Procedural Details for ACD NMR Spec Manager

Note Clicking on a Operation toolbar produces a new toolbar appears as a third row with two options, on the left. First a green check  mark to accept changes or a red X mark to reject changes before exiting the current mode. Using these options allows cycling through various options: Phase Correction, Base Line Correction, Arithmetic, Peak Picking, Integration, Reference, Annotation, and Multiplet. Each option has several sub-options.

Processing FID Spectra (for a spectra imported into SpecManager). Save time by complete all processing of the spectrum before spectrum analysis, i.e. label, integrate, etc.

1. Select the Icon to do a Fourier transform of the FID current data set or Apodization, an example.

2 The NMR manager has a very handy feature: Interactive Apodization. This mode allows interactively application of the following options: Fourier Transform and Phase Correction. This feature permits interactive and quick adjustment of the Window Functions and phase correction parameters for each spectrum.

After processing a file with VHelper then open/import a FID and click Apodization. Entering the Apodization mode for the first time produces a new toolbar. This command allows interactively: Fourier Transform and Phase Correction. This feature permits interactive and quick adjustment of the Window Functions and phase correction parameters for any spectrum.

3. The Power Spectrum or Magnitude Spectrum modes disable some of the processing options which produces beautiful spectra but is not normally used.

4. There are several ways to correct a spectrum for non-zero phase: Auto Phasing Simple, Auto Phasing by Baseline Optimization, Auto Phasing by Symmetrical Lines, and Manual Phasing, which allows use of a mouse to optimize phasing interactively. This mode allows adjusting any phase-correction using the mouse. Click on the Phase Correction toolbar or choose this command. Dragging with the left mouse button controls the first phase parameter (Ph0); dragging with the right mouse button changes the second phase parameter (Ph1) or enter a new value for Ph0 and/or Ph1 by degrees from the degree windows. Manual phase adjustment helps to fine-tune the phase-correction obtained using the automatic methods.

5. Zoom Control Enlarge the spectrum in the following ways: Using the Horizontal Zoom tool or Rectangular Zoom tool Both tools have the same principle of operation Click either of these buttons and drag over the spectral region to be enlarged. The spectrum display area is split into two areas. The top area displays the entire non- expanded spectrum with the shaded area denoting the enlarged region; the bottom area displays the enlarged view. To see details in different sections of the spectrum drag or resize the shaded area of the spectrum in the top area. Or enlarge or reduce the spectrum view in vertical direction only, using the Vertical Zoom commands or Page Up or Page Down keys on the keyboard. The tools differ in that the rectangular zoom will magnify the y-axis as well as the x-axis. Select Zoom In or Manual from the View menu or click In the dialog box that appears enter the coordinates of the area and click OK. Note: To cancel the Zoom-In mode and to get back to the full spectrum view use the button on the General toolbar. Right-clicking on the spectrum enables the Horizontal Zoom tool. CTRL + right-click on the spectrum enables the Rectangular Zoom tool. Click on the spectrum with the Horizontal Zoom tool active and the spectrum will be enlarged three times around the clicked point.  Hold down the CTRL key when dragging with either the Horizontal or Rectangular tool active and the area is zoomed, symmetrically around the starting point.

Analyzing FT Spectra

1. To label peaks in a spectrum select peak picking: auto peak picking, picking by setting the peak level and manual peak picking. Information on each selected peak is placed into the Table of Peaks .This table can also be displayed on screen and if values are truncated the column width can be increased.

2. To assign peaks first draw the structure and place it on the NMR spectrum. Then select Analysis and Assignment either by individual peaks, multiplets, or region. See Additional Procedures for drawing molecules with ChemSketch.

3. This mode allows peaks to be labeled peaks. There are three ways of peak picking: auto peak picking, picking by setting the peak level and manual peak picking. Information on each selected peak is placed into the Table of Peaks. Default gives two decimal places for peak position. The number of significant figures can be increased or decreased under Options/ Preferences/Peak/Numeric Display. Similarly, the number of significant figures displayed in a table can modified by opening a Table of Peaks or Integrals, then right clicking anywhere inside the table to bring up the Edit Box. Select Options and then Integer Field to change the amount of space for digits and the number of digits displayed.

4. Annotation allow text to be placed by individual or groups of peaks. Double click on the annotation to edit text or remove it.

5. Integration includes a manual integration mode and an automatic integration function. Moreover, the bias (slope or tilt) of the integral curves can be adjusted. The value of an integral can be set after selecting the integral then under options select Reference Integral and set the number, e.g. of protons to 1, 2, 3.5, 5, etc.

6. Select set reference point (TMS, etc.) for the currently opened spectrum either manually or automatically.

7. The Multiplet mode allows definition any spectral region as multiplet and then defining coupling (J values) constants within it, as well as convert assigned regions to multiplets. First expand the multiplet region with the rectangular zoom. Set a multiplet by holding the left mouse button down while dragging the cursor across the set of peaks; the multiplet area will be marked. To define individual J values within each multiplet click the first peak with the left mouse and then click on the second peak with the left mouse button. Repeat the process. The tentative J values are displayed after each set of peaks have been defined and can be listed in a table.

8. Measure Peak to Peak Distance Measures the distance between any two specified peaks. The area may be measured may be enlarged using either the Horizontal or Rectangular Zoom tools. To measure the distance: with this tool active point to the starting point and click, then move the mouse to another peak of the spectrum and click again.

9. Distance between two any specified points -- The distance can be enlarged if required with either the Horizontal or Rectangular Zoom tools. To measure the distance: with this tool active point to the starting point and click, then move the mouse to another point of the spectrum and click again. The results of measuring are displayed on the bottom status bar:

Reporting and Printing

1. Dialog box allows users to specify the settings for spectrum report page. The dialog box is displayed when selecting either the Copy to Report Editor or Print command from the File menu. Many options include: whole and/or expanded spectra, tables of peaks, integrals, reference, annotations, multiplets, etc.

2. Copy the active spectrum to a new report page in the ChemSketch Window. Displays the Report Page Setup dialog box allows specific settings for the report page. Before using this command, ensure that the NMR spectrum that copy to the ChemSketch Window is represented correctly in the window. For example, first insert any structure or Table of Peaks in the Spectrum Window. Once the spectrum is copied to the ChemSketch Window, changes in the spectral modes or settings can not be made, although it is possible to change the style, size, and location of the NMR picture as a graphical object using the Objects Panel. Spectra data can be copied into a Report on a single page or on multiple pages. For instance, the whole spectra might be copied on the first page with expanded spectra for multiplets on subsequent pages and another page used exclusively for tables. All spectra and/or just tables may be imported into any Windows program for presentation or publication.

Multi-spectral Operations

1. Arithmetic Operations -- This mode allows arithmetic operations (adding and subtracting) with two spectra at a time. Arithmetic operations can only be applied to spectra of the same nucleus type and having the same frequency. However, spectra can have different number of points and width or can be shifted relative each other along Y-axis (if this is a case apply the Synchronize option). Before starting subtracting or adding spectra make sure that two required spectral windows are selected and it is recommended to switch to the Tile mode. Click the button on the Operation toolbar the Arithmetic toolbar appears. Fix Result of Operation To permanently fix the results of adding or subtracting, for example, for subsequent arithmetic operations, click this button. Add Spectra Click this button the spectrum from the selected spectral window will be added to the one from the active window. For more details click here. Subtract Spectra Click this button and one of the two selected spectra will be subtracted from another (active one). For more details click here. Coefficient field Both the sum and difference of two spectra are calculated with the use of k factor (Sum=A+k*B and Diff=A-k*B, where A is an active spectrum). Change this factor to obtain the desired result.

Step-by-step procedure: first turn on the New Windows and Tile Modes and under Windows Set Scrolling to a number greater than two. Open the two files make the first spectrum active and then use the SHIFT key to select the second spectrum (the file tab will turn light blue). Use the Synchronize button to assure both spectra are synchronized. Click on the Arithmetic button and then either Addition or Subtraction. Select the 'k' coefficient, type the number and Enter. Use Page Up or Page Down to zoom the spectrum and see the peaks disappear or appear. If the results are not satisfactory click the addition/subtraction button. Or to accept the results select Fix Results and accept the changes

2. Replace Mode If this mode is active (the corresponding button is depressed on the General toolbar), any spectra loaded (open, import or copy from DB) will replace the content of the active spectral window. Alternatively, select either the Add mode or the New Window mode.

3. Add Mode If this option is active (the corresponding button is depressed on the General toolbar), the newly loaded spectra (opened, imported or transferred from the Database Window) will be added to the same spectral window. This mode is useful to compare several spectra.

4. New Window Mode If this mode is active all the spectra loaded (open, import or copy from database) will be placed into a separate window.

5. Synchronous Mode Sometimes spectra to be compared belong to different ranges of X. This command allows representation of spectra in a form convenient for comparing them. Switch to the Tile mode and select several windows before applying this option. As this command is selected or by clicking on the corresponding button, the X-axis of each selected window will be represented so that they line up. If necessary, the units of measurements will be recalculated. If any of the Zoom options are applied (View menu) with this button active, all the selected spectra will be zoomed simultaneously.

6. Table of Windows Lists the spectral windows that are currently opened in the Spectrum window. This table contains useful information on the spectrum from each window. Click on any portion of the dialog box to get more information: Use this table to switch among opened windows: double-click on the line containing the required spectrum and the corresponding spectrum will become active. Right-clicking within the table opens the context menu with the commands that will allows management of open files. To edit the table representation choose the Options command from the context menu.

Additional Procedures -- ChemSketch

ChemSketch is an integrated software package from ACD for drawing chemical structures, reactions, schematic diagrams, and designing other chemistry-related reports and presentations. ChemSketch has the following features: Structure mode for drawing chemical structures and calculating their properties as well as the draw mode for text and graphics processing.

Note: switch between Structure and Draw mode using the buttons in the top left corner of the ChemSketch Window, in the General toolbar or the Space Bar is a toggle between the modes.

Molecular Structure

1. Create chemical structures using the Structure toolbar, Atoms toolbar and References toolbar. Instantly see either the elemental composition or the formula and molecular weight of the drawn structure or chemical property of the selected structure on the status bar. After the structure is drawn it can be imported into the spectrum window.

2. At the lower left hand corner of the ChemSketch window select either Spectrum or Chemsketch. Select Spectrum after drawing a structure and it can be imported by selecting Attach Structure to Current Spectrum or the first choice is to Switch to the Spectrum Window, without the structure.

3. Assignment This mode allows the assignment peaks in the spectrum to corresponding atoms in the structure and vice versa. There are three ways of assigning peaks: auto assignment, assignment by peak and assignment by region. Note that to make this mode available first insert a structure. Select the Assignment button on the Operation Toolbar, the Assignment toolbar appears. It includes the following selection to allows assignment by peak, region, or multiplet.

By Peak Choose this command or click the corresponding button on the Assignment toolbar. Place the mouse pointer over the peak/atom. Click on the peak/atom when it is highlighted. Note that the red line stretches to the cursor. Drag from the peak/atom to the corresponding atom/peak and click to assign it.

Notes: If an atom has been assigned to a peak and if the selected atom has already been assigned to any other peaks, the ''old'' assignment is deleted and the selected atom is assigned to a new peak. When assigning a peak to an atom and if the selected atom has already been assigned to any other peaks, the ''old'' assignment is not deleted so it can be assigned to either one atom to several peaks. View the assigned peaks and corresponding numbers of atoms in the Table of Assignments by clicking or choosing the Show Table of Assignments command from the View menu.

ChemSketch and Draw
Several hints to make using the program a bit simpler.

Reseizing and Moving a Molecule -- After a molecule is drawn and if it is not centered or the proper size first click on the molecule to select select it. A selected molecule will be enclosed in a box with eight small dark squares. Resize the molecule by dragging the two arrow cursor from any corner to make it larger or smaller. Dragging from the sides will increase the width or length of a molecule, but not proportionality. To move the molecule to another place select the ALT key select a 4-arrow curser which allows movement of the whole molecule.

There are two modes in ChemSketch. One for drawing a molecular Structure and one to Draw. The later may be useful to form equations, add text, or diagrams.

For specific applications procedures see ADC: ACD software for NMR is described:  http://www.acdlabs.com/products/spec_lab/exp_spectra/nmr/