Help Page
Getting Help
Throughout The Merck Index*
Online website, we have tried to make all of
the information and search tools easy to understand and use. If you are having difficulties
when using the site, we hope that the following information will help you to resolve
your problem. But in the eventuality that you still need assistance we encourage
you to contact us directly by
email.
Where further assistance is required we are happy to provide support, by email,
telephone, or as interactive online training.
The Merck Index* Online Search Help
The Quick Search
The Quick Search interface is located on the home page for The Merck Index* Online.
This search is designed to allow you to perform a limited set of searches and get
results quickly. You can perform the following types of search:
- Name
- Molecular formula
- Molecular weight
Name
You can search The Merck Index*
Online using any text identifier, within
The Merck Index*
Online we have monographs relating to: Plants, Food additives/components,
Nutrients, Minerals, Proteins, Enzymes, Antibodies and commonly isolated complex
mixtures as well as a wide range of chemical species including polymers.
Examples include:
Nutmeg, Gelatin, Thiamine, Anatase, Gluten, Glucose oxidase, Arcitumomab or Blackstrap
Molasses
Thinking specifically about searching for (small molecule) compounds, you can search
using:
A Trivial name (Aspirin), a Trade name (Testogel), Systematic name (1H-Indole-3-ethanamine),
an abbreviation (AIBN) or a Registry Number (1134-47-0)
Important: By default, when you enter a name, your query
is submitted as a sub-string search.
For example, a search for Tryptophan,
will return: Tryptophan, Tryptophan hydrochloride, N-Methyl tryptophan, etc...
If you wish to perform an exact search, use the equals operator (=), e.g. =tryptophan
Molecular formula
You can also choose to search The Merck Index* Online by molecular formula.
To do this: Enter the molecular formula that you are interested in surrounded by
square brackets ( [ ] ). For example, [C6H10BNaO6] returns Sodium triacetoxyborohydride.
(Note: the order of the elements is not important, so [NaC6H10BO6], works
just as well)
When performing a molecular formula search from the Quick Search interface the search
will only return records that are an exact match. For more complex searches use
the interface on the main Search page.
Molecular weight
The Quick Search interface also accepts searches on molecular weights. You can choose
to search for an Exact weight or search over a molecular weight range.
- Exact weight – If you enter a single
value; for example, 368 (g/mol) you will obtain a list of records that
match that weight +/- 1 mass unit (e.g. 367-369).
- Weight range – If you enter a range
(separated with a hyphen), for example, 220.25-225.90, you will obtain
a list of records that have a molecular weight that falls between your boundary
conditions, ordered from lowest molecular weight to highest.
Search page
The main search page is designed to allow you to search across a large variety of
different types of data using text or numerical values.
Many of the fields can be used in combination, e.g. you can construct a search for
a compound that has the following properties,
Compound name contains: triazole,
Human Therapeutic Use is: Antiviral,
Molecular weight is in the range 240 – 250 g/mol
Important: When performing a search using multiple parameters,
the individual queries are combined in an additive manner, which means that in the
above example you will only obtain results where there are records that match all
criteria:
Compound name contains: triazole,
AND Human Therapeutic Use is: Antiviral,
AND Molecular weight is in the range 240 – 250 g/mol.
Each of the search fields on the page has a Question Mark icon next to it, if you
click on these then you will open a balloon containing some basic data on the types
of input that it takes (and in some cases a link to further help).
Description of searches
Text Searches Section
Compound Name
- This field accepts any name/synonym that might be used in The Merck Index* Online,
e.g.
Trivial names (Aspirin), Trade names (Testogel), Systematic names (1H-Indole-3-ethanamine),
Abbreviations (AIBN) or Plants, Food additives/components, Nutrients, Minerals,
Proteins, Enzymes, Antibodies and commonly isolated complex mixtures as well as
a wide range of chemical species including polymers.
Important: By default, when you enter a name, your query
is submitted as a sub-string search.
For example, a search for Tryptophan,
will return: Tryptophan, Tryptophan hydrochloride, N-Methyl tryptophan, etc...
If you wish to perform an exact search, use the equals operator (=), e.g. =tryptophan
When performing an exact search on the Compound Name field, all other fields are
ignored/disabled.
CAS Registry Number
- This search only accepts a query that matches the format of the CAS registry number.
When performing a search on the CAS registry number field, all other fields are
ignored/disabled.
Literature References and Notes
- This field Searches across the Literature and Notes sections of the monographs.
Useful search terms for this field might be Journal Title, or Author Name. Other
useful search terms might be classifications of the reference (Preparation, Isolation,
Determination, Review, etc.)
Veterinary Therapeutic Use
- Specify a Veterinary Therapeutic Use category. E.g. Antibacterial.
Non-Medical Use
- Perform a free text search of the Use section of a monograph. E.g. Solvent, oxidant,
catalyst, dye, pesticide, or a role/application in a manufacturing or analytical
process.
Human Therapeutic Use
- Select one or more Human Therapeutic Use categories. E.g. Antiviral.
To select a Human Therapeutic Use category, Click on the Select Category button,
this will open a pop-up window, this will display a tree view, showing the main
categories, some of which possess sub-categories. Once you have selected the terms
which you wish to search on you can close the pop-up, and you will see the categories
that you have selected next to the field.
Manufacturer
- Search across the manufacturers that have registered trade names that are included
in a monograph.
Full Text
- This field allows you to perform a free text search across all of the fields contained
within the monographs.
Properties Search Section
The Properties Search Section consists primarily of numeric searches across experimentally
measured data. Many of the fields accept two inputs, a main value together with
an input that allows you to specify the boundary conditions for the search. For
example,
Boiling point: 200 °C +/-5 °C - allows you to search a range of 10 °C around your
specified value e.g. 195-205 °C
By default the Boundary conditions are a set to a sensible non-zero value, however,
you can adjust the boundary conditions (there are limits on how wide you can set
your boundary conditions). It is also possible to change the Boundary conditions
value to zero – which turns this query in to an exact match search.
Molecular Formula
- In contrast to the Quick Search interface, you do not need to use brackets in your
query when you search using the Molecular Formula field in the Search page.
For example, C6H10 returns a number of results. When searching using this
field, the query returns not only results that are an exact match i.e. has the molecular
formula C6H10, but also results for monographs that contain C6H10, so you can also
get matches for molecular formulae such as C6H10N, C6H10O, C6H10O2 etc.
Search by Molecular Formula Range
It is also possible to specify that the molecular Formula Search covers a range
of molecular of Molecular formulae e.g. C10-12 H22 O2, will match C10H22O2, C11H22O2
and C12H22O2
Molecular weight
- You can choose to search for an Exact weight (boundary condition = 0) or over a
range of molecular weights.
Both the main value and boundary conditions fields allow you to enter values to
an accuracy of 2 d.p.
Boiling Point
- You can search The Merck Index* Online by specifying an exact boiling point
or a range (in °C).
Both the main value and boundary conditions fields allow you to enter values to
an accuracy of 2 d.p.
Melting Point
- You can search The Merck Index* Online by specifying an exact melting point
or a range (in °C).
Both the main value and boundary conditions fields allow you to enter values to
an accuracy of 2 d.p.
pKa
Log P
- You can search The Merck Index* Online by specifying a Log P value (the
Partition Coefficient)
point or a range.
Density
- You can search The Merck Index* Online by specifying a particular density
or a range.
Both the main value and boundary conditions fields allow you to enter values to
an accuracy of 3 d.p.
Index of Refraction
- You can search The Merck Index* Online by specifying a particular Index
of Refraction or a range. Both the main value and boundary conditions fields allow
you to enter values to an accuracy of 3 d.p.
Optical Rotation
- You can search The Merck Index* Online by specifying a particular Optical
Rotation or a range. Note: Please be aware that within the database the Optical
Rotation data is often listed at different concentrations and in different solvents.
Both the main value and boundary conditions fields allow you to enter values to
an accuracy of 3 d.p.
Flash Point
- You can search The Merck Index* Online by specifying an exact flash point
or a range. You have the option of searching the data either in °C or °F.
Both the main value and boundary conditions fields allow you to enter values to
an accuracy of 2 d.p.
Absorption Max
- Search by Absorption Max value, this field expects a wavelength that should be provided
in nanometres (nm). Both the main value and boundary conditions fields allow you
to enter values to an accuracy of 3 d.p.
Toxicity
- Search against toxicity (this may be either LC50 or LD50 data) specified in mg/kg,
e.g. 375 and the range of your search can be narrowed or widened by altering the
Boundary Conditions.
Structure searching
The Structure Search page allows you to search The Merck Index* Online by
chemical structure. This can be an exact structure search or you can perform Substructure
or Similarity searches to allow you to find any monographs that have structures
related to your query structure.
When performing a Substructure or Similarity search it is possible to combine your
structure search with queries from the Text or Properties section.
Structure Search interface
The Structure Search interface provides a box that displays the structure to be
searched on together with buttons that allow you to modify or input a new structure(s).
The
Options menu allows you to perform Exact, Substructure and Similarity
Searches (see subsections for more details)
Entering (and editing a new structure)
There are two buttons displayed in the Top-left corner of the Structure display
box; Convert and Edit.
The Convert option can be used to input complex chemical structures quickly, based
on conversion of a text identifier to a structure.
When you click on OK, the system will attempt to generate the structure that corresponds
to your input. At this point you can perform a search on the structure as is, or
use the Edit option to modify the structure.
The Edit option can be used to draw from scratch or modify a chemical structure.
We have integrated two structure editor interfaces:
- JChemPaint (http://jchempaint.github.com/
in browsers that do not support HTML 5). Additionally, JChemPaint provides the ability
to paste structures drawn in other editors directly into the editor and also the
option to open a file that contains a structure (e.g. mol, sdf, rxn)
Clicking on the Edit button will open the structure editor interface in a pop-up.
By default JSDraw is displayed, but you can easily change to JChemPaint by selecting
the tab near the top of the pop-up.
Note: Only JChemPaint supports the ability to cut and paste structures in
(and out) of the editor from external programs such as ChemDraw or ChemSketch.
Once you have entered your structure, click OK to close the structure Editor interface.
Search Options
The Structure Search options work as follows:
Exact search
When selecting this option the system will search for the molecule exactly as drawn
including any stereochemistry or isotopic labelling that you have defined
This option is useful for searching when your input structure may be depicted in
more than one tautomeric form, e.g. Ethyl malonate, which can be drawn as a keto-ester
or an enol ester.
- Allow isotopes and stereoisomers
This option is useful for performing a slightly more general search to see whether
there are any related stereoisomers or isotopomers in The Merck Index* Online
database
Substructure search
The Substructure Search allows you to search The Merck Index*
Online for
molecules that contain the structural fragment that you have specified.
Note:
We do not currently support any special structural wildcards.
You can choose to restrict your search to the particular tautomer that you have
drawn, or allow matching of any tautomeric structure (where relevant)
Important: When performing a Substructure Search it is advisable
to choose a large, functionalised structure as a starting point and then simplify
the query structure gradually to widen your results set.
Similarity search
The Similarity Search option allows you to find compounds that are similar to (but
do not necessarily match all of the features of) your specified structure. It is
possibility to change the level of similarity that the results must have with your
input structure (From >99% to >70%) as well as the method of determining the similarity:
Tanimoto,
Tversky
or
Euclidian.
Important: When performing a Similarity Search we would always
advise you to start by specifying a high degree of similarity and then decrease
the level of similarity incrementally as needed.
Viewing your results
Whenever you perform a search a new page will be displayed, this results page will
show the number of results that were obtained and the search parameters that you
specified. If any matching monographs were found you will see these listed below.
You can then choose to view individual monographs by:
Clicking on the monograph title (this will open the monograph in the same browser
tab)
Or use the buttons provided to open the monograph in a new window or a new tabs
(if this is supported by your browser)
If you are logged into The Merck Index*
Online as an authenticated user
you will be able to see the full monograph. Guest users will see a basic monograph
landing page which contains an image, molecular formula and weight.
Tweak your query
When you perform a search from the Search or Structure Search page, your search
parameters are shown as a "Tag list", each option that was specified is shown in
its own tag. You can choose to remove one of the parameters by clicking the cross
next to the parameter and your revised search will be run automatically.
Refine your query
If you perform a search and decide that you need to change one or more parameters,
you can use the Change Query button, this will take you back to the search interface,
which will contain your previously entered search parameters, so that you can change
your query without having to start from scratch.
Browse page
The Browse page allows you to explore all of the content of The Merck Index* Online alphabetically.
By selecting a letter of the alphabet you can see a list of the monographs whose title begins with that letter. Prefixes such as locants, stereodescriptors ((
R)-, (
S)-,
cis-,
trans-, etc.) and structural descriptors (
n-,
sec-,
tert-, etc.) are not included in the alphabetical ordering; for example,
N-bromoacetamide and
tert-butyl acetate are both found under the letter B.
Named Reactions
The Merck Index*
Online contains summaries of a large number of (Organic)
Named Reactions (>500 different reactions).
There are two ways to explore this data:
Browse by first letter
By selecting a letter of the alphabet from the list on the Named Reactions pages
you can see a list of all of the Named Reactions that begin with that letter.
Search Named Reactions
The search box on the Named Reactions page allows you to perform a free text search
across all of the text in the Named Reactions records, this means that as well as
searching by the name of the reaction you can search by reagent, functional group
or class of compound, or even author name.
When performing such searches, it should be noted that in some cases a search term
may return a match that is unexpected because the term occurs in particular context.
