SEL Reference Desk.

Beilstein Today

• The Beilstein database is still being compiled, but now under the auspices of Reed-Elsevier, the giant European publisher.
• The print edition of Beilstein is no longer being published; the Fifth Supplement was the last in that form.
• However, data from 1980 through the present is still being compiled for the electronic version of Beilstein.
• Today, data is being gathered from over 175 journals in organic chemistry.
• In addition to the traditional physical and chemical properties, Beilstein now indexes pharmacological and ecological properties of compounds. See the Beilstein Data Structure poster for a full list of properties indexed.

The Many Faces of Beilstein

• Currently, incoming data from the organic literature is being published in several forms:
• Beilstein Online
  • Available on STN online system. Note that the database summary sheet was last updated in 2006, and does not reflect the transfer of the Beilstein database to Elsevier when Elsevier sold MDL, Inc. to Symyx.
  • Searchable by chemical name, numeric data and chemical structure.
  • Includes checked data from H-E(IV), unchecked data from E(V), plus new data from the current literature.
  • Online versions of Beilstein have the advantage of crossfile searching with other chemical information files (e.g. Chemical Abstracts (CAPLUS), CA Registry File).
• Beilstein Abstracts, Beilstein Facts, Beilstein Reactions
  • On the online vendor DIALOG, the Beilstein database is split into three parts, Beilstein Abstracts, Beilstein Facts and Beilstein Reactions. The first contains bibliographic information (and, from 1980, titles and abstracts) for the sources from which Beilstein data is derived. The second contains data organized by compound, and the third reaction data for those comounds. There is no structure searching capability at present.
  • Beilstein Abstracts is also available as a separate database on STN.
• CrossFire
  • CrossFire is a subscription only electronic version of the Beilstein database, containing all up-to-date Beilstein data.
  • Searchable by names, structures, data, with special features for searching reactions, cross-references. Abstracts of papers published since 1980 are available. The database currently contains: over 8 million compounds, over 9 million reactions, over 35 million associated chemical property and bioactivity records, and over 750,000 abstracts and titles indexed from the primary organic chemical literature since 1980.
  • The CrossFire system is very fast, and very powerful.
  • Uses its own client software, CrossFire Commander (now in Version 6 for the Mac and Version 7 for Windows.) Can download data directly to Microsoft Excel with a special add-on.
  • We will cover CrossFire Beilstein in detail in the next lecture.
  • The CrossFire interface for Beilstein will be dropped by Elsevier at the end of 2010.
• DiscoveryGate
  • DiscoveryGate is a Web-based product from Symyx, oriented toward scientists in the pharmaceutical industry, though MDL is now making a big push for academic customers. It provides integrated access to Beilstein, Gmelin (see below), as well as a large number of other databases of synthetic methodology, pharmacology, metabolism and toxicology, chemical safety and chemical source information. It is designed to integrate with MDL's ISIS chemical database system and other MDL products. It is now available for Windows 2000 or XP and Mac OS 10.4 or higher computers. (Note: The DiscoveryGate site above only works with Internet Explorer V.6 or higher on PC's or Safari on the Mac.)
• Reaxys
  • Reaxys is a newly-released Web interface for the Beilstein, Gmelin (see below) and Patent Chemistry databases from Elsevier. In Reaxys, the databases are integrated.
  • It supports both Windows and Mac OS X systems (requiring the Java Runtime Environment to be installed.)
  • It has all the searching features of the CrossFire Commander client, with new tools to facilitate the development of multi-step synthetic pathways.
  • It is not yet known whether the University of California will migrate to the Reaxys interface in 2010.

Gmelin Handbook of Inorganic and Orgamometallic Chemistry

(Ref QD 151 .G52)

• Begun in 1817 by Leopold Gmelin, it went through seven editions before the current on began in 1924.
• Originally focused on classic inorganic; organometallic was recently added to the title to reflect the vast growth of the latter field.
• Volumes before 1980 are in German; volumes since 1980 are in English.
• The future of the Gmelin Handbook had been in doubt; no new volumes have been published since 1996 because of a cutoff of funding from the German government. A handful of volumes which were already in the editorial pipeline are expected to appear shortly.
• Late in 1999, an agreement was reached between the creators of the Gmelin database, and Reed-Elsevier, the owners of the Beilstein database, to restart Gmelin, including coverage of the "missing years". Gmelin is now once again being produced, and the "missing years" are being filled in, in the CrossFire Gmelin database. Print Gmelin, like its Beilstein counterpart, is dead.

Organization of Gmelin

• Gmelin published print volumes entirely according to editorial choice, reflecting mainly the volume of research in a given area since the last such volume.
• Gmelin does not attempt to cover chronological periods in a block. Each volume is devoted to a particular aspect of the chemistry of a single element, with a specified closing date. Examples:
  • Magnesium has had eight volumes published -- none since 1952.
  • Iron has had over 30 volumes on its organometallic chemistry since 1974, with eleven volumes on ferrocenes alone!
  • Uranium has special volumes on nuclear fuel behavior, extraction and purification.
  • Under oxygen: water desalination

Choice of Primary Element

• Gmelin uses its own Principle of Latest Entry. Whichever is the "latest" element in the compound is one chosen.
• The general order of preference is:
  • "Noble gases": He, Ne, Ar, Kr, Rn in one volume.
  • Hydrogen
  • Oxygen
  • Nitrogen (except ammonium compounds, see below, between K and Rb)
  • Halogens: F, Cl, Br, I, At
  • Group VIA: S, Se, Te, Po
  • Group VA: P, As, Sb, Bi
  • Boron
  • Silicon
  • Group IA: Li, Na, K, NH4+, Rb, Cs, Fr
  • Group IIA: Be, Mg, Ca, Sr, Ba, Ra and IIB: Zn, Cd, Hg
  • Group IIIA: Al, Ga, In, Tl
  • Sc, Y, Lanthanides
  • Group IVA: Ge, Sn, Pb and Group IVB: Ti, Zr, Hf plus Th
  • Group VB: V, Nb, Ta, plus Pa
  • Group VIB: Cr, Mo, W, plus U
  • Mn
  • Group VIII: Fe, Co, Ni, Ru, Rh, Pd, Os, Ir, Pt
  • Group IB: Cu, Ag, Au
  • Tc, Re, transuranics
• Volume Examples:
  • NaCl -- Sodium is Vol. 21; Chlorine is Vol. 6. Therefore, Vol. 21
  • Ferrocene - Carbon is Vol. 14; Hydrogen is Vol. 2; Iron is Vol. 59. Therefore Ferrocene appears in Vol. 59
  • (NH4)2Cr2O7 -- Chromium is Vol 52; Ammonium gets its own volume, 23: Oxygen is Vol. 2. Therefore: Vol. 52.
• The printed version of Gmelin ceased publishing in 1997.

Indexing in Gmelin

• Gmelin has comprehensive formula indexes, in three parts: 1924-74, 1974-79, and 1980-87. The index for 1988-1992 is now being published.
• Formulas are listed alphabetically using an inverted form of Hill notation
  • If no carbon is present, all elements in alphabetical order: e.g. ClNa, H2O4S
  • If carbon is present, then all other elements first, followed by carbon and hydrogen if any.

Electronic Forms of Gmelin

• Gmelin is available online commercially from STN. It is searchable by names, formula, physical properties and structures. Note that this version of the file has ot been updated since 1997. Note, too, that the database summary sheet was last updated in 2006, and does not reflect the transfer of the Gmelin database to Elsevier when Elsevier sold MDL, Inc. to Symyx.
• Gmelin is also available in client-server form on the CrossFire system with similar search capabilities to CrossFire Beilstein.
• The database contains 1.6 million compounds, 1.3 million structures, 1.3 million reactions, and 900,000 citations, including titles and abstracts from 1995. CrossFire Gmelin is fully searchable by structures, substructures, and reactions. The data are indexed from 62 journals. See the Gmelin Data Structure for a full list of data types indexed.
• The CrossFire Gmelin database, like Beilstein, is a part of Symyx's DiscoveryGate system, as well (see above.)
• CrossFire Gmelin also is (or will be soon) part of the Reaxys system as well (see above.)
• Neither electronic form contains the full text of the old printed volumes, but they instead concentrate on specific types of data (physical data, preparations, etc.) In addition, while more than 99 % of the material from the original Gmelin Handbook up to the year 1975 is in CrossFire Gmelin. Some is omitted: for example, some organic-related material was folded into CrossFire Beilstein (a matter of definition) and some volumes that do not deal with chemistry were not included, like one about Geology of Iron.
  The handbooks published after 1975 are not included in CrossFire Gmelin, however the excerpts of the 120 most important journals (Year 1976 to 1995) are in the database. This would be the source of the handbooks that would have made their way into CrossFire Gmelin anyway, so there is no loss (according to the publishers). Data from 1995-2001 was added by the original database creators, and since 2001 Elsevier Science Publishers is responsible for the data, in partnership with the German Chemical Society (Gesellschaft Deutscher Chemiker e.V., GDCh for short).
• Net result: For Gmelin, much more than for Beilstein, access to the printed volumes is still useful. The UCSB Library's collection in print contains much of the pre-1980 material, and a complete run from 1980 to 1991.
• We will cover CrossFire Gmelin in detail in the next lecture.

This page created by Chuck Huber (huber@library.ucsb.edu).
Updated: 01/19/10 01:12:01