Introduction to ACD version 12 NMR Software

Transcription

1 ACD v12 guidebook 2011 pg 1 Introduction to ACD version 12 NMR Software The ACD NMR software provides a complete set of software tools for processing and visualisation of 1D and 2D NMR data, for spectrum prediction and for databasing of NMR spectra. Once installed the various program modules can be accessed through: Start => Programs => ACDLABS 12.0 There are numerous movie tutorials for each module with in ACD12 which can be accessed in the MOVIES menu. 1) Installing ACD labs version 12 a) Chemistry networked PCs The software can be found on the Chemistry server at: \\chem-ds5\nmrstore\nmr Software\ACD 12 If you are not using a CHEM domain login on your PC you may have to map this folder as a network drive to gain access. To install the software use the setup.exe application and the process will begin. When the license server window appears, enter chem-ds5 as the server Address and Port 7200, as below. NOTE: The port number must be as below and is different from that used for ACD 11 (7199)! When this is complete you should copy the DMILLIB.DLL patch from the ACD 12 folder and place this in the C:\Program Files\ACD12 folder on your local PC (replacing the existing copy) [This patch is necessary for the on-line prediction tools (I-Lab) to operate correctly]. The on-line prediction tools (accessed within ChemSketch drawing program that is installed as part of the ACD suite) requires the following options to be configured for access to the server (if you have an older ACD installation this information may already be shown correctly): Under I-Lab -> Options enter the server URL address as below:

2 ACD v12 guidebook 2011 pg 2 Tick the Server authentication box and enter the User ID and Password that gives you access to the Chemical Data Service at Daresbury. Individual user IDs and passwords can be obtained by completing the simple registration form at: This requires you to have a valid Oxford University address. b) Laptop A free to use (academic) version of the 1D and 2D NMR processing software can be installed from the ACD website, and is now recommended for use on laptops away from the department: This requires you to register on-line with ACD before use. This may be installed in parallel with the networked version if desired, in which case a separate folder name (eg ACD12-Laptop) must be defined for this installation. The free academic version is for processing only and will do give access to any of the data basing facilities described below. When installation is complete you should copy the DMILLIB.DLL patch from the Chem-ds5 ACD_12 folder and place this in the C:\Program Files\ACD12-Laptop folder (or as defined for the installation) on your local PC (replacing the existing copy). [This patch is necessary for the on-line prediction tools (I-Lab) to operate correctly] The on-line prediction tools (accessed within ChemSketch drawing program that is installed as part of the ACD suite) requires the following options to be configured for access to the server (if you have an older ACD installation this information may already be shown correctly): Under I-Lab -> Options enter the server URL address as in the figure above. Tick the Server authentication box and enter the User ID and Password that gives you access to the Chemical Data Service at Daresbury. Individual user IDs and passwords can be obtained by completing the simple registration form at: This requires you to have a valid Oxford University address.

3 ACD v12 guidebook 2011 pg 3 2) Chemsketch module: Drawing molecules Select ChemSketch to draw your molecule in the same way you would using ChemDraw use the various template Options (e.g. template window, periodic table, dictionary, table of radicals etc) available to you. You may also import Chemdraw (or other formats) using the File => Import option. 3) NMR Spectrum Prediction Using The Prediction module makes use of the ACD ilab predictors at the Chemical Database Service (Daresbury) and in run from Chemsketch. Once in Chemsketch, under the Session tab in I-Lab => Options you may like to select the Login at Startup option so that you automatically connect to the prediction server every time ChemSketch is started. When you connect to the server you should see the following welcome screen, after which you can start predictions. You can select NMR, Naming or Phys-Chem options. In NMR you can predict 1 H, 13 C, 31 P, 19 F or 15 N spectral predictions as well as investigating whether your or similar compound(s) are represented in ACD s databases Prediction allows you to see a computed spectrum, based on proven assignments from the same or similar compounds taken from over 150,000 compounds in the literature. 13 C is particularly powerful and tends to be most reliable and accurate.

4 ACD v12 guidebook 2011 pg 4 The phys-chem options also allow you pka, solubility, logp etc predictions 4) NMR Data Processing First step: Copy & Paste an NMR data folder onto your local computer from one of the NMR data servers or from the spectrometer. The easiest route to interacting with your NMR data is to import the processed NMR data (spectrum) file generated by the spectrometer. For Bruker data the processed data files are called: 1r- for a 1D spectrum and 2rr- for a 2D spectrum. These are found in the pdata/1 folders associated with each NMR data set and once imported can be viewed directly in ACD. If these do not exist (the processed data may have been deleted to save disk space, for example, or are not usually supplied as with Varian data) it will be necessary to import the raw (unprocessed) NMR data and process this within ACD. For Bruker data, these files are found above the pdata folder level and will be called: fid- for a 1D data set and ser- for a 2D data set For Varian data, open the appropriate name.fid folder and select the fid file. Open 1D NMR Manager

5 ACD v12 guidebook 2011 pg 5 Go to File => Import an 1r/ 2rr spectrum (or fid/ser file) from the selected NMR data folder (make sure that file of type has (AutoDetect) flagged). Please note that ACD/NMR WorkBook appears on the left hand side. This functionality is recommended for more experienced users (see 8) and can be toggled off under the View menu. The easy way to process raw data is to opt for the Shortcut button (toggled on/off on the left of the Text Toolbar; see figure below) and your spectrum appears before your eyes; you can then save your spectrum in ACD format. The layout of the processor window is labelled below. Menus Icon Toolbar Text Toolbar (context sensitive) Window selector Module selector (context sensitive) At this point, you can attach a structure to your spectrum by clicking (on the Module Selector) Structure => Draw in ChemSketch or Attach from File, and select Attach structure to current spectrum in ChemSketch. The longer, more interactive way to spectral processing of the fid is: 1. Apply Zero Filling (double the size of original points count). 2. Apply Window Function (Using Exponential): i. For 1 H set LB = 0.3, for 13 C set LB = Fourier Transform the fid.

6 Spectrum interaction using the Text Toolbar options ACD v12 guidebook 2011 pg 6 ` Note - each operation can be saved with the tick or negated with the cross. Phase the spectrum Use Auto Simple for 1 H and Auto Symm for 13 C. Baseline Correct the spectrum Use Auto function. Integrate the spectrum Use Manual mode, to integrate each multiplet drag across the peak (cyan vertical lines mark each red integral, reference to number of protons using Reference on the toolbar). NB: the Show Integral Curves tab on the Icon Toolbar must be toggled on view traces). Peak Pick the spectrum Use Auto or use Peak Level where red cross hairs define peaks above horizontal. Peaks can be picked or un-picked by toggling Peak by Peak. NB: the Show Labels tab on the Icon Toolbar must be toggled on view traces). Referencing the spectrum Use Auto - most solvents e.g. CDCl 3 or C 6 D 6 etc are automatically recognised, if they are not selected properly use the option facility and choose the appropriate solvent. Annotation with the cursor you can annotate your spectra. Multiplets allows you to define coupling constants, only if they are first order, (Note, it cannot handle second order multiplets). Having carefully peak-picked only those peaks that comprise the multiplet of interest, and having integrated your spectrum in terms of whole numbers of protons, use option Auto. Your spectrum will be automatically subdivided into multiplets from right to left, M01, M02 M0N. Etc. Select J-Coupler and home in on a particular multiplet of interest and you will see calculated coupling constants. The Multiplet analysis box (see below) is flexible enough to allow you to pick/unpick peaks which are or are not part of a multiplet, it allows you to measure J-values manually and it also allows you to re-define the coupling pattern. Assignment Easiest way is by Multiplet. Point cursor from the proton of interest and to its corresponding multiplet, a link is automatically generated and the associated proton and multiplet are highlighted.

7 ACD v12 guidebook 2011 pg 7 5) Generate a Report Reports are used to output your spectra and generate ChemSketch files for printing, storage etc. Click Edit => Create Report selecting either Standard or Report By Template and choose appropriate options. If you want your own template report, you will need to create it in Chemsketch using the small Report Template icon on the bottom left hand side selecting appropriate boxes e.g. If you use Standard option, the report is produced instantly and you can tailor it to your needs. 6) 2-D NMR Processing First, it is recommended that you save the 1-D proton (and carbon) spectra to an ACD Spectrum file (*.esp) in your folder which you will subsequently use as a projection in F1 and/or F2 1D spectra. File - Import a Bruker ser file or Varian fid from 2-D Directory with File of Type (AutoDetect), and Full FT => OK gives the spectrum.

8 ACD v12 guidebook 2011 pg 8 In order to display your 1-D projections select Setup 1D Curves on the Text Toolbar. Select Horiz. and Spectrum and select your saved proton esp file (F2), then select Vert. and Spectrum and select a corresponding esp file (F1: 1 H, 13 C etc). You can scale the 1-D projections in the scale icon e.g. 300% both horizontally and vertically. Note, whilst in Setup 1D Curves, you can precisely align the 1-D projection peaks with their 2-D counterparts by using the crosshairs and left hand mouse button: drag from the 2D peak to the 1D peak position to align. Note that Page Up and Page Down on your keyboard allows you to change the contour levels (or use the mouse wheel). There are icons for block intensity plots or contour plots. The Option => Preferences pop-up window (above right) allows you to change contour colours, background and numbers of contours. Peak Picking is best done with Manual rather than Auto (which picks everthing!). You can use the Gridlines to help you accurately pick the cross peaks. When complete you can Clear them, as they only serve to define the peaks clearly. For heteronuclear spectra, both proton and carbon contours are conveniently labelled on the spectrum, a feature not so easily available in Topspin!

9 ACD v12 guidebook 2011 pg 9 2-D Assignment Once peaks are picked, assignment is simply done by placing the cursor on the cross peak and locating the two proton that are J-coupled or correlated to each other. 2D Phasing Many 2D experiments are phase-sensitive and as such have to be phased manually eg HSQC, NOESY, TOCSY (unless you can access the previously phased spectrum 2rr Bruker file from your folder). If the 2rr file is not present you need to import the ser file, transform and phase it. o File - Import a Bruker ser file from 2-D Directory with File of Type (AutoDetect), and Full FT, OK. It may look poorly phased as in the edited-hsqc example below:

10 ACD v12 guidebook 2011 pg 10 o Select Phase => Horiz. and place the cursor on a contour peak and horizontal crosshairs appear, click the left hand cursor and a horizontal row from the 2-D spectrum appears, use Add to select another contour from a different part of the spectrum. Use the Phase tabs Horizontal Ph0 (zero-order phase correction) and Ph1 (first-order phase correction) to perform the horizontal phasing in F2 and likewise use the tabs Vertical Ph0 and Ph1 to perform the vertical phasing in F1. o phase o Having phased the spectrum, you can perform baseline correction with a noise correction e.g.2. 7) ACD/NMR WorkBook This option is recommended for the more experienced and frequent user. It allows you to open several spectra simultaneously in one spectral folder e.g. 1 H, COSY, HSQC and 13 C. It is useful to view the demo movie: To initialise its use, you need to go to View and ensure ACD/NMR_WorkBook is ticked, then File => New NMR Project, where upon a new set of icons appears in the left hand corner.

11 ACD v12 guidebook 2011 pg 11 Select the icon entitled Add Raw Data from Folder (with the + sign) and tick the spectra you require processing. After a few seconds all the automatically processed spectra appear in tile mode on the screen. It is a good idea to turn on the NMR Sync icon, (6 th Workbook icon from the left) and the top right icon called Synchronise which allow you to align multiplets between spectra and to attach 1-D spectra to all your 2-D spectra. The first icon on the top right toggles between different horizontal and vertical tiles, the second one allows you to view one spectrum at a time. Some words of warning using ACD/NMR WorkBook: The edited-hsqc spectra may not be automatically phased correctly and will need manual phasing, there may also be extraneous 1-D spectra taken from 2-D rows that are used by Bruker automation (eg expt. numbers 998, 999 etc) which are inadvertently carried forward. You will need to deselect these when you open your files or close these down afterwards, File => Close. The synchronisation of spectra is not perfect and is often lost half-way through manipulation. The tiled views are often small and irritating. 8) Spectral User database The use of User databases (either Group or Personal) is an extremely powerful and useful tool, allowing you to archive your spectra with attached structures, assignments and coupling constants from which your results can also be automatically tabulated in various Journal formats. Its application is highly recommended.

12 ACD v12 guidebook 2011 pg 12 Generating a new database In ChemSketch go to ACD/Labs menu and open up Spectrum Database, give it a name ****.nd9, allow compression, give the new database a password, then open it. Inputting Spectra to a database Having opened your Spectrum Database, open your processed spectrum in the NMR Processor module from File => Open => From 1D NMR Directory or File => Import => From 1D NMR Directory. Click the icon at the top that looks like a thunder-bolt and the spectrum is immediately entered into the database. You can toggle between Processor and Database using the Module Selector tabs at the bottom of the screen, allowing new additions and changes to your spectrum to be updated in the Database. The Structure User Data if double clicked allows the input of any other data using New e.g X-ray, mass spectra, melting points, and you can also link the spectral data to other files on your computer, making it very versatile.

13 ACD v12 guidebook 2011 pg 13 Note If a structure already exists in a database, the user will be prompted to create a new record, replace the current record or add to the record during the update process. Remember to select the appropriate option when this occurs. When used routinely, the database can be searched for user, structure, name etc. and will become a very valuable archiving system for you and your group, since each spectrum always keeps an associated structure alongside it. Revised Sept 2011