Molecular quantification

Tl. Thompson, J. D., Brodsky, I., and Yunis, J. J., Molecular quantification of residual disease in chronic myelogenous leukemia after bone marrow transplantation. Blood 79, 1629-1635 (1992). 

Brisco MJ, Condon J, Hughes E et al. Outcome predietion in childhood acute lymphoblastic leukaemia by molecular quantification of residual disease at the end of induction. Lancet 1994 343 196-200. 

The basic premise of this method is that the magnitude of the detector output, as measured by hj for a particular fraction, is proportional to the weight of that component in the sample. In this sense the chromatogram itself presents a kind of picture of the molecular weight distribution. The following column entries provide additional quantification of this distribution, however. 

Analytical Approaches. Different analytical techniques have been appHed to each fraction to determine its molecular composition. As the molecular weight increases, complexity increasingly shifts the level of analytical detail from quantification of most individual species in the naphtha to average molecular descriptions in the vacuum residuum. For the naphtha, classical techniques allow the isolation and identification of individual compounds by physical properties. Gas chromatographic (gc) resolution allows almost every compound having less than eight carbon atoms to be measured separately. The combination of gc with mass spectrometry (gc/ms) can be used for quantitation purposes when compounds are not well-resolved by gc. 

Molecular Connectivity Indexes and Graph Theory. Perhaps the chief obstacle to developing a general theory for quantification of physical properties is not so much in the understanding of the underlying physical laws, but rather the inabiUty to solve the requisite equations. The plethora of assumptions and simplifications in the statistical mechanics and group contribution sections of this article provide examples of this. Computational procedures are simplified when the number of parameters used to describe the saUent features of a problem is reduced. Because many properties of molecules correlate well with stmctures, parameters have been developed which grossly quantify molecular stmctural characteristics. These parameters, or coimectivity indexes, are usually based on the numbers and orientations of atoms and bonds in the molecule. 

DB Turner, SM Tyrell, P Willett. Rapid quantification of molecular diversity for selective database acquisition. I Chem Inf Comput Sci 37 18-22, 1997. 

The most common application of dynamic SIMS is depth profiling elemental dopants and contaminants in materials at trace levels in areas as small as 10 pm in diameter. SIMS provides little or no chemical or molecular information because of the violent sputtering process. SIMS provides a measurement of the elemental impurity as a function of depth with detection limits in the ppm—ppt range. Quantification requires the use of standards and is complicated by changes in the chemistry of the sample in surface and interface regions (matrix efiects). Therefore, SIMS is almost never used to quantitadvely analyze materials for which standards have not been carefiilly prepared. The depth resoludon of SIMS is typically between 20 A and 300 A, and depends upon the analytical conditions and the sample type. SIMS is also used to measure bulk impurities (no depth resoludon) in a variety of materials with detection limits in the ppb-ppt range. 

SALI compares fiivorably with other major surface analytical techniques in terms of sensitivity and spatial resolution. Its major advantj e is the combination of analytical versatility, ease of quantification, and sensitivity. Table 1 compares the analytical characteristics of SALI to four major surfiice spectroscopic techniques.These techniques can also be categorized by the chemical information they provide. Both SALI and SIMS (static mode only) can provide molecular fingerprint information via mass spectra that give mass peaks corresponding to structural units of the molecule, while XPS provides only short-range chemical information. XPS and static SIMS are often used to complement each other since XPS chemical speciation information is semiquantitative however, SALI molecular information can potentially be quantified direedy without correlation with another surface spectroscopic technique. AES and Rutherford Backscattering (RBS) provide primarily elemental information, and therefore yield litde structural informadon. The common detection limit refers to the sensitivity for nearly all elements that these techniques enjoy. 

Relative photoionization cross sections for molecules do not vary gready between each other in this wavelength region, and therefore the peak intensities in the raw data approximately correspond to the relative abundances of the molecular species. Improvement in quantification for both photoionizadon methods is straightforward with calibration. Sampling the majority neutral channel means much less stringent requirements for calibrants than that for direct ion production from surfaces by energetic particles this is especially important for the analysis of surfaces, interfaces, and unknown bulk materials. 

Survey spectra using the MPI method are used primarily for quantification of surface components in inorganic materials, with a detection limit of ppm to ppb. The same mode coupled with SPI can be used for molecular characterization of polymer films. 

The limitations of SIMS - some inherent in secondary ion formation, some because of the physics of ion beams, and some because of the nature of sputtering - have been mentioned in Sect. 3.1. Sputtering produces predominantly neutral atoms for most of the elements in the periodic table the typical secondary ion yield is between 10 and 10 . This leads to a serious sensitivity limitation when extremely small volumes must be probed, or when high lateral and depth resolution analyses are needed. Another problem arises because the secondary ion yield can vary by many orders of magnitude as a function of surface contamination and matrix composition this hampers quantification. Quantification can also be hampered by interferences from molecules, molecular fragments, and isotopes of other elements with the same mass as the analyte. Very high mass-resolution can reject such interferences but only at the expense of detection sensitivity. 

Surface analysis by non-resonant (NR-) laser-SNMS [3.102-3.106] has been used to improve ionization efficiency while retaining the advantages of probing the neutral component. In NR-laser-SNMS, an intense laser beam is used to ionize, non-selec-tively, all atoms and molecules within the volume intersected by the laser beam (Eig. 3.40b). With sufficient laser power density it is possible to saturate the ionization process. Eor NR-laser-SNMS adequate power densities are typically achieved in a small volume only at the focus of the laser beam. This limits sensitivity and leads to problems with quantification, because of the differences between the effective ionization volumes of different elements. The non-resonant post-ionization technique provides rapid, multi-element, and molecular survey measurements with significantly improved ionization efficiency over SIMS, although it still suffers from isoba-ric interferences. 

Although the diffraction techniques are unique in providing detailed information on the structural organization at the molecular level in the different crystalline forms, there are other characterization techniques which are sensitive to the chain conformation and in some cases to the chain packing, which can be used advantageously (and in some case more efficiently than diffraction techniques) in the recognition and quantification of the different polymorphs in polymeric materials. 

Factors may be classified as quantitative when they take particular values, e.g. concentration or temperature, or qualitative when their presence or absence is of interest. As mentioned previously, for an LC-MS experiment the factors could include the composition of the mobile phase employed, its pH and flow rate [3], the nature and concentration of any mobile-phase additive, e.g. buffer or ion-pair reagent, the make-up of the solution in which the sample is injected [4], the ionization technique, spray voltage for electrospray, nebulizer temperature for APCI, nebulizing gas pressure, mass spectrometer source temperature, cone voltage in the mass spectrometer source, and the nature and pressure of gas in the collision cell if MS-MS is employed. For quantification, the assessment of results is likely to be on the basis of the selectivity and sensitivity of the analysis, i.e. the chromatographic separation and the maximum production of molecular species or product ions if MS-MS is employed. 

In practice, the valne depends on the type of analysis being attempted. Structural studies may require the extent of fragmentation to be maximized, while quantification may require the opposite, i.e. the efficient prodnction of a small number of ions of different m/z ratios, in order to maximize sensitivity. Selectivity may be obtained simply by monitoring of the molecular ions formed. On occasions, when significant background is observed, this may not be adequate and fragmentation of the molecnlar species may be necessary to provide a number of ions to be monitored. Some componnds may be ionized very effectively under positive-ionization conditions, while others may require the formation of negative ions to allow analysis. 

The advantages of SIMS are its high sensitivity (detection limit of ppms for certain elements), its ability to detect hydrogen and the emission of molecular fragments that often bear tractable relationships with the parent structure on the surface. Disadvantages are that secondary ion formation is a poorly understood phenomenon and that quantification is often difficult. A major drawback is the matrix effect secondary ion yields of one element can vary tremendously with chemical environment. This matrix effect and the elemental sensitivity variation of five orders of magmtude across the periodic table make quantitative interpretation of SIMS spectra oftechmcal catalysts extremely difficult. 

The use of HPLC for quantification of phenols is often limited to a single class of phenolics and then often only to low-molecular weight compounds that are available as standards. It is, therefore, often necessary to use colorimetric assays such as the Folin-Ciocalteau assay which rely on the reducing ability of phenols to quantify the amount of total phenolics in a sample (Waterman and Mole, 1994 Singleton et al, 1999 Schofield et al, 2001). The degree of condensation of polyphenols can be quantified by colorimetric assays such as the acid-butanol assay and the vanillin assay (Waterman and Mole, 1994 Schofield et al, 2001). 

Caramel color interacts with other food components. As an example, a concentration higher than 700 ppm caramel in cola increased the rate of hydrolysis of the aspartame, forming alpha-L-aspartyl-L-phenylalanine. Caramelization products inhibited enzymic browning by 85.8 and 72.2% when heated at pH 4 and 6, respectively, for 90 min. The highest inhibitory activity was found for the fraction with molecular weight of 1000 to 3000. Caramel is often used for adulteration of juices and other foods like honey or coffee. It can be determined by quantification of marker molecules such as 5-HMF, 4-Mel, and DFAs. ... 

The definition of "concepts" must be accompanied by explicit recipes for computing them is actual cases. There is no more space in theoretical chemistty for "driving forces", "effects, etc. not accompanied by specific rules for their quantification. The impact of a new "concept will be greater if the rules of quantifications are not restricted to ad hoc methods, but related to methods of general use in molecular quantum mechanics. A concept based exclusively on some specific features of a given method, e g. the extended Hiickel method, is less robust than a concurrent concept which may be quantified also using other levels of the theory. 

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