NMR Database

A PC-based H-nmr database, which includes fiiU spectmm search capabiHty, is being constmcted by the Toyohashi University of Technology (67). Speclnfo, owned by Chemical Concepts, offers a 150,000 spectra Hbrary and database system for mainframe computers, which includes H, F, "O,... 

The Novosibirsk Institute of Organic Chemistry has developed a method for computer-aided retrieval of stmctural information from H-nmr using its database of 50,000 spectra (72). Eraser WUHams Ltd. (Scientific Systems) has special software to search its E-nmr database (73). Protein nmr data have been compiled into a relational database at the University of Wisconsin (74). 

F. Uhlig, U. Herrmann and H. Marsmann, 29Si NMR Database System, http //oc30. uni-paderbon.de/ chemie/fachgebiete/ac/ak marsmann or http //platon.chemie.uni-dortmund. de/acii/fulilig, 2000. 

A recent review by Bifulco et al. covers the methods for determining relative configuration by NMR with the aid of computational methods, including /-based analysis, the Universal NMR Database and the quantum mechanical calculation of NMR parameters.120... 

ACD/Labs (www.acdlabs.com) markets several extensive NMR databases. The H database now exceeds 600,000 experimental chemical shifts and 110,000 coupling constants from 81,000 molecules, and that for 13C is based on more than 900,000 chemical shifts. Databases for 19F and 31P each have more than 20,000 chemical shifts. The databases are linked to programs that predict NMR spectra for given molecular structures and substructures. 

Chemical Concepts (www.wiley-vch.de/cc/) markets similar NMR databases in conjunction with vibrational spectral and mass spectral collections, with a total of more than 600,000 entries. 

Fig. 14.5 LOO (leave-one-out) analysis of the NMR database contained in ACD/Labs NNMR chemical shift and coupling constant prediction package. The calculation was done by removing one shift and then calculating the shift in question using the remaining structures and data contained in the database.

Glycan NMR database that is integrated with CarbBank. 

Carabddian, M. and Dubois, J.-E. (1998). Large Virtual Enhancement of a C NMR Database. A Structural Crowing Extrapolation Method Enabling Spectral Data Transfer. J.Chem.lnf. Comput.Sci.,38,100-107. 

Metabolomics is often employed in early discovery projects and used for the identification of biomarkers. In mammalian systems, the metabolites so identified are often contained in NMR databases, which, depending on the database, are either commercially or freely available to the public (e.g., Human Metabolome Database).37 There is considerably less nonmammalian NMR information available in these databases. While this is an obvious problem for plant biochemists, it can also impact biomarker discovery utilizing other organisms,... 

A new release of version 1.0 of an open access, open submission, open source NMR database NMRShiftDB has been... 

Fig. 6. LOO (Leave-One-Out) analysis of the NMR database contained in ACD/Labs NNMR chemical shift and coupling constant prediction package. The calculation was performed by removing one N shift and then calculating the N shift in question using the remaining structures and data contained in the database. The resulting analysis gave a correlation coefficient of = 9.91 over 21,244 points. The presentation shows a plot of a number of chemical shifts vs. the difference between the experimental and predicted chemical shift values. Approximately 250 shifts out of >21,000 have a deviation of >20 ppm.

Ralph, S. A., Landncci, L. L., and Ralph, J. (2005) NMR database of lignin and cell wall model componnds. Available at http //ars.usda.gov/Services/docs.htm7docid = 10449 (previously http //www.dfrc.ars.usda.gov/software.html), updated at least annually since 1993. 

NMR techniques used in combination with databases is helpful for carbohydrate analysis. For example, SUGABASE is a carbohydrate-NMR database that combines CarbBank complex carbohydrate structure data (CCSD) with proton and carbon chemical shift values (151). 

The combination of the new methods for optimizing and pruning search trees described above, and the backtracking technique, makes the Chen-Robien algorithm a very fast MCSS algorithm. It has become a central mainstay of several other commands within the CSEARCH-NMR database system [69]. 

Spectra of saccharides can be accessed from NMR database of Glycosciences at http // glycosciences.de/sweetbase/mnr/. 

In synthetic organic and organometaUic chemistry, solution-state NMR means a 300—500 MHz NMR spectrometer, high-precision glass sample tubes, 2 ml of deuterated solvent (typicaUy fully deuterated chloroform, acetone, benzene, or dichlorobenzene), several milligrams of pure sample, and a basic suite of H and NMR experiments [3 7]. With several hours of spectrometer time and data interpretation, the stuctures of new compounds with molecular weights up to 2000 Da can be determined, espedaUy when analyzed along with results from NMR databases and mass spectroscopy. 

All Figures have been generated using the CSEARCH-NMR-database system Kalchhauser H., Robien W.,/. Chem. Inf. Comput. Sci., 1985, 25, 103-108. 

Another valuable role of model compound studies is the generation of NMR databases that have been extremely important for NMR studies on isolated LCC preparations [59-65]. 

Multidimensional NMR techniques can potentially provide valuable information on the carbohydrate sites involved in ether LCC linkages. However, these efforts were so far unsuccessful, as the region where these signals should be located (ca. 65-75/3.0-4.0 ppm) is heavily overlapped and a very accurate NMR database is required to unambiguously assign the signals in this region. 

Thus, a precise and unbiased assignment of carbohydrate moieties in complex LCC preparatiOTis (as well as in dissolved ceU wall preparations) is not possible without a detailed NMR database for sugar moieties acquired in DMSO-de as it has been indicated earlier [21,48,82]. Most of the current carbohydrates databases were acquired in D2O, while the best NMR solvent for the study of LCC preparations is OMSO-dg. The difference in the chemical shift values between D2O and DMSO-de is often comparable with the difference between different types of carbohydrate units and fliis makes their reliable assignment difficult. Therefore, attempts of detailed assignment of various carbohydrate moieties are unreasonable before that kind of database is generated. 

It has an NMR database (web database) for organic structures and their NMR spectra. It allows for spectrum prediction ( C, H, and other nuclei) as well as for searching spectra, structures, and other properties. It also has a collection of peer-reviewed datasets by its users. 

C.-W. von der Lieth, NMR Databases and Tools for Automatic Interpretation of Spectra of Carbohydrates , in Bioinformatics for Glycobiology and Glycomics An Introduction, eds. C.-W. Von der Lieth, T. Luetteke and M. Frank, John Wiley Sons Ltd., Chichester, UK, 2009, p. 295. 

Bio-Rad Laboratories, Informatics Division, Philadelphia, PA (www.bio-rad.com), publishes the electronic Sadtler spectra collections of high-resolution proton and C NMR spectra, and specialty NMR databases for metabolites, monomers, and polymers. Bio-Rad offers a powerful informatics tool called KnowItAll , which permits spectral processing, search, analysis, and prediction, among other tools. As of 2012, the proton and carbon NMR databases contained over 560,000 spectra, and the other elements NMR databases such as B, P, N, and Si had over 90,000 spectra. 

Leftin, A. and Brown, M.R 2011. An NMR database for simulations of membrane dynamics. Biochim. Biophys. Acta Biomembranes 1808 818-839. 

The results described in this section show that spectroscopy in the liquid state can be applied to the analysis of both colloidal metal particles and species adsorbed on colloidal metals in a manner reminiscent of the spectroscopic investigations of molecular compounds in solution. There are established infrared and NMR databases from the molecular and solid state literature on which to base analyses of colloid spectra. The NMR data presented suggest that the study of metal particles in the important size range where tranritions from the molecular to the metallic state take place will be greatly facilitated by this method. In addition, the use of NMR in observing the adsorption of small molecules promises to open the way for the development of the surface chemistry of nanoscale colloidal metal particles. 

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