Fragment data base

In principle, two different classes of structure generators can be distinguished, namely empirical approaches,. such as fragment-based or rule- and data-based... 

The program system COBRA [118, 119] can be regarded as a rule- and data-based approach, but also applies the principles of fragment-based (or template-based) methods extensively (for a detailed description sec Chapter 11, Sections 7.1 and 7.2 in the Handbook). COBRA uses a library of predefined, optimized 3D molecular fragments which have been derived from crystal structures and foi ce-field calculations. Each fi agment contains some additional information on... 

D structures can be generated with fragment-based, data-based, and numerical methods. 

In this context it should be mentioned that some fragmentation data for compounds 127-13152 and 132-14353 have also been given. Compounds 127-131 do not exhibit peaks for the parent ions at all. Their base peaks are m/z 93 (anilinium ion, compounds 127-129) and m/z 172 ([M - R] +, compounds 130-131). 

For the confirmatory procedure, it is recommended that the sponsor develop spectral data based on at least three structurally specific ions that completely define the marker residue molecule. These ions may or may not include the molecular ion. The use of water loss and isotopic ions is usually unacceptable and CVM concurrence should be sought when water loss ions or isotopic ions are selected for the confirmatory analysis. The proposed fragment ion structures should be consistent with the fragmentation pattern, and justification for specificity of selected ions or scan range should be included. All confirmation criteria should be specified in the standard operating procedure. 

Fragment search in the Cambridge Crystallographic Data Base reveals 127 hits out of 42381 entries (state May 1985) having dimethyl sulfoxide as the search query and allowing for the presence of metal atoms. In absence of such elements, the number of hits is reduced to 27. 

The simplest representation of a molecule, with respect to computing physicochemical properties, is to assume the property to be the sum of the property values of the individual constituent atoms, or groups of atoms. Extensive data bases (1,2) of atomic and group (fragment) property values have been compiled to facilitate implementation of this model. The most notable physicochemical properties employed in QSARs using an additive property model are ... 

The novel approaches in LC-MS-based lipidomics, such as ultra-high performance LC (UHPLC), combined with high-resolution MS methodologies allow fast and reliable analysis of various classes of lipids (33). The modem instruments, with fast duty cycles, allow acquisition of high and low collision energy data simultaneously to provide both data on precursor ions and fragmentation data for all detectable molecular ions (34). 

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