Reaxys Introduction and Basic Navigation

Reaxys Introduction and Basic Navigation
Leow.Pei.Shan – Aug 2012 Regional Product Sales Manager – PBT (APAC) Reaxys ® is a registered trademark owned and protected by Elsevier Properties SA and used under license.

Agenda Reaxys Overview Basic Navigation Reaxys Xcelerate Quizz Time
February 25, 2019 Agenda Reaxys Overview Basic Navigation Exercise 1 : Reactions Search Exercise 2 : Substances and Properties search Exercise 3 : Synthesis Plan - Stereo Selective Synthesis Query Exercise 4 : Literature Search Reaxys Xcelerate Analysis View Enhanced Report Autoplan Quizz Time

Reaxys Overview Basic description of key icons at header. My alerts and my settings only for users with remote ids. Very personalized and customized. -History icons shows your history of search at your desk. So if time out, just click on refresh icon and click history, you will be able to back trace your search history. But, not all the time. However, if one is using remote ID, the history stays. Report – for you to generate reports and send to your partners with ease. But, as we go along, you will see another way to generate output of your search history. Am generally impatient, so will not look or conduct bliblographic search, but say if you obviously know that you are doing a bibliographic search for an article, a particular issue, volume, then go ahead, it will be like what one generally does in a literature search database. Begin by looking at substances and properties – green icon – under marvin sketch and properties (basic and advance) and then the reactions tab just to see how it looks different. In using this tab, what we have in mind is to either use the name to search or to draw the end molecule or similar molecule that we have in mind.

Reaxys Overview Excerption Chemical Structures Physicochemical
February 25, 2019 Reaxys Overview Chemical Structures Physicochemical Properties Excerption Pharmacology Chemical Synthesis Just to explain a few key features of Reaxys which makes it unique: 1st, the source of information that makes up the Rx work tool comprise of up to 400+ carefully selected journals that touches across organic/inorganic/organometallic chemistry data. In terms of chronological coverage, it covers information from 1771 to present day, including Euro, US and world patent office. As such, this is suitable for med chem/catalysis and/or material science/ synthetic chemists/ Biochemist/ polymer science, whether you are looking into total organic synthesis of natural products/asymmetric synthesis. 2ndly, what Elsevier did which was to extract valuable chemical information from these journals and patents and present them using specific excerption algorithm, specific to the search needs of the researcher both in academia and commerical settings. We excerpt Chemical structures even if they appear in footnotes, Physiochemical properties, Chemical Synthesis, Pharmacology details. We excerpt all data, regardless of whether they support main theme of the publication or are just some facts. Most other competitor excerpt base on main theme. In terms of physiochemical properties, Reaxys excerpt up to 450 different properties such that if say you are in biodiesel research and is keen to look into specific azeotropes properties, you can also get access to that. Space groups/crystallography related search, you can also drill down to those topics. All the data are experimentally obtained. For articles that are published with calculated data, we will not excerpt them and so will not come up when you do a reaction search although when one does a literature search, it will still be available for reading. Experimental procedures also tag along with each reaction steps as long as it has been prepared before. And of course, the way to export your search data is also designed to be intuitive, even when you send them across to your research partners overseas. for certain customers, we are always open to customization of this database. As an example, we worked quite closely with certain commercial set-ups to combine their in-house research papers into this database 3rdly, it will be the synthesis planning tool that can help you plan your retro synthesis steps. You could continue to click on the synthesis button to conduct re-tro synthesis steps. Further to this, you could also view chemical availability. Need to stress that this is very US centric and so for each country, we need to consider if these chemicals can pass the regulatory body to be imported into [country]. Click. We excerpt all data, regardless whether they support the main theme of the publication or are just some facts

Basic Navigation 1.0 – Reactions
Use Ibuprofen as example.

Reaxys Generics Template Library Atoms Mapping Snapshot of marvin sketch and properties data. By default, we are at ChemAxon, Dotmatics Elemental is an alternative. If you like to use other structure editiors like chemdraw/accelrys/infochem,you will need to download the applets off the reaxys webpage – under the segment call “ system support” Just to highlight some features of this sketch – template library, Reaxys generics – to explain what the generics refers to. Object icon…. How to enlarge the sketch.

Actual Search Query Exercise 1…..Making use of Reactions tab. Aim:
-Formation of a dipropylethylamino chain on a fused ring. To do: -Search in Reaxys for similar reactions. Possible starting material could be dipropylamine. -View experimental procedures, look for other reaction details, SDS of reagents, cost, commercial availability so as to find the most suitable and quickest way to carry out the cooking.

Actual Search Query – Exercise 1
S 6, meaning allows for substitution. No limit to the number of substituents possible. 2- Point cursor to blank space and type .S 6. Move cursor to the C of interest and click to indicate maximum substitution. select drop down and select “single reaction arrow”. Explain about how in this example, we are not fixing the N to N atom. .S6 refers to maximum number of substituion. If one wants to limit it to only 4 substituents and below, type .S4 into the blank space.

Line 1 – Refers to Bromo group Line 2 refers to Tosyl group.. Stress that similarly, one can view all the related information : experimental procedures /patent information / analytical information / other reactions / what each icons means, Title/Abstract / Full text / Show Details.

Basic Navigation 2.0 – Substances and Properties
On substances and properties tab.

Basic Navigation 2.1 – Substance and Properties
Reaxys Generics Template Library Atoms Mapping Snapshot of marvin sketch and properties data. By default, we are at ChemAxon, Dotmatics Elemental is an alternative. If you like to use other structure editiors like chemdraw/accelrys/infochem,you will need to download the applets off the reaxys webpage – under the segment call “ system support” Just to highlight some features of this sketch – template library, Reaxys generics – to explain what the generics refers to. Object icon…. How to enlarge the sketch.

Basic Navigation 2.1 – Substance and Properties
Physical data search very much focus on properties. This is the 450 properties that one can play around with and make a selection or filter on. If you have a lot of criteria, once the filters are executed, it will all be taken into considerations and filter accordingly. Help icon for further explanations…

Actual Search Query Exercise Making use of Substance and Properties tab Aim: To find reactions and properties data for 1st and 2nd generation GRUBBS catalysts. To do: Create an atom list Use of generic query atom icons Selecting bond order Organometallic eg. An important area that has a lot of industrial applications, as catalyst in polymer chemistry, as additive in oil and gas industry, as anticancer drug. Titanocence dichloride, eg. R-M-X CpTiCl2

1- Click to select “Ru”. (Alternatively, just type “Ru” onto the white space) 2- Click , place cursor to Ru and upon seeing a round circle, click on it to draw a single bond. 3- Click , click the drop down button to select “lasso selection”. Lasso “Ru” and 1 “C” 4- Click Object  Bond  Type  Any 5- Select 2 of the “C” and click Click “Atom list” and select “C”, “P”. Click close. 6- Select the other 2 “C” and select Select “X” (Alternatively, just point cursor to the “C” and type in “X”) 7- Click Transfer Query. MMC- coupling M-C M-C=O M-C=O-M M-X MM-C=O

To return this hit, one must select “substructure” and as “catalyst” under search in the properties tab. Purple grid – 5 parts of icons. Availability / Molecular weight / 3D/ Triangle icon for report Synthesize icon. 11 prep out of 173 rxn means what? Blue grid – Correlation between physical data and physical data below the identification. 534 = no of reference.

Actual Search Query – Exercise 2 – Tsetse Fly
Search the substance fields, “Basic Index” to find 85 compounds tested on the tsetse fly. ……and this substance with data in the Bioactivity field showing that although ticks were the target, the substance also killed tsetse flies Results include, for example, this substance with data in the Ecotoxicology field ……this substance from a patent for a tsetse fly-related use (Use field)

Actual Search Query – Exercise 4 – Tsetse Fly
How many of these compounds are from natural products? Filter by “Natural Product” – Left Column For example:

Actual Search Query Exercise You face a synthetic challenge of halogenating a double bond in a ring that has substituents attached to both atoms of the ring double bond. Furthermore, you wish to do so in a stereo selective manner, with the two halogen atoms added in an anti-configuration. You need to determine if there are any examples of this type of addition in the literature and to create a report of what you find. Aim: To do comprehensive stereoselective search on both chiral centers and double bonds. To do: Setting the query as simply but able to return results as accurately that is needed. Create the synthesis plan Create the report

1- Use of Marvin sketch to plot this query reactions in total but atoms not mapped may return unwanted hits when sorted according to MW. See below. 1- Look at MW distribution and will see 1,2,3 as false hits.

1- Atoms are mapped. See 1 and 2. 2- Narrowed to 513 reactions. See below. 3- Structure of interest are highlighted in blue.

1- Atoms are mapped. 2- Narrowed to 16 possibilities after specifying absolute stereochemistry See below. 3- If “H” atoms are being drawn as well, search will be narrowed to 12 possible reactions to only give exact “Z” conformations

1- Atoms are mapped. 2- Specified that all the 4 C must be in a ring. Not necessary to code “cis” or “stereo” search as Reaxys X is intuitive enough to know that once it’s a ring, “cis” conformation will be the likely formation. out of 513 as search in step 2 is filtered through.

1- Atoms are mapped. 2- We are looking for substituents group as well and not “H”. 3- Use of “G” and not “G* ” and atoms must also be mapped. 4- 3 hits are returned. G* will cause it to also cause it to look at G combined to open groups at the C below it where S4 is at, since S4 refers to opening the site up for substitution. - Remember to map G to G atom as well.

Synthesis Planning

Output

Actual Search Query Exercise 4.....Plant Pollinators Aim: To do:
To make use of Literature Search to obtain meaningful data. To do: - Make search on Literature->Formed Base->Quick Search - Retrieve abstracts, journals name, patent citations, view citation articles

Search titles and abstracts for plant pollinators. Retrieve a list of journal and patent citations View abstracts…. And patent Front Page information View structures and reactions from any patent or article with structures. ….And link to the substance record.

.And link to the substance record. View the list of articles that cite this article ..without ever leaving Reaxys

Reaxys Xcelerate – Close View Analysis
Selecting Solvents (classified) … Close tab analysis allows one to correlate and analysis 2 different properties of interest. …shows number of records that has Yield of different range (in yellow)

Reaxys Xcelerate – Enhance Report
Ibuprofen Synthesis

Reaxys Xcelerate – Auto Plan
Ibuprofen Synthesis route/rxn routes are selected base on what criteria we have set-forth. If we only want to see more than 50 % yield, then, we can select that under My alerts. Only for those who have access to remote IDs. If only want to see 10 rxns at one go, we can also set that in place. Allows one to see the top 10 reactions in 1 sec as well as their synthesis plan.

Reaxys Xcelerate On Reaxys On Rx Xcelerate February 25, 2019
Reaxys Xcelerate Feature On Reaxys On Rx Xcelerate Report Getting 1 reaction and the key spectra into one document requires leaving Reaxys and merging 2 documents Collecting data across contexts eliminates the step of collating data from various documents Autoplan Creating 1 effective synthesis path requires ~ 15 minutes 10 effective synthesis plans available in 1 minute Close View Analysis It is not possible to see for example which solvent brings the highest yields. The correlation of two data types, like solvent and yield, is an insight unavailable on Reaxys Taxonomies Similar solvents, catalysts or reactions can’t be grouped Viewing similar data types in correlation is producing valuable insights especially if the user is looking for similarities Chat All customer issues, whether easy or complex, go through the same channel. Instant and direct access to experts 2D alignment For each compound in a hit set the query structure is oriented depending on the total structure Instant recognition of your core drawing, overview enabled Report Features and annotation features. Autoplan features. Close View Analysis Feature Taxonomies – means what – grouping of similar functional groups together, methanol / propanol / ethanol all together under 1 grouping. Chat line – not so quick for set-up yet mainly because we want questions to be specific to the technical part, in particular the formation of queries. 2D alignment – this is a feature that makes it more intuitive, like if you draw the core structure, it will be able to recognize the parts. February 25, Slide 41

Quizz Time As a cosmetic RnD chemist, you have been tasked to work with your biology colleagues to look into anti-hair loss strategies. A normal strand of hair stays on our scalp for about 4 years before dropping off naturally from the hair follicle. An active on the market, Oleanolic Acid, at certain concentration, has been known to inhibit the activity of 5-alpha 1 and 5-alpha 2 reductases. These 2 enzymes are responsible for producing dihydrotestosterone (DHT). DHT is a male hormone that shortens the hair growth cycle and thus cause hair follicles to become smaller and eventually lead to hair loss. You need to : Look at current natural sources of Oleanolic Acid that were successfully extracted. Look at possible synthetic pathways to see the type of yields, raw materials availability as you are competing with your colleagues in biology who are actively looking at bio-fermentation processes which are viewed to be “cleaner” and “greener”. Look at other side groups other than –COOH, synthesize them and pass them to your med chem/biology colleagues to screen for potential bio/pharmaco- activities.

Quizz Time Look at current natural sources of Oleanolic Acid that were successfully extracted. What should you do? Wikipedia Erm…Well…. ScienceDirect Party this Friday night…For sure… Wikipedia may not be able to provide all the sources and will not be able to tell you exactly which could be successfully extracted. ScienceDirect …well….depends on your personality and timeframe of your research really… 2 ways to search on Reaxys, 1- Through Substances and Properties Tab and 2 – Literature tab.\ Finding information like this is meaningful especially from a sustainability point of view / green routes point of view.

Quizz Time Look at possible synthetic pathways to see the type of yields, raw materials availability as you are competing with your colleagues in biology who are actively looking at bio-fermentation processes which are viewed to be “cleaner” and “greener”. What should you do? -> > Erm…Well… -> > > If you are on Reaxys -> > > If you are on Reaxys X

Quizz Time Look at other side groups other than –COOH, synthesize them and pass them to your med chem/biology colleagues to screen for potential bio/pharmaco- activities. What should you do? -> > -> > > > Give up. Look for a/another job. 2nd option can be the first step and then, explore the use of Marvin Sketch further to look into specific rxns.

Thank you Q & A? Complete Training Survey ……………………………………………………………………
Reaxys Lifeline Support Reaxys website: Reaxys (Taiwan): (Karen Liu)

Reaxys Introduction and Basic Navigation

Similar presentations

Presentation on theme: "Reaxys Introduction and Basic Navigation"— Presentation transcript:

Similar presentations

About project

Feedback

Log in

Auth with social network:

Reaxys Introduction and Basic Navigation

Similar presentations

Presentation on theme: "Reaxys Introduction and Basic Navigation"— Presentation transcript:

Similar presentations

About project

Feedback