Searching CrossFire Beilstein Using DiscoveryGate. DiscoveryGate Version 2.2 Participant s Guide

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1 Searching CrossFire Beilstein Using DiscoveryGate DiscoveryGate Version 2.2 Participant s Guide

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3 Searching CrossFire Beilstein using DiscoveryGate DiscoveryGate Version 2.2 Participant s Guide Elsevier MDL 2440 Camino Ramon San Ramon, CA Copyright MDL Information Systems, Inc. ( Elsevier MDL ). All rights reserved. No part of this document may be reproduced by any means except as permitted in writing by Elsevier MDL. Beilstein Database: Copyright Beilstein-Institut zur Förderung der Chemischen Wissenschaften licensed to Beilstein GmbH and MDL Information Systems GmbH. Used under permission from MDL Information Systems GmbH. All rights reserved. U.S. GOVERNMENT RESTRICTED RIGHTS NOTICE The materials are provided with RESTRICTED RIGHTS. Use, duplication or disclosure by: (i) the Department of Defense ("DOD") shall be subject to MDL Information System, Inc.'s standard commercial license and (ii) by any unit or agency of the U.S. Government other than the DOD, shall be governed by clause (c) of the FAR (or any successor regulations) and (iii) by NASA, shall be governed by clause (a) (or any successor regulations) and, in any such case, the U.S. Government acquires only "restricted rights" in the materials. Contractor/Manufacturer is: MDL Information Systems, Inc Camino Ramon, San Ramon, CA MDL and DiscoveryGate are registered trademarks in the United States, of Elsevier MDL. All other product names may be trademarks or registered trademarks of their respective holders in the United States and other countries. Developed: June 2006, Instructional Design & Development, Elsevier MDL. TRDG-34V2.2PG

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5 TABLE OF CONTENTS INTRODUCTION Searching CrossFire Beilstein using DiscoveryGate Course objectives Login to the application Configure the CrossFire Beilstein database Select a database Default query form Form controls STRUCTURE SEARCHING Structure searching objectives Create the structure query Structure field index controls Structure search options Global search options Exact match search results View the details View the synthetic scheme Substructure query Substructure results Generalize a query Atom query features Allow and Prohibit atom features Beilstein generic groups Applying substitution Varying the amount of substitution Applying the Beilstein generic group Generic search query and results Stereochemical search query Bond query features Stereochemical considerations Stereochemical search results Retrieve a list of reactions Find preparations of this compound Find reactions of this compound Exercise descriptions i

6 Conduct a series of structure searches for 4-amino-indole Retrieve benzodiazepine derivatives Retrieve the preparation of a compound REACTION SEARCHING Reaction searching objectives Types of reaction queries Create a reaction query Reaction field index controls Reaction search options Global search options Structural fragment search results Reaction search details Trace the synthetic pathway Create a partial reaction query Mark atom reaction sites Marking reaction centers Partial reaction query and results Create a full reaction query Analyzing the results Mapping a reaction Results of mapping a query Find similar reactions InfoChem ClassCodes Reaction Classification search results Narrow results Return to the CrossFire Beilstein results Exercise descriptions Retrieve synthetic methods for 6-nitro-nicotinic acid Retrieve examples of Knorr Pyrrol synthesis Search for synthesis of quinolines with defined starting materials Search for similar reactions DATA SEARCHING Data searching objectives Predefined query forms Customized query forms Factual search features Data operators and wildcards ii

7 Data Look up tables Chemical Name search results Details CAS Number search results Multiple search criteria Display the citation details Show Substances for this Citation link Show Reactions for this Citation link Structure/data combination search Structure/data search results Use a data search to retrieve reactions Formulate the query Search results Reaction details Exercise descriptions Conduct a Chemical Name search to retrieve ibuprofen Combination factual/structure search Retrieve reactions using a factual query Retrieve citations by an author on a particular topic EXPORTING SEARCH RESULTS Exporting search results Structure search results Creating a report Selected options Detail page report Report Outline Saving a report Exporting a report Selecting records to export Export records Selecting fields to export Exporting an SDfile SDfile Exporting a tabbed file Tab-delimited file read by ISIS for Excel Exporting citations Selecting citation records Export selected citations Citation text file Reaction search results iii

8 Exporting an RDfile Exporting reaction citations Exercise descriptions Creating, saving, and exporting a report Exporting an SDfile Exporting a tab-delimited file Exporting citations iv

9 Introduction 1-1 Searching Exploring CrossFire DiscoveryGate Beilstein using DiscoveryGate Welcome to the Searching CrossFire Beilstein using DiscoveryGate course. In this course, you will search the CrossFire Beilstein database using the MDL Database Browser in DiscoveryGate. If you are unfamiliar with the DiscoveryGate application, see the Introduction to DiscoveryGate course for complete instructions on using the application and its capabilities. You are also expected to know how to draw basic structures. If you are not familiar with this, see the Drawing Molecules course for complete instructions.

10 1-2 Searching CrossFire Beilstein using DiscoveryGate Course objectives In this course, you will learn how to: Conduct structure searches Conduct reaction searches Conduct data searches Apply query features to atoms and bonds Review the search history, save a list, create a report, and export results In this course, you will learn the how to conduct stucture, reaction, data, and combination searches in the CrossFire Beilstein database only. You will learn how to apply query features to atoms and bonds. You will save a list of results, review the search history, create a report, and export results.

11 Introduction 1-3 Login to the application A Quick Start Guide and basic training videos (not database specific) are available within the application. Launch the internet browser and enter the DiscoveryGate URL: To log in, enter your user name and password, and then click Go. Within the application, you can access a printable Quick Start guide. You also have access to learning videos to take you through a workflow scenario, prompting you to navigate within the simulated environment. At the end of the video, you can print out instructions that will allow you to practice the same steps within the actual application.

12 1-4 Searching CrossFire Beilstein using DiscoveryGate Configure the CrossFire Beilstein database Linked to the online help Configure the CrossFire Beilstein database as your default database. You have the ability to set the CrossFire Beilstein database as your default database. To do this, click the <your name> Settings tab to personalize your configuration of DiscoveryGate. After modifying a settings category, click Update to enact the changes.

13 Introduction 1-5 Select a database Search Databases launches the MDL Database Browser. Under Database, choose CrossFire Beilstein. DiscoveryGate uses the MDL Database Browser to search individual databases. CrossFire Beilstein is one of the individual database selections. It is an essential source of information for generating leads, planning syntheses, and determining bioactivity and physical properties.

14 1-6 Searching CrossFire Beilstein using DiscoveryGate Default query form Structural (compound and reaction) queries are entered here. Factual (data) queries are entered here. Additional fields can be accessed using the Field Index located in the pane to the left. Every database opens to a default form that can be used to create your query. Create your structural query using the MDL Draw structure editor.

15 Introduction 1-7 Form controls Each of the four tabbed forms has its own set of command buttons. DiscoveryGate uses a series of tabbed forms to search and view data. Each form has it own set of command buttons to accommodate operations required for the specified process.

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17 Structure searching 2-1 Structure searching objectives In this section, you will learn how to: Conduct a structure search for a specific compound Conduct a substructure search Conduct a search using a generic structure Conduct a structure search for a defined stereochemical compound Use a structure query to retrieve a list of reactions Apply query features to atoms and bonds In this section, you will learn how to conduct structure searches to retrieve the items listed in the slide. You will also learn how to apply query features to atoms and bonds.

18 2-2 Searching CrossFire Beilstein using DiscoveryGate Create the structure query DiscoveryGate uses the MDL Draw structure editor. Click the Done button to transfer the structure to the CrossFire Beilstein database in the MDL Database Browser. Knowledge of the MDL Draw structure editor is required to successfully use this module. Drawing is not taught during this session. See the Drawing Molecules course or the Creating Structure Queries self-paced module for complete instructions on creating structures and reactions.

19 Structure searching 2-3 Structure field index controls Structure search options Global search options Field index controls The Structure field index has a series of structure search options and global search options that affect how the search will be conducted. There are structure controls that allow you to reset the default settings, delete structure or data fields and controls, duplicate data field and its controls, or access information in the help box.

20 2-4 Searching CrossFire Beilstein using DiscoveryGate Structure search options Retrieves a list of molecules and associated properties for the compound specified. Retrieves a list of reactions where the compound is a product. Click the Synthesize Reactant(s) link for the preparation information. Retrieves a list of reactions where the compound is either a reactant or a product. Retrieves a list of citations for the specified compound. Find this compound and its properties retrieves a list of molecules, based on the structure entered. Find preparations of this compound retrieves a list of reactions where the structure entered is a reactant. Find reactions of this compound retrieves a list of reactions where the structure entered is either a reactant or a product. Find citations of this compound retrieves a list of citations that reference the structure entered.

21 Structure searching 2-5 Global search options Allows or disallows tautomeric forms of the target structure. Allows for substitution on all atoms, therefore excludes tautomeric forms. Allows rings to form from chains at atoms that you specify with substitution. Allows structures that contain isotopes, charged species, or radicals. Allows for the retrieval of the target structure and its mirror image as designated. Allows two or more non-bonded fragments to be retrieved in separate compounds. The global search options directly affect the results of a structure search. The first two settings lock in the ability to accept substituents only at positions drawn directly onto the original structure query. Unlike the first two settings, the Unlimited substitution on all atoms, exclude tautomers setting allows for substitution on any atom that has an open valence. When the Allow boxes are checked, you allow the retrieval of structures that contain the specified characteristics.

22 2-6 Searching CrossFire Beilstein using DiscoveryGate Exact match search results Allows you to view information for this compound that was found in another database. Allows you to select specific records to store in a results set. Indicates that there is pharmacological or toxicological data available for this compound. Allows you to view the detailed record or the synthetic scheme. We spoke about the global search options. To retrieve an exact match of the structure, you must uncheck all the Allow options. You must also set the substitution to retrieve only what you have drawn. When the search is complete, you are automatically transferred to the results form. A green BIO label in the upper right corner indicates that the compound retrieved has pharmacological or toxicological data present in the detailed results.

23 Structure searching 2-7 View the details Click a link, in the Available Data table, to view specific data for the compound retrieved. To view the associated data, click the Details link. The structure table is replaced with a detailed display of the data. The available data for the compound can be displayed by clicking the links for Substance (displayed by default), or any field found in the Available Data table. The additional information is added to the bottom of the display.

24 2-8 Searching CrossFire Beilstein using DiscoveryGate View the synthetic scheme To view the synthetic scheme for a compound, click the Synthesize link found below the structure result. This takes you to the rxn schemes tab. The rxn schemes tab displays a hierarchy of retrosynthetic pathways beginning with the final product. To expand the reaction tree, double-click a substance or a reaction folder (or click the plus sign). When multiple synthetic schemes are available the folder structure is ordered based on yield and the most recent information added.

25 Structure searching 2-9 Substructure query An exact match retrieves the structure you entered. The rules of a substructure search are: the core structure must be embedded in all hits retrieved, and substitution can occur at any open valence. You will conduct a substructure search on the same compound and compare the results. The Query Highlighting box is enabled and the effects are shown on the next slide.

26 2-10 Searching CrossFire Beilstein using DiscoveryGate Substructure results substituents The core structure is highlighted in blue when the Query Highlighting box (on the query form) is checked. The substructure search retrieved more hits than the previous exact match search. This is expected because you are opening the possibility of substitution at all the atom sites. The core structure is highlighted when you check the Query Highlighting box below the structure box on the query form.

27 Structure searching 2-11 Generalize a query Original substructure query Generalized substructure query O N Predefined generic group ALK N O C* Cl Substitution query feature You can modify a structure to specify only those portions that are required. In this example, you want to retrieve any alkyl-substituted oxaziridines. You will use query features to introduce flexibility or to make the search more focused. You will apply a substitution feature and a predefined generic group on the structure fragment.

28 2-12 Searching CrossFire Beilstein using DiscoveryGate Atom query features Allows selection of any atom from the periodic table. Allows you to assign a specific Charge, Isotope, Valence, or Radical to an atom site. Allows you to specify the number of hydrogens at an atom site. Allows you to specify the number of free sites at an atom. Allows you to specify that the atom must be part of a cyclic or acyclic system. Allows you to specify the number of times an atom can appear. Removes any applied atom property. The first selection allows you to select any atom from the periodic table. The next grouping allows you to assign a specific charge, specify an isotope, specify a valence, and specify a radical at an atom site. The next two selections allow you to specify the number of free atoms or the number of hydrogens at an atom site. There is also a feature that allows you to specify whether the atom must be part of a cyclic or an acyclic system. The Remove Properties selection removes any features previously placed on the structure.

29 Structure searching 2-13 Allow and Prohibit atom features Allow Prohibit There are two additional selections that allow or prohibit certain atom types from being retrieved. For Allow these atoms, you find the generic atoms A, Q, X, and M. A is any atom except hydrogen. Q is any atom except carbon or hydrogen. X is any halogen. M is any metal. For the Prohibit these atoms, you find Atom List, NOT X, NOT M, and Off. The Atom List allows you to select any atoms from the periodic table to exclude from the search. The NOT X excludes any halogens, and the NOT M excludes any metal atom.

30 2-14 Searching CrossFire Beilstein using DiscoveryGate Beilstein generic groups G Any Group G* Any Group with ring closure ACY Acyclic CYC Cyclic ABC Carbacyclic AHC Heteroacyclic N CHC Heterocyclic N CXX Cyclic, no carbon N N N CBC Carbocyclic ALK Alkyl AEL Alkenyl AYL Alkynyl AOX Alkoxy O HAR Heteroaryl(6) N ARY Aryl CAL Cycloalkyl CEL Cycloalkenyl The last atom feature introduces the Beilstein generic groups. They are shown in this slide. You will use the ALK generic group for this query to represent alkyl substitution.

31 Structure searching 2-15 Applying substitution Right-click the atom and select the query feature from the drop-down list. Choose the amount of additional substitution. Right-click the atom site and select Additional substituents from the dropdown list. Choose the amount of additional substitution from the dialog box that opens.

32 2-16 Searching CrossFire Beilstein using DiscoveryGate Varying the amount of substitution ALK N O C * Any number of additional substituents (327 records retrieved) ALK ALK N N C O *1 Up to that number of substituents (197 records retrieved) O C No additional substituents, as drawn (4 records retrieved) Placing explicit substituents allows substitution only at the sites you specify. When you apply a specific number, the search retrieves compounds having up to that number of additional substituents at that site. This is only true when searching the CrossFire Beilstein or the CrossFire Gmelin databases. When you specify Any # at an atom, the number of additional substituents is limited only by its valence.

33 Structure searching 2-17 Applying the Beilstein generic group Right-click the atom site and select Beilstein generic group from the dropdown list. Navigate the submenu selections to open individual dialog boxes displaying the appropriate generic groupings.

34 2-18 Searching CrossFire Beilstein using DiscoveryGate Query: Generic search query and results Results: The global search options are set to allow substitution as drawn. This allows substitution at the designated carbon atom only. All compounds retrieved contain the oxaziridine substructure and any alkyl group.

35 Structure searching 2-19 Stereochemical search query In this example, you will search using a structure with defined asymmetric, or chiral, centers. Alter the Search Stereoinformation settings and compare the results.

36 2-20 Searching CrossFire Beilstein using DiscoveryGate Bond query features Allows you to specify Single, Double, or Triple bond order. Allows you to specify an Up, Down, or Either stereobond. Allows you to specify an Any bond, a Single or Double bond, or a Double or Triple bond. Removes any applied bond property. Allows you to specify that the bond must be in a cyclic or acyclic system. Allows you to specify the cis or trans configuration. There are a series of bond features that can be used when conducting a structure search that will make the query more flexible or more focused. The selections are described in the slide.

37 Structure searching 2-21 Stereochemical considerations As drawn retrieves compounds with the absolute stereochemical representation. Off retrieves all stereochemical representations. Plus mirror image retrieves racemic compounds. Or mirror image retrieves compounds with the relative stereochemical representation. You can use the Search Stereoinformation drop-down list to search for the compound shown in the structure box and its mirror image as follows: - As drawn - Off (stereoinformation is not important) - Plus mirror image (racemic mixture) - Or mirror image (relative search, for isomer as drawn or its enantiomer)

38 2-22 Searching CrossFire Beilstein using DiscoveryGate Stereochemical search results As drawn O Chiral Off, Plus mirror image, or Or mirror image Chiral E E O R S R Absolute Relative Off Z E O R O R R Cis R Trans You can see the variation in the retrieved results when you alter the Search Stereoinformation settings and use specific stereochemical tools on the structure.

39 Structure searching 2-23 Retrieve a list of reactions Retrieves a list of reactions using a structure query It is possible to retrieve a list of reactions using a structure query. Previously, you were shown the structure search options. The Find preparations of this compound and the Find reactions for this compound generate a list of reactions when used in the search.

40 2-24 Searching CrossFire Beilstein using DiscoveryGate Find preparations of this compound Retrieves the compound as a product. The Find preparations of this compound retrieves all reactions where the specified compound is found in the product.

41 Structure searching 2-25 Find reactions of this compound Retrieves the compound as a reactant or a product. The Find reactions of this compound retrieves all reactions where the specified compound is found as a reactant or a product.

42 2-26 Searching CrossFire Beilstein using DiscoveryGate Exercise descriptions The following descriptions explain the goal of each exercise. If you like to figure things out on your own, use the descriptions to conduct the exercises. If you prefer step-bystep instructions, go to the page listed below the description. Exercise 1 Conduct an exact structure and substructure search for 4- amino-indole. Conduct an exact structure search. N N Use the Synthesize link to view preparation data. Conduct a substructure search. For a step-by-step solution, see page Exercise 2 Conduct a substructure search. Search for benzodiazepine derivatives. Use predefined generic groups and an X halogen atom to generalize the query. View all fields. G N O X N ARY For a step-by-step solution, see page 2-31.

43 Structure searching 2-27 Exercise 3 Conduct a structure search using indole to retrieve a list of preparation reactions. For a step-by-step solution, see page 2-33.

44 2-28 Searching CrossFire Beilstein using DiscoveryGate Conduct a series of structure searches for 4-aminoindole Exercise 1 Conduct a structure search for 4-amino-indole. View the preparation methods. Then conduct a substructure search on the same structure. N N Start DiscoveryGate 1. If you have already started the application, go to Step 3. Launch your internet browser and enter the DiscoveryGate URL ( 2. Enter your user name and password. (If necessary, enter your company id.) Click Go. 3. Under Applications, click Search Databases. Open the CrossFire Beilstein database 4. Under Database, click CrossFire Beilstein. 5. Double-click the Structure box. Draw 4-amino-indole. Click Done. Set the Structure search options 6. In the Structure search option area, select Find this compound and its properties. Set the Global search options 7. Under the Global search options, select Substitution as drawn, exclude tautomers. Uncheck all other options. 8. Under Search Stereoinformation, select Off.

45 Structure searching Click start search. 10. Click the Details link. View the preparative methods 11. Click the Synthesize link found under the structure graphic. 12. Click the plus sign next to Substance Click the plus sign next to Reaction Under the reaction graphic, click the Details for Reaction link. 15. Click the refine query button on the top menu bar. Conduct the substructure search 16. In the MDL Database Browser select: - Find this compound and its properties

46 2-30 Searching CrossFire Beilstein using DiscoveryGate - Unlimited substitution on all atoms, exclude tautomers - Under Allow, check Multi-component substances, Ring closure through substitution, Isotopes, Charges, and Radicals. - Search Stereoinformation, select Off 17. Click start search and view the results.

47 Structure searching 2-31 Retrieve benzodiazepine derivatives Exercise 2 Conduct a substructure search for benzodiazepine derivatives. Use predefined generic groups and an X halogen atom to generalize the query. G is the abbreviation for any group. ARY is the abbreviation for aryl groups. G N O X N ARY Prepare for a new search 1. Click the queries tab. 2. To the right of the structure box, click Reset. 3. Double-click the Structure box. Draw the core structure. 4. To place the ARY designation, right-click the atom, and then choose Beilstein generic group > Cyclic group > Carbon atoms only. In the dialog box, choose ARY. Click to select the terminal carbon atom on the C-C single bond. Type X and press Enter. Right-click the terminal carbon atom on the C-N single bond. Choose Beilstein generic group > Any group. In the dialog box, choose G.

48 2-32 Searching CrossFire Beilstein using DiscoveryGate 5. Click Done. 6. In the MDL Database Browser select: - Find this compound and its properties - Unlimited substitution on all atoms, exclude tautomers - Under Allow, check Multi-component substances, Ring closure through substitution, Isotopes, Charges, and Radicals. - Search Stereoinformation, select Off 7. Click start search and view the results.

49 Structure searching 2-33 Retrieve the preparation of a compound Exercise 3 Conduct a structure search using indole to retrieve a list of preparation reactions. Prepare for a new search 1. Click the queries tab. 2. To the right of the structure box, click Reset. 3. Double-click the Structure box. Draw indole. 4. Click Done. 5. In the MDL Database Browser select: - Find preparations of this compound - Substitution as drawn, exclude tautomers - Under Allow, uncheck Multi-component substances, Ring closure through substitution, Isotopes, Charges, and Radicals. - Search Stereoinformation, select Off

50 2-34 Searching CrossFire Beilstein using DiscoveryGate 6. Click start search and view the results.

51 Reaction searching 3-1 Reaction searching objectives In this section, you will learn how to: Conduct a reaction search using structural fragments Conduct a reaction search using a partial reaction query Conduct a reaction search using a full reaction query Mark reaction centers Apply atom-atom mapping Find similar reactions In this section, you will learn how to create a partial and full reaction query. You will learn how to mark the reacting centers and apply atom-atom mapping to your reaction query. You will also learn how to retrieve similar reactions using InfoChem ClassCodes.

52 3-2 Searching CrossFire Beilstein using DiscoveryGate Types of reaction queries Partial reaction reactant(s) product(s) Cl C* N O + C* S O Full reaction reactant(s) product(s) C C C* C* + ALK X ALK C C C* C* When you search for reactions, you specify the role of each molecule. You can search using a partial reaction. A partial reaction is defined as only reactants or only products. You can search using a full reaction. A full reaction can have one reactant and one product, or you can have multiple reactants and products.

53 Reaction searching 3-3 Create a reaction query Used to create a valid reaction Draw the reaction and click the Done button to transfer to the MDL Database Browser. Create your structural query using the MDL Draw structure editor. MDL Draw uses the Arrow tool to define the reactant and product structures. Placement of the arrow is important. The reactants must be to the left of the arrow and the products must be to the right of the arrow. MDL Draw uses the Plus tool to specify that there are multiple components on either side of the reaction arrow.

54 3-4 Searching CrossFire Beilstein using DiscoveryGate Reaction field index controls Reaction search options Global search options Above the reaction box, you have reaction search options. To the right of the reaction box, you have a grouping of Global search options. The selections in both areas affect how the system searches.

55 Reaction searching 3-5 Reaction search options Retrieves the reaction shown and the reaction conditions used during the synthesis. Retrieves a list of citations for the reaction specified. The Find this reaction and its conditions allows you to retrieve a list of reactions and the associated reacting conditions, based on the structural information entered. Find citations of this reaction retrieves a list of citations that reference the reaction entered. In this example, you have a compound that contains, among other groups, an amine and oxime. You want to react the amine with a sulfinyl chloride, but you would like to know what happens to the oxime during the reaction.

56 3-6 Searching CrossFire Beilstein using DiscoveryGate Global search options Controls the substitution on atoms including or excluding tautomeric forms. Allows for the retrieval of: mixtures rings formed through substitution isotopes charged species radicals Controls the inclusion or exclusion of atom mapping features in the search. Allows for the retrieval of the target structure and its mirror image as designated. Allows two or more non-bonded fragments to be retrieved in separate compounds. The first few settings lock in the ability to accept or exclude substituents. The next grouping allows you to retrieve mixtures, ring systems, isotopes, charged species, and radicals. The Ignore atom mapping feature allows you to exclude any mapping features on the reaction from being considered during the search. The Keep fragments separate allows two or more non-bonded fragments to be retrieved in separate compounds.

57 Reaction searching 3-7 Structural fragment search results The advantage of using a partial reaction query is that you can retrieve many types of transformations that you cannot retrieve when using a fully defined reaction query. When the search is complete, you are automatically transferred to the results form.

58 3-8 Searching CrossFire Beilstein using DiscoveryGate Reaction search details Click to view the retrosynthetic pathway Reaction identification information Reaction details Initially, you will only see the reactions associated with the retrieved record. To view the associated data, click the Details link. The reaction identification information for the reactant(s) and product(s) is shown. Reaction details that display the citation information, the reaction classification, and other reacting conditions are also shown.

59 Reaction searching 3-9 Trace the synthetic pathway Click the plus sign to open the Rxn Tree. The rxn schemes tab displays a hierarchy of reaction pathways. To expand the reaction tree, double-click a substance or a reaction folder (or click the plus sign). As you expand the reaction tree, you see the full synthetic scheme appear in the window at the right.

60 3-10 Searching CrossFire Beilstein using DiscoveryGate Create a partial reaction query Substitution feature In this example, you will continue to use a partial reaction query, but this time we are going to specify only the product. Since there is no mechanistic implication associated with this query, you will use the mark reaction centers feature to assign one. You want to retrieve compounds where all ring closures produce benzo[b]thiopenes and the new bonds are made into an existing thiophene ring in the same preparation.

61 Reaction searching 3-11 Mark atom reaction sites Must change in reaction the selected atom must be part of the reaction. Must NOT change in reaction the selected atom cannot be part of the reaction. Off turns off any atom role feature. A reacting center can be defined on an atom or a bond. When you right-click an atom in MDL Draw, one of the Atom Property choices will be Atom role in reactant or Atom role in product. Select Must change in reaction when you want the atom to take part in the reaction. Select Must NOT change in reaction when you do not want the atom to play a part in the reaction. Off turns the feature off.

62 3-12 Searching CrossFire Beilstein using DiscoveryGate Marking reaction centers Breaks in reaction the selected bond in the reactant is broken during the reaction. Forms in reaction the selected bond in the product is formed during the reaction. Changes the selected bond undergoes a bond order or topology change during the reaction. Must NOT change the selected bond cannot change during the reaction. Off turns off any Bond role feature. A reacting center is defined when a bond changes in the reactant and in the product. Markings on the structure specify exactly how each bond does or does not change in the reaction. You can specify that a bond is made or broken, changes bond order, or is not changed in the reaction. Off turns the feature off.

63 Reaction searching 3-13 Query: Partial reaction query and results Results: A larger number of reactions are retrieved when the reacting centers are left undefined. You will retrieve a variety of extraneous reactions.

64 3-14 Searching CrossFire Beilstein using DiscoveryGate Create a full reaction query Predefined generic group Substitution feature Predefined atom In the next example, you will create a full reaction query to retrieve those reactions that show the alkylation of naphthalenes. In the process, you will use predefined atoms, predefined generic groups, and atom-atom mapping.

65 Reaction searching 3-15 Analyzing the results + + Cl Cl When you analyze the results, note that most conform to the criteria specified in the query. H O + I Some results do not fit the criteria specified in the query. Se O H + I Although you created a searchable query, the application can only do a broad interpretation of what you presented and will retrieve some results that do not satisfy exactly what you were trying to retrieve. To refine this query, you will use a feature called atom-atom mapping.

66 3-16 Searching CrossFire Beilstein using DiscoveryGate Mapping a reaction Atom-Atom Mapping tool Delete Atom-Atom Mapping tool To be more precise when you are searching for reactions, you can use atom-atom mapping to require that a specific atom in the reactant correspond to a specific atom in the product. Not all of the reactions in the Beilstein database are mapped. When you search with atom mapping, you are limiting your search to about 70% of the database. To apply the atom mapping, choose the Atom-Atom Mapping tool. Click an atom in the reactant, and then click the corresponding atom in the product.

67 Reaction searching 3-17 Results of mapping a query Scenario Results Reaction search unmapped 44 Reaction search carbon mapped 18 Reaction search carbon and alkyl group mapped 14 It is possible to retrieve ambiguous records when you do not map a reaction. If you do not use atom-atom mapping, you can retrieve ambiguous hits. When mapping, it is recommended that you map as few atoms as possible. If you map too many atoms, you increase the chance that the reactions in the database will not be mapped the same way, and therefore will not be retrieved. The slide shows a difference of approximately 30 records by performing the search on a reaction query mapped and unmapped.

68 3-18 Searching CrossFire Beilstein using DiscoveryGate Find similar reactions + Cl Target applications: Click the Find Similar Reactions link to use InfoChem ClassCodes to retrieve similar reactions. A dialog box opens in which you can select the appropriate database. The available target applications are listed in the drop-down list.

69 Reaction searching 3-19 InfoChem ClassCodes Class Codes : Broad, Medium, Narrow N C N N C N H H Reaction Similarity (RX.BCODE): Broad Only reaction centers are compared. C C N N C C N N H H Reaction Similarity (RX.MCODE): Medium Reaction centers and the alpha atoms and bonds are compared. C C C N N C C C N N H H Reaction Similarity (RX.NCODE): Narrow Reaction centers and alpha & beta atoms and bonds are compared. Reactions in all MDL reaction databases are indexed using InfoChem Reaction ClassCodes. Similar reactions have the same ClassCodes in all databases. It is possible to use the InfoChem ClassCodes to retrieve similar reactions in the CrossFire Beilstein and other MDL databases. These databases are indexed using the InfoChem ClassCodes. The reactions are analyzed and are assigned a reaction ClassCode. The class codes are: Broad, Medium, and Narrow.

70 3-20 Searching CrossFire Beilstein using DiscoveryGate Reaction Classification search results Automatically switches to target database selected. DiscoveryGate automatically switches to the target application selected and conducts the search. The similarity search retrieves all classification levels (Broad, Medium, and Narrow). To view reactions in a specific level, click the link for that level.

71 Reaction searching 3-21 Narrow results To view data from a different classification level, you do not need to conduct a separate search. Click Return to Reaction Classification Search Results and select the appropriate link. Viewing the number of hits retrieved, you will see that a Broad similarity search retrieves more hits than the Narrow similarity search. You receive different results due to the different atoms and bonds involved in the search.

72 3-22 Searching CrossFire Beilstein using DiscoveryGate Return to the CrossFire Beilstein results Select the CrossFire Beilstein database. Click the History tab on the results form. Double-click the last search list. To return to the CrossFire Beilstein database, select it from the drop-down database list. To view the last set of retrieved results, click the History tab on the results form and double-click the last list in the Today s Searches folder.

73 Reaction searching 3-23 Exercise descriptions The following descriptions explain the goal of each exercise. If you like to figure things out on your own, use the descriptions to conduct the exercises. If you prefer step-bystep instructions, go to the page listed below the description. Exercise 1 Conduct a partial reaction search to retrieve methods for the synthesis of 6-nitro-nicotinic acid. O N N O O O For a step-by-step solution, see page Exercise 2 Conduct a full reaction search to retrieve examples of Knorr Pyrrol synthesis. Draw the query shown. Use predefined generic groups to generalize the structure query. Mark the reacting centers. O G + G N [RC] N [RC] O For a step-by-step solution, see page Exercise 3 Conduct a full reaction search to retrieve examples of the synthesis of quinolines with anilines and glycerol as the starting materials. Draw the reaction, assign molecule roles in the reaction, apply atom-atom mapping, and mark the reacting center.

74 3-24 Searching CrossFire Beilstein using DiscoveryGate Ṅ 1. C(s*) C(s*) C(s*) C (s*)c(s*) + O O O.2. Ṅ C(s*) C(s*) C(s*) C(s*) For a step-by-step solution, see page Exercise 4 Find similar reactions in the MDL Synthetic Methodology Database for the retrieved reaction Reaction ID: from Exercise 3. View the results for the narrow classification. Return to the original list of results in the CrossFire Beilstein database. For a step-by-step solution, see page 3-33.

75 Reaction searching 3-25 Retrieve synthetic methods for 6-nitro-nicotinic acid Exercise 1 Conduct a partial reaction search to retrieve methods for the synthesis of 6-nitro-nicotinic acid. O N N O O O Prepare for a new search 1. Click the queries tab. 2. To the right of the structure box, click Reset. 3. Double-click the structure box and draw 6-nitro-nicotinic acid using MDL Draw. 4. Click the Arrow tool and place a reaction arrow to the left of the structure. 5. Click Done. Set the search options 6. In the Reaction search option area, select Find this reaction and its conditions. 7. Under the Global search options, select Substitution as drawn, exclude tautomers. 8. Under Allow, check Multi-component compounds, Ring closure through substitution, Isotopes, Charges, and Radicals.

76 3-26 Searching CrossFire Beilstein using DiscoveryGate 9. Under Search Stereoinformation, choose Off. O N N O O O 10. Click start search and view the results. 11. Click the Details link and scroll though the information.

77 Reaction searching 3-27 Retrieve examples of Knorr Pyrrol synthesis Exercise 2 Retrieve examples of Knorr Pyrrol synthesis by conducting a structural search. Use predefined generic groups to generalize the structure query. Mark the reacting centers. Use short display to view multiple reactions at the same time. O G + G N [RC] N [RC] O Prepare for a new search 1. Click the queries tab. 2. To the right of the structure box, click Reset. 3. Double-click the structure box and the core reaction using MDL Draw. Add a predefined generic group 4. Right-click the terminal carbon on the second reactant. Choose Beilstein generic group > Any group > G.

78 3-28 Searching CrossFire Beilstein using DiscoveryGate 5. Repeat Step 4 to apply the same generic group to the product molecule. Apply reacting centers 6. Using the Lasso tool, right-click the nitrogen in the second reactant. Choose Atom role in reactant > Must change in reaction.

79 Reaction searching Using the Lasso tool, right-click the nitrogen in the product. Choose Atom role in product > Must change in reaction. 8. Click Done. Set the search options 9. In the Reaction search option area, select Find this reaction and its conditions. Under the Global search options, select Substitution as drawn, exclude tautomers. Under Allow, check Multi-component compounds, Ring closure through substitution, Isotopes, Charges, and Radicals. Under Search Stereoinformation, choose Off. 10. Click start search and view the results.

80 3-30 Searching CrossFire Beilstein using DiscoveryGate Search for synthesis of quinolines with defined starting materials Exercise 3 Search for synthesis of quinolines with anilines and glycerol as the starting materials. Map the reaction and mark the reacting center. Ṅ 1. C(s*) C(s*) C(s*) C (s*)c(s*) + O O O.2. Ṅ C(s*) C(s*) C(s*) C(s*) Prepare for a new search 1. Click the queries tab. 2. To the right of the structure box, click Reset. 3. Double-click the structure box and draw the core reaction using MDL Draw. Add the substitution feature 4. Using the Lasso tool, select the nine carbon atoms shown. Right-click one of the designated carbon atoms and choose Additional substituents > Any #.

81 Reaction searching 3-31 Apply reacting centers 5. Using the Lasso tool, right-click the C-N bond in the product molecule. Choose Bond role in product > Forms in reaction. Apply atom-atom mapping 6. Using the Atom-Atom Mapping tool:

82 3-32 Searching CrossFire Beilstein using DiscoveryGate - click the nitrogen atom in reactant 1 and then in the product - click the carbon atom in the first C-O bond of reactant 2 and then the carbon atom in the C-N double bond of the product - click the carbon atom for the last C-O bond in reactant 2 and the carbon atom in the C-C bond in the product as shown. 7. Click Done. Set the search options 8. In the Reaction search option area, select Find this reaction and its conditions. Under the Global search options, select Substitution as drawn, exclude tautomers. Under Allow, check Multi-component compounds, Ring closure through substitution, Isotopes, Charges, and Radicals. Under Search Stereoinformation, choose Off. 9. Click start search and view the results.

83 Reaction searching 3-33 Search for similar reactions Exercise 4 Find similar reactions in the MDL Synthetic Methodology Database for the retrieved reaction Reaction ID: from Exercise 3. View the results for the narrow classification. Return to the original list of reactions in the CrossFire Beilstein database. Find similar reactions 1. Click the Find Similar Reactions link found under the reaction graphic for Reaction ID: from Exercise 3. Select the target application 2. Select Synthetic Methodology MDL Database Browser as the target from the drop-down list. 3. Click the Start Search button. View the Narrow classification results 4. Click the Classification Narrow link.

84 3-34 Searching CrossFire Beilstein using DiscoveryGate 5. Scroll through the results. Return to the CrossFire Beilstein database 6. Under Database, choose CrossFire Beilstein. 7. Click the results tab. 8. On the History tab, click the plus sign to open the Today s Searches folder. 9. Double-click the last search list.

85 Data searching 4-1 Data searching objectives In this section, you will learn how to: Conduct data searches using individual data entries Conduct data searches using multiple data entries Conduct data searches using a combination of data and structural entries Use predefined and customized forms to conduct your searches In this section, you will learn how to conduct data searches to retrieve compounds based on their chemical name, CAS number, and physical or chemical properties. You will learn how to use the predefined EDS forms, and create your own custom forms.

86 4-2 Searching CrossFire Beilstein using DiscoveryGate Predefined query forms Predefined query forms are located on the Field Index tab in the Easy Data Search (EDS) folder. There is a section on the Field Index tab called Easy Data Search. This category contains a number of predefined forms that have common search criteria. The forms are organized by search area. The data fields on an EDS (Easy Data Search) form are predefined and can be text or numeric fields.

87 Data searching 4-3 Customized query forms Custom query forms can be created by double-clicking a data field in any of the other folders found on the Field Index tab. In this example, we added the Chemical Name and Molecular Weight fields from the Substance Identification folder and the Effect field from the Pharmacological Data folder to create a small customized form. Custom forms can be created by doubleclicking a data field in any of the folders found on the Field Index tab.

88 4-4 Searching CrossFire Beilstein using DiscoveryGate Factual search features Data field Operators used to connect multiple search criteria Operators used with text and/or numeric search entries Data field index controls When using text or numeric fields, you can use any of the operators shown in the slide.

89 Data searching 4-5 Data operators and wild cards Operators Use to retrieve records that: AND satisfy both criteria OR satisfy either criterion NOT do not satisfy the criterion = satisfy the exact entry < are less than the specified entry <= are less than or equal to the specified entry > are greater that the specified entry >= are greater than or equal to the specified entry <> are not included as an entry Is have the exact entry Starts with begin with the entry Ends with end with the entry Contains have the term contained within Wildcards Use in text string to represent:? One character?? Two characters When using multiple fields, you must use some of the following data operators. In the next example, you are shown two ways to retrieve the compound acyclovir using data entries.

90 4-6 Searching CrossFire Beilstein using DiscoveryGate Data Look up tables Chemical Name search CAS number search Data Lookup tables display the specified value and the number of occurrences found in the database. The DiscoveryGate application uses a Data Lookup feature for the text fields. This feature allows you to view the contents of the database and indicates the number of occurrences for that data entry. By default, Find any of these terms (OR operator) is selected. This means that an OR operator will be used to connect each value you have selected. Select Find all of these terms (AND operator) to require that every value is present. Select Find all of these terms adjacent to one another in order to search for a string of values adjacent to one another.

91 Data searching 4-7 Chemical Name search results Results are displayed on a separate form in a structural format. In some of the result panels, you will notice the green BIO indicator. This label indicates that the compound has pharmacological or toxicological data associated with it.

92 4-8 Searching CrossFire Beilstein using DiscoveryGate Details Click a link to obtain specific data for the retrieved compound. Click to link to reactions or citations for this substance The Substance Identification data is shown, which includes identification information such as registry numbers, molecular formula, CAS number, and chemical name. To obtain specific data for the compound, click a link in the Available Data table. If you would like to use this structure in a new query, click the Use as Query link.

93 Data searching 4-9 CAS Number search results The details view confirms the retrieval of the data entry.

94 4-10 Searching CrossFire Beilstein using DiscoveryGate Multiple search criteria Use a predefined EDS form Author can be Erik Jacobsen, Erik Jacobson, Eric Jacobsen, or Erik Jacobson Use Data lookup table In the next example, you will conduct a data search to find publications authored by Eric Jacobsen. You are not sure of the exact spelling of the author s first and last name. You will narrow the list to those references that discuss epoxidation reactions. When you attempt to find eric jacobsen, you learn that authors are indexed using the format last name, first name. Your query must contain the appropriate format for the author s name.

95 Data searching 4-11 Display the citation details The hit list consists of citations published by Eric Jacobsen that discuss epoxidation chemistry.

96 4-12 Searching CrossFire Beilstein using DiscoveryGate Show Substances for this Citation link There are 12 substances reported in this citation. To view additional data about a substance, click the Details link found under the structure graphic. To view synthetic routes to the substance, click Synthesize.

97 Data searching 4-13 Show Reactions for this Citation link There are 4 reactions reported in this citation. To view additional data about a reaction, click the Details link found under the reaction graphic. To learn how to synthesize the reactants in a reaction, click Synthesize Reactant(s).

98 4-14 Searching CrossFire Beilstein using DiscoveryGate Structure/data combination search To locate a field, expand the Field Index or use the Find in Field Index box In the next example, you want to conduct a search for the synthesis of para-acetophenone compounds, limiting the list to only those reactions that use methanol as a solvent. When searching for reaction conditions, it is best to use the data fields from the Chemical Properties folder.

99 Data searching 4-15 Structure/data search results Conducting the structural search retrieves greater than 300 records. Conducting the structure/data search retrieves approximately 189 records. Using a partial reaction query does not limit us to a specific type of reaction. Doing the structural portion of the search alone retrieves too many results. Inclusion of a data parameter focuses the list.

100 4-16 Searching CrossFire Beilstein using DiscoveryGate Use a data search to retrieve reactions Custom Search forms contain only those data fields specifically selected for the search. Select data field twice or click Duplicate to add the same data field to the form. In this example, you are interested in retrieving hydrogenation reactions that use Raney-Ni as a reagent or a catalyst, and acetic acid as a reagent. Due to the inconsistencies of how authors report various reagents and catalysts in the literature, catalyst information can be stored in the catalyst and/or reagent field. To obtain a complete listing of information, you must search both data fields.

101 Data searching 4-17 Formulate the query You must use brackets to create the correct query logic. The substance, Raney Ni, occurs in the database using different entries. Use wildcards to include all occurrences of the catalyst and the reagent in the query. Use parentheses to force your search condition. You want to create an OR between the reagent and catalyst fields for Raney Ni.

102 4-18 Searching CrossFire Beilstein using DiscoveryGate Search results You retrieved a list of over 600 reactions.

103 Data searching 4-19 Reaction details The Reactions Details display the data entries required for the search.

104 4-20 Searching CrossFire Beilstien using Discoverygate Exercise descriptions The following descriptions explain the goal of each exercise. If you like to figure things out on your own, use the descriptions to conduct the exercises. If you prefer step-bystep instructions, go to the page listed below the description. Exercise 1 Conduct a Chemical Name search to retrieve ibuprofen. Review the results. Conduct a second search for only those ibuprofen compounds that display pharmacological data. Review the results and link to the pharmacological data. For a step-by-step solution, see page Exercise 2 Conduct a combination factual/structure search to retrieve all compounds that have a phenobarbital core structure and a melting point restriction greater than or equal to 150 o C. O N O N O For a step-by-step solution, see page Exercise 3 Conduct a factual search to retrieve reactions where the product was derived from a demethylation of various groups. For a step-by-step solution, see page Exercise 4 Conduct a search to retrieve articles published by Larry Overman that contain the term heck reaction in the abstract. View the substances reported in a citation. View the reactions reported in a citation. For a step-by-step solution, see page 4-26.

105 Data searching 4-21 Conduct a Chemical Name search to retrieve ibuprofen Exercise 1 Conduct a Chemical Name search to retrieve ibuprofen. Review the results. Conduct a second search for only those ibuprofen compounds that display pharmacological data. Review the results and link to the pharmacological data. Prepare for a new search 1. Click the queries tab. 2. Click the clear form button on the top menu bar. Click OK. Use an Easy Data Search form 3. On the Field Index tab, click the plus sign to open the Easy Data Search folder. Double-click the Substance Identification Data folder. 4. For the Chemical Name field, select the Contains operator. 5. Click the Data Lookup link below the text entry box. Use the Data Lookup table 6. In the Data Look up Chemical Name dialog box, type ibuprofen in the Find text box and click the Find button. 7. In the Frequency: Values: box, double-click the ibuprofen entry. 8. When the entry appears in the Your Query box, click OK.

106 4-22 Searching CrossFire Beilstien using Discoverygate 9. On the Field Index tab, double-click Pharmacological Data. 10. Check the Pharmacological data exists box. 11. Click start search. 12. Click the Details link below the structure graphic and view the data.

107 Data searching 4-23 Combination factual/structure search Exercise 2 Conduct a combination factual/structure search to retrieve all compounds that have a phenobarbital core structure and a melting point restriction greater than or equal to 150 o C. O N O N O Prepare for a new search 1. Click the queries tab. 2. Click the clear form button on the top menu bar. Click OK. Create a custom form 3. On the Field Index tab, double-click the Structure field. 4. In the Find in Field Index text box, type melting point. 5. In the Field Index Tree, the Melting Point folder is highlighted. Open the folder and double-click the Melting Point data field. 6. Double-click the structure box and draw phenobarbital using MDL Draw. Click Done. 7. In the MDL Database Browser select: - Find this compound and its properties - Substitution as drawn, exclude tautomers - Under Allow, check Multi-component substances, Ring closure through substitution, Isotopes, Charges, and Radicals.

108 4-24 Searching CrossFire Beilstien using Discoverygate - Search Stereoinformation, select Off 8. If necessary, choose the AND operator between the fields. 9. For the melting point field, select the greater than or equal to (>=) operator and enter 150 in the text box. 10. Click start search and view the results. 11. Click the Details link for BRN Under Available Data, click the Melting Point link. Scroll through the occurrences.

109 Data searching 4-25 Retrieve reactions using a factual query Exercise 3 Conduct a factual search to retrieve reactions where the product was derived from a demethylation of various groups. Prepare for a new search 1. Click the queries tab. 2. Click the clear form button on the top menu bar. Click OK. Create a custom form 3. On the Field Index tab, type conditions in the Find in Field Index text box. The Other Conditions data field in the reaction Details folder is highlighted. (If this field is not highlighted, click the Next button until you obtain that field.) 4. Double-click the Other Conditions data field. If necessary, select the Contains operator and type demethylation in the text box on the form. 5. Click start search. 6. Click the Details link for any compound and view the results.

110 4-26 Searching CrossFire Beilstien using Discoverygate Retrieve citations by an author on a particular topic Exercise 4 Conduct a search to retrieve articles published by Larry Overman that contain the term heck reaction in the abstract. View the substances and reactions reported in a citation. Prepare for a new search 1. Click the queries tab. 2. Click the clear form button on the top menu bar. Click OK. Use an Easy Data Search form 3. On the Field Index tab, double-click Bibliographic Data. 4. Under the Authors data field, click Data Lookup. Type overman, larry and click Find. Use Data Lookup 5. Double-click to add the terms overman, larry e., overman,l.e., and overman,l.e. et al. to the Your Query box. Click OK.

111 Data searching 4-27 Add the abstract data to the query form 6. Under the Abstract data field, click Data Lookup. Type heck reactions and click Find. You see that there are no entries for this text.

112 4-28 Searching CrossFire Beilstien using Discoverygate 7. Remove reactions from the data entry and click the Find button. Double-click to add the heck entry. Click OK.

113 Data searching Check your parenthetical statement (created by selecting more than one author entry). 9. Click start search. 10. Click Details for any retrieved citation. 11. In the Available Data table, click Abstract link. Show Substances for this Citation 12. Click the Show Substances for this Citation link. View the results.

114 4-30 Searching CrossFire Beilstien using Discoverygate 13. Click the Return to Search Results link. Show Reactions for this Citation 14. Click the Details link. 15. Click the Show Reactions for this Citation link. View the results. 16. Click the Return to Search Results link.

115 Exporting search results 5-1 Exporting search results In this section, you will learn how to: Create and save reports Export reports as HTML files Export records as SDfiles, RDfiles, and tabbed files Export citations as RIS and text files After you complete a search, you have several options for exporting the search results. In this section, the procedures are demonstrated using results from specific molecule and reaction searches. However, the export procedures are applicable for any search results obtained using any search queries.

116 5-2 Searching CrossFire Beilstein using DiscoveryGate Structure search results Previously, you used a substructure query to obtain these search results. The search results in this example are obtained by conducting a substructure search using the Olmesartan structure. A total of six compounds are retrieved. You will be shown to create a printable report from the search results. On the results tab, click copy to report.

117 Exporting search results 5-3 Creating a report A new report is created initially. Thereafter, each time you click copy to report, you will have the option of creating another report, or appending to the current report. Copies molecule records in grid format or in detail format Specifies which records to copy to the report Check to view report immediately On the Copy to Report dialog box, click the radio buttons for the report options. Then click OK.

118 5-4 Searching CrossFire Beilstein using DiscoveryGate Selected options Using the options selected above, a new report will be generated using the information provided on the standard details page. (This is the same information that appears when you click the Details link located below the structure in the structure grid.) The records to be copied are from the Current Page. In this case, data for all six records will be copied to the report. Alternatively, you could have clicked All records, or entered 1-6 for Specify Record Numbers. The box for View report now is checked, so you will be taken to the report tab as soon as the report is finished.

119 Exporting search results 5-5 Detail page report This slide shows the Detail page for the first compound, located at the top of the report. Scroll the display to see the full report. Detail pages for all six compounds are included. At this point, you could use your browser s Print function to print the report.

120 5-6 Searching CrossFire Beilstein using DiscoveryGate Report Outline Right-click a section to hide or show it, or to change its position within the report. Each database record forms its own section within the report. The left pane contains two tabs, Outline and History. You see that the folder for Today s Report - Report #1 contains six sections. The Detail page for each database record forms a section. Right-click a section, and then use the menu options (Hide/Show, Move Up, Move Down) to hide or show a section, or to change its position within the report.

121 Exporting search results 5-7 Saving a report To save a report: The report is listed on the History tab. On the History tab, all reports from the current day are saved in the Today s Reports folder. All reports older than one day are automatically moved to the Previous Reports folder. To save the current report, click save on the top menu bar. Saved reports are stored in the Saved Reports folder. To retrieve a report, go to the appropriate folder on the History tab, and then double-click the report. To delete or rename a report, right-click the report, and then use the Delete or Rename menu option.

122 5-8 Searching CrossFire Beilstein using DiscoveryGate Exporting a report The exported report is saved as an HTML file. To export a report, it must first be displayed. Then click export on the top menu bar. You will be prompted for a file name for the report. The exported report is saved in HTML format. You must have the Chime software to view the structures in the HTML file.

123 Exporting search results 5-9 Selecting records to export Check the boxes for the records you want to export, or click Select All. The structures and data for the database records can also be exported. SDfiles are a flat file format that can store compound structures, but not reactions. This format is suitable for import to Isentris, ISIS/Base, and ISIS for Excel databases. In this example, you will be exporting the six database records to an SDfile. As shown in the slide, you have the option of checking individual boxes for the records you want to export, or you can click Select All to select all of the records on the current page.

124 5-10 Searching CrossFire Beilstein using DiscoveryGate Export records You can override the default record selection by clicking a different radio button To export the selected records, click export records on the top menu bar. On the slide above, you see that the record range is automatically set to the three records that you checked on the results grid. However, you can override the range selection by clicking a different radio button in the dialog box. For example, you can click All Records to export all six records instead. Click OK to continue the export process.

125 Exporting search results 5-11 Selecting fields to export Double-click from Database Fields to add to Exporting Fields. The database fields available for export are listed in the Database Fields pane. Open the folders to see the individual field names. To add a field to the Exporting Fields pane, you can click the field name and then click Add, or simply double-click the field name. To export all of the database fields, including the compound structure, double-click the MOL parent field at the top of the tree.

126 5-12 Searching CrossFire Beilstein using DiscoveryGate Exporting an SDfile With the entire MOL tree copied to the Exporting Fields pane, click Export SDfile to continue the export process. Enter a file name, and then click Save.

127 Exporting search results 5-13 SDfile Part of the exported SDfile is shown in the slide above. The compound structure is represented by an atom table that describes each atom and its connection to the other atoms in the molecule. Following the atom table are entries for each field that contain the field name in arrow brackets, and then the data value. This format is repeated for each of the exported records.

128 5-14 Searching CrossFire Beilstein using DiscoveryGate Exporting a tabbed file Database records can also be exported as a tab-delimited file. The structures are exported as Chime strings. This file format is suitable for import by ISIS for Excel. You must install the ChemScape plug-in for ISIS for Excel to display the structures. To export the selected fields to a tabdelimited file, click Export TAB. Enter the file name, and then click Save.

129 Exporting search results 5-15 Tab-delimited file read by ISIS for Excel Chime strings are represented as structures This slide shows the tab-delimited file read by ISIS for Excel. With the ChemScape plug-in enabled, ISIS for Excel displays the Chime strings as structures.

130 5-16 Searching CrossFire Beilstein using DiscoveryGate Exporting citations To export citations, display the citations first. Click Details. Click Show Citations for this Substance. Next we will look at exporting citations for database records. To begin, you must display the citations on the results tab. In this example, you are starting from the structure grid on the results tab. Click the Details link below the compound structure. Then click the link for Show Citations for this Substance.

131 Exporting search results 5-17 Selecting citation records Check the individual Export citation boxes, or click Select all citations. The citation information is added to the Details display. Check the individual Export citation boxes for the citations you want to export, or click Select all citations located at the top of the Details page.

132 5-18 Searching CrossFire Beilstein using DiscoveryGate Export selected citations An RIS file can be read by Procite or EndNote. To export the selected citations, click the export selected citations option on the top menu bar. The citations can be exported as an RIS file, or as a Text file. The RIS file format is suitable for use by the Procite and EndNote applications. The Text file format can be read by any text editor.

133 Exporting search results 5-19 Citation text file In this example, the Text file format is selected. Click Export to continue the export process. Enter a file name, and then click Save. A portion of the exported text file is shown on the slide above.

134 5-20 Searching CrossFire Beilstein using DiscoveryGate Reaction search results Earlier, you retrieved these search results by searching for preparations of the olmesartan substructure. The procedures for exporting reaction search results are very similar to what you have already seen. In this example, the reaction search results are obtained by using the Olmesartan structure as a substructure query to search for compound preparations.

135 Exporting search results 5-21 Exporting an RDfile When you click export records on the main menu, you see the same dialog boxes for selecting the record range and the exporting fields as you did for the molecule search results. In this case, however, you will click Export RDfile to export the reaction records. An RDfile is a hierarchical file format suitable for storing reactions and data. RDfiles can be imported to Isentris and ISIS/Base databases.

136 5-22 Searching CrossFire Beilstein using DiscoveryGate Exporting reaction citations To export citations, display the citations on the Details page. Check the Export boxes for the citations you want to export. Then click Export selected citations. The process for exporting reaction citations is the same as for substance citations. Display the citations that you want to export by going to the Details page for the reaction. Click the Export boxes for the citations you want to export. Then click Export selected citations on the top menu bar. You have the same options for exported file formats: RIS files and Text files.

137 Exporting search results 5-23 Exercise descriptions The exercises in this section use the same examples shown during the lecture and demonstration. You can also substitute your own search results for the purpose of practicing the export process. Exercise 1 Create a report for the current page of records using the detail page format. Save the report, and then export it as an HTML file. For a step-by-step solution, see page Exercise 2 Export selected records to an SDfile, using all of the data fields for the MOL parent. For a step-by-step solution, see page Exercise 3 Export the same search results as in Exercise 2 to a tabdelimited file. For a step-by-step solution, see page Exercise 4 Export the citations for a compound to a text file. For a step-by-step solution, see page 5-30.

138 5-24 Searching CrossFire Beilstein using DiscoveryGate Creating, saving, and exporting a report Exercise 1 Create a report for the current page of records using the detail page format. Save the report, and then export it as an HTML file. This exercise assumes that you are currently on the results tab, with the results of a compound search displayed in the grid format. For example: Copy the search results to a report 1. On the results tab, click copy to report on the top menu bar. 2. In the Copy to Report dialog box, choose the following options: Create a new report View detail results in report Current Page View report now

139 Exporting search results Click OK. You are taken to the report on the reports tab. Save the report 4. On the reports tab, click save on the top menu bar. 5. Enter a name for the report. 6. Click OK. The report is stored in the Saved Reports folder on the History tab.

140 5-26 Searching CrossFire Beilstein using DiscoveryGate Export the report 7. Click export on the top menu bar. 8. Enter the file name for the report. 9. Click Save.

141 Exporting search results 5-27 Exporting an SDfile Exercise 2 Export selected records to an SDfile, using all of the data fields for the MOL parent. Select the records to export 1. Click the results tab to return to the search results used in Exercise Check the export boxes for some of the records. For example: 3. Click export records on the top menu bar.

142 5-28 Searching CrossFire Beilstein using DiscoveryGate 4. Click OK. Select the fields to export 5. In the Export Database Results dialog box, double-click the MOL parent field in the Database Fields pane. The entire data tree is added to the Exporting Fields pane. Export the SDfile 6. Click Export SDfile. 7. Enter a file name for the SDfile. Then click Save.

143 Exporting search results 5-29 Exporting a tab-delimited file Exercise 3 Export the same search results as in Exercise 2 to a tabdelimited file. 1. Click export records on the top menu bar. 2. Click OK to accept the default for the range of export records. 3. In the Export Database Results dialog box, double-click the MOL parent field in the Database Fields pane. The entire data tree is added to the Exporting Fields pane. 4. Click Export TAB. 5. Enter a file name, and then click Save.

144 5-30 Searching CrossFire Beilstein using DiscoveryGate Exporting citations Exercise 4 Export the citations for a compound to a text file. Display the citations to be exported 1. On the results tab, click the Details link below one of the compound structures. For example: 2. On the Details page, click Show Citations for this Substance. Select the citations 3. Click the Export citation check boxes for the citations you want to export. For example:

145 Exporting search results 5-31 Export the citations as a text file 4. Click export selected citations on the top menu bar. 5. In the dialog box, click the radio button for Text file. 6. Click Export. 7. Enter a name for the text file. Then click Save.