Searching CrossFire Gmelin

Transcription

1 Searching CrossFire Gmelin Training Guide CrossFire Commander Version 7.1

2

3 Searching CrossFire Gmelin CrossFire Commander Version 7.1 Training Guide CrossFire Software Copyright , Elsevier Information Systems GmbH. CrossFire Beilstein Database: Copyright , Elsevier Information Systems GmbH. Gmelin Database: Copyright , Gesellschaft Deutscher Chemiker, licensed to Elsevier Information Systems GmbH; , Gmelin Institut fuer Anorganische Chemie und Grenzgebiete der Max-Planck-Gesellschaft zur Förderung der Wissenschaften. All rights reserved. This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in other ways, and storage in data banks. Duplication of this publication or parts thereof is only permitted under the provisions of the German Copyright Law of September 9, 1965, in its version of June 24, 1985, and a copyright fee must always be paid. Violations fall under the prosecution act of the German Copyright Law. The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and are therefore free for general use. Furthermore the Elsevier CrossFire system is subject to the license agreement and the terms and conditions for the CrossFire Beilstein data and database system. Training Guide: May 2008, for Elsevier CrossFire Commander Version 7.1

4

5 TABLE OF CONTENTS INTRODUCTION Searching CrossFire Gmelin Module objectives What is a Gmelin compound? Elements included in Gmelin Sources Time coverage Compound types STRUCTURE SEARCHING Structure searching Retrieval of coordination compounds CrossFire Structure Editor Apply the substitution query feature Query options for atoms Implicit versus explicit free sites Set implicit free sites Allow query options Extended query options Implicit search results Explicit search results Using generics and atom lists Generic atoms Predefined generic groups Creating an atom list Add data constraints Bonding considerations Bond query features Search results Inorganic Editmode Atom Attributes dialog box Gmelin database descriptors Polyhedra descriptors Predefined templates Exercises descriptions Exercise 1: Conduct a structure search for lead tetrahalogens Exercise 2: Combined structure search Exercise 3: Conduct structure searches for nickel tetracarbonyl compounds

6 CHARACTERIZATION OF COMPOUNDS Characterization of compounds Characterization data structure Chemical name search Predefined form Identification Results based on wildcard placement Accessing UV spectral data Viewing spectral data Molecular formula searching Molecular formula fields Fields related to molecular formula Enter query EDS form MOFO versus MF List manipulation List manipulation results Formula data parameter search Formula search query View the hitset Search for multi-component compounds Type of Substance field Query results with and without exclusions Search for alloys Alloy table Alloy results Conduct the subset search Subset search results Ligand formula search Ligand molecular formula (LIGMF) field Ligand formula (LIGFO) field Enter search criteria Ligand results Exercises descriptions Exercise 1: Conduct a chemical name search Exercise 2: Molecular formula search Exercise 3: Search for alloys, glass and ceramic materials Exercise 4: Search for copper alloys containing trace amounts of iron PHYSICAL PROPERTY SEARCHING Physical property searching Physical properties data structure Electrical conductivity search Predefined form Electrical Data

7 Electrical conductivity results Expansion coefficient search Predefined form Thermal Data Expansion coefficient results Modified expansion coefficient query View the hitset Combination data/structure search Create the structural query Enter data constraints Search with and without values Results of the combination search Magnetization diagram search Tabular Query data entry Magnetization diagram data entry Magnetization results Exercises descriptions Exercise 1: Retrieving melting point data Exercise 2: Retrieve crystal structure data Exercise 3: Retrieve the adsorption diagram of Hg 2+ ions CHEMICAL PROPERTY SEARCHING Chemical property searching Chemical properties data structure Retrieve preparation methods Enter reaction preparation data Check database occurrence Preparative search results Hyperlink to the reaction Modify the query Catalyst preparation Create the query Search results Hyperlink to the catalysis data Hyperlink to the journal articles Full reaction search Create the full reaction query Full reaction results Factual reaction search Factual reaction search query Reaction results Convert the hitset Converted citation hitset Citation searching Managing your results

8 Exercises descriptions Exercise 1: Retrieve inorganic reactions Exercise 2: Conduct a reaction search Exercise 3: Preparation of CO bridged cyclopentadienyl metal complexes

9 Introduction 1-1 Searching CrossFire Gmelin Welcome to the Searching CrossFire Gmelin module. In this module, you will use the CrossFire Commander 7.1 to search the Gmelin database. The focus of this course is to present only information that is unique to the Gmelin Database. General information about how to use the CrossFire Commander can be found in the manual Searching CrossFire Databases- based on CrossFire Beilstein.

10 1-2 Searching CrossFire Gmelin Module objectives Review the definition of a Gmelin compound Review Sources & Time Coverage of Gmelin Use your knowledge of searching with the XFire Commander 7.1 to retrieve information from Gmelin Retrieve lists of Gmelin compounds based on structural criteria incorporating query features characterization criteria physical and chemical property values In this module, you will learn the qualifications used to define a compound as a Gmelin compound. You will learn how to apply the features learned on XFire Commander 7.1 to the Gmelin database, with specific examples. You will view how to find desired information resulting from structural criteria, various characterization criteria, and physical or chemical property values.

11 Introduction 1-3 What is a Gmelin compound? Compounds included in Gmelin: All compounds without carbon Elemental carbon Alloys and multi-component systems with carbon components, carbides, and carbideoxides, carbonic acids and the thio- and seleno-analogues, as well as small molecules like CO, CS, CO 2, CS 2, or phosgene. Substances, which contain carbon, containing at least one Gmelin element The Gmelin database contains structures, synthesis, and property data for compounds that meet the criteria shown. The Gmelin database covers all compounds without carbon. The compounds in Gmelin are available with their structures. However, only molecular structures are indexed. Compounds such as alloys, glasses, and ceramic materials have no structures in the database.

12 1-4 Searching CrossFire Gmelin Elements included in Gmelin H Elements, in combination with carbon, included in Gmelin are shaded in the periodic table. The elements, in combination with carbon, included in the Gmelin database are shaded in the periodic table.

13 Introduction Million Sources Primary Literature: - Journals Gmelin Handbook of Inorganic Chemistry: - Journals - Patents - Monographs Data is excerpted from the following sources to include in the Gmelin database. From 1817 until 1975, data was taken from the Gmelin Handbook of Inorganic Chemistry (journals, patents, and monographs) and included values for all physical properties. From 1975 until present, data is taken from the primary literature (journals).

14 1-6 Searching CrossFire Gmelin Time coverage Time coverage from 1772 to present Gmelin Handbook of Inorganic Chemistry from its beginning in 1817 up to 1975 Primary literature from 1975 onwards, currently about 62 journals This slide shows a summary of the time frames for the excerption of data. The list of the journals considered in the Gmelin database is available at nals.pdf

15 Introduction 1-7 Compound types >1339,000 Coordination 121,300 compounds Alloys 42,000 Glasses and 65,100 ceramic Solid solutions materials 4,200 Minerals 46,200 Catalysts 32,600 Polymers This slide displays the types and frequency of the compounds found in this database. There are greater than 1339,000 coordination compounds, and approximately 121,300 alloys, 65,100 solid solutions, 42,000 glass and ceramic materials, 46,200 catalysts, 32,600 polymers, and 4,200 minerals (GM0704). The residual compounds are other inorganic compounds, such as an element (chemical), small molecules (like water), inorganic salts, solid-state compounds, and organic reactants.

16

17 Structure searching 2-1 Structure searching In this section, you will learn how to apply the features learned with XFire Commander 7.1, to the Gmelin database: Application of to query features to atoms and bonds Application of structure search parameters Conduction of a combination search 1 In this section, you will conduct structure searches in Gmelin to learn how to use and apply some query features for atoms and bonds. You will learn how to set the structure search parameters and conduct a combination search. On the next example, you will work first with coordination compounds.

18 2-2 Searching CrossFire Gmelin Retrieval of coordination compounds Scenario: Retrieve coordination compounds, from the Gmelin database, containing the same core structure. Modify your query to show the effects of implicit versus explicit substitution. Further modify the search by applying search features. apply atom query features Compare explicit and implicit substitution query options 2 In this example, we will search for coordination compounds with the same core structure. In the process, we will use atom query features and compare implicit and explicit substitution query options.

19 Structure searching 2-3 CrossFire Structure Editor Select the following tools to create the compound: 3 As you already know, various structure editors (Please consult the CrossFire Administration Guide for details) can be used for the drawing of a structure; but the CrossFire Structure Editor (default) is recommended to avoid possible query feature discrepancies between the Commander and other structure editors. Choose Options > Select Structure Editor to make your selection You have to draw the needed core structure, and to click on the red cross to return to the Commander. On the next slides you will review how to create explicit (and implicit) free sites, and the differences between the two.

20 2-4 Searching CrossFire Gmelin Apply the substitution query feature Max free sites N Co * N 4 Using explicit Free Sites controls substitution. Free Sites allow any substituent, any bond order, and ring closure. You can set Max Free Sites or a specific number (in this case, do not forget that you will allow substitution up to this number).

21 Structure searching 2-5 Query options for atoms Options > Define Atom or Click the atom with the Edit tool Indicates that one further substituent is allowed, but not required, at an atom site Sets the valence of an atom from the default to another allowed value Sets the minimum and maximum number of implicit hydrogens attached to the atom Sets the negative or positive charge of an atom Sets the mass of an atom from the default to another occurring isotope Sets the number of unpaired electrons associated with the atom Determines whether an atom is part of a ring, chain, or either 5 In the Define Atom dialog box, you can specify the number of Free Sites, the valence, the charge, the mass (isotope), the appearance of radicals, the hydrogen count, and the atom topology. The number of Free Sites is zero by default. When you specify a number greater than zero, you are allowing, but not requiring, additional substituents on that site, up to the number chosen. The Elsevier CrossFire Commander will not permit selection of multiple sites when applying a query feature. To change multiple sites, check the Set to Current box.

22 2-6 Searching CrossFire Gmelin Implicit versus explicit free sites Explicit free sites Applied to specific atoms Specify the number of free sites Co * N N Max free sites Implicit free sites Applied to the entire structure N Co *1 N 1 free site (0 or 1 addl substituent) Co N N N Co *2 N 2 free sites (0,1 or 2 addl substituents) 6 Implicit Free Sites allows substitution at any open valence. Explicit Free Sites 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. When you specify MAX Free Sites at an atom, the number of additional substituents is limited only by its valence.

23 Structure searching 2-7 Set implicit free sites 7 To specify the implicit Free Sites, you have to be in the Query Builder section of the CrossFire Commander. The Structure Query Options area, located to the right of the structure box, allows you to specify Free Sites on hetero atoms only, or on all atoms. When you check this last Free Sites option, you will automatically allow presence of salts, additional rings, isotopes, charges and radicals.

24 2-8 Searching CrossFire Gmelin Allow query options Allows or excludes multifragment structures such as salts or charge-transfer complexes Allows or excludes ring closures between atoms or groups with free sites. Allows or excludes isotopes Allows or excludes charged compounds to be retrieved in the search. Allows or excludes compounds containing radicals to be retrieved in the search. 8 Of course, you can always decide that salts, isotopes, charges, radical and additional rings will be present or absent from the search results.

25 Structure searching 2-9 Extended query options Tautomers of the drawn structure will also be retrieved in the search Sets the total number of atoms to be found in the retrieved structure When more than one isolated component is drawn in the query, this switch defines that they are to be retrieved as separate components Sets the total number of fragments to be found in the retrieved structure Sets the total number of rings to be found in the retrieved structure If atom-atom mappings have been defined in a reaction query, this option will ignore those mappings in the search 9 Some global restrictions can be defined for a search. Minimum and maximum values can be set independently. The total number of atoms (including hydrogen atoms) to be found in the retrieved structure can be set. The total number of fragments to be found in the retrieved structures can also be set; for example, salts & addition compounds can be set. The total number of rings allowed in the retrieved structures, defined as the smallest number of ring bonds which must be broken to convert the structure into an acyclic structure, can be set.

26 2-10 Searching CrossFire Gmelin Implicit search results example 10 All compounds retrieved contain the cobalt complex as a substructure. Those two searches are made with implicit Free Sites; but the top query excludes the retrieval of salts, additional rings, isotopes, charges, and radicals and results then in fewer hits than the second one.

27 Structure searching 2-11 Explicit search results example 11 In these queries, substitution was explicitly allowed on the cobalt only and not on the nitrogens. If you compare with the hits retrieved on the previous page, you will see that query with explicit substitution retrieves a more focused list of results; this is because only the Cobalt can accept substituents. Rmq : All the queries were launched with Autosearch On & Stop Autosearches after 1 st result features checked.

28 2-12 Searching CrossFire Gmelin Using generics and atom lists Scenario: Conduct a search to retrieve reactions producing a metal tetraalkyl, where the metal is defined as lead (Pb), tin (Sn), or germanium (Ge), and having a yield greater than 90%. Isolate the list to only those reactions using tetrahydrofuran (THF) as the solvent. apply generics and an atom list create a partial reaction create a combination search using an PSF form 12 In this example, we will conduct a search to retrieve reactions that produce a metal tetraalkyl. You will apply generic atoms, create a user-defined atom list, and create a partial reaction; if you don t remember in details how to use those features, have a look to the Searching CrossFire Databases based on CrossFire Beilstein training guide, as we will only show you a summary here.

29 Structure searching 2-13 Generic atoms Generic atoms: A - any atom except hydrogen Q - any atom except hydrogen/carbon M - any metal X - any halogen Predefined generic groups Creates user-defined atoms and user-defined generic groups 13 In the Define User Atom dialog box, query atoms can be found under the Symbol location. Selected predefined generic atoms are displayed. The generic atoms are A, Q, M, and X. A is any atom except hydrogen; Q is any heteroatom (any atom except carbon or hydrogen); M is any metal and X is any halogen. A user-defined generic group allows the possible substituents to be described precisely. In a user-defined generic group, a substituent can be defined as being either a full structure or a substructure.

30 2-14 Searching CrossFire Gmelin Predefined generic groups G Any Group G* Any Group with ring closure ACY Acyclic CYC Cyclic ABC Carbacyclic AHC CHC CXX Heteroacyclic Heterocyclic Cyclic, N N no carbon N N N CBC Carbocyclic ALK Alkyl AEL Alkenyl AYL Alkynyl AOX Alkoxy O HAR Heteroaryl(6) N ARY Aryl CAL CEL Cycloalkyl Cycloalkenyl 14 On this slide, you have a list of some Predefined Generic Groups. For each group, a symbol exists with the last letter replaced by an H, allowing the mentioned group and also hydrogen. The predefined generic groups allow structural elements to be represented that have certain basic tautologic features without the need to specify them completely. Predefined generic groups can only have one bond to the parent structure (at the exception of G and G*) and setting explicit free sites is not allowed.

31 Structure searching 2-15 Creating an atom list 15 To introduce flexibility into the query, we will create an atom list (user-defined atom). An atom list can only be defined after the corresponding symbol has been placed in the parent structure. In the Structure Editor, you can create as many as 50 user-defined atoms for your query. The atoms are numbered A0 through A49. We will now add the data constraints requested by the scenario.

32 2-16 Searching CrossFire Gmelin Add data constraints Data query form Search query form Example results : 16 Due to the general nature of our structure query, we will use data constraints to minimize the number of extraneous results. We will add a defined yield (%) for the reaction, and a solvent requirement. Each of the structures retrieved is a metal complex with one of the specified metals from the user-defined atom list.

33 Structure searching 2-17 Bonding considerations Scenario: You are interested in retrieving organometallic compounds such as triphenylphosphine manganese halides with and without bonds between the phosphorus, manganese, and halogen atoms. apply bond query features Cl Cl Mn (III) F F F F C (V) C (V) C (V) C (V) Mn (VIII) P (IV) P (IV) O F F O (III) O (III) F F F 17 In this example, we will retrieve organometallic compounds by modifying the bonding factor.

34 2-18 Searching CrossFire Gmelin Bond query features Options > Define Bond or Click the atom with the Edit tool Determines whether a bond is part of a ring, chain, or either Retrieves structures containing any stereo configuration where applied Retrieves structures where the cis or trans configuration is considered where applied Retrieves structures containing any type of bond where applied Retrieves structures containing either single or double bonds where applied Retrieves structures containing either double or triple bonds where applied 18 The query bond features are: - Any retrieves structures containing any type of bond where applied. - Single/Double retrieves structures containing either single or double bonds where applied. - Double/Triple retrieves structures containing either double or triple bonds where applied. Use the bond topology to specify that a specific bond is part of a ring or chain. The Any bond is particularly useful when searching for organometallic substances, or when they may be an ionic or covalent bond between two elements.

35 Structure searching 2-19 Queries: Search results Number of hits: In the first example, you retrieve all compounds where any bond order is found connecting the phosphorus, manganese, and halide atoms. In the second example, you eliminate the retrieval of compounds having a manganese-halide (Mn-X) bond. In the third example, you eliminate the retrieval of compounds having a phosphorus-manganese (P-Mn) and/or manganese-halide (Mn-X) bond.

36 2-20 Searching CrossFire Gmelin Inorganic Editmode The Inorganic Editmode must be selected to assign the polyhedra descriptors for atoms within the Gmelin database. 20 You have access to two variations of the CrossFire Structure editor, an organic (default choice) and an inorganic drawing mode. In the next example, we will show you how to set the Inorganic Draw mode and the various polyhedra descriptors available. As you will see on the next slide, selecting Inorganic Editmode will allow you to play with the connectivity of the atoms in inorganic molecules (use of some stereodescriptors).

37 Structure searching 2-21 Atom Attributes dialog box Editmode > Organic Editmode > Inorganic Determines the connectivity of atoms and stereodescriptors 21 A location named Polyeder is added in the Atom Attributes dialog box. Special polyhedra descriptors are assigned that allow you to set the connectivity of atoms, and stereodescriptors.

38 2-22 Searching CrossFire Gmelin Gmelin database descriptors Simple polyhedra: Descriptor P-3 T-4 SP-4 SP-5 TB-5 OC-6 TP-6 PB-7 CU-8 SA-8 DD-8 HB-8 TPS-9 HB-9 Polyhedron triagonal pyramid tetrahedron square planar square pyramid triagonal bipyramid octahedron trigonal prism pentagonal bipyramid cube square antiprism dodecahedron hexagonal bipyramid tricapped trigonal prism heptagonal bipyramid 22 The above descriptors assign possible polyhedra in the Gmelin database. These descriptors are available for searching.

39 Structure searching 2-23 Polyhedra descriptors Two polyhedra, linked by a chain of bonds: Descriptor 22E 22S 23E 23S 33E 33S 24E 24S 25E 25S 44E 44S 45E 45S 55E 55S Polyhedron two triangles (eclipsed) two triangles (staggered) triangle plus tetrahedron (eclipsed) triangle plus tetrahedron (staggered) two tetrahedra (eclipsed) two tetrahedra (staggered) triangle plus square pyramid (eclipsed) triangle plus square pyramid (staggered) triangle plus octahedron (eclipsed) triangle plus octahedron (staggered) two square pyramids (eclipsed) two square pyramids (staggered) square pyramid plus octahedron (eclipsed) square pyramid plus octahedron (staggered) two octahedra (eclipsed) two octahedra (staggered) 23 Other more advanced polyhedra descriptors, shown on this slide, exist. These examples are two polyhedra linked together by a chain of bonds. These descriptors cannot be used for searching; they are only for display.

40 2-24 Searching CrossFire Gmelin Predefined templates File > Group Template Template File button displays first the last.bsd file selected 24 As you know, there are a series of template pages within the application that speed the drawing process. The majority of the templates support organic molecules. One template that is very useful for the Gmelin database is the Polyatom.bsd file. It has a series of structures where the ligands are numbered in the polyhedra; therefore you can specify the absolute stereochemical center. To select a series of templates, choose File > Group Template and select a.bsd file, or click on the Template File button, and select the needed templates, if it isn t the last one used.

41 Structure searching 2-25 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 structure search to retrieve lead tetrahalogenides. Review the results in the Display Hits window. Modify the query to exclude multi-fragment compounds. Draw the lead tetrahalogen structure. Return to CrossFire Commander and start the search. X X Pb X X For a step-by-step solution, see page Exercise 2 Conduct a search to retrieve compounds containing oxalate and water. Draw the oxalate and water structures. Return to CrossFire Commander and perform the search. O O O O - O - H H For a step-by-step solution, see page Exercise 3 Conduct a search to retrieve nickel tetracarbonyl compounds. Then modify the query to isolate 13 C isotopes of the nickel tetracarbonyl. Lastly, modify the query to retrieve any metal tetracarbonyls. View the hitsets.

42 2-26 Searching CrossFire Gmelin Draw the nickel tetracarbonyl structure. Return to CrossFire Commander and perform the search. O O Ni O O Modify the query to isolate the 13 C isotopes. O 13 C O 13 C Ni 13 C O 13 C O Modify the query to retrieve any metal tetracarbonyl. O O M O O View the hitsets. For a step-by-step solution, see page 2-34.

43 Structure searching 2-27 Conduct a structure search for lead tetrahalogenides Exercise 1 Conduct a structure search to retrieve lead tetrahalogenides. Modify the query to exclude multi-fragment compounds. Start the CrossFire Commander If you have already started the software, go to Step 3. Doubleclick the CrossFire Commander icon to start the software. Click the Connect button to log on to the server. Enter your User ID and Password. Click OK. Choose Options > Structure Editors and select CrossFire Structure Editor. Double-click the Structure window. CrossFire Structure Editor instructions Click the Def. Atom drop-down list and select Elements. Select Pb from the periodic table and click OK.

44 2-28 Searching CrossFire Gmelin Click once in the drawing window. Click the Single bond tool. Click the Def. Atom drop-down list and select the X atom. Drag to draw four single bonds with an X atom at the terminal site. X X Pb X X Click the To Commander button. Under Allow, to the right of the structure box, check salts., isotopes, charges, radicals, and additional rings. Click Start Search. Click the View button and view the hitset.

45 Structure searching 2-29 Click the Query Tab button. Click the More button. Under Number of fragments, in the Extended Structure Query Options area, select 1 as minimum and as maximum. Click OK. Click Start Search. Click the View button and view the hitset. Click the Details button.

46 2-30 Searching CrossFire Gmelin Browse through the hitset. Notice that many of the hits from the first list have been removed.

47 Structure searching 2-31 Combined structure search Exercise 2 Conduct a search to retrieve compounds containing oxalate and water. View the hitset. 1. Click the Query Tab button and clear the previous query. 2. Double-click the Structure window. CrossFire Structure Editor instructions 3. Select the Carbon atom and the Single Bond tools from the tool bar. Draw the structural backbone shown below. 4. Select the Double Bond tool from the tool bar. Shiftclick two bonds to modify the structure as shown. 5. Select the oxygen atom from the tool bar. Shift-click the terminal carbons on the oxalate core structure and the junction carbon on the water core structure. O O O O O

48 2-32 Searching CrossFire Gmelin 6. Using the Edit tool, select one of the single bonded terminal oxygen atoms. The Atom Attributes dialog box opens. Assign atom charge 7. Set the charge to 1 and check the Set to Current box. Click OK. 8. Shift-click the second single bonded terminal oxygen atom to place the negative charge on the second oxygen atom. 9. Click the Def. Atom drop-down list and select H. Shift-click the terminal carbon atoms on the water core structure to draw hydrogen atoms. O O O O - O - H H 10. Click the To Commander button. 11. Under Free Sites, to the right of the structure box, check all atoms.

49 Structure searching Click Start Search. 13. Click the View button and view the hitset.

50 2-34 Searching CrossFire Gmelin Conduct structure searches for nickel tetracarbonyl compounds Exercise 3 Conduct a search to retrieve nickel tetracarbonyl compounds. Then modify the query to isolate 13 C isotopes. Lastly, modify the query to retrieve any metal tetracarbonyl. View the hitsets. 1. Click the Query Tab button and clear the previous query. 2. Double-click the Structure window. CrossFire Structure Editor instructions 3. Click the Def. Atom drop-down list and select Elements. 4. Select Ni from the periodic table and click OK.

51 Structure searching Click once in the drawing window to draw the nickel atom. 6. Click the Single bond tool and the carbon atom from the tool bar. 7. Starting at the Ni atom, press and drag to draw four single bonds. 8. Click the Triple bond tool and the oxygen atom from the tool bar. 9. Starting at the terminal carbon atoms, press and drag to draw four C-O triple bonds. 10. Click the To Commander button.

52 2-36 Searching CrossFire Gmelin 11. Under Allow, to the right of the structure box, verify that the boxes next to salts, isotopes, charges, radicals, and additional rings are checked. 12. Click Start Search. 13. Click the View button and view the hitset. 14. Click the Query Tab. 15. Double-click the structure window to return to the CrossFire Structure Editor. 16. Using the Edit tool, click one of the carbon atoms. Assign the isotope value 17. In the Atom Attributes dialog box, set the Mass to 13 and check the Set to Current box.

53 Structure searching Click OK. 19. Shift-click the other three carbon atoms to assign the mass value. 20. Click the To Commander button. 21. Click Start Search. 22. Click View and view the hitset.

54 2-38 Searching CrossFire Gmelin 23. Click the Query Tab. 24. Double-click the structure window to return to the CrossFire Structure Editor. 25. Using the Edit tool, click one of the carbon atoms. Change the Mass value 26. In the Atom Attributes dialog box, set the Mass to * and check the Set to Current box. 27. Click OK. 28. Shift-click the other three carbon atoms to assign the mass value. 29. Using the Edit tool, click the Ni atom.

55 Structure searching 2-39 Assign the generic metal atom 30. In the Atom Attributes dialog box, under Symbol, select M. 31. Click OK. 32. Click the To Commander button to return to the CrossFire Commander. 33. Click Start Search. 34. Click the View button and view the hitset.

56 2-40 Searching CrossFire Gmelin 35. Click the Details button.

57 Characterization of compounds 3-1 Characterization of compounds In this section, you will learn how to: Conduct a search to retrieve characterization data for compounds Conduct a search using multiple data parameters Search over a subset Manipulate hitsets In this section, we will conduct a series of data searches to retrieve compounds and specific information from the Gmelin database. We will not enter in the details during the description of those actions, as there are already described in the Searching CrossFire Databases based on CrossFire Beilstein guide. We will use the Predefined Search Forms and the Fact/Text Search Area to enter factual searches. We will set the subset and search over that subset, and manipulate hitsets.

58 3-2 Searching CrossFire Gmelin Characterization data structure The characterization data structure consists of: identification data for substances, formula search data, composition data, and information on the ligands around a metal.

59 Characterization of compounds 3-3 Chemical name search Scenario: Retrieve various ferrocene compounds using a chemical name search. Review the UV spectral data. use an predefined search form include data operators C (V) C (V) C (V) C (V) Fe (X) C C (V) (V) C (V) C (V) Cl S O O C (V) C (V) C (V) C (V) C -(V) N Fe 2+(XII) C (V) C (V) C -(V) C (V) C (V) N O C (V) C (V) Fe (X) C (V) C (V) C (V) C (V) C (V) C (V) Previous searches performed have involved a structural component. We will now perform a factual search. We will retrieve all compounds with a ferrocene core structure in common using a chemical name search.

60 3-4 Searching CrossFire Gmelin Predefined Search form Identification Check for the occurrence in the database This query form provides search criteria specific to fields related to substance identification data. As you know, you have access to a list of Predefined Search forms, linked to the type of properties you would use for your research. The Predefined Search form selected here provides search criteria specific to fields related to Substance Identification Data. The chemical name fields are free text fields, and they are listed as they appear in the original literature articles. You have to check the presence of the entry in the database (List button).

61 Characterization of compounds 3-5 Results based on wildcard placement Query Results Examples cn=ferrocene 21 ferrocene cn=ferrocene* 228 ferrocene (1+) cn=*ferrocene 3371 bromoferrocene cn=*ferrocene* 7807 acetylferrocene-chi 3 GM0801 All text fields can be searched using wild card (truncation) symbols. The two wildcards are the asterisk (*) and the question mark (?). Both can be used at the beginning, in the middle, or at the end of an entry. The asterisk (*) allows any number of characters, including zero. The single question mark (?) requires any single character. The double question mark (??) requires any two characters.

62 3-6 Searching CrossFire Gmelin Accessing UV spectral data Click the UV link in the Field Availability List Choose View > Field Availabiity As you want to check the UV data, click the UV dynamic link to go directly to the ultraviolet spectral data. To return to the Substance Identification information, click the Home button. The Field Availability dialog box allows you to move directly to specific information. Double-click the field name, or select the field name and click the Go to button.

63 Characterization of compounds 3-7 Viewing spectral data Click to return to top of page Check to print or copy fact Click to copy selected lines Whenever you use an internal link, such as the UV data field code, you can quickly return to the top of the page by clicking the home icon, found in the upper right corner of each fact. Next to this icon, you have the blank check box, allowing you, as in all CrossFire databases, to print or copy a particular fact. As usually, if you are interested in copying a number of lines of information, not the entire fact, select the lines and click the last icon found in this position.

64 3-8 Searching CrossFire Gmelin Molecular formula searching Scenario: Use the molecular formula to retrieve various ferrocene compounds. Eliminate multi-fragment compounds from your search results. In the Gmelin database, there are a number of compounds that cannot be retrieved using a structural query. Inorganic salts, solid-state compounds, alloys, glasses, or ceramic materials cannot be searched using a structure, only a molecular formula. In the next couple of examples, we will use various methods to retrieve compounds based on a molecular formula search. In this example, we want to retrieve ferrocene compounds using the molecular formula. We will also eliminate multi-fragment compounds from the hitset.

65 Characterization of compounds 3-9 Molecular formula fields To retrieve Use the field Example Compounds containing Molecular Formula MF=C2H3NaO2 the molecular formula Compounds containing Search MF Range MOFO=YBa2Cu3O(6-8) the molecular formula range Compounds defined as Alloy Search Field ALLOY=B2O3, CAO, multi-component alloys Eu2O3(W%) and are specified by their formula and percentage Compounds containing Linearized Structure LSF=FeCl3*6NH3 the linear representation of Formula the structure of a compound Compounds containing Fragment Molecular FRAGMF=MnO4(1-):1 the molecular formula Formula of a given fragment MF (Molecular Formula field) retrieves compounds having a component with the exact molecular formula specified, and MOFO (Search MF Range field) finds compounds with molecular formula matching the specified range. ALLOY (Alloy Search field) retrieves multicomponents alloys, glasses or ceramic materials where one or more of the components are specified by their formula and percentage in the material. LSF (Linearized Structure Formula field) retrieves compounds having the exact mol. formula and net charge specified; FRAGMF (Fragment Molecular Formula) retrieves all compounds with a given fragment, and the fragments also.

66 3-10 Searching CrossFire Gmelin Fields related to molecular formula To retrieve Use the field Example The total number Number of Components NC=1 of components The total number Number of Fragments NFRAG=1 of fragments The total number of Number of Elements NE=2 elements in the MF The total number of atoms Number of Atoms NA=6-8 in the MF (use <, >, =, or specify a range with a dash) The respective count of Element Count ELC=Fe2.00 a particular element The symbol of each Element Symbol ELS=Fe particular element Most of the fields related to molecular formula searching can be accessed only through the Fact/Text Search area; there are listed on this slide.

67 Characterization of compounds 3-11 Enter query Predefined Search Forms Four fields relating to molecular formula can be accessed using an PSF form: Molecular Formula (MOFO) Component Molecular Formula (MF) Number of Fragments (NFRAG) Alloy Search Field (ALLOY) Type data directly into the PSF box. When you open the Predefined Search form called Substance Identification Data, you see that there are only four fields related to molecular formula searching that can be accessed. The rest of the molecular formula fields must be accessed using the Fact/Text Search area, as already mentionned. The two fields needed for our query can be found on the chosen form.

68 3-12 Searching CrossFire Gmelin MOFO versus MF Component Molecular Formula (MF) must be entered using Hill order: carbon first (if none carbon, then enter elements in alphabetical order) hydrogen next additional elements in alphabetical order Query Results MOFO= Fe(C5H5)2 and NF= 1 29 MF= Fe(C5H5)2 and NF= 1 0 MF= C10H10Fe and NF= 1 19 GM0801 Component molecular formulas must be entered in Hill order: - carbon atoms are entered first (if no carbon atoms are present, enter all other elements in alphabetical order) - hydrogen atoms are entered next - additional elements are added in alphabetical order It is thus important to understand which molecular formula field was selected when entering a query, reviewing results. The MOFO data field isn t a component molecular formula field; it is why the atoms can be entered using any format. The MF data field is a component molecular formula field, and therefore you must follow rules when entering elements to perform an accurate search.

69 Characterization of compounds 3-13 List manipulation Items from list Q17 excluded from list Q15 To easily view the differences in the lists, combine your lists. As explained in the Searching CrossFire Databases- based on CrossFire Beilstein guide, double click the needed lists from the Hitsets Tab to add it on the Fact/Text Search area, and select the right operator between the selected lists. Alternatively, if you know the hitset number, you can enter the information manually.

70 3-14 Searching CrossFire Gmelin List manipulation results There is a difference of 10 records retrieved when you use the molecular formula (MOFO) field versus the component molecular formula (MF) field. There are 10 records retrieved when using the molecular formula (MOFO) search field that are not present when using the component molecular formula (MF) field. Using the MOFO field, you will retrieve different isotopes of the core structure and with the MF field you will not. If you specified a defined isotope, when using the MF field, this compound will be retrieved. For example, MF=C 10 H Fe.

71 Characterization of compounds 3-15 Formula data parameter search Scenario: Retrieve a single compound containing two iron atoms per formula, copper atom(s), and no oxygen atom(s). There are ways to retrieve records from the database that are formula related, but do not use the molecular formula directly. It is what we will do in the next few examples, where we will use formula data (element count, number of elements, or ) to retrieve a hitset.

72 3-16 Searching CrossFire Gmelin Formula search query Our query must contain information to retrieve compounds with two iron atoms, copper atom(s), and no oxygen atoms. This cannot be done directly using the Predefined Search forms; it is why we have to locate the needed fields on the Search Fields tab, using the Find Field or Form button. Once the field is found, it is added into the Fact/Text Search area by a double click on it; then the needed operator is selected (and, or, not). One-component compounds are substances like elements, molecules, salts, complexes, adducts, mixed crystals (in simple formula descriptions), alloys, glasses and ceramic materials (in formula description).

73 Characterization of compounds 3-17 View the hitset There are records in the Gmelin database that do not have defined structures. You have retrieved single compounds containing specific elements, and excluding others.

74 3-18 Searching CrossFire Gmelin Search for multi-component compounds Scenario: Conduct a formula search to retrieve the BaO/CuO/Y2O3 system. Exclude alloys and glass/ceramic materials from the list of results. Multi-component compounds are heterogeneous compounds like systems or solutions of two or more compounds. Doped compounds, mixed crystals (in complex formula descriptions), alloys, glasses and ceramic materials (in tabular description) are also considered homogeneous compounds. We will retrieve the BaO/CuO/Y2O3 multi-component system excluding alloys, and glass and ceramic materials.

75 Characterization of compounds 3-19 Type of Substance field The Type of Substance (STYPE) field searches for the following classes of compounds: - Alloys - Coordination compounds - Dopants - Glass or ceramic materials - Isomorphous or diadochous compounds, solid solution - Isotope or isotope containing compound - Mineral (assigned to natural minerals) - Polymer When the chemical classification of the substances is unknown, you can use the Type of Substance (STYPE) field. The following classes are searchable: - Alloys - Coordination compounds - Dopants - Glass or ceramic materials - Isomorphous or diadochous compounds, solid solution - Isotope or isotope containing material - Mineral (assigned to natural minerals) - Polymer

76 3-20 Searching CrossFire Gmelin Query results with and without exclusion Query: mf=bao and mf=cuo and mf=o3y2 and nc=3 not (stype=alloy or stype=glass*) Query: mf=bao and mf=cuo and mf=o3y2 and nc=3 A number of compounds that are defined as glass/ceramic material are eliminated from the hitset when using the exclusion statement; only one compound is then retrieved. In the second assay, we re-run the query removing the type restriction. A number of compounds, defined as glass/ceramic material are then retrieved.

77 Characterization of compounds 3-21 Search for alloys Scenario: Conduct a search to retrieve brass alloys where the percentage of copper is unspecified, and the percentage of zinc is restricted between 5-30% by weight. Isolate the results to those with thermodynamic data. use the Fact/Text Search area use the Refine results feature Alloys, glass and ceramic materials can be retrieved using a formula search or percentage composition. For this scenario, we will use the percentage composition.

78 3-22 Searching CrossFire Gmelin Alloy table Percentage Types: A atom W weight V volume X mole fraction The alphanumerical search field, Alloy Search Field, allows the search of alloys, glasses and ceramic materials specified by percentages. A percentage value or percentage range can specify the content of each constituent, an element, or compound. A real number or range is used for the percentage value. The percentage choices are: - A to set the atom or mol percentage - W to set the weight percentage - V to set the volume percentage - X to set an indefinite percentage Compounds must be entered in Hill order; constituents in trace amounts are specified as 0%.

79 Characterization of compounds 3-23 Alloy results Note the various percentages retrieved for the zinc compound.

80 3-24 Searching CrossFire Gmelin Conduct the subset search Enter the Thermodynamic Data field parameter Select from hitset list To isolate the list to only to those compounds with thermodynamic data, we will perform a second search over the retrieved list of results. Choose the last list retrieved as your new search domain and enter the new data query. All lists generated during your work session can be found in the Hitsets Tab.

81 Characterization of compounds 3-25 Subset search results Subset searching is one method for reducing the size of a retrieved hit list.

82 3-26 Searching CrossFire Gmelin Ligand formula search Scenario: Conduct a search to retrieve dinuclear coordination compounds that contain at least one substituted cyclopentadiene ligand. The retrieved compounds must include the metal chromium and one or more carbonyl ligands. Substances can also be searched based on a ligand classification. This classification allows you to search for certain types of ligands in a generalized manner without having to draw complicated structures. One form of molecular formula searching that we have not spoken about is the ligand molecular formula, that we will use with this scenario.

83 Characterization of compounds 3-27 Ligand molecular formula (LIGMF) field Ligand molecular formulas must be ordered as follows: 1. All metal centers, alphabetically 2. Ligand codes ordered as follows: A, CN, CNO, CNR, CNS, CO, CS, D, L, Q, X within the same ligand types, they are ordered on ascending denticity (frequency is not considered) The Ligand Molecular Formula (LIGMF) field is an alphanumerical search field containing the linearized formula of the coordination centers and all ligand codes of a compound. Ligand molecular formulas must follow a specific ordering system. That system is outlined in this slide.

84 3-28 Searching CrossFire Gmelin Ligand formula (LIGFO) field The Ligand Formula field contains ligand codes which describe the elements (in groups) and the number of atoms that are connected to the central metal atom(s). Code L A D Q X Atom C B, Si, Ge N, P, As, Sb O, S, Se, Te H, F, Cl, Br, I, At The Ligand Formula (LIGFO) field contains ligand codes that describe the elements and the number of atoms that are connected to the central metal atom(s). The codes include the elements shown above in this slide. There are also special ligands available. They are: CO, CS, CN, CNS, CNO, and CNR (where the substituent R has no further bonds to the metal atoms).

85 Characterization of compounds 3-29 Enter search criteria The denticity of a ligand is placed in parentheses before the ligand code. Allows for the chromium metal. Allows for the inclusion of carbonyl groups. To enter a value you must place the denticity of the ligand in parentheses before the ligand code. For example, benzene would be (6)L, and cyclopentadiene would be (5)L. If there is a combination of codes, they are ordered alphabetically. We already mentioned that there were special ligands; CO, representing carbonyl group, is one of them. The search field Element Count (ELC) contains the respective counts of the distinct elements in a component molecular formula.

86 3-30 Searching CrossFire Gmelin Ligand results Review the Ligand fields available in the Display Hits window.

87 3-32 Searching CrossFire Gmelin 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-by-step instructions, go to the page listed below the description. Exercise 1 Conduct a chemical name search to retrieve salen complexes. Review the results. For a step-by-step solution, see page Exercise 2 Conduct a molecular formula search to retrieve all potassium sulfate compounds. Modify the query to retrieve only single component potassium sulfate compounds. Review the results. For a step-by-step solution, see page Exercise 3 Conduct a search to retrieve borate glass with the CaO and Eu 2 O 3 components in weight percent. View the results. For a step-by-step solution, see page Exercise 4 Conduct a search to retrieve copper alloys containing trace amounts of iron. View the results. For a step-by-step solution, see page 3-42.

88 Characterization of compounds 3-33 Conduct a chemical name search Exercise 1 Conduct a chemical name search to retrieve salen complexes. Review the results. 14. Click the Query Tab and clear the previous query. 15. Double-click Substance Identity Data from the Predefined Search Forms window. Enter the chemical name 16. Type *salen* in the Chemical Name box. 17. Click OK. 18. Click Start Search. 19. Click View button and view the hitset.

89 3-34 Searching CrossFire Gmelin 20. Click the Query Tab. Delete the current query. 21. Double-click Substance Identity Data from the Predefined Search Forms window 22. Type salen into the Chemical Name Segment box. Click OK. 23. Click Start Search. 24. Click View button and note the differences from the first hitset.

90 Characterization of compounds 3-35 Molecular formula search Exercise 2 Conduct a molecular formula search to retrieve all potassium sulfate compounds. Modify the query to retrieve only single component potassium sulfate compounds. Review the results. 1. Click the Query Tab and clear the previous query. 2. Double-click the Search Fields Tab. Click on the Find Fields or Form button, and type mf range. Click OK. Enter the molecular formula 3. Double click the Search MF Range field. 4. Type K2SO4 in the Field Content column. 5. Click OK. 6. Click Start Search. 7. Click the View button and view the hitset.

91 3-36 Searching CrossFire Gmelin 8. Click the Details button. Note that some of the examples retrieved are multi-component compounds. These appear due to crosssearching effects, i.e. the elements are located in different components. To remove these extraneous records, set the number of components equal to one (nc=1). Modify the query Enter component restriction 9. Click the Query Tab Click the Find Field or Form button and type components. Click OK. 11. Double click on the Number of Components (NC) field.

92 Characterization of compounds Click in the Field Content column and type Click Start Search. 14. Click the View and view the hitset.

93 3-38 Searching CrossFire Gmelin 15. Click the Details button.

94 Characterization of compounds 3-39 Search for alloys, glass and ceramic materials Exercise 3 Conduct a search to retrieve borate glass with the CaO and Eu 2 O 3 components in weight percent. View the results. 1. Click the Query Tab and clear the previous query. 2. Click the Search Fields tab. 3. Click the Find Fields or Forms button and type alloy. 4. Click OK. Enter the alloy requirements 5. Double click on the Alloy Search Field (ALLOY). 6. Click the List button. 7. In the Component Formula column of the Alloy Table, type B2O3.

95 3-40 Searching CrossFire Gmelin 8. Press Tab twice and type CaO in the Component Formula column. 9. Press Tab twice and type Eu2O3 in the Component Formula column.

96 Characterization of compounds 3-41 Enter the percentage parameter 10. Select W from the Percentage Type drop-down list. 11. Click OK. 12. Click Start Search. 13. Click the View button and view the hitset.

97 3-42 Searching CrossFire Gmelin Search for copper alloys containing trace amounts of iron Exercise 4 Conduct a search to retrieve copper alloys containing trace amounts of iron. View the results. 1. Click the Query Tab and clear the previous query. 2. Click the Search Fields tab. Click on the Find Fields or Forms button. Enter alloy requirements 3. Type alloy in the Find Fields window. Double click on the Alloy Search field. 4. Click the List button. 5. In the Component Formula column of the Alloy Table, type Cu. Press Tab twice and type Fe in the Component Formula column. Press Tab and enter 0 in the Percentage column of the Alloy Table dialog box. Select X from the Percentage Type drop-down list.

98 Characterization of compounds Click OK. 7. Click Search. 8. Click the View button and view the hitset.

99 3-44 Searching CrossFire Gmelin

100

101 Physical property searching 4-1 Physical property searching In this section, you will learn how to: Conduct searches to retrieve physical property data In this section, you will learn how to conduct searches to retrieve physical property information specific to the CrossFire Gmelin database.

102 4-2 Searching CrossFire Gmelin Physical Properties data structure The Gmelin file contains more than 100 search fields with numeric data for chemical and physical properties of substances. In addition, there are many search fields for various topics using group codes or keywords. The physical properties data structure consists of: electric, magnetic, mechanical, molecular, optical, thermal, thermodynamic, spectroscopic, information on condensed phases, and phase transition properties.

103 Physical property searching 4-3 Electrical conductivity search Scenario: Conduct a search to retrieve compounds with an electrical conductivity value between 1x10 10 and 1x Restrict the list of compounds to those that have superconductivity data reported. conduct a data search using a Predefined Search Form In this scenario, you will retrieve compounds having a specified range for the electrical conductivity. You will have to restrict the compounds retrieved to only those that additionally indicate superconductivity. The electric conductivity of a substance is its time rate of electricity flowing across unit area, per unit potential gradient. The superconductivity is the abrupt increase of electric conductivity of some materials at low temperatures.

104 4-4 Searching CrossFire Gmelin Predefined Search form Electrical Data This query form provides search criteria specific to fields related to electrical data. The Electrical Data query form has an area to create a general occurrence search for electric data, photoconductivity, dielectric constants, electric conductivity, superconductivity, and thermoelectric effect; and a search where detailed values can be entered. Electrical conductivity values are entered using an upper or lower case E. In our example, 1x10 10 through 1x10 12 is written 1E10-1E12. In addition to the electric conductivity search, you can also create specific searches for superconductivity and dielectric constants using the lower portion of the Electric Data dialog box.

105 Physical property searching 4-5 Electrical conductivity results We retrieved only those compounds where the electrical conductivity is between 1x10 10 and 1x10 12 having also superconductivity values.

106 4-6 Searching CrossFire Gmelin Expansion coefficient search Scenario: Conduct a search to retrieve compounds having an expansion coefficient less than zero. Then modify the query to retrieve compounds having a cubic expansion coefficient less than zero. conduct the initial search using a Predefined Search Form modify the query using the Search Fields The Predefined Search Forms are useful to perform quick searches over general fields in the database; unfortunately, it is not always possible to use those forms. With the second portion of this example, you want to vary the search to include the cubic expansion coefficient; this field is not available in a Predefined Search Form, so you will have to locate the field using the Search Fields tab.

107 Physical property searching 4-7 Predefined Search form Thermal Data This query form provides search criteria specific to fields related to thermal property data. This query form provides search criteria specific to fields related to thermal data. The Thermal Data dialog box has an area to create a general occurrence search for thermal conductivity and the thermal expansion coefficient. You can also create specific searches for these two fields in the lower portion of the Thermal Data dialog box. The thermal expansion coefficient is the ratio in the change in length per unit length, or change in volume per unit volume, to the change of temperature.

108 4-8 Searching CrossFire Gmelin Expansion coefficient results Using the Thermal Data Predefined Search form, we can easily retrieve records to satisfy the expansion coefficient less than zero; but we have too many records to review (459 hits in GM 2008/01). Setting a second parameter will help qualify these records; unfortunately we cannot retrieve the cubic expansion coefficient using the Thermal Data form. You will then locate it in the Search Fields tab, using the Find Field or Form button. If you don t remember how to locate a field, jump to the Searching CrossFire Databases based on CrossFire Beilstein manual.

109 Physical property searching 4-9 Modified expansion coefficient query Field values are not always specific data entries. In this example, entering a numeric value of zero would produce an error in the search. A Flag Field controls the Cubic Expansion data field. A Flag Field is one type of data indexing. The other two forms used for indexing are numerical and text string entries.

110 4-10 Searching CrossFire Gmelin View the hitset We will only retrieve those compounds where the expansion coefficient is less than zero and the cubic expansion coefficient is entered.

111 Physical property searching 4-11 Combination data/structure search Scenario: Conduct a search to retrieve the stability, solubility, and 1H NMR data for the antimetastatic reagent trans- RuCl 2 (DMSO) 4. use the Inorganic Mode to create the structure use the Search Fields In this new example, we will retrieve information about the stability, solubility, and H NMR data for the antimetastatic reagent. There are various possibilities to formulate combination queries. We are using one data constraint and one structure entry.

112 4-12 Searching CrossFire Gmelin Create the structural query DMSO ligand can bond to metal centers by either the S or the O atom; there are times when both complexes can be retrieved in the same search if a general structure is used. The complexes can be fragmented if the connectivity is unknown; here we want the S connection to the Ru to be retrieved. We want to find only the trans-complex. Use the OC-6 template as core structure; include Cl atoms in the trans-position and the DMSO complex attached via the sulfur atom in the other positions. Set the polyhedra descriptor OC-6 on the Ru atom and search using the absolute stereochemical designation.

113 Physical property searching 4-13 Enter data constraints Applying absolute stereo ensures retrieval of only the trans configuration. Applying absolute stereo will avoid retrieval of any cis configurations. You will then add the needed fields needed in the Text/Fact area table: the Description of Stability (STAB), the Description of Solubility (SLB) and the Nucleus (NMR.NUC) fields. When you conduct a combined search, both the data in the Test/Fact Search area and the structure in the Structure window must be satisfied.

114 4-14 Searching CrossFire Gmelin Search with or without values What does it mean? Searching a field without a value retrieves hits that have any entry in that field. What kind of entries are allowed? Phrases - search for specific terms or with wildcard * Numeric values - search for specific values or range Existence - no entry is necessary, relation is: exists Some fields can be searched with values or for existence only (solubility/slb) On this slide, you can see the entries allowed within Crossfire Commander 7.1. If a field is a folder in the Search Fields tab, you can search it without entering a value. There are two types of folders, those that can be expanded and those that cannot be expanded (called group codes ). If a field is included in a folder, and the last in the hierarchy in the Search Fields tab, you must enter a value to search that field. For example, stability is a folder; therefore we are not required to enter a value.

115 Physical property searching 4-15 Results of the combination search We retrieved the defined structure having solubility, stability, and NMR data.

116 4-16 Searching CrossFire Gmelin Magnetization diagram search Scenario: Conduct a search to retrieve compounds having only the elements Fe, B, and Nd. Include information for the retrieval of a magnetization diagram for the compounds. conduct the search using the Search Fields We have done extensive searching using the various methods for retrieving compounds based on their molecular formula. In this scenario, we want to retrieve compounds specifying certain elements as a requirement. This can be an extremely general search. We will control the list retrieved by requiring that the compounds found must have a magnetization diagram available.

117 Physical property searching 4-17 Search Text/Fields data entry Brackets can be used to combine parts of a query. Use the Find Field or Form button to locate the needed fields on the Search Fields tab. Use the - Element Symbol field (ELS) to specify an element that must be retrieved. - Number of Elements field (NE) to restrict the total number of elements in the molecular formula that can be retrieved. - Number of Components field (NC) to retrieve compounds with a specific number of components.

118 4-18 Searching CrossFire Gmelin Magnetization diagram data entry The magnetization diagram data field is also a flag field and requires the use of special indexing to run the query properly.

119 Physical property searching 4-19 Magnetization results Further magnetization data can be displayed: information on the magnetic anisotrophy, magnetic structure, magnetic space group, or further magnetic phenomenon.

120 4-20 Searching CrossFire Gmelin 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 search to retrieve compounds having a melting point above 4000 o C. View the results. For a step-by-step solution, see page Exercise 2 Use the Crystal Structure Data PSF form to conduct a search for compounds with the A cell parameter range of Angstroms and the C cell parameter range of Angstroms as determined by single crystal diffraction. View the results. For a step-by-step solution, see page Exercise 3 Search for the adsorption of Hg 2+ ions on a cellulose containing material. View the results. For a step-by-step solution, see page 4-25.

121 Physical property searching 4-21 Retrieve melting point data Exercise 1 Conduct a search to retrieve compounds having a melting point above 4000 o C. View the results. 25. Click the Query Tab and clear the previous query. 26. Double-click Physical Data from the Predefined Search Forms tab. 27. In the Detailed values section of the Physical Data query form, choose the greater than (>) symbol for the melting point value or range. Enter the physical data 28. Press Tab and type 4000 in the Melting Point box. Check for the occurrence 29. Click the List button to check for the occurrence in the database. 30. Click Cancel.

122 4-22 Searching CrossFire Gmelin 31. Click OK. 32. Click Start Search. 33. Click the View button and view the hitset. View the melting point data 34. Choose View > Hit only. 35. Choose View > Highlight Hits.

123 Physical property searching 4-23 Retrieve crystal structure data Exercise 2 Use the Crystal Structure Data PSF form to conduct a search for compounds with the A cell parameter range of Angstroms and the C cell parameter range of Angstroms as determined by single crystal diffraction. View the results. 16. Click the Query Tab and clear the previous query. 17. Double-click Crystal Structure Data from the Predefined Search Forms tab. Enter Angstrom data restrictions 18. Type in the Lattice Length A box. 19. Click to select the Lattice Length C box. Type Enter detection method 20. In the Detailed values section of the Crystal Structure Data query form, choose is for the Method operator. 21. Click to select the Method box. Click the List tool. Select single crystal x-ray diffraction. 22. Click OK.

124 4-24 Searching CrossFire Gmelin 23. Click Start Search. 24. Click the View button and view the hitset.

125 Physical property searching 4-25 Retrieve the adsorption diagram of Hg 2+ ions Exercise 3 Search for the adsorption of Hg 2+ ions on a cellulose containing material. View the results. 1. Click the Query Tab and clear the previous query. 2. Click the first line of the Search Text/Field area (Table). Enter the data query 3. Type mofo in the Field Name column. 4. Press Tab and type Hg(2+). 5. Click the Search Fields tab. Locate the data field 6. Expand the Properties of / in Systems (MCS) folder. 7. Double-click the Other Component (SPOF.PA) field in the Sorption of Title Compound (SPOF) folder. 8. Type cellulose in the Field content column. Check for occurrence 9. Click the List button to check the occurrence in the database.

126 4-26 Searching CrossFire Gmelin 10. Click Cancel. 11. Click Start Search. 12. Click the View button and view the hitset.

127 Chemical property searching 5-1 Chemical property searching In this section, you will learn how to: Conduct searches to retrieve chemical property data In this section, you will learn how to conduct searches to retrieve chemical property data.

128 5-2 Searching CrossFire Gmelin Chemical Properties data structure The chemical properties data structure consists of: chemical behavior, surface reactions, reaction data, reaction details.

129 Chemical property searching 5-3 Retrieve preparation methods Scenario: Conduct a search to retrieve information on the preparation of the hexagonal modification of barium titanate. Modify the search to retrieve the solid phase preparation of barium titanate. use the Search Fields use hyperlinks to view the reaction We have already mentioned that not every compound record in the CrossFire Gmelin database can be retrieved using a structural query. This poses a challenge when trying to retrieve reaction information. Those reaction records that do not contain a structure are designated as non-graphical reactions. To retrieve these types of records, you must use information about their preparation. In this example, we will retrieve the reaction records for the preparation of hexagonal barium titanate.

130 5-4 Searching CrossFire Gmelin Enter reaction preparation data Use List button to check entries A number of the reaction fields must be accessed using the Tabular Query form. It is important to check for the occurrence of the data values for these fields.

131 Chemical property searching 5-5 Check database occurrence The combination entry does not retrieve any records. Although BaTiO3 occurs in the database, running this search will produce no hits. You have always to check the occurrence of the entry using the List button. The database displays batio3 and batio3 barium titanate as valid entries. Selecting both obtains barium titanate compounds, while showing that the entry is more detailed than just the molecular formula.

132 5-6 Searching CrossFire Gmelin Preparative search results In the reaction section of the Display Hits window, you will find information on the preparation of this compound. Reagents, solvents, and general conditions are shown. Clicking the displayed link can access details for the starting materials.

133 Chemical property searching 5-7 Hyperlink to the reaction Hyperlinks are available throughout the Display Hits window to allow you to view various pieces of retrieved information. Use the Reaction ID hyperlink to view the preparative methods. Clicking the Show button opens a window displaying the structural representation, if available.

134 5-8 Searching CrossFire Gmelin Modify the query The second part of the scenario asks us to modify the query to retrieve the reaction records for the solid phase preparation of barium titanate. The structure for the product is not shown. The correct molecular formula can be viewed below the reactant.

135 Chemical property searching 5-9 Catalyst preparation Scenario: Ziegler/Natta complexes are important catalysts in the polymer industry. Conduct a search to retrieve information on the synthesis of these compounds. Use hyperlinks to access the catalysis data and the journal articles. use a partial reaction query use hyperlinks to access the catalysis data and journal articles We will conduct a search to retrieve information on the synthesis of Ziegler/Natta complexes. We will then use hyperlinks to access information on the catalysis data and the original journal article.

136 5-10 Searching CrossFire Gmelin Create the query Apply an atom list where M=Ti, Zr, or Hf Set as product for the search feature To create the structural query, you will need to apply a user-defined atom list and designate the compound as a product. In a user-defined atom list, a substituent can be defined as only an atom. A quick method to define the substance as a reactant or as a product is to use the Structure Query Options area. 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.

137 Chemical property searching 5-11 Search results Click the Product(s) (GRN) hyperlink To view the catalysis data, you must first hyperlink to the product information.

138 5-12 Searching CrossFire Gmelin Hyperlink to the catalysis data Click the Behavior as Catalyst (BCAT) hyperlink. We previously mentioned that you can view information using the View>Field Availability command, or by clicking the hyperlinks in the Field Availability List. Click on the CAT hyperlink; there are 125 occurrences (GM 2008/01) for the Behavior as Catalyst data field. Click one of the Full Text button to view the original journal article. Some references list only the title while others list the title and abstract.

139 Chemical property searching 5-13 Hyperlink to the journal articles Zirconium-catalyzed methylalumination of heterosubstituted arylethynes: Factors affecting the regio-, stereo-, and chemoselectivities A click on the View Details button, for the second occurrence of Behavior as Catalyst data, allows you to jump to the citation and gives the title and abstract. Examine the abstract entry.

140 5-14 Searching CrossFire Gmelin Full reaction search Scenario: Conduct a search to retrieve the simple synthesis of the catalyst Cp 2 ZrCl 2 where the reactant is defined as ZrCl 4. create a full reaction query We have retrieved reactions using : - factual chemical properties as our query. - a partial reaction search We will now search using a full reaction query. In this example, we want to retrieve synthetic methods for the preparation of the CP 2 ZrCl 2 catalyst using a full reaction query.

141 Chemical property searching 5-15 Create the full reaction query Reaction Attributes mode In Reaction Attributes mode: Select ZrCl4 and click the Reactant button Select CpZrCl2 and click the Product button To create a full reaction query, you must use one of the structure editors and define the reactant(s) and product(s) (cf Searching CrossFire Databases based on CrossFire Beilstein manual). CrossFire Structure Editor has two modes: Molecule Attributes and Reaction Attributes. You will use the Molecule Attributes mode to draw the compounds. The Reaction Attributes mode will allow you to assign a molecule role in a reaction, to specify the reacting center, and to map a reaction.

142 5-16 Searching CrossFire Gmelin Full reaction results Results can be viewed using the Full or Short view.

143 Chemical property searching 5-17 Factual reaction search Scenario: Conduct a factual search to retrieve reactions that produce hexachlorodisilane without using solvents. Convert the hitset to a list of citations. use a Predefined Search form to retrieve the reaction use the Get all conversion In this scenario, you will conduct a factual search to retrieve a list of reactions. You will then convert the hit list to a list of associated citations.

144 5-18 Searching CrossFire Gmelin Factual reaction search query This query form provides search criteria specific to fields related to reaction data. This query form provides search criteria specific to fields related to reaction data. The Reaction Data Predefined Search Form allows you to search the fields: - Starting Material name - Product Name - Catalyst Name - Reagent - Yield - Solvent Catalysts are stored with their identification data and can be searched using GRN number or name. Structures of catalysts are available, but they cannot be entered in the graphical reaction mode with the role of catalyst.

145 Chemical property searching 5-19 Reaction results Notice the Product(s) GRN naming convention. The product is Si 2 Cl 6 hexachlorodisilane. Without an operator we would not have retrieved this example. Text fields use operators that are different from those used with numeric entries. The text field operators used are: - Is which finds the exact entry. - Starts with which enters a wildcard at the end of the entry. - Ends with which enters a wildcard at the beginning of the entry. - Contains which enters wildcards at the beginning and the end of the entry.

146 5-20 Searching CrossFire Gmelin Convert the hitset Click the Get all button and select: Get All Related Citations A single reaction is often published multiple times with different reaction details or conditions. To find more about this reaction, you might want to view the list of citations that report it. A lit can be converted to one of the two other contexts.

147 Chemical property searching 5-21 Converted citation hitset Sort for newest Article The Grid Display contains summary information for the citations that report the reaction. By default, the most current citations are at the end of the list, and can be sorted by Year or by Source Title/Patent Number by clicking on the hyperlinked header of the two last columns. The Details Display includes the article title and abstract where available, all compounds, and all reactions reported in the concerned citation.

148 5-22 Searching CrossFire Gmelin Citation Searching For information about Citation Searching, please consult the Searching CrossFire Databases- based on CrossFire Beilstein training guide.

149 Chemical property searching 5-23 Managing Your Results For information about Printing, creating Report, Exporting, and Alerts, please consult the Searching CrossFire Databases- based on CrossFire Beilstein training guide.

150 5-24 Searching CrossFire Gmelin 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-by-step instructions, go to the page listed below the description. Exercise 1 Conduct a search to retrieve inorganic reactions catalyzed using aluminum trichloride (AlCl 3 ) published after View the hitset. For a step-by-step solution, see page Exercise 2 Conduct a search to retrieve reactions with chromium hexacarbonyl (Cr(CO) 6 ) in ethanol under irradiation. View the hitset. For a step-by-step solution, see page Exercise 3 Conduct a search to retrieve reactions for the preparation of CO bridged cyclopentadienyl iron or ruthenium complexes using two CO bridges. Allow for maximum substitution on the metal. View the hitset. Modify the query to allow substitution on all available atoms. View the hitset. Draw the metal CO cyclopentadienyl complex. Return to CrossFire Commander and perform the search. For a step-by-step solution, see page 5-33.

151 Chemical property searching 5-25 Retrieve inorganic reactions Exercise 1 Conduct a search to retrieve inorganic reactions catalyzed using aluminum trichloride (AlCl 3 ) published after View the hitset. 36. Click the Query Tab and clear the previous query. 37. Click the Search Fields tab. 38. Expand the Chemical Properties (CHE) folder. 39. Expand the Reaction Details (RX) folder. 40. Double-click the Catalyst(s)(Name) (RX.CAT) field. Enter the chemical data 41. Type AlCl3 in the Field content box. 42. Click the List button to check the occurrence in the database. 43. Select alcl3 aluminum trichloride and click the double arrows (>>). Click OK.

152 5-26 Searching CrossFire Gmelin 44. Click the Search Field tab. 45. Click the Find Fields or Forms button and type publication. 46. Click OK. Enter the data restriction 47. Double-click the Publication Year (PY) field. 48. Choose > as operator, and type 1999 in the Field content box.

153 Chemical property searching Click Start Search. 50. Click the View button and view the hitset.

154 5-28 Searching CrossFire Gmelin Conduct a reaction search Exercise 2 Conduct a search to retrieve reactions with chromium hexacarbonyl (Cr(CO) 6 ) in ethanol under irradiation. View the hitset. 1. Click the Query Tab and clear the previous query. 2. Type cn in the Field Name column of the Search Text/Fields contents area 3. Type chromium hexacarbonyl in the field content box. 4. Click the List button to check for the occurrence in the database. 5. Click the Search Fields tab. 6. Expand the Chemical Properties (CHE) folder. 7. Expand the Reaction Details (RX) folder. 8. Double-click the Solvent (RX.SOL) field.

155 Chemical property searching 5-29 Enter the solvent information 9. Type ethanol in the Field content box. 10. Double-click the Special Conditions (RX.SCON) field. Enter special conditions

156 5-30 Searching CrossFire Gmelin 11. Click the List button. 51. Double-click irradiation (uv/vis) and click OK.

157 Chemical property searching Click OK. 53. Click Start Search. 54. Click the View button and view the hitset.

158 5-32 Searching CrossFire Gmelin 55. Click the Details button to view the full record. 56. If necessary, choose View > Hits only. 57. If necessary, choose View > Highlight Hits.

159 Chemical property searching 5-33 Preparation of CO bridged cyclopentadienyl metal complexes Exercise 3 Conduct a search to retrieve reactions for the preparation of CO bridged cyclopentadienyl iron or ruthenium complexes. Allow for maximum substitution on the metal. View the hitset. Modify the query to allow substitution on all available atoms. View the hitset. 25. Click the Query Tab and clear the previous query. 26. Double-click the Structure window. CrossFire Structure Editor 27. Click the cyclopentadiene template from the tool bar. 28. Using the Edit tool, click once in the drawing window. Click the disconnected atom to open the Atom Attributes dialog box. 29. Type A0 in the Symbol box, set the Free Sites to MAX and click OK. 30. Using the Edit tool, select the Carbon atom and the Single Bond tool. Click to draw two ethylene groups coming off the A0 atom.

160 5-34 Searching CrossFire Gmelin 31. Draw single bonds connecting each of the carbons on the cyclopentadiene to the A0 atom. 32. Select the Single/Double Bond tool. Shift-click to create the bonds shown below. 33. Select the O atom from the tool bar. Shift-click to create the oxygen atoms shown below.

161 Chemical property searching Using the Edit tool, select the C atom from the tool bar. Click one of the carbon atoms on the C-O bond. This opens the Atom Attributes dialog box. Set Free Sites 35. Set Free Sites to Max., check the Set to Current box, and click OK. 36. Shift-click the carbon atom on the second C-O bond to apply the max free sites to the carbon atom. 37. Click the Atom List tool. If necessary, set the Atom List number to A0 and click OK. 38. Select Fe and Ru from the periodic table and click OK.