Searching CrossFire Gmelin Training Guidein the manual “Searching CrossFire Databases- based on...

Searching CrossFire Gmelin

Training Guide

CrossFire®

Commander Version 7.1


CrossFire

® Commander Version 7.1

Training Guide

CrossFire

® Software Copyright © 1995-2008, Elsevier Information Systems GmbH.

CrossFire Beilstein Database: Copyright © 2007-2008, Elsevier Information Systems GmbH. Gmelin Database: Copyright © 2000-2008, Gesellschaft Deutscher Chemiker, licensed to Elsevier Information Systems GmbH; © 1988-1999, 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

TABLE OF CONTENTS

INTRODUCTION

Searching CrossFire Gmelin ............................................................................................ 1-1

Module objectives ............................................................................................................ 1-2

What is a Gmelin compound? .......................................................................................... 1-3

Elements included in Gmelin ........................................................................................... 1-4

Sources ............................................................................................................................. 1-5

Time coverage .................................................................................................................. 1-6

Compound types .............................................................................................................. 1-7

STRUCTURE SEARCHING

Structure searching........................................................................................................... 2-1

Retrieval of coordination compounds .............................................................................. 2-2

CrossFire Structure Editor ............................................................................................... 2-3

Apply the substitution query feature ................................................................................ 2-4

Query options for atoms................................................................................................... 2-5

Implicit versus explicit free sites ..................................................................................... 2-6

Set implicit free sites ........................................................................................................ 2-7

Allow query options ......................................................................................................... 2-8

Extended query options.................................................................................................... 2-9

Implicit search results .................................................................................................... 2-10

Explicit search results .................................................................................................... 2-11

Using generics and atom lists ........................................................................................ 2-12

Generic atoms ................................................................................................................ 2-13

Predefined generic groups.............................................................................................. 2-14

Creating an atom list ...................................................................................................... 2-15

Add data constraints ....................................................................................................... 2-16

Bonding considerations .................................................................................................. 2-17

Bond query features ....................................................................................................... 2-18

Search results ................................................................................................................. 2-19

Inorganic Editmode ........................................................................................................ 2-20

Atom Attributes dialog box ........................................................................................... 2-21

Gmelin database descriptors .......................................................................................... 2-22

Polyhedra descriptors ..................................................................................................... 2-23

Predefined templates ...................................................................................................... 2-24

Exercises descriptions .................................................................................................... 2-25

Exercise 1: Conduct a structure search for lead tetrahalogens ...................................... 2-27

Exercise 2: Combined structure search .......................................................................... 2-31

Exercise 3: Conduct structure searches for nickel tetracarbonyl compounds................ 2-34

CHARACTERIZATION OF COMPOUNDS

Characterization of compounds ....................................................................................... 3-1

Characterization data structure ........................................................................................ 3-2

Chemical name search ..................................................................................................... 3-3

Predefined form – Identification ...................................................................................... 3-4

Results based on wildcard placement .............................................................................. 3-5

Accessing UV spectral data ............................................................................................. 3-6

Viewing spectral data ....................................................................................................... 3-7

Molecular formula searching ........................................................................................... 3-8

Molecular formula fields.................................................................................................. 3-9

Fields related to molecular formula ............................................................................... 3-10

Enter query – EDS form ................................................................................................ 3-11

MOFO versus MF .......................................................................................................... 3-12

List manipulation .......................................................................................................... 3-13

List manipulation results ................................................................................................ 3-14

Formula data parameter search ...................................................................................... 3-15

Formula search query .................................................................................................... 3-16

View the hitset ............................................................................................................... 3-17

Search for multi-component compounds ....................................................................... 3-18

Type of Substance field ................................................................................................. 3-19

Query results with and without exclusions .................................................................... 3-20

Search for alloys ............................................................................................................ 3-21

Alloy table ...................................................................................................................... 3-22

Alloy results ................................................................................................................... 3-23

Conduct the subset search .............................................................................................. 3-24

Subset search results ...................................................................................................... 3-25

Ligand formula search ................................................................................................... 3-26

Ligand molecular formula (LIGMF) field ..................................................................... 3-27

Ligand formula (LIGFO) field ....................................................................................... 3-28

Enter search criteria ....................................................................................................... 3-29

Ligand results ................................................................................................................. 3-30


Exercise 1: Conduct a chemical name search ................................................................ 3-32

Exercise 2: Molecular formula search ........................................................................... 3-34

Exercise 3: Search for alloys, glass and ceramic materials ........................................... 3-38

Exercise 4: Search for copper alloys containing trace amounts of iron ......................... 3-41

PHYSICAL PROPERTY SEARCHING

Physical property searching ............................................................................................. 4-1

Physical properties data structure .................................................................................... 4-2

Electrical conductivity search .......................................................................................... 4-3

Predefined form – Electrical Data .................................................................................... 4-4

Electrical conductivity results .......................................................................................... 4-5

Expansion coefficient search ........................................................................................... 4-6

Predefined form – Thermal Data ..................................................................................... 4-7

Expansion coefficient results ........................................................................................... 4-8

Modified expansion coefficient query ............................................................................. 4-9

View the hitset ............................................................................................................... 4-10

Combination data/structure search ................................................................................. 4-11

Create the structural query ............................................................................................. 4-12

Enter data constraints ..................................................................................................... 4-13

Search with and without values ..................................................................................... 4-14

Results of the combination search ................................................................................. 4-15

Magnetization diagram search ....................................................................................... 4-16

Tabular Query data entry ............................................................................................... 4-17

Magnetization diagram data entry ................................................................................. 4-18

Magnetization results ..................................................................................................... 4-19


Exercise 1: Retrieving melting point data ...................................................................... 4-21

Exercise 2: Retrieve crystal structure data ..................................................................... 4-23

Exercise 3: Retrieve the adsorption diagram of Hg2+

ions ............................................ 4-25

CHEMICAL PROPERTY SEARCHING

Chemical property searching ........................................................................................... 5-1

Chemical properties data structure................................................................................... 5-2

Retrieve preparation methods .......................................................................................... 5-3

Enter reaction preparation data ........................................................................................ 5-4

Check database occurrence .............................................................................................. 5-5

Preparative search results ................................................................................................. 5-6

Hyperlink to the reaction ................................................................................................. 5-7

Modify the query.............................................................................................................. 5-8

Catalyst preparation ......................................................................................................... 5-9

Create the query ............................................................................................................. 5-10

Search results ................................................................................................................. 5-11

Hyperlink to the catalysis data ....................................................................................... 5-12

Hyperlink to the journal articles .................................................................................... 5-13

Full reaction search ........................................................................................................ 5-14

Create the full reaction query ......................................................................................... 5-15

Full reaction results ........................................................................................................ 5-16

Factual reaction search ................................................................................................... 5-17

Factual reaction search query......................................................................................... 5-18

Reaction results .............................................................................................................. 5-19

Convert the hitset ........................................................................................................... 5-20

Converted citation hitset ................................................................................................ 5-21

Citation searching .......................................................................................................... 5-22

Managing your results.................................................................................................... 5-23


Exercise 1: Retrieve inorganic reactions........................................................................ 5-25

Exercise 2: Conduct a reaction search ........................................................................... 5-28

Exercise 3: Preparation of CO bridged cyclopentadienyl metal complexes .................. 5-33

Introduction 1 - 1

Notes


Key points

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”.

1 - 2 Searching CrossFire Gmelin

Notes

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

Key points

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.

Introduction 1 - 3

Notes

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, CO2, CS2, or

phosgene.

Substances, which contain carbon, containing at

least one “Gmelin element”

Key points

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.


Notes

Elements included in Gmelin

Elements, in combination with carbon, included in

Gmelin are shaded in the periodic table.

H

Key points

The elements, in combination with

carbon, included in the Gmelin database

are shaded in the periodic table.

Introduction 1 - 5

Notes

Sources

2.5+ Million

1817 1975 2008

Gmelin Handbook of

Inorganic Chemistry:

- Journals

- Patents

- Monographs

Primary Literature:

- Journals

Key points

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).


Notes

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

Key points

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

http://info.crossfiregmelin.com/GMJour

nals.pdf

http://info.crossfiregmelin.com/GMJournals.pdf

http://info.crossfiregmelin.com/GMJournals.pdf

Introduction 1 - 7

Notes

Compound types

4,200

Minerals

4,200

Minerals

>1339,000

Coordination

compounds

>1339,000

Coordination

compounds

42,000

Glasses and

ceramic

materials

42,000

Glasses and

ceramic

materials

46,200

Catalysts

46,200

Catalysts

65,100

Solid solutions

65,100

Solid solutions

121,300

Alloys

121,300

Alloys

32,600

Polymers

32,600

Polymers

Key points

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.

Structure searching 2 - 1

Notes

1

Structure searching

Application of to query features to atoms

and bonds

Application of structure search parameters

Conduction of a combination search

In this section, you will learn how to apply the features

learned with XFire Commander 7.1, to the Gmelin database:

Key points

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.


Notes

2

Retrieval of coordination compounds

apply atom query features

Compare explicit and implicit substitution query options

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.

Key points

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.


Notes

3

CrossFire Structure Editor

Select the following tools to create the compound:

Key points

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.


Notes

4

Apply the substitution query feature

Max free sites

N

Co

N

*

Key points

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).


Notes

5

Query options for atoms

Sets the number of unpaired

electrons associated with the atom

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 negative or

positive charge of an atom

Sets the mass of an atom

from the default to

another occurring isotope

Determines whether

an atom is part of a

ring, chain, or either

Sets the minimum

and maximum number

of implicit hydrogens

attached to the atom

Key points

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.


Notes

6

Implicit versus explicit free sites

Max free sites

1 free site(0 or 1 addl substituent)

2 free sites(0,1 or 2 addl substituents)

Explicit free sites

Applied to specific atoms

Specify the number of free sites

N

Co

N

*

N

Co

N

*1

N

Co

N

*2

Implicit free sites

Applied to the entire structure

N

Co

N

Key points

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.


Notes

7

Set implicit free sites

Key points

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.


Notes

8

Allow query options

Allows or excludes charged compounds

to be retrieved in the search.

Allows or excludes compounds containing

radicals to be retrieved in the search.

Allows or excludes ring closures

between atoms or groups with free sites.

Allows or excludes isotopes

Allows or excludes multifragment

structures such as salts or charge-transfer

complexes

Key points

Of course, you can always decide that

salts, isotopes, charges, radical and

additional rings will be present or absent

from the search results.


Notes

9

Extended query options

Sets the total number

of rings to be found in

the retrieved structure

Sets the total number

of fragments to be

found in the retrieved

structure

Sets the total

number of atoms

to be found in the

retrieved structure

Tautomers of the drawn

structure will also be

retrieved in the search

When more than one isolated

component is drawn in the

query, this switch defines that

they are to be retrieved as

separate components

If atom-atom mappings have been

defined in a reaction query, this option

will ignore those mappings in the search

Key points

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.


Notes

10

Implicit search resultsexample

Key points

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.


Notes

11

Explicit search results example

Key points

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

1st result‟ features checked.


Notes

12

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

Key points

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.


Notes

13

Generic atomsGeneric 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

Key points

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.


Notes

14

Predefined generic groups

Any GroupG

O

AlkoxyAOX

N NHeterocyclic

CHC

AcyclicACY

CarbacyclicABC

N N

Nno carbon

Cyclic,CXX

CarbocyclicCBC

CyclicCYC

NHeteroaryl(6)

HARAlkynylAYL

AlkenylAEL

AlkylALK

CycloalkenylCEL

CycloalkylCAL

ArylARY

HeteroacyclicAHC

Any Group with ring closure

G*

Key points

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.


Notes

15

Creating an atom list

Key points

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.


Notes

16

Add data constraintsData query form

Search query form

Example results :

Key points

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.


Notes

17

Bonding considerationsScenario: 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

O

F

F

F

F

F

F

F

FF

Mn(VIII)

P(IV)

C(V)

C(V)

C(V)

C(V)

O(III)

O(III)

P(IV)

Mn(III)

ClCl

Key points

In this example, we will retrieve

organometallic compounds by

modifying the bonding factor.


Notes

18

Bond query features

Determines whether

a bond is part of a

ring, chain, or either

Options > Define Bond or Click the atom with the Edit tool

Retrieves structures

containing any type

of bond where applied


containing either

single or double

bonds where applied


containing either

double or triple bonds

where applied


containing any

stereo configuration

where applied


where the cis or trans

configuration is

considered

where applied

Key points

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.


Notes

19

Search results

Queries:

Number of hits:

59 301 607

Key points

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.


Notes

20

Inorganic Editmode

The Inorganic Editmode must be selected to assign the polyhedra

descriptors for atoms within the Gmelin database.

Key points

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).


Notes

21

Atom Attributes dialog boxEditmode > Organic Editmode > Inorganic

Determines the connectivity of atoms

and stereodescriptors

Key points

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.


Notes

22

Gmelin database descriptors

Simple polyhedra: Descriptor Polyhedron

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

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

Key points

The above descriptors assign possible

polyhedra in the Gmelin database.

These descriptors are available for

searching.


Notes

23

Polyhedra descriptors

Two polyhedra, linked

by a chain of bonds:

22E

Descriptor Polyhedron

22E

22S

23E

23S

33E

33S

24E

24S

25E

25S

44E

44S

45E

45S

55E

55S

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)

Key points

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.


Notes

24

Predefined templates

File > Group Template

Template File button displays first the

last .bsd file selected

Key points

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.


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.

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.

P b

X

XX

X

For a step-by-step solution, see page 2-27.

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


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.

Exercise descriptions

Exercise 1

Exercise 2

Exercise 3


Draw the nickel tetracarbonyl structure. Return to


Ni

O

O

O

O

Modify the query to isolate the

13C isotopes.

Ni

C13

C13

C13

C13

O

O

O

O

Modify the query to retrieve any metal tetracarbonyl.

M O

O

O

O

View the hitsets.



Conduct a structure search for lead

tetrahalogenides

Conduct a structure search to retrieve lead tetrahalogenides.

Modify the query to exclude multi-fragment compounds.

If you have already started the software, go to Step 3. Double-

click 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.

Click the Def. Atom drop-down list and select Elements.

Select Pb from the periodic table and click OK.

Exercise 1

Start the CrossFire Commander

CrossFire Structure Editor instructions


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.

P b

X

XXX

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.


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.


Browse through the hitset. Notice that many of the hits

from the first list have been removed.


Combined structure search

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.

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. Shift-

click 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.

OO

O O

O

Exercise 2



6. Using the Edit tool, select one of the single bonded

terminal oxygen atoms. The Atom Attributes dialog

box opens.

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.

OO

O- O

- H

O

H

10. Click the To Commander button.

11. Under Free Sites, to the right of the structure box, check

all atoms.

Assign atom charge


12. Click Start Search.

13. Click the View button and view the hitset.


Conduct structure searches for nickel

tetracarbonyl compounds

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.


3. Click the Def. Atom drop-down list and select

Elements.

4. Select Ni from the periodic table and click OK.

Exercise 3



5. 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.



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.



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.

17. In the Atom Attributes dialog box, set the Mass to 13

and check the Set to Current box.

Assign the isotope value


18. Click OK.

19. Shift-click the other three carbon atoms to assign the

mass value.



22. Click View and view the hitset.



24. Double-click the structure window to return to the

CrossFire Structure Editor.

25. Using the Edit tool, click one of the carbon atoms.

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.

Change the Mass value


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.



Assign the generic metal atom


35. Click the Details button.

Characterization of compounds 3 - 1

Notes

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

Key points

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.


Notes

Characterization data structure

Key points

The characterization data structure

consists of: identification data for

substances, formula search data,

composition data, and information on the

ligands around a metal.


Notes

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

F e(X)

C(V)

C(V)

C(V)

C(V)

C(V)

C(V)

C(V) C

(V)

Fe(X)

C(V)

C(V)C

(V)C

(V)

C(V)C

(V) C(V)C

(V)

S

C l

O

O

Fe2+(XII)

C(V)C

(V)

C-(V)C

(V)

C(V)

C(V)

C(V)

C-(V)

C(V)

C(V)

N

N

O

Key points

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.


Notes

Predefined Search form – Identification

This query form

provides search

criteria specific to

fields related to

substance

identification data.

Check for the

occurrence in

the database

Key points

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).


Notes

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-CHI3

GM0801

Key points

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.


Notes

Accessing UV spectral dataClick the UV link in the

Field Availability ListChoose View > Field Availabiity

Key points

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.


Notes

Viewing spectral data

Click to return

to top of page

Check to print or copy fact

Click to copy

selected lines

Key points

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.


Notes

Molecular formula searching

Scenario: Use the molecular formula to retrieve various ferrocene

compounds. Eliminate multi-fragment compounds from

your search results.

Key points

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.


Notes

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 containing Linearized Structure LSF=FeCl3*6NH3

the linear representation of Formula

the structure of a compound

Compounds defined as Alloy Search Field ALLOY=B2O3, CAO,

multi-component alloys Eu2O3(W%)

and are specified by their

formula and percentage

Compounds containing Fragment Molecular FRAGMF=MnO4(1-):1

the molecular formula Formula

of a given fragment

Key points

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.


Notes

Fields related to molecular formula

The respective count of Element Count ELC=Fe2.00

a particular element

The total number of atoms Number of Atoms NA=6-8

in the MF (use <, >, =, or

specify a range with a dash)

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 symbol of each Element Symbol ELS=Fe

particular element

Key points

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.


Notes

Enter query – Predefined Search Forms

Four fields relating to molecular formula can be accessed using an PSF form:

Type data directly into

the PSF box.

– Molecular Formula (MOFO)

– Component Molecular Formula (MF)

– Number of Fragments (NFRAG)

– Alloy Search Field (ALLOY)

Key points

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.


Notes

MOFO versus MFComponent 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

Key points

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.


Notes

List manipulation

Items from list Q17 excluded from list Q15

Key points

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.


Notes

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.

Key points

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=C10H1057

Fe.


Notes

Formula data parameter search

Scenario: Retrieve a single compound containing two iron atoms

per formula, copper atom(s), and no oxygen atom(s).

Key points

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.


Notes

Formula search query

Key points

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).


Notes

View the hitset

There are records

in the Gmelin database

that do not have

defined structures.

Key points

You have retrieved single compounds

containing specific elements, and

excluding others.


Notes

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.

Key points

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.


Notes

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

Key points

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


Notes

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

Key points

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.


Notes

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

Key points

Alloys, glass and ceramic materials can

be retrieved using a formula search or

percentage composition.

For this scenario, we will use the

percentage composition.


Notes

Alloy table

Percentage Types:

A – atom

W – weight

V – volume

X – mole fraction

Key points

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%.


Notes

Alloy results

Key points

Note the various percentages retrieved

for the zinc compound.


Notes

Conduct the subset search

Select from hitset list

Enter the Thermodynamic

Data field parameter

Key points

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”.


Notes

Subset search results

Key points

Subset searching is one method for

reducing the size of a retrieved hit list.


Notes

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.

Key points

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.


Notes

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)

Key points

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.


Notes

Ligand formula (LIGFO) field

L

A

D

Q

X

B, Si, Ge

N, P, As, Sb

O, S, Se, Te

H, F, Cl, Br, I, At

C

Code Atom

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).

Key points

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).


Notes

Enter search criteria The denticity of a ligand is placed in

parentheses before the ligand code.

Allows for the inclusion

of carbonyl groups.Allows for the

chromium metal.

Key points

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.


Notes

Ligand results

Key points

Review the Ligand fields available in the

Display Hits window.


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.

Conduct a chemical name search to retrieve salen complexes.

Review the results.


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.


Conduct a search to retrieve borate glass with the CaO and Eu2O3

components in weight percent. View the results.


Conduct a search to retrieve copper alloys containing trace amounts of

iron. View the results.



Exercise 1

Exercise 2

Exercise 3

Exercise 4


Conduct a chemical name search

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.

16. Type *salen* in the Chemical Name box.

17. Click OK.


19. Click View button and view the hitset.

Exercise 1

Enter the chemical name


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.


24. Click View button and note the differences from the first hitset.


Molecular formula search

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.


2. Double-click the Search Fields Tab. Click on the Find Fields

or Form button, and type mf range.

Click OK.

3. Double click the Search MF Range field.

4. Type K2SO4 in the Field Content column.

5. Click OK.



Exercise 2

Enter the molecular formula


8. Click the Details button. Note that some of the examples retrieved

are multi-component compounds. These appear due to cross-

searching 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).

9. Click the Query Tab..

10. Click the Find Field or Form button and type components. Click

OK.

11. Double click on the Number of Components (NC) field.

Modify the query

Enter component restriction


12. Click in the Field Content column and type 1.


14. Click the View and view the hitset.


15. Click the Details button.


Search for alloys, glass and ceramic materials

Conduct a search to retrieve borate glass with the CaO and Eu2O3

components in weight percent. View the results.


2. Click the Search Fields tab.

3. Click the Find Fields or Forms button and type alloy.

4. Click OK.

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.

Exercise 3

Enter the alloy requirements


8. Press Tab twice and type CaO in the Component Formula

column.

9. Press Tab twice and type Eu2O3 in the Component Formula

column.


10. Select W from the Percentage Type drop-down list.

11. Click OK.



Enter the percentage parameter


Search for copper alloys containing trace amounts of

iron

Conduct a search to retrieve copper alloys containing trace amounts of

iron. View the results.


2. Click the Search Fields tab. Click on the Find Fields or

Forms button.

3. Type alloy in the Find Fields window. Double click on the

Alloy Search field.


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.

Exercise 4

Enter alloy requirements


6. Click OK.

7. Click Search.


Physical property searching 4 - 1

Notes

Physical property searching


Conduct searches to retrieve physical property data

Key points

In this section, you will learn how to

conduct searches to retrieve physical

property information specific to the

CrossFire Gmelin database.


Notes

Physical Properties data structure

Key points

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.


Notes

Electrical conductivity search

Scenario: Conduct a search to retrieve compounds with an

electrical conductivity value between 1x1010 and 1x1012.

Restrict the list of compounds to those that have

superconductivity data reported.

conduct a data search using a Predefined Search Form

Key points

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.


Notes

Predefined Search form – Electrical Data

This query form provides search criteria

specific to fields related to electrical data.

Key points

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, 1x1010

through 1x1012

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.


Notes

Electrical conductivity results

Key points

We retrieved only those compounds

where the electrical conductivity is

between 1x1010

and 1x1012

having also

superconductivity values.


Notes

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

Key points

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.


Notes

Predefined Search form – Thermal Data

This query form provides search criteria specific

to fields related to thermal property data.

Key points


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.


Notes

Expansion coefficient results

Key points

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.


Notes

Modified expansion coefficient query

Field values are

not always specific

data entries.

Key points

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.


Notes

View the hitset

Key points

We will only retrieve those compounds

where the expansion coefficient is less

than zero and the cubic expansion

coefficient is entered.


Notes

Combination data/structure search

Scenario: Conduct a search to retrieve the stability, solubility, and 1HNMR data for the antimetastatic reagent trans-

RuCl2(DMSO)4.

use the Inorganic Mode to create the structure

use the Search Fields

Key points

In this new example, we will retrieve

information about the stability,

solubility, and HNMR data for the

antimetastatic reagent.

There are various possibilities to

formulate combination queries. We are

using one data constraint and one

structure entry.


Notes

Create the structural query

Key points

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.


Notes

Enter data constraintsApplying “absolute stereo” ensures

retrieval of only the trans configuration.

Key points

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.


Notes

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)

Key points

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.


Notes

Results of the combination search

Key points

We retrieved the defined structure

having solubility, stability, and NMR

data.


Notes

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

Key points

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.


Notes

Search Text/Fields data entry

Brackets can be used to

combine parts of a query.

Key points

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.


Notes

Magnetization diagram data entry

Key points

The magnetization diagram data field is

also a flag field and requires the use of

special indexing to run the query

properly.


Notes

Magnetization results

Key points

Further magnetization data can be

displayed: information on the magnetic

anisotrophy, magnetic structure,

magnetic space group, or further

magnetic phenomenon.


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.

Conduct a search to retrieve compounds having a melting point

above 4000oC. View the results.


Use the Crystal Structure Data PSF form to conduct a search

for compounds with the A cell parameter range of 4.5-4.6

Angstroms and the C cell parameter range of 2.9-3.0

Angstroms as determined by single crystal diffraction. View

the results.


Search for the adsorption of Hg2+

ions on a cellulose containing

material. View the results.



Exercise 1

Exercise 2

Exercise 3


Retrieve melting point data

Conduct a search to retrieve compounds having a melting

point above 4000oC. View the results.


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.

28. Press Tab and type 4000 in the Melting Point box.

29. Click the List button to check for the occurrence in the

database.

30. Click Cancel.

Exercise 1

Enter the physical data

Check for the occurrence


31. Click OK.



34. Choose View > Hit only.

35. Choose View > Highlight Hits.

View the melting point data


Retrieve crystal structure data

Use the Crystal Structure Data PSF form to conduct a search

for compounds with the A cell parameter range of 4.5-4.6

Angstroms and the C cell parameter range of 2.9-3.0

Angstroms as determined by single crystal diffraction. View

the results.


17. Double-click Crystal Structure Data from the

Predefined Search Forms tab.

18. Type 4.5-4.6 in the Lattice Length A box.

19. Click to select the Lattice Length C box. Type 2.9-3.0.

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.

Exercise 2

Enter Angstrom data restrictions

Enter detection method


Retrieve the adsorption diagram of Hg2+

ions

Search for the adsorption of Hg2+

ions on a cellulose containing

material. View the results.


2. Click the first line of the Search Text/Field area

(Table).

3. Type mofo in the Field Name column.

4. Press Tab and type Hg(2+).


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.

9. Click the List button to check the occurrence in the

database.

Exercise 3

Enter the data query

Locate the data field

Check for occurrence


10. Click Cancel.



Chemical property searching 5 - 1

Notes

Chemical property searching


Conduct searches to retrieve chemical property data

Key points

In this section, you will learn how to

conduct searches to retrieve chemical

property data.


Notes

Chemical Properties data structure

Key points

The chemical properties data structure

consists of:

chemical behavior,

surface reactions,

reaction data,

reaction details.


Notes

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

Key points

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.


Notes

Enter reaction preparation data

Use List button to check entries

Key points

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.


Notes

Check database occurrence

The combination entry does

not retrieve any records.

Key points

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.


Notes

Preparative search results

Key points

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.


Notes

Hyperlink to the reaction

Key points

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.


Notes

Modify the query

Key points

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.


Notes

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

Key points

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.


Notes

• Apply an atom list where M=Ti, Zr, or Hf

Create the query

• Set “as product” for the search feature

Key points

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.


Notes

Search results

Click the Product(s) (GRN) hyperlink

Key points

To view the catalysis data, you must first

hyperlink to the product information.


Notes

Hyperlink to the catalysis data

Click the Behavior as Catalyst

(BCAT) hyperlink.

Key points

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.


Notes

Hyperlink to the journal articles

Zirconium-catalyzed methyl-

alumination of heterosubstituted

arylethynes: Factors affecting the

regio-, stereo-, and chemoselectivities

Key points

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.


Notes

Full reaction search

Scenario: Conduct a search to retrieve the “simple” synthesis of the

catalyst Cp2ZrCl2 where the reactant is defined as ZrCl4.

create a full reaction query

Key points

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 CP2ZrCl2 catalyst using a full

reaction query.


Notes

Create the full reaction query

In Reaction Attributes mode:

• Select ZrCl4 and click the

Reactant button

• Select CpZrCl2 and click the

Product buttonReaction Attributes mode

Key points

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.


Notes

Full reaction results

Key points

Results can be viewed using the Full or

Short view.


Notes

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

Key points

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.


Notes

Factual reaction search query


specific to fields related to reaction data.

Key points


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‟.


Notes

Reaction results

Key points

Notice the Product(s) GRN naming

convention. The product is Si2Cl6

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.


Notes

Convert the hitset

Click the Get all button and select:

Get All Related Citations…

Key points

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.


Notes

Converted citation hitset

Sort for newest Article

Key points

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.


Notes

Citation Searching

Key points

For information about Citation

Searching, please consult the Searching

CrossFire Databases- based on

CrossFire Beilstein training guide.


Notes

Managing Your Results

Key points

For information about Printing, creating

Report, Exporting, and Alerts, please

consult the Searching CrossFire

Databases- based on CrossFire Beilstein

training guide.


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.

Conduct a search to retrieve inorganic reactions catalyzed using

aluminum trichloride (AlCl3) published after 1999. View the hitset.


Conduct a search to retrieve reactions with chromium hexacarbonyl

(Cr(CO)6) in ethanol under irradiation. View the hitset.


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




Exercise 1

Exercise 2

Exercise 3


Retrieve inorganic reactions

Conduct a search to retrieve inorganic reactions catalyzed using

aluminum trichloride (AlCl3) published after 1999. View the

hitset.



38. Expand the Chemical Properties (CHE) folder.

39. Expand the Reaction Details (RX) folder.

40. Double-click the Catalyst(s)(Name) (RX.CAT) field.

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.

Exercise 1

Enter the chemical data


44. Click the Search Field tab.

45. Click the Find Fields or Forms button and type publication.

46. Click OK.

47. Double-click the Publication Year (PY) field.

48. Choose > as operator, and type 1999 in the Field content box.

Enter the data restriction


Conduct a reaction search

Conduct a search to retrieve reactions with chromium hexacarbonyl

(Cr(CO)6) in ethanol under irradiation. View the hitset.


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.


6. Expand the Chemical Properties (CHE) folder.

7. Expand the Reaction Details (RX) folder.

8. Double-click the Solvent (RX.SOL) field.

Exercise 2


9. Type ethanol in the Field content box.

10. Double-click the Special Conditions (RX.SCON) field.

Enter the solvent information

Enter special conditions



51. Double-click irradiation (uv/vis) and click OK.


52. Click OK.




55. Click the Details button to view the full record.

56. If necessary, choose View > Hits only.

57. If necessary, choose View > Highlight Hits.


Preparation of CO bridged cyclopentadienyl metal

complexes

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.



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.

Exercise 3

CrossFire Structure Editor


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.


34. 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.

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.

Set Free Sites



40. Under Search, to the right of the structure box, select as

product.

41. Under Allow, to the right of the structure box, check, isotopes,

charges, radicals, and additional rings.


43. Click View and view the hitset.



45. Under Free Sites, to the right of the structure box, check all

atoms.



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