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Tips and tricks chemistry

Tips and TricksChemistry

November 2005


Chemical abstracts service cas
Chemical Abstracts Service, CAS

  • CAS... we are scientists, creating and delivering the most complete and effective digital information environment for scientific research and discovery

  • CAS is a self-sustaining division of the American Chemical Society

  • CAS employs 1250 staff members in Columbus, Ohio


Chemical abstracts service cas1
Chemical Abstracts Service, CAS

  • CAS Content... the world’s largest collection of chemical and related scientific information for the research community including:

  • Most authoritative collection of substance information available

  • Worldwide coverage of current and comprehensive journals and patents


Scifinder content
SciFinder content

  • CAplus from CAS with 25.6 mil references, abstracts and detailed indexing from 1907-

    • Sources: 9,500 journals, patents from 50 offices, internet journals and preprint servers, conferences, theses and report

    • Citations from journals and patents 1997-

  • Registry from CAS with ~83.5 mil substances

    • Small molecules, biosequences, polymers, inorganics, alloys, complexes

    • Single compounds have experimental data from InfoChem and CAS and have calculated data from ACDlabs


Scifinder content1
SciFinder content

  • CASREACT from CAS with 9.2 mil single and multi-step reactions

    • From journals and patents, 1907-

  • ChemCats from CAS with supplier data from 914 catalogues

    • Screening compounds, fine chemicals and some bulk for 8 mil compounds

  • Chemlist from CAS with regulatory information

  • Medline from NLM with 15.5 mil records from 1950-

    • Sources: 3200 journals



Scifinder benefits
SciFinder benefits

  • Easy access to largest database covering chemistry and related sciences relevant to drug discovery

    • Solid look at IP status for substances and biosequences

    • Advanced analysis tools to handle larger answer sets in a creative way

    • Powerful alerting due to high currency of the information

    • Content and interface designed by scientists for scientists

    • Big time save not having to run experiments that are well documented in the literature

    • Big money save not having to continue projects that have already received patent protection by competition


Agenda
Agenda

  • Structure searching features

  • Substance viewer features

  • Get related feature

  • Reaction searching in SF2006

  • Novel compound or freedom to operate?


Structures in scifinder
Structures in SciFinder

  • The CAS Registry file contains over 26.4 million small molecules or small sequences

  • At present over 6.2 mil structures have defined stereochemistry in the structure

  • Stereochemistry is not available for certain classes of compounds

    • Coordination compounds, allenes and cumulenes (not searchable), stereo bond between two ring systems


Structure searching in sf
Structure searching in SF

  • SciFinder and Scholar use a broader structure search, which includes tautomers and related compounds

    • Double bond geometry may be impacted by a tautomer

    • Carbohydrates and hemiacetals may have different configurations (included as hits)




Absolute stereo answers

These answers will have the R-stereoisomers pictured either with the bond into the plane or out of the plane. The author must have provided complete configuration of the stereo node.

Absolute stereo answers


Absolute stereo mirror image answers

These answers will have the S-stereoisomers pictured either with the bond into the plane or out of the plane. It is also called the “meso” compound of our structure.

Absolute stereo mirror image answers


Relative stereo answers

These answers will have the stereochemistry defined relative to another chiral center. The stereochemistry could be shown as R,S or S,R being identical for relative stereoisomers. Relative stereo answers can be useful for structure searches with multiple chiral centers.

Relative stereo answers


Stereo answers not matching

These answers do not have the desired stereochemistry at the node we searched, but there is stereochemistry elsewhere in the molecule. In this case it is the Z double bond geometry. If we had searched a compound with R,R bonds, we would also see the R,S and S,R answers in this set.

Stereo answers not matching


No stereo in answer structure

These answers will be completely flat structures (or racemic mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

No stereo in answer structure


Three types of structure searches
Three types of structure searches mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

  • Exact search

  • Substructure search

  • Similarity search

  • Additional filters


Example warfarin 81 81 2
Example: Warfarin (81-81-2) mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.


Exact structure search
Exact structure search mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

  • Retrieves 135 answers

    • 47 single compound substances

      • 14 unlabelled compounds

      • 33 radio-labelled compounds

    • 88 salts and mixtures

  • Of these there are 26 tautomers


Substructure search
Substructure search mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

  • Retrieves 613 answers

    • 424 single compound substances

      • 375 unlabelled compounds

      • 49 radio-labelled compounds

    • 189 salts and mixtures

  • There are 57 tautomers

  • There are 38 compounds with a mol weight of >500

  • All 135 answers of the exact search are included in this answer


Similarity search
Similarity search mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

  • Ranks the compounds according to their Tanimoto similarity score based on structural attributes

The 109 compounds with a score of ≥ 99 are the same as the 135 exact compounds minus the 26 tautomers


Substructure is very different from similarity search
Substructure is very different from similarity search mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Unique answer for substructure search

Unique answer for similarity search


Additional analyze features
Additional analyze features mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

  • Analyze by real-atom attachment

    • Useful to see a breakdown of the types of substitution at different nodes of your query

  • Analyze by ring skeleton

    • Beware this only analyzes the rings that are part of the query structure, not any ring

  • Analyze by precision

    • Separates out the exact structure, close and loose tautomer answers


Example query structure
Example query structure mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

X = any

Halogen

R1=O/N

You may define an R-group as the VAP node; you may define multiple VAP nodes to the same ring system


Classes of substances
Classes of substances mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Substance class or the type of study can be selected using the additional options before the search


Analyze your answers
Analyze your answers mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.


Real atom attachment
Real atom attachment mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Makes a distinction between C and Ak and Cb

Select option to refine your search


Real atom attachment 2
Real atom attachment (2) mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Halogen attachments are in addition to the X drawn at a variable position

Cannot analyze a node that is part of a repeating group.


Variable node analyze
Variable node analyze mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Compounds may have additional halogen substitution on the phenyl ring, so numbers may be higher


Precision analyze
Precision analyze mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Conventional structure match exactly

Closely assoc. tautomers have 1 bond shifted or created

Loosely assoc. tautomers have bigger variation

Make a selection to remove unwanted answers


Precision analyze close tautomer
Precision analyze: close tautomer mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

This compound is considered a close tautomer, because the second double bond in the ring, could also be drawn as a keto substituent, which would have matched the query.


Ring skeleton analyze
Ring skeleton analyze mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Option to analyze only the shape, the shape and atoms, the shape, atoms and bonds or rings that have at least one atom in common with the query structure


Refine substances
Refine substances mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.


Refine want a maximum of 2 halogens anywhere on the phenyl
Refine: want a maximum of 2 halogens anywhere on the phenyl mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Replaced the specific phenyl with a generic Cb node. One X is drawn; second optional halogen is defined as R2=H,X. The tool “lock substitution” prevents additional substituents


Agenda1
Agenda mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

  • Structure searching features

  • Substance viewer features

  • Get related feature

  • Reaction searching in SF2004

  • Novel compound or freedom to operate?


Search options from substance viewer
Search options from substance viewer mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

= Same as Get References

= View 3D (Accelrys software)

= Commercial suppliers

= Search exact compound in

a reaction explore

= Regulatory information


Exact reaction link specify the role in the reaction
Exact reaction link: specify the role in the reaction mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Could work very well for reactions in water or reactions with a specific catalyst


Exact reaction link results
Exact reaction link results mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Leads to 871 reactions from 258 documents


Get reference link
Get Reference Link mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Records from 1907-1966 are not associated to any roles


Get reference link1
Get Reference link mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

Not all publications in Chemical Abstracts are selected for CASREACT !! (only 258 out of 480 with reaction indexing)


Agenda2
Agenda mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

  • Structure searching features

  • Substance viewer features

  • Get related feature

  • Reaction searching in SF2004

  • Novel compound or freedom to operate?


Get related feature
Get related feature mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

  • Starting your search from a text explore

  • Obtain all the substances indexed in the reference list

    • Answer set must be <1000 references

    • Refine with structure fragments or calculated properties

  • Obtain all reactions indexed from the listed references

  • Obtain the older cited references or forward citing references

    • Answer set must be <500 references


Rc metathesis 2000 2005
RC metathesis (2000-2005) mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.


Limit the related substances that are indexed as products
Limit the related substances that are indexed as products mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.


All indexed products
All indexed products mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

We are interested in compounds with a ring 10-30 atoms


All indexed products1
All indexed products mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.


411 large rings as products
411 large rings as products mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.


Get references again
Get References again mixtures) with no other stereochemistry in the structure that was searched. Some compounds with stereochemistry in the name may still be found in this set.

SciFinder didn’t remember the original search at this point



Agenda3
Agenda compounds

  • Structure searching features

    Substance viewer features

  • Get related feature

  • Reaction searching in SF2004

  • Novel compound or freedom to operate?


Reaction searching in sf sfs
Reaction Searching in SF/SFS compounds

  • CASREACT database offers full reaction searching

    • Reactions from CAS cover 1985-present

    • Reactions from InfoChem 1974-1991

    • Common enzymatic reactions

    • Reactions from INPI 1840-1984

  • Contains new/novel reactions not all reactions

  • Details of solvents, catalysts, reagents not routinely indexed in CAplus


Searching in casreact
Searching in CASREACT compounds

  • By structure fragments for products, reactant/reagents

    • Indicate reacting bond (reaction site)

    • Indicate reaction map (identical atom in reactant and product)

    • Compounds indexed as solvents or catalysts cannot be searched by structure

  • By functional groups

    • Indicate role: product, reactant, reagent, or non-reacting


Searching by functional groups
Searching by Functional Groups compounds

Non-reacting role allows for searching reactions “in the presence of” a group


Reaction searching in sf sfs1
Reaction Searching in SF/SFS compounds

  • Registry and CAplus

    • All preparative literature with most reaction participants indexed with CASRN

    • Solvents, catalysts only indexed if novel or emphasized by the author

    • Pre-1967 literature partially indexed by CAS RNs

      • Use older names or formulas for the substance



Reaction example
Reaction example compounds

  • Run a closed or open structure search

  • New up front limitation options


Reaction example1
Reaction example compounds

  • As soon as you move over any substance in the reaction display the formula or the structure becomes a button to request more information

Click substance


Reaction example2
Reaction example compounds

Information from patents and journals

Single step and

multi-step reactions; click the microscope for intermediate reaction steps


Reaction example3
Reaction example compounds

Scroll down for all steps; the mouse wheel is now enabled for power-scrolling


View options
View options compounds

Get only one sample reaction per document

Hypertext link to other query hit reactions from that document



Commercial availability or retrosynthetic steps
Commercial availability or retrosynthetic steps compounds

Click on a substance for more info


Reaction example4

Reactions will search the compound itself as a reaction participant

Reaction example

  • References will show the list of references limited by the usual roles

  • Substance details for the Registry record

  • Commercial sources from Chemcats

  • Regulatory info from Chemlist



Reaction example5
Reaction example participant

Retrieves new reactions with this substance as the reaction product


Reaction information
Reaction Information participant

  • Creates an infinite path of reaction browsing

  • Can use the [BACK] button to go to the previous reaction answers

  • Is only available to SF subscription users and SciFinder Scholar users




Reaction searching
Reaction searching participant

  • Remember, CASREACT has a focus on novel reactions

  • For a more comprehensive preparative answer, search the substance in Registry and refine by the preparation role

  • If necessary search by names or by CAS number without roles for information from 1907-1966



More comprehensive answers
More comprehensive answers participant

Compare to 8 documents from

our reaction search !!


Searching for specific catalysts
Searching for specific catalysts participant

  • Catalysts and solvents are not structure searchable in the reaction explore

  • Possibility to search them via the exact, substructure or similarity search and select “Get Reactions” with the appropriate reaction role

  • Example: finding reactions catalyzed by similar compounds to Proline, a well known organocatalyst






Agenda4
Agenda participant

  • Structure searching features

  • Substance viewer features

  • Get related feature

  • Reaction searching in SF2004

  • Novel compound or freedom to operate?


Chemical patent protection can be very complex
Chemical patent protection can be very complex participant

  • SciFinder provides access to 85 mil chemical compounds

  • Specific substances from patent claims and examples have been registered

  • Broad “Markush” claims in patents can describe thousands of compounds

  • For freedom-to-operate searching you need to have a search done for prophetic compounds hidden in large Markush claims


Markush answers
Markush answers participant

  • A search in CAS’ Marpat database revealed compound theoretically matches the Markush definition in 7 patents

    • e.g., WO2005058292by AstraZeneca


Markush answers1
Markush answers participant

  • If these are answers you need to know, contact your information professional, a patent office, or CAS’ Science IP


Tips and tricks chemistry1

Tips and Tricks participantChemistry


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