acd specmanager NMR from ACD. See?
ACD's SpecManager is a powerful suite to help in the management of spectroscopic data ranging from NMR to UV, IR, and Raman, by way of mass spectra and chromatography-coupled MS techniques. It also functions within the ChromManager module for liquid chromatography coupled with gas chromatography. Now at version 6.0, it's easy to use, intuitive, and can process heaps of data. This review delves into the module that handles NMR.
Hydrogen, carbon, fluorine, nitrogen, phosphorusÉall the elemental ingredients of a good and proper NMR portfolio. Now, with ACD's SpecManager, one can put together an innovative menu and make the most of available and predicted spectral data. The NMR Module of ACD's SpecManager can handle all the common forms of nuclear magnetic resonance spectra: proton, carbon-13, nitrogen-15, fluorine-19, and phosphorus-31.
It quickly processes experimentally acquired data to create an accurate database of spectra, together with pertinent spectral parameters and the chemical structure that underpins each spectrum. Furthermore, peaks from an experimental spectrum can be assigned to a structure or structures generated using a plug-in called ChemSketch. The NMR module encompasses the basic, underlying components of ACD/SpecManager, which are ChemSketch, the general structure drawing and modelling module, and the Spec DB Module, which provides the database functions. In addition, ChemSketch and the NMR predictors allow the incorporation of a generated structure(s)with its theoretical spectrum. The ChemSketch program also allows one to easily print the structures and their respective spectra to documents, using user-defined layouts or readily available templates.
After several decades of acquiring NMR spectra, chemists have built up a massive library, thus enabling significantly improved spectral predictions. ACD's database uses over 1.2 million chemical shifts for predicting proton NMR spectra. Calculated spectra can be processed, analysed, and saved in much the same way as the experimental spectra in one's database.
New features, such as forms of zoom and zoom history, have been added since the last version. One form of zoom, the horizontal zoom, allows the user to enlarge the spectrum simply by dragging the zoom tool across the display. The area is zoomed in symmetrically in all directions around the starting point. The rectangular zoom, on the other hand, allows one to enlarge (obviously) a rectangular area of the spectrum; this can be done symmetrically in all directions about a starting point by holding the control key while one drags the zoom tool. Zoom history allows the user to step back through different views, one zoom at a time, while the 'zoom out' is just a click from displaying the full spectrum again. The most aesthetically pleasing improvements involve the 3D View mode where new perspectives, zooming, rotation, and measuring distances and angles are now possible, together with the ability to apply new surface types to structures, contour, wireframe, solid colours, etc.
SpecManager uses basic and advanced spectral manipulations for both 1D and 2D NMR data sets. These include zero-filling, Fourier Transform, phase correction (done manually or automatically), baseline correction, calibration, integration, peak picking (manual and automatic), peak fitting, multiplet operation, and peak assignment. One rather interesting feature of the system is that it allows one to select impurities and artefact signals and hide them from view. Alternatively, peaks can be singled out above a certain threshold. The module allows estimates of purity to be obtained too, so that mixtures can be spotted. The dark regions formed in this way can be implemented manually or through a macro. Moreover, there is a fine adjustment for the spectrum's phase to compensate for drift problems due to the recording spectrometer.
Chemical shifts and coupling constants are the mainstay of NMR spectroscopy - providing the primary information that betrays the environment of each atomic nucleus in a molecule or other system. It is possible to extract a listing of these with a single click. Moving your mouse over any atom (a hydrogen in a proton NMR spectrum, obviously) displays the peaks associated with that atom, assuming it has been assigned. Zooming in on a particular set of peaks then allows them to be expanded, so that a cluster of what may appear to be a single spectral spike reveals its true nature as a doublet, for instance. Moreover, the built-in J-coupler will carry out the analysis of the various doublets, triplets, tented quartets, and other such spectral characteristics, and provide fundamental information about the atoms associated with each region. And, within the program's main window, each open spectrum is available by clicking a tab, so that multiple spectra can be manipulated in the same session. It is now also possible to synchronize spectra, while an Autodifferentiate function can display assigned and unassigned atoms in different colours.
The samples files provided with the software give a useful set of test compounds and spectra to help one become familiar with the package. According to the ACD literature, the NMR module can import all the major FID (free induction decay) and Fourier transform data formats: Bruker DISNMR, Bruker UXNMR/XWIN-NMR, Bruker WIN_NMR, Chemagnetics, GE Omega, Jeol Lambda, Jeol Alpha, Jeol Delta, Jeol Generic, Jeol AL95, Jeol DX, Jeol EX, TecMag, Varian VNMR, ASCII, Galactic, Felix, JCAMP, Lybrics, Nuts, MACNMR, and Nicolet GE/QE -300.
However, let's take the proton NMR spectrum of catechin for example (a bioflavonoid found in Green Tea).
Open the file, and the multi-tab preferences dialogue box allows one to choose how a spectrum can be loaded into the main processor window. Choose the Spectrum tab and you can tweak the various settings to taste. One can change the colour of the spectral lines, display them as lines, points or crosses, and toggle on and off the horizontal and vertical scales and gridlines. The other tabs - structure, labels, integrals, peaks, and multiplets - allow the user to adjust how other spectral characteristics, such as the area under a peak or integral, which represents the number of protons giving rise to each signal, are displayed.
The View menu command allows quick access to any commentary on spectral origin and details. Of course, the software doesn't allow the user to contravene Good Laboratory Practice (GLP) - and modify the spectrum parameters.
The spectrum processing allows the user to shift the experimental free induction decay of any spectrum. The software can apply a weighting function to the FID - transform the FID file into a Fourier transform spectrum. When carrying out a Fourier transformation, the program allows one to dampen out small oscillations in the FID that would otherwise result in a noisy FT spectrum. Various dampening functions are available. One can apply an exponential weighting function to the FID, which improves the signal-to-noise ratio. A Lorentzian/Gaussian function command improves the spectral resolution, but only marginally improves signal-to-noise. Three other functions: TRAF, sine bell, and shifted sine bell can also be used to improve a spectrum's resolution. The resulting FT spectrum can then be phase corrected and subsequently baseline corrected. Other tools such as solvent removal and setting dark regions, as mentioned above, are all very straightforward too.
Fourier transformations can be carried out as direct or inverse. The software can be run in default mode, which will then automatically work out which type of direct Fourier transform would suit - either Complex or Bruker - or one can click to make a personal choice. Inverse FT simply reverts to the original spectrum.
One feature that ACD/Labs describe in their literature as 'very handy' is the interactive apodization. In this mode, Fourier transform and phase correction parameters can be adjusted 'on the fly' to help the user produce the optimum resolution, corrected spectrum with the best signal-to-noise ratio displayable.
By directly incorporating interpretative information on one's spectrum, it is possible to produce a self-contained visual that reveals much if not all of the key points about a spectrum. ACD/SpecManager allows peaks to be labelled by automatic or manual methods, the distances between peaks to be measured, the spectrum adjusted to different reference points, and notes added to peaks and regions of the spectrum. The spectrum's integral can be calculated and displayed, and peaks themselves optimised by the peak fitting routine.
SpecManager is much more than a spectral database with various methods for garnering the most information from the spectral data and displaying the results in different useful formats. With macros to assist in the automation, one can begin to appreciate the power of NMR spectroscopy to its full extent, with the ability to compare multiple spectra both experimentally and predicted from one's compounds and unsynthesised molecules, and to create detailed reports on the whole result.
ACD/SpecManager comes with a fairly hefty online manual but it follows the usual kinds of rules for menus and buttons. It is properly intuitive after becoming familiar with some of the more complex tasks in order to understand the various variables and parameters that can be tweaked and fine-tuned. In addition, easy accessible help files are provided with each window or dialog box. However, to get a quick grasp of what is possible with the system there is a set of exercises to be done that would take about 50 to 70 minutes, although, one would also have to be reasonably familiar with ChemSketch and ACD/Dictionary to be able to get up to working speed in that time.
ACD's NMR software can run as a local or global data system via the SpecDB module or the SpecDB SQL module (for global work). Of increasing importance in the digital publishing world, is the ability to add an electronic signature; this makes publishing and the inbuilt emailing function more secure. The program also comes with a built-in automatic update program that allows online updates to be carried out by connecting to the ACD servers.