2. Who is it for ?
Research chemists in chemical companies
and at universities.
Research areas:
Chemistry (Dyes, Intermediates, Agriculture
Polymers)
Petro Chemistry
Pharmaceutical and Medical Chemistry
Biotechnology
Cosmetics
Food Industry
3. RxnFinder - What does it do ?
RxnFinder answers questions around chemical reactions:
A+B
Reagents
C
Product
How to synthesize a potential drug?
What reaction conditions lead to the best yield?
What catalyst has been used for this functional
group transformation?
What chemistry can I find beyond my query?
How to synthesize this reagent?
Is there information if this reaction fails?
4. Facts:
Scope of chemistry covered:
synthetic organic and
organometallic chemistry
Chemical reactions:
about 2 million
Number of substances:
over 1,7 million
Updating:
inhouse quarterly/online monthly
Journals covered:
about 100 (the most important ones)
Dates covered:
1990 - present
(100,000 reactions added per year)
5. The abstracts in the ChemInform provide you with the
latest developments in preparative chemistry, including:
novel catalysts and reagents
protecting groups
functional group transformations
approaches to heterocyclic scaffolds
new strategies in natural product synthesis
6. Search in the pool of ChemInform reactions for:
structures and substructures
reaction types
experimental conditions (e.g. reagent, solvent, yield, e.e.)
bibliographic data (e.g. author, journal, year, title)
combinations thereof
7. Unique Features:
Focus on NOVEL or improved methods, new reagents and
catalysts.
Full reaction schemes show the scope and limitations of the
reaction, electronic, structural and stereochemical effects.
Elimination of spurious or duplicated results through rigorous
selection criteria.
‘Failed reactions’ are also included (Yield = 0).
8. Chemical Reactions
One of the main tasks of researchers in chemical and
pharmaceutical Industry is to synthesize new chemical
compounds applied in the areas agriculture, pharma,
intermediates, dyes and more.
Most efficient tool to make this work succesful is
reaction databases with carefully selected and curated
experimental data.
Besides the reaction centers conditions and yield is the
Information the researcher is interested in
Reactant
Product
Catalyst
Temperature
Solvent
Yield
9. Table-of-contents
Section 1: The RxnFinder User Interface
Section 2: Transformational Search, Schemes,
Reaction Details
Section 3: Substructure Search, Filters, Cluster
Analysis
Section 4: From RxnFinder to Wiley‘s Smart
Article
10. Section 1: RxnFinder User Interface
Tabs:
Query, Results, Details, Retrosy
nthesis, Hitlist handling
Query Fields:
Reaction, Molecule, Cit
ation, All
Reaction Search:
Exact, Similarity, Substructure, T
ransformational
Upload or Draw structure
queries
Query Handling: Save, History
11. Section 2: Transformational Search, Schemes,
Reaction Details
Use case: One of the most powerful reaction
searches is the reaction center search or
transformational search. Reactions with similar
reaction centers can be identified using this
technique. An example is the functional group
transformation, e.g., from a trifluoromethyl to a
carboxyl group.
12. Section 2
Select the Search Type
Transformation broad (default)
Submit Query
Upload or Draw the reaction
query
13. 13 Hits match the Query
Open the Reaction Scheme
Section 2
14. Section 2
….the Transformation he was
looking for
….other Transformations which
might also be of Interest
The scheme is a
comprehensive
summary of the
most important
reactions in an
article.
At a glance
the chemist
gets the
crucial
details of
reactions…..
16. Section 2
This reaction
details page
displays:
• Products
Reactants
• Catalysts
• Solvents
and
• Keywords
• Structure
Properties
• Yield
• Temperature
17. Section 3: Substructure Search, Filters, Cluster
Analysis
Use case: Geipavarin is a natural compound
known as a potential anti-cancer drug
A pharma researcher identifies the 5-membered
ring as being a potential pharmacophore
(important part of the molecule) and wants to
find products including this ring.
18. Section 3
The structure is
sent to the
Editor
The geipavarin
structure is
uploaded
The left part of
the molecule is
removed using
the lasso/
delete function
of the editor
19. Section 3
The arrow on
the left of the
structure
indicates that a
search for
products will
take place
Reaction Substructure Search
has been chosen
Submit query
To restrict the results, only
recent articles are selected
20. Section 3
The Cluster
Analysis provides
another tool to
refine hit lists.
56 hits result
The researcher
may be interested
in a certain
reagent and
selects it
21. Section 3
One article
remains. The
reaction scheme
again contains
information about
the context
No OH
protection
required if
the R
substituents
are aliphatic
Protection
required if
the R
substituents
are aromatic
22. Section 4: From RxnFinder to Wiley‘s Smart
Article
Use Case : A research chemist who works on
heterocycles wants to start from nicotinaldehyde as
the reagent. The products shall have molecular weights
in the range 300 to 500 Dalton (see Lipinsky‘s „Rule of
5“ defining drug likeness with 5 criteria)
What has recently been published in the Journal of
Heterocyclic Chemistry on this research field?
23. Draw/ Upload
Nicotinaldehyde as reagent
Section 4
Select the Journal JHET
Exact search
Recent literature
Molecular
weight range
25. Section 4
All compounds identified by the author as
primary are displayed on the Abstract page
26. The Featured Compounds are the
Chemistry Gateway to Wiley Online
Library
Section 4
Exact structure search in
Wiley Online Library
Views all instances of
the compound in the
article
Links to the compound
record with
properties, molfile
export, external links to
Google, PubChem, Che
mSpider
In the followin sections the basic functionality of RXNFinder will be demonstrated based on use cases. After a brief introduction of the user interface a transformational search will we performed followed by a discussion of reaction schemes and reaction details. A following substructure search demonstrates the application of filters and cluster analaysis. In the last section the seamless connection to Wiley‘s Smart Article will be shown as part of a use case.
This is the the web client of RXNFinder. The functionality is organised in Tabs. The reaction query tab is activated by default. Result, details, retrosynthesis and selected hits tabs are populated when a search has been taken place.On the left the detailed query fields are displayed with the sub-sections Reaction, Molecule, Citation, All. These fields are used to restrict the search results appropriately. In the middle three buttons are placed to open the structure drawing tool, acces a library of structure templates and upload a structure in standard formats such as SDFile or Molfile.On the right the various search functions are available:Exact search retrieves reactions which include the identical query structureReaction Similarity search takes into account the reaction centers and a molecular similarity. The latter is based on a set of structure features such as existence of rings, arrangment of heteroatoms etc.Reaction substructure search can be performed with or without autmapping of the query. Automapping usually reduces the result set by supressing reactions which are not consistent with the query.Transformational search is based on the comparison of reaction centers in reactants and productsOn the bottom left features for query handling are available.
Transformational broad: only the reaction center is compared. The result set is large.Transformational medium: the reaction center and the atoms in the first sphere are taken into account. The result sets are significantly smallerTransformation narrow: first and second sphere are taken into account. The result sets a small, often zero.
Upload transformation.rxn from the local disk. The trifluoromethyl group is transformed into a carboxyl group.The rest of the molecule is not taken into account in the search. Transformation broad search (see explaination on slide 3) has been chosen. Submit query sends the reaction query to the cartridge.
13 hits result from the transformational broad search. The 3rd hit has been chosen for further explaination of featureson the result list.If a chemist wants to get more information about the chemistry in the article he needs to go to that article andread it. A time saving alternative is to look at the reaction scheme.
The reaction scheme is a unique feature of ChemInform. It includes a summary of the featured reactions described in an article. The chemist sees immediately what chemistry is discussed in the article. Not only his query is shown in the scheme but also relatedInformation. The schemes have been generated by chemists at Wiley Information Service who compiled the most important information and rejectedsecondary or trivial chemistry. Other database vendors usually collect everything with the disadvantage that valuable information isoften hidden in large result sets.
Open articles will be discussed in another use case. The link show details opens a page where reactant, conditions and products are displayed in more details
Products, Reactants, Catalysts and solvents are listed in separate sections. If the reaction is part of a multistep synthesis the individual steps would show upon the left. In the given case we have a single step reaction.Structure descriptors such as molecular formula, molecular weight and INCHI‘sare assigned to the compounds. Other data typical for reactions such as yield and reaction temperature are also displayed in the details record.
In the next section the focus will be on substructure search, filtering and hitlist refinement. We again start from a use case: see text(A pharmacophore is a part of a molecule which is responsible for biological effects)
Geiparvarin.mol is uploaded from the disk. A click on the edit button opens the structure in the structure editor. The lasso functionality (top left) is used to mark the structure part in the molecule which has to be removed. A click with the eraser removes the selected part. Now an arrow is drawn on the left side of the structure fragment and the query is ready for search. Transfer to query moves the structure into the query field.
