INTRODUCTION TO THE BEILSTEIN AND GMELIN DATABASES Margarete Bower Chemistry Library

BEILSTEIN HANDBOOK OF ORGANIC CHEMISTRY (In German originally)  Friedrich Konrad Beilstein (1838 – 1906)  Worked to collect all properties and reactions of organic compounds together in one book or set of books  Checked all data to determine if it was reliable  Last edition would fill more than fifty shelves

Database includes:  > 8 million organic compounds  > 5 million chemical reactions  > 35 million chemical property data  > 200 types of properties and information to search  References to the original reports in journal articles. Some as old as the 1770’s.

Types of compounds:  Organics  Organometallics (limited types)  Some biological molecules

Search for a compound by:  Structure  Exact match to structure  Substructure search  Chemical formula  Chemical name or part of a name

Search for reactions by:  Compound as a product  Compound as a reactant  Both product and reactant  Reactions using specific catalysts, reagents or solvents

Other types of searches:  Chemical or physical property  For example, compounds that melt at a particular temperature  Compounds that have reports of a particular property  For example, compounds that have been isolated from natural products  Compounds that have vapor pressure data reported  Combine structure and property search  For example, all the esters of acetic acid that boil above 120 degrees

Types of properties that may be reported: ( Not all compounds have all properties.)  Crystal structure, bond lengths, bond angles  Boiling point, melting point, triple point, critical temperature and pressure, vapor pressure  Thermodynamic properties: enthalpy of formation, fusion, and vaporization; free energy of formation; entropy; heat capacity  Dissociation constants (pKa)

Ionization energy  Optical data: index of refraction, circular dichroism  Electrochemical data  Spectra data: IR, NMR, UV-Vis, MS, Raman, luminescence, fluorescence  Isolation from natural products  Properties of mixtures  Pharmacological data  Safety data

Search by compound name  Not usually the best method because of many variations in the form of chemical names  Choose “Substance Identification” from the list at the left  Double click on “Chemical Name” or “Chemical Name Segment”  Use menu under “Relation” to choose the type of search  Is = exact match to your term  Contains = your term appears anywhere in the name  Type your search term in the box under “ Field content”  Click on “Start Search”

Search by molecular formula  Count all the atoms of each kind  List atoms in the order : C, H, all others in alphabetical order  For example:  C 8 H 10 N 4 O 2  C 7 H 6 BrNO, not BrC 6 H 4 CONH 2

Property search example:  Find a list of compounds that boil between 150 and 200 degrees and have data reported for the refractive index  Choose:  Boiling point > 150  Boiling point < 200  Refractive index (Leave Field Content box blank)

Structure search  Click on “Draw Structure”  In “Structure Editor” window select the pencil icon to draw or edit a structure.  Choose the type of atom, bond, and ring to draw from the row at the top.  Select the “erase” icon on the left and click on an atom or bond to remove it.  To change an atom or bond to another kind or to add a charge or change other properties of an atom, click on it. Use the window that opens.

 The computer fills in hydrogen atoms. You do not need to draw them all.  Transfer the structure to the search window by clicking on the red crossed arrows.  Check any options for the search conditions, if desired. The box at the bottom should say “Substances”.  Click on “Start Search”  When the “Search Status Report” window opens, click on “View” to see the answers.  Click on a structure to see the full record for the compound.

Combining structure and data search

Reaction search  Variation on a structure search  Draw a structure for a product or a reactant or both  Under “Editmode” from the top list choose “Reaction”  Use the cursor to put a box around the chemical structure  Click on either “Reactant” or “Product”  Transfer the reaction to the search window by clicking on the red crossed arrows  The box at the bottom should say “Reactions”  Click on “Start Search”

AUTONOM  Draw the structure of an organic molecule  Transfer the structure to the Autonom window by clicking on the crossed red arrows  Click on “Generate name”  Autonom generates a systematic chemical name

GMELIN HANDBOOK OF INORGANIC CHEMISTRY (In German orginally)  Leopold Gmelin (1788 – 1853)  Similar to Beilstein, but covers:  Inorganic compounds  Organometallics  Coordination compounds  Metals and alloys  Minerals  Elements

Search by:  Structure  Chemical formula  Chemical name or chemical name fragment  Reaction  Chemical or physical property

Properties that may be available: ( not every compound has all properties)  Crystal structure data, interatomic distances and angles.  Physical properties: boiling point, melting point, vapor pressure  Bond dissociation energies, ionization energies  Dielectric constant, dipole moment  Thermodynamics data: enthalpies of formation, fusion and vaporization; entropy; heat capacity