Structural elucidation software

In addition to software tools to help postacquisition processing, software tools to help mass spectral interpretation, particularly MS/MS, have taken new strides as well (Heinonen et al., 2008). One example of such a software tool is the MathSpec program. The details of the MathSpec approach have been explained (Sweeney, 2003). MathSpec software is used in conjunction with MS/MS spectra obtained under high-resolution conditions. The software systematically attempts to assemble possible parts (from the MS/MS fragment data) of the molecule into a rational molecule. Other examples of structure elucidation software include HighChem s Mass Frontier and ACD/Labs ACD/MS Manager (Bayliss et al., 2007). Other metabolite prediction software tools such as Meteor are also being incorporated into LC-MS software as tools to help accelerate metabolite detection and characterization (Testa et al., 2005 Ives et al., 2007). 

Williams, A. Recent advances in NMR prediction and automated structure elucidation software. Curr. Opin. Drug... 

Williams, T., Blinov, K., Elyashberg, M. and Martisrosian, E. Recent Advances in the Use of NMR Prediction and Automated Structure Elucidation Software for Natural Product Characterization, presented at the SMASH NMR Conference. Argonne, IL, 2000. 

B. J. Stockman, Flow NMR Spectroscopy in Drug Discovery , p. 269 A. Williams, Recent Advances in NMR Prediction and Automated Structure Elucidation Software , p. 298... 

Since the data obtained by low resolution instruments, like QqQ, are enough simple to interpret if compared with the huge amount of data obtained by a HR instrument, interpretation of a product ion spectrum generated by the QqQ is often not straightforward, because of the complex dissociation mechanisms for formation of fragment ions. However, a structure elucidation software, such as ACD/MS Fragmenter or Mass Frontier, developed to predict the fragment ions formed by Cff), has been used to assist the spectral interpretation of unknown structures. 

Basic conditions for efficient structure elucidation are the collection of spectroscopic data in centralized databases and easy access by all spectroscopic laboratories. Besides the classical similarity searches for structures and spectra, the prediction of data is of increasing importance. Database-supported spectrum predictions not only have the advantage of being very precise but they also enhance their precision automatically when new data are introduced. Another application of structure-oriented spectral databases is their use in partially or fully automated structure elucidation software. 

There are many software tools available to help with the acquisition, processing and interpretation of NMR data. Attempts have been made to automate the verification process and even perform full structural elucidations of unknown compounds. As you might guess from the complexity of the interpretation chapters, these software solutions are not foolproof It remains to be seen whether they ever will be good enough but there have certainly been some major steps forward in all of these areas. 

In order to obtain detailed structure, a knowledge of diffraction intensities is essential, the intensities being related to the structure factor. Computer-controlled single-crystal X-ray diffractometers with structure (software) packages have made structure elucidation a routine matter. The availability of synchrotron X-radiation of continuously variable wavelength has made X-ray diffraction a still more powerful structural tool for the study of solids. A technique of great utility to solid state chemists is the Rietveld treatment of powder X-ray diffraction profiles (Rietveld, 1969 Manohar, 1983). Automated structure packages for the determination of unknown structures by this method are now commercially available (see section 2.2.3). In Fig. 2.1, we show a typical set of profile data. 

Finally, for routine applications, our software provides a database management system called BASIS for storage and manipulation of chemical information. BASIS can access generally available spectral libraries from three different spectroscopic techniques (MS, H-NMR and F13C-NMR, IR), and permits the creation of new libraries. For structure elucidation and substructure search of unknown compounds, library search algorithms allow the retrieval of identical and structurally similar spectra. 

Even if improved hardware and/or software is feasible for the "generate" and/or "test" phases of structure elucidation, it would appear that improvements in the first phase for derivation of structure information could substantially reduce the effort required for these latter two phases, and similarly increase the proportion of unknowns for which the interpreter can derive a satisfactory answer only aided by STIRS. (The availability of infrared absorption data from GC/IR/MS would be particularly helpful.)... 

Solid-state NMR spectroscopy has been demonstrated as a well established technique for characterization of zeolites and other porous materials with respect to structure elucidation, pore architecture, catalytic behaviour and mobility properties. The latest progress in the development of NMR techniques, both with respect to software and hardware improvements, has contributed to the present state of the art for NMR within the field of characterization of zeolitic materials. Furthermore, the introduction of NMR imaging (110), two-dimensional quintuple-quantum NMR spectroscopy (111) and transfer of populations in double resonance (TRAPDOR) NMR (112,113) will extent the horizons of zeolite characterization science. As a final example, the Al => Si TEDOR experiment directly proves, for the first time, that silicon substitutes for phosphorous atoms in the framework of SAPO-37 (114). The Al... 

Although solution-state NMR has revealed much regarding the chemical structural composition of humic substances and dissolved organic matter (5), the development of more sophisticated software, pulse sequences, probes in recent years have not been exploited much in the field of soil science. Most of the novel applications have strictly relied on conventional one-dimensional spectroscopy. Two-dimensional NMR methods have become the mainstay of the chemical research field, especially for the structural elucidation of complex soluble biopolymers. The complexity of humic substances along with other inherent physical properties such as limited solubility and the presence of paramagnetics... 

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