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1. Cj ta 0 N e LSJ LEJ CU Bg 1 ed sy Draw Bond C H 0 18 Hs implicit Zoomfactor 100 Moreover please note that in the case of no existing mol file JCP will open a dummy file consisting of an ethan molecule If no changes are made JCP should be closed with out saving otherwise the ethan molecule will be copied in the current dataset Saving newly created molecules or modified structures will overwrite already existing mol files 12 Z4D11813 Z33040 Rev 01 Data Analysis 6 9 Prediction Clicking the tab Prediction opens a pdf document that shows the prediction information used for the automated spectra analysis The upper part displays the spectrum including the integrals red numbers below the baseline and proton numbers abbreviation nP above the signals for each peak cluster The lower part of this graphic indicates the pre dicted chemical shift ranges The grey bars in the first line correspond to the integration regions of the peak clusters of the acquired spectrum Each of the following lines repre sents the predicted chemical shift ranges depicted as blue bars for each atom speci fied in squared brackets Spectrum P1 P3 P P P2 Fa P3 P6 OD O N 0 ag in oO a a Q DO N Po o 130 125 120 115 110 105 100 95 90 85 80 60 55 50 45 40 35 30 25 2 0 16 10 O86 75 Chemical shift ppm Predicted chemical shift ranges Chemical shift ppm 130 125 120 115 110 10
2. In order to perform the transformation of the NMR signal apply the window function mul tiplication by clicking OK in the corresponding dialog and enter the command ft on the command line Z4D11813 Z33040 Rev 01 47 Data Processing 5 2 2 Phase Correction Subsequently the phase can be either corrected manually by clicking the tab Di Phase or automatically by choosing one of the various modi accessible via the down arrow on the right side of the Di Phase tab 5 2 2 1 Automatic Phase Correction Jimak CR seel jak iF riese FFL all 9 Dam Process Analyse Report since Yew O ii Process Spadium Phaser Baseines Cobb Aise Burial a aua D Diem O Hh T amp ASA Phase Beer irua Wang PRACT pa kie MM 2 AE in l mat N LE 3 A Cite tel iier Gorren ion papi n R 4 TT OE Orie rare tn Coty jan EE LULU alia TE TE d f EER a ai Di Merrie Adige fs 2 ae 1 if h i I 11 i 4 J a MLS LY 3 Phase Spectrum Using PHCO PHC1 pk perform phase correction with existing values for Oth and 1st order Oth 1st Order Correction apk adjust phase with automatically determined val ues for Oth and 1st order Oth Order Correction Only apk0 phase spectrum automatically using only Oth order phase correction Alternate Algorithm 1 apks apply an alternate algorithm for Oth and 1st order phase correction Alternate Algorithm 2 apkm Oth and 1st order phase correction usi
3. e CMC assist Bruker User Manual Version 001 Innovation with Integrity Copyright by Bruker Corporation All rights reserved No part of this publication may be reproduced stored in a retrieval system or transmitted in any form or by any means without the prior consent of the publisher Product names used are trademarks or registered trademarks of their respective holders This manual was written by CMC Service Team September 13 2011 Bruker Corporation Fallanden Switzerland P N Z33040 DWG Nr Z4D11813 For further technical assistance on the CMC assist please do not hesitate to contact your nearest BRUKER dealer or contact us directly at BRUKER BioSpin AG Industriestrasse 26 CH 8117 Fallanden Switzerland Phone 41 44 82591 11 FAX 49 44 825 96 96 E mail service_cmc bruker ch Internet www bruker com 1 HUE OCU eiie a AE EA EE EE EE N EE N T 1 1 ADOT ME SER Manual ee Ee ER EEEE ER EK ED ED ER EE i 7 1 1 1 Font CONV CIOS soene SE Oe Rok oe oe ENE Se Ee ee ee ee Janeth Be Ro eie 7 1 1 2 Available DocumentatiON ese eek ee EE ee RE ER EE ee ee Ee RE ee ee ee Ee ee ee ee ee ee ee 7 1 2 eie ORE ME ee ecco tbat esac scant ae cassie AG Baai RD EEN 8 1 3 CMC assist License ie eke oe ORE ee ee ES DE RE RE SR Re ee RE RE RE Ee Re 8 2 cema Starled is Es ER RE Re DE ER Ee Ed Re Ne Ee ER 9 2 1 VREES E a RE N EE N N EE EE 9 2 2 Stdr
4. Z4D11813 Z33040 Rev 01 15 Reporting CMC assist Eewa hot_candidate 1 1 C BrukenCMCAldatalChemical Synthesistnmr F ede 125 120 15 110 WS 100 35 30 85 6 0 7 5 70 65 6 0 5 5 5 0 45 40 35 3 0 25 20 15 10 ppm DS a Pa i Le rr fo Be wh pd i F E N ET dT 15 2 a 15 2 4 8 15 i a ef da jg Oo Naa Non 11 1 Ti s mm m s m om at 12 244 ppm at 7 189 ppm AS 1H 2H 2H p ag 20 20 EET TEE 12 35 12 30 12 25 12 20 ppm 7 25 7 20 ppm 715 7 10 ppm Scale 0 02699 pprvom 10 00 Harm Sep 12 2011 3 07 50 PM Page 3 of 8 Furthermore via the down arrow on the right side of the tab the Report Settings can be altered This includes adding of an originator label to the first page of the report or switching of the page size between letter and A4 7 3 Patent String Clicking the tab Patent String opens a dialog which gives the opportunity to select different journal types and copy the appropriate patent string Assignments as Patent String Journal type Mu Re de ei eee MH NMR 400 MHz DMSO 12 24 1H s 7 21 7 17 2H m 7 12 7 09 2H m 3 63 4H q J 7 0 Hz 2 43 2 40 2H m 1 85 1 77 1H m 1 34 3H d J 7 3 Hz 0 87 0 85 GH m Copy OK 76 Z4D11813 Z33040 Rev 01 Reporting 7 4 Print Clicking on the tab amp Print will print the currently active data window Alternatively the down arrow on the right side of the tab offers several file ty
5. Z4D11813 Z33040 Rev 01 71 Data Analysis 6 7 Line Shape Analysis 6 8 The Line Shape Analysis tab uses the CMC i package and the current structure to calcu late a prediction and match factor by automated cost analysis ACA For further details regarding this software package please refer to the manual Documentation for PERCH ACA available via the amp help button In addition please note that this functionality requires a separate license Molecular Structure 6 8 1 The structure editor JChemPaint is an integrated part of the software package CMC assist that enables drawing and modifying of chemical structures Besides this editor the Structure menu also offers the option to view predicted chemical shift ranges for the given molecular structure Adding mol Files 6 8 2 This submenu jj Add MOL file within the Structure menu allows loading a new struc ture in the format of a mol file into the current dataset Editing Structures with the JCP Editor The tab JCP Editor starts the program JChemPaint an editor for 2D molecular structures in a separate window For further information on creating or modifying molecular struc tures please consult the JCP manual available via the He p button in the upper right cor ner of the window 210 File Edit View Atom Bond Tools Templates Help M Insert namaggid aase oo Val IE e AN IG IN Ve O AN ROOOO MIE
6. Spectrum colors Print black and white only Color of 1st 1D spectrum Color of 2nd 1D spectrum Color of 3rd 1D spectrum Color of 4th 1D spectrum Color of 5th 1D spectrum Color of 6th 1D spectrum Color of 7th 1D spectrum Color of 8th 1D spectrum Color of axis Color of grid lines Color of zoom area Fonts Printer font Dialoginput plain Plain 10 Spectrum extras Use thick lines Title Color of title Parameters Color of parameters Axis Font for the axes integral peak labels Dialog bold Bold 14 Change Change Change Change Change Change Change Change Change Change r Change Change Change Search In addition the displayed content of the active data window can be saved in a graphics file of selectable type png jpg joeg bmp emf and wmf via the Export option in the file menu 14 Z4D11813 Z33040 Rev 01 Getting Started 2 4 Automated Analysis of Spectra The CMC assist also offers the opportunity to analyse 1D 1H NMR spectra in full auto mation with respect to concentration determination and structure consistency check Clicking on the tab Analyse Spectrum starts this automated interpretation of the currently displayed spectrum If the analysis runs for the first time on a dataset it might be necessary to give some additional information The appearing dialog shows the reguired information that con sists of the number of suppre
7. For precise analysis a reference spectrum is essential that should be acquired prefera bly under the same conditions as the molecule of interest In addition the reference sub stance should be highly soluble in the solvent used and the exact amount of compound has to be known Please note that the most suitable window function for spectra pro cessing for quantification purposes is an exponential function After appropriate acquisi tion and processing this reference spectrum has to be defined as reference First of all at least one signal within the reference spectrum has to be integrated Subse quently it has to be stated on which signal s the reference concentration is based by right clicking on the respective integral s and ticking the option Calculate concentration by this integral Stairs Prodan Conten Inlegral 723 7 15 pe Annalaan F Dak ulate concentration fry this integral Afterwards the down arrow on the right side of the tab Quantification offers the possibil ity to define the marked and integrated signal s as reference PH Define Integrals as Eretic Reference x Enter Parameters Concentration 1 0 mmou Integral Range Integral Atoms Peak Integ Ratio 7 231 7 148 2 0000 2 1 0000 OK Cancel Z4D11813 Z33040 Rev 01 69 Data Analysis 6 5 Clicking the submenu Define as Eretic Reference opens up a dialog where the assigned proton number for each labeled and integrat
8. Select Save As in the file menu or use the shortcut Crtl s Tick Save other file Choose as File type processed data as new PROCNO Enter a processing number procno Save Acquisition Data 3 2 4 Select Save As in the file menu or use the shortcut Crtl s Tick Save other file Choose as File type acqu data as new EXPNO Enter a experiment number expno Save Processed Data as Pseudo Raw Data 3 3 Select Save As in the file menu or use the shortcut Crtl s Tick Save other file Choose as File type 1r 1i as fid Enter a experiment number expno Deleting Data 3 3 1 Delete a Specific Dataset 3 3 2 e Right click on the dataset name expno or procno and select Delete e Right click on a data directory and choose Remove Selected Data Dir Delete Types of Datasets Select the option Delete in the file menu or enter delete on the command line Z4D11813 Z33040 Rev 01 23 Data Handling Define the type of data for removing via the various criteria of the appearing window x Browse Options An entire data set with all EXPNOs PROCNOs C Acquisition data Processed data C Data acquired at certain dates C 1D raw data fid C 1D processed data 11 1i C 2D 3D etc raw data ser 2D processed data 2rr 2ii C Imaginary processed data 1i_ C Macro AU program Python program C Pulse program C Parameter list Misc
9. Bruker CMCA data Screening_Compounds nmr 1 wetdc 2008 05 31 01 44 25 compound_13 1 1 C Bruker CMCA data Screening_Compounds nmr 1 wetdc 2008 05 30 16 27 57 Display Display In New Window Display As 2D Projection Sort This Column Sort Reverse v Show Details Save selection in file Add selection to dataset group File Properties Files Process Selected Datasets Save Selection In File save the list of selected datasets in a text file Add Selection To Dataset Group add selected datasets to an existing dataset group or define a new group for the selected datasets File Properties show main dataset parameters like dimension pulse program acquisition date nuclei spectrometer frequency and solvent Z4D11813 Z33040 Rev 01 27 Data Handling Files display the files within the processed data directory procno of the selected dataset Process Selected Datasets perform serial processing on the selected datasets see Chapter 5 4 Save for TopSpin The tab Save for TopSpin exports assignment information and spectrum analysis features to standard Bruker TopSpin files This will overwrite any existing information previously generated by TopSpin for example peak integral and multiplet lists created after data acquisition Z4D11813 Z33040 Rev 01 4 1 CMC assist Interface The CMC assist possesses a workflow based interface with its available functionalities
10. arranged according to diverse working processes like data handling data processing data analysis etc The CMC assist Window 4 1 1 The CMC assist window consists of data area data browser toolbars and menubar The data browser can be inactive Ctrl d or clicking the tab Browser in the menu Data or displayed as a separate window The following figure shows the CMC assist window with two data windows in the data area and the browser as an integral part ey i TIETE 5 Dein Broom Anasa Report Stu wew 12 a wa DE O tb T amp LM ble mi Gash mi LE ox A Teaser mis Groups Dipa imiia i bcaa a ME pi OM 7 a 5 4 2 i a 4 Menubar The menubar includes the following menus e Data performing data file handling tasks e Process data processing e Analyse automatic and manual data analysis e Report generating various types of reports and patent strings e Structure adding and modifying chemical structures e View display properties Z4D11813 Z33040 Rev 01 29 CMC assist Interface Toolbar Experienced users might prefer to work with the command line rather than the toolbar buttons A mouse contact of the toolbar buttons opens a balloon help that shows the corresponding commands and shortcuts in square brackets behind the explanation of the button s functionality Create new dataset new Ctrl n va Open dataset open Ctrl o Save current dataset sa
11. y Ji Toggle grid mode between fixed axis off gr aA Start distance measurement xi Setup frequency list for pulse programs freglist W Switch overview spectrum on off ov Multiple display md Chemical Shift Distance Measurement 4 1 2 2 As long as the icon TI Start distance measurement is highlighted in yellow the function ality of the cursor line changes in order to measure chemical shift distances Left clicking at one peak position and moving the mouse to another peak position will measure the distance in ppm and Hertz Right clicking in the data window or moving the cursor out of the data window will leave the distance measurement mode Discesa a 0 0098 ppa 191 He T T T T lg T T T T T T T T T T T T T T f T t TA 73 72 74 TE 69 63 ppm Overview Spectrum In addition to a certain region of the spectrum the spectrum overview can be displayed at the top of the data window with the zoomed region highlighted in green by clicking the 4 icon an Switch overview spectrum on off Simply click hold this green area in the over Z4D11813 Z33040 Rev 01 31 CMC assist Interface view spectrum and moving the mouse will shift the displayed region at the bottom of the data window sd EXP fe iins a m A Ac rye en oO AS 11 ODCIS ANT pom 2567 8953 He T ft T EE 6a ppm 4 1 2 3 Multiple Display The multiple display mode enables superimposition of mul
12. ANG AR EE AO E O E 22 3 2 1 Save an Entire Dataset ccc se ee Ee EER ER EE ee EE ee Ee ee ee ee ee ee ee ee ee Ee ee ee 23 3 2 2 Save Processed Data ccccccccscccscccsscccueccueecsecceeeceuecsueesueesueeeeeesseesaeesseesseesaees 23 3 2 3 Save Acquisition ala eo GE EE Ne Ge Ee naii ee EE 23 3 2 4 Save Processed Data as Pseudo Raw Data sees sesse Ee ee Ee ee ee ee ee ee ee ee ee 23 3 3 Deleng Dali EE Ee Oe De N ee oe T 23 3 3 1 Delete a Specific Dataset ss ee ER EE ER ee ER ee EE Re RE ee Ee ee ee ee RE ee ee ee ee ee 23 3 3 2 Delete Types of Dataset is ee EE ER EE ee EE ER Re ER ee EE Re ee Ee ee ee ee ee Re ee Ee ee EE ee ee 23 3 4 Data IMIG UD Alice osse EE eo ER EE DE ge E EE EG EE Ee 25 3 4 1 EE EE N EE N EE OE N EE 25 3 4 2 OS BAS a as Ee Ee mane dase Ee ee Ee De ee 25 3 4 3 Eie EE RE OE OON N N ON OE OE OE ER ON 26 3 4 4 le EE OE EE OE OE OE EE N EE 26 3 4 5 IV TON WO eo ii EE OE 28 ZAD11813 Z33040 Rev 01 CMC assist Intertace tea asec N eee GE Re RE OR EE Ee We ee 29 4 1 The EME assist WiINAGW ate ie oe GE oos Ge ed GEE ee EG Ge 29 4 1 1 BL MO A pce acter ER OE OO 29 4 1 2 MONO A saris EA AT OR N EE EE EE EE N 30 4 1 2 1 Chemical Shift Distance Measurement sees esse ee ee Re Ee ER ee ee ee Re ee Ee 31 4 1 2 2 Overview Spectrum eie ee ese EE ee EER EE ER EE ER ER EE AA ER EE ee Ee ee ee Ee ee Re RE ee ee ee 31 4 1 2 3 MUDIE DS Oy esse EG RR EE AR E eg Se Ee Pe ED ee 32 4
13. F1 F2 absf n adjust baseline the same way as abs n just within the defined range F1 F2 Automatic Alternate Algorithm absd n apply an alternate algorithm for automatic baseline correction 5 2 3 2 Manual Baseline Correction Besides clicking the submenu Manual correction mode entering basl on the command line also switches to the baseline correction mode and replaces the standard CMC 50 Z4D11813 Z33040 Rev 01 Data Processing assist toolbar by the toolbar specific for baseline correction A The yellow button indicates that the baseline correction mode is active ER EABGD El ae WA Al a Polynomial Baseline Correction Left click the following button a for polynomial baseline correction In the data window a red horizontal line will appear as well as the equation that describes the polynomial function f x A Bx Cx Dx Ex Left click hold the button for variable A and move the mouse until the red line coin cides with the first point of the spectrum Repeat the procedure of variable A for all the other variables B C D and E until the red line matches the entire baseline of the spectrum b Sine Baseline Correction Left click the following button jy for sine baseline correction In the data window a red horizontal line will appear as well as the eguation that describes the sine function f x A Bsin Cx D Left click hold the button for vari
14. For further information about the handling of this tool please refer to the manual Documentation for Multiplet Analy sis available via the 3 help button 70 Z4D11813 Z33040 Rev 01 Data Analysis Ed EE ET ii Lenie VALA lata eea proljeca yae algia MIRRE Haa iha Tele LXK niy ARE di ieobulvinhenriErainEsd in DASO fret OG ae TEE 171 074 He Ander T4841 1451 Valus Bdke 0 cel TR EE EE EE AE es EE AE AE ER es MA gr FEE EE eee th 4 4 q i G 4 lan sd 4 ta 6 6 Consistency The ae Consistency tab opens a dialog that enables changing of the consistency status as well as adding of individual comments in the fields Result Summary and Result Details ee Project Status Description i x Consistency OK by automatic analysis OK C NOT OK UNCLEAR Result Source Automatic analysis generated by Bruker CMC 3466 Manually edited by user Result Summary Automatic evaluation Spectrum and Structure are in agreement Result Details Automatic evaluation All elements of the structure could be assigned to regions in the spectrum and all major signals in the spectrum are assigned A quantification result is available These manual changes and or comments as well as statements from the automated spectra analysis are printed on the first page of the report generating the report see Chapter 7 1
15. Peaks within this outer region only experience minor disturbances from the suppres sion For the automated spectra interpretation these peaks are analysed with respect to their multiplicity however their integrated proton numbers are classified as not reli able unsuppressed spectrum suppressed spectrum remove 80Hz q_ inner 160Hz E _ otter 400H2 c d Eretic Signal in Spectrum If the spectrum contains an artificial signal for quantification this box must be ticked and 62 Z4D11813 Z33040 Rev 01 Data Analysis its position within the spectrum has to be stated The artificial signal may either be a real hardware ERETIC signal or it may be a signal introduced digitally after the data acquisition e e Decoupling This box indicates whether the spectra were acquired with or without GC decoupling f Import Expert Settings In the case the settings have already been adjusted according to the individual condi tions previously or for different data these settings can be imported for the current data set e Current Dataset This option imports the settings of the last automated analysis of the current dataset This functionality is intended for minor changes of the previous settings and avoids edit ing of the parameters from scratch If the spectrum interpretation should run again with the same settings as before except for an addition
16. Proportional ball size CABruker CMCA Serial Processing Lis Show Table Close Clicking on any of the colored balls will open the corresponding spectrum in the data window of the CMC assist and highlight the respective entry in the table of the other batch window The same applies for selecting an entry from the table 3 4 3 Browser Clicking on the tab J Browser displays and hides the CMC assist browser respec tively 3 4 4 Find Searching for certain data can be performed according to various criteria The respective dialog will pop up when clicking the tab EA Find entering the command find on the command line or hitting the shortcut Ctrl f Enter the search items in the upper part of the dialog Exact matching is performed for the dataset variables NAME EXPNO and PROCNO if the corresponding checkbox at the right is ticked Entries in the fields Title and Pulse Prog cause searching for items containing these specified strings The search can be restricted to data created between specified dates referring to the acquisition dates Select the Data directories to be searched in the lower part of the dialog if no direc tories are selected all directories will be used for search Clicking OK starts the search and a list of data that fulfill the defined criteria will appear 26 Z4D11813 Z33040 Rev 01 Data Handling x Searching will be performed in all data directories
17. and the concentration can be calculated based on this integral 66 Z4D11813 Z33040 Rev 01 Data Analysis Delete delete the selected integral Protons list proton numbers in order to set a new proton content for the selected integral Signal Type enable setting of the status of the selected integral as substance mix ture or impurity 6 3 2 Multiplet Analysis Clicking on the toolbar icon na Define new multiplets activates the multiplet analysis mode and the cursor line becomes dashed e Define multiplet Left click on the peaks which belong to one multiplet Right click in the data window and choose Finish Multiplet Definition Depending on the number of peaks which define the multiplet a dialog appears that lists all possible multiplet configurations Selecting any of the listed options will display the corresponding multiplicity in the data window If none of the suggested multiplet configurations is appropriate it still leaves the possibility to tick Report multiplet type as m which results in reporting no multiplicity and no coupling con stant In addition the labeling of the multiplet can be changed e Exit multiplet analysis Left click the yellow highlighted button 7 If the created multiplet needs to be deleted again leave the multiplet analysis mode right click on the multiplet and choose Delete from the appearing window Z4D11813 Z33040 Rev 01 67 Data
18. correction save current baseline correction values and leave the baseline correction mode J Return and discard any changes f Cubic Spline Baseline Correction Click the following button it to define points for the cubic spline baseline correction Z4D11813 Z33040 Rev 01 Data Processing 5 3 The toolbar of the data window will change and the cursor line turns red If a list of base line points already exists a pop up dialog gives the opportunity to either overwrite or append to these points Append displays the labels of the existing points on the screen whereas Overwrite does not show any labels However the existing points are only overwritten when new baseline points are defined and saved In order to define new baseline points move the cursor line to an appropriate baseline position and left click at that position This has to be done for at least five baseline points The actual baseline correction is only performed when clicking the save button in the spline baseline and the interactive baseline mode Existing points can also be deleted by right clicking on the corresponding point position and choosing Delete Current from the pop up menu The same applies for removing all existing points just select Delete All from the appearing window Apart from the buttons for returning from the cubic spline baseline mode with or without saving mentioned above right clicking in the data window offers the options Save am
19. data stored in special formats C Open other file rRequired parameters Browser type File Chooser v Cancel Help Subsequently a standard file browser allows navigation to the desired data directory Clicking Display will replace the content of the currently active window with the selected dataset If no data window was displayed a new one will be created 10 Z4D11813 Z33040 Rev 01 Getting Started Look in nmr aa Arbeitsplatz Netzwerkum File name C Bruker CMCA data Open_Access nmr Display Files of type Topspin NAME EXPNO PROCNO or top file v Cancel The file browser will also pop up by entering reb on the command line 2 3 2 Open Data from the Browser First of all the desired data directories have to be added to the data browser Move the cursor into the browser area Right click and choose Add New Data Dir in the pop up menu PH Bruker CMC assist 1 0 b 12 build 1791 a Data i Process Analyse Report Structure View VT 842 QQ Oea FB AA H si QA gt a est 2 LE Ox Browser Last50 Groups P Chemical Synthesis H E Open Access Streng Compounds Display Display In New Window Scroll to Active Dataset Fully Expand Selection v Show PULPROG Title Show Date Sort by Date Copy File Properties Delete Rename Files Remove Selected Data Dirs Browser Preferences Browse for
20. defined in the list as well as the number of datas ets for which the spectra interpretation is completed In addition it provides the opportunity to hold and resume or abort the batch analysis Please note that the maxi mum capacity of one batch is restricted to 96 datasets in order to enable visual inspec tion of the batch result Modifying Results from Automated Analysis 6 2 1 Integrals Integration regions can be easily changed just move the cursor to the edge of the blue bar till the vertical boundary line turns red Left click hold and move the mouse in order to expand or reduce the integration region The bars of the integration regions are colored differently depending on their signal type Blue bars correspond to signals originating from the investigated compound grey bars label impurities and striped bars indicate a mixture of substance and impurity The status of the signal type can be altered by right clicking on the integral and choosing the appropriate status via the submenu Signal Type Furthermore the dialog that appears when right clicking on the integral offers additional options like calibrating the integral cutting the integral and changing the correlated proton number 64 Z4D11813 Z33040 Rev 01 DEV WAIN ATE As soon as an integral has been modified in some way the integral and the proton num ber are printed italic A EE acl 1 HEET TEE eer MEE id s m a ME en e E a a l
21. integration as described above Z4D11813 Z33040 Rev 01 43 CMC assist Interface i 1 Cira HCA piaia aa dier TT fi FI TT T T Al EE sr w ra E a OS tren 5 KO afosyt LLL 4 919 ppa T2P EAT He Rol ciplet Multiplicity st 3 7 Hz 6 050 ppa papige co stows 27 J o Mule thy Resine Mutil Deele i Clear Assignment 4 l Hew Muted Hera Inle graad I I EE EE NEE ee ee fh 5 TH TH TH 2H TH TH TH mm or or 22 ED 123 13 d E l 0 TE Ta 5 GE 55 ppm Assignment If an assignment already exists moving the cursor to any atom of the displayed structure will highlight this atom as well as the corresponding multiplet The same holds true the other way around moving the cursor line to any multiplet will highlight the atom s of the molecule assigned to this multiplet There are two different ways to connect a signal in the spectrum with the respective atom s of the molecular structure depending on the cursor position Z4D11813 Z33040 Rev 01 CMC assist Interface 4 3 5 e Cursor at highlighted atom of the molecule Left click hold on any atom of the molecule and move the mouse to the corresponding multiplet will assign this atom to the selected multiplet e Cursor at highlighted multiplet Left click hold on any multiplet and move the mouse to the appropriate atom of the dis played structure will connect the selected multiplet with this atom Mol
22. line are in Arial bold italic e Menus buttons and icons that can be clicked or selected are in Arial italic Available Documentation Clicking on the help button 2 provides the following information and documentation e CMC assist Manual e Documentation for PERCH ACA Z4D11813 Z33040 Rev 01 T Introduction 1 2 e Documentation for Multiplet Analysis e Version Info e License Info Functionality 1 3 CMC assist is a software package intended for e Processing 1D 1H NMR spectra e Analysing NMR spectra manually e Automated spectra analysis e Generating NMR spectra reports and patent strings in various formats CMC assist License The CMC assist requires a license for startup A license can be ordered online from www bruker biospin de NMR nmrsoftw Licenses index html A short instruction on updating the license file for Windows operating systems C flexlm Bruker licenses license dat and for systems running under Linux usr local flexlm Bruker licenses license dat will be sent together with the license The following programs are distributed as part of the CMC assist but require a separate license e PERCH NMR prediction only for Windows operating systems e Line Shape Analysis only for Windows operating systems Z4D11813 Z33040 Rev 01 2 1 Getting Started This chapter shortly describes the installation of the software package CMC assist and the first steps to start the
23. marked in the data directories list below The checkboxes at the right will enforce exact matching if enabled NAME EXPNO 1 PROCNO fi Vv Title Pulse Prog Dimension Any v Data type Any z Date from mm dd yy Date till mm dd yy Data directories f C Bruken CMCA data Chemical_ Synthesis nmralias Chemical_ Synthesis C BrukenCMCA data Open_Access nmr alias Open_Access i C BrukenCMCA data Screening_Compounds nmr alias Screening Compounds OK Reset mask Cancel Help Right click on a list entry offers the following options Display display the selected dataset s in the current data window Display In New Window show selected dataset s in a new data window Sort This Column sort the column in ascending alphabetical order in relation to the dataset title numbers before letters Sort Reverse sort the column in descending alphabetical order in relation to the dataset title numbers after letters Show Details switch display of expno pulse program and acquisition date on off x Found 6 Data Sets Please right click in a list for more options Ajmalicin 1 1 C Bruker CMCA data Chemical_Synthesis nmr 1 zg30 2006 08 22 14 08 15 Isobutylphenylpropionicacid 1 1 C Bruker CMCA data Chemical_Synthesis nmr 1 zg30 2006 08 22 16 19 33 alpha_Satonin 1 1 C Bruker CMCA data Chemical_Synthesis nmr 1 zg30 2006 08 25 15 15 59 compound_0815 1 1 C
24. tab A Calib Axis will set the frequency of this reference signal to 0 ppm Serial 5 4 1 The command Serial allows the handling of whole batches of datasets Generating a Serial Processing List First of all a serial processing list has to be created in order to define the different paths of the spectra that should be processed or analysed the same way This serial process ing list can be generated as follows 54 Z4D11813 Z33040 Rev 01 Data Processing Clicking on the tab Serial opens a new submenu with the tabs Define List Define Command and Execute The down arrow on the right side of the tab Define List offers the option Build data Set list using find which opens up a dialog sa aldl ed 3 Data Process Analyse Repot Stuur Ver O T Back Define List Define Command Execute Ban Q Em OD Mi Tt amp Aa Cait Dustasel ini ble mi SR ik t i LE 3 A el fobs KAR in aban in Des Deseret aste Grou T CP pa f Mee di m lal UL l 4 J MEE MJ 3 Search will be performed in all data directories marked in the data directories list and can be further specified by certain entries for EXPNO PROCNO Dimension etc Find data x Searching will be performed in all data directories marked in the data directories list below The checkboxes at the right will enforce exact matching if enabled NAME A EXPNO li Vv PROC
25. the data like processing integration multiplet analysis etc made within the CMC assist are saved automatically Apart from that the option Save As in the file menu provides the opportunity to save the dataset in several different formats CT x Options Copy data set to a new destination C Save data set in a ZIP file C Save data set in a JCAMP Dx file C Save data set as experiment to CCPN project Save data of currently displayed region in a text file Save parameters as a new experiment C Save digital as analog filtered data C Save other file rReruired parameters File type processed data as new PROCNO Cancel Help The choices of the pop up dialog correspond to the following command line commands Copy the current dataset to a new destination name or expno wrpa Save the selected dataset in ZIP format tozip Convert the current dataset to JCAMP DX format tojdx Save the selected dataset in CCPN format toccpn Convert the current dataset to text format totxt Write parameterset wpar Save digitally filtered data as analog filtered data convdta 22 Z4D11813 Z33040 Rev 01 Data Handling 3 2 1 Save an Entire Dataset 3 2 2 Select Save As in the file menu or use the shortcut Crtl s Choose Copy dataset to a new destination Specify dataset variable name or expno Save Processed Data 3 2 3
26. the desired data directory Optionally a shortcut can be defined for the selected data directory Z4D11813 Z33040 Rev 01 11 Getting Started MEN Please enter a new NMR data directory DIR Full path of dir containing nmr datasets ALIAS Shortcut for DIR if filled in DIR C BruKkenCMCA data Quantification ALIAS Quantification OK Cancel Browse Afterwards the data can be displayed from the browser as follows Expand the directory in the browser to the level of the data name expno or procno Select the desired spectrum and drag it into the data area 2 3 3 Expand a Spectral Region In order to expand a certain spectral region left click hold on one side of the region drag the cursor to the other side and release the mouse Rimi 270611 3 1 yin OAA date Ven ACE omer sl ET Me ese a RE bid PER abbo a07 Hz DO The expansion can be canceled by moving the cursor out of the data area while still dragging the mouse and release it Besides this mouse button functionality the corresponding toolbar buttons for zooming can be used as described in Chapter 3 1 Z4D11813 Z33040 Rev 01 Getting Started 2 3 4 Show Peaks Integrals Multiplet Labels etc For displayed spectra several options exist in order to show additional information together with the spectrum like for example title status parameters concentration etc e Choose the co
27. 1 3 Command EE N OE EE EE OE EE EN 35 4 1 3 1 Senes Ol Command S ses ee oe Ee Ge GE ee ER Eb DEE er ge dk 36 4 1 3 2 Command Line HistOFV ies see ee ee ee ee ee ee AR ee AR Ee ee Re ee Re ee Re ee Re ee ee ee ee ee ee ee ee 36 4 1 4 Data WiInNdOW RA EE N ER EE N OE OE EE ENG 36 4 1 4 1 Move and Resize Data WindOWS eie ees ee ee ee Re cee ee ee Re ee ee ee ee ee ee ee ee 37 4 1 4 2 Activate a Data WINKOW eie ees see ee ccc Ee cece ee ee Ee Ee ee ee Re ee ee ee ee ee ee ee Re ee ee 37 4 2 CMC assist Toolbar ets N ON EE ER RE ke ee GE De IE ne ENG 38 4 2 1 CMC assist Toolbar Buttons c ccccccessceseeessessuecesecessuvecessauesaeeceesceesavenevenees 38 4 2 2 CMC assist Toolbar FunctionalitieS iese see ee ee ee ee ee ER ee ee ee ee Re ee ee ee 38 4 2 2 1 ZOOM to Quantification Range ees ee ee ee Ee ee RE Ee ee ee ee ee ee ee ee 38 4 2 2 2 Define New Integrals ccccccccccssecceeeeceeeeeeecceeseeeeeeeeeeeeeeeeeeueeseeeseeeeseesseeeees 39 4 2 2 3 Define New Multiplet ese ee EE ee EE Ee EE ee EE ee EE Re RE ee EE ee Re ee ee ee ee ee ee Re ee ee ee ee ee 39 4 2 2 4 Show Display Options cccccccccsccccseeecesecececeseeceeeceseeceseeeeseeeeseeeeseeeseeeeseeeeas 40 4 2 2 5 Show and Edit Project Status InformatiON ees ee ee ee ee Ee ee ee ee RR ee ee ee 41 4 3 CMC assist Data WiINdOW ee ee ee ee ee ee ee Re cece Re ee ee ee ee ee ee ee ee ee ee Ee 41 4 3 1 BaSe ae 6
28. 131110 HI Screening Compounds compound 0815 1 wetdc compound 0815 HDMSO Off resonance 2 544 3 462ppm Wi 23 compound_13 H compound_42 The Browser Tab The browser shows data directory trees that can be expanded or collapsed Furthermore various additional information can be displayed together with the data directory like the pulse program the title of the spectrum or the acquisition date Just Z4D11813 Z33040 Rev 01 17 Data Handling right click on the respective directory and select the desired option from the appearing dialog W Bruker CMC assist 1 0 b 12 build 1791 E i Data Process Analyse Report Structure a 8 2 lt 2 CD Gah Mo k l i T GO 3 2 2 OOS wa HY J Browser Last50 Groups 5 4 Chemical_Synthesis BIO Ajmaiicin BID alpha Satonin ED Isobutylphenylpropionicacid EE 1 27930 Isobutylphenylpropionicacid in DMSO HO Open Access Display B DAB 070311 Display In New Window EE FH 250611 EH 3 2930 FH 250611 CDCI3 i 1 FH 250611 CDCI3 BEKO 310511 BE SC 020111 Scroll to Active Dataset Fully Expand Selection Show Date E XY_131110 Sort by Date a Screening_Compounds compound 0815 Copy BE 1 wetdc compound 0815 HDMS File Properties 2 compound 13 Deiis H compound 42 Rename Files Add New Data Dir Remove Selected Data Dirs Browser Preferences Display display dataset in cu
29. 195s 11 gt n ao DE Ee Mi eee ed Ee N ee ee 41 4 3 2 Bel gs Uie AE IE EE OR N 42 4 3 3 MullipletAiial Y SIS use ee NE ee oe ee ee ED ed one N Do de ENAS 43 4 3 4 PRS S MIAN SIM OE AE EE EE OT Ne 44 4 3 5 Molecular SUC MIE re Eie ee AE EE Gee ie ek ve Ein 45 4 3 5 1 Clear Existing Assignment cccccseeccceeeecceeeeeceeeeecesceceueeessegeeseeueessuseesseneenes 45 4 3 5 2 Moving the Displayed Molecule ees ee ER AR RA ee Re Re ee ee ee 45 4 3 5 3 Changing Display Options ccccccccccseccceeeeeeeeeceeeeeeeeceeceseeeeseeceseeeeseneeseeesaees 45 4 3 6 Increasing Horizontal ScaliNg esse esse ees ee ee se ee ee ee ee Ee ee ee ee ee ee ee ee ee ee ee ee ee 46 BEA WO SOS ae EE AA EE EE RE EE AT 5 1 Automati Processing sesse es se een sole Ee enaa se WE sal os Di 47 5 2 interactive PFOCESSING iis sn Ee AG Ke eb ee n n EG Ek dag oe ee 47 5 2 1 Ig eed dip ede AE N ER OE EE AE OE 47 5 2 2 PAS SC ONS CU OM Ma ee oe Oe on ie Ge Re EEE ie Ge Ge ea 48 5 2 2 1 Automatic Phase Corre ction ccccccecceccceeceeeeececeeceneeeseeeeeneeeeeeeeneeuseegeeeeeeeeneees 48 5 2 2 2 Manual Phase CorreclOn issie as ee GE Ge ga Ed Ge Ge Ge Ek de 48 5 2 3 Baseline Correction i ss ES EN RS n dante ais land ve Ges ei ei Ge ee 50 5 2 3 1 Automatic Baseline Correction ees ee ee ee ee Re ER ee ee ee ee ee ee ee ee ee ee ee 50 5 2 3 2 Manual Baseline Correction cccccccccecceeecececeeeeeeeeeeeeeeaueeeeeeeeeaeeeee
30. 1D 1H NMR spectra Consequently only this type of spectra can be processed with the soft ware package CMC assist The corresponding Process menu gives the opportunity to manually process the acquired data or to process single spectra as well as batches of spectra in automation Automatic Processing 5 2 Bruker 1D 1H NMR spectra can be processed in a fully automated way After opening appropriate NMR data clicking the tab X Process Spectrum will execute a standard processing for 1D spectra including an exponential window function fourier transforma tion automated phase correction and automated baseline correction Interactive Processing 5 2 1 Besides the automatic processing it is also possible to interactively process the NMR data Advanced users who are familiar with the software package TopSpin can enter all the known single commands for processing 1D spectra on the command line Window Function By clicking the down arrow on the right side of the tab X Process Spectrum one can choose any window function for multiplication together with their required parameters A Window function em xX Options 7 _ Manual window adjustment i Required parameters Window function type WDW Line broadening LB Hz 03 Gaussian max position 0 lt GB 1 lo Sine bell shift SSB 0 1 2 _ 0 Left trapezoid limit 0 lt TM1 lt 1 0 Right trapezoid limit 0 TM2 1 0 OK Cancel Help
31. 5 100 95 90 85 80 75 70 65 60 55 50 45 40 35 30 25 20 15 10 OS Integration regions g ii f ll i 15 nP 3 Ey 13 nP 3 Ed 14 nP 1 EI 12 nP 1 11 np 3 SSS EE 5 nP 1 add aard 12 nP 1 E aa Explanstion stom numbers number of protons nP Alternatively the tab Prediction provides the opportunity to run the prediction software PERCH Clicking the down arrow on the right side of the tab makes the submenu Run PERCH shift prediction accessible This prediction software calculates a theoretical spectrum for the current structure and superimposes it with the experimental data for manual comparison Please note that this software package requires an additional license Z4D11813 Z33040 Rev 01 13 Data Analysis 14 Z4D11813 Z33040 Rev 01 l 7 1 Reporting The software package CMC assist enables generation of a short report of one page a detailed report of several pages and also a text file including patent strings in various formats All these options are available via the Report menu Short Report 7 2 The tab Short Report creates an one page assignment report displaying the consis tency status the molecular structure the spectrum interpretation based on the automat ically generated assignment and or the manually edited assignment the determined concentration and any comments made regarding the summary of results or any rele vant details e CM
32. AE 66 6 3 2 Mluliip let al SIE si EK SE Ee E ED EN Ee EE O 67 6 3 3 sen sp Se OR EE A A A I 68 6 4 Eie EO eee oe EE nee en see ee ee eee eee ee eee eee 69 6 5 Analysis of Complex Multiplet S iss ee ee ee ee Ee ee ee ee ee Ee ee ee ee ee ee ee ee ee ee 70 6 6 IVS GE ve EE EE N EE E N OE NE EE nites 71 6 7 Line Snaps ANalySIS ia Ek eo Re EE RA ge ER oe VG ee 72 6 8 Molecular EIE Ee ee ee re ent eee eee ene eee eee eer Tee 72 6 8 1 PACING ATION Files see es Ee ak GE n ee ie 72 6 8 2 Editing Structures with the JCP Editor esse ee ss es ee se ee ee ee ee ee ee ee ee ee ee ee 72 6 9 asie ie EE EE dg ager OE maa 73 T REDOUN E E E 75 7 1 ole AA RODO KEN RE EE N EE EE N EO ON a 15 7 2 Be CUM TPS se EE ON cine EE N OE EE EE 15 7 3 FU AE SCN EE N OE N EE OE E N 76 7 4 PAL ENE e OE DE OER OO N EE OE RE did ee OY N EE EE EE 77 8 COMICI AE acces recesses EE recone ek cence Ed 19 ZAD11813 Z33040 Rev 01 6 Z4D11813 Z33040 Rev 01 1 1 Introduction The software package CMC assist is designed for processing and analysis of acquired 1D 1H NMR data Its user friendly and well structured interface enables new CMC assist users as well as experienced Bruker software users to benefit from the comprehensive range of functionalities About the User Manual The User Manual describes the main aspects of Bruker s software package CMC assist It intends to give an overview of the various functionalities of the CMC as
33. Analysis ET TE RR NET Id AI OE OOR GM adel ee GR amp Satin m3 lsobutvlphenvipropionicaad in DMSO 1 653 pow 661 204 Tr PT TAT ET TA t 134 itt ae Beata err f Ee HR d DEFILE SEY MULTIPLET NOOR Lefteclick to define peaks Fight click jor tool butten te finish multiplet 6 3 3 Assignment There are two different ways to connect a signal in the spectrum with the corresponding atom s of the molecular structure Left click hold on any atom of the molecule and move the mouse to the respective multiplet will assign this atom to the selected multiplet Left click hold on any multiplet and move the mouse to the appropriate atom of the displayed structure will assign the selected multiplet with this atom lsoiotyiphermyipo eed N 1 Leser Ti PA edele ieena Byl ien r ae e gt ad AE oo mu RRR fsobukdokarsiaropiariarid in MESO L 20 ppa S07 4e7 Hz Huletpler d MultipltELEF A 2 0 He 1 4 pou Asien fo ae dt Z4D11813 Z33040 Rev 01 68 Data Analysis 6 4 Moving the cursor line to any multiplet will highlight the atom s of the molecule assigned to this multiplet The same applies the other way around positioning the cursor at any atom of the displayed structure will highlight the connected multiplet Quantification The tab Quantification enables concentration determination of the measured substance
34. C assist BROKER Anale atwyats gecerates by Broker CMC 3511 j AL amfa have bee gate acts hy by mulveretic arm bysin Repon generated by Becher CMC aasid 1 0 5 12 on P1727 wn Gr Osta set on candi 1 1 OE her MORA OO herrie ad By riese ructue C Afsutu he reke Dye skater oar a Vetructure mal Acqeieiten due August 22 2006 4 10 33 PM CEST Sower 6 mn PABBI 1HO BB LORD ZE203010131 C Btu OCA Oeria Crete rotaen Satoni pdala eroti Summary of results Interpretation Automatic evaluation Spectrum and Structure are in agreement Position coup ng integral Assignment 1224 ppm 5 1H 10 7 19 ppm m 2H 143 7 10 ppm m 2H 245 3 63 ppm q 7 0Hz 1H 7 3 34 ppm s OH not assigned Details 2 51 ppm dd 1 8 1 6Hz OH mot assigned Automatic evaluation All elements of the structure could be assigned to 2 42 ppm m 2H ae 12 regions in the spectrum and all major signals in the spectrum are assigned 1 61 ppm m TH 14 A quantification result is available 1 34 ppm d 7 3Hz 3H 11 0 86 ppm m 6H 15413 Sep 12 2011 3 02 42 PM Page 1 of 1 Full Report The first page of the full report available by the corresponding tab L Full Report is identical to the short report In addition the following pages show a more detailed inter pretation of the spectrum including integration multiplicity and assignment for each peak and finally the last page presents the complete assignment in various Journal for mats
35. NO i iw Title Pulse Prog Dimension Any w Data type Any Date from mm dd yy Date till mm dd yy Data directories CA Bruke CMCA data Chemical _Synthesis inmr alias Chemical_Synthesis C Bruke CMCA data Open_Access nmr alias Open_Access C Brukern CMCA data Screening_Compounds nmr alias Screening_ Compounds OK Reset mask Cancel Help Enter the search items in the upper part of the dialog Z4D11813 Z33040 Rev 01 55 Data Processing Exact matching is performed for the dataset variables NAME EXPNO and PROCNO if the corresponding checkbox at the right is ticked Entries in the fields Title and Pulse Prog cause searching for items containing these specified strings The search can be restricted to data created between specified dates referring to the acquisition dates Select the Data directories to be searched in the lower part of the dialog if no direc tories are selected all directories will be used for search OK starts the search and the results will be displayed within a new dialog Found 6 Data Sets Please right click in a list for more options Ajmalicin 1 1 C Bruker CMCA data Chemical_Synthesis nmr Isobutylphenylpropionicacid 1 1 C Bruker CMCA data Chemical_Synthesis nmr alpha_Satonin 1 1 C Bruker CMCA data Chemical_Synthesis nmr compound_0815 1 1 C Bruker CMCA data Screening_Compounds nmr compound_13 1 1 C Bruker CMCA data Scre
36. T T T T T 10 B a 4 2 pem Move and Resize Data Windows 4 1 4 2 Several data windows can be opened within the CMC assist data field by just selecting Display in New Window every time a new dataset is loaded These data windows can be arranged individually by moving or resizing the windows e Move a data window Left click hold the title bar and move the mouse e Resize a data window Move the cursor to the window edge until it becomes a double headed arrow Left click hold that position and move the mouse Depending on the position of the double headed arrow the window can be changed in height width or both Activate a Data Window All functionalities of the toolbar and commands from the command line only correspond to and act on the active data window readily identifiable by the highlighted title bar Activate a data window Left click in the desired data window or left click its title bar Left click one of the colored buttons above the data area the pressed button indi cates the currently activated data window Hit the F6 key to activate the next window and repeat hitting the key until the desired window is the active one Z4D11813 Z33040 Rev 01 37 CMC assist Interface 4 2 CMC assist Toolbar 4 2 1 CMC assist Toolbar Buttons Zoom to quantification range on dataset opening J Define new integrals ha Define new multiplets J Show display options we Un
37. a new win dow where these impurities can be defined CMC q Analysis Define Impurities Known Impurities C TMS MF TSP l H20 I MeOH l DMSO_D5 I DMSO_H6 V Dimethylsulfon l EtOH l Acetone CH3CN l Ethylacetate m MP 1 from 1 16 to 1 21 ppm Multipiicity other Coupling Hz Proton Number Delete Vv MP 2 from 7 29 to 7 35 ppm Multiplicity s Coupling Hz Proton Number Delete Create Impurity Clear All Entries Save Cancel On the one hand some typical impurities regularly found within spectra of synthesized chemical compounds can be selected by just ticking the corresponding boxes In addi tion special or rarely appearing impurities can be defined individually In order to add an impurity click the tab Create Impurity and fill in any known information Please note that the individually entered impurities have to activated the same way as the predefined ones by ticking the respective boxes Before leaving this dialog any changes should always be saved c Suppression Frequency For automatic spectra analysis information about the number of suppression frequen cies is essential In the case the data were acquired unsuppressed all expected signals 60 Z4D11813 Z33040 Rev 01 Data Analysis should be visible within the spectrum Whereas the suppression of solvent signals might result in missing peaks that should appear within the suppression region All the required inf
38. able A and move the mouse until the red line coin cides with the first point of the spectrum Repeat the procedure of variable A for all the other variables B C and D until the red line matches the entire baseline of the spectrum c Exponential Baseline Correction Left click the following button for exponential baseline correction In the data window a red horizontal line will appear as well as the equation that describes the exponential function f x A Bexp Cx Z4D11813 Z33040 Rev 01 51 Data Processing Left click hold the button for variable A and move the mouse until the red line coin cides with the first point of the spectrum Repeat the procedure of variable A for the other variables B and C until the red line matches the entire baseline of the spectrum d Previewing Baseline Corrected Spectrum Before actually performing the baseline correction the result can be previewed by click ing the following button A Preview corrected spectrum The corrected spectrum will be displayed in red If the baseline is correct click the save button j If further correction is needed click the yellow highlighted preview button A again to show the original spectrum and the red correction line e Button Functionalities Reset red correction line to zero Increase double mouse sensitivity inc t Decrease halve mouse sensitivity dec I Reset the mouse sensitivity H Execute baseline
39. al impurity importing the previous set tings would be helpful e Browse In the case the desired settings for the current dataset have already been adjusted for a different dataset they can be imported via the Browse function select the cmcq file in the procno of the automatically analysed spectrum in order to apply the same settings for the automated interpretation of the current dataset 6 1 2 Automatic Analysis of Batch Spectra Besides the interpretation of a single spectrum a batch of datasets can also be anal ysed enc iojxi OS OA Analysis 20 C Single Analysis Batch Analysis CiBruker CMCA Serial Processing ListsiScreening Compoundstd Browse Expert Analysis Expert Analysis I Expert Analysis Details Batch Control Current Dataset Hold Abort all Current Batch Start Analysis Save Cancel Z4D11813 Z33040 Rev 01 63 Data Analysis 6 2 Clicking the submenu Batch Analysis opens a dialog where a serial processing list has to be defined before starting the analysis in the batch mode How to generate this serial processing list a text file made up of the data path for every single spectrum of the desired batch dataset is described in Chapter 5 4 After starting the batch analysis the Batch Control in the lower part of the window shows the path of the dataset currently analysed the file name of the specified serial process ing list and the number of all datasets
40. ata have not been acquired with respective Bruker software packages plus the analysis runs for the first time on a dataset some basic parameters have to be specified for the automatic analysis Hence by clicking the tab Analyse Spectrum a dialog appears that shows the required information These consist of the number of suppression frequencies any known impuri ties that should be excluded from the analysis possible RC decoupling existence of an eretic signal including its position and for quantification purposes the path to the required calibration file All these settings can be changed any time by the submenu Analysis Settings accessi ble by the down arrow on the right side of the tab Analyse Spectrum a Calibration File Directory Quantification of a dataset requires a reference spectrum of a molecule with known con centration The data path to this reference spectrum has be specified in order to calcu late the concentration of the compound of interest Please note that an already existing calibration file will not be overwritten and the concentration determination will be based on the previously defined reference b Known Impurities Besides substance signals the spectrum might also comprise peaks originating from impurities If any impurities are known to occur within the acquired dataset these should be declared for the spectrum interpretation Clicking the button Edit on the right side of the field Known Impurities opens
41. ata window s Add Selected Data Window add active data window to this group Add All Open Data Windows add all open data windows to this group Collapse All Groups collapse all expanded groups to top level Toggle Dim Pulprog Title switch dimension pulse program title display on off Add new Dataset Group create new group and define its name Close All Group Windows close all data window s belonging to this group 20 Z4D11813 Z33040 Rev 01 Data Handling Remove Selected Groups remove selected group s from the list Right clicking on a dataset within the group provides some additional features Display display dataset in current data window Display In New Window display dataset in new data window Update Window Bounds amp Display Limits update window bounds and display limits Remove Selected Datasets From Group remove selected dataset s from group Process Selected Datasets enter the serial command see Chapter 5 4 File Properties show dataset properties Files list files in selected entry expno or procno Copy copy dataset to clipboard 3 1 4 Put Focus in the Browser Hit the F2 key or click inside the browser 3 1 5 Expand Collapse a Folder in the Browser e Expanding a collapsed folder Left click the button to the left of the folder Double click the folder Hit the right arrow key while the folder is highlighted e Fully expand
42. ay Options 3 datasets were selected for display Please choose from the following options Display each dataset in its own window A Open a new window and show the vs datasets in layered multiple display mode A Add the datasets to the active window vs in layered multiple display mode If this button if is highlighted in yellow the multiple display mode is active and the stan dard CMC assist toolbar of the data window is replaced by the toolbar of the multiple dis play mode Furthermore the browser is split in two parts with an additional lower part that lists the datasets displayed in the active data window Z4D11813 Z33040 Rev 01 33 CMC assist Interface b Select Deselect and Remove Datasets e Select a single dataset Left click the small square at the upper right of the spectrum Left click the corresponding entry in the lower part of the browser e Select several datasets Hold down the Ctrl key and click the desired datasets Hold down the Shift key and click two datasets to select these two and all datasets in between Selected datasets can be recognized by a filled small square at the upper right of the spectrum and its highlighted entry in the lower part of the browser respectively Note that none selected spectrum equates to all spectra selected Moreover the scale and shift buttons of the data window toolbar only work on selecte
43. d spectra e Deselect a single dataset Select another dataset e Deselect all datasets Click the button Ts for deselecting all datasets e Remove datasets from multiple display Select the desired dataset s and click the button 2 for removing the selected data from the multiple display c Display Sum or Difference Spectra A Show the difference between the first and the sum of the other datasets gt Show the sum of all datasets in the multiple display window The displayed difference or sum spectrum can be saved by clicking the save button F and specifying the destination procno in the pop up box d Display the Next or Previous Name or Expno To compare a series of spectra the dataset name or expno can be interactively incre mented or decremented A dataset name is incremented according to the IlconNMR naming convention of increasing extensions e g name 001 name 002 etc E Show previous name expno procno of current dataset E Show next name expno procno of current dataset E Set increment options Z4D11813 Z33040 Rev 01 CMC assist Interface Data set increment options Increment C Procno C Expno Name Expno increment Preserve individual scaling e Toggle Between Superimposed and Stacked Spectra in Toggle between superimposed and stacked display f Shift and Scale Individual Spectra In order to compare the intensity and chemical shift of corresponding peaks spectra can b
44. do last action ex Redo last action P Show and edit project status information 4 2 2 CMC assist Toolbar Functionalities 4 2 2 1 Zoom to Quantification Range In order to activate this zoom mode click the button the zoom mode is active as long as the corresponding button appears yellow Another click on this button deacti vates the zoom mode again iden ELETE Er pola Tt ic wey mu ane j 1 Cirer CMS dele ipen Aar un raar T 72 ne Eg 54 BA ppml This special zoom mode becomes effective for every dataset that is newly loaded in the 38 Z4D11813 Z33040 Rev 01 CMC assist Interface data window and was analysed in automation previously Instead of the entire spectrum only a certain region of the spectrum is displayed This zoomed region shows the multi plet used for quantification including the calculated concentration at the center of the data window In the case no quantification information exists for the opened dataset the entire spectrum will be displayed as usual 4 2 2 2 Define New Integrals If the integration mode is active the corresponding toolbar icon is highlighted in yel low and the cursor line turns red e Define integral Left click hold and move the mouse e Exit integration mode Left click the yellow highlighted button Right click in the data window and select End Integral Definition 4 2 2 3 Define New Multiplet This yellow highlighted toolbar icon hd i
45. e g em ft apk or macros e g xmac my macro After finishing the serial processing a feedback dialog pops up Finally the Back button will exit the Serial submenu 5 5 Viewing Spectra If more than one internal window is opened all these windows can be arranged Side by Side or Stacked by clicking the corresponding tabs in the menu View Me 15 ren j A AJ W Jl A ts m T T T r T T T r ym r T T r r T sy T P T r T T 2 r r T T 6 5 4 3 2 ppa so In addition the spectrum display properties can be changed via the tab Spectrum These properties toggle for example the visibility of atom number chemical shift and multiplicity for each assigned atom together with the molecular structure Furthermore showing the calculated concentration the status parameters the cursor information or the title can be switched on or off Z4D11813 Z33040 Rev 01 of Data Processing OJ Da Process Aam Beet Structure we B m Spectum Stacked D Shie by Sida ae z nd a 4858 ia tov EE A al PETF s ee oe imanen in mso tack me i a ma EE ES 58 Z4D11813 Z33040 Rev 01 6 1 Data Analysis The software package CMC assist offers the possibility to run a fully automated spectra analysis as well as to interpret the NMR data manually including integration multiplet analysis and quantification All the features associated with the spectra inter
46. e shifted and scaled individually using the following buttons Note that the scale and shift buttons of the data window toolbar only work on selected spectra 5 Scale the selected spectra left click hold the button and move the mouse to align the intensity Shift the selected spectra left and right left click hold the button and move the mouse to align the peak position 2 Increase intensity of the selected spectra by a factor of 2 f va Decrease intensity of the selected spectra by a factor of 2 Ts Shift selected spectra vertically R Reset individual scaling and shift g Button Functionalities 4 Move selected spectrum one place up in the list 4 Move selected spectrum one place down in the list in Switch on off display of data paths and scaling factors A Calibrate multiple spectra 4 Return from multiple display mode 4 1 3 Command Line To execute a command via the command line the command line has to be activated first by the Esc key or clicking inside the command line All commands that have been entered on the command line since CMC assist was started are stored and can be Z4D11813 Z33040 Rev 01 35 CMC assist Interface 4 1 3 1 retrieved by the Up Arrow key to go back to previously entered commands and the Down Arrow key to scroll forward to recently entered commands The Left Arrow and Right Arrow keys move the cursor within the command line Series of Commands 4 1 3 2 Besides si
47. eafuiviphenrirmaienteerd in Dads L732 ppa JOD Fee Ez Peak Cluster Substance 1 protea LnEegeel 1 0 aaekgeed to mom 14 6 2 2 Multiplets In the case the automatically analysed multiplicity needs to be changed right click on the multiplet and select Multiplicity HEET ENTE EET EE Er E alas TERE SR TAYE eh oo Hz Biltipies q Mabetpliciny g 3 0 HE 1 821 ppa Aeshgeed to atoa T fei Hiirt Conlara T Report stipe type as nT e j Me Car TENK TA OS ME Tr TEM TE HE TE TENK TEN HE lee ox ese The pop up window lists all possible multiplet configurations depending on the number Z4D11813 Z33040 Rev 01 65 Data Analysis of peaks which define the multiplet Selecting any of the listed options will display the corresponding multiplicity in the data window In addition right clicking on the multiplet provides the opportunity to redefine the multi plet which means that the currently displayed multiplet will be deleted and the multiplet analysis mode will be entered in order to newly define the multiplicity 6 2 3 Assignment Moving the cursor line to any multiplet will highlight the atom s of the molecule assigned to this multiplet The same applies the other way around positioning the cursor at any atom of the displayed structure will highlight the connected multiplet Before any signal in the spectrum can be newly assigned the existing assignment has to be cleared This opt
48. ecular Structure 4 3 5 1 Clear Existing Assignment Right clicking on any atom of the molecular structure gives the opportunity to clear the 4 3 5 2 assignment for this atom Moving the Displayed Molecule 4 3 5 3 Left click hold anywhere close to the molecule except on any highlighted atom and drag the structure to the desired position Changing Display Options Right clicking on any atom of the structure or anywhere close to the molecule offers the possibility to show or hide chemical shifts atom numbers and multiplicities for each assigned atom together with the molecule Z4D11813 Z33040 Rev 01 45 CMC assist Interface Furthermore right clicking anywhere close to the molecule except on any highlighted atom opens a window that allows changing the size of the structure and in addition enables resetting of all modifications made aliz TERES OT EN ener 1OETTEF o rd at ee mu o Comsteney OK KO 310501 D 3105 CDCIS od 5 032 ppa 213 40 Wz i tren 4 3 6 Increasing Horizontal Scaling Shift left click hold always enables increasing the horizontal scaling zoom in Besides only left click hold also allows increasing the horizontal scaling zoom in if the cursor is positioned below the baseline or above any multiplet 46 Z4D11813 Z33040 Rev 01 5 1 Data Processing The software package CMC assist is designed to view process and analyse
49. ed signal has to be entered as well as the exact concentration of the reference substance all the given information will be saved in a file called eretic In order to calculate the concentration of the compound of interest this reference has to be specified for the respective dataset via the submenu Browse for Reference accessi ble by the down arrow on the right side of the tab Quantification Please note that the required path of the reference spectrum has to consist of all levels including procno A I IU x An Eretic file is needed for the quantification of this spectrum Please specify the Eretic reference file you want to use Reference file C Bruker CMCA data Chemical_Synthesis nmrsobutylphenylp Cancel For quantification of the investigated compound right click on the desired integral s on which the concentration determination should be based select Properties and tick the box for Calculate concentration by this integral The calculated concentration will be dis played in green numbers above the selected integral s EE EE NN Ja J kije e aR ma TT cn In DUST maer 5 a i m AE Ly J JUI Analysis of Complex Multiplets Besides the multiplet analysis mode accessible via the toolbar icon T Define new mul tiplets another multiplet tool is offered that allows creation of multiplets for more com plex coupling systems Clicking on the tab N Multiplets starts this multiplet tool
50. ellaneous file Required parameters Name f Data directory C Bruker CMCA data Open_Acces Specify the Required parameters note that question mark can be used for any single character and asterix for any character and any number of characters Select dataset entries for deletion from the pop up dialog showing the matching datasets x Data directory C Bruker CMCA data Open_Access nmr Options Delete the selected PROCNOs Delete the processed data files of the selected PROCNOs OK Cancel Help 24 Z4D11813 Z33040 Rev 01 Data Handling 3 4 Data Menubar 3 4 1 File In order to open a new dataset in the data window click on the tab wy File and browse for the desired dataset the new dataset will replace the currently displayed dataset 3 4 2 Open Batch Apart from single spectra a whole collection of spectra can be displayed and analysed Opening a batch of spectra requires a serial processing list that can be generated by the command serial see Chapter 5 4 Furthermore this feature is intended for manual inspection of automatically analysed batches of datasets for batch analysis see Chapter 6 1 To show the batch data click the tab HH Open Batch and browse for the appropri ate serial processing list Besides the standard CMC assist interface two additional win dows will appear One window lists all molecules with the availab
51. ening_Compounds nmr BY AA mk compound 42 1 1 C Bruken CMCA data Screening Compounds nmr Display Display In New Window Display As 2D Projection Z930 Z030 zg30 wetdc wetdc Sort This Column Sort Reverse Show Details Save selection in file Add selection to dataset group File Properties Eiles In order to save these search results as a serial processing list all entries of the list have to be marked using Ctrita Right clicking on the marked list provides the Process Selected Datasets 2006 08 22 14 08 15 2006 08 22 16 19 33 2006 08 25 15 15 59 2008 05 31 01 44 25 2008 05 30 16 27 57 2008 05 30 20 57 57 opportunity Save Selection In File to save the selection in a text file 5 4 2 Executing Serial Commands If a serial processing list already exists clicking on the tab Define List enables browsing for the respective text file Enter the dataset list s filepath or browse Serial Processing Lists screening_C ompounds txt Browse OK Cancel Subsequently the serial processing command has to be entered via the tab Define Com mand and executed via the corresponding tab 56 Z4D11813 Z33040 Rev 01 Data Processing xi Please enter serial command em ftapk OK Cancel The defined serial command can consist of just a single command e g efp as well as several commands separated by semicolon
52. ing a collapsed folder Right click the folder and choose Fully Expand Selection e Collapsing an expanded folder Left click the button to the left of the folder Double click the folder Hit the left arrow key while the folder is highlighted 3 1 6 Open Data From the Browser e Left click hold a dataset and drag it into the data area the new dataset will replace the currently displayed dataset e Right click on a dataset and choose Display from the pop up menu the new dataset will replace the currently displayed dataset e Right click on a dataset and select Display in New Window from the appearing dialog the dataset will be opened in a new data window In order to load multiple spectra hold the Ctrl key and left click on the desired datasets to select them or hold the Shift key and left click two datasets to select these two and Z4D11813 Z33040 Rev 01 21 Data Handling all in between Executing any of the options described above will open a new dialog that offers three different ways of presenting the selected multiple datasets Display Options 3 datasets were selected for display Please choose from the following options Display each dataset in its own window a a Open a new window and show the vAN datasets in layered multiple display mode a a Add the datasets to the active window VA in layered multiple display mode 3 2 Saving Data In principle all modifications of
53. ion can be selected from the dialog available by right clicking on the multiplet or the atom Subsequently there are two different ways to connect a signal in the spectrum with the corresponding atom s of the molecular structure Left click hold on any atom of the molecule and move the mouse to the respective multiplet will assign this atom to the selected multiplet Left click hold on any multiplet and move the mouse to the appropriate atom of the displayed structure will assign the selected multiplet with this atom 6 3 Manual Spectra Analysis 6 3 1 Integration To define new integrals click the corresponding toolbar icon The integration mode is active when the icon is highlighted in yellow and the cursor line turns red e Define integral Left click hold and move the mouse e Exit integration mode Left click the yellow highlighted button J Right click in the data window and select End Integral Definition After integration it might be necessary to adjust the integrals and proton numbers Right clicking on the integration region provides several options Calibrate Current Integral enable calibration of the selected integral Cut Current Integral cut the integral according to the cursor position Properties allow editing of several properties like definition of the status sub stance mixture or impurity and the appropriate proton number for the selected integral Furthermore an annotation can be made
54. itip EME asSiS Is EE n SE EE DEE EO EG OR EE EE 9 2 2 1 Under WING OW ER EO OE EN N EE N OE venice 9 2 2 2 2 are E oe AA EES EE EE ER ER EE ae ee 10 2 3 Displaying DEE ii AE SE EDE Re EE Ed Re Ee Er ee ee 10 2 3 1 Open Data from the Me nu cccccceeccceeccceeeeeeeeeceeeeseeeeeeceseeeesseeeseeeesseeesaeeees 10 2 3 2 Open Data from the BrowSel ccccccccceecceeececeececeeeeseeeeseeeeseeeeseessegeeseneeseeeees 11 2 3 3 Expand a Spectral Region see see ee EE ee ee ee EE ee ee ee ee ee Ee ee ee ee ee ee ee ee ee 12 2 3 4 Show Peaks Integrals Multiplet Labels tC ee see see Ee ee EE ee Ee ee ee ee ee ee ee 13 2 3 5 Print or Export Contents of a Data WIiNdOW ee ees ee ee ee Ee ee ee ee ee EE 14 2 4 Automated Analysis of Spectra ee ee ee Ee ee Ee ee Re ee Re ee Ee ee ee ee ee ee 15 3 Data Haidee sedes ERG N EE Ge GEE RE VR Ee EG RE RE Ee Ge 17 3 1 CMC assist BrOWSET ii essens ese EN oe kk N ee Ed ke be ks RR en Ee ER Se BR ee ke Be eie sant 17 3 1 1 The Browser ab ad EE EE RE Ee eee eee ee ae 17 3 1 2 Tel sd Tab ee ER EE RR ee Re ee nn EE epee RE De EE Ee ES EE 19 3 1 3 The Groups ME or EE EE EE EE EO i 20 3 1 4 Put FOCUS in the BIOWS GP see Asteke ee ee Se ie AE DE EE 21 3 1 5 Expand Collapse a Folder in the BrowSel ccccsscccesceceececeececeeceeseeeseeeesseees 21 3 1 6 Open Data From the Browser ccccccccsececeececaeeeceeeeeaeeeseeeeseeeeseeeeseeeeseeeseeeeas 21 3 2 SING
55. le information from the automatic analy sis like concentration consistency status water content etc The content of this table can be exported H to spreadsheet format csv xls and document format pdf html or printed 8 PB batch C Oruker CMCA Serial_ Processing Lists Screening Compounds txt de Cc a sil SUS Structure used lt 26 ds Caza 29241644 yes T052776_COS 1 1 10 7 49 3H 1 950 27 fy CO Cy 4gN 0 5Cl 268 71936 yes 1052842 DOS 1 1 6 0 15 90 2H 7 978 2 TE CyHy7NO 207 26888 yes ST052851_F05_1_1 60 11 23 1H 6 580 i 29 pes Czas 304 36899 yes ST052887_FO5_1_1 60 150 1H 7115 The second window represents a 96 well plate graphically displaying the determined concentration and structural consistency dark blue means consistent and light blue stands for inconsistent Moreover it offers the option to additionally show the values of the concentration and to size the displayed balls proportional to this concentration If the bars for the expected concentration and its expected deviation are adjusted samples within this concentration range have a white background whereas the ones outside this range are highlighted in grey hd x ZAD11813 Z33040 Rev 01 26 Data Handling amp Batch C Bruker CMCA Serial Processing Lists Expected conc mmol _ 1000 Expected range 50 00 l Concentration values M
56. low the baseline opens the integration menu whereas right clicking above the baseline enters the multiplet menu Right clicking below the baseline opens a pop up window with the following choices Calibrate Current Integral enable calibration of the selected integral Cut Current Integral cut the integral exactly at the corresponding cursor position Properties allow editing of several properties like definition of the status sub stance mixture or impurity and the appropriate proton number for the selected integral Furthermore an annotation can be made and the concentration can be calculated based on this integral Delete delete the selected integral Protons list proton numbers in order to set a new proton content for the selected integral Signal Type another way to define the status of the selected integral as substance mixture or impurity New Multiplet single multiplet definition as mentioned above New Integral single integration as described above 42 Z4D11813 Z33040 Rev 01 CMC assist Interface 1E NE Ciim OME A dato ern Anew er ET lT A lj mu aR 3 J5 KO TEF P LAL pom TDs He ful tiple E Multiplicity a Z F Ms 4 029 ppe asiguri to miram I7 H gol o 1 Li MA A N Th 2 ma me pam EER L 1 10 22 Protons 3 7 T F e T 7 i 1 T r Spa Type a 3 T r 4 aa TE Ta Mew Bugil io ES Ipem 4 3 3 Multiple
57. matic phase correction of zero order according to the calculated value d Button Functionalities 9 Perform 90 zero order phase correction ph90 90 Perform 90 zero oder phase correction phm90 180 Perform 180 zero order phase correction ph180 R Reset zero and first order phase values phr Increase double mouse sensitivity inc t Decrease halve mouse sensitivity dec Z4D11813 Z33040 Rev 01 49 Data Processing I Reset mouse sensitivity Execute phase correction save current phase correction values and leave the phase correction mode 4 Return and discard any changes 5 2 3 Baseline Correction For the baseline correction all available options manual and automatic are listed in the submenu whereas the tab A Baseline itself executes an automatic baseline correction using polynomial degree absn 5 2 3 1 Automatic Baseline Correction kary OM apai lbs i F fhail EFS ale sd J Dats Process Analyse Repot She Yew O j P process Specs OF Phage Baseline Colb Ads Serial Zant Gen 8 Haai T di AA Manus correction age Daal be wad San i LE Sa A ETE d 1 LR aa Oe M Range FUTZ Bee EE add sa dr EP EIE l Afr Marmas Aires abad rj gi Wo UU A NL H i E fil f f Li UL Automatic Using Polynomial of Degree ABSG abs n perform automatic baseline correction using a polynomial function of degree ABSG Like abs Only In Range
58. n the dataset In addition the field Number of suppression frequencies has to be edited and must match with the number of entries in the frequency list NMR Parameter O1P Choose this option for on resonant solvent suppression By definition this type of sup pressed spectra possesses only one suppression frequency whose frequency corre sponds to the NMR parameter O1P e Custom In the unlikely case that none of the above mentioned variations of suppressed spectra matches the type of acquired data number and position of the suppression frequencies can be specified individually Z4D11813 Z33040 Rev 01 61 Data Analysis e Remove region around solvent The range in Hertz Hz defined in this field is completely ignored for spectra analysis Typically it covers the suppression frequency itself including the nearby suppression artefacts Please note that a setting of 60 HZ means a region of 30 Hz around the sup pression frequency Besides each suppression frequency requires one entry where the left entry in the dialog is related to the suppression frequency with the lower ppm value Inner region around solvent This region refers to the area close to the suppression frequency that is still signifi cantly influenced by the suppression Peaks within this specified range are taken into account for the analysis however their multiplicity and proton number is not inter preted Outer region around solvent
59. ncy status statements concerning the result summary or result details can be edited All the entered information will be taken over and marked as manually modified if creating a short or full report for this dataset 4 3 CMC assist Data Window It is also possible to analyse a spectrum just using the mouse button functionalities Depending on the position of the cursor within the data window different actions are exe cutable 4 3 1 Basic Functionalities When the cursor line resides next to any integral or multiplet without any highlighted region right clicking offers the following basic functionalities New Multiplet activates the button Define new multiplet multiplet analysis as men tioned above and automatically exits the mode after defining one multiplet Z4D11813 Z33040 Rev 01 41 CMC assist Interface New Integral enters the integration mode integration as described for the button Define new integrals and automatically quits the mode after a single integration Toggle Concentration switches between displaying and hiding the calculated con centration 4 3 2 Integration If the signals of the spectrum have been analysed with respect to integral and multiplic ity the functionalities available via the mouse buttons depend on the position of the cur sor within the data window When the cursor line highlights a multiplet integration region right clicking with the cursor be
60. nded to accept the default path for the flexLM installation for Windows C flexim and for Linux usr local flexim Any user defined path may cause problems with other applications accessing the FlexLM Startup CMC assist 2 2 1 Under Windows e Start CMC assist using the icon on the desktop Double click the CMC assist icon on the desktop Z4D11813 Z33040 Rev 01 Getting Started e Start CMC assist from a Command Prompt Click Start select Run and enter cmd enter cd cmcahome in the Command Prompt enter cmca in the Command Prompt 2 2 2 Under Linux Open a Linux Shell or Terminal Window enter cd lt cmcahome in the Shell enter cmca in the Shell 2 3 Displaying Spectra With the CMC assist nmr data can be located in any arbitrary directory like in the follow ing formats lt dir gt data lt user gt nmr lt dataset name gt lt expno gt pdata lt procno gt e g C Bruker CMCa data guest nmr quinine 1 pdata 1 or lt dir gt lt name gt lt expno gt pdata lt procno gt e g C nmrdata sucrose 10 pdata 1 2 3 1 Open Data from the Menu The file menu is accessible via the button Ej Select Open and just leave the predefined settings options open NMR data stored in standard Bruker format required parame ters browser type file chooser in the appearing dialog xi rOptions Open NMR data stored in standard Bruker format C Open NMR
61. ndicates that the multiplet analysis mode is active and the cursor line becomes dashed e Define multiplet Left click on the peaks which belong to one multiplet Right click in the data window and choose Finish Multiplet Definition Depending on the number of peaks which define the multiplet a dialog appears that lists all possible multiplet configurations Selecting any of the listed options will Z4D11813 Z33040 Rev 01 39 CMC assist Interface display the corresponding multiplicity in the data window If none of the suggested multiplet configurations is appropriate it still leaves the possibility to tick Report multiplet type as m which results in reporting no multiplicity and no coupling con stant In addition the labeling of the multiplet can be changed iden 10511 1 1 ilo OPA lets ope Anessa ner pile TEL sen ew ji Sen KO MOEITE BERK LDLT 1 1491 ppa DOT He k Fi eas Soo be Pour 293 285 HE Pop 245 NEG he enter labeing of meester Right clicking in the data window after peak picking gives also the opportunity to delete all the peaks by choosing Cancel e Exit multiplet analysis Left click the yellow highlighted button 4 2 2 4 Show Display Options i This toolbar icon opens a window that enables setting of the display options xl Molecule I Atom numbers I Multiplet shift I Multiplicity Scaling ET Concentration M Sho
62. ng another alternate algorithm 5 2 2 2 Manual Phase Correction Besides clicking the e Phase tab entering ph on the command line also switches to the phase correction mode and replaces the standard CMC assist toolbar by the toolbar specific for interactive phase correction The yellow button indicates that the phase correction mode is active 48 Z4D11813 Z33040 Rev 01 Data Processing a 1D Interactive Phase Correction Left click hold the button and move the mouse until the reference peak is in pure absorption mode Left click hold the button 1 and move the mouse until the entire spectrum is in pure absorption mode Left click the button H to save the corrected phase and return to the standard CMC assist toolbar SE Li ALO 1R AREA R A pivot 1 1 pa Fhar income 0 30 phd 0 00 p li 0 00 rel Ainahan an DAME LM ppa 2055 5071 Hs ex Looe Le Talus D 0035TL rel 1s Bet Pret Pol Cal ulaie DER 0 5 EE Jul HH b Setting the Phase Pivot Point By default the pivot point is set to the peak with the highest intensity of the displayed region of the spectrum recognizable by the red line In order to change the pivot point right click on the desired position and select Set Pivot Point from the pop up menu aa c Default Zero Order Phase Correction Right clicking in the data window opens a dialog with the option Calculate phO that exe cutes an auto
63. ngle commands a series of commands separated by semicolons can also be entered on the command line e g em ft apk If this series of commands will be used regularly it can be stored as a macro by right clicking in the command line and selecting Save As A Macro to edit this macro enter edmac lt macro name gt to execute it enter its name on the command line Command Line History 4 1 4 To open a command history control window right click in the command line and choose Command Line History or type cmdhist on the command line This history shows all commands that have been entered on the command line since CMC assist was started After marking one or several commands the following functions can be applied Execute execute the selected command s Append append the first selected command to the command line Save Macro the selected command s are stored as macro to edit this macro enter edmac lt macro name gt to execute it enter its name on the command line a Command History cmdhist Execute Append Save Macro Cancel Data Window The CMC assist data window consists of data field title bar and toolbar Besides the name of the dataset currently displayed in the data field the entire data path of the spec trum is written in the title bar 36 Z4D11813 Z33040 Rev 01 CMC assist Interface 4 1 4 1 ah a m ETE o ba kg a 1 t F F T T T T T T T
64. orld class market leading range of analytical solutions for your molecular and material research needs Our solution oriented approach enables us to work closely with you to identify your specific needs and determine the best solution package for you from our comprehensive range Furthermore we offer you the opportunity to collaborate with us on new de velopments Our ongoing efforts and substantial investment in research and develooment demonstrate our long term commitment to tech nological innovation on behalf of our customers With 50 years of experience in meeting the needs of the scientific community across a range of specialist disciplines Bruker has built a sound rapport with professionals from the community through under Standing specific requirements This cooperative relationship with our customers allows us to provide them with effective solutions and a service of un matched quality Bruker Corporation info bruker com www bruker com Bruker Corporation Z33040
65. ormation on the suppression frequencies can be edited in another dia log that will pop up when clicking the tab Edit on the right side of the field Suppression Frequency e Unsuppressed CMC q Edit Suppression Frequencies Suppression Frequencies Location Unsuppressed Suppression Frequency File C NMR Parameter O1P C Custom Edit Suppression Frequencies Filename for suppression frequencies solvents 11 list Number of suppression frequencies 24 Suppression frequency ppm Remove region around solvent Hz s8 8 Inner region around solvent Hz 41604 1604 Outer region around solvent H 4004 40044 Reset All Entries Save Cancel In the case the data were acquired unsuppressed just select this option and no further specification is required e Suppression Frequency File Suppressed spectra can be acquired in various ways depending on the number and position of the solvent signal Consequently the information about the suppression fre quencies can be stored in different parameters or files If several solvent signals have to be suppressed or the suppression frequency is off resonant all the information about number and position of the suppression frequencies is typically stored in a frequency file In this case the filename has to be specified in the lower part of the dialog this file should be automatically generated during acquisition and located at the level of the expno withi
66. p Quit or Quit respectively Calibrate Axis Clicking the tab A Calib Axis or entering cal on the command line replaces the stan dard CMC assist toolbar by the toolbar of the calibration mode This calibration mode enables manual definition of the reference frequency A The yellow button indicates that the calibration mode is active Z4D11813 Z33040 Rev 01 53 Data Processing 5 3 1 Calibrate to the Center of the Spectrum 5 3 2 On the one hand the reference frequency can be changed by redefining the frequency of the center of the spectrum Clicking on the button opens a dialog where the new frequency for the center of the spectrum can be entered x spectrum calibration frequency Calibration frequency for center of spectrum ppm SES OK Cancel Redefining the Reference Frequency 9 3 3 On the other hand the reference frequency can be modified by positioning the red cur sor line at the desired peak left clicking at that position and entering the new frequency of this peak in the upcoming dialog x spectrum calibration frequency Cursor frequency ppm 4 4807 OK Cancel In both cases the spectrum will be calibrated and the calibration mode will be closed automatically Set Reference Substance to 0 ppm 5 4 If the acquired spectrum includes a signal originated from a reference substance e g TMS clicking on the down arrow on the right side of the
67. pes for saving of the dis played data window e g pdf png or jpg file O Das Process Analyse Repoti Since Wew Shot Repet Ful Repert Palani string Print Copy wa Fe OD Hd o An ie mak phe teal ma gt LE Sst A Deseret gmt Gotu ETE TR LIne N harem year kaas nm am PIE Duits a alie FE crema Sytem da TE Me mn Ed EER N D 4 gim Coulee np eons a L Sve oe PHG lta Diret eat alglsd m Pra Gurari regn fave mm POT irai foe pa d Hd RAL i d Oar me 7 5 Copy The selected spectrum can also be copied to the clipboard by clicking on the tab Copy and pasted into a word processor or a presenter program Z4D11813 Z33040 Rev 01 dd Reporting 78 Z4D11813 Z33040 Rev 01 8 Contact Manufacturer Bruker BioSpin AG Industriestrasse 26 CH 8117 Fallanden Switzerland Phone 49 44 825 9111 http www bruker biospin com NMR Hotlines Contact our NMR service centers Bruker BioSpin NMR provide dedicated hotlines and service centers so that our special ists can respond as quickly as possible to all your service requests applications ques tions software or technical needs Please select the NMR service center or hotline you wish to contact from our list avail able at http www bruker biospin com hotlines_nmr html Z4D11813 Z33040 Rev 01 79 80 Z4D11813 Z33040 Rev 01 Bruker your solution partner Bruker provides a w
68. pretation are combined in the Analyse menu Automatic Spectra Analysis 6 1 1 The CMC assist offers an automatic analysis of 1D 1H NMR spectra with respect to inte gration regions proton numbers multiplet interpretation assignment concentration determination and structure consistency check Automatic Analysis of Single Spectra 6 1 1 1 Clicking on the tab Analyse Spectrum starts this automated interpretation of the currently displayed spectrum In the case the data have also been acquired in automation using the software package CMC q available under TopSpin or the feature Fast Lane NMR integrated within Icon NMR all information needed for the automated analysis already exists within the data set Thus clicking the tab Analyse Spectrum directly interprets the current dataset Analysis Settings Pcie 14 69 Analysis Mode Single Analysis C Batch Analysis C Bruker CMCA Serial_Processing_Lists Screening Compounds xt Browse Expert Analysis Expert Analysis M Expert Analysis Details Calibration File Directory Browse Known Impurities Edit Suppression Frequency unsuppressed Edit Eretic Signal in Spectrum T E 0 ppm 13C Decoupling Vv Import Expert Settings Current Dataset Browse Batch Control Current Dataset Hold Abort all current Batch Start Analysis Save Cancel Z4D11813 Z33040 Rev 01 59 Data Analysis In the case the d
69. rrent data window Display In New Window display dataset in new data window Scroll to Active Dataset scroll to procno of active data window Fully Expand Selection fully expand selected data directory Show PULPROG Title switch pulse program title display on off Show Date show acq date expno or last mod date name Sort by Date sort data by last modified date Copy copy dataset to clipboard File Properties show dataset properties Delete delete selected entry name expno or procno Rename rename dataset name expno or procno Files list files in selected entry expno or procno Add New Data Dir add new top level data directory Remove Selected Data Dir remove selected top level data directory Browser Preferences set display options Z4D11813 Z33040 Rev 01 Data Handling 3 1 2 The Last50 Tab Clicking the Last50 tab will list the last 50 displayed datasets Every time a new dataset is opened it is automatically added to this list In order to reopen any of these datasets in the current window double click on a dataset or hit the Enter key after highlighting a dataset by left clicking on it Right clicking on any list entry opens a dialog that enables modification of the list load ing of spectra or getting additional information on the dataset amp Bruker CMC assist 1 0 b 12 build 1791 d Data _ Process Analyse Report Structure e
70. rresponding entry accessible via the tab Spectrum menu View alah Fe_250611 ref MAAT ppa 3160 4675 He e Click the button Ta Show display options in the CMC assist toolbar xi Molecule l Atom numbers I Multiplet shift F Multiplicity Scaling se ET Concentration MF Show concentration Default offset for molecule in new data sets O lt x y lt 1 oos EET OK Cancel Please note that the selected information can only be shown in the spectrum if avail able For example molecule and concentration can only be displayed if an appropriate structure file exists and the concentration has been determined respectively Z4D11813 Z33040 Rev 01 13 Getting Started 2 3 5 Print or Export Conte nts of a Data Window The displayed content of the active data window can be printed as follows Use the shortcut Ctrl p e Choose the Print option in the file menu Genera Name Print R Print Service Status Info Page Setup Appearance Microsoft XPS Document Writer Properties Accepting jobs Type I Print To Eile ange rCopies All Number of copies h C Pages fi To fi F Collate Cancel e Selecting the Print option in the Report menu allows modification of the print settings H Spectra Printing Preferences Spectrum colors Fonts Spectrum extras Title Parameters Axis
71. seneeaeenseeaneeas 50 5 3 Calibrate FASE N EE a a a aaee ee EG ane teen nage 53 5 3 1 Calibrate to the Center of the SpectFUM ees ee ee see ee EE ee EE ee EE ee ee ee ee ee ee ee 54 5 3 2 Redefining the Reference Frequency cccccccseececeeeeeeeeeeaeeeeeeeeeseeeeseeesseeeeseneens 54 Z4D11813 Z33040 Rev 01 5 3 3 Set Reference Substance to 0 ppm eie ee ee EE RR ee Ee Ee ee Ee ee ee ee ee 54 5 4 os PR N N OE scan E ncaa oan A N 54 5 4 1 Generating a Serial Processing List sk RA Re Re ee ee ee ee ee ee ee ee 54 5 4 2 Executing Serial COMMAMNAS ccccccccsseeccceeeecceeeeecsaeeecseucessuseeecseeeessueeesseeeeess 56 5 9 Viewing be ve ii OE OE EO EE R aa N N of 6 BELET GEE OE EO OE OE OE NE 59 6 1 Automatic Spectra AnalySIS cccccccccesceceseeceeeeceseeceeeeseseeseseesesseesseeseneesnseseas 59 6 1 1 Automatic Analysis of Single Spectra sesse Ee ee Ee ee Re ee ee ee ee ee ee ee 59 6 1 1 1 Analysis eu eN EE IE EE RE 59 6 1 2 Automatic Analysis of Batch Spectra ie see ee ee ee ee ee ee ee ee ee ee 63 6 2 Modifying Results from Automated Analysis ees ses se ee ee RR Ee ee ee ee ee ee ee ee 64 6 2 1 WAL GOI CNS RR EE OE OE N OR OO ER RE 64 6 2 2 VA ie E EE Ee A RE EE AE ON EN 65 6 2 3 ale id n RE EE N RE OE N 66 6 3 Manual Spectra AnalysiS iss see se ee EE ee EE Re EE ee Re EE ee Ee Re EE Re EE ee ER Re EE ee EE Re Ee Re ee 66 6 3 1 MARS GAUL OMN VEE N N EE OE EE OE
72. sist providing an easy way to process and analyse acquired NMR data In order to facilitate navigation through the manual the chapters are arranged according to a typical workflow e Chapter 2 shortly describes the installation of the software package and the first steps to display and analyse a spectrum e Chapter 3 addresses the handling of NMR data This covers the different options of the Data menu as well as managing the data within the CMC assist browser including loading new data saving or deleting data e Chapter 4 explains all functionalities associated with the CMC assist interface This comprises the toolbar icons the command line and the data window with its specific toolbar e Chapter 5 deals with processing of NMR data In addition to manually processing sin gle datasets the corresponding menu gives the opportunity to process single spectra or a batch of spectra in automation e Chapter 6 describes all available functionalities regarding the analysis of NMR data Besides carrying out a manual interpretation of the spectra complete analysis of the spectra including integration multiplet analysis concentration determination and structural consistency check can be performed automatically Chapter 7 lists several possibilities to document the gained results such as generating reports printing data or exporting assignments in patent string format Font Conventions e Commands that can be entered on the command
73. software to load new NMR data to display a spectrum to print spectra and to analyse a spectrum in automation For more detailed information please refer to the following chapters Installation 2 2 The software package CMC assist is provided together with Bruker s software TopSpin The installation always covers both programs it is not possible to install these software packages separately However each program requires its own license After successful installation two icons will appear on the desktop Topspin amp CMC assist Top Spin and respectively CMC assist can be started by double clicking the corresponding icon This section briefly describes the installation of CMC assist For more detailed informa tion please read the instruction available on the installation DVD Log in as Local Administrator Close all windows on the desktop Insert the DVD Start of installation If the automatic start of the DVD is enabled a window will automatically appear If this window does not appear automatically autorun is probably switched off Open the Window Explorer select the DVD device and double click install cmd The appearing window will guide through the installation The only decision that has to be made during the setup is the destination directory for CMC assist and Top Spin respectively After successful installation the computer should be restarted Please note that it is strongly recomme
74. ssion frequencies any known impurities that should be excluded from the analysis possible 13 decoupled existence of an eretic signal includ ing its position and for quantification purposes the path to the required calibration file lol x OK HY Analysis Mode Single Analysis Batch Analysis c Bruker CMCA Serial_Processing_Lists Sc reening_Compounds txt Expert Analysis Expert Analysis M Expert Analysis Details Calibration File Directory Browse Known Impurities Edit Suppression Frequency unsuppressed Edit Eretic Signal in Spectrum T ET ppm 13C Decoupling Iv Import Expert Settings Current Dataset Browse Batch Control Current Dataset Hold Abort all Current Batch Start Analysis Save Cancel The result of the automated spectrum analysis will be displayed within the data window The status of the consistency check will be written next to the CMC assist toolbar and color coded according to the gained result green meaning spectrum and structure are in good agreement whereas red indicates mismatches between the structure and the spectrum In the case the molecular structure coincides with the spectrum the software provides an interpretation of each peak including integration proton number multiplicity and assignment Besides the assignment all the available information is readily displayed together with the spectrum In order to visualize the assignmen
75. t move the cursor line on the desired peak and the corresponding atom will be highlighted in yellow within the molecular structure Z4D11813 Z33040 Rev 01 15 Getting Started leoes GEFI ppa DTT Hr Peak Chusece jadimedj Bibeeance praan integral Lol assigned to anma LU 16 Z4D11813 Z33040 Rev 01 3 3 1 Data Handling The following chapter addresses the handling of NMR data This covers the different options of the Dafa menu as well as managing the data within the CMC assist browser like loading new data saving or deleting data CMC assist Browser 3 1 1 The browser appears at the left of the CMC assist window and can be shown or hidden with Ctrl d or by clicking the arrow buttons at the upper right of the browser Its dialog offers the following tabs e Browser data browser displaying the data directory hierarchy e Last50 list of the 50 last open datasets e Groups list of user defined groups of datasets PM Bruker CMC assist 1 0 b 12 build 1791 3 Data y Process Analyse Report Structure R 2 lt a CD phn Mo k 32 T H OS an OOP wah RY EE Browser Lastso Groups a Chemical Synthesis RE Ajmaiicin BI alpha_Satonin BS Isobutylphenylpropionicacid EH 1 z930 Isobutylphenylpropionicacid in DMSO HI Open Access BE AB 070311 EMO FH_250611 B 3 2930 FH_250611 CDC amp 4 FH_250611 CDCI HKO 310511 HE Sc_020111 RED XY_
76. t Analysis In the case that integral and multiplicity are defined for one signal the cursor line has to highlight a multiplet integration region and the cursor has to be positioned anywhere above the baseline in order to access the multiplet menu Otherwise right clicking underneath the baseline will open the integration menu Right clicking above the baseline makes the following functionalities available Multiplicity open a dialog that lists all possible multiplet configurations depending on the number of peaks which define the multiplet Selecting any of the listed options will display the corresponding multiplicity in the data window If none of the suggested multiplet configurations is appropriate it still leaves the possibility to tick Report multiplet type as m which results in reporting no multiplicity and no cou pling constant In addition the labeling of the multiplet can be changed Redefine Multiplet delete the current multiplet and enter the multiplet analysis mode to newly define this multiplet Properties allow editing of several properties like redefining the multiplicity and the assigned atoms for the selected multiplet Furthermore an annotation can be made and the label can be changed Delete delete the selected multiplet Clear Assignments clear the connection of the selected multiplet to any atom New Multiplet single multiplet definition as mentioned above New Integral single
77. t the top of the Last50 browser 3 1 3 The Groups Tab The Groups tab shows the list of user defined dataset groups Defining a group might be helpful if working on several projects where each project involves multiple datasets Cre ating groups is an easy way to organize projects and to access all data belonging to a certain project In addition several options exist to edit or modify these groups by right clicking on the respective dataset group Pf Bruker CMC assist 1 0 b 12 build 1791 3 Data Process Analyse Report Structure es n h 1 ops Hz D e th Be O kaw Tt me a i E z 1 A o gt OS snr QQA Ik aa LEE Browser Last50 Groups 5j Calibration References compound 42 1 1 wetdc compound_42 HDMSO Off resonance 2 544 3 compound_13 1 1 wetdc compound_13 HDMSO Off resonance 2 544 3 s3 Cooperation_University FH 2506113 1 zg30 FH_250611 CDCI3 KO_310511 3 1 zg30 KO_310511 CDCIS SC 0201113 1 zg30 SC_020111 CDCIS Isobutylphenylpropionicacid Display Display In New Window Display Group Add All Open Data Windows Update Window Bounds amp Display Limits Remove Selected Datasets From Group Collapse All Groups Toggle Dim Pulprog Title Add new Dataset Group Close All Group Windows Process Selected Datasets File Properties Files Copy Display Group display all dataset s belonging to this group in new d
78. tiple spectra in which each spectrum can be shifted and scaled individually allowing an exact alignment of corre sponding peaks in different spectra a Read Multiple Spectra One way to superimpose data in multiple display is to read one dataset switch to multi ple display mode and add other datasets Read a 1D dataset Click the AA button or type md on the command line The data window will switch to multiple display mode Add a dataset by Left click hold the dataset in the browser and drag it into the data window Right click the dataset in the browser and select Display from the pop up menu Enter re on the command line and specify the additional dataset in the appearing dialog box Another way to superimpose data in multiple display is to read multiple datasets simulta neously 32 Z4D11813 Z33040 Rev 01 CMC assist Interface Select multiple datasets by Hold down the Ctrl key and click the desired datasets Hold down the Shift key and click two datasets to select these two and all datas ets in between Right click any of the selected datasets and choose Display or Display In New Win dow from the pop up menu The appearing dialog provides the following options Display each dataset in its own data window Open a new data window and show the datasets in layered mode Add the datasets to the active data window in layered multiple display mode Displ
79. v Ctrl s amp Print active window print Ctrl p 8 Increase intensity by a factor of 8 8 2 Increase intensity by a factor of 2 2 8 Decrease intensity by a factor of 8 8 2 Decrease intensity by a factor of 2 2 ka Change intensity smoothly Reset intensity scale baseline position remains unchanged vr Ctrl Alt PgUp CU Zoom in out smoothly ppm Exact zoom via dialog zx MH H Reset zooming to full spectrum leave intensity scale hr Zoom in to the center of the displayed region increasing horizontal scaling zi Q Zoom out from the center of the displayed region decreasing horizontal scaling zo 5 Show last zoom z ra Show full spectrum reset intensity scale all Toggle interactive zoom method zoommode fill Retain expansion and scale when changing dataset keep Is Shift to left end of spectrum s 0 Shift to right end of spectrum sr0 Shift spectrum to the left half of the displayed region s Shift spectrum to the right half of the displayed region sr to Shift baseline up down while pressing left mouse button T Shift spectrum left right while pressing left mouse button T Shift baseline to center of displayed region su Alt UpArr IE Shift baseline to bottom of displayed region sd AltDwnArr 30 Z4D11813 Z33040 Rev 01 CMC assist Interface 4 1 2 1 E Toggle between Hertz and ppm axis units hz t Switch y axis labeling between abs rel off
80. w concentration Default offset for molecule in new data sets 0 lt x y lt 1 oos 010 OK Cancel 40 Z4D11813 Z33040 Rev 01 CMC assist Interface Besides changing the size and position of the molecular structure within the data win dow further additional information regarding the molecule can be selected that will be presented with the structure Please note that the information on multiplet shift and mul tiplicity is only available for previously assigned multiplet shifts and defined multiplicities The same applies for the concentration which can only be shown if determined either manual or in automation 4 2 2 5 Show and Edit Project Status Information Description and status of the current project can be modified or generated via the dialog that pops up when clicking on the corresponding toolbar icon es es Project Status Description F x Consistency OK by automatic analysis OK C NOT OK UNCLEAR Result Source Automatic analysis generated by Bruker CMC 3466 Manually edited by user Result Summary Automatic evaluation Spectrum and Structure are in agreement Result Details Automatic evaluation All elements of the structure could be assigned to regions in the spectrum and all major signals in the spectrum are assigned A quantification result is available Degradation observed Poor Solubility a OK Cancel In addition to the definition of the consiste
81. y 8 42 S DE OAD T a WS s2 3 QQ oh espe LE Browser Last50 Groups M Show Spectra Thumbnails Display Display In New Window Display As 2D Projection Show PULPROG Title Copy SC 020111 3 1 C Bruken CMCA j i ie AAR E File Properties Eiles Remove Selected items From List Open Saved Last50 List Remove Non Existing Datasets From List Browser Preferences Display display dataset in current data window Display In New Window display dataset in new data window Show PULPROG Title switch pulse program title display on off Copy copy dataset entry to clipboard File Properties show dataset properties Files list files in selected entry expno or procno Remove Selected Items From List remove selected dataset s from list Open Saved Last50 List open a dialog to select a Last50 list Save Last50 List As open a dialog for saving the current Last50 list Remove Non Existing Datasets From List remove entries with non existing data paths from the list Z4D11813 Z33040 Rev 01 19 Data Handling Browser Preferences set display options Each line of the Last50 list corresponds to one dataset including its path and name Apart from just presenting the data path for every entry of the list a thumbnail of the spectrum can be displayed in addition to each data path by ticking the box Show Spectra Thumbnails a

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