Professor Damon Ridley was our special guest speaker for this webinar. Damon was Professor of Chemistry at the University of Sydney until 2002 when he left to become Head of the Chemistry Department at Silverbrook Research – which then was Australia’s largest privately owned research organization. He has published over 150 scientific papers and is an inventor named in over 50 patents granted by the US Patent Office. However, he also is very well known internationally for his work and publications in scientific information retrieval. In this webinar Damon shared his years of experience with us and focused in particular on searching for substances in Reaxys.

1. WEBINAR:
SEARCHING FOR
SUBSTANCES IN REAXYS
24 MARCH, 2015
1
Damon Ridley

2. Overview of searching for substances in Reaxys
2
1. Search
by
Substance-
identifying
terms
(in substance
records)
2. Search
by
Words
(in bibliographic
records)

3. DATABASE PRODUCER:
ADDED VALUE
A RECORD IN REAXYS
3
AUTHORS
Searched and
displayed in
Substance
Records
Searched and
displayed in
Bibliographic
Records

4. Classes of Substances
4
CLASSIC ORGANICS
CLASSIC INORGANICS NUCLEIC ACIDS &
PROTEINS
POLYMERS
ORGANOMETALLICS
COORDINATION
COMPOUNDS
Found in KEYWORDS in REAXYS BIBLIOGRAPHIC
RECORDS
CERAMICS
ALLOYS & METALS
Found in REAXYS SUBSTANCE RECORDS
… and …
Search Substances Search Literature

5. However, for more
complex substances
• systematic names
can get very
complicated
• different indexers
use different
index terms
In simple cases,
systematic names
and indexing are
easy to follow and
easy to use
• 4-chloro-2-butanol
• p-nitroaniline
A personal opinion about naming and indexing of substances
5
For > 100 years
chemical
scientists and
indexers have
sought ways to
systematically
name and index
substances
By structure and by simple name (morphine)
How do scientists refer to, and like to search for, morphine?

6. That is, most
polymers are very
difficult to describe
in systematic terms
(name, structure,
formula, shape,
molecular weight)
6
However, for many
substances
“indexing” requires a
number of “rules”
• which in turn may
be very complex &
• which may not tell
the “whole story”
A personal opinion about naming and indexing of substances

7. INDEXING OF POLYMERS AS “SUBSTANCES”
7
• “Issues” arise from inter alia:
• The “shape” of the polymer
• The organisation of monomers in the polymer backbone
• Post-treated polymers (i.e., polymers to which additional groups are later added)
• Polymer blends (how are blends/mixtures of polymers indexed?)
• The conditions under which polymers are formed (e.g., different monomer ratios,
different reaction conditions such as temperatures or catalysts, give different
“substances”)
The shape of the polymer backbone
The organisation of monomers in the
polymer backbone

8. 8
• Very few scientists know how complex polymers are indexed
• For example, ask any polymer scientist (or polymer indexer) how the product from
the following reaction would be (systematically) indexed!
Index this product!
A personal opinion about naming and indexing of substances

9. We need different systems to “index” different classes of substances
9
Easy to describe by structure and/or formula? Yes No
Easy to describe by common chemical name? Yes (if: morphine) No
Easy to index as a substance?
=> registry number
Yes (the structure defines
the substance)
No
Easy to describe in text terms (excluding common name)? No Yes
We need different ways to search for polymers,
and the same applies to ceramics, ceramers, and
indeed to the many classes of substances of most
interest to scientists in the materials sciences, in
biochemistry, in molecular biology …

10. There is an enormous
amount of information
on such “substances”
in Reaxys
(we just search in a different way)
Reaxys has Index
Keywords to help us
search for these
“substances”
Polymers, ceramics,
materials and
proteins/nucleic acids may
be most effectively
searched by WORDS
Indexing of “SUBSTANCES” in Reaxys: WORDS
10

11. 11
CLASSIC ORGANICS
CLASSIC INORGANICS NUCLEIC ACIDS &
PROTEINS
POLYMERS
ORGANOMETALLICS
COORDINATION
COMPOUNDS
Found in KEYWORDS in REAXYS BIBLIOGRAPHIC
RECORDS
CERAMICS
ALLOYS & METALS
Found in REAXYS SUBSTANCE RECORDS
… and …
1 2
Search Substances Search Literature

12. Searching for Substances in Substance Records
(commonly used fields)
12
Click Substances to search in
the Substance Database
Note the Search Context
Ask Reaxys when you have
a simple name for the
substance
1
Search by Structure when a
clearly defined structure (or
part-structure) is the best way
to find substances that meet
your needs
2
Try ligand search fields for
coordination compounds
3
Search for formulas or
part-formulas
4
Search for chemical names
or part-names
5
Search for alloys, ceramics
and related substances
6
Search Querylets

13. 13
Search Querylets
Enter
term(s)
But how do
we know
what to
enter?
Numeric Field
Text Field
Auto-
truncation
Just start
typing or
click
Lookup
Auto-
suggest

14. 14
Ask Reaxys when you have a simple name for the substance1
Ask Reaxys searches
both options for us
WORDS in Bibliographic Records
Substance Records

15. 15
Ask Reaxys when you have a simple name for the substance1
SUBSTANCE RECORD
BIBLIOGRAPHIC RECORD

16. 16
Ask Reaxys when you have a simple name for the substance1
Ask Reaxys
Enter
“Simple Names”
Substances
• Usually “specific” substance searched
will be at the top of the list
• Will retrieve other substances
(stereoisomers, salts, and some
substances related by name)
Show Query =>
Ask Reaxys – Analysis
References
• Name of substance is searched in Title,
Abstract or Keyword Fields

17. Exact Structure
Part-Structure
Similarity
Include:
• Tautomers
• Markush
Exclude:
• Salts
• Mixtures
• Isotopes
• Charges
• Radicals
17
Structure and Sub-structure Search2
Structure Query Editor
used to:
• Lock atoms/rings
• Specify isotopes,
charges, radicals
• Repeat groups
• Block substitution
and so forth
Keep Queries Simple
For further information:
bdtraining@elsevier.com

18. 18
Ligand Search Fields for Coordination Compounds3
• The variety and complexity of the structures of
coordination compounds present many challenges for
the author, the database developer, and for the
searcher
• Even such an important and common ligand such as
ethylenediamine tetraacetic acid (EDTA) presents
problems in that the 2 nitrogens and 4 oxygens in EDTA
may coordinate to a central metal or to two metals,
or some of the coordination sites may be replaced by
other ligands such as water
• To cover possibilities of interest in a single structure
search may be challenging
• Reaxys offers another solution through the ability to
search for ligands through formulas
The metal is Co
Another ligand is
attached through N
2
2
Another ligand is
attached through C
3
3
The main ligand has
2 N’s and 2 O’s
1
1
There are three parts of a ligand formula
• The metal
• The ligands attached to the metal
• Each ligand is
enclosed in { }
• The coordinating atoms,
grouped in codes, e.g.
Numbers are assigned when >1

19. 19
Ligand Search Fields for Coordination Compounds3
1
326 substances
3
170 substances
2
518 substances
4
259 substances

20. 20
Search for Formulas or Part-Formulas4
• We may enter the formula in the Molecular Formula
Querylet …
• The Formula Builder allows us to build:
• Full or part formulas
• Formulas with groups (e.g., Transition Metals)
• Formulas with variable numbers of elements or
groups
• Formulas that may include other elements
• The Formula Builder is particularly useful for finding:
• Substances that are related by formula rather
than by structure or name
• Inorganics and organometallics
• Substances with non-standard formulas, e.g.,
radicals, carbocations and other intermediates
• Groups of substances with variable formulas
Example 1: Find calcium hydrides

21. 21
Search for Formulas or Part-Formulas4
Example 2: Find transition metal halides with 2-4 transition metals

22. 22
Search for Formulas or Part-Formulas4
Example 3: Find dilithio hydrocarbons

23. 23
Search for Names or Part-Names5
Example: Find nitrogen-containing organic radicals

24. Search for radicals by Part-Name
Search for radicals by Part-Formula
24
5 Search for Names or Part-Names5
Provide search functions and scientists will use them creatively

25. 25
Search for Alloys, Ceramics and Related Substances6

26. 26
Search for Alloys, Ceramics and Related Substances6

27. Searching for substances in Substance Records
(commonly used fields)
27
Click Substances to search in
the Substance Database
Note the Search Context
Ask Reaxys when you have
a simple name for the
substance
1
Search by Structure when a
clearly defined structure (or
part-structure) is the best way
to find substances that meet
your needs
2
Try ligand search fields for
coordination compounds
3
Search for formulas or
part-formulas
4
Search for chemical names
or part-names
5
Search for alloys, ceramics
and related substances
6
Ask Reaxys when you have
a simple name for the
substance
1
Search by Structure when a
clearly defined structure (or
part-structure) is the best way
to find substances that meet
your needs
2
Try ligand search fields for
coordination compounds
3
Search for formulas or
part-formulas
4
Search for chemical names
or part-names
5
Search for alloys, ceramics
and related substances
6
Ask Reaxys: morphine
 Subs + Text answers
Ask Reaxys: cis-platin (Google)
1
Numerous Search Functions
8 Different Structure Search
Editors
bdtraining@elsevier.com
2
Search for substances with
specific ligands
3
Calcium hydrides
(Trm)2-4
halides
Di lithio hydrocarbons
4
C, N – containing radicals
5
Ti V alloys
Aluminium/Titanium Oxides
Ask Reaxys: titanium vanadium alloys
6

28. 28
CLASSIC ORGANICS
CLASSIC INORGANICS NUCLEIC ACIDS &
PROTEINS
POLYMERS
ORGANOMETALLICS
COORDINATION
COMPOUNDS
Found in KEYWORDS in REAXYS BIBLIOGRAPHIC
RECORDS
CERAMICS
ALLOYS
S
e
a
r
c
h
S
u
b
s
t
a
n
c
e
s
Found in REAXYS SUBSTANCE RECORDS
… and …
1 2
Search Substances Search Literature

29. Searching for Substances in Bibliographic Records
29

30. 30
Search Querylets
Text Field
Auto-
truncation
Enter
term(s)
But how do
we know
what to
enter?
Just start
typing or
click
Lookup
Auto-
suggest

31. in Substance Records
31
HIMBACINE
Searching for Substances

32. Searching for Substances in Bibliographic Records:
Ask Reaxys
32
Key points about Ask Reaxys
• Still being developed
• Enter a few (and simple) terms – nothing too complex
• No truncation or proximity allowed
• Singulars  plurals not searched automatically

33. Searching for Substances in Bibliographic Records:
Citation Basic Index Querylet
33

34. 34
Searching for Substances in Bibliographic Records:
Citation Basic Index Querylet
Found in REAXYS SUBSTANCE RECORDS … and … Found in KEYWORDS in REAXYS BIBLIOGRAPHIC RECORDS

35. 35
Polymers: Ask Reaxys

36. 36
Polymers: Citation Basic Index Querylet
Start typing here
Highlight term(s) of interest

37. 37
Polymers: Citation Basic Index Querylet
Precision vs Comprehension
Different Fields
More/Fewer Terms
Truncation/No truncation
Filter by: Analysis View

38. 38
Enzymes: Citation Basic Index Querylet
APOBEC (apolipoprotein B mRNA editing enzyme)

39. 39
Difficult “Substances”: Citation Basic Index Querylet
STRANGE IONS – CH5
+ STRANGE PARTICLES
ALUMINA ZIRCONIA CERAMICS GAMMA-AMINOBUTYRIC ACID RECEPTORS

40. Summary: Searching for “substances” that are “not simple”
40
• Reaxys provides extensive and flexible keyword search functions which greatly assist
retrieve information on these classes of substances through:
• Ask Reaxys
• Citation Basic Index Querylet, e.g.:
• Auto-suggest text for single terms and phrases
• Automatic or user-driven truncation
• Proximity operators
• In general, Reaxys does not index a number of classes of substances by “Registry Number”
• (That is, they do not appear as separate substances in Reaxys Substance Records)
• The classes involved include:
• Instead, Reaxys “indexes” these classes of substances through Index Keywords in
Bibliographic Records
POLYMERSCERAMICS(Some) ALLOYS CERAMERS PROTEINSNUCLEIC ACIDS

41. Searching for Information on Substances
41
STRUCTURES & PART-
STRUCTURES
NAMES &
PART-NAMES
FORMULAS &
PART-FORMULAS
LIGANDS
WORDS IN TITLES &
ABSTRACTS
INDEX KEYWORDS
Provide search functions and
scientists will use them creatively
ORGANOMETALLICSCLASSIC INORGANICS
POLYMERS
ALLOYS
CERAMICS
NUCLEIC ACIDS
COORDINATION
COMPOUNDS
CLASSIC ORGANICS
PROTEINS
AUTO-
TRUNCATION
AUTO-SUGGEST
POST-PROCESSING
Some Functions
Some Substance Classes
Some Search Types
Know your options …
… and TRY THEM!

42. Send email to:
bdtraining@elsevier.com
Further Information
42