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Copyright 2010 Elsevier Properties SA. All rights reserved.Reaxys is a trademark owned and protected by Elsevier Properties SA and used under license.

Reaxys Quick Reference Guide


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Table of Contents

Last revision 11-Feb-10.

1 The basics where to find what?

2 Homepage

3 My Settings

4 Generate a structure from a name

Reactions

5 Query tab

6 Query tab Conditions (Form-based)

7 Query tab Conditions (Advanced)

8 Results general overview

9 Results reactions tab

10 Results filter by

11 Synthesis Plans

12 Output

13 History

14 My Alerts

Substances and properties

15 Query tab

16 Query tab Properties (Form-based)

17 Query tab Properties (Advanced)

18 Results overview

19 Substances (Table) tabSubstances (Grid) tab

20 Text, authors and more

21 Query tab

22 Citations tab


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The basicsWhere to find what?

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To start Reaxys, go to www.reaxys.com

To find more user tips, go to www.info.reaxys.com. Here you can find:

Registration form for the Reaxys newsletter

Training & Support information, with

o Training Center giving access to various instructional materials (demos, videos, manuals)

o Webinar schedule offering regular training sessions and registration form

o Frequently Asked Questions

o Downloads of software (plug-ins, structure editors) and of documentation (training materials)

o Customer Care Contact details:

Europe, Middle East, Asia and Africa +49 69 5050 4268 [email protected]

Americas +1 888 615 4500

+1 212 462 1978 if calling outside USA & Canada

[email protected]

Japan +81 3 5561 5034 [email protected]


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Homepage

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How to find the preparation of a compound?1. Ensure the reaction tab is selected and double click the drawing pane2. Draw the desired compound structure in your preferred editor and click Transfer Query3. Click the search button and browse the result.

Note: an Auto-Search algorithm starts if an "As Drawn" search has no hits; Reaxys performs a "substructure onheteroatoms" search, and then a "substructure on all atoms (if no hits are found). When a structure/reactionquery is combined with a factual query, this feature is turned off.

1 Main Navigation:The following screens are available- Query- Results- Synthesis Plans- History- My Alerts- My Settings- Help & Register, Login

2 Query tabs- Reactions- Substances and properties- Text, authors and more

3 Generate structure from nameA chemical name will be translatedinto a structure.

4Structure/reaction windowWindow to add a structure or reactionwith additional search possibilities.

5 Add Reaction/Bibliographic dataThe Conditions (Form-based) andConditions (Advanced) links allowentering further reaction orbibliographic data constraints.

6Search buttonLaunch a search.

7 Command buttonsClear, load or save a query. The Loadfeature also supports batch querying.


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My Settings

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Note: the default search settings can be changed through the My Settings menu. Click the Save button and aconfirmation that your settings have been updated is displayed. The new settings will be effective from thenext time you login.

1 My SettingsSelect this tab to- Modify application settings- Modify personal data- Change password

2 Modify Application SettingsSelect this item to specify yourpreferred Structure editor, Reaction &Substance default search options, Nbof hits per page and Highlights colors.

3 Structure editorChoose your preferred editor. Findinformation on download of the pluginrequired for the use of externalstructure editors.

4Reaction/Substance searchoptionsDefine the default search options forreactions and/or substances query.

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Hits per pageSelect preferred number of displayedhits on the Results menu.

Highlights colorsSelect preferred colors to highlight thesearched structure and/or text/data.

7 Back & Save buttonsConfirm new settings with Save oruse Back to return to the item list.


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Generate a structure from name

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Available on the Reactions andSubstances & Properties query tabs.

Generate structure from namebuttonClick this button to open an input field.

2 Input fieldEnter a chemical name as systematicname or trivial name, an InChI key, aCAS Registry number or a SMILESstring. Click submit to launchstructure generation.

3 Structure/reaction windowThe generated structure is displayed

in the structure/reaction window, youcan now:

a) Start the search immediately.b) Edit the structure by double

clicking the box (or by doing aright-click); modify it in theStructure editor.

c) Define the search type, add

further search conditions or/andselect additional query options.

Note: this option only works if the corresponding compounds are available in the Reaxys database.


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Reactions query tab

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How to load a saved query?1. Ensure you are on the query tab and click the load query button2. Browse to locate your saved XML file and click open

1 Structure/reaction boxThis window contains the requestedstructure or reaction, with additionalquery features. It is also possible tocopy the structure to the Substancesand Properties query tab.

2 Search as/byIf needed, define the role of thesubstance.

3 Select the search typeSelect how the structure should besearched: asdrawn (includingpossible query features added in yourstructure) or as substructure search.(In a substructure search the resultsinclude additional substituents).

4 Additional query optionsSelect additional options to refineyour search.

5 Add further search conditionsClick the Conditions (Form-based) orthe Conditions (Advanced) links torefine your search by adding furtherreaction or bibliographic data

constraints (e.g. a yield or/and authorconstraint).

6 SearchClick this button to launch the search.A search progression box appearsallowing you to cancel your researchor to view your hits retrieved.


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Reactions query tabConditions (Form-based)

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Note: the Conditions (Form-based) link opens up forms containing commonly used fields for the given searchform; they are grouped as either Reaction Data (such as yield or reagent name) or Bibliographic Data (such asjournal title or patent assignee). The All Reaction fields and Title/Abstract/Keywords fields are text fields; useBoolean operators to search these fields.

1 Reaction dataSpecifyreactant name, productname, reagent, yield and/or allreaction fields.Various selected fields are combinedwith the Boolean operator AND.

2 OperatorsSelect the appropriate operator fromthe drop-down menu.

3 Selection listSelection appears when typing entry.

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Numeric FieldFor a numeric field select theoperator followed by entering thenumber or range in the text box.

Bibliographic dataSpecifyauthors, patent assignee,journal title, title, patent number,patent country code, publication yearand/or title/abstract/keywords.Various selected fields are combinedwith the Boolean operator AND.

Expand Index feature (for allsearch fields)

The box allows convenient indexbrowsing and multiple entryselections. Click the Transferbuttonto add the selected data to the query.

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Reactions query tabConditions (Advanced)

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Note: the Conditions (Advanced)allows entry of complex and sophisticated property queries in combinationwith the structure or reaction queries following two ways:1. Type the query directly into the query box, with single quotes around the field data,

2. If the necessary field code is unknown, locate it using the Show fields and Operators hyperlink.

1 Show Fields and OperatorsExpand the fields list. Manually selectthe field code from the hierarchicallist or use Search for Field button.

2 Fields CategoryClick the + sign to expand theneeded fields list.

3 Search for Field buttonType the name of the desiredconstraint, and click this button tolocate the field.

4 OperatorsSelect the appropriate operation fromthe drop-down menu.

5 Expand Index feature (for all

search fields)The box allows convenient indexbrowsing and multiple entryselections.

6 Transfer the field dataSelect the needed data entry(ies).Click the Transferbutton to add thedata to the query

7 Check SyntaxAllows query verification in case ofmanual entry.


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Reactions resultsGeneral overview

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Have a look at the breadcrumbs at the top of the screen; it shows the actions done on your initial hitset. Clickone of the red-framed boxes to quickly jump to a previous set of data or initial query.

1 BreadcrumbsGraphical navigation helps keep trackof your results analysis.

2 Create AlertClick this link to create an alert.

3 Reactions/citations tabReactions tab is displayed by default,

but you can switch to the citationstab.

4 Filtered byRefine results by applying filterslinked to the reaction (yield, recordtype, reagent/catalyst, solvent,reaction type, no. of steps) or linkedto bibliographic data (document type,authors, patent assignee, journal title

and publication year).

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Tool barAccess Limit to Selection, Output,and Sort by features.

Maximizer/minimizer toolIncrease or decrease the size of yourdisplayed structures.

Reaction results

Gives a quick overview of the resultsdisplayed with key data in a table.Display the title and the abstract, theoriginal article or patent (Full Text)and access related information inScopus (View citing articles).


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Reactions resultsReactions tab

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The navigation tool to the right of the screen allows you to easily jump from one hit to another, or to thefirst/last hit, without need of scrolling down multiple times.Note: information on the citations tab of the reactions results window can be found on page 22.

Click or a structure to get a pop-upmenu with information or sub items.

1 Display further options & dataReaxys RN (Reaxys registrynumber), MF (molecular formula),CAS-RN (CAS registry number),show details (display information asphysical-, spectral- data etc), copystructure to Clipboard/Query screen,

copy reaction to Query screen.

2 Access bibliographic detailsDisplay the title/abstract, the full textof your reference and view citingarticles in Scopus. Show experimentalprocedure excerpted from patents.View scheme of multi-steps sequenceas a synthesis plan.

3 Commercial availabilityAccess the commercial availability ofa substance and leads to appropriatecompanies (eMolecules/Symyx ACD).

4 Limit to selectionSelect the important hits and click thisbutton to restrict your hitset.

5 OutputExport data in the desired format.

6 Sort bySort results ascending ordescending by Reaxys-RxID,reactant & product availability, Nb ofreferences, yield, MW of product orReaxys ranking (default).


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Reactions results tabFilter by

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Note: filter by feature allows for rapid and easy refinement of your results. Click the double arrows to expandthe selection list. Two filter options are available for each reaction specification:

1. To retrieve a pre-defined selection list, use the by Group tab.2. To specify a filter value or range (flexible filter), select the by Value tab.

1 Filter bySelect filter(s) linked to reactionspecifications:- Yield- Record type- Reagent/catalyst- Solvent- Reaction type

- No. of steps

2 By Value tab: flexible filterEnter a specific value or a range torefine result sets with more options.

3 By Group tab: pre-defined listCheck boxes to limit or excludeentries of the pre-defined selection.

4Limit to/exclude buttons

Click the appropriate button.

5 Refine on Filter fieldClick the More button to expand thescope of the selection, and to furtherrefine the filter by feature. Sort thechosen data by Value or byOccurrence.

6 Filter bySpecify filter(s) linked to bibliographicdata:- Document type- Authors- Patent assignee- Journal title- Publication year

Effect of Filter by Yield on Breadcrumbs

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Filter by Value

Filter by Group

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Synthesis plans

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Note: the overall scheme of multi-step reactions can be displayed in the synthesis plans page. A click on the

View Scheme hyperlink opens the multi-step sequence as a new synthesis plan for a better overview.

ClickSynthesize below any chemicalstructure in any of the results tabs toget the Synthesis Plans page.

1 Undo, open and save buttonsTo undo last action, open or savesynthesis plans. Click on the X of thetab to delete an unnecessary plan.

2 Copy plan to new pageOpens a new tab of your currentsynthesis plan, where you candevelop another retrosynthesis.

3 OutputExport Synthesis plan

4 Synthesis plans representationChoose horizontal tree or vertical treefor the display of your plan.

5 ModifyModify discards the already definedsynthetic step and proposes otherpreparations for the compound.

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SynthesizeClick the synthesize link to display

various preparations for a compound.Click the add button of the selectedstep to incorporate it in your plan.

Commercial availabilityAccess the commercial availability ofa substance and leads to appropriatecompanies (eMolecules/ACD).


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Output

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Note: output function is available on each of the results screens; it allows the export of any type of hitset(reactions, substances and bibliographic data) in any desired format. In the substance details table, clickselectdata to choose the type of property you want to export.

1 OutputChoose the type of results to export:

2 toDefine the format of exported file:PDF/Print, XML, Microsoft Word orExcel, TXT for LiteratureManagement Systems, or RD File.

3 Include the following headline

Check the box and enter a headlinethat will be shown on each page ofthe document.

4 Output rangeDefine the hits to export: all hits,selected hits (select it before clickingthe output button), or a range (enter itin the box).

5 Output containsDefine the type of data to export.Reactions output: include structuresand/or experimental procedure, allavailable data or identification dataonly.Substances output: include structuresand all available data or identificationdata only or select data.

Citations output: include structuresand/or abstracts

6 OK buttonClick the OK button to launch yourexport. Click cancel to stop thisaction.

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History

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Note: the history table displays all current-session hitsets resulting from queries or from any analysis of yourresults; the most recent hitsets are shown at the top of the list. Here you can also graphically combine hitsets.

1 Temporary listsThe upper part of the table shows allhitsets from the current session.Click View to display a list as activehitsets in the results page.Click Store (enter a filename andcomment) to save a list.

2 Saved listsThe lower part of the table shows the

hitsets stored by the user. All savedhitsets are displayed if the user islogged in to Reaxys.Click remove to delete a saved list.

3 Query columnClick Edit to display the queryassociated with the hitset in the querypage

Note that hitsets resulting fromfiltering will not display the query inthis column

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Combine hitsetsSelect two or more lists by checkingthe box closed to the query column;the combine hitsets button becomesavailable and will provide graphicaltools to combine the selected hitsets

in various ways.

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If 2 hits selected If >2 hits selected

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My Alerts

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Note: alerts are user-defined search queries stored on the Reaxys server, so that they can be accessed andretrieved any time you log-in to Reaxys. You can choose to run it either monthly or each time the database isupdated. You will receive an alert notification by email with a link to Reaxys allowing you to access the Alertresults. Alerts are by default sorted by their Name.

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My Alerts menu displays the list ofavailable alerts together with thegiven result sets.How to create an alert?Create and run a query. On theresults menu, click the Create Alertlink located just below the Querybreadcrumb. Fill in the Alert form and

click the Save button.

2 View results buttonClick this link to jump to the Resultsmenu and access the hits linked toyour alert.

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Modify alertModify the options of your alert(Name of Alert, Copy to,

Comment/Description, FrequencyandEmail format). Click the Save button.

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DeleteCheck the box closed to the alertname column; the delete buttonbecomes available and will discardthe concerned alert.

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Substances and propertiesQuery tab

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How to find information on specific compounds?1. Ensure the substances & properties tab is selected and double click the drawing pane

2. Draw the desired compound structure in your preferred editor and return to Reaxys by clicking thetransfer button

3. Click the search button and browse the result.

Note: Reaxys remembers the last query form used, and will reopen it in the next session; the substances andproperties query tab can then become an entry form.

1 Structure/reaction boxThis window contains the neededstructure, with additional queryfeatures. Two buttons enable thestructure to be copied to the reactionsquery tab, and also to delete it.

2 Search asDefine the type of structure search: as

drawn (including possible queryfeatures added on your structure), orSubstructure search.

3 Additional query optionsSelect additional options to refine thesearch.

4 Further optionsIf needed, add further options, such

as Include related Markush orNumber of Ring Closures

5 Add further search conditionsClick the Properties (Form-based) orthe Properties (Advanced) links toenter further substance orbibliographic data constraints.

6 SearchClick this button to start searching


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Substances query tabProperties (Form-based)

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Note: the Properties (Form-based) link opens up forms containing commonly used fields for the given search

form; they are grouped as either Substance Data (such as spectra or solubility data) or Bibliographic Data(such as journal title or patent assignee). The Search text in all facts and Title/Abstract/Keywords fields aretext fields; use Boolean operators to search these fields.

1 Substance dataSpecifySearch text in all facts/Search for (to add several terms inthis text box, separate them with a ;;they will be combined with theBoolean operator OR), identificationdata,physical data, spectroscopicdata, bioactivity data and/or

ecotoxicological data.Various selected fields are combinedwith the Boolean operator AND.

2 OperatorsSelect the appropriate operation fromthe drop-down menu; for a numericfield enter the number or range in thetext box.

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Bibliographic dataSpecifyauthors, patent assignee,journal title, title, patent number,patent country code, publication yearand/ or title/abstract/keywordsVarious selected fields are combinedwith the Boolean operator AND.

Selection listSelection appears when typing entry.

5 Expand Index featureThe box allows convenient indexbrowsing and multiple entryselections. Click the Transferbuttonto add the selected data to the query.


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Substances query tabProperties (Advanced)

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Note: The Properties (Advanced)allows entry of complex and sophisticated property queries in combinationwith the structure queries following two ways:1. Type the query directly into the query box, with single quotes around the field data,2. If the necessary field code is unknown, locate it using the Show fields and Operators hyperlink.

1 Show Fields and OperatorsExpand the fields list. Manually selectthe field code from the hierarchicallist or use Search for Field button.

2 Fields CategoryClick the + sign to expand theneeded fields list.

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Search for Field buttonType the name of the desiredconstraint, and click this button tolocate the needed field.

OperatorsSelect the appropriate operation fromthe drop-down menu.

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Expand Index feature (for all fields)The box allows convenient indexbrowsing and multiple entryselections.

Transfer the field dataSelect the needed data entry(ies).Click the Transfer button to add thedata to the query.

7 Check SyntaxIn case of manual entry of the queryinto the Advanced search box, checkthe used syntax by using the CheckSyntax hyperlink.


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Substances and propertiesResults overview

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Note: information on the citations tab of the substances results window can be found on page 22.

1 BreadcrumbsGraphical navigation helps keepingtrack of your result analysis.

2 Substances (grid)/substances(table)/citations tabThe substances (table) tab isdisplayed by default, but you canswitch to the substances (grid) or

citations tab.

3 Filtered byRefine results by applying filterslinked to the substance (molecularweight, number of fragments,physical data, spectroscopic data,bioactivity and natural product) orlinked to bibliographic data (docu-

ment type, authors, patent assignee,journal title and publication year).

4 Tool barAccess limit to selection, output, sortby features.

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Maximizer/minimizer tool

Increase or decrease the size ofdisplayed structures.

Substances and properties resultsGives an overview of the resultsdisplayed with key data in a table.Show details & data hyperlinks allowdisplaying properties for each hit.


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Substances and propertiesSubstances (Table) tab

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Click a specific link in the available data column to only expand the needed data.

Click or a structure to get a pop-upmenu with information or sub items.

1 Additional information / sub itemsReaxys RN (Reaxys registrynumber), MF (molecular formula), MW(molecular weight), CAS-RN (CASregistry number), Show details (displayinformation as Structure/compounddata), Copy Structure to Clipboard/

Query screen, View related Markush.

2 Commercial availabilityAccess the commercial availability of asubstance and leads to appropriatecompanies (eMolecules/ACD).

3 Show/Hide details button

4 Structure/compound dataFind details about structure/compound.

5 Available dataLinks to Hit Data and to All AvailableData (from organic, inorganic &organometallic sources). Dataexcerpted from Gmelin has a fromGmelin flag.

6 Sort bySort results ascending ordescending by Reaxys-RN, CommAvailability, Molec Formula, NbFragments, Publication Year, MolWeight and Nb of References (default).


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Substances and propertiesSubstances (Grid) tab

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1 Grid viewFor a quick overview results aredisplayed in a grid.

2 Additional Information/sub itemsClick a structure to get a pop-upmenu leading to additional informationor sub items.Reaxys RN: Reaxys registry numberMF: molecular formulaMW: molecular weightCAS-RN: CAS registry numberShow Details: display information asStructure/compound dataPlan a synthesis: develop yourretrosynthesisCopy structure to clipboard

3 Commercial availabilityAccess the commercial availability ofa substance and leads to appropriatecompanies (eMolecules/ACD).

4 OutputExport results in the desired format.

5 Available data for this substanceVarious red hyperlinks display theinformation available by substance.


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Text, Authors and moreQuery tab

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Note: in the Quick Search box you can use and enter the following Boolean operators: AND, OR, PROXIMITY,NEAR and NEXT.

1 Search pageEnterQuick Search,author(s)/assignee(s), journal title,patent number, patent country,and/or publication year.

Different specified fields arecombined with the Boolean operator

AND.

2 Quick SearchEnter free text and combine it withthe Boolean operators of your choice.If needed use truncations.Truncation:* = any number of characters? = one character

3 Text field/selection listSelection appears when typing entry.

4 Expand Index featureThe box allows convenient indexbrowsing and multiple entryselections.If several terms are chosen in onefield, they are combined with the

Boolean operator OR (;).

5 Entry exampleHints how to enter your search termare displayed below each of the fielddata boxes.

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Text, authors and moreCitations tab

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Reactions - and Substances & Properties - citations tabs have almost the same layout and content as thebibliographic citations tab. The only differences are the presence of one additional link on each of those tabsand additional filters:- Reactions results/citations tab: presence ofHit Reactions in this article (# out of total #) link

- Substances & properties results/citations tab: presence ofHit Substances in this article (# out of total #) link

1 Filter byRefine search results by applyingbibliographic (document type,authors, patent assignee, journal titleand publication year), reaction orsubstance filters.

2 OutputExport results in an appropriate

format.

3 Sort bySort results ascending ordescending by Document Type,Authors, Journal Title or PublicationYear (default).

4 Abstract/Reactions/SubstancesDisplay the abstract, and show all

reactions or show all substanceswhich are related to the article.

5 SourceFind here the literature reference.Display the original text with the FullText link and access relatedinformation from Scopus with theView citing articles link.The Times cited column displays thenumber of articles from Scopus citinga specific reference.

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