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Reaxys training Dr. Charles Martinez
Reaxys training
Dr. Charles Martinez
Table of Contents
• What is Reaxys?• What do Chemists want to know?• Who uses Reaxys?• Reaxys 2013 expansion• Examples
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What is Reaxys?
• Elsevier’s premier workflow tool for research chemists & related science
• An extensive repository of chemical properties and reaction data presented with chemistry as the organizing principle
• A resource for accurate and validated experimental data. High quality answers you can use with confidence.
• A simple interface, easy to work with. Analysis and planning tools offer new, and fast functions that help identify and plan the synthesis of molecules.
• A web-based product that makes chemistry research more efficient, and helps to achieve better results. Simply access at www.reaxys.com
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Chemistry as organizing principle
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One Record
Publication In Tetrahedron
Patent
Patent
Publication In Am Chem Soc
across time, documents and publishers
How do we collect the content?
PhysicochemicalProperties
Pharmacology
Chemical Structures
Chemical Syntheses
All Data, independent from main theme of the article
Relevant Data can be in footnotes, descriptive texts, schemes, tables…
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What do chemistswant to know?
1. What is this?• Is it novel? Patented?• What are its physical characteristics
(weight, melting point, etc?)2. What does it do?• Is it a reagent? Solvent?• What is its bioactivity?
Pharmacology?• Is it toxic?3. How can I make it?• How can I change it?• How can I make it better?
Who uses Reaxys?
1 Massachusetts Institute of Technology (MIT) 2 University of California, Berkeley (UCB)3 Harvard University4 Stanford University (with faculty on Reaxys Advisory Board)5 California Institute of Technology (Caltech)6 University of Oxford7 University of California, Los Angeles (UCLA)8 University of Cambridge9 University of Hong Kong10 Imperial College London (with faculty on Reaxys Advisory Board)
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In addition, we have 84 of the top 100
What exactly is Reaxys?
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A workflow solution for scientists in chemistry R&D
The largest resource for experimentally validated substance properties and reaction data presented with chemistry as the organizing principle
The most effective solution for synthesis planning
A fully integrated chemistry database
2013 Expansion
Content Expansion 2013
Agricultural and Biological SciencesBiochemistry, Genetics and Molecular BiologyChemical EngineeringChemistryDentistryEarth and Planetary SciencesEnergyEngineering
2013 onwards
15,973 periodicals: chemistry, life sciences, engineering, pharmacology, environmental sciences & more (including journal articles, book series & conference proceedings)
Relevant chemistry patents
Historical chemistry data (from 1771), new periodical backfiles from 1823 onwards
Environmental ScienceImmunology and MicrobiologyMaterials ScienceMedicineNeurosciencePharmacology, Toxicology and PharmaceuticsPhysics and AstronomyVeterinary
Reaxys coverage has been extended from the core chemistry focus to include
Worked Examples
Worked examplesExample 1Use the Generate Structure from Name feature
Example 2Find Substances with a general structure and information containing these keyword fragments
Example 3Operators
Example 4Find Antibiotics isolated from marine organisms
Example 5Using the Quantum Chemistry field
Example 6Isomerization of azobenzene
Example 7Find the Elastic properties of brass
Example 8Searching for LCD properties of a particular compound/s
Example 9Whatever happened to polymers?
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Example 1Use the Generate Structure from Name feature
• CAS number 139755-83-2
• Vanadium oxide
• Diiodoacetylene
• Diazepam(Smiles): CN1c2ccc(cc2C(=NCC1=O)c3ccccc3)Cl
• Codeine: OROGSEYTTFOCAN-DNJOTXNNSA-N
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Example 2Find Substances with a general structure and information containing keyword fragments (diabetes or pregnancy)
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Draw or generate structure from name
Benzoic Acid
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Example 3Search Operators
Operator Definition Example Query
AND Retrieves records containing data in both fields
Looking for compounds with melting point between 20-25C containing 2 elements
MP.MP='20 - 25' AND IDE.NE='2'
OR Retrieves records containing at least one of the fields
Looking for reactions using water, methanol or coal as a catalyst
RXD.RGTCAT = 'water' OR RXD.RGTCAT = 'methanol' OR RXD.RGTCAT = 'coal'
NOT Retrieves records with the first field selected and not the second
Looking for compounds with a dielectric constant greater than 6 but not at temperatures less than -100C
DIC.DIC>'6' NOT DIC.T<='-100'
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Example 5Search Operators
Operator Definition Example Query
NEXT Retrieves records where the first field appears before the second
Looking for compounds that have shown to improve heart conditions
PHARM.RE = ‘improved' NEXT PHARM.RE = ‘heart'
NEAR Retrieves records were the requested fields appear adjacent to each other
Looking for products isolated from the fermentation of beer
INP.INP = 'beer' NEAR INP.INP = 'fermentation'
PROXIMITY Retrieves records where the content of both fields relate to each other
Looking for compounds with a refractive index of 3.4 at temperatures over 20C
RI.RI='3.4' PROXIMITY RI.T>'20'
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Example 4Find Antibiotics isolated from marine organisms
• A group of chemists/biochemists working on new antibiotics isolated from marine organisms.
• They want to know more about compounds which show a common sub-structure, such as steroids, and whether they also show more than one pharmacological effect.
• Promising candidates need to be investigated to find other compounds with same sub-structure but not showing any effect.
• Those compounds then need to be synthesized for testing.
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Create a substance query which finds all compounds isolated from marine organisms and which show antibacterial effects.
Open Reaxys and select the substance query tab. Switch to advanced mode and open the datafield tree. Find natural product and expand on marine.
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Do the same for pharmacological effect “antibacteria”. Ensure that you do a wildcard search
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Check the resulting compounds for interesting candidates by browsing in the grid view, e.g. compounds with a dioxybridge show additional pharmacological effects.
Select one of the interesting compounds and transfer it to the query window. There create a sub-structure query and run the search.
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Exclude all compounds with bioactivity data from the list of found compounds by applying a bioactivity filter
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Find ways to synthesize the remaining compounds, which are not commercially available, by using the synthesis planner and/or reaction queries
Example 5Using the Quantum Chemistry field
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Example 6Isomerization of azobenzene by light or heat
Enter cis-azobenzene and generate structure by name, then select it as the product
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Switch to advanced mode and open the datafield tree. Find reaction data, reaction details, other conditions and expand on light.
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Do the same for reaction condition “heat”.
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Your query should then read as follows
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Limit your results to isomerization reactions
Example 7Find a publication detailing the Elastic properties of brass
Search for elastic properties of brass via molecular formula, Cu(0.5-100)Zn(0.5-100).
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First, do a search for the Molecular Formula range.
Apply data filter to the substance hit set (by using Physical Data >Mechanical Properties)
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Or do an advanced search
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Example 8LCD properties of a compound
Use the structure generator to draw the following structure:
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An Alkyl or Aryl -4’-cyanobiphenyl
We are interested in the words liquid and crystalline/crystal appearing adjacent to each other and in the order shown, it would also be wise to search for instances of the words hyrdrophobic or hydrophobicity
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Example 9Whatever happened to polymers?
Searching on explicit Polymer names as chemical names is useless, such as poly(styrene)
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You can search on chemical name containing “poly” or “polymer” and find lots of polymers.
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For *polymer*, you get over 38000 substances.
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You can also search by monomer structure. For example if you want information on a copolymer of ethylene and propylene, draw both (or several) monomers (NOT the repeat units) and run the search.
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Lets try again with methyl methacrylate/styrene
