Landolt-Börnstein
Numerical Data and Functional Relationships in Science and Technology
New Series / Editor in Chief: W. Martienssen
Index of Organic Compounds
Subvolume K (Supplement to Subvolumes B, E and H)
Compounds with 8 to 12 Carbon Atoms
Electronic Version
Editor: V. Vill
Authors: C. Bauhofer, G. Peters
A simple introduction into the abilities of the Landolt-Börnstein Organic Index
The database-tool SciDex is very easy to use, and most functions should be self-explanatory. As a
short information about what can be done, read this document, for more detailed informations
about single topics, refer to the help-file IndexAI.hlp. In all parts of the program it is possible to
simply press the "F1"-key and get context-sensitive help pertaining directly to the currently active
window.
What is ...
... SciDex?
... Landolt-Börnstein, Index of Organic Compounds?
... a search?
... an extraction?
... a comparison?
How To ...
... start the program
... print information of a compound
... see more and detailed information
... search a compound by CAS-RN
... search a compound by Chemical Structure
... search a compound by Name
... get a single compound out of a list
... extract references from compound list
... print references
... get a single reference out of a list
... unclutter the screen
... search compounds by keyword
... compare compounds
... make a compound list from a comparison
And finally ...
What has not been mentioned here?
What is SciDex?
SciDex is a newly developed object-oriented database system basing on the three main record
types of compounds, properties and references. All of these main record types have lots of
subrecords, so has for example a compound a drawing of the chemical structure ("connectivity"),
several names, etc., and a reference has for example an author, a source, keywords, etc.
All records are crosslinked. e.g. a compound can have several properties and references and all of
the main record-types can be searched via each of the other record types.
(See also, "What is an extraction")
What is Landolt-Börnstein, Index of Organic Compounds?
This index is a guide to organic compounds which have material constants of general interest
described in the Landolt-Börnstein / New Series. Compiled are volumes containing molecular
constants, density, surface tension, dielectric constants, refractive index, vapor pressure, phase
transition temperatures and transition enthalpies, spectroscopy, microwave, NMR, structure and
viscosity data. This database contains a cumulative index of all compounds contained in the
subvolumes A through I of the organic index.
What is a search?
There are specific search-functions for the three main types of records (compounds, properties
and references). A search creates always a hit-list, which can be used for further operations, e.g.
print, combine lists, save. Each main type of records has its own class of list, but it’s possible to
convert one type of list into another by using the extract-functions.
What is an extraction?
To convert a list of e.g. compounds into a list of associated properties, or associated references,
an extraction can be used. For example if a compound has three properties recorded somewhere,
the ExtractProperties function can be used to create a list of these three properties, which is then
available for further operations.
What is a comparison?
Scientists nearly always want to compare some things with others. So for example, how would a
melting temperature change, when a methyl-group is substituted with the next homologue, an
ethyl-group. This Organic Index contains only two simple forms to create lists of pairs from a
comparison: Compare by Name and Compare by Elements.
How to start the program
Start the program using the file "INDEXAI.exe", the program will always start with a compound
window as active window.
The database is very easily browsable, using the navigation bar
on top of this
window. This window is of course not a search, but just a "window into the database". SciDex can
display many windows concurrently at the same time. Most functions of menu-entries apply only
to the currently topmost window on the screen, e.g. print, or extract.
How to see more and detailed information
In some cases, like in the above displayed window for the reference (lower right corner), the
information in the window is only partially shown. In these cases, a "magnifying glass" can be
applied by pressing the right mouse-button with the cursor over the area which one wants to see
complete. For the reference in the above case:
While
pressing
the right
mousebutton
the detailed view is visible
How to print information of a compound
To print either all, or part of the information in the current window, there are two possibilites.
from the shortcut bar and second, one can choose from the
First, one can click on the button
menu File → Print:
In the following dialog-box, one can then choose, which information shall be printed, and which
isn't wanted and shall be omitted.
For Windows of the type "Single Compound", "Compound List" and "Compound Pairs" the
above selection is shown. The first four boxes are referring to the content of the four parts of the
window, the "First page" and "Last page" refers to pages in the window.
To start each compound on a separate sheet of paper, select the last checkbox, "Each compound
starts on a new page". If this box is unchecked (default), then multiple compounds will be printed
directly one after the next, with as many on one sheet of paper as will fit.
How to search a compound by CAS-RN
There are four different possibilities to search for Compounds:
1)
by Registration Numbers
2)
by Drawing of the Chemical Structure
3)
by other Compound identifications
4)
by extracting lists of References or lists of Properties
A Chemical Abstracts Number is a registration number of compounds, so one should start with
Search → Registration Numbers ...
... then continue by selecting Compounds: CAS-RN in the dialog-box ...
... and typing the searched for CAS-RN in the dialog box.
Added bonus: The number can be typed with at most one mistake, but then has to be specified as
unsecure CAS-RN, with a tilde (~) as first character, e.g. "~1493-15-6". The tilde indicates that
exactly one (or none) of the digits may be wrong.
One other special character is allowed, the "*" alone, for searching all compounds that have a
CAS-Number registered. To find all compounds that have no CAS-RN, type "*" here, and invert
the hitlist afterwards (via Search → Combine Lists)
This particular search "~1493-15-6" produces a list with three hits referring to the CAS-RNs
1493-13-6 (changed digit), 1493-15-8 (changed digit) and 149-31-5 (removed digit):
A 'normal' search without the tilde in front of the number would of course not allow a mistaken
digit in the CAS-RN, and then produce for the above number 1493-15-6 no list, as this CAS-RN
does not exist.
How to search a compound by Chemical Structure
The next possibility, and perhaps the most flexible of all, is to search for all compounds which
contain a particular chemical structure, either as a partial or as a complete match.
Start with Search → Structure Drawing ...
... then continue by drawing a structure in the new window by simply clicking into the drawing
canvas for each atom (carbon-atom and single-bond is the default setting); click the right mousebutton when finished with drawing:
For detailed information on how to draw and modify a structure in this window, please refer to
the helpfile (press F1 in SciDex, while this window is active). Of course it is also possible to take
a chemical strcuture drawn in a separate chemical drawing program, like ChemWindow,
ChemFrontier or ChemDraw and copy the structure via clipboard into the drawing canvas, using
the function Edit → Paste Image.
The checkbox "chain is chain" at the bottom prevents the propyl-chain in the
above structure to be interpretable as part of a ring-system. If unchecked, then
for example the structure to the right will also be among the compounds found:
The checkbox "exact" allows to find an exact structure, and will disable the usual substructure
algorithm, when checked, i.e. the search will only find one compound or none. More than one
compound can be found, if there are deuterated derivatives of the same compound in the
database.
How to search a compound by Name
Compounds can be searched by complete or partial names using the "Search Compounds" dialog
box, the search for names can also be combined in the same dialog box with a search for a
molecular formula and/or a search for a particular molecular mass or a range of masses.
Start with Search → Compounds ...
... then continue by filling the appopriate fields in the following dialog box
In this example, we are interested in all compounds that contain the fragments "cyclo" and
"pentane". The order in which these parts appear in the names are irrelevant. So this search would
find among others: "cyclopentane", "cyclo-pentane", "pentane, cyclo-" (different variants to
name the same compound, all of which would be found by this search) but also cyclohexyl
pentane; bicyclo[1.1.1]-pentane; 1,3-diazacyclopentane; and lots of others.
The search for names will go through all names of each compound, even if the subsequently
shown hitlist window shows only the first name of the compound, which does not necessarily
need to contain the searched-for name parts. See the following example, in which the compound
"housane" has the alternative name bicyclo[2.1.0]pentane.
Note: when specifying an "exact name" (checkbox to the left), then the names textbox may not
contain multiple parts, but must be typed as one would expect to find the name in the database
How to get a single compound out of a list
The search result from the above example looks as follows:
Now to find out, why "housane" was found in a search for cyclopentane, and to get the full
information on this compound, just doubleclick on the compound identification number [3081]
and a new Single Compound window will be opened with this compound.
The names are contained in the scrollable window to the upper right. Scroll down and the
names will be shown:
How to extract references from compounds
To get a list of all the literature references in which a particular compound is mentioned, there are
from the shortcut bar and second, one can
two possibilities. First, one can click on the button
choose from the menu Search → Extract References:
The result will be a list of the three references of the volumes II/6, II/14a and IV/20a, in
which data of this particular compound are stored.
How to print references
This works just like "print compounds", only that the dialog-box looks slightly different. To print
either all, or part of the information in the current window, there are two possibilities. First, one
from the shortcut bar and second, one can choose from the menu
can click on the button
File → Print (see way at the beginning of this document). The dialog-box for choosing what to
print looks as follows:
"Reference details" refers to what one sees in the Single Reference window (see below) and what
is also shown when the magnifying function is invoked (see way at the top of this document)
"Reference summary" is the two-line display that will be shown in the Reference list window, and
is present in the Single Compound window as well. The only difference on printing this is, that it
will not be cut off at the end of the page like on the screen, but it will be wrapped around to the
next line, if the entry is too long.
For example, double-click on the line II/14a and you get the following:
How to unclutter the screen
After some time of working with the database, it can happen that the screen becomes fairly
crowded. The maximum number of windows that can be displayed at the same time is somewhere
around 20, which can be quite a lot. To clean the screen up, one can instead of closing each
window separately choose the menu-entry Window → Close all Windows ...
... and the result will be a virginally clean screen...
How to search compounds by keyword
As visible in the screenshot of the previous example, the "Keywords" which are stored in the
database belong to the Reference, i.e. to search for all compounds pertaining to a particula
keyword, one needs to search for References first, and then extract all Compounds from those
References.
So, start with Search → References:
The dialog-box for Search References will appear:
The Keywords are one of the "Other Fields", so choose in that bombo-box the entry Keywords,
and a list of keywords recorded in the database will be shown in the list-box to the right.
If you are interested in, say, Refractive Indices, search in the listbox for that term and click it, and
the term will be copied to the text-box to the left. If you are searching for multiple topics, just
click the others as well, then choose „and“ or „or“, to define an inclusive or exclusive search.
The result of this search is a list of four references:
To get the list of all compounds of which the properties are described in these four references,
choose either Search → Extract Compounds from the menu, or click the icon
from the
shortcut bar to get the list of 8440 compounds which are described in volumes III/38 and VIII/5.
How to compare compounds
There are two methods to create a list of pairs of compounds:
1)
Compare Compounds by exchanging one chemical element by another
2)
Compare Compounds by exchanging parts of the name
In both cases, a list of compound pairs will result, where both compounds of a pair are identical,
with the exception of the difference specified in these dialog-boxes.
First example, Comparison "Cl ←→ Br" (List A): exactly one Cl-atom is replaced by a Br-atom
(in the search: "Way of Replacement: Single"). The compound CHBr3 for example is not part of
this list, but it would be, if "Way of Replacement: Multiple" (one or more atoms exchanged) or
"Way of Replacement: Complete" had been chosen.
For the second example (List B) the part "hex" is substituted by the part "oct" in the Compound
name, so that methylenecycloHEXane and methylenecycloOCTane create a pair of compounds.
Likewise it would make a pair of HEXatriacontane (C 36) and OCTatriacontane (C 38).
For comparison of the names the algorithm uses all names of a compound, even if the pairwindow shows only the first name. To get all names, doubleclick on the compound in question
and use the scrollbar in the top-left part of the Single ompound window.
How to make a compound list from a comparison
If the list of compound-pairs shall be made into a regular list of compounds, which can then be
used to combine it with other compound lists, choose the function Search → Extract Compounds
from the shortcut bar. You will then see the following
from the menu, or click the button
dialog box:
Here you can choose, whether to make a compound list only from the first row of compounds (In
the examples above the compounds with more chlorine, or with HEX in their name, respectively),
or to create a list from the second row, or to include both in one list.
What has not been mentioned here?
Lots of things probably. Most things should be more or less self-explanatory, however, and for
every window there is an entry in the help-file. Whenever something does not seem clear, press
from the shortcut bar and you should find the information
the key F1 or select the help-icon
needed therein.