Combining structural information

The atom-type E-state indices combine structural information about the electron accessibility associated with each atom type, an indication of the presence or absence of a given atom type and a count of the number of atoms of a given atom type. 

The Comparative Structurally Assigned Spectral Analysis (CoSASA) is another QSAR approach that is based on C-NMR spectra where chemical shifts at selected positions in the molecule backbone template are previously identified [Beger, Buzatu et al., 2001, 2002 Beger and Wilkes, 2001a]. This approach combines structural information from molecules with the assigned simulated C-NMR chemical shifts. 

Both molecular and transition dipole moment orientation can be probed within the solid state samples, especially upon combining structural information with polarized absorption measurements. Small-area electron diffraction experiments are also effective since they allow the orientation of crystalline regions within polymer nanofibers to be probed. Most of these techniques are already well established from the study of polymer alignment in thin-films. Improved analysis methods, which make use of combined polarized Raman spectroscopy and UV-visible absorption data, are especially worthwhile to be mentioned as valuable tools to investigate the orientational properties of light-emitting polymer systems. We will come back in depth to optical properties of polymer nanofibers in Chapter 5. 

The hybrid can be used with El, Cl, FI, FD, LSIMS, APCI, ES, and MALDI ionization/inlet systems. The nature of the hybrid leads to high sensitivity in both MS and MS/MS modes, and there is rapid switching between the two. The combination is particularly useful for biochemical and environmental analyses because of its high sensitivity and the ease of obtaining MS/MS structural information from very small amounts of material. The structural information can be controlled by operating the gas cell at high or low collision energies. 

Rost, B., Sander, C. Combining evolutionary information and neural networks to predict secondary structure. Proteins 19 55-72, 1994. 

The last three detection schemes apply only under very special circumstances. Transmission EXAFS is strictly a probe of bulk structure, i.e., more than about a thousand monolayers. The electron- and ion-yield detection methods, which are used in reflection rather than transmission schemes, provide surface sensitivity, 1-1,000 A, and are inherendy insensitive to bulk structure. X-ray fluorescence EXAFS has the widest range of sensitivity—from monolayer to bulk levels. The combination of electron or ion yield and transmission EXAFS measurements can provide structural information about the X-ray absorbing element at the surface and in the bulk, respectively, of a sample. 

With the microfocus instrument it is possible to combine the weak Raman scattering of liquid water with a water-immersion lens on the microscope and to determine spectra on precipitates in equilibrium with the mother liquor. Unique among characterization tools, Raman spectroscopy will give structural information on solids that are otherwise unstable when removed from their solutions. 

Tandem mass spectrometry (MS/MS) is a method for obtaining sequence and structural information by measurement of the mass-to-charge ratios of ionized molecules before and after dissociation reactions within a mass spectrometer which consists essentially of two mass spectrometers in tandem. In the first step, precursor ions are selected for further fragmentation by energy impact and interaction with a collision gas. The generated product ions can be analyzed by a second scan step. MS/MS measurements of peptides can be performed using electrospray or matrix-assisted laser desorption/ionization in combination with triple quadruple, ion trap, quadrupole-TOF (time-of-flight), TOF-TOF or ion cyclotron resonance MS. Tandem... 

The combination of the flash vacuum pyrolysis (FVP) technique169 with mass spectrometry proved to be particularly useful in identification and characterization of both the fragmentation/rearrangement patterns, intermediates and/or final products formed (see Section IV.E.l). Usually, no structures are indicated in the mass spectra, although ionization and appearance potential can, in principle, provide structural information. 

The examples chosen above have illustrated how CVF or MS-MS may be used to generate useful structural information but these do not always provide sufficient detail to allow an unequivocal structural assigmnent. There may still be instances where it might be necessary to probe fragmentation pathways further. This can be accomplished by combining MS-MS with CVF, i.e. use CVF to effect fragmentation of an ion of interest and then study one of the product ions so formed by using conventional MS-MS. This may be considered to be MS-MS-MS . 

TEM is still the most powerful technique to elucidate the dispersion of nano-filler in rubbery matrix. However, the conventional TEM projects three-dimensional (3D) body onto two-dimensional (2D) (x, y) plane, hence the structural information on the thickness direction (z-axis) is only obtained as an accumulated one. This lack of z-axis structure poses tricky problems in estimating 3D structure in the sample to result in more or less misleading interpretations of the structure. How to elucidate the dispersion of nano-fillers in 3D space from 2D images has not been solved until the advent of 3D-TEM technique, which combines TEM and computerized tomography technique to afford 3D structural images, incidentally called electrontomography . 

Combining structural and biochemical information, MacLennan and his colleagues [8,11,42,45,48,87] constructed a hypothetical model of the tertiary structure of Ca " -ATPase that has interesting mechanistic implications (Fig. 2). The structure was divided into three major parts, designated as the cytoplasmic headpiece, the stalk domain and the transmembrane domain each was assigned distinct functional... 

An example of quantum mechanical schemes is the oldest and most widely used Mulliken population analysis [1], which simply divides the part of the electron density localized between two atoms, the overlap population that identifies a bond, equally between the two atoms of a bond. Alternatively, empirical methods to allocate atomic charges to directly bonded atoms in a reasonable way use appropriate rules which combine the atomic electronegativities with experimental structural information on the bonds linking the atoms of interest. A widely used approach included in many programs is the Gasteiger-Hiickel scheme [1]. 

As with GC, the combination of MS and MS/MS detection with LC adds an important confirmatory dimension to the analysis. Thermospray (TSP) and particle beam (PB) were two of the earlier interfaces for coupling LC and MS, but insufficient fragmentation resulted in a lack of structural information when using TSP, and insufficient sensitivity and an inability to ionize nonvolatile sample components hampered applications using PB. Today, atmospheric pressure ionization (API) dominates the LC/MS field for many environmental applications. The three major variants of API... 

By utilizing different probe wavelengths and time-scales, several different intermediates and their reactions were characterized by TR spectroscopy. These results in combination with fs-TA and fs-KTRF experiments provide important kinetics and structural information that enable an overall mechanistic characterization for the photophysical and photochemical events taking place after photolysis of pHP caged phosphates in various solvent environments. 

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