Presentation on theme: "Reaxys training Dr. Charles Martinez. Table of Contents What is Reaxys? What do Chemists want to know? Who uses Reaxys? Reaxys 2013 expansion Examples."— Presentation transcript:
Table of Contents What is Reaxys? What do Chemists want to know? Who uses Reaxys? Reaxys 2013 expansion Examples Slide 2
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 Slide 3
Chemistry as organizing principle Slide 4 One Record across time, documents and publishers
How do we collect the content? Physicochemical Properties Pharmacology Chemical Structures Chemical Syntheses All Data, independent from main theme of the article Relevant Data can be in footnotes, descriptive texts, schemes, tables…
Slide 6 What do chemists want 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 University 4 Stanford University (with faculty on Reaxys Advisory Board) 5 California Institute of Technology (Caltech) 6 University of Oxford 7 University of California, Los Angeles (UCLA) 8 University of Cambridge 9 University of Hong Kong 10 Imperial College London (with faculty on Reaxys Advisory Board) Slide 7 In addition, we have 84 of the top 100
What exactly is Reaxys? Slide 8 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 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
Content Expansion 2013 Agricultural and Biological Sciences Biochemistry, Genetics and Molecular Biology Chemical Engineering Chemistry Dentistry Earth and Planetary Sciences Energy Engineering 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 Science Immunology and Microbiology Materials Science Medicine Neuroscience Pharmacology, Toxicology and Pharmaceutics Physics and Astronomy Veterinary Reaxys coverage has been extended from the core chemistry focus to include
Worked examples Example 1 Use the Generate Structure from Name feature Example 2 Find Substances with a general structure and information containing these keyword fragments Example 3 Operators Example 4 Find Antibiotics isolated from marine organisms Example 5 Using the Quantum Chemistry field Example 6 Isomerization of azobenzene Example 7 Find the Elastic properties of brass Example 8 Searching for LCD properties of a particular compound/s Example 9 Whatever happened to polymers? Slide 12
Example 1 Use 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 Slide 13
Example 3 Search Operators OperatorDefinitionExampleQuery ANDRetrieves 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' ORRetrieves 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' NOTRetrieves 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' Slide 18
Example 5 Search Operators OperatorDefinitionExampleQuery NEXTRetrieves 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' NEARRetrieves 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' PROXIMITYRetrieves 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' Slide 19
Example 4 Find 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. Slide 20
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. Slide 21
Do the same for pharmacological effect “antibacteria”. Ensure that you do a wildcard search Slide 22
Slide 23 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. Slide 24
Exclude all compounds with bioactivity data from the list of found compounds by applying a bioactivity filter Slide 25 Find ways to synthesize the remaining compounds, which are not commercially available, by using the synthesis planner and/or reaction queries
Example 5 Using the Quantum Chemistry field Slide 26
Example 6 Isomerization of azobenzene by light or heat Enter cis-azobenzene and generate structure by name, then select it as the product Slide 27
Switch to advanced mode and open the datafield tree. Find reaction data, reaction details, other conditions and expand on light. Slide 28
Do the same for reaction condition “heat”. Slide 29
Your query should then read as follows Slide 30 Limit your results to isomerization reactions
Example 7 Find 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). Slide 31 First, do a search for the Molecular Formula range.
Apply data filter to the substance hit set (by using Physical Data >Mechanical Properties) Slide 32 Or do an advanced search
Example 8 LCD properties of a compound Use the structure generator to draw the following structure: Slide 34 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 Slide 35
Example 9 Whatever happened to polymers? Searching on explicit Polymer names as chemical names is useless, such as poly(styrene) Slide 36
Slide 37 You can search on chemical name containing “poly” or “polymer” and find lots of polymers.
Slide 38 For *polymer*, you get over 38000 substances.
Slide 39 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.
Slide 40 Lets try again with methyl methacrylate/styrene