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1. 4 A AA VM 2800 2600 2400 2200 2000 1800 1500 1400 1200 1000 800 600 400 Three different windows set up the browser of the band assignment chart The upper window shows a chart which includes the names of the functional groups and their respective band positions in the form of bars The spectra are displayed in the lower window which abscissae are always conform with the respective band positions in the upper window To the left of the spectrum window the molecular structure of the functional group selected is displayed in the so called structure window Apart from the functional group name the band assignment chart also includes information on the position and peaks of the bands created by the functional group Wavenumber ranges which may include bands are highlighted by a colored bar The color intensity indicates the band peaks The less the color intensity of the bar the less pronounced will be the band expected To compare spectra with the band assignment chart select the Load File command from the File menu Load or drag amp drop one spectrum from the Bruker Optik GmbH OPUS SEARCH 49 Editing Libraries OPUS browser window to the spectrum window of the band assignment browser The latest spectrum only which has been loaded and drawn into the spectrum window will be displayed Now a spectrum search will be performed in the band assignment chart and the entries of the upper window will be sorted accordin
2. OPUS Spectroscopy Software User Manual SEARCH gt lt BRUKER LL 2006 BRUKER OPTIK GmbH Rudolf Plank StraBe 27 D 76275 Ettlingen www brukeroptics com All rights reserved No part of this manual may be reproduced or transmitted in any form or by any means including printing photocopying microfilm electronic systems etc without our prior written permission Brand names registered trademarks etc used in this manual even if not explicitly marked as such are not to be considered unprotected by trademarks law They are the property of their respective owner The following publication has been worked out with utmost care However Bruker Optik GmbH does not accept any liability for the correctness of the information Bruker Optik GmbH reserves the right to make changes to the products described in this manual without notice This manual is the original documentation for the OPUS spectroscopic software Table of Contents 1 JIO a LAA 1 1 1 Library Si tlet le 2cvs aci sin aos ce VO P d Ad uia T V as 2 2 UBS A Se ALEA 5 2 1 OPUS SEARCH ICONS S 14x cse oe ee SG he REIN nate E EE Eia 5 22 Selecting A Library a aia AE acea e Voc duc UB ace bao ace eat Gre 6 2 3 Spectr m Seatehia E 8 231 Search Parameters ze suns egE eei seas MERE Te VN 10 2 3 2 Excluded Regions Guide bt eurt ew een hus eb ne es 13 2 3 9 Delect Libraries a eis Va EIER Ei aa 14 2 3 4 Library View and SEARCH Report u z 14 2 4 Pe
3. You can also load and edit an existing method file Click on the Load Method button If you do not store a method file created the Save File dialog automatically pops up when clicking on the OK button On the OPUS Parameters tab you define the parameters which are to be stored with each spectrum in the library Library methods x Method Parameters OPUS Parameters r Parameter types Sample C Data status C Acquisition Instrument Fourier transform Plot List of all parameters List of selected method parameters Annotation Text ATX 10 Ch 2 Filename NA2 10 Copyright message CPR 10 Experiment IEE IDI gt gt Experiment Path DEE IDI Filename NAM 10 History of Last Operation HIS 10 Instrument Status ISI IOI Measurement DLL Parameter MCP 10 Measurement Path DETK IDI Operator Name CNM 10 Path of File PAT IDI lt lt Sample Form SFM 10 Sample Name SNM 10 TRS Method name RAT 10 EA Cancel Apply Figure 22 Library Methods OPUS Parameters tab The parameters have been grouped into different types You can switch between these types by clicking on the respective option buttons The List of all Parameters selection field shows all parameters available and the List of selected Method Parameters includes the parameters which have been added to the library To move a parameter from one selection field to the other first select the particular parameter and then click on the re
4. Digital Resolution 34 F Frequency Regions Interactive Selecting 13 Manual Selecting 13 I Information Search 1 5 21 Choosing Text 24 Combined Search 26 Info Item 23 Molecular Formula Search 25 Numerical Search 24 Operator 22 Value 23 L Libraries Editing 41 Library Browser 46 Editing 42 47 48 Editor 41 Entries 38 43 Initializing 31 Parameters 37 Status 7 Storing Spectra 36 Structure 2 View 15 Library Window 14 P Peak Search 1 5 18 Algorithm Calculate Hit Quality 20 Count Matching Peaks 20 Hit If All Peaks Match 20 Hit If One Peak Matches 20 Parameters 19 Peak List 18 S Sadtler Libraries 7 Search Datablock 14 Parameters 16 Report 14 Search Algorithm Spectrum Correlation 11 Search Icons 5 Spectrum Search 1 5 8 Algorithm 10 Peak Intensities 10 Peak Table 11 Standard 10 Hit Quality 12 Report 15 Sensitivity 11 Structure Import 51 Structure Search 1 5 26 Sub Structures 28 Structure Search Parameters Match Embedded 28 Match Exact 28
5. Peak Search command from the Evaluate menu or click on the a icon 2 4 1 Peak List for Peak Search x Peak List for Peak Search Parameters Select Libraries i fasst Mee Load Peak List Save Peak List v Show search report immediately Use search report for searching Search Library Cancel Help Figure 12 Peak Search Peak List for Peak Search tab 18 OPUS SEARCH Bruker Optik GmbH Peak Search On the Peak List for Peak Search tab a peak table is displayed to be used to enter the peak position tolerance as well as the intensity of the peaks you want to search for The Range and Intensity columns provide drop down lists for convenient data input Click on one of the columns to activate this drop down list In the Range column you can enter a tolerance value as wavenumbers This tolerance range will be added to both sides of the peak If you use a frequency of 1000cm and a tolerance range of 20cm all peaks between 980 and 1020cm will be considered In the ntensity column you can set the intensity of peaks at 3 different levels i e strong medium and weak The range is calculated relatively to the strongest peak 100 and covers the following areas Weak 0 50 Medium 50 75 Strong 50 100 If you do not want to consider the intensity select the any option from the drop down list in the ntensity column To save the peak list click on the Save Pea
6. be stored in the library with an information text added You can also replace an existing entry by selecting the Replace entry option button Make sure to specify which entry you want to replace by entering the corresponding entry number into the Entry Number field It is also possible to replace only the info text of an existing library entry In this case check the Replace info option button Furthermore you can add and replace a structure by the Add replace structure option button In both cases you have to specify which entry you want to replace by entering the corresponding entry number into the Entry number field Bruker Optik GmbH OPUS SEARCH 37 Generating Library Files Additionally you can define how to proceed with spectra which do not have an INFO data block If you check the Add Information manually option button and click on the Store button you will be prompted to enter the relevant spectra information To automatically create an INFO data block select the Create standard information block automatically option button This kind of INFO data block is based on the sample parameter data available for the sample name sample type and operator Together with the spectrum this data block is stored in the library If you check the Do not store spectrum in library option button all spectra which do not have an information block will NOT be stored in the library 3 2 5 Library Entries Click on the Library Entries tab to
7. f RAOPUS LIBS ETCALIBRARYASOLVENTS SO1 60 f RAOPUS LIBS ETEALIBRARYALIB AQNBASF 501 3923 C not found f RAOPUS LIBS ETCALIBRARYALIB ADSNAGASPH SOT 189 Librar Entries QAPROGRAMMENOPUSNDATANLIBRARYADEMOLIB f RAOPUS LIBS ETCALIBRARYASOLVENTS S01 60 of RNOPUS LIBS ETCALIBRARYALIB AQNBASF SO1 3929 d test failed of RAOPUS LIBS ETCALIBRARYALIB IADENIAGASPH SO1 189 Figure 4 Different library status 2 3 Spectrum Search Start the Spectrum Search command either from the Evaluate menu or the tool bar p and load the spectrum by drag amp drop from the OPUS browser window into the Files to Search selection field figure 5 When using the Spectrum Search option transmission spectra will automatically be converted into absorption spectra to get a reasonable result However both the query spectrum and the search results will be displayed in transmission If you store transmission spectra they will automatically be converted into absorption spectra This conversion will be performed internally and will not have any influence on the original spectrum Note If you have created a library using transmittance spectra it is recommended to convert the spectra into absorption spectra OPUS SEARCH Bruker Optik GmbH Spectrum Search Spectrum Search xj Spectrum Search Search Parameters Excluded Regions Select Libraries Files to search C ProgrammeSOPUS D ata4bboe05 0 1 IV Show search report
8. if one Peak matches Yields 203 hits and each hit has a hit quality of 1000 Count matching Peaks A total of 203 hits can be ranked according to the number of matching peaks 2 5 Information Search The information search allows to search for all data stored e g general compound information or spectral data You can simultaneously search for several parameters combining different types of search criteria To perform an information search click on the Information Search command in the Evaluate menu or click on the e icon Bruker Optik GmbH OPUS SEARCH 21 Library Search 2 5 1 Query for Information Search Information Search x Query for Information Search Choose Information Text Select Libraries Ho Sample name SNM 10 Reference Charge Number Comment Sample name SNM 10 Sample form SFM 10 Operator name CNM 10 Maximum number of hits fed Load Info Query Save Info Query M Show search report immediately Use search report for search Search Library Cancel Help Figure 14 Information Search Query for Information Search tab On the Query for Information Search tab you set the search criteria Each row of the table displayed corresponds to a parameter and its corresponding value to be searched You can either type the entries manually or select them from a drop down list which will be activated as soon as you click on one of the
9. immediately Use search report for searching Search Library Cancel Help Figure 5 Spectrum Search dialog If you activate the Show search report immediately check box a library window will automatically be displayed after the search If you activate the Use search report for searching check box a dialog pops up from which you can select an already existing search report In this case the search will not be performed by means of the settings made on the Select Libraries tab but only by those spectra which are included in the search report This enables to refine a search previously performed Bruker Optik GmbH OPUS SEARCH 9 Library Search 2 3 1 Search Parameters Spectrum Search Xj Spectrum Search Search Parameters Excluded Regions Select Libraries Search algorithm i Sock das dy o dei seb uuu UE EE EO ES s UE ae LU I Similarity Search sensitivity Identity Maximum number of hits 30 Minimum hit quality EO Search Library Cancel Help Figure 6 Spectrum Search Search Parameters tab Use the drop down list to select between 4 search algorithms a Basic This algorithm requires a peak table in addition to the search spectrum This peak table will temporarily be generated during the search b Standard This algorithm is similar to the Basic algorithm and additionally takes into account whether the respective peaks in the search or library spectr
10. lines You can limit the number of hits save a search query once created and reload it and restrict the search to an existing search report The search items set cannot be individually configured for each library There is only a global set of information fields which is the same for all libraries This may cause empty result lists if there is no information available at all in the specific library file searched Therefore it is recommended to check the libraries using the library browser The functions of each column will be explained in the following a Operator A logical combination of several search criteria in one query can be achieved by using the boolean operators AND OR OR NOT and AND NOT e OR only one search criterion has to be met to generate a hit AND all conditions combined with AND have to be met to generate a hit OR AND NOT are the negations of the above operators i e these conditions may must not be met to generate a hit 22 OPUS SEARCH Bruker Optik GmbH Information Search b Info Item In this column you define the parameters to be searched for The parameters available depend on the libraries selected for the search Specify the corresponding info item by the drop down list c Comparative Operators Select the comparative operator for the parameters defined There are operators for text a A A A and numerical comparison lt gt a A case insensitive text compariso
11. new method click on the Setup New Method button The following dialog opens Library Methods E Method Parameters OPUS Parameters Description Genera Library IR x Startpoint 4000 x Endpoint 600 Digital resolution 4 Loaded method Load Method Save Method Cancel Appl Help Figure 21 Library Methods Method Parameters tab On the Method Parameters tab you specify the frequency ranges x startpoint x endpoint and digital resolution of the library spectra Additionally you have to define a description of the method The digital resolution determines the number of data points required to save spectra by using this method This feature has a direct effect on the space needed by the library on the hard disk As a rule of thumb in case of a library using the DEFAULT method 4 000 400cm digital resolution deri you can anticipate a disk space of about 6 7Mbyte per 1 000 spectra 34 OPUS SEARCH Bruker Optik GmbH Initializing Library Note The digital resolution refers to the spectra saved which are used for correlation algorithms the display plot and in case of mixtures the subtraction However the digital resolution does not have any influence on the quality of spectrum searches for the standard algorithm If you want to differentiate very identical spectra and if you depend on the correlation algorithm we recommend a digital resolution of 2 or 1
12. that the Select Libraries tab will be the same for all search methods The following example have been created by using the Spectrum Search command Click on this command and select the Se ect Libraries tab 6 OPUS SEARCH Bruker Optik GmbH Selecting a Library Spectrum Search xj Spectrum Search Search Parameters Excluded Regions Select Libraries Entries CAPROGRAMMESOPUS TEST 5 SDATASLIBRARY SDEMOLIB Add Libraries Remove Library Remove All libraries Change List Save Library List Check Libraries Search Library Cancel Help Figure 3 Spectrum Search Select Libraries tab As the libraries selected during the last query will automatically be included in the Library selection field the DEMOLIB library is displayed in figure 3 You can add libraries to or remove libraries from the library list by clicking on the Add Libraries or Remove Library buttons The libraries displayed in the Library selection field will be used for the query Frequently used library lists can be saved and re loaded by clicking on the Save Library List and Change List buttons You can also load Sadtler libraries into the Library selection field Sadtler libraries have the file extension DX Any library in OPUS and Sadtler format can be combined for one search Sadtler libraries are protected by a dongle You have to install the dongle drivers which are stored on the OPUS CD directory SENTINEL and copy the JR C
13. 1 3 Methyl Bruker Optik GmbH OPUS SEARCH 23 Library Search 2 5 2 Choose Information Text The Choose Information Text tab is only relevant if you use more than one library for the search In general an information search employing several libraries does only make sense if all libraries have an identical information mask Therefore the info data sets of all libraries loaded are displayed on the Choose Information Text tab Information Search Ea Query for Information Search Choose Information Text Select Libraries EZ DEMOLIB SOLVENTS Select DEMOLIB Select SOLVENTS E Compound Name Compound Name Compound Name I3 Molecular Formula amp Molecular Weight Molec ular Formula Molecular Formula Molecular Weight 5 CAS Registry Number Y y Number CAS Number Melting Point ting P oint Melting Point EZ Boiling Point 8 Sample Preparation Boiling Point Sample Preparation Boiling Point Sample Technique a Sample Quantity le Quantity Sample Quantity H0 Manufacturer Commercial Name Reference 2 Charge Number har E e Number Manufacturer B Reference M3 Comment omment Registry Number Sample name SNM 10 nple name Spectrum Number Sample form SFM 10 ample form SFM 10 Analysis Number Search Library Cancel Help Figure 15 Information Search Choose Information Te
14. 3 103 34 4 107 38 2 592 84 7 107 87 3 37 334 71 40 38 82 8 75 854 123 54 6 103 86 4 111 77 3 140 11 4 127 19 6 38 01 1 38 00 0 111 27 3 E Store Cancel Help Figure 25 Store Spectrum in Library Library Entries tab Bruker Optik GmbH OPUS SEARCH 39 Generating Library Files 40 OPUS SEARCH Bruker Optik GmbH Library Editor Editing Libraries The library editor allows to maintain self generated libraries and provides the following options Loading library entries Deleting library entries Editing library descriptions Editing information text 4 1 Library Editor Click on the Library Editor command in the Evaluate menu or click on the b icon The following dialog opens Library Editor xj Edit Library Library Entries Contents of Info Setfs m Current library Library path Library name Total entries Valid entries Deleted entries C Program DATAALIBRARY DEMOLIB User library 352 352 0 Change Library Load entry m Enter number or select entry on next page C Delete entry General Library IR C Change description Change info definition Change Info Current info C PROGRAM SDATASLIBRARYSDEM Create Into New info m o ooo ee Figure 26 Library Editor Edit Library tab Bruker Optik GmbH OPUS SEARCH 41 Editing Libraries 4 1 1 Edit Library The Current Library group field on the Edit Li
15. Initialize Library E Library Initialization Method and Info Selection Infotext file D OPUS METHODS DEFAULT TXD Browse Setup New Info Text Method file D OPUS METHODS CIBA MTD Browse Setup New Method Execute Cancel Help Figure 19 Initialize Library Method and Info Selection tab 32 OPUS SEARCH Bruker Optik GmbH Initializing Library a Infotext File The infotext file determines which kind of information from the INFO data blocks GEN of OPUS files will be added to the library For further details on how to create and work with infotext files refer to the OPUS Reference Manual If you click on the Browse button you can load an existing infotext file To create a new infotext file click on the Setup New Info Text button Infotext files have the file extension 7XD The infotext file used to create a library has to be identical to the one used for the Setup Info Mask command in the Edit menu This applies to all spectra to be added to the library b Setup New Info Text To create a new infotext file click on the Setup New Info Text button The Setup Information Mask dialog opens Setup Information Mask x 1 11 12 25 Current info mask Load Test Definition Restore Original Clear All Line1 CompoundName tne2 MoecuarFomda Tr Une3 MoecdarWeght 7 Line 4 CAS Registry Number SSCS Line 5 Melting Poit ss S Lines Boing Pont 77
16. L FORMATE Molecular Formula O C9H12 3 1 METHOXY 2 PROPANOL Molecular Weight O 120 2 4 BUTYL FORMATE SS CAS Registry NumberO 98 82 8 5 METHYL PROPYL KETONE Boiling Point O 152 6 TETRAHYDROFURFURYL ALC Sample Preparation O NEAT 7 N AMYL ALCOHOL 1 PENTA 8 CUMENE a TERT AMYL ALCOHOL ACETYLACETONE ETHYLENE GLYCOL MONOME DIETHYLENE GLYCOL MONOM BENZYLACETATE N N DIMETHYLACETAMIDE FURFURAL d FURFURYL ALCOHOL 1 HEXANOL 2 HEXANONE ISOPROPYL METHYL KETONE 2 METHOXYETHYL ACETATE NITROBENZENE NITROETHANE Adei Pall EE D STYRENE 0 50 0 00 ed 3500 3000 2500 2000 1500 1000 A F General Library IF EE Change Library Hep Signed by Bruker Optik 2002 01 30 11 53 24 UTC 1 with qualified Figure 30 Library browser The library browser consists of four different windows All the entries of the library selected are displayed on the left side It is distinguished between entry number compound name molecular formula molecular weight and CAS number If you select a particular entry the information data defined for this entry will be displayed in the respective windows i e the molecular structure in the middle compound information upper window and the spectrum lower window To change the sorting order click on the respective column header and the table will be sorted in ascending order according to the column selected To change to a different library click on the Change Lib
17. Line 7 Sample Preparation SS Line 8 ERE Line 3 Manufacturer 77 Line 10 Reference m EmN Nest Page Cancel Apply Help Figure 20 Initialize Library Wizard Setup Information Mask dialog If you click on the Load Text Definition button you have access to an existing info mask which you can use as template The two tabs 1 11 and 12 26 indicate the number of lines displayed The content of each line will later be available as entry field for the spectrum information input For the information input use the Information Input command from the Edit menu Bruker Optik GmbH OPUS SEARCH 33 Generating Library Files The Setup Info Mask dialog box provides two different possibilities to correct all the changes made If you click on the Restore Original button the original settings of the template will be restored To get a template without any entries click on the Clear All button If you click on the OK button the Save File dialog opens and allows to store the newly created or modified text mask The Method and Info Selection tab figure 19 will be displayed again c Method file A method file defines the frequency range and digital resolution of spectra used for the library to be created Besides you can also select different OPUS parameters which have to be stored for each spectrum in the library Method files have the extension MTD Use the Browse button to load an existing method file figure 19 To create a
18. TL Sadtler control file to the OPUS directory This CTL file is either stored on the Sadtler libraries CD or on a different disk supplied To activate the dongle driver you have to reboot the PC The library status is indicated in different ways Library entries checked by a green check mark have been tested and are correct An exclamation mark indicates an error whereas a dot means that the library integrity has not been tested Bruker Optik GmbH OPUS SEARCH F Library Search Therefore click on the Check Libraries button figure 3 If the library is OK it will be checked by a green check mark A red cross indicates the library could not be found This may occur if the library has been deleted or the directory changed If you want to load the library from CD insert the CD into the CD drive and keep the CD in the drive during the search run If the library has been tested the number of library entries will be displayed Library Entries QAPROGRAMMENOPUSNDATANLIBRARYADEMOLIB RAOPUS LIBS ETC LIBRARYSSOLVENTS S01 60 a not checked RAOPUS LIBS ETCALIBRARYALIB AQNBASF SO1 3929 RAOPUS LIBS ETCALIBRARYALIB IADSNIAGASPH SOI 189 Library Entries f QAPR GRAMMENOPUSNDATANLIBRARYNDEMOLIB f RAOPUS LIBS ETC LIBRARYSSOLVENTS SO1 60 b test passed of RAOPUS LIBS ETC LIBRARYLIB AQ BASF S01 3929 f RAOPUS LIBS ETC LIBRARYSLIB4AOSVAGASPH SO1 189 Library Entries 3X QAPROGRAMMENOPUSNDATANLIBRARYADEMOLIB
19. ak Neate Nie AAA 18 2 4 1 Peak List for Peak Search za ou yop Re we ERI PES SD 18 24 2 Parameters estia Soest eatenus etwaige I e SOUS eee Rane da ar 19 2 5 Information Search ed esie ae ess Ea E V da arratea Zia 21 2 5 1 Query for Information Search 0 0 cece eee eee 22 2 5 2 Choose Information Text 545 sce vba DICERE OD OE be Ws 24 2 6 Structure Searels GER iis Pes MONA van eats PEU VES NES HS 26 GR Str cture Search ooo ges e Lt eie e detu 27 2 6 2 Search Parameters a 4 oed Od e gitura deira lerarako 27 210 3 Select Bie ANEA 29 3 Generating Library Files 0 ccc cc cece eee eee eee eens 31 34 Initializing Bl any etch oec une d Sce esto a ede et sd e Oe eei eC 31 3 1 1 Adding existing spectra to new DRO 32 3 1 2 Creating empty a AAA 32 3 2 Storing Spectra in a Library erar atarata pi er px he du o Pais 36 EE Store Spectr mM AAE 36 3 224 Parameter wena ey ATEKA A Sa hype baieie 37 3 237 Ebrary ONAE 38 4 Editing PAd eie 41 4 1 Library Sa 41 AAA Edit Library 452 23 r igea ad Ue re ad 42 4 1 2 Library ATA 43 413 Contents of the Info Set s A atera gd bar ae AO SE dE ba Ps 45 4 2 BEREGAN ES Eto 46 4 3 Band Assignment rt ear ai bbw a ETE a a aay 49 OG HE ee AEE EAEE ahha EAE A Eat EE SI iii iv Introduction OPUS SEARCH allows to identify unknown spectra by comparing them to spectra libraries You can use commercially available libraries e g Sadtler and create your ow
20. alue between 6 and 10 It is recommended however to perform several test runs applied to spectra of known samples to learn about the influence of the Sensitivity parameter As a general rule of thumb settings greater than 15 rarely produce useful results Bruker Optik GmbH OPUS SEARCH 11 Library Search Maximum Number of Hits Specify the number of hits which will be saved in the search report Minimum Hit Quality A hit quality of 1000 would be a perfect conformity whereas a value of 0 is obtained if there is no correlation at all In general the search algorithm produces a value of gt 0 even if there are no or negligible similarities between spectra Therefore it is reasonable not to include all hits below a certain limit default setting 300 into the search report As the Minimum hit quality also depends on the data acquisition method it first should be evaluated by measuring reference samples Only if such a search yields no hits should you set the Minimum hit quality to a lower value If you have set all parameters click on the Search Library button to start a search The search result will be stored in a search report For further details on the influence of certain search parameters refer to chapter 2 3 4 12 OPUS SEARCH Bruker Optik GmbH Spectrum Search 2 3 2 Excluded Regions It is also possible to exclude certain spectral regions from the search If you click on the Excluded Regions tab the following d
21. and converts an already existing structure from the OPUS format to the Molfile format and writes the structure into a temporary file BIRSY MOL stored in the OPUS sub directory SEARCH If you now open an appropriate structure editor the name and path of the temporary file is added to the structure editor using the command line The temporary file will be loaded and the structure automatically displayed You can now make as many changes on the structure as you like Save the changed structure which will be rewritten into the original structure data block Creating a new structure is similar to editing a structure except for the fact that an empty temporary file is created before starting the editor Bruker Optik GmbH OPUS SEARCH 51 The minimum requirements for a structure editor are The editor has to be compatible with Windows NT 2000 XP The editor has to be able to read and write structures in Molfile format Recommended functionality The editor should be able to automatically load and display Molfile format structures e If a structure is edited or redrawn the editor should automatically save this new structure in the Molfile format in the particular file defined If you click on the Edit Create Structure command in the Edit menu the following dialog opens Edit Create Structure x Edit Structure Choose Editor New structure file C AProgramme sO PU S D ata 4bboe Edit Create Structure Canc
22. arch Parameters Select Libraries v Show search report immediately Use search report for search Search Library Cancel Help Figure 16 Structure Search Structure Search tab Drag amp drop the structure blocks created by the editor to the selection field on the Structure Search tab The check boxes are the same as described for the Spectrum Search see section 2 3 2 6 2 Search Parameters The Search Parameters tab provides two different options for the specifications of the search parameters Bruker Optik GmbH OPUS SEARCH 27 Library Search Structure Search x Structure Search Search Parameters Select Libraries C Match embedded Match exact Maximum number of hits 20 Search Library Cancel Help il Figure 17 Structure Search Search Parameters a Match Embedded In the query structure this algorithm replaces all hydrogen atoms by free valences which still can have all sorts of remnants Therefore molecules even qualify as a hit if the query structure is part of their structure b Match Exact This algorithm only searches for structures and sub structures that exactly match your query Define the maximum number of hits in the corresponding entry field 2 6 2 1 Entering Sub Structures If you work with an external molecular structure editor e g CHEMWIN or ISISDRAW you can use apart from element symbols which allow to enter a co
23. arch Sensitivity parameter will not be available Depending on the measurement you can additionally define whether the spectrum to be searched for contains one component in case of a single substance or multiple components in case of compounds e Spectrum Correlation This algorithm calculates the sum of the squared deviations between the query spectrum and the result spectrum for the data points of the range defined The summation can be limited to a spectral range selected by the user If you use this algorithm the Search sensitivity slider is replaced by two additional drop down lists Normalization Method and Derivative For details on these methods see chapter 8 in the OPUS Reference Manual The search algorithms described can also be used for Sadtler libraries However the Standard search algorithm might differ in quality compared to the search in OPUS libraries due to the different file formats of Sadtler libraries Therefore it is recommended to test the algorithms first and use a correlation algorithm if you do not get unambiguous results Sensitivity The Search sensitivity allows you to influence the search result As the search result substantially depends on the type and quality of the spectra acquired it is not possible to give a general recommendation on how to optimally set the sensitivity value In the case of spectra obtained from KBr pellets with a normal signal to noise ratio you can start with a sensitivity v
24. brary tab includes information about the currently active library e g library name path and description as well as information on the number of entries distinguished between Valid and Deleted You can change to a different library by clicking on the Change Library button You can select between the following editing options Load Entry Check the Load entry option button to extract an entry from the library and save it as a spectral data file by the file name ENTRYx 0 with x being the entry number in the library Note that you first have to define an entry number either manually or by a double click on the specific entry number on the Library Entries tab Delete Entry Check the Delete entry option button to delete an entry from the library Note that you first have to define an entry number either manually or by a double click on the specific entry number on the Library Entries tab The number of entries deleted will be displayed in the Current Library group field Change Description Check the Change description option button to change the library description and enter the new description into the entry field on the right Change Info Definition Check the Change info definition option button to change the info mask assigned to a library Either select an existing mask by clicking on the Change Info button or create a new mask by clicking on the Create Info button The Change Info Definition option button should only be checke
25. browse through the different parameters of all entries The parameters include e g the entry number compound name molecular formula molecular weight and the CAS registry number If you click on a particular column header e g Compound Name the entire table entries will be sorted in ascending order according to the column selected If you click on the particular column header again the table entries will be sorted in descending order A double click on a particular entry would automatically transfer you to the Parameter tab The number of the entry selected will be added to the Entry Number field 38 OPUS SEARCH Bruker Optik GmbH Storing Spectra in a Library Store Spectrum in Library Store Spectrum Parameter Library Entries Double click on entry number to select entry for editor Erk Compoure Neme__ Molecular Formula Molecular Weight CAS Number wom Doe woh METHYL FORMA ETHYL FORMATE 1 METHOXY 2 P BUTYL FORMATE METHYL PROFY TETRAHYDROF N AMYL ALCOHO CUMENE TERT AMYL ALC ACETYLACETONE ETHYLENE GLY DIETHYLENE GL BENZYLACE TATE N N DIMETHYLA FURFURAL FURFURYL ALC 1 HEXANOL C2H402 C3H602 C4H1002 C5H1002 C5H1001 C5H1002 C5H1201 C3H12 C5H1201 C5H802 C3H802 C5H1203 C3H1002 C4H3N101 C5H402 C5H6502 C6H1401 60 05 74 08 30 12 102 13 85 13 102 13 88 15 120 2 88 15 100 12 76 1 120 15 150 18 87 12 36 03 38 1 102 18 107 31
26. ck on the Browse button to select the editor from the dialog that pops up Define the Scaling Factor for the structure display The standard setting is 100 which is adequate for most structure editors Change the scaling factor only if the structure in the editor is displayed in too large or too small a size Attach Structure The Attach Structure command is used to convert a Molfile structure and add the STR data block to an existing spectrum file Click on the Attach Structure command and the following dialog opens 54 OPUS SEARCH Bruker Optik GmbH Attach Structure b x Attach Structure to OPUS File Select OPUS spectrum As ae C NOPUSSDATANAbboe 05 0 1 Select structure file CNDPUSNDATANTEST Browse Ges Ire Figure 36 Attach Structure Attach Structure to OPUS File tab Select the OPUS file which the structure will be attached to and drag amp drop it into the Select OPUS spectrum selection field Define the path and file name of the structure file to be converted or click on the Browse button and select the path and file name from the dialog that pops up If you click on the Attach Structure button the structure file will be converted and an STR data block will be added to the spectrum file Bruker Optik GmbH OPUS SEARCH 55 56 OPUS SEARCH Bruker Optik GmbH Index A Attach Structure 54 B Band Assignment Chart 49 Structure 49 C Comparative Operators 23 D
27. cursor on the edges of the spectral ranges and press the left mouse button you can re size the ranges Bruker Optik GmbH OPUS SEARCH 13 Library Search 2 3 3 Select Libraries The Select Libraries tab is the same as described for Spectrum Search see section 2 3 2 3 4 Library View and SEARCH Report The search result is added to the query spectrum in the form of a SEARCH data block areu see figure 9 All these SEARCH reports have the same structure regardless of the search method used A report will automatically be displayed after a search provided you have activated the Show Search Report immediately check box see figure 5 Compound Namel METHYL FORMATE H Molecular Formulal C2H402 NS Molecular Weight 60 05 CAS Registry Number 107 31 3 Boiling Point 32 Sample Preparation NEAT O a 336 METHYL FORMATE E E 2 580 POLY METHYL METHACRYLATE a L 3 538 DIMETHYL DIETHYLMALONATE 298 O 4 527 METHYL METHACRYLATE 153 5 526 2 HEXANONE 18 L B 526 MALONIC ACID 36 52 IBUPROFEN 61 v Exit General Library IR E Jl User Library Figure 8 Library windows 14 OPUS SEARCH Bruker Optik GmbH Spectrum Search The library view consists of four different windows which can be re sized by moving the window borders figure 8 The bottom window includes the total number of search hits ranked according to their hit quality Additional features of the hit list are the compound name entry number of
28. d entries n Store Cancel Help Figure 23 Store Spectrum in Library Store Spectrum tab Drag amp drop the spectra from the OPUS browser window to the selection field on the Store Spectrum tab If a warning symbol is displayed on the Store Spectrum tab the data block does not match the settings made on the Parameters tab Note that the option buttons checked on the Parameters tab for 36 OPUS SEARCH Bruker Optik GmbH Storing Spectra in a Library a previous operation will automatically be selected by default Data blocks displayed in red will not be added to the library The Library Properties group field identifies the library as a user library The library description entered during the setup will also be displayed together with some library statistics You also have the possibility to use a different library by clicking on the Change Library button 3 2 4 Parameter On the Parameter tab you define how to store data into the library Store Spectrum in Library x Store Spectrum Parameter Library Entries Add new entry C Replace entry C Replace info C Add replace structure Entry number a If spectrum contains no info block Add Information manually C Create standard information block automatically C Do not store spectrum in library Store Cancel Help Figure 24 Store Spectrum in Library Parameter tab If you select the Add new entry option the spectrum will
29. d to append lines to an existing mask or to edit typos in an existing mask 42 OPUS SEARCH Bruker Optik GmbH Library Editor 4 1 2 Library Entries If you click on the Library Entries tab the following dialog opens Library ea x EditLibrary Library Entries Contents of Info Set s Double click on entry number to select entry for editor Entry Compound Name Molecular Formula Molecular Weight CAS Number 1 METHYL FORMA C2H402 60 05 107 31 3 2 ETHYLFORMATE C3H602 74 08 103 34 4 3 T METHOXY 2 P C4H1002 90 12 107 38 2 4 BUTYLFORMATE C5H1002 102 13 592 84 7 5 METHYL PROFY C5H1001 86 13 107 87 9 6 TETRAHYDROF C5H1002 102 13 37 334 GZ N AMYLALCOHO C5H1201 88 15 71 40 8 CUMENE C3H12 120 2 38 82 8 3 TERT AMYL ALC C5H1201 88 15 75 854 10 ACETYLACETONE C5H802 100 12 123 54 6 11 ETHYLENE GLY C3H802 76 1 109 86 4 12 DIETHYLENE GL C5H1203 120 15 111 77 3 13 BENZYLACETATE C9H1002 150 18 140 11 4 14 MN DIMETHYLA C4HSN101 87 12 127 19 6 15 FURFURAL C5H402 36 03 38 01 1 16 FURFURYL ALC C5HEO2 38 1 98 00 0 17 1 HEXANOL C6H1401 102 18 111 27 3 4 A Edit Cancel Help Figure 27 Library Editor Library Entries tab The Library Entries tab lists all entries of the active library including the entry number compound name molecular formula and weight as well as the CAS number If you click on a particular column header e g Compound Name the
30. e Exit button 50 OPUS SEARCH Bruker Optik GmbH Appendix Structure Handling in OPUS The OPUS base package offers the possibility to import edit and print structures There are three functions available in the Edit menu Structure Import Edit Create Structure Attach Structure Structure Import The Structure Import command converts structures which have been stored in the Molfile format to the internally used OPUS format Files stored in this format have the extension MOL The Molfile format developed by the company MDL has become a quasi standard over the last years Almost all structure programs available can process structures in the Molfile format The format is published and can be used without any restrictions Click on the Structure Import command a dialog opens and shows all files with the extension MOL Select one or more structure files and click on the Open button All files are converted into the OPUS format and loaded The file name is identical to the original file name and the extension 0 is automatically added Double click on the STR data block Saf in the OPUS browser window to have the structure displayed Edit Create Structure The Edit Create Structure command allows to edit a structure or create a new one OPUS however does not include a structure editor but you can load any appropriate structure editor by means of the Edit Create Structure command The Edit Create Structure comm
31. e between these two peak positions the lower will be the resulting hit quality b Hit if all Peaks match A spectrum is only considered to be identical if it includes all peaks specified in the peak list In this case the hit quality is always 1000 c Hit if one Peak matches A spectrum is considered to be identical if it includes at least one peak specified in the peak list In this case the hit quality is always 1000 d Count matching Peaks This algorithm indicates the number of peaks found as hit quality At least one peak has to be congruent with the peak list in order for the spectrum to be included in the hit list The result of a peak search will also be stored in a SEARCH data block see section 2 3 4 The Select Libraries tab is the same as described for spectrum search see section 2 2 20 OPUS SEARCH Bruker Optik GmbH Information Search Example Select the SEARCH3 0 file as query spectrum and the DEMOLIB library as the only library Enter the following peaks into the peak list on the Peak List for Peak Search tab of the Peak Search command Frequency Region Intensity 3434 20 middle 1452 20 middle 1111 20 strong 973 20 middle Use all 4 algorithms to perform a peak search Calculate Hit Quality The correct spectrum is listed as the first hit with a hit quality of 901 Hit if all Peaks match The only hit is the correct spectrum e Hit
32. earch E Query for Information Search Choose Information Text Select Libraries Ei Operator Info item xj Lal Molecular Formula A C59 a AND Boilinq Point 250 AND Boiling Point gt 150 a AND Compound Name a A__ methyl i5 ANDNOT Compound Name a A di methyl The following search retrieves substances which have between 5 and 9 carbon atoms with a boiling point in the range of 150 C to 250 C In addition methyl should also be part of the name regardless of whether it is capitalized or not Di methyl and di methyl are excluded from the name 2 6 Structure Search A structure search is used for the convenient and reliable identification of compoundis in libraries This type of query often yields better results in less time than a spectrum search as you may not always know the exact spelling of the compound names In addition you can also search for a molecular sub structure to selectively refine and filter certain compound groups Searching structures in Sadtler libraries is supported by OPUS SEARCH 4 and higher Prior to performing a search the molecular structure has to be entered using the structure editor Details on the structure handling can be obtained from the appendix Click on the Structure Search command in the Evaluate pull down menu or on the S icon 26 OPUS SEARCH Bruker Optik GmbH Structure Search 2 6 1 Structure Search Structure Search x Structure Search Se
33. el Help Figure 33 Edit Create Structure Edit Structure tab Select a file and drag amp drop it from the OPUS browser into the selection field of the Edit Structure tab If an STR data block already exists you can edit the structure If no structure is available a new structure will be attached If you activate the New structure file check box the Edit Create Structure dialog box changes as follows OPUS SEARCH Bruker Optik GmbH Edit Create Structure x Edit Structure Choose Editor IV New structure file Path c SOPUSSDATA d File name TEST Path for Structure File x c opus data Cancel Help ZO Library ZO Search Edit Create Structure Drives b Network Figure 34 Edit Create Structure Edit Structure tab Enter the path for the new structure file into the Path entry field or click on the E button to browse the path Define the file name with extension for the new structure file in the File Name entry field Click on the Choose Editor tab to open the following dialog Bruker Optik GmbH OPUS SEARCH 53 Edit Create Structure xj Edit Structure Choose Editor Structure editor FNCHEMWINACHEMWIN EXE Browse Scaling factor 2 100 Edit Create Structure Cancel Help Figure 35 Edit Create Structure Choose Editor tab Enter the path and file name of the structure editor into the Structure editor entry field or cli
34. entire table entries will be sorted in ascending order according to the column selected If you click on the particular column header again the table entries will be sorted in descending order Double clicking on an entry number automatically copies the entry number into the destined entry field on the Edit Library tab see the mark in figure 26 which will immediately be displayed Deleting one or more entries from the library will be noted next to the particular entry number see figure 28 Bruker Optik GmbH OPUS SEARCH 43 Editing Libraries Library Editor x Edit Library Library Entries Contents of Info Set s Double click on entry number to select entry for editor Enty CompeundNams Molecular Formula Molecular Weight METHYL FORMA C2H402 107 31 3 Deleted Entry 1 METHOXY 2 P C4H1 002 107 38 2 E dit Cancel Help Figure 28 Library Editor Contents of Info Set s tab 44 OPUS SEARCH Bruker Optik GmbH Library Editor 4 1 3 Contents of the Info Set s If you click on the Contents of the Info Set s tab the following dialog opens Library Editor x Edit Library Library Entries Contents of Info Set s Current info New info m Special entries 1 Compound Name 1 es Missing 2 Molecular Formula 2 Missing 3 Molecular Weight 3 e Missing 4 CAS Registry Number d Missing Name gt Compound Namel Formula gt Molecu
35. f a spectrum search since the original data files will always be employed for the search Optionally you can define the Substance Name Molecular Formula Molecular Weight and CAS Number information lines It is however recommended to create these lines at random position in the info mask If the Substance Name line e g cannot be found in the info mask the content of the first info mask line will automatically be used OPUS SEARCH Bruker Optik GmbH Library Structure Library Method Entry 1 Entry 2 Entry 3 Spectrum Chemical Spectrum Information Structure Parameter Figure 1 Internal structure of a library entry Bruker Optik GmbH OPUS SEARCH 3 Introduction 4 OPUS SEARCH Bruker Optik GmbH OPUS SEARCH Icons Library Search The aim of any library search is to identify an unknown substance by its optical spectrum As already mentioned in chapter four different search methods are available a Spectrum Search An unknown spectrum is compared with the library spectra Library spectra which show distinct similarities to the unknown spectrum are detected and reported b Peak Search One or several band positions can be entered manually This allows searching for spectra which are not available in a digital format i e only a hard copy exists c Information Search An information search refers to the kind of information stored together with the spectra E
36. g to the result of this particular search This means that those functional groups which spectra come very close to the spectrum displayed in the spectrum window are shown at the farthest end of the list Thus you can quickly get an overview about the functional groups in the substance which forms the basis for the spectrum If you right click on the spectrum window a menu pops up and provides the most important functions required to edit the spectrum display e g Zoom and Scale Depending on the spectrum section displayed in the spectrum window the chart in the upper window changes accordingly This allows to quickly check whether the band positions in the spectrum and the chart are conform with each other If you double click on the functional group name you can have the molecular structure displayed in the structure window The functional group name will be highlighted in light gray in the upper window Double click again on the name to undo the selection To change to a different band assignment chart click on the Change Chart button A dialog pops up to be used to select a different band assignment chart The information provided by the band assignment chart are stored in the OPUS library format Therefore it is practically possible to display OPUS libraries in the browser of the band assignment chart which is however not very useful Use the Help button to open the online help To close the band assignment chart browser click on th
37. h Report AB Number of Hits SER eport of Spectrum Search 1 General Library IR AB User Library 2 General Library IR User Library Hit No Hit Quality Compound Name Entry No Lib Index 1 540 GLYCEROL 106 1 2 540 GLYCEROL 106 z 3 514 ETHYLENE GLYCOL 35 1 4 514 ETHYLENE GLYCOL 35 2 5 502 1 7 DIAMINOHEPTANE 186 1 Figure 10 Search report window Expand the Report of Spectrum Search directory to have the search parameters displayed Bruker Optik GmbH OPUS SEARCH 15 Library Search Report of Spectrum Search Algorithm Standard Number of Hits 30 Date 2003 12 05 Time 11 01 50 GMT 1 Searched Method 1 Library CAOPUSIDATAYLIBRARSADEMOLIB 2 Library C WPROGRAMME OPUS DATAILIBRARY DEMOLIB 501 Searched Spectrum C ProgrammeVOPUSTDATAYAbboe05 0 Search Sensitivity 13 Figure 11 Search parameters The Search Parameters include all relevant details about the search Search algorithm used Number of hits e Date of the search Time ofthe search Search method List of libraries used for the search with name and directory Directory and name of the query spectrum Sensitivity value used for the search Note The last two parameters are only valid for the spectrum search If you use the peak information or structure search the parameters will indicate information on Band search number of bands band position Information search number of queries query Structure search name
38. ialog opens Spectrum Search xj Spectrum Search Search Parameters Excluded Regions Select Libraries Restore Last Ranges Clear Ranges From frequency To frequency Save Ranges as Load Ranges Interactive Range Selection Search Library Cancel Help Figure 7 Spectrum Search Excluded Regions tab There are several possibilities to define the regions you want to exclude You can enter the ranges manually into the table If you want to use the frequency ranges of previous search runs click on the Restore Last Ranges button Sometimes it may be advisable to delete CO bands from an MIR spectrum Click on the Clear Ranges button to delete the table entries and enter the new ranges you want to use for the next query To delete single lines only click on the respective line number and press the DEL button on the PC keyboard If you have completed the frequency table save the settings by clicking on the Save Ranges as button To restore the data sets saved click on the Load Ranges button If you prefer to interactively select the frequency ranges click on the nteractive Range Selection button A window opens and displays the query spectrum Right click on the spectrum and select the Add Region button from the pop up menu The spectral ranges to be excluded are displayed on a white background If you position the
39. ibrary Click on the Yes button to perform the adding operation The spectrum is added to the library as a new entry at the end of the library list Make sure that the spectra you want to add does include an INFO data block In case of spectra without any INFO data block a warning pops up and you will automatically be routed to the Store Spectrum in Library dialog described in section 3 2 d Editing compound information If you have selected an entry in the library list you can edit the corresponding compound information Double click on the Compound Information window The Add Information dialog will be displayed and you can make the necessary changes Bruker Optik GmbH OPUS SEARCH 47 Editing Libraries Add Information x 1 11 12 26 f E APragrammeNOPL SS earchNE ntryDO7 1 1 Load Text Mask woe Restore Original ew file Text definition From Info Block Compound Namel TESTER RB B ES Molecular Formula C5H 1201 Molecular W eight 88 15 CAS Registry urteta Melting Pont st s lt s sSOSO C Bailing Pana SS Sample Preparation NEAT Sample Geri Mandacued Referencel Charge Number Add Cancel Help Figure 31 Add Information If you click on the Add button a window pops up and asks whether to store the changes into the library Confirm the procedure b
40. item options are limited to a text search the Molecular Weight info item option to a numerical search If the content of a field is recognized as Molecular Formula the Molecular Formula Search see below will automatically be performed The remaining info item options will be treated according to their values If the first entry in a line is a number this number will always be stored in numerical form a following string will be stored as text The 500 Degrees Decomposition entry e g will be stored in a library as a numerical value of 500 0 and as Degree Decomposition text This allows both a numerical as well as a text search Even a search query like Melting Point a A 500 would generate a hit Molecular Formula Search Information Search X Query for Information Search Choose Information Text Select Libraries seme wem 7 bue 1 Molecular Formula a A C5 6H5 8 This setting retrieves all entries with 5 or 6 carbon atoms and 5 to 8 hydrogen atoms Molecular formula search queries have the following general syntax El n m E2 n m E3 n m Bruker Optik GmbH OPUS SEARCH 25 Library Search Example El and E2 represent the chemical element Additionally you can use X as a wild card for halogens and Ht for hetero atoms N and m specify the range for the number of atoms n being the minimum number and m the maximum number in the molecular formula Combined Search Information S
41. k List button To use a peak list previously created click on the Load Peak List button A peak list will always be saved as separate file with the extension PKL When starting a search the current peak list is automatically saved in the DEFAULT PKL file However the file content will be updated during the next search run When using the Peak Search algorithm it is also possible to restrict the search to the range of an existing search report as described in section 2 3 2 4 2 Parameters On the Parameters tab you select the search algorithm the maximum number of hits as well as the minimum hit quality The Minimum Hit Quality entry field is only available if you have selected the Calculate Hit Quality algorithm see figure 13 Bruker Optik GmbH OPUS SEARCH 19 Library Search Peak Search x Peak List for Peak Search Parameters Select Libraries Algorithm Calculate Hit Quality Calculate Hit Quality Za Hit if all peaks match Minimum Hit if one peak matches Count matching peaks Maximum number of hits 3 Search Library Cancel Help Figure 13 Peak Search Parameter tab The following algorithms are available a Calculate Hit Quality The results produced by this algorithm are similar to those produced by using the Spectrum Search algorithm It calculates a hit quality from the difference between the position of the search peak and the peak found in the library The larger the differenc
42. lar Formulal Weight gt Molecular Weight CAS gt CAS Registry Number Melting Point Boiling Point Sample Preparation Sample Quantity Manufacturerl Referencel Charge Number Comment E dit Cancel Help Figure 29 Library Editor Contents of Info Set s tab The Contents of Info Set s tab displays the current info text definition of the selected library in the left selection field If you have checked the Change info definition option button on the Edit Library tab see figure 26 the info mask of the file to be newly assigned will be displayed in the right selection field Thus it will be easier to see whether the new and the old info mask are compatible The new info mask must contain all fields included in the old one and may also list additional fields The Special Entries group field lists entries that will be automatically assigned to a library Compound Name Molecular Formula Molecular Weight and CAS Registry Number These entries are selected in the respective selection fields Bruker Optik GmbH OPUS SEARCH 45 Editing Libraries 4 2 Library Browser SLibrary Display default ows 5 Operator Default Administrator The Library Browser command in the Evaluate menu allows to visualize the contents of a library It is possible to make changes in the library displayed Ent Compound Name RE Compound Information D METHYL FORMATE n Tb Compound Name O CUMENE 2 ETHY
43. mall deviations from the identity methyl propyl ketone remains hit quality no 1 The absolute hit quality of the spectrum correctly searched is the lowest compared to the other sensitivity setting as even the smallest deviations are considered We know from experience that sometimes too extreme a sensitivity value produces results which could hardly be interpreted Therefore it is advisable to test several sensitivity settings and whether the values found make sense Bruker Optik GmbH OPUS SEARCH 17 Library Search 2 4 Peak Search A peak search is a very simple but powerful search option You can perform a search on one or more bands which will then be compared to the selected libraries using different algorithms The result of a peak search performed on a Sadtler library substantially depends on the number of bands stored in this library According to our experience sometimes minor peaks may not be recorded in the Sadtler database The search for strong and medium bands should however yield identical results Different algorithms can be used To reasonably limit the search results you can enter a tolerance limit and intensity criteria for each band This search type is often applied to data obtained from older instruments where the results are plotted on paper and digital data is not available But it can also be used to get an answer to the question Which spectra show a peak at To perform a peak search select the
44. mplete structure different symbols which allow to define specific sub structures R replaces any sub structure except hydrogen Z replaces any sub structure including hydrogen Y replaces any single element except hydrogen Ht replaces any single hetero atom X replaces any single element 28 OPUS SEARCH Bruker Optik GmbH Structure Search 2 6 2 2 Structure Search Example Search the following structures in the DEMOLIB library Cyclohexane Benzene Benzene with substitute R Benzene with substitute X Acetic Acid Use both search algorithms and compare the results 2 6 3 Select Libraries On the Select Libraries tab you select the libraries for the search Structure Search also generates a SEARCH data block which includes the search result Bruker Optik GmbH OPUS SEARCH 29 Library Search 30 OPUS SEARCH Bruker Optik GmbH Initializing Library Generating Library Files Generating library files can be facilitated by the Initialize Library command from the Evaluate menu This command however does not provide the possibility to generate or edit library files for Sadtler libraries 3 1 Initializing Library Use the nitialize Library command to integrate several spectra into a new library or to create an empty library and add different spectra to this library Select the ntitialize Library command or click on the f icon Initialize Library E Library Initialization Method and Info Selectio
45. n Spectra to add to a new library D SQPUSSDAT Abe DI IDMOEUSMDATANObeiai 1 D AOPUSSDATA SS ylhex2a 0 1 Library name AAA Library path JDABrukerLibraries Browse Library description Copyright note ea Je Figure 18 Initialize Library Library Initialization tab Define the different entry fields You can change the default library path by clicking on the Browse button There are two possibilities to proceed Bruker Optik GmbH OPUS SEARCH 31 Generating Library Files 3 1 1 Adding existing spectra to new library Load the respective spectra by the Load File command from the File menu to the OPUS browser Drag amp drop the spectra data blocks into the Spectra to add to a new library selection field figure 18 Note that only ratio data blocks e g AB TR KM RAM Refl or logRefl will be accepted If you create the library in this way the library parameters will be derived from the first spectrum displayed in the selection field This is the reason why all functions on the Method and Info Selection tab are completely deactivated 3 1 2 Creating empty library If the Spectra to add to a new library selection field does not include any spectrum you have to define certain parameters on the Method and Info Selection tab You can e g define the frequency range of each library spectrum or specify which kind of spectra information type of each spectrum has to be added to the library
46. n e A A case sensitive text comparison e equality of numbers including the decimals e gt the number in the library must be greater than the number defined here e lt the number in the library must be less than the number defined here e gt the number in the library must be greater than or equals the number defined here e lt the number in the library must be less than or equals the number defined here If Molecular Formula has been selected as info item the comparing text operators will not be available d Value Enter the value to be searched for in this column Depending on the comparison operator the value is treated as text or as a number In case of text comparison there is an additional set of control characters available to allow a more specific sub string search e the string following the character must be at the beginning of the text e replaces the rest of a string wild card e replaces exactly one character of a string e d replaces a number e l replaces a character e p replaces either a number or a character e w replaces any sign which is neither a number nor a character ignores blanks Example benzene returns benzene and methyl benzene Sbenzene returns benzene but not nitro benzene benzoi returns benzoin and benzoic benz returns benzoin benzoic benzpyrene etc d Methyl returns e g 1 Methyl 2 Methyl etc Yop d Methyl returns e g 3 Methyl and
47. n individual libraries OPUS SEARCH can be classified by two functional parts e Library Search to identify unknown substances Library Editor to create individual spectral libraries The Library Search option enables you to search existing libraries You can select between four different types of search methods a Spectrum Search To identify unknown substances b Peak Search To search for one or more specific peaks c Information Search To search for names material characteristics molecular formulae d Structure Search To search for complete or partial substance structures A structural formula editor helps you to create the respective structural formulae The result of such a library search is stored in the form of a report in the SEARCH data block amp sex This report includes links to each spectrum of the substances found To compare these spectra with the query spectrum it is possible to have them displayed in one window SEARCH reports can also be used as a basis for further search requests which also may refine the search method The library editor comprises all tools needed to create and maintain your own spectral libraries Note OPUS SEARCH utilizes the user name which you have defined for the specific workspace to be able to internally access the database system Note that this user name will be shortened to 9 characters and that it only has to include letters and figures Do not use any special character
48. of the structure file Example Search using the standard algorithm Load the Search 5 0 file from the OPUS DATA directory This file includes a methyl propyl ketone spectrum Perform several queries using the sensitivity settings listed below 16 OPUS SEARCH Bruker Optik GmbH Spectrum Search Sensitivity 10 30 Hits Hit Qual Compound Name Entry No be 1 9 METHYL PROPYL KETONE 5 Bl jz 7 2 HEXANONE 18 L 3 595 DIISOBUTYL KETONE 297 4 536 3 HEPTANONE 57 ls 47 ISOPROPYL METHYL KETONE 19 e 464 ISOOCTANE 263 O7 45 DIETHYL KETONE 36 Methyl propyl ketone has a substantially higher hit quality than all the other substances listed This kind of setting produces an unambiguous result Sensitivity 1 30 Hits Hit Qual Compound Name Entry Mo 1 950 METHYL PROPYL KETONE 5 a les 935 2 HEXANONE 18 l ere DIISOBUTYL KETONE 297 4 638 ISOPROPYL METHYL KETONE 19 IK 623 4 HYDROXY 4 METHYL 2 PENTANONE 33 e 604 ETHYL BUTYRATE 32 Ll 53 4 METHYL 2 PENTANOL 40 Again methyl propyl ketone has been identified as hit no 1 However the criterion of spectra identity is less stringent Even hit no 2 produces a high hit quality Sensitivity 20 30 Hits Hit Qual Compound Name Entry No 1 828 METHYL PROPYL KETONE 5 B jz 706 2 HEXANONE 18 Tb de ACETONE 93 Tik Sa 1 PROPANOL 107 TIK se 3 HEPTANONE 57 le sa 3 PENTANOL 147 Cir se ISOBUTANOL 131 Even in case of this very extreme setting which allow only very s
49. rary button A dialog pops up from which you can select a different library Click on the Exit button to close the library browser If you open the library browser again by the Library Browser command in the Evaluate menu the library previously selected will be displayed There are several possibilities to edit the library However all the editing options can only be used in connection with unprotected libraries i e libraries which have been created by the user 46 OPUS SEARCH Bruker Optik GmbH Library Browser a Extracting spectra from the library Select one entry or several entries in the library list If you right click on the library list a window pops up from which you select the Extract Spectra command The entry files are now displayed in the OPUS browser window and the entry spectra are displayed in the spectrum window b Deleting spectra from the library Select one entry or several entries in the library browser If you right click on the selection a window pops up from which you select the Delete Spectra command Before the entries are definitely deleted you will be asked whether you want to continue the deleting operation which is irreversible c Adding spectra to the library If you have loaded a spectrum in a different window you can add it to the library Drag amp drop the particular data block AB or TM into the library list A dialog pops up and asks whether you want to add this spectrum to the l
50. s e g or umlauts e g as this would cause an error message when trying to access the library system Bruker Optik GmbH OPUS SEARCH 1 Introduction 1 1 Library Structure A library consists of several files which have the same file name but different file name extensions This facilitates the providing of backup copies for a library FILENAME DO1 FILENAME D02 FILENAME D03 FILENAME D04 FILENAME D05 FILENAME D06 FILENAME D07 FILENAME D08 FILENAME D09 FILENAME D10 FILENAME D11 FILENAME D12 FILENAME D13 FILENAME KO01 FILENAME K02 FILENAME K03 FILENAME S01 FILENAME D02 FILENAME TXD A numbered entry is allocated for each substance within one library The entry number helps to address the single entries Each entry additionally includes an information text which is extracted from the spectrum INFO data block aes The info text mask has to be defined when creating the library and is mandatory for the information input The library is restricted to spectra acquired by one single spectroscopic method Therefore the library may either include NIR MIR or Raman spectra but not a mixture of these types of spectra Furthermore you can specify additional OPUS parameters in the method which will be saved together with the spectrum The spectrum will then be cut off according to the frequency limits specified and transformed to the digital resolution selected However this does not influence the quality o
51. spective arrow button If you click on the OK button the Save File As dialog pops up Save the method file created or modified The Method and Info Selection tab will be displayed again figure 19 If you click on the Execute button the library will be created This kind of library can also be used for the searching procedure in libraries provided the library does include the respective spectra Bruker Optik GmbH OPUS SEARCH 35 Generating Library Files To store spectra in a library use the Store Spectrum in Library command which will be explained in more detail in the next chapter 3 2 Storing Spectra in a Library Load all spectra you want to store in the library into the OPUS browser and select the spectral data blocks Make sure that each file includes an INFO data block which actually contains the information you want to add to the library To get reasonable search results the spectra to be added should only be absorption or Raman spectra If you use transmission spectra they will be converted into absorption spectra and also saved as absorption spectra Select the Store Spectrum in Library command from the Evaluate menu or click on the TZ icon The Store Spectrum in Library opens 3 2 3 Store Spectrum x Store Spectrum Parameter Library Entries Change Library C Programme OPUS DATASLIBRARYSDEMOLIB Library properties User library Description General Library IF Total entries 352 Valid entries 352 Delete
52. the substance molecular formula molecular weight and the CAS number Generally the first hit is automatically checked and its spectrum is displayed together with the structural formula and compound information You can deactivate the first hit and activate a different one Use the Show Query Spectrum button figure 8 to have the query spectrum displayed Spectra are automatically displayed in transmittance if the query spectrum is a transmittance spectrum If you have clicked on the Show Query Spectrum button the button will change into Hide Query Spectrum Right to this button you can see the library description and copyright Closing the library window adds a SEARCH data block figure 9 to the query spectrum file in the OPUS browser window If you right click on the data block the Show Report menu pops up Click on this menu to open the corresponding report window fid Display default ows 1 Operator Def SE AbboeU5 0 1 AE SEARCHIHISTORY Show Report Figure 9 SEARCH data block and Show Report menu The report window includes its own browser which helps you to navigate figure 10 On the right side the number of hits are displayed as well as the library number which is important if several libraries have been used for the search Additional information on the query are displayed on the lower part of the search report window CAProgrammeYOPUSTDATAYAbboe05 0 1 Report of Spectrum Search 30 E Searc
53. um have similar intensities Depending on the substance measured you can also define whether the spectrum to be searched for contains one component in case of a single substance or multiple components in case of compounds In the first case the hit quality achieved is reduced by a certain factor if the number of bands in the library spectrum is less than the number of bands in the query spectrum c Weigthed Peak Matching In case of this algorithm all pieces of band information which are available from the query and library spectrum are reflected in the hit quality The information contains the position relative intensity and half width of each band A library spectrum band is considered to be identified in the query spectrum if this spectrum contains a band 10 OPUS SEARCH Bruker Optik GmbH Spectrum Search which position does deviate from the position in the library spec trum by less than the half width which difference between the half widths and relative intensities is less than factor 2 respectively This algorithm also allows to further specify the search result Select the appropriate option button to define whether the measurement of the query spectrum has been performed by one main component or by multiple components d Use Existing Peak Table This algorithm uses an already existing peak table which enables you to suppress the influence of peaks originating from the substrate If you use this algorithm the Se
54. xample if you search for spectra of substances which have a specific molecular weight you can narrow down the number of spectra searched for d Structure Search This is the only reliable method to find single substances or compound classes in a library A complete or partial molecular structure is compared with the data stored in the library Before starting any search load the unknown spectrum into the OPUS browser window OPUS provides a DEMOLIB demo library which has been used for most of the following examples 2 1 OPUS SEARCH Icons All OPUS SEARCH commands can easily be accessed by specific OPUS SEARCH icons in the tool bar which you first have to configure For further details on how to configure the tool bar refer to the OPUS Reference Manual OPUS SEARCH commands are listed in the OPUS Evaluate menu Bruker Optik GmbH OPUS SEARCH 5 Library Search Spectrum Search A Peak Search Information Search Structure Search Initialize Library Store Spectrum in Library Library Editor Library Browser di SES al Eb Eh Bb Gh Band Assignment Chart m fio iu Em ds b At ze Figure 2 OPUS SEARCH functions 2 2 Selecting a Library You have to define one or more libraries to be used for the search irrespective of the search method you select Select any search method described either by defining the respective search command A from the Evaluate menu or clicking on the respective icon on the tool bar B Note
55. xt tab Fig 15 shows the info data sets of three libraries loaded for an information search The first two info data sets are identical whereas the third set differs from the others in some parameters The deviations are indicated in red Click on the Search Library button to start the search query The result will be stored in a SEARCH data block see chapter 2 3 4 Further information search examples will be described below Example Numerical Search x Query for Information Search Choose Information Text Select Libraries Molecular Weight 60 This setting generates only one hit if a library entry contains a molecular weight value of 60 A value of 60 05 would not qualify as a hit 24 OPUS SEARCH Bruker Optik GmbH Information Search Example Information Search x Query for Information Search Choose Information Text Select Libraries Molecular Weight AND Molecular Weight This setting retrieves all entries with a molecular weight between 60 and 61 Information Search x Query for Information Search Choose Information Text Select Libraries ree uem TT 3 Boilinq Point AND Boiling Point aA Ge Sometimes a numerical field also includes additional text e g Decomposition in the second line The string can either be searched separately or in combination with the numerical value The Compound Name and CAS Registry Number info
56. y clicking on the Yes button e Adding data blocks from a loaded file to a library entry Select the specific library entry to which you want to add an INFO or structure STR data block Drag amp drop the respective data block from the OPUS browser to the library list A dialog pops up and if you confirm the operation the respective data block will be added to the entry selected If the entry already includes such a data block type this data block will automatically be replaced 48 OPUS SEARCH Bruker Optik GmbH Band Assignment Chart 4 3 Band Assignment Chart The Band Assignment Chart command in the Evaluate menu allows to visually assign spectrum bands to functional groups Amides Secondary Amides Tertiary Amines Amines Amines Amines Primary Aliphatic Primary Aromatic Secondary Aliphatic Secondary Aromatic 3j as PO Amines Tertiary Aliphatic Amines Tertiary Aromatic Nitriles Aliphatic Nitriles Aromatic Isonitriles Aliphatic Isonitriles Aromatic Nitro Compounds Aliphatic Nitro Compounds Aromatic Nitro Compounds Nitrates Nitro Compounds Nitrites Halogenes RI Halogens RCI Carboxylic Acids Dimer Alcohols free OH Alcohols Intermol Esters Formates Alcohols Acetal Esters Acetates 1 25 4000 3600 3400 LZ change chat pe Figure 32 Band Assignment Chart A FA 3200 3000 hl M

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